Starting phenix.real_space_refine on Sun Jul 21 14:59:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v2z_42938/07_2024/8v2z_42938_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v2z_42938/07_2024/8v2z_42938.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v2z_42938/07_2024/8v2z_42938.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v2z_42938/07_2024/8v2z_42938.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v2z_42938/07_2024/8v2z_42938_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v2z_42938/07_2024/8v2z_42938_neut.cif" } resolution = 2.72 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= 0.003 sd= 0.036 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 110 5.16 5 C 9230 2.51 5 N 2455 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 PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 157": "OD1" <-> "OD2" Residue "A ASP 184": "OD1" <-> "OD2" Residue "A GLU 241": "OE1" <-> "OE2" Residue "B PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 100": "OE1" <-> "OE2" Residue "B GLU 107": "OE1" <-> "OE2" Residue "B PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 157": "OD1" <-> "OD2" Residue "B GLU 241": "OE1" <-> "OE2" Residue "C PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 157": "OD1" <-> "OD2" Residue "C ASP 184": "OD1" <-> "OD2" Residue "D PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 157": "OD1" <-> "OD2" Residue "D GLU 241": "OE1" <-> "OE2" Residue "E TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 157": "OD1" <-> "OD2" Residue "E GLU 226": "OE1" <-> "OE2" Residue "E GLU 241": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 14635 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2899 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: 2899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2899 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: 2899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2899 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: 2899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2899 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: 2899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2899 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: 8.87, per 1000 atoms: 0.61 Number of scatterers: 14635 At special positions: 0 Unit cell: (105.93, 77.04, 193.67, 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 110 16.00 P 10 15.00 Mg 5 11.99 O 2825 8.00 N 2455 7.00 C 9230 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: 6.42 Conformation dependent library (CDL) restraints added in 2.7 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: 100 helices and 30 sheets defined 49.2% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.59 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.596A pdb=" N HIS A 101 " --> pdb=" O PRO A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.799A 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 removed outlier: 3.545A pdb=" N ILE A 175 " --> pdb=" O PRO A 172 " (cutoff:3.500A) No H-bonds generated for '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 Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.594A 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 289 through 295 Processing helix chain 'A' and resid 302 through 306 removed outlier: 4.001A 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 369 through 374 removed outlier: 3.509A pdb=" N CYS A 374 " --> pdb=" O VAL A 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.667A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.795A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 removed outlier: 3.514A pdb=" N GLY B 146 " --> pdb=" O LEU B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 removed outlier: 3.540A pdb=" N ILE B 175 " --> pdb=" O PRO B 172 " (cutoff:3.500A) No H-bonds generated for '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 Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.652A 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 295 removed outlier: 3.645A pdb=" N ARG B 290 " --> pdb=" O ASP B 286 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LYS B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ASP B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 306 removed outlier: 3.990A 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 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 removed outlier: 3.556A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.837A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 removed outlier: 3.531A pdb=" N GLY C 146 " --> pdb=" O LEU C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 removed outlier: 3.539A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 172 through 175' Processing helix chain 'C' and resid 181 through 194 removed outlier: 3.731A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.540A 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: 3.680A 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 289 through 295 Processing helix chain 'C' and resid 302 through 306 removed outlier: 4.017A 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 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: 3.649A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.810A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 removed outlier: 3.526A pdb=" N GLY D 146 " --> pdb=" O LEU D 142 " (cutoff:3.500A) Processing helix 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 Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.651A 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: 3.582A pdb=" N ARG D 290 " --> pdb=" O ASP D 286 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LYS D 291 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N ASP D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 306 removed outlier: 4.018A 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: 3.720A pdb=" N GLU E 100 " --> pdb=" O ALA E 97 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N HIS E 101 " --> pdb=" O PRO E 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 97 through 101' Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.790A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 146 removed outlier: 3.523A pdb=" N GLY E 146 " --> pdb=" O LEU E 142 " (cutoff:3.500A) 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 Processing helix chain 'E' and resid 222 through 233 Processing helix chain 'E' and resid 252 through 257 removed outlier: 3.599A 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: 3.597A pdb=" N ARG E 290 " --> pdb=" O ASP E 286 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LYS E 291 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N ASP E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 306 removed outlier: 4.049A 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: 6.547A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.314A 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: 6.309A 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: 4.110A 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: 6.568A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.297A 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: 6.344A 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: 4.127A 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: 6.574A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.300A 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: 6.452A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 6.337A 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: 4.207A 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: 6.520A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.312A 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: 6.388A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 6.377A 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: 6.505A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.290A 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: 6.381A 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 241 732 hydrogen bonds defined for protein. 1887 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: 5.56 Time building geometry restraints manager: 6.61 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: 4707 1.34 - 1.46: 3390 1.46 - 1.58: 6662 1.58 - 1.70: 16 1.70 - 1.83: 185 Bond restraints: 14960 Sorted by residual: bond pdb=" CE1 HIC E 73 " pdb=" NE2 HIC E 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.54e+00 bond pdb=" CE1 HIC A 73 " pdb=" NE2 HIC A 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.54e+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 7.54e+00 bond pdb=" CE1 HIC D 73 " pdb=" NE2 HIC D 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.45e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.401 -0.054 2.00e-02 2.50e+03 7.35e+00 ... (remaining 14955 not shown) Histogram of bond angle deviations from ideal: 97.63 - 105.34: 375 105.34 - 113.06: 8036 113.06 - 120.77: 6979 120.77 - 128.49: 4820 128.49 - 136.20: 100 Bond angle restraints: 20310 Sorted by residual: angle pdb=" CA PRO C 367 " pdb=" N PRO C 367 " pdb=" CD PRO C 367 " ideal model delta sigma weight residual 112.00 99.68 12.32 1.40e+00 5.10e-01 7.75e+01 angle pdb=" CA PRO E 367 " pdb=" N PRO E 367 " pdb=" CD PRO E 367 " ideal model delta sigma weight residual 112.00 104.89 7.11 1.40e+00 5.10e-01 2.58e+01 angle pdb=" CB MET B 227 " pdb=" CG MET B 227 " pdb=" SD MET B 227 " ideal model delta sigma weight residual 112.70 127.32 -14.62 3.00e+00 1.11e-01 2.37e+01 angle pdb=" CB GLN A 354 " pdb=" CG GLN A 354 " pdb=" CD GLN A 354 " ideal model delta sigma weight residual 112.60 120.56 -7.96 1.70e+00 3.46e-01 2.19e+01 angle pdb=" CA GLN A 354 " pdb=" CB GLN A 354 " pdb=" CG GLN A 354 " ideal model delta sigma weight residual 114.10 123.18 -9.08 2.00e+00 2.50e-01 2.06e+01 ... (remaining 20305 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.54: 8394 24.54 - 49.07: 545 49.07 - 73.61: 53 73.61 - 98.14: 3 98.14 - 122.68: 5 Dihedral angle restraints: 9000 sinusoidal: 3625 harmonic: 5375 Sorted by residual: dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 177.32 122.68 1 2.00e+01 2.50e-03 3.70e+01 dihedral pdb=" O1B ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PB ADP B 401 " pdb=" PA ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 -173.21 113.21 1 2.00e+01 2.50e-03 3.35e+01 dihedral pdb=" O1B ADP E 401 " pdb=" O3A ADP E 401 " pdb=" PB ADP E 401 " pdb=" PA ADP E 401 " ideal model delta sinusoidal sigma weight residual -60.00 -172.01 112.00 1 2.00e+01 2.50e-03 3.30e+01 ... (remaining 8997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1982 0.082 - 0.164: 260 0.164 - 0.247: 3 0.247 - 0.329: 3 0.329 - 0.411: 2 Chirality restraints: 2250 Sorted by residual: chirality pdb=" CB ILE A 287 " pdb=" CA ILE A 287 " pdb=" CG1 ILE A 287 " pdb=" CG2 ILE A 287 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.22e+00 chirality pdb=" CB ILE C 287 " pdb=" CA ILE C 287 " pdb=" CG1 ILE C 287 " pdb=" CG2 ILE C 287 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" CB ILE D 151 " pdb=" CA ILE D 151 " pdb=" CG1 ILE D 151 " pdb=" CG2 ILE D 151 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 2247 not shown) Planarity restraints: 2600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 366 " 0.133 5.00e-02 4.00e+02 1.91e-01 5.85e+01 pdb=" N PRO C 367 " -0.330 5.00e-02 4.00e+02 pdb=" CA PRO C 367 " 0.109 5.00e-02 4.00e+02 pdb=" CD PRO C 367 " 0.088 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 366 " 0.108 5.00e-02 4.00e+02 1.60e-01 4.12e+01 pdb=" N PRO E 367 " -0.277 5.00e-02 4.00e+02 pdb=" CA PRO E 367 " 0.088 5.00e-02 4.00e+02 pdb=" CD PRO E 367 " 0.081 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 366 " -0.047 5.00e-02 4.00e+02 7.19e-02 8.27e+00 pdb=" N PRO D 367 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO D 367 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO D 367 " -0.040 5.00e-02 4.00e+02 ... (remaining 2597 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 801 2.73 - 3.27: 13248 3.27 - 3.81: 24604 3.81 - 4.36: 31508 4.36 - 4.90: 52777 Nonbonded interactions: 122938 Sorted by model distance: nonbonded pdb=" O3B ADP B 401 " pdb="MG MG B 402 " model vdw 2.186 2.170 nonbonded pdb=" O3B ADP A 401 " pdb="MG MG A 402 " model vdw 2.237 2.170 nonbonded pdb=" O GLY E 156 " pdb=" OG1 THR E 303 " model vdw 2.272 2.440 nonbonded pdb=" O3B ADP C 401 " pdb="MG MG C 402 " model vdw 2.273 2.170 nonbonded pdb=" O GLY D 156 " pdb=" OG1 THR D 303 " model vdw 2.280 2.440 ... (remaining 122933 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 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: 0.020 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 43.320 Find NCS groups from input model: 0.820 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: 0.010 Load rotamer database and sin/cos tables:11.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 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 : 0.005 0.116 14960 Z= 0.301 Angle : 0.777 14.616 20310 Z= 0.399 Chirality : 0.052 0.411 2250 Planarity : 0.008 0.191 2600 Dihedral : 15.424 122.676 5560 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.51 % Allowed : 17.52 % Favored : 81.97 % 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: -1.04 (0.19), residues: 1835 helix: -1.57 (0.16), residues: 730 sheet: 0.41 (0.28), residues: 355 loop : -0.04 (0.24), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 79 HIS 0.003 0.001 HIS B 161 PHE 0.022 0.002 PHE C 127 TYR 0.008 0.001 TYR C 362 ARG 0.005 0.000 ARG A 206 *********************** 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 102 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 94 time to evaluate : 1.723 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 100 average time/residue: 1.6606 time to fit residues: 180.1499 Evaluate side-chains 95 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 91 time to evaluate : 1.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain D 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: 0.7980 chunk 140 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 94 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 145 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 chunk 107 optimal weight: 0.4980 chunk 168 optimal weight: 5.9990 overall best weight: 1.8382 ------------------------------------------------------------------------------- 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 41 GLN A 225 ASN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 GLN B 162 ASN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN D 225 ASN E 225 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.0753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14960 Z= 0.221 Angle : 0.561 6.860 20310 Z= 0.266 Chirality : 0.043 0.128 2250 Planarity : 0.005 0.110 2600 Dihedral : 7.579 101.704 2094 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.78 % Allowed : 16.43 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.20), residues: 1835 helix: 0.12 (0.19), residues: 740 sheet: 0.53 (0.28), residues: 350 loop : 0.44 (0.24), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 340 HIS 0.003 0.001 HIS B 161 PHE 0.008 0.001 PHE C 262 TYR 0.007 0.001 TYR B 188 ARG 0.001 0.000 ARG B 39 *********************** 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 119 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 91 time to evaluate : 1.718 Fit side-chains REVERT: A 314 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.8156 (tt0) REVERT: B 176 MET cc_start: 0.8790 (OUTLIER) cc_final: 0.8460 (mtp) REVERT: B 354 GLN cc_start: 0.8694 (pp30) cc_final: 0.8136 (pp30) outliers start: 28 outliers final: 3 residues processed: 110 average time/residue: 1.7495 time to fit residues: 207.9047 Evaluate side-chains 95 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 90 time to evaluate : 1.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 260 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 7.9990 chunk 52 optimal weight: 8.9990 chunk 139 optimal weight: 7.9990 chunk 114 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 168 optimal weight: 7.9990 chunk 181 optimal weight: 0.9990 chunk 149 optimal weight: 9.9990 chunk 166 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 135 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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** C 12 ASN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 14960 Z= 0.420 Angle : 0.617 7.234 20310 Z= 0.298 Chirality : 0.047 0.142 2250 Planarity : 0.004 0.086 2600 Dihedral : 7.602 105.265 2087 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.48 % Allowed : 15.35 % Favored : 82.17 % 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: 0.73 (0.20), residues: 1835 helix: 0.51 (0.19), residues: 770 sheet: 0.86 (0.29), residues: 325 loop : 0.53 (0.24), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 79 HIS 0.006 0.001 HIS B 161 PHE 0.010 0.001 PHE C 262 TYR 0.009 0.001 TYR B 188 ARG 0.003 0.000 ARG B 254 *********************** 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 130 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 91 time to evaluate : 1.774 Fit side-chains REVERT: A 314 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.8177 (tt0) REVERT: A 354 GLN cc_start: 0.8765 (pp30) cc_final: 0.8464 (pp30) REVERT: B 47 MET cc_start: 0.6322 (pp-130) cc_final: 0.6085 (pp-130) REVERT: B 107 GLU cc_start: 0.9136 (OUTLIER) cc_final: 0.8736 (tt0) REVERT: B 176 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.8463 (mtp) REVERT: B 269 MET cc_start: 0.9156 (mtp) cc_final: 0.8919 (mtp) REVERT: B 314 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.7587 (tp40) REVERT: B 354 GLN cc_start: 0.8689 (pp30) cc_final: 0.8142 (pp30) REVERT: C 6 THR cc_start: 0.9098 (OUTLIER) cc_final: 0.8843 (p) REVERT: C 325 MET cc_start: 0.8801 (mmp) cc_final: 0.8524 (mmp) REVERT: D 354 GLN cc_start: 0.8486 (pp30) cc_final: 0.8124 (pp30) outliers start: 39 outliers final: 7 residues processed: 117 average time/residue: 1.5241 time to fit residues: 194.1062 Evaluate side-chains 102 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 90 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain E residue 151 ILE 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: 2.9990 chunk 87 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 chunk 113 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 178 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 160 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 41 GLN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 GLN C 12 ASN C 162 ASN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14960 Z= 0.204 Angle : 0.541 6.904 20310 Z= 0.253 Chirality : 0.044 0.133 2250 Planarity : 0.004 0.072 2600 Dihedral : 7.288 97.290 2087 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.85 % Allowed : 15.61 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.20), residues: 1835 helix: 0.84 (0.20), residues: 770 sheet: 1.07 (0.29), residues: 330 loop : 0.62 (0.24), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 79 HIS 0.003 0.001 HIS B 161 PHE 0.007 0.001 PHE C 255 TYR 0.006 0.001 TYR E 69 ARG 0.001 0.000 ARG D 210 *********************** 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 121 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 92 time to evaluate : 1.590 Fit side-chains REVERT: A 314 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.8133 (tt0) REVERT: A 354 GLN cc_start: 0.8772 (pp30) cc_final: 0.8513 (pp30) REVERT: A 355 MET cc_start: 0.9321 (OUTLIER) cc_final: 0.8882 (mtm) REVERT: B 47 MET cc_start: 0.6372 (pp-130) cc_final: 0.6159 (pp-130) REVERT: B 95 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.8164 (mtm110) REVERT: B 314 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.7590 (tp40) REVERT: B 354 GLN cc_start: 0.8642 (pp30) cc_final: 0.8128 (pp30) REVERT: C 325 MET cc_start: 0.8773 (mmp) cc_final: 0.8512 (mmp) REVERT: C 354 GLN cc_start: 0.8908 (mp10) cc_final: 0.8590 (mp10) REVERT: D 354 GLN cc_start: 0.8535 (pp30) cc_final: 0.8112 (pp30) REVERT: E 6 THR cc_start: 0.9132 (OUTLIER) cc_final: 0.8633 (t) outliers start: 29 outliers final: 10 residues processed: 110 average time/residue: 1.6328 time to fit residues: 194.5183 Evaluate side-chains 106 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 91 time to evaluate : 1.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 128 ASN Chi-restraints excluded: chain E residue 151 ILE 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: 4.9990 chunk 2 optimal weight: 5.9990 chunk 133 optimal weight: 0.9990 chunk 73 optimal weight: 9.9990 chunk 152 optimal weight: 7.9990 chunk 123 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 160 optimal weight: 8.9990 chunk 45 optimal weight: 0.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 41 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN E 12 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 14960 Z= 0.424 Angle : 0.607 7.240 20310 Z= 0.290 Chirality : 0.047 0.144 2250 Planarity : 0.004 0.060 2600 Dihedral : 7.454 100.696 2087 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.42 % Allowed : 15.03 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.20), residues: 1835 helix: 0.97 (0.20), residues: 770 sheet: 1.06 (0.28), residues: 330 loop : 0.66 (0.24), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 79 HIS 0.005 0.001 HIS B 161 PHE 0.008 0.001 PHE A 127 TYR 0.008 0.001 TYR A 188 ARG 0.002 0.000 ARG B 254 *********************** 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 129 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 91 time to evaluate : 1.764 Fit side-chains REVERT: A 314 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.8157 (tt0) REVERT: A 354 GLN cc_start: 0.8805 (pp30) cc_final: 0.8503 (pp30) REVERT: A 355 MET cc_start: 0.9316 (OUTLIER) cc_final: 0.9022 (mtp) REVERT: B 95 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.8212 (mtm110) REVERT: B 107 GLU cc_start: 0.9138 (OUTLIER) cc_final: 0.8674 (tt0) REVERT: B 176 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.8413 (mtp) REVERT: B 215 LYS cc_start: 0.9224 (OUTLIER) cc_final: 0.8926 (mttm) REVERT: B 314 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.7610 (tp40) REVERT: B 354 GLN cc_start: 0.8662 (pp30) cc_final: 0.8123 (pp30) REVERT: C 51 ASP cc_start: 0.8975 (OUTLIER) cc_final: 0.8670 (p0) REVERT: C 246 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8093 (mt0) REVERT: C 325 MET cc_start: 0.8903 (mmp) cc_final: 0.8557 (mmp) REVERT: C 354 GLN cc_start: 0.8920 (mp10) cc_final: 0.8574 (mp10) REVERT: D 354 GLN cc_start: 0.8570 (pp30) cc_final: 0.8177 (pp30) outliers start: 38 outliers final: 17 residues processed: 119 average time/residue: 1.5744 time to fit residues: 205.4761 Evaluate side-chains 115 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 89 time to evaluate : 1.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 128 ASN Chi-restraints excluded: chain E residue 151 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 6.9990 chunk 161 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 104 optimal weight: 0.0570 chunk 44 optimal weight: 0.8980 chunk 178 optimal weight: 3.9990 chunk 148 optimal weight: 7.9990 chunk 82 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 overall best weight: 0.7900 ------------------------------------------------------------------------------- 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 41 GLN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 GLN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 ASN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN E 12 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14960 Z= 0.136 Angle : 0.523 6.825 20310 Z= 0.242 Chirality : 0.043 0.134 2250 Planarity : 0.003 0.058 2600 Dihedral : 7.120 95.534 2087 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.91 % Allowed : 15.54 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.21), residues: 1835 helix: 1.23 (0.20), residues: 770 sheet: 1.20 (0.29), residues: 330 loop : 0.70 (0.24), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 79 HIS 0.002 0.000 HIS E 161 PHE 0.006 0.001 PHE A 255 TYR 0.007 0.001 TYR E 69 ARG 0.002 0.000 ARG A 206 *********************** 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 124 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 94 time to evaluate : 1.734 Fit side-chains REVERT: A 354 GLN cc_start: 0.8734 (pp30) cc_final: 0.8395 (pp30) REVERT: A 355 MET cc_start: 0.9281 (OUTLIER) cc_final: 0.9000 (mtp) REVERT: B 354 GLN cc_start: 0.8591 (pp30) cc_final: 0.8093 (pp30) REVERT: C 325 MET cc_start: 0.8828 (mmp) cc_final: 0.8588 (mmp) REVERT: C 354 GLN cc_start: 0.8952 (mp10) cc_final: 0.8611 (mp10) REVERT: D 246 GLN cc_start: 0.8759 (mt0) cc_final: 0.8552 (mt0) REVERT: D 314 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.8172 (tt0) REVERT: D 354 GLN cc_start: 0.8593 (pp30) cc_final: 0.8245 (pp30) REVERT: D 355 MET cc_start: 0.9436 (mtm) cc_final: 0.9151 (mtm) REVERT: E 355 MET cc_start: 0.9223 (mtp) cc_final: 0.8840 (mtm) outliers start: 30 outliers final: 7 residues processed: 113 average time/residue: 1.5591 time to fit residues: 191.2558 Evaluate side-chains 101 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 92 time to evaluate : 1.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain E residue 128 ASN 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: 7.9990 chunk 101 optimal weight: 3.9990 chunk 130 optimal weight: 8.9990 chunk 150 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 178 optimal weight: 7.9990 chunk 111 optimal weight: 10.0000 chunk 108 optimal weight: 8.9990 chunk 82 optimal weight: 0.6980 chunk 110 optimal weight: 8.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- 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 41 GLN C 12 ASN C 246 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 14960 Z= 0.474 Angle : 0.629 9.768 20310 Z= 0.299 Chirality : 0.048 0.143 2250 Planarity : 0.004 0.049 2600 Dihedral : 7.430 101.439 2087 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.78 % Allowed : 15.16 % Favored : 83.06 % 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: 1.29 (0.20), residues: 1835 helix: 1.16 (0.20), residues: 770 sheet: 1.11 (0.28), residues: 330 loop : 0.59 (0.24), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 79 HIS 0.006 0.001 HIS B 161 PHE 0.009 0.001 PHE E 127 TYR 0.010 0.001 TYR B 188 ARG 0.003 0.000 ARG B 39 *********************** 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 120 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 92 time to evaluate : 1.677 Fit side-chains REVERT: A 314 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.8146 (tt0) REVERT: A 354 GLN cc_start: 0.8814 (pp30) cc_final: 0.8466 (pp30) REVERT: A 355 MET cc_start: 0.9322 (OUTLIER) cc_final: 0.9020 (mtp) REVERT: B 82 MET cc_start: 0.9234 (OUTLIER) cc_final: 0.8958 (tpp) REVERT: B 95 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.8207 (mtm110) REVERT: B 132 MET cc_start: 0.9181 (ppp) cc_final: 0.8977 (OUTLIER) REVERT: B 314 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.7630 (tp40) REVERT: B 354 GLN cc_start: 0.8623 (pp30) cc_final: 0.8129 (pp30) REVERT: C 6 THR cc_start: 0.9118 (OUTLIER) cc_final: 0.8875 (p) REVERT: C 325 MET cc_start: 0.8936 (mmp) cc_final: 0.8674 (mmp) REVERT: C 354 GLN cc_start: 0.8935 (mp10) cc_final: 0.8575 (mp10) REVERT: D 314 GLN cc_start: 0.8558 (OUTLIER) cc_final: 0.8068 (tp40) REVERT: D 354 GLN cc_start: 0.8687 (pp30) cc_final: 0.8438 (pp30) REVERT: E 99 GLU cc_start: 0.9268 (OUTLIER) cc_final: 0.8770 (pm20) REVERT: E 355 MET cc_start: 0.9221 (mtp) cc_final: 0.8821 (mtm) outliers start: 28 outliers final: 12 residues processed: 113 average time/residue: 1.5742 time to fit residues: 193.0225 Evaluate side-chains 109 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 90 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 128 ASN Chi-restraints excluded: chain E residue 151 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 35 optimal weight: 0.0970 chunk 34 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 121 optimal weight: 0.1980 chunk 88 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 140 optimal weight: 5.9990 chunk 162 optimal weight: 8.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 162 ASN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 GLN C 12 ASN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN D 162 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14960 Z= 0.131 Angle : 0.531 7.332 20310 Z= 0.245 Chirality : 0.042 0.135 2250 Planarity : 0.003 0.056 2600 Dihedral : 7.091 95.181 2087 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.96 % Allowed : 16.11 % Favored : 82.93 % 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 (0.20), residues: 1835 helix: 1.36 (0.20), residues: 770 sheet: 1.22 (0.29), residues: 330 loop : 0.75 (0.24), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 79 HIS 0.002 0.000 HIS E 161 PHE 0.007 0.001 PHE E 255 TYR 0.007 0.001 TYR E 69 ARG 0.002 0.000 ARG A 206 *********************** 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 107 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 92 time to evaluate : 1.703 Fit side-chains REVERT: A 44 MET cc_start: 0.9213 (mmm) cc_final: 0.6689 (pmt) REVERT: A 354 GLN cc_start: 0.8717 (pp30) cc_final: 0.8377 (pp30) REVERT: A 355 MET cc_start: 0.9254 (OUTLIER) cc_final: 0.8985 (mtp) REVERT: B 354 GLN cc_start: 0.8556 (pp30) cc_final: 0.8047 (pp30) REVERT: C 325 MET cc_start: 0.8858 (mmp) cc_final: 0.8605 (mmp) REVERT: C 354 GLN cc_start: 0.8978 (mp10) cc_final: 0.8617 (mp10) REVERT: D 246 GLN cc_start: 0.8752 (mt0) cc_final: 0.8475 (mt0) REVERT: D 314 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.8039 (tp40) REVERT: D 354 GLN cc_start: 0.8591 (pp30) cc_final: 0.8339 (pp30) REVERT: E 355 MET cc_start: 0.9215 (mtp) cc_final: 0.8848 (mtm) outliers start: 15 outliers final: 7 residues processed: 101 average time/residue: 1.5533 time to fit residues: 170.5218 Evaluate side-chains 100 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 91 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 151 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 1.9990 chunk 155 optimal weight: 0.5980 chunk 166 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 72 optimal weight: 8.9990 chunk 130 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 150 optimal weight: 0.0770 chunk 157 optimal weight: 6.9990 chunk 165 optimal weight: 6.9990 chunk 109 optimal weight: 4.9990 overall best weight: 1.5344 ------------------------------------------------------------------------------- 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 41 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14960 Z= 0.196 Angle : 0.548 8.664 20310 Z= 0.251 Chirality : 0.043 0.130 2250 Planarity : 0.003 0.049 2600 Dihedral : 7.077 94.451 2087 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.02 % Allowed : 16.11 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.21), residues: 1835 helix: 1.42 (0.20), residues: 770 sheet: 1.25 (0.29), residues: 330 loop : 0.72 (0.25), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 79 HIS 0.003 0.001 HIS B 161 PHE 0.007 0.001 PHE E 127 TYR 0.005 0.001 TYR B 188 ARG 0.001 0.000 ARG C 254 *********************** 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 108 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 92 time to evaluate : 1.834 Fit side-chains REVERT: A 44 MET cc_start: 0.9216 (mmm) cc_final: 0.6693 (pmt) REVERT: A 314 GLN cc_start: 0.8754 (OUTLIER) cc_final: 0.8091 (tt0) REVERT: A 354 GLN cc_start: 0.8724 (pp30) cc_final: 0.8373 (pp30) REVERT: A 355 MET cc_start: 0.9276 (OUTLIER) cc_final: 0.8998 (mtp) REVERT: B 354 GLN cc_start: 0.8551 (pp30) cc_final: 0.8063 (pp30) REVERT: C 325 MET cc_start: 0.8877 (mmp) cc_final: 0.8592 (mmp) REVERT: C 354 GLN cc_start: 0.8949 (mp10) cc_final: 0.8574 (mp10) REVERT: D 246 GLN cc_start: 0.8763 (mt0) cc_final: 0.8482 (mt0) REVERT: D 314 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.8030 (tp40) REVERT: D 354 GLN cc_start: 0.8552 (pp30) cc_final: 0.8249 (pp30) REVERT: E 6 THR cc_start: 0.9213 (OUTLIER) cc_final: 0.8801 (t) REVERT: E 355 MET cc_start: 0.9204 (mtp) cc_final: 0.8837 (mtm) outliers start: 16 outliers final: 8 residues processed: 103 average time/residue: 1.6553 time to fit residues: 185.1266 Evaluate side-chains 103 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 91 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 151 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 3.9990 chunk 107 optimal weight: 0.0670 chunk 83 optimal weight: 3.9990 chunk 122 optimal weight: 7.9990 chunk 184 optimal weight: 8.9990 chunk 169 optimal weight: 6.9990 chunk 146 optimal weight: 9.9990 chunk 15 optimal weight: 8.9990 chunk 113 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 overall best weight: 2.0122 ------------------------------------------------------------------------------- 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 41 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 14960 Z= 0.233 Angle : 0.558 8.714 20310 Z= 0.257 Chirality : 0.044 0.130 2250 Planarity : 0.003 0.051 2600 Dihedral : 7.115 94.669 2087 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.15 % Allowed : 15.86 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.21), residues: 1835 helix: 1.43 (0.20), residues: 770 sheet: 1.26 (0.29), residues: 330 loop : 0.80 (0.24), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 79 HIS 0.003 0.001 HIS B 161 PHE 0.008 0.001 PHE E 127 TYR 0.007 0.001 TYR B 133 ARG 0.001 0.000 ARG C 254 ********************** 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 111 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 93 time to evaluate : 1.677 Fit side-chains REVERT: A 44 MET cc_start: 0.9219 (mmm) cc_final: 0.6690 (pmt) REVERT: A 314 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8076 (tt0) REVERT: A 354 GLN cc_start: 0.8727 (pp30) cc_final: 0.8390 (pp30) REVERT: A 355 MET cc_start: 0.9291 (OUTLIER) cc_final: 0.8994 (mtp) REVERT: B 354 GLN cc_start: 0.8540 (pp30) cc_final: 0.8056 (pp30) REVERT: C 325 MET cc_start: 0.8890 (mmp) cc_final: 0.8602 (mmp) REVERT: C 354 GLN cc_start: 0.8960 (mp10) cc_final: 0.8570 (mp10) REVERT: D 246 GLN cc_start: 0.8771 (mt0) cc_final: 0.8541 (mt0) REVERT: D 314 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.8031 (tp40) REVERT: D 354 GLN cc_start: 0.8588 (pp30) cc_final: 0.8373 (pp30) REVERT: E 6 THR cc_start: 0.9214 (OUTLIER) cc_final: 0.8801 (t) REVERT: E 355 MET cc_start: 0.9202 (mtp) cc_final: 0.8823 (mtm) outliers start: 18 outliers final: 8 residues processed: 107 average time/residue: 1.5637 time to fit residues: 182.1869 Evaluate side-chains 104 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 92 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 151 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 135 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 129 optimal weight: 4.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 41 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.047388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2510 r_free = 0.2510 target = 0.037493 restraints weight = 42854.874| |-----------------------------------------------------------------------------| r_work (start): 0.2513 rms_B_bonded: 2.87 r_work: 0.2374 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 14960 Z= 0.231 Angle : 0.560 9.359 20310 Z= 0.258 Chirality : 0.044 0.133 2250 Planarity : 0.003 0.049 2600 Dihedral : 7.117 94.725 2087 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.02 % Allowed : 15.92 % Favored : 83.06 % 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: 1.64 (0.21), residues: 1835 helix: 1.45 (0.20), residues: 770 sheet: 1.26 (0.29), residues: 330 loop : 0.81 (0.24), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 79 HIS 0.003 0.001 HIS B 161 PHE 0.008 0.001 PHE E 127 TYR 0.006 0.001 TYR B 188 ARG 0.001 0.000 ARG C 254 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4014.63 seconds wall clock time: 72 minutes 4.22 seconds (4324.22 seconds total)