Starting phenix.real_space_refine on Fri Feb 16 18:45:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z7h_14532/02_2024/7z7h_14532_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z7h_14532/02_2024/7z7h_14532.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z7h_14532/02_2024/7z7h_14532.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z7h_14532/02_2024/7z7h_14532.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z7h_14532/02_2024/7z7h_14532_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z7h_14532/02_2024/7z7h_14532_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 5 5.21 5 S 109 5.16 5 C 10165 2.51 5 N 2720 2.21 5 O 3100 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 56": "OD1" <-> "OD2" Residue "D TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 80": "OD1" <-> "OD2" Residue "D GLU 83": "OE1" <-> "OE2" Residue "D PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 100": "OE1" <-> "OE2" Residue "D GLU 117": "OE1" <-> "OE2" Residue "D PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 167": "OE1" <-> "OE2" Residue "D TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 224": "OE1" <-> "OE2" Residue "D GLU 237": "OE1" <-> "OE2" Residue "D TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 253": "OE1" <-> "OE2" Residue "D PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 288": "OD1" <-> "OD2" Residue "D ASP 292": "OD1" <-> "OD2" Residue "D TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 311": "OD1" <-> "OD2" Residue "D GLU 334": "OE1" <-> "OE2" Residue "D TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 120": "OE1" <-> "OE2" Residue "F GLU 128": "OE1" <-> "OE2" Residue "F PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 160": "OE1" <-> "OE2" Residue "F TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 186": "OD1" <-> "OD2" Residue "F GLU 199": "OE1" <-> "OE2" Residue "F ASP 213": "OD1" <-> "OD2" Residue "F ASP 215": "OD1" <-> "OD2" Residue "F TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 222": "OD1" <-> "OD2" Residue "F GLU 231": "OE1" <-> "OE2" Residue "F ARG 233": "NH1" <-> "NH2" Residue "F ASP 244": "OD1" <-> "OD2" Residue "F PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 282": "NH1" <-> "NH2" Residue "B TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 56": "OD1" <-> "OD2" Residue "B TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 80": "OD1" <-> "OD2" Residue "B GLU 83": "OE1" <-> "OE2" Residue "B PHE 90": "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 GLU 117": "OE1" <-> "OE2" Residue "B PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 167": "OE1" <-> "OE2" Residue "B TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B GLU 237": "OE1" <-> "OE2" Residue "B TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 253": "OE1" <-> "OE2" Residue "B PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 288": "OD1" <-> "OD2" Residue "B ASP 292": "OD1" <-> "OD2" Residue "B TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 311": "OD1" <-> "OD2" Residue "B GLU 334": "OE1" <-> "OE2" Residue "B TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 56": "OD1" <-> "OD2" Residue "E TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 80": "OD1" <-> "OD2" Residue "E GLU 83": "OE1" <-> "OE2" Residue "E PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 100": "OE1" <-> "OE2" Residue "E GLU 117": "OE1" <-> "OE2" Residue "E PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 167": "OE1" <-> "OE2" Residue "E TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 224": "OE1" <-> "OE2" Residue "E GLU 237": "OE1" <-> "OE2" Residue "E TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 253": "OE1" <-> "OE2" Residue "E PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 288": "OD1" <-> "OD2" Residue "E ASP 292": "OD1" <-> "OD2" Residue "E TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 311": "OD1" <-> "OD2" Residue "E GLU 334": "OE1" <-> "OE2" Residue "E TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 56": "OD1" <-> "OD2" Residue "C TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 80": "OD1" <-> "OD2" Residue "C GLU 83": "OE1" <-> "OE2" Residue "C PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 100": "OE1" <-> "OE2" Residue "C GLU 117": "OE1" <-> "OE2" Residue "C PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 167": "OE1" <-> "OE2" Residue "C TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C GLU 237": "OE1" <-> "OE2" Residue "C TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 253": "OE1" <-> "OE2" Residue "C PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 288": "OD1" <-> "OD2" Residue "C ASP 292": "OD1" <-> "OD2" Residue "C TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 311": "OD1" <-> "OD2" Residue "C GLU 334": "OE1" <-> "OE2" Residue "C TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 56": "OD1" <-> "OD2" Residue "A TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 80": "OD1" <-> "OD2" Residue "A GLU 83": "OE1" <-> "OE2" Residue "A PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 100": "OE1" <-> "OE2" Residue "A GLU 117": "OE1" <-> "OE2" Residue "A PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 167": "OE1" <-> "OE2" Residue "A TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A GLU 237": "OE1" <-> "OE2" Residue "A TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 253": "OE1" <-> "OE2" Residue "A PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 288": "OD1" <-> "OD2" Residue "A ASP 292": "OD1" <-> "OD2" Residue "A TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 311": "OD1" <-> "OD2" Residue "A GLU 334": "OE1" <-> "OE2" Residue "A TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16111 Number of models: 1 Model: "" Number of chains: 12 Chain: "D" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, '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: "F" Number of atoms: 1427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1427 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 12, 'TRANS': 168} Chain: "B" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, '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: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, '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: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, '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: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, '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: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'ADP': 1, 'APR': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'NCA': 1} Classifications: {'undetermined': 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: "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} 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: "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} Time building chain proxies: 8.87, per 1000 atoms: 0.55 Number of scatterers: 16111 At special positions: 0 Unit cell: (124.2, 88.2, 197.1, 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 109 16.00 P 12 15.00 Mg 5 11.99 O 3100 8.00 N 2720 7.00 C 10165 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.67 Conformation dependent library (CDL) restraints added in 2.8 seconds 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3774 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 109 helices and 27 sheets defined 44.6% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.32 Creating SS restraints... Processing helix chain 'D' and resid 55 through 60 Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'D' and resid 79 through 92 removed outlier: 3.550A pdb=" N TRP D 86 " --> pdb=" O MET D 82 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR D 91 " --> pdb=" O HIS D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 100 No H-bonds generated for 'chain 'D' and resid 98 through 100' Processing helix chain 'D' and resid 113 through 127 removed outlier: 3.654A pdb=" N ILE D 122 " --> pdb=" O MET D 119 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N THR D 126 " --> pdb=" O MET D 123 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N PHE D 127 " --> pdb=" O PHE D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 removed outlier: 3.522A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA D 144 " --> pdb=" O LEU D 140 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER D 145 " --> pdb=" O SER D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 174 No H-bonds generated for 'chain 'D' and resid 172 through 174' Processing helix chain 'D' and resid 182 through 196 removed outlier: 3.503A pdb=" N LYS D 191 " --> pdb=" O ASP D 187 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG D 196 " --> pdb=" O ILE D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 216 removed outlier: 3.618A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL D 209 " --> pdb=" O GLU D 205 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG D 210 " --> pdb=" O ARG D 206 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE D 212 " --> pdb=" O ILE D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 232 removed outlier: 3.533A pdb=" N SER D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 236 No H-bonds generated for 'chain 'D' and resid 234 through 236' Processing helix chain 'D' and resid 252 through 262 removed outlier: 4.302A pdb=" N CYS D 257 " --> pdb=" O ARG D 254 " (cutoff:3.500A) Proline residue: D 258 - end of helix Processing helix chain 'D' and resid 264 through 266 No H-bonds generated for 'chain 'D' and resid 264 through 266' Processing helix chain 'D' and resid 274 through 283 Processing helix chain 'D' and resid 289 through 295 removed outlier: 3.520A pdb=" N TYR D 294 " --> pdb=" O ARG D 290 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 305 Processing helix chain 'D' and resid 309 through 320 Processing helix chain 'D' and resid 335 through 348 removed outlier: 4.368A pdb=" N VAL D 339 " --> pdb=" O ARG D 335 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N TRP D 340 " --> pdb=" O LYS D 336 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY D 343 " --> pdb=" O VAL D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 355 Processing helix chain 'D' and resid 359 through 365 Processing helix chain 'D' and resid 367 through 372 Processing helix chain 'F' and resid 119 through 125 Processing helix chain 'F' and resid 138 through 148 removed outlier: 3.954A pdb=" N PHE F 148 " --> pdb=" O PHE F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 167 Processing helix chain 'F' and resid 173 through 183 Processing helix chain 'F' and resid 274 through 276 No H-bonds generated for 'chain 'F' and resid 274 through 276' Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 79 through 93 Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 113 through 127 removed outlier: 3.637A pdb=" N PHE B 127 " --> pdb=" O MET B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 144 removed outlier: 3.727A pdb=" N ALA B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 182 through 196 removed outlier: 3.703A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 removed outlier: 3.664A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 232 removed outlier: 3.582A pdb=" N SER B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 236 No H-bonds generated for 'chain 'B' and resid 234 through 236' Processing helix chain 'B' and resid 252 through 262 removed outlier: 4.218A pdb=" N CYS B 257 " --> pdb=" O ARG B 254 " (cutoff:3.500A) Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 264 through 266 No H-bonds generated for 'chain 'B' and resid 264 through 266' Processing helix chain 'B' and resid 274 through 283 Processing helix chain 'B' and resid 289 through 295 Processing helix chain 'B' and resid 302 through 305 Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 335 through 348 removed outlier: 4.224A pdb=" N VAL B 339 " --> pdb=" O ARG B 335 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N TRP B 340 " --> pdb=" O LYS B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 355 Processing helix chain 'B' and resid 359 through 365 Processing helix chain 'B' and resid 367 through 372 Processing helix chain 'E' and resid 55 through 60 Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 79 through 92 Processing helix chain 'E' and resid 98 through 100 No H-bonds generated for 'chain 'E' and resid 98 through 100' Processing helix chain 'E' and resid 114 through 127 Processing helix chain 'E' and resid 137 through 144 removed outlier: 3.549A pdb=" N ALA E 144 " --> pdb=" O LEU E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 182 through 196 Processing helix chain 'E' and resid 202 through 216 Processing helix chain 'E' and resid 223 through 232 removed outlier: 3.648A pdb=" N SER E 232 " --> pdb=" O ALA E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 236 No H-bonds generated for 'chain 'E' and resid 234 through 236' Processing helix chain 'E' and resid 252 through 262 removed outlier: 3.502A pdb=" N ARG E 256 " --> pdb=" O GLU E 253 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N CYS E 257 " --> pdb=" O ARG E 254 " (cutoff:3.500A) Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 264 through 267 Processing helix chain 'E' and resid 274 through 283 Processing helix chain 'E' and resid 289 through 295 Processing helix chain 'E' and resid 302 through 305 Processing helix chain 'E' and resid 309 through 320 Processing helix chain 'E' and resid 335 through 348 removed outlier: 4.339A pdb=" N VAL E 339 " --> pdb=" O ARG E 335 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N TRP E 340 " --> pdb=" O LYS E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 355 Processing helix chain 'E' and resid 359 through 365 Processing helix chain 'E' and resid 367 through 372 Processing helix chain 'C' and resid 55 through 60 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 79 through 92 Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 114 through 127 Processing helix chain 'C' and resid 137 through 144 removed outlier: 3.516A pdb=" N ALA C 144 " --> pdb=" O LEU C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 182 through 196 Processing helix chain 'C' and resid 203 through 216 removed outlier: 3.700A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 232 removed outlier: 3.512A pdb=" N SER C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 236 No H-bonds generated for 'chain 'C' and resid 234 through 236' Processing helix chain 'C' and resid 252 through 262 removed outlier: 4.276A pdb=" N CYS C 257 " --> pdb=" O ARG C 254 " (cutoff:3.500A) Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 264 through 266 No H-bonds generated for 'chain 'C' and resid 264 through 266' Processing helix chain 'C' and resid 274 through 283 Processing helix chain 'C' and resid 289 through 295 Processing helix chain 'C' and resid 302 through 305 Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 336 through 348 removed outlier: 4.020A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLY C 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU C 346 " --> pdb=" O GLY C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 355 Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'C' and resid 367 through 372 Processing helix chain 'A' and resid 55 through 60 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 79 through 92 Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 114 through 127 Processing helix chain 'A' and resid 137 through 144 removed outlier: 3.560A pdb=" N ALA A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 182 through 196 removed outlier: 3.611A pdb=" N ARG A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 216 removed outlier: 3.620A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 232 removed outlier: 3.706A pdb=" N SER A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 262 removed outlier: 4.221A pdb=" N CYS A 257 " --> pdb=" O ARG A 254 " (cutoff:3.500A) Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 264 through 267 Processing helix chain 'A' and resid 274 through 283 Processing helix chain 'A' and resid 287 through 295 Processing helix chain 'A' and resid 302 through 305 Processing helix chain 'A' and resid 309 through 320 Processing helix chain 'A' and resid 336 through 348 removed outlier: 4.138A pdb=" N VAL A 339 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY A 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU A 346 " --> pdb=" O GLY A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 355 Processing helix chain 'A' and resid 359 through 365 Processing helix chain 'A' and resid 367 through 372 Processing sheet with id= A, first strand: chain 'D' and resid 8 through 10 removed outlier: 3.520A pdb=" N ALA D 29 " --> pdb=" O ALA D 19 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 34 through 38 removed outlier: 3.578A pdb=" N VAL D 35 " --> pdb=" O LYS D 68 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 103 through 107 Processing sheet with id= D, first strand: chain 'D' and resid 297 through 300 removed outlier: 6.512A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE D 165 " --> pdb=" O GLY D 150 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL D 163 " --> pdb=" O VAL D 152 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 238 through 241 Processing sheet with id= F, first strand: chain 'F' and resid 107 through 115 removed outlier: 3.562A pdb=" N ASP F 115 " --> pdb=" O PRO F 208 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LEU F 209 " --> pdb=" O HIS F 280 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 192 through 195 removed outlier: 3.611A pdb=" N SER F 265 " --> pdb=" O HIS F 258 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA F 220 " --> pdb=" O ASN F 227 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 8 through 10 removed outlier: 3.803A pdb=" N VAL B 17 " --> pdb=" O PHE B 31 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE B 31 " --> pdb=" O VAL B 17 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA B 19 " --> pdb=" O ALA B 29 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA B 29 " --> pdb=" O ALA B 19 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 34 through 38 removed outlier: 3.537A pdb=" N THR B 66 " --> pdb=" O ARG B 37 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 103 through 107 Processing sheet with id= K, first strand: chain 'B' and resid 298 through 300 removed outlier: 3.560A pdb=" N MET B 176 " --> pdb=" O ASN B 162 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 238 through 241 Processing sheet with id= M, first strand: chain 'E' and resid 8 through 11 removed outlier: 3.753A pdb=" N LYS E 18 " --> pdb=" O ASP E 11 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE E 31 " --> pdb=" O VAL E 17 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA E 19 " --> pdb=" O ALA E 29 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA E 29 " --> pdb=" O ALA E 19 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 35 through 38 Processing sheet with id= O, first strand: chain 'E' and resid 103 through 107 Processing sheet with id= P, first strand: chain 'E' and resid 298 through 300 removed outlier: 3.520A pdb=" N SER E 155 " --> pdb=" O SER E 300 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 238 through 241 Processing sheet with id= R, first strand: chain 'C' and resid 8 through 10 removed outlier: 3.882A pdb=" N ALA C 29 " --> pdb=" O ALA C 19 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 34 through 38 removed outlier: 3.723A pdb=" N ARG C 37 " --> pdb=" O THR C 66 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR C 66 " --> pdb=" O ARG C 37 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 103 through 107 Processing sheet with id= U, first strand: chain 'C' and resid 298 through 300 Processing sheet with id= V, first strand: chain 'C' and resid 238 through 241 Processing sheet with id= W, first strand: chain 'A' and resid 8 through 10 removed outlier: 3.631A pdb=" N PHE A 31 " --> pdb=" O VAL A 17 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A 19 " --> pdb=" O ALA A 29 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA A 29 " --> pdb=" O ALA A 19 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'A' and resid 65 through 69 removed outlier: 3.731A pdb=" N THR A 66 " --> pdb=" O ARG A 37 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG A 37 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'A' and resid 103 through 107 removed outlier: 3.806A pdb=" N GLU A 107 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'A' and resid 298 through 300 Processing sheet with id= AA, first strand: chain 'A' and resid 238 through 241 620 hydrogen bonds defined for protein. 1506 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: 4.89 Time building geometry restraints manager: 7.89 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: 5200 1.34 - 1.46: 3174 1.46 - 1.58: 7876 1.58 - 1.69: 20 1.69 - 1.81: 196 Bond restraints: 16466 Sorted by residual: bond pdb=" C1' APR D 403 " pdb=" O4' APR D 403 " ideal model delta sigma weight residual 1.393 1.639 -0.246 2.00e-02 2.50e+03 1.52e+02 bond pdb=" C4' APR D 403 " pdb=" O4' APR D 403 " ideal model delta sigma weight residual 1.430 1.632 -0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" C2 APR D 403 " pdb=" N1 APR D 403 " ideal model delta sigma weight residual 1.331 1.531 -0.200 2.00e-02 2.50e+03 1.00e+02 bond pdb=" C6 APR D 403 " pdb=" N1 APR D 403 " ideal model delta sigma weight residual 1.338 1.527 -0.189 2.00e-02 2.50e+03 8.93e+01 bond pdb=" C7 NCA F 300 " pdb=" N7 NCA F 300 " ideal model delta sigma weight residual 1.340 1.525 -0.185 2.00e-02 2.50e+03 8.57e+01 ... (remaining 16461 not shown) Histogram of bond angle deviations from ideal: 94.25 - 103.12: 249 103.12 - 111.98: 8010 111.98 - 120.85: 9170 120.85 - 129.71: 4816 129.71 - 138.57: 103 Bond angle restraints: 22348 Sorted by residual: angle pdb=" C1' APR D 403 " pdb=" O4' APR D 403 " pdb=" C4' APR D 403 " ideal model delta sigma weight residual 111.27 94.25 17.02 3.00e+00 1.11e-01 3.22e+01 angle pdb=" O1A APR D 403 " pdb=" PA APR D 403 " pdb=" O2A APR D 403 " ideal model delta sigma weight residual 121.71 107.08 14.63 3.00e+00 1.11e-01 2.38e+01 angle pdb=" C MET A 283 " pdb=" N LYS A 284 " pdb=" CA LYS A 284 " ideal model delta sigma weight residual 121.94 112.61 9.33 2.00e+00 2.50e-01 2.18e+01 angle pdb=" O1B APR D 403 " pdb=" PB APR D 403 " pdb=" O2B APR D 403 " ideal model delta sigma weight residual 122.24 108.72 13.52 3.00e+00 1.11e-01 2.03e+01 angle pdb=" N MET A 283 " pdb=" CA MET A 283 " pdb=" C MET A 283 " ideal model delta sigma weight residual 111.71 116.48 -4.77 1.15e+00 7.56e-01 1.72e+01 ... (remaining 22343 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.61: 9354 22.61 - 45.21: 491 45.21 - 67.82: 75 67.82 - 90.43: 15 90.43 - 113.03: 5 Dihedral angle restraints: 9940 sinusoidal: 4052 harmonic: 5888 Sorted by residual: dihedral pdb=" CA PHE F 126 " pdb=" C PHE F 126 " pdb=" N PRO F 127 " pdb=" CA PRO F 127 " ideal model delta harmonic sigma weight residual 180.00 150.64 29.36 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" C5' ADP D 401 " pdb=" O5' ADP D 401 " pdb=" PA ADP D 401 " pdb=" O2A ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 53.04 -113.03 1 2.00e+01 2.50e-03 3.34e+01 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 50.80 -110.79 1 2.00e+01 2.50e-03 3.25e+01 ... (remaining 9937 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 2035 0.082 - 0.164: 412 0.164 - 0.245: 33 0.245 - 0.327: 1 0.327 - 0.409: 3 Chirality restraints: 2484 Sorted by residual: chirality pdb=" C4' APR D 403 " pdb=" C3' APR D 403 " pdb=" C5' APR D 403 " pdb=" O4' APR D 403 " both_signs ideal model delta sigma weight residual False -2.54 -2.95 0.41 2.00e-01 2.50e+01 4.18e+00 chirality pdb=" C1' APR D 403 " pdb=" C2' APR D 403 " pdb=" N9 APR D 403 " pdb=" O4' APR D 403 " both_signs ideal model delta sigma weight residual False 2.40 2.78 -0.39 2.00e-01 2.50e+01 3.73e+00 chirality pdb=" C4D APR D 403 " pdb=" C3D APR D 403 " pdb=" C5D APR D 403 " pdb=" O4D APR D 403 " both_signs ideal model delta sigma weight residual False -2.49 -2.16 -0.33 2.00e-01 2.50e+01 2.70e+00 ... (remaining 2481 not shown) Planarity restraints: 2849 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 117 " 0.160 9.50e-02 1.11e+02 8.76e-02 3.46e+01 pdb=" NE ARG F 117 " -0.042 2.00e-02 2.50e+03 pdb=" CZ ARG F 117 " 0.095 2.00e-02 2.50e+03 pdb=" NH1 ARG F 117 " -0.034 2.00e-02 2.50e+03 pdb=" NH2 ARG F 117 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 89 " 0.018 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" C THR B 89 " -0.061 2.00e-02 2.50e+03 pdb=" O THR B 89 " 0.023 2.00e-02 2.50e+03 pdb=" N PHE B 90 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 89 " 0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C THR A 89 " -0.059 2.00e-02 2.50e+03 pdb=" O THR A 89 " 0.022 2.00e-02 2.50e+03 pdb=" N PHE A 90 " 0.020 2.00e-02 2.50e+03 ... (remaining 2846 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 90 2.40 - 3.03: 10598 3.03 - 3.65: 24067 3.65 - 4.28: 34001 4.28 - 4.90: 56302 Nonbonded interactions: 125058 Sorted by model distance: nonbonded pdb=" O1B ADP D 401 " pdb="MG MG D 402 " model vdw 1.777 2.170 nonbonded pdb=" O1B ADP B 401 " pdb="MG MG B 402 " model vdw 1.829 2.170 nonbonded pdb=" O1A ADP D 401 " pdb="MG MG D 402 " model vdw 1.853 2.170 nonbonded pdb=" O3A ADP B 401 " pdb="MG MG B 402 " model vdw 1.873 2.170 nonbonded pdb=" O1B ADP A 401 " pdb="MG MG A 402 " model vdw 1.964 2.170 ... (remaining 125053 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' and (resid 5 through 375 or resid 401 through 402)) 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.300 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: 7.410 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 46.060 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.120 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.246 16466 Z= 0.705 Angle : 1.248 17.017 22348 Z= 0.687 Chirality : 0.064 0.409 2484 Planarity : 0.007 0.088 2849 Dihedral : 14.273 113.033 6166 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % 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: -0.19 (0.17), residues: 2009 helix: -0.49 (0.17), residues: 617 sheet: 0.72 (0.24), residues: 440 loop : -0.14 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.004 TRP E 356 HIS 0.019 0.003 HIS D 371 PHE 0.032 0.004 PHE D 31 TYR 0.033 0.006 TYR A 294 ARG 0.097 0.011 ARG F 117 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 261 time to evaluate : 1.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 123 MET cc_start: 0.8850 (mmp) cc_final: 0.8555 (tpp) REVERT: F 183 TYR cc_start: 0.8305 (m-80) cc_final: 0.7876 (m-80) REVERT: F 212 ILE cc_start: 0.8540 (mt) cc_final: 0.8326 (pt) REVERT: F 282 ARG cc_start: 0.7291 (ptt-90) cc_final: 0.7077 (mpp-170) REVERT: B 34 ILE cc_start: 0.9248 (mt) cc_final: 0.8901 (tp) REVERT: B 153 LEU cc_start: 0.8834 (tp) cc_final: 0.8492 (tt) REVERT: E 65 LEU cc_start: 0.7066 (mt) cc_final: 0.6708 (mt) REVERT: E 78 ASN cc_start: 0.7159 (t0) cc_final: 0.6898 (t0) REVERT: E 356 TRP cc_start: 0.7091 (m100) cc_final: 0.6534 (m100) REVERT: C 9 VAL cc_start: 0.9438 (t) cc_final: 0.9232 (m) REVERT: C 155 SER cc_start: 0.8644 (t) cc_final: 0.8379 (m) REVERT: A 123 MET cc_start: 0.8228 (mmp) cc_final: 0.7963 (mmt) outliers start: 0 outliers final: 0 residues processed: 261 average time/residue: 0.2855 time to fit residues: 110.2581 Evaluate side-chains 152 residues out of total 1726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 171 optimal weight: 6.9990 chunk 153 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 82 optimal weight: 0.9980 chunk 159 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 118 optimal weight: 0.9990 chunk 184 optimal weight: 6.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 111 ASN D 252 ASN B 111 ASN B 115 ASN B 162 ASN B 252 ASN E 59 GLN ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN C 111 ASN C 162 ASN A 59 GLN ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 252 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16466 Z= 0.207 Angle : 0.724 8.444 22348 Z= 0.368 Chirality : 0.046 0.264 2484 Planarity : 0.004 0.042 2849 Dihedral : 8.528 88.922 2321 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.62 % Allowed : 8.05 % Favored : 90.32 % 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: 0.85 (0.19), residues: 2009 helix: 0.40 (0.19), residues: 716 sheet: 1.00 (0.25), residues: 377 loop : 0.73 (0.22), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 79 HIS 0.008 0.001 HIS D 371 PHE 0.019 0.002 PHE E 90 TYR 0.017 0.002 TYR B 294 ARG 0.005 0.001 ARG C 196 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 180 time to evaluate : 1.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 183 TYR cc_start: 0.8311 (m-80) cc_final: 0.8072 (m-80) REVERT: B 34 ILE cc_start: 0.9327 (mt) cc_final: 0.9054 (tp) REVERT: B 227 MET cc_start: 0.8644 (ttp) cc_final: 0.8363 (ttp) REVERT: B 325 MET cc_start: 0.7981 (tpp) cc_final: 0.7307 (mmp) REVERT: E 65 LEU cc_start: 0.6983 (mt) cc_final: 0.6653 (mt) REVERT: E 78 ASN cc_start: 0.6591 (t0) cc_final: 0.6191 (t0) REVERT: E 325 MET cc_start: 0.5882 (ttm) cc_final: 0.5498 (ptm) REVERT: E 356 TRP cc_start: 0.6909 (m100) cc_final: 0.6662 (m100) REVERT: C 65 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7696 (mt) REVERT: C 269 MET cc_start: 0.8361 (tpp) cc_final: 0.7731 (mtt) REVERT: C 299 MET cc_start: 0.8642 (OUTLIER) cc_final: 0.8439 (ttp) REVERT: A 9 VAL cc_start: 0.8932 (OUTLIER) cc_final: 0.8699 (p) REVERT: A 225 ASN cc_start: 0.8303 (p0) cc_final: 0.8088 (p0) REVERT: A 313 MET cc_start: 0.8071 (mmm) cc_final: 0.7498 (mmm) outliers start: 28 outliers final: 12 residues processed: 195 average time/residue: 0.2645 time to fit residues: 78.5089 Evaluate side-chains 152 residues out of total 1726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 137 time to evaluate : 1.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain F residue 107 LYS Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 137 ASP Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 186 ASP Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 289 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 102 optimal weight: 7.9990 chunk 57 optimal weight: 10.0000 chunk 153 optimal weight: 0.6980 chunk 125 optimal weight: 9.9990 chunk 50 optimal weight: 20.0000 chunk 184 optimal weight: 3.9990 chunk 199 optimal weight: 0.2980 chunk 164 optimal weight: 9.9990 chunk 183 optimal weight: 9.9990 chunk 62 optimal weight: 9.9990 chunk 148 optimal weight: 6.9990 overall best weight: 3.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 246 GLN ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 16466 Z= 0.325 Angle : 0.728 7.395 22348 Z= 0.368 Chirality : 0.046 0.249 2484 Planarity : 0.004 0.055 2849 Dihedral : 7.757 78.544 2321 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.85 % Allowed : 9.73 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.19), residues: 2009 helix: 0.42 (0.19), residues: 715 sheet: 0.96 (0.26), residues: 375 loop : 0.64 (0.22), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 79 HIS 0.011 0.002 HIS D 371 PHE 0.031 0.002 PHE A 352 TYR 0.015 0.002 TYR F 183 ARG 0.005 0.001 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 142 time to evaluate : 1.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 123 MET cc_start: 0.8853 (tpp) cc_final: 0.8637 (tpp) REVERT: D 283 MET cc_start: 0.8259 (mmp) cc_final: 0.8006 (mmp) REVERT: D 325 MET cc_start: 0.7133 (OUTLIER) cc_final: 0.6855 (mtm) REVERT: F 183 TYR cc_start: 0.8446 (m-80) cc_final: 0.8128 (m-80) REVERT: F 214 MET cc_start: 0.6144 (tpp) cc_final: 0.5829 (tpp) REVERT: B 34 ILE cc_start: 0.9426 (mt) cc_final: 0.9080 (tp) REVERT: B 227 MET cc_start: 0.8645 (ttp) cc_final: 0.8305 (tpp) REVERT: B 325 MET cc_start: 0.8026 (tpp) cc_final: 0.7336 (mmp) REVERT: E 44 MET cc_start: -0.0658 (mmt) cc_final: -0.0955 (mpp) REVERT: E 65 LEU cc_start: 0.7086 (mt) cc_final: 0.6698 (mt) REVERT: E 78 ASN cc_start: 0.6968 (t0) cc_final: 0.6508 (t0) REVERT: E 325 MET cc_start: 0.6459 (ttm) cc_final: 0.5956 (ptm) REVERT: E 356 TRP cc_start: 0.6848 (m100) cc_final: 0.6556 (m100) REVERT: C 123 MET cc_start: 0.8877 (mmt) cc_final: 0.8594 (mmt) REVERT: C 132 MET cc_start: 0.8343 (tpp) cc_final: 0.8138 (tpt) REVERT: C 226 GLU cc_start: 0.8152 (tp30) cc_final: 0.7924 (tp30) REVERT: C 227 MET cc_start: 0.8385 (ttp) cc_final: 0.8120 (ttm) REVERT: C 269 MET cc_start: 0.8729 (OUTLIER) cc_final: 0.8285 (mtt) REVERT: C 283 MET cc_start: 0.7843 (mmp) cc_final: 0.7387 (mmp) REVERT: C 325 MET cc_start: 0.7812 (mtt) cc_final: 0.7490 (pmm) REVERT: A 9 VAL cc_start: 0.9031 (OUTLIER) cc_final: 0.8660 (p) REVERT: A 44 MET cc_start: 0.8768 (tpp) cc_final: 0.8560 (tpp) REVERT: A 225 ASN cc_start: 0.8385 (p0) cc_final: 0.8152 (p0) outliers start: 32 outliers final: 18 residues processed: 162 average time/residue: 0.2558 time to fit residues: 64.3083 Evaluate side-chains 150 residues out of total 1726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 129 time to evaluate : 2.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 10 CYS Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 374 CYS Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 137 ASP Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 215 ASP Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 260 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 182 optimal weight: 2.9990 chunk 138 optimal weight: 8.9990 chunk 95 optimal weight: 20.0000 chunk 20 optimal weight: 9.9990 chunk 88 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 185 optimal weight: 9.9990 chunk 196 optimal weight: 7.9990 chunk 96 optimal weight: 0.0060 chunk 175 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 overall best weight: 2.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN C 161 HIS A 40 HIS ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16466 Z= 0.216 Angle : 0.635 7.244 22348 Z= 0.315 Chirality : 0.044 0.200 2484 Planarity : 0.004 0.047 2849 Dihedral : 7.163 80.253 2321 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.09 % Allowed : 10.31 % Favored : 87.60 % 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 (0.19), residues: 2009 helix: 0.73 (0.20), residues: 690 sheet: 0.89 (0.25), residues: 375 loop : 0.64 (0.22), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 79 HIS 0.008 0.001 HIS D 371 PHE 0.019 0.002 PHE C 352 TYR 0.013 0.001 TYR A 306 ARG 0.005 0.000 ARG C 196 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 144 time to evaluate : 2.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 123 MET cc_start: 0.8912 (tpp) cc_final: 0.8680 (tpp) REVERT: F 183 TYR cc_start: 0.8423 (m-80) cc_final: 0.8061 (m-80) REVERT: F 214 MET cc_start: 0.6157 (tpp) cc_final: 0.5646 (tpp) REVERT: B 227 MET cc_start: 0.8609 (ttp) cc_final: 0.8344 (tpp) REVERT: B 269 MET cc_start: 0.8204 (mmm) cc_final: 0.7903 (mtp) REVERT: B 283 MET cc_start: 0.8272 (mmp) cc_final: 0.8066 (mmp) REVERT: B 325 MET cc_start: 0.7944 (tpp) cc_final: 0.7388 (mmp) REVERT: E 78 ASN cc_start: 0.6972 (t0) cc_final: 0.6591 (t0) REVERT: E 107 GLU cc_start: 0.5078 (OUTLIER) cc_final: 0.4766 (mt-10) REVERT: E 241 GLU cc_start: 0.7770 (tp30) cc_final: 0.7545 (tp30) REVERT: E 297 ASN cc_start: 0.8521 (t0) cc_final: 0.7989 (t0) REVERT: E 325 MET cc_start: 0.6420 (ttm) cc_final: 0.6133 (ptm) REVERT: E 356 TRP cc_start: 0.6818 (m100) cc_final: 0.6348 (m100) REVERT: C 132 MET cc_start: 0.7963 (tpp) cc_final: 0.7704 (tpt) REVERT: C 226 GLU cc_start: 0.8168 (tp30) cc_final: 0.7893 (tp30) REVERT: C 269 MET cc_start: 0.8708 (tpp) cc_final: 0.8327 (mtt) REVERT: C 283 MET cc_start: 0.7792 (mmp) cc_final: 0.7516 (mmp) REVERT: C 325 MET cc_start: 0.7945 (mtt) cc_final: 0.7476 (pmm) REVERT: A 9 VAL cc_start: 0.9033 (OUTLIER) cc_final: 0.8642 (p) REVERT: A 44 MET cc_start: 0.8695 (tpp) cc_final: 0.8449 (tpp) REVERT: A 129 VAL cc_start: 0.8358 (m) cc_final: 0.8043 (p) REVERT: A 187 ASP cc_start: 0.8429 (m-30) cc_final: 0.8067 (t0) REVERT: A 225 ASN cc_start: 0.8419 (p0) cc_final: 0.8195 (p0) REVERT: A 313 MET cc_start: 0.8054 (mmm) cc_final: 0.7566 (mmm) outliers start: 36 outliers final: 18 residues processed: 167 average time/residue: 0.2449 time to fit residues: 64.7816 Evaluate side-chains 153 residues out of total 1726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 133 time to evaluate : 1.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 10 CYS Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 215 ASP Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 317 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 163 optimal weight: 0.0770 chunk 111 optimal weight: 7.9990 chunk 2 optimal weight: 0.0570 chunk 146 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 chunk 167 optimal weight: 10.0000 chunk 135 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 chunk 176 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 overall best weight: 2.8262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 HIS C 87 HIS ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.4418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 16466 Z= 0.232 Angle : 0.635 11.219 22348 Z= 0.312 Chirality : 0.044 0.155 2484 Planarity : 0.004 0.046 2849 Dihedral : 6.937 82.207 2321 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.09 % Allowed : 12.63 % Favored : 85.28 % 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: 0.88 (0.19), residues: 2009 helix: 0.72 (0.20), residues: 690 sheet: 0.80 (0.24), residues: 400 loop : 0.58 (0.22), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 356 HIS 0.009 0.001 HIS D 371 PHE 0.018 0.002 PHE E 262 TYR 0.014 0.001 TYR F 183 ARG 0.005 0.001 ARG E 312 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 138 time to evaluate : 1.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 44 MET cc_start: 0.7786 (ttt) cc_final: 0.7042 (tmm) REVERT: D 123 MET cc_start: 0.8962 (tpp) cc_final: 0.8726 (tpp) REVERT: F 183 TYR cc_start: 0.8453 (m-80) cc_final: 0.8170 (m-80) REVERT: F 214 MET cc_start: 0.6385 (tpp) cc_final: 0.5786 (tpp) REVERT: B 227 MET cc_start: 0.8618 (ttp) cc_final: 0.8393 (tpp) REVERT: B 325 MET cc_start: 0.7864 (tpp) cc_final: 0.7412 (mmp) REVERT: E 78 ASN cc_start: 0.7071 (t0) cc_final: 0.6679 (t0) REVERT: E 82 MET cc_start: 0.6941 (tpt) cc_final: 0.6621 (mmp) REVERT: E 107 GLU cc_start: 0.5348 (OUTLIER) cc_final: 0.4783 (mt-10) REVERT: E 297 ASN cc_start: 0.8582 (t0) cc_final: 0.8243 (t0) REVERT: E 325 MET cc_start: 0.6720 (ttm) cc_final: 0.6381 (ptm) REVERT: E 356 TRP cc_start: 0.6771 (m100) cc_final: 0.6280 (m100) REVERT: C 132 MET cc_start: 0.7844 (tpp) cc_final: 0.7623 (tpt) REVERT: C 226 GLU cc_start: 0.8215 (tp30) cc_final: 0.7893 (tp30) REVERT: C 269 MET cc_start: 0.8797 (OUTLIER) cc_final: 0.8353 (mtt) REVERT: C 283 MET cc_start: 0.7881 (mmp) cc_final: 0.7564 (mmp) REVERT: C 325 MET cc_start: 0.7887 (mtt) cc_final: 0.7481 (pmm) REVERT: A 9 VAL cc_start: 0.8993 (OUTLIER) cc_final: 0.8611 (m) REVERT: A 80 ASP cc_start: 0.9476 (OUTLIER) cc_final: 0.9234 (p0) REVERT: A 129 VAL cc_start: 0.8375 (m) cc_final: 0.8073 (p) REVERT: A 187 ASP cc_start: 0.8421 (m-30) cc_final: 0.8110 (t0) REVERT: A 225 ASN cc_start: 0.8403 (p0) cc_final: 0.8162 (p0) REVERT: A 313 MET cc_start: 0.8082 (mmm) cc_final: 0.7591 (mmm) outliers start: 36 outliers final: 19 residues processed: 162 average time/residue: 0.2513 time to fit residues: 63.7870 Evaluate side-chains 152 residues out of total 1726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 129 time to evaluate : 1.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 10 CYS Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 374 CYS Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain F residue 215 ASP Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 352 PHE Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 352 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 66 optimal weight: 10.0000 chunk 176 optimal weight: 0.5980 chunk 38 optimal weight: 10.0000 chunk 115 optimal weight: 9.9990 chunk 48 optimal weight: 9.9990 chunk 196 optimal weight: 1.9990 chunk 163 optimal weight: 9.9990 chunk 90 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 87 HIS F 103 ASN E 162 ASN ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.4992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 16466 Z= 0.351 Angle : 0.722 9.455 22348 Z= 0.359 Chirality : 0.046 0.152 2484 Planarity : 0.004 0.045 2849 Dihedral : 7.283 81.507 2321 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.84 % Allowed : 13.73 % Favored : 83.43 % 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: 0.44 (0.19), residues: 2009 helix: 0.58 (0.20), residues: 684 sheet: 0.44 (0.25), residues: 400 loop : 0.17 (0.21), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 356 HIS 0.013 0.002 HIS D 371 PHE 0.027 0.002 PHE E 352 TYR 0.018 0.002 TYR A 279 ARG 0.005 0.001 ARG D 335 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 126 time to evaluate : 1.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 44 MET cc_start: 0.7894 (ttt) cc_final: 0.7128 (tmm) REVERT: D 227 MET cc_start: 0.7139 (tpp) cc_final: 0.6871 (tpp) REVERT: F 122 MET cc_start: 0.5309 (ttt) cc_final: 0.5010 (mtp) REVERT: F 183 TYR cc_start: 0.8600 (m-80) cc_final: 0.8238 (m-80) REVERT: F 214 MET cc_start: 0.6492 (tpp) cc_final: 0.5845 (tpp) REVERT: F 231 GLU cc_start: 0.8169 (pt0) cc_final: 0.7786 (pm20) REVERT: F 237 MET cc_start: 0.7005 (OUTLIER) cc_final: 0.6721 (mmm) REVERT: B 283 MET cc_start: 0.8314 (mmp) cc_final: 0.8032 (mmp) REVERT: B 325 MET cc_start: 0.7840 (tpp) cc_final: 0.7444 (mmp) REVERT: E 82 MET cc_start: 0.7163 (tpt) cc_final: 0.6836 (mmp) REVERT: E 107 GLU cc_start: 0.5665 (OUTLIER) cc_final: 0.4866 (mt-10) REVERT: E 297 ASN cc_start: 0.8624 (t0) cc_final: 0.8276 (t0) REVERT: E 325 MET cc_start: 0.7043 (ttm) cc_final: 0.6562 (ptm) REVERT: E 356 TRP cc_start: 0.6760 (m100) cc_final: 0.6139 (m100) REVERT: C 115 ASN cc_start: 0.8094 (OUTLIER) cc_final: 0.7804 (t0) REVERT: C 132 MET cc_start: 0.7849 (tpp) cc_final: 0.7640 (tpt) REVERT: C 269 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8491 (mtt) REVERT: C 283 MET cc_start: 0.7939 (mmp) cc_final: 0.7613 (mmp) REVERT: C 325 MET cc_start: 0.7929 (mtt) cc_final: 0.7563 (pmm) REVERT: A 9 VAL cc_start: 0.8846 (OUTLIER) cc_final: 0.8552 (m) REVERT: A 80 ASP cc_start: 0.9491 (OUTLIER) cc_final: 0.9083 (p0) REVERT: A 187 ASP cc_start: 0.8451 (m-30) cc_final: 0.8202 (t0) REVERT: A 225 ASN cc_start: 0.8418 (p0) cc_final: 0.8195 (p0) outliers start: 49 outliers final: 24 residues processed: 162 average time/residue: 0.2375 time to fit residues: 61.0787 Evaluate side-chains 155 residues out of total 1726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 125 time to evaluate : 1.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 10 CYS Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 196 ILE Chi-restraints excluded: chain F residue 237 MET Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 352 PHE Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 352 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 189 optimal weight: 7.9990 chunk 22 optimal weight: 20.0000 chunk 111 optimal weight: 10.0000 chunk 143 optimal weight: 7.9990 chunk 165 optimal weight: 0.8980 chunk 109 optimal weight: 10.0000 chunk 195 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 90 optimal weight: 9.9990 chunk 121 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.5171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 16466 Z= 0.188 Angle : 0.608 9.104 22348 Z= 0.296 Chirality : 0.043 0.145 2484 Planarity : 0.004 0.044 2849 Dihedral : 6.864 85.427 2321 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.85 % Allowed : 15.24 % Favored : 82.91 % 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: 0.54 (0.19), residues: 2009 helix: 0.56 (0.20), residues: 715 sheet: 0.75 (0.25), residues: 370 loop : 0.20 (0.22), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 340 HIS 0.006 0.001 HIS D 371 PHE 0.020 0.001 PHE B 223 TYR 0.012 0.001 TYR F 183 ARG 0.003 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 138 time to evaluate : 2.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 44 MET cc_start: 0.7801 (ttt) cc_final: 0.7136 (tmm) REVERT: D 227 MET cc_start: 0.7154 (tpp) cc_final: 0.6883 (tpp) REVERT: F 105 GLN cc_start: 0.8961 (pm20) cc_final: 0.8683 (pm20) REVERT: F 122 MET cc_start: 0.4821 (ttt) cc_final: 0.4581 (mtp) REVERT: F 163 LYS cc_start: 0.7532 (tmtt) cc_final: 0.6736 (pttt) REVERT: F 183 TYR cc_start: 0.8557 (m-80) cc_final: 0.7854 (m-80) REVERT: F 214 MET cc_start: 0.6578 (tpp) cc_final: 0.5905 (tpp) REVERT: F 231 GLU cc_start: 0.8128 (pt0) cc_final: 0.7761 (pm20) REVERT: B 325 MET cc_start: 0.7814 (tpp) cc_final: 0.7332 (mmp) REVERT: E 8 LEU cc_start: 0.8853 (mt) cc_final: 0.8472 (mt) REVERT: E 33 SER cc_start: 0.8303 (t) cc_final: 0.7880 (p) REVERT: E 82 MET cc_start: 0.7078 (tpt) cc_final: 0.6732 (mmp) REVERT: E 107 GLU cc_start: 0.5632 (OUTLIER) cc_final: 0.4870 (mt-10) REVERT: E 297 ASN cc_start: 0.8637 (t0) cc_final: 0.8317 (t0) REVERT: E 325 MET cc_start: 0.6968 (ttm) cc_final: 0.6557 (ptt) REVERT: E 356 TRP cc_start: 0.6688 (m100) cc_final: 0.6108 (m100) REVERT: C 82 MET cc_start: 0.8664 (tpt) cc_final: 0.8353 (mmm) REVERT: C 132 MET cc_start: 0.7627 (tpp) cc_final: 0.7397 (tpt) REVERT: C 226 GLU cc_start: 0.8287 (tp30) cc_final: 0.8003 (tp30) REVERT: C 269 MET cc_start: 0.8794 (tpp) cc_final: 0.8350 (mtt) REVERT: C 325 MET cc_start: 0.7927 (mtt) cc_final: 0.7523 (pmm) REVERT: A 9 VAL cc_start: 0.8941 (OUTLIER) cc_final: 0.8662 (m) REVERT: A 80 ASP cc_start: 0.9475 (OUTLIER) cc_final: 0.9219 (p0) REVERT: A 129 VAL cc_start: 0.8437 (m) cc_final: 0.8138 (p) REVERT: A 187 ASP cc_start: 0.8391 (m-30) cc_final: 0.8175 (t0) REVERT: A 225 ASN cc_start: 0.8408 (p0) cc_final: 0.8167 (p0) REVERT: A 313 MET cc_start: 0.8063 (mmm) cc_final: 0.7750 (mmm) REVERT: A 317 ILE cc_start: 0.7972 (OUTLIER) cc_final: 0.7673 (tp) outliers start: 32 outliers final: 16 residues processed: 159 average time/residue: 0.2622 time to fit residues: 64.5293 Evaluate side-chains 152 residues out of total 1726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 132 time to evaluate : 1.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 352 PHE Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 371 HIS Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 352 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 78 optimal weight: 8.9990 chunk 116 optimal weight: 0.8980 chunk 58 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 37 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 chunk 133 optimal weight: 10.0000 chunk 96 optimal weight: 0.6980 chunk 18 optimal weight: 8.9990 chunk 153 optimal weight: 6.9990 chunk 177 optimal weight: 9.9990 overall best weight: 4.5186 ------------------------------------------------------------------------------- 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 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.5447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 16466 Z= 0.331 Angle : 0.696 10.673 22348 Z= 0.345 Chirality : 0.045 0.151 2484 Planarity : 0.004 0.046 2849 Dihedral : 7.053 82.578 2321 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.38 % Allowed : 15.30 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.19), residues: 2009 helix: 0.54 (0.20), residues: 690 sheet: 0.38 (0.25), residues: 400 loop : -0.01 (0.21), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 356 HIS 0.011 0.002 HIS D 371 PHE 0.024 0.002 PHE C 352 TYR 0.020 0.002 TYR F 183 ARG 0.005 0.001 ARG D 335 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 128 time to evaluate : 1.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 44 MET cc_start: 0.7911 (ttt) cc_final: 0.7199 (tmm) REVERT: D 123 MET cc_start: 0.8956 (tpp) cc_final: 0.8643 (tpp) REVERT: D 227 MET cc_start: 0.7100 (tpp) cc_final: 0.6833 (tpp) REVERT: F 122 MET cc_start: 0.5071 (ttt) cc_final: 0.4748 (mtp) REVERT: F 183 TYR cc_start: 0.8514 (m-80) cc_final: 0.8220 (m-80) REVERT: F 214 MET cc_start: 0.6678 (tpp) cc_final: 0.5985 (tpp) REVERT: F 231 GLU cc_start: 0.8188 (pt0) cc_final: 0.7785 (pm20) REVERT: B 227 MET cc_start: 0.8199 (tpp) cc_final: 0.7892 (mpp) REVERT: B 283 MET cc_start: 0.8197 (mmp) cc_final: 0.7925 (mmp) REVERT: B 325 MET cc_start: 0.7848 (tpp) cc_final: 0.7396 (mmp) REVERT: E 8 LEU cc_start: 0.8842 (mt) cc_final: 0.8452 (mt) REVERT: E 82 MET cc_start: 0.7187 (tpt) cc_final: 0.6924 (mmp) REVERT: E 107 GLU cc_start: 0.5748 (OUTLIER) cc_final: 0.4800 (mt-10) REVERT: E 297 ASN cc_start: 0.8629 (t0) cc_final: 0.8291 (t0) REVERT: E 325 MET cc_start: 0.7191 (ttm) cc_final: 0.6720 (ptt) REVERT: E 356 TRP cc_start: 0.6680 (m100) cc_final: 0.5978 (m100) REVERT: C 269 MET cc_start: 0.8925 (tpp) cc_final: 0.8473 (mtt) REVERT: C 325 MET cc_start: 0.7944 (mtt) cc_final: 0.7482 (pmm) REVERT: A 9 VAL cc_start: 0.8867 (OUTLIER) cc_final: 0.8565 (m) REVERT: A 80 ASP cc_start: 0.9494 (OUTLIER) cc_final: 0.9102 (p0) REVERT: A 187 ASP cc_start: 0.8442 (m-30) cc_final: 0.8190 (t0) REVERT: A 225 ASN cc_start: 0.8379 (p0) cc_final: 0.8149 (p0) REVERT: A 313 MET cc_start: 0.8096 (mmm) cc_final: 0.7873 (mmm) REVERT: A 317 ILE cc_start: 0.8059 (OUTLIER) cc_final: 0.7772 (tp) outliers start: 41 outliers final: 24 residues processed: 154 average time/residue: 0.2524 time to fit residues: 60.8780 Evaluate side-chains 151 residues out of total 1726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 123 time to evaluate : 2.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 10 CYS Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 352 PHE Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 371 HIS Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 352 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 187 optimal weight: 6.9990 chunk 171 optimal weight: 10.0000 chunk 182 optimal weight: 5.9990 chunk 109 optimal weight: 10.0000 chunk 79 optimal weight: 6.9990 chunk 143 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 164 optimal weight: 7.9990 chunk 172 optimal weight: 5.9990 chunk 181 optimal weight: 5.9990 chunk 119 optimal weight: 0.9980 overall best weight: 5.1988 ------------------------------------------------------------------------------- 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 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.5797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 16466 Z= 0.373 Angle : 0.733 10.259 22348 Z= 0.367 Chirality : 0.046 0.153 2484 Planarity : 0.004 0.047 2849 Dihedral : 7.335 81.986 2321 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.32 % Allowed : 15.64 % Favored : 82.04 % 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: -0.16 (0.19), residues: 2009 helix: 0.23 (0.20), residues: 720 sheet: 0.19 (0.25), residues: 393 loop : -0.39 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 356 HIS 0.010 0.002 HIS D 371 PHE 0.030 0.002 PHE C 352 TYR 0.018 0.002 TYR A 279 ARG 0.010 0.001 ARG E 254 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 125 time to evaluate : 2.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 44 MET cc_start: 0.7930 (ttt) cc_final: 0.7175 (tmm) REVERT: D 123 MET cc_start: 0.9028 (tpp) cc_final: 0.8716 (tpp) REVERT: D 227 MET cc_start: 0.7099 (tpp) cc_final: 0.6828 (tpp) REVERT: F 105 GLN cc_start: 0.8994 (pm20) cc_final: 0.8758 (pm20) REVERT: F 122 MET cc_start: 0.5204 (ttt) cc_final: 0.4897 (mtp) REVERT: F 183 TYR cc_start: 0.8559 (m-80) cc_final: 0.8003 (m-80) REVERT: F 214 MET cc_start: 0.6730 (tpp) cc_final: 0.6019 (tpp) REVERT: F 231 GLU cc_start: 0.8166 (pt0) cc_final: 0.7785 (pm20) REVERT: B 283 MET cc_start: 0.8224 (mmp) cc_final: 0.7957 (mmp) REVERT: B 325 MET cc_start: 0.7788 (tpp) cc_final: 0.7373 (mmp) REVERT: E 8 LEU cc_start: 0.8879 (mt) cc_final: 0.8320 (mt) REVERT: E 82 MET cc_start: 0.7311 (tpt) cc_final: 0.6980 (mmp) REVERT: E 107 GLU cc_start: 0.5934 (OUTLIER) cc_final: 0.5604 (tt0) REVERT: E 297 ASN cc_start: 0.8646 (t0) cc_final: 0.8299 (t0) REVERT: E 356 TRP cc_start: 0.6625 (m100) cc_final: 0.5760 (m100) REVERT: C 269 MET cc_start: 0.9003 (tpp) cc_final: 0.8546 (mtt) REVERT: C 325 MET cc_start: 0.7945 (mtt) cc_final: 0.7480 (pmm) REVERT: A 80 ASP cc_start: 0.9471 (OUTLIER) cc_final: 0.9081 (p0) REVERT: A 187 ASP cc_start: 0.8412 (m-30) cc_final: 0.8177 (t0) REVERT: A 313 MET cc_start: 0.8064 (mmm) cc_final: 0.7849 (mmm) REVERT: A 317 ILE cc_start: 0.8168 (OUTLIER) cc_final: 0.7898 (tp) outliers start: 40 outliers final: 28 residues processed: 149 average time/residue: 0.2593 time to fit residues: 61.1337 Evaluate side-chains 151 residues out of total 1726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 120 time to evaluate : 2.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 10 CYS Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 372 ARG Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 352 PHE Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 371 HIS Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 352 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 192 optimal weight: 8.9990 chunk 117 optimal weight: 7.9990 chunk 91 optimal weight: 7.9990 chunk 134 optimal weight: 2.9990 chunk 202 optimal weight: 7.9990 chunk 186 optimal weight: 0.9990 chunk 161 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 124 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 127 optimal weight: 10.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- 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 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.5879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 16466 Z= 0.247 Angle : 0.655 10.500 22348 Z= 0.323 Chirality : 0.044 0.142 2484 Planarity : 0.004 0.046 2849 Dihedral : 7.014 84.918 2321 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.62 % Allowed : 16.34 % Favored : 82.04 % 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: 0.00 (0.19), residues: 2009 helix: 0.39 (0.20), residues: 720 sheet: 0.17 (0.25), residues: 400 loop : -0.26 (0.22), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 356 HIS 0.008 0.001 HIS D 371 PHE 0.031 0.002 PHE C 352 TYR 0.014 0.001 TYR A 279 ARG 0.004 0.000 ARG E 254 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 126 time to evaluate : 2.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 44 MET cc_start: 0.7855 (ttt) cc_final: 0.7228 (tmm) REVERT: D 123 MET cc_start: 0.8960 (tpp) cc_final: 0.8653 (tpp) REVERT: D 227 MET cc_start: 0.7100 (tpp) cc_final: 0.6839 (tpp) REVERT: D 355 MET cc_start: 0.8607 (mtp) cc_final: 0.8283 (mmm) REVERT: F 105 GLN cc_start: 0.8963 (pm20) cc_final: 0.8729 (pm20) REVERT: F 122 MET cc_start: 0.5134 (ttt) cc_final: 0.4872 (mtp) REVERT: F 214 MET cc_start: 0.6706 (tpp) cc_final: 0.5995 (tpp) REVERT: F 231 GLU cc_start: 0.8110 (pt0) cc_final: 0.7750 (pm20) REVERT: B 44 MET cc_start: 0.8038 (mtp) cc_final: 0.7770 (mtp) REVERT: B 227 MET cc_start: 0.8264 (tpp) cc_final: 0.7915 (mpp) REVERT: B 283 MET cc_start: 0.8169 (mmp) cc_final: 0.7896 (mmp) REVERT: B 325 MET cc_start: 0.7735 (tpp) cc_final: 0.7358 (mmp) REVERT: E 8 LEU cc_start: 0.8878 (mt) cc_final: 0.8312 (mt) REVERT: E 82 MET cc_start: 0.7288 (tpt) cc_final: 0.7024 (mmp) REVERT: E 107 GLU cc_start: 0.5785 (OUTLIER) cc_final: 0.4955 (mt-10) REVERT: E 297 ASN cc_start: 0.8667 (t0) cc_final: 0.8336 (t0) REVERT: E 356 TRP cc_start: 0.6687 (m100) cc_final: 0.5837 (m100) REVERT: C 269 MET cc_start: 0.8959 (tpp) cc_final: 0.8467 (mtt) REVERT: C 325 MET cc_start: 0.7983 (mtt) cc_final: 0.7445 (pmm) REVERT: A 9 VAL cc_start: 0.8937 (OUTLIER) cc_final: 0.8545 (m) REVERT: A 80 ASP cc_start: 0.9470 (OUTLIER) cc_final: 0.9090 (p0) REVERT: A 187 ASP cc_start: 0.8423 (m-30) cc_final: 0.8204 (t0) REVERT: A 313 MET cc_start: 0.8111 (mmm) cc_final: 0.7900 (mmm) REVERT: A 317 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7926 (tp) outliers start: 28 outliers final: 22 residues processed: 144 average time/residue: 0.2629 time to fit residues: 60.6811 Evaluate side-chains 151 residues out of total 1726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 125 time to evaluate : 1.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 352 PHE Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 371 HIS Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 352 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 171 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 148 optimal weight: 9.9990 chunk 23 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 161 optimal weight: 0.8980 chunk 67 optimal weight: 5.9990 chunk 165 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 chunk 141 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.065599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.056229 restraints weight = 87347.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.057755 restraints weight = 48759.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.058812 restraints weight = 32130.722| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.5970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16466 Z= 0.203 Angle : 0.634 11.427 22348 Z= 0.308 Chirality : 0.043 0.152 2484 Planarity : 0.004 0.046 2849 Dihedral : 6.770 86.970 2321 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.56 % Allowed : 16.45 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.19), residues: 2009 helix: 0.50 (0.20), residues: 720 sheet: 0.26 (0.25), residues: 400 loop : -0.14 (0.22), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 356 HIS 0.007 0.001 HIS D 371 PHE 0.037 0.002 PHE C 352 TYR 0.033 0.001 TYR F 183 ARG 0.004 0.000 ARG E 254 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2636.92 seconds wall clock time: 49 minutes 41.42 seconds (2981.42 seconds total)