Starting phenix.real_space_refine on Sun Dec 10 16:56:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ahn_11787/12_2023/7ahn_11787_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ahn_11787/12_2023/7ahn_11787.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ahn_11787/12_2023/7ahn_11787_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ahn_11787/12_2023/7ahn_11787_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ahn_11787/12_2023/7ahn_11787_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ahn_11787/12_2023/7ahn_11787.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ahn_11787/12_2023/7ahn_11787.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ahn_11787/12_2023/7ahn_11787_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ahn_11787/12_2023/7ahn_11787_updated.pdb" } resolution = 2.9 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= 0.002 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 15 5.49 5 Mg 5 5.21 5 S 100 5.16 5 C 9455 2.51 5 N 2490 2.21 5 O 2875 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ASP 24": "OD1" <-> "OD2" Residue "C TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 80": "OD1" <-> "OD2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 205": "OE1" <-> "OE2" Residue "C GLU 207": "OE1" <-> "OE2" Residue "C TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 222": "OD1" <-> "OD2" Residue "C GLU 226": "OE1" <-> "OE2" Residue "C ASP 244": "OD1" <-> "OD2" Residue "C GLU 276": "OE1" <-> "OE2" Residue "C TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 364": "OE1" <-> "OE2" Residue "C ARG 372": "NH1" <-> "NH2" Residue "C PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 24": "OD1" <-> "OD2" Residue "A TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 80": "OD1" <-> "OD2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 205": "OE1" <-> "OE2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "A TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 222": "OD1" <-> "OD2" Residue "A GLU 226": "OE1" <-> "OE2" Residue "A ASP 244": "OD1" <-> "OD2" Residue "A GLU 276": "OE1" <-> "OE2" Residue "A TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 364": "OE1" <-> "OE2" Residue "A ARG 372": "NH1" <-> "NH2" Residue "A PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 24": "OD1" <-> "OD2" Residue "E TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 80": "OD1" <-> "OD2" Residue "E TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 205": "OE1" <-> "OE2" Residue "E GLU 207": "OE1" <-> "OE2" Residue "E TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 222": "OD1" <-> "OD2" Residue "E GLU 226": "OE1" <-> "OE2" Residue "E ASP 244": "OD1" <-> "OD2" Residue "E GLU 276": "OE1" <-> "OE2" Residue "E TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 364": "OE1" <-> "OE2" Residue "E ARG 372": "NH1" <-> "NH2" Residue "E PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 24": "OD1" <-> "OD2" Residue "D TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 80": "OD1" <-> "OD2" Residue "D TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 205": "OE1" <-> "OE2" Residue "D GLU 207": "OE1" <-> "OE2" Residue "D TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 222": "OD1" <-> "OD2" Residue "D GLU 226": "OE1" <-> "OE2" Residue "D ASP 244": "OD1" <-> "OD2" Residue "D GLU 276": "OE1" <-> "OE2" Residue "D TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 364": "OE1" <-> "OE2" Residue "D ARG 372": "NH1" <-> "NH2" Residue "D PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 24": "OD1" <-> "OD2" Residue "B TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 80": "OD1" <-> "OD2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 205": "OE1" <-> "OE2" Residue "B GLU 207": "OE1" <-> "OE2" Residue "B TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 222": "OD1" <-> "OD2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B ASP 244": "OD1" <-> "OD2" Residue "B GLU 276": "OE1" <-> "OE2" Residue "B TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 364": "OE1" <-> "OE2" Residue "B ARG 372": "NH1" <-> "NH2" Residue "B PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 14940 Number of models: 1 Model: "" Number of chains: 10 Chain: "C" Number of atoms: 2877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2877 Classifications: {'peptide': 367} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 347} Chain breaks: 1 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: 2877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2877 Classifications: {'peptide': 367} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 347} Chain breaks: 1 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: 2877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2877 Classifications: {'peptide': 367} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 347} Chain breaks: 1 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: 2877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2877 Classifications: {'peptide': 367} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 347} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2877 Classifications: {'peptide': 367} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 347} Chain breaks: 1 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: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 111 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1, 'RLZ': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 189 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1, 'RLZ': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 111 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1, 'RLZ': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 111 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1, 'RLZ': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 8.12, per 1000 atoms: 0.54 Number of scatterers: 14940 At special positions: 0 Unit cell: (95.55, 92.4, 193.2, 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 100 16.00 P 15 15.00 Mg 5 11.99 O 2875 8.00 N 2490 7.00 C 9455 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.65 Conformation dependent library (CDL) restraints added in 2.8 seconds 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3410 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 95 helices and 25 sheets defined 45.8% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.12 Creating SS restraints... Processing helix chain 'C' and resid 56 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 91 Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 113 through 125 Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.544A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER C 145 " --> pdb=" O SER C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 182 through 196 removed outlier: 3.686A pdb=" N LYS C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 removed outlier: 3.513A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 252 through 261 removed outlier: 3.905A pdb=" N ARG C 256 " --> pdb=" O GLU C 253 " (cutoff:3.500A) removed outlier: 4.678A 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 267 Processing helix chain 'C' and resid 274 through 283 Processing helix chain 'C' and resid 287 through 296 removed outlier: 4.333A pdb=" N LYS C 291 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASN C 296 " --> pdb=" O ASP C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 304 No H-bonds generated for 'chain 'C' and resid 302 through 304' Processing helix chain 'C' and resid 309 through 320 removed outlier: 3.695A pdb=" N LYS C 315 " --> pdb=" O ASP C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 348 removed outlier: 5.483A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA C 347 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 354 removed outlier: 3.872A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 351 through 354' Processing helix chain 'C' and resid 359 through 371 Proline residue: C 367 - end of helix removed outlier: 4.888A pdb=" N VAL C 370 " --> pdb=" O GLY C 366 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N HIS C 371 " --> pdb=" O PRO C 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 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 91 Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 113 through 125 Processing helix chain 'A' and resid 137 through 145 removed outlier: 3.543A pdb=" N LEU A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 182 through 196 removed outlier: 3.687A pdb=" N LYS A 191 " --> pdb=" O ASP A 187 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ARG A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 216 removed outlier: 3.513A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 252 through 261 removed outlier: 3.905A pdb=" N ARG A 256 " --> pdb=" O GLU A 253 " (cutoff:3.500A) removed outlier: 4.679A 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 296 removed outlier: 4.333A pdb=" N LYS A 291 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ASP A 292 " --> pdb=" O ASP A 288 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN A 296 " --> pdb=" O ASP A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 304 No H-bonds generated for 'chain 'A' and resid 302 through 304' Processing helix chain 'A' and resid 309 through 320 removed outlier: 3.695A pdb=" N LYS A 315 " --> pdb=" O ASP A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 348 removed outlier: 5.482A pdb=" N VAL A 339 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ALA A 347 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 354 removed outlier: 3.871A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 351 through 354' Processing helix chain 'A' and resid 359 through 371 Proline residue: A 367 - end of helix removed outlier: 4.887A pdb=" N VAL A 370 " --> pdb=" O GLY A 366 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N HIS A 371 " --> pdb=" O PRO A 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 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 91 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 113 through 125 Processing helix chain 'E' and resid 137 through 145 removed outlier: 3.543A pdb=" N LEU E 142 " --> pdb=" O ALA E 138 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER E 145 " --> pdb=" O SER E 141 " (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 removed outlier: 3.687A pdb=" N LYS E 191 " --> pdb=" O ASP E 187 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU E 195 " --> pdb=" O LYS E 191 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ARG E 196 " --> pdb=" O ILE E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 216 removed outlier: 3.512A pdb=" N GLU E 207 " --> pdb=" O THR E 203 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASP E 211 " --> pdb=" O GLU E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 232 Processing helix chain 'E' and resid 252 through 261 removed outlier: 3.905A pdb=" N ARG E 256 " --> pdb=" O GLU E 253 " (cutoff:3.500A) removed outlier: 4.678A 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 287 through 296 removed outlier: 4.333A pdb=" N LYS E 291 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ASP E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN E 296 " --> pdb=" O ASP E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 304 No H-bonds generated for 'chain 'E' and resid 302 through 304' Processing helix chain 'E' and resid 309 through 320 removed outlier: 3.695A pdb=" N LYS E 315 " --> pdb=" O ASP E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 348 removed outlier: 5.482A pdb=" N VAL E 339 " --> pdb=" O LYS E 336 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA E 347 " --> pdb=" O SER E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 354 removed outlier: 3.871A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 351 through 354' Processing helix chain 'E' and resid 359 through 371 Proline residue: E 367 - end of helix removed outlier: 4.887A pdb=" N VAL E 370 " --> pdb=" O GLY E 366 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N HIS E 371 " --> pdb=" O PRO E 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 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 91 Processing helix chain 'D' and resid 98 through 100 No H-bonds generated for 'chain 'D' and resid 98 through 100' Processing helix chain 'D' and resid 113 through 125 Processing helix chain 'D' and resid 137 through 145 removed outlier: 3.544A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 3.628A 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: 3.686A pdb=" N LYS D 191 " --> pdb=" O ASP D 187 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ARG D 196 " --> pdb=" O ILE D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 216 removed outlier: 3.512A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASP D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 232 Processing helix chain 'D' and resid 252 through 261 removed outlier: 3.905A pdb=" N ARG D 256 " --> pdb=" O GLU D 253 " (cutoff:3.500A) removed outlier: 4.678A 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 267 Processing helix chain 'D' and resid 274 through 283 Processing helix chain 'D' and resid 287 through 296 removed outlier: 4.334A pdb=" N LYS D 291 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ASP D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASN D 296 " --> pdb=" O ASP D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 304 No H-bonds generated for 'chain 'D' and resid 302 through 304' Processing helix chain 'D' and resid 309 through 320 removed outlier: 3.696A pdb=" N LYS D 315 " --> pdb=" O ASP D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 348 removed outlier: 5.482A pdb=" N VAL D 339 " --> pdb=" O LYS D 336 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ALA D 347 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 354 removed outlier: 3.871A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 351 through 354' Processing helix chain 'D' and resid 359 through 371 Proline residue: D 367 - end of helix removed outlier: 4.888A pdb=" N VAL D 370 " --> pdb=" O GLY D 366 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N HIS D 371 " --> pdb=" O PRO D 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 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 91 Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 113 through 125 Processing helix chain 'B' and resid 137 through 145 removed outlier: 3.544A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 182 through 196 removed outlier: 3.687A pdb=" N LYS B 191 " --> pdb=" O ASP B 187 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 removed outlier: 3.512A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASP B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 252 through 261 removed outlier: 3.906A pdb=" N ARG B 256 " --> pdb=" O GLU B 253 " (cutoff:3.500A) removed outlier: 4.678A 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 267 Processing helix chain 'B' and resid 274 through 283 Processing helix chain 'B' and resid 287 through 296 removed outlier: 4.333A pdb=" N LYS B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ASP B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASN B 296 " --> pdb=" O ASP B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 304 No H-bonds generated for 'chain 'B' and resid 302 through 304' Processing helix chain 'B' and resid 309 through 320 removed outlier: 3.695A pdb=" N LYS B 315 " --> pdb=" O ASP B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 348 removed outlier: 5.482A pdb=" N VAL B 339 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ALA B 347 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 354 removed outlier: 3.872A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 351 through 354' Processing helix chain 'B' and resid 359 through 371 Proline residue: B 367 - end of helix removed outlier: 4.888A pdb=" N VAL B 370 " --> pdb=" O GLY B 366 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N HIS B 371 " --> pdb=" O PRO B 367 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'C' and resid 8 through 10 Processing sheet with id= B, first strand: chain 'C' and resid 65 through 69 Processing sheet with id= C, first strand: chain 'C' and resid 103 through 107 Processing sheet with id= D, first strand: chain 'C' and resid 297 through 300 removed outlier: 6.336A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 238 through 241 Processing sheet with id= F, first strand: chain 'A' and resid 8 through 10 Processing sheet with id= G, first strand: chain 'A' and resid 65 through 69 Processing sheet with id= H, first strand: chain 'A' and resid 103 through 107 Processing sheet with id= I, first strand: chain 'A' and resid 297 through 300 removed outlier: 6.336A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 238 through 241 Processing sheet with id= K, first strand: chain 'E' and resid 8 through 10 Processing sheet with id= L, first strand: chain 'E' and resid 65 through 69 Processing sheet with id= M, first strand: chain 'E' and resid 103 through 107 Processing sheet with id= N, first strand: chain 'E' and resid 297 through 300 removed outlier: 6.336A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 238 through 241 Processing sheet with id= P, first strand: chain 'D' and resid 8 through 10 Processing sheet with id= Q, first strand: chain 'D' and resid 65 through 69 Processing sheet with id= R, first strand: chain 'D' and resid 103 through 107 Processing sheet with id= S, first strand: chain 'D' and resid 297 through 300 removed outlier: 6.336A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 238 through 241 Processing sheet with id= U, first strand: chain 'B' and resid 8 through 10 Processing sheet with id= V, first strand: chain 'B' and resid 65 through 69 Processing sheet with id= W, first strand: chain 'B' and resid 103 through 107 Processing sheet with id= X, first strand: chain 'B' and resid 297 through 300 removed outlier: 6.336A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'B' and resid 238 through 241 525 hydrogen bonds defined for protein. 1305 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: 4.98 Time building geometry restraints manager: 6.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3348 1.33 - 1.45: 3329 1.45 - 1.57: 8403 1.57 - 1.69: 20 1.69 - 1.81: 175 Bond restraints: 15275 Sorted by residual: bond pdb=" C31 RLZ D 404 " pdb=" C32 RLZ D 404 " ideal model delta sigma weight residual 0.228 1.538 -1.310 2.00e-02 2.50e+03 4.29e+03 bond pdb=" C31 RLZ A 404 " pdb=" C32 RLZ A 404 " ideal model delta sigma weight residual 0.228 1.538 -1.310 2.00e-02 2.50e+03 4.29e+03 bond pdb=" C31 RLZ B 404 " pdb=" C32 RLZ B 404 " ideal model delta sigma weight residual 0.228 1.537 -1.309 2.00e-02 2.50e+03 4.29e+03 bond pdb=" C31 RLZ A 405 " pdb=" C32 RLZ A 405 " ideal model delta sigma weight residual 0.228 1.537 -1.309 2.00e-02 2.50e+03 4.29e+03 bond pdb=" C31 RLZ C 404 " pdb=" C32 RLZ C 404 " ideal model delta sigma weight residual 0.228 1.537 -1.309 2.00e-02 2.50e+03 4.28e+03 ... (remaining 15270 not shown) Histogram of bond angle deviations from ideal: 95.29 - 103.54: 288 103.54 - 111.78: 6774 111.78 - 120.03: 7212 120.03 - 128.27: 6326 128.27 - 136.51: 135 Bond angle restraints: 20735 Sorted by residual: angle pdb=" C27 RLZ A 404 " pdb=" C28 RLZ A 404 " pdb=" N29 RLZ A 404 " ideal model delta sigma weight residual 180.00 117.72 62.28 3.00e+00 1.11e-01 4.31e+02 angle pdb=" C27 RLZ A 405 " pdb=" C28 RLZ A 405 " pdb=" N29 RLZ A 405 " ideal model delta sigma weight residual 180.00 117.72 62.28 3.00e+00 1.11e-01 4.31e+02 angle pdb=" C27 RLZ D 404 " pdb=" C28 RLZ D 404 " pdb=" N29 RLZ D 404 " ideal model delta sigma weight residual 180.00 117.72 62.28 3.00e+00 1.11e-01 4.31e+02 angle pdb=" C27 RLZ B 404 " pdb=" C28 RLZ B 404 " pdb=" N29 RLZ B 404 " ideal model delta sigma weight residual 180.00 117.72 62.28 3.00e+00 1.11e-01 4.31e+02 angle pdb=" C27 RLZ C 404 " pdb=" C28 RLZ C 404 " pdb=" N29 RLZ C 404 " ideal model delta sigma weight residual 180.00 117.76 62.24 3.00e+00 1.11e-01 4.30e+02 ... (remaining 20730 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 8800 35.93 - 71.87: 160 71.87 - 107.80: 62 107.80 - 143.74: 28 143.74 - 179.67: 10 Dihedral angle restraints: 9060 sinusoidal: 3745 harmonic: 5315 Sorted by residual: dihedral pdb=" O1B ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PB ADP B 401 " pdb=" PA ADP B 401 " ideal model delta sinusoidal sigma weight residual 300.00 160.19 139.81 1 2.00e+01 2.50e-03 4.23e+01 dihedral pdb=" O1B ADP A 401 " pdb=" O3A ADP A 401 " pdb=" PB ADP A 401 " pdb=" PA ADP A 401 " ideal model delta sinusoidal sigma weight residual 300.00 160.25 139.74 1 2.00e+01 2.50e-03 4.23e+01 dihedral pdb=" O1B ADP D 401 " pdb=" O3A ADP D 401 " pdb=" PB ADP D 401 " pdb=" PA ADP D 401 " ideal model delta sinusoidal sigma weight residual 300.00 160.27 139.72 1 2.00e+01 2.50e-03 4.23e+01 ... (remaining 9057 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.546: 2245 0.546 - 1.092: 5 1.092 - 1.639: 0 1.639 - 2.185: 0 2.185 - 2.731: 15 Chirality restraints: 2265 Sorted by residual: chirality pdb=" C27 RLZ A 404 " pdb=" C28 RLZ A 404 " pdb=" C76 RLZ A 404 " pdb=" N24 RLZ A 404 " both_signs ideal model delta sigma weight residual False -0.34 2.39 -2.73 2.00e-01 2.50e+01 1.86e+02 chirality pdb=" C27 RLZ C 404 " pdb=" C28 RLZ C 404 " pdb=" C76 RLZ C 404 " pdb=" N24 RLZ C 404 " both_signs ideal model delta sigma weight residual False -0.34 2.39 -2.73 2.00e-01 2.50e+01 1.86e+02 chirality pdb=" C27 RLZ A 405 " pdb=" C28 RLZ A 405 " pdb=" C76 RLZ A 405 " pdb=" N24 RLZ A 405 " both_signs ideal model delta sigma weight residual False -0.34 2.39 -2.73 2.00e-01 2.50e+01 1.86e+02 ... (remaining 2262 not shown) Planarity restraints: 2625 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C50 RLZ B 404 " -0.112 2.00e-02 2.50e+03 5.43e-01 8.11e+03 pdb=" C51 RLZ B 404 " -0.421 2.00e-02 2.50e+03 pdb=" C52 RLZ B 404 " -0.424 2.00e-02 2.50e+03 pdb=" C53 RLZ B 404 " -0.121 2.00e-02 2.50e+03 pdb=" C54 RLZ B 404 " 0.164 2.00e-02 2.50e+03 pdb=" C55 RLZ B 404 " 0.200 2.00e-02 2.50e+03 pdb=" C58 RLZ B 404 " 1.389 2.00e-02 2.50e+03 pdb=" N49 RLZ B 404 " -0.198 2.00e-02 2.50e+03 pdb=" N56 RLZ B 404 " -0.836 2.00e-02 2.50e+03 pdb=" N57 RLZ B 404 " 0.007 2.00e-02 2.50e+03 pdb=" O77 RLZ B 404 " 0.353 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C50 RLZ D 404 " -0.112 2.00e-02 2.50e+03 5.43e-01 8.10e+03 pdb=" C51 RLZ D 404 " -0.421 2.00e-02 2.50e+03 pdb=" C52 RLZ D 404 " -0.425 2.00e-02 2.50e+03 pdb=" C53 RLZ D 404 " -0.121 2.00e-02 2.50e+03 pdb=" C54 RLZ D 404 " 0.163 2.00e-02 2.50e+03 pdb=" C55 RLZ D 404 " 0.199 2.00e-02 2.50e+03 pdb=" C58 RLZ D 404 " 1.389 2.00e-02 2.50e+03 pdb=" N49 RLZ D 404 " -0.198 2.00e-02 2.50e+03 pdb=" N56 RLZ D 404 " -0.835 2.00e-02 2.50e+03 pdb=" N57 RLZ D 404 " 0.007 2.00e-02 2.50e+03 pdb=" O77 RLZ D 404 " 0.353 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C50 RLZ A 405 " -0.112 2.00e-02 2.50e+03 5.43e-01 8.10e+03 pdb=" C51 RLZ A 405 " -0.421 2.00e-02 2.50e+03 pdb=" C52 RLZ A 405 " -0.425 2.00e-02 2.50e+03 pdb=" C53 RLZ A 405 " -0.121 2.00e-02 2.50e+03 pdb=" C54 RLZ A 405 " 0.164 2.00e-02 2.50e+03 pdb=" C55 RLZ A 405 " 0.199 2.00e-02 2.50e+03 pdb=" C58 RLZ A 405 " 1.389 2.00e-02 2.50e+03 pdb=" N49 RLZ A 405 " -0.198 2.00e-02 2.50e+03 pdb=" N56 RLZ A 405 " -0.835 2.00e-02 2.50e+03 pdb=" N57 RLZ A 405 " 0.007 2.00e-02 2.50e+03 pdb=" O77 RLZ A 405 " 0.353 2.00e-02 2.50e+03 ... (remaining 2622 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.24: 15 2.24 - 2.91: 5930 2.91 - 3.57: 20501 3.57 - 4.24: 38023 4.24 - 4.90: 63979 Nonbonded interactions: 128448 Sorted by model distance: nonbonded pdb=" O SER C 199 " pdb=" O25 RLZ C 404 " model vdw 1.580 3.040 nonbonded pdb=" O SER A 199 " pdb=" O25 RLZ A 405 " model vdw 1.600 3.040 nonbonded pdb=" O SER B 199 " pdb=" O25 RLZ B 404 " model vdw 1.788 3.040 nonbonded pdb=" O SER D 199 " pdb=" O25 RLZ D 404 " model vdw 1.858 3.040 nonbonded pdb=" O2B ADP E 401 " pdb="MG MG E 402 " model vdw 1.930 2.170 ... (remaining 128443 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' and resid 5 through 375) selection = (chain 'B' and resid 5 through 375) selection = (chain 'C' and resid 5 through 375) selection = (chain 'D' and resid 5 through 375) selection = (chain 'E' and resid 5 through 375) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.220 Check model and map are aligned: 0.230 Set scattering table: 0.150 Process input model: 42.220 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 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 : 0.058 1.310 15275 Z= 4.069 Angle : 2.587 62.285 20735 Z= 0.967 Chirality : 0.228 2.731 2265 Planarity : 0.029 0.543 2625 Dihedral : 19.714 179.673 5650 Min Nonbonded Distance : 1.580 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % 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: -2.47 (0.18), residues: 1800 helix: -2.87 (0.13), residues: 775 sheet: -0.93 (0.29), residues: 250 loop : -0.21 (0.23), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.006 TRP C 356 HIS 0.009 0.003 HIS E 161 PHE 0.014 0.003 PHE E 31 TYR 0.023 0.006 TYR D 133 ARG 0.067 0.014 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 272 time to evaluate : 1.838 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 1 residues processed: 272 average time/residue: 1.5768 time to fit residues: 464.7273 Evaluate side-chains 138 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 137 time to evaluate : 1.773 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.1751 time to fit residues: 2.5028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 0.6980 chunk 136 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 46 optimal weight: 8.9990 chunk 92 optimal weight: 5.9990 chunk 72 optimal weight: 0.7980 chunk 141 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 105 optimal weight: 0.7980 chunk 163 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN C 49 GLN ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 ASN ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 ASN B 297 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 15275 Z= 0.238 Angle : 1.126 22.479 20735 Z= 0.443 Chirality : 0.053 0.404 2265 Planarity : 0.006 0.058 2625 Dihedral : 21.278 178.818 2190 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.41 % Allowed : 8.87 % Favored : 89.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.20), residues: 1800 helix: -1.10 (0.17), residues: 770 sheet: -0.97 (0.32), residues: 235 loop : 0.88 (0.24), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 79 HIS 0.003 0.001 HIS D 161 PHE 0.013 0.001 PHE B 31 TYR 0.009 0.001 TYR D 169 ARG 0.007 0.001 ARG A 372 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 161 time to evaluate : 1.812 Fit side-chains outliers start: 22 outliers final: 5 residues processed: 173 average time/residue: 1.4259 time to fit residues: 269.7510 Evaluate side-chains 119 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 114 time to evaluate : 1.802 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 1 average time/residue: 0.1750 time to fit residues: 2.6481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 136 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 163 optimal weight: 0.4980 chunk 176 optimal weight: 4.9990 chunk 145 optimal weight: 3.9990 chunk 162 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 ASN ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 162 ASN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 15275 Z= 0.357 Angle : 1.052 21.916 20735 Z= 0.419 Chirality : 0.054 0.392 2265 Planarity : 0.005 0.062 2625 Dihedral : 20.792 171.783 2190 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.57 % Allowed : 10.61 % Favored : 86.82 % 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: -0.31 (0.20), residues: 1800 helix: -0.67 (0.18), residues: 785 sheet: -0.73 (0.33), residues: 235 loop : 0.81 (0.24), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 79 HIS 0.006 0.001 HIS A 88 PHE 0.014 0.001 PHE B 31 TYR 0.011 0.001 TYR E 279 ARG 0.003 0.001 ARG C 206 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 141 time to evaluate : 1.823 Fit side-chains outliers start: 40 outliers final: 9 residues processed: 169 average time/residue: 1.5084 time to fit residues: 278.8714 Evaluate side-chains 125 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 116 time to evaluate : 1.771 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 1 average time/residue: 1.3050 time to fit residues: 3.7200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 164 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 GLN ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 GLN E 161 HIS D 173 HIS B 162 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 15275 Z= 0.342 Angle : 1.038 22.479 20735 Z= 0.411 Chirality : 0.054 0.394 2265 Planarity : 0.006 0.076 2625 Dihedral : 20.415 178.818 2190 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.12 % Allowed : 11.45 % Favored : 86.43 % 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: -0.19 (0.20), residues: 1800 helix: -0.46 (0.18), residues: 785 sheet: -0.73 (0.33), residues: 235 loop : 0.76 (0.24), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 79 HIS 0.005 0.001 HIS A 88 PHE 0.014 0.001 PHE A 31 TYR 0.016 0.001 TYR D 166 ARG 0.010 0.001 ARG D 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 126 time to evaluate : 1.769 Fit side-chains outliers start: 33 outliers final: 15 residues processed: 149 average time/residue: 1.2002 time to fit residues: 199.1395 Evaluate side-chains 131 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 116 time to evaluate : 1.732 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 12 residues processed: 3 average time/residue: 1.1856 time to fit residues: 6.2176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 8.9990 chunk 98 optimal weight: 4.9990 chunk 2 optimal weight: 0.5980 chunk 129 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 148 optimal weight: 0.5980 chunk 120 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 88 optimal weight: 4.9990 chunk 156 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 ASN C 314 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 15275 Z= 0.296 Angle : 1.028 22.280 20735 Z= 0.403 Chirality : 0.053 0.385 2265 Planarity : 0.005 0.074 2625 Dihedral : 20.157 176.790 2190 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.32 % Allowed : 11.96 % Favored : 85.72 % 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: 0.06 (0.20), residues: 1800 helix: -0.23 (0.18), residues: 770 sheet: -0.72 (0.32), residues: 235 loop : 0.89 (0.24), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 79 HIS 0.006 0.001 HIS E 161 PHE 0.014 0.001 PHE A 31 TYR 0.028 0.001 TYR D 166 ARG 0.007 0.000 ARG D 95 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 121 time to evaluate : 1.893 Fit side-chains outliers start: 36 outliers final: 17 residues processed: 149 average time/residue: 1.2034 time to fit residues: 199.6055 Evaluate side-chains 129 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 112 time to evaluate : 1.804 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 15 residues processed: 2 average time/residue: 1.1309 time to fit residues: 4.7004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 6.9990 chunk 156 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 102 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 174 optimal weight: 5.9990 chunk 144 optimal weight: 8.9990 chunk 80 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 GLN A 297 ASN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 15275 Z= 0.356 Angle : 1.035 22.204 20735 Z= 0.407 Chirality : 0.053 0.379 2265 Planarity : 0.005 0.081 2625 Dihedral : 20.157 176.564 2190 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.74 % Allowed : 13.05 % Favored : 85.21 % 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: 0.05 (0.20), residues: 1800 helix: -0.22 (0.18), residues: 770 sheet: -0.72 (0.32), residues: 235 loop : 0.86 (0.24), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 356 HIS 0.005 0.001 HIS E 161 PHE 0.014 0.001 PHE A 31 TYR 0.015 0.001 TYR D 166 ARG 0.003 0.000 ARG D 95 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 111 time to evaluate : 1.554 Fit side-chains outliers start: 27 outliers final: 22 residues processed: 132 average time/residue: 1.3125 time to fit residues: 191.7802 Evaluate side-chains 132 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 110 time to evaluate : 1.587 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 18 residues processed: 4 average time/residue: 1.2448 time to fit residues: 7.7761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 99 optimal weight: 0.8980 chunk 127 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 146 optimal weight: 0.0770 chunk 97 optimal weight: 0.9990 chunk 173 optimal weight: 3.9990 chunk 108 optimal weight: 7.9990 chunk 105 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 overall best weight: 1.3542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 ASN E 162 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15275 Z= 0.243 Angle : 1.007 22.112 20735 Z= 0.390 Chirality : 0.051 0.383 2265 Planarity : 0.005 0.072 2625 Dihedral : 19.789 179.254 2190 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.93 % Allowed : 13.12 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.20), residues: 1800 helix: -0.03 (0.19), residues: 770 sheet: -0.60 (0.32), residues: 235 loop : 0.89 (0.24), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 340 HIS 0.005 0.001 HIS E 161 PHE 0.014 0.001 PHE A 31 TYR 0.012 0.001 TYR D 166 ARG 0.004 0.000 ARG E 147 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 127 time to evaluate : 1.650 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 20 residues processed: 150 average time/residue: 1.2329 time to fit residues: 206.1979 Evaluate side-chains 133 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 113 time to evaluate : 1.699 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 18 residues processed: 2 average time/residue: 1.1609 time to fit residues: 4.8747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 110 optimal weight: 6.9990 chunk 118 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 15275 Z= 0.232 Angle : 1.008 22.144 20735 Z= 0.392 Chirality : 0.051 0.389 2265 Planarity : 0.005 0.076 2625 Dihedral : 19.719 179.600 2190 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.61 % Allowed : 13.57 % Favored : 84.82 % 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: 0.31 (0.20), residues: 1800 helix: 0.05 (0.19), residues: 770 sheet: -0.57 (0.32), residues: 235 loop : 0.92 (0.24), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 340 HIS 0.005 0.001 HIS E 161 PHE 0.014 0.001 PHE A 31 TYR 0.010 0.001 TYR D 166 ARG 0.004 0.000 ARG B 147 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 114 time to evaluate : 2.040 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 19 residues processed: 134 average time/residue: 1.2806 time to fit residues: 191.0062 Evaluate side-chains 129 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 110 time to evaluate : 1.774 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 18 residues processed: 1 average time/residue: 1.1883 time to fit residues: 3.5112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 3.9990 chunk 166 optimal weight: 9.9990 chunk 151 optimal weight: 1.9990 chunk 161 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 70 optimal weight: 7.9990 chunk 126 optimal weight: 0.6980 chunk 49 optimal weight: 6.9990 chunk 146 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 15275 Z= 0.232 Angle : 1.008 22.144 20735 Z= 0.392 Chirality : 0.051 0.389 2265 Planarity : 0.005 0.076 2625 Dihedral : 19.722 179.600 2190 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.16 % Allowed : 14.21 % Favored : 84.63 % 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: 0.31 (0.20), residues: 1800 helix: 0.05 (0.19), residues: 770 sheet: -0.57 (0.32), residues: 235 loop : 0.92 (0.24), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 340 HIS 0.005 0.001 HIS E 161 PHE 0.014 0.001 PHE A 31 TYR 0.010 0.001 TYR D 166 ARG 0.004 0.000 ARG B 147 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 110 time to evaluate : 1.840 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 18 residues processed: 128 average time/residue: 1.2577 time to fit residues: 179.0716 Evaluate side-chains 128 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 110 time to evaluate : 1.740 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 18 residues processed: 0 time to fit residues: 2.3382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 8.9990 chunk 104 optimal weight: 0.0980 chunk 81 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 179 optimal weight: 0.3980 chunk 165 optimal weight: 2.9990 chunk 142 optimal weight: 6.9990 chunk 14 optimal weight: 7.9990 chunk 110 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 15275 Z= 0.232 Angle : 1.008 22.144 20735 Z= 0.392 Chirality : 0.051 0.389 2265 Planarity : 0.005 0.076 2625 Dihedral : 19.730 179.600 2190 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.16 % Allowed : 14.28 % Favored : 84.57 % 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: 0.31 (0.20), residues: 1800 helix: 0.05 (0.19), residues: 770 sheet: -0.57 (0.32), residues: 235 loop : 0.92 (0.24), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 340 HIS 0.005 0.001 HIS E 161 PHE 0.014 0.001 PHE A 31 TYR 0.010 0.001 TYR D 166 ARG 0.004 0.000 ARG B 147 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 110 time to evaluate : 1.763 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 18 residues processed: 128 average time/residue: 1.3216 time to fit residues: 188.3352 Evaluate side-chains 128 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 110 time to evaluate : 1.817 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 18 residues processed: 0 time to fit residues: 2.3442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 143 optimal weight: 0.4980 chunk 59 optimal weight: 0.9990 chunk 146 optimal weight: 0.3980 chunk 18 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 125 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 ASN ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.099611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.085243 restraints weight = 24655.922| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.23 r_work: 0.2985 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 15275 Z= 0.198 Angle : 1.011 22.331 20735 Z= 0.392 Chirality : 0.051 0.391 2265 Planarity : 0.005 0.074 2625 Dihedral : 19.593 178.701 2190 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.41 % Allowed : 14.21 % Favored : 84.37 % 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: 0.39 (0.20), residues: 1800 helix: 0.14 (0.19), residues: 770 sheet: -0.47 (0.32), residues: 235 loop : 0.92 (0.24), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 340 HIS 0.004 0.001 HIS E 161 PHE 0.014 0.001 PHE A 31 TYR 0.010 0.001 TYR D 166 ARG 0.004 0.000 ARG B 147 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4491.07 seconds wall clock time: 81 minutes 26.55 seconds (4886.55 seconds total)