Starting phenix.real_space_refine on Tue Apr 9 02:07:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ahn_11787/04_2024/7ahn_11787_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ahn_11787/04_2024/7ahn_11787.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ahn_11787/04_2024/7ahn_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_11787/04_2024/7ahn_11787_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ahn_11787/04_2024/7ahn_11787_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ahn_11787/04_2024/7ahn_11787.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ahn_11787/04_2024/7ahn_11787.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ahn_11787/04_2024/7ahn_11787_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ahn_11787/04_2024/7ahn_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-dev-5288/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: 8.40, per 1000 atoms: 0.56 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: 5.79 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: 3.03 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: 4.86 Time building geometry restraints manager: 6.28 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: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.360 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 42.300 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.620 ------------------------------------------------------------------------------- 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 : 1.714 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 44 MET cc_start: 0.7010 (tpp) cc_final: 0.6642 (tpt) REVERT: E 280 ASN cc_start: 0.8234 (m-40) cc_final: 0.7947 (m110) REVERT: B 123 MET cc_start: 0.8083 (mmt) cc_final: 0.7739 (mmt) outliers start: 0 outliers final: 1 residues processed: 272 average time/residue: 1.6083 time to fit residues: 472.8085 Evaluate side-chains 138 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 137 time to evaluate : 1.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 287 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 0.9980 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: 0.8980 chunk 105 optimal weight: 0.8980 chunk 163 optimal weight: 5.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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: 0.8052 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 15275 Z= 0.237 Angle : 1.126 24.155 20735 Z= 0.443 Chirality : 0.053 0.399 2265 Planarity : 0.006 0.058 2625 Dihedral : 21.422 177.565 2192 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.48 % Allowed : 8.75 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.20), residues: 1800 helix: -1.10 (0.17), residues: 775 sheet: -0.96 (0.32), residues: 235 loop : 0.81 (0.24), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 79 HIS 0.003 0.001 HIS C 88 PHE 0.013 0.001 PHE D 31 TYR 0.009 0.001 TYR D 306 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: 23 poor density : 160 time to evaluate : 1.857 Fit side-chains REVERT: A 314 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7809 (tp40) REVERT: D 334 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.6786 (pt0) outliers start: 23 outliers final: 5 residues processed: 173 average time/residue: 1.4845 time to fit residues: 280.0670 Evaluate side-chains 119 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 112 time to evaluate : 2.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 354 GLN Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 350 SER 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: 4.9990 chunk 111 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 163 optimal weight: 1.9990 chunk 176 optimal weight: 0.8980 chunk 145 optimal weight: 3.9990 chunk 162 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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** B 162 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15275 Z= 0.296 Angle : 1.040 21.816 20735 Z= 0.410 Chirality : 0.052 0.384 2265 Planarity : 0.005 0.059 2625 Dihedral : 20.679 170.666 2190 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.64 % Allowed : 10.35 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.20), residues: 1800 helix: -0.59 (0.18), residues: 785 sheet: -0.73 (0.33), residues: 235 loop : 0.84 (0.24), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 79 HIS 0.005 0.001 HIS A 88 PHE 0.014 0.001 PHE B 31 TYR 0.010 0.001 TYR E 279 ARG 0.004 0.000 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 182 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 141 time to evaluate : 1.829 Fit side-chains REVERT: C 314 GLN cc_start: 0.7711 (OUTLIER) cc_final: 0.7468 (tt0) REVERT: A 291 LYS cc_start: 0.6447 (mmtt) cc_final: 0.6242 (mmtt) REVERT: A 314 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.7830 (tp40) REVERT: E 269 MET cc_start: 0.8195 (ttm) cc_final: 0.7993 (ttm) REVERT: D 44 MET cc_start: 0.3893 (tpt) cc_final: 0.3622 (mmm) REVERT: D 334 GLU cc_start: 0.7057 (OUTLIER) cc_final: 0.6766 (pt0) outliers start: 41 outliers final: 10 residues processed: 167 average time/residue: 1.5180 time to fit residues: 277.0948 Evaluate side-chains 129 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 116 time to evaluate : 1.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 350 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 6.9990 chunk 123 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 109 optimal weight: 0.3980 chunk 164 optimal weight: 1.9990 chunk 173 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- 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** ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 15275 Z= 0.333 Angle : 1.030 22.088 20735 Z= 0.407 Chirality : 0.053 0.385 2265 Planarity : 0.005 0.071 2625 Dihedral : 20.149 175.367 2190 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.12 % Allowed : 11.58 % Favored : 86.30 % 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: -0.13 (0.20), residues: 1800 helix: -0.40 (0.18), residues: 785 sheet: -0.66 (0.33), residues: 235 loop : 0.78 (0.24), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 356 HIS 0.005 0.001 HIS A 88 PHE 0.014 0.001 PHE A 31 TYR 0.008 0.001 TYR E 279 ARG 0.006 0.001 ARG B 147 *********************** 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 163 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 130 time to evaluate : 1.667 Fit side-chains REVERT: C 314 GLN cc_start: 0.7731 (OUTLIER) cc_final: 0.7489 (tt0) REVERT: A 314 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7849 (tp40) REVERT: E 269 MET cc_start: 0.8252 (ttm) cc_final: 0.8046 (ttm) REVERT: D 334 GLU cc_start: 0.6980 (OUTLIER) cc_final: 0.6675 (pt0) outliers start: 33 outliers final: 11 residues processed: 154 average time/residue: 1.3298 time to fit residues: 226.0781 Evaluate side-chains 132 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 118 time to evaluate : 1.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 350 SER 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: 8.9990 chunk 2 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 148 optimal weight: 0.9980 chunk 120 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 88 optimal weight: 4.9990 chunk 156 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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 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: 0.8129 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 15275 Z= 0.317 Angle : 1.027 22.232 20735 Z= 0.404 Chirality : 0.053 0.386 2265 Planarity : 0.005 0.074 2625 Dihedral : 20.009 176.746 2190 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.57 % Allowed : 11.77 % Favored : 85.66 % 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: 0.07 (0.20), residues: 1800 helix: -0.23 (0.18), residues: 775 sheet: -0.65 (0.32), residues: 235 loop : 0.87 (0.24), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 356 HIS 0.005 0.001 HIS A 88 PHE 0.014 0.001 PHE A 31 TYR 0.013 0.001 TYR D 166 ARG 0.005 0.000 ARG E 147 *********************** 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 163 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 123 time to evaluate : 1.730 Fit side-chains revert: symmetry clash REVERT: C 314 GLN cc_start: 0.7731 (OUTLIER) cc_final: 0.7510 (tt0) REVERT: A 314 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7834 (tp40) REVERT: E 269 MET cc_start: 0.8264 (ttm) cc_final: 0.8057 (ttm) REVERT: D 334 GLU cc_start: 0.6982 (OUTLIER) cc_final: 0.6674 (pt0) REVERT: B 178 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7890 (mt) outliers start: 40 outliers final: 19 residues processed: 152 average time/residue: 1.3129 time to fit residues: 220.7932 Evaluate side-chains 139 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 116 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 350 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 10.0000 chunk 156 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 174 optimal weight: 0.9990 chunk 144 optimal weight: 8.9990 chunk 80 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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** ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 15275 Z= 0.317 Angle : 1.027 22.232 20735 Z= 0.404 Chirality : 0.053 0.386 2265 Planarity : 0.005 0.074 2625 Dihedral : 20.009 176.746 2190 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.48 % Allowed : 13.38 % Favored : 85.14 % 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: 0.07 (0.20), residues: 1800 helix: -0.23 (0.18), residues: 775 sheet: -0.65 (0.32), residues: 235 loop : 0.87 (0.24), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 356 HIS 0.005 0.001 HIS A 88 PHE 0.014 0.001 PHE A 31 TYR 0.013 0.001 TYR D 166 ARG 0.005 0.000 ARG E 147 *********************** 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 139 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 116 time to evaluate : 1.757 Fit side-chains revert: symmetry clash REVERT: C 314 GLN cc_start: 0.7751 (OUTLIER) cc_final: 0.7510 (tt0) REVERT: A 314 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7834 (tp40) REVERT: E 269 MET cc_start: 0.8267 (ttm) cc_final: 0.8057 (ttm) REVERT: D 334 GLU cc_start: 0.6980 (OUTLIER) cc_final: 0.6674 (pt0) REVERT: B 178 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7890 (mt) outliers start: 23 outliers final: 19 residues processed: 136 average time/residue: 1.3655 time to fit residues: 205.0993 Evaluate side-chains 138 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 115 time to evaluate : 1.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 350 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 0.0570 chunk 19 optimal weight: 4.9990 chunk 99 optimal weight: 0.9990 chunk 127 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 146 optimal weight: 0.4980 chunk 97 optimal weight: 0.8980 chunk 173 optimal weight: 4.9990 chunk 108 optimal weight: 7.9990 chunk 105 optimal weight: 0.9980 chunk 80 optimal weight: 7.9990 overall best weight: 0.6900 ------------------------------------------------------------------------------- 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** ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 15275 Z= 0.317 Angle : 1.027 22.232 20735 Z= 0.404 Chirality : 0.053 0.386 2265 Planarity : 0.005 0.074 2625 Dihedral : 20.011 176.746 2190 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.48 % Allowed : 13.44 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.20), residues: 1800 helix: -0.23 (0.18), residues: 775 sheet: -0.65 (0.32), residues: 235 loop : 0.87 (0.24), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 356 HIS 0.005 0.001 HIS A 88 PHE 0.014 0.001 PHE A 31 TYR 0.013 0.001 TYR D 166 ARG 0.005 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 138 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 115 time to evaluate : 1.653 Fit side-chains revert: symmetry clash REVERT: C 314 GLN cc_start: 0.7752 (OUTLIER) cc_final: 0.7510 (tt0) REVERT: A 314 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7834 (tp40) REVERT: E 269 MET cc_start: 0.8267 (ttm) cc_final: 0.8056 (ttm) REVERT: D 334 GLU cc_start: 0.6980 (OUTLIER) cc_final: 0.6674 (pt0) REVERT: B 178 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7890 (mt) outliers start: 23 outliers final: 19 residues processed: 135 average time/residue: 1.4400 time to fit residues: 214.0931 Evaluate side-chains 138 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 115 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 350 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 0.0980 chunk 69 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 52 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 136 optimal weight: 4.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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** ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 15275 Z= 0.318 Angle : 1.027 22.232 20735 Z= 0.403 Chirality : 0.053 0.416 2265 Planarity : 0.005 0.074 2625 Dihedral : 20.088 177.414 2190 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.48 % Allowed : 13.44 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.20), residues: 1800 helix: -0.23 (0.18), residues: 775 sheet: -0.65 (0.32), residues: 235 loop : 0.87 (0.24), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 356 HIS 0.005 0.001 HIS A 88 PHE 0.014 0.001 PHE A 31 TYR 0.013 0.001 TYR D 166 ARG 0.005 0.000 ARG E 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 138 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 115 time to evaluate : 1.794 Fit side-chains revert: symmetry clash REVERT: C 314 GLN cc_start: 0.7752 (OUTLIER) cc_final: 0.7510 (tt0) REVERT: A 314 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7834 (tp40) REVERT: E 269 MET cc_start: 0.8267 (ttm) cc_final: 0.8057 (ttm) REVERT: D 334 GLU cc_start: 0.6980 (OUTLIER) cc_final: 0.6673 (pt0) REVERT: B 178 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7890 (mt) outliers start: 23 outliers final: 19 residues processed: 135 average time/residue: 1.3775 time to fit residues: 205.0039 Evaluate side-chains 138 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 115 time to evaluate : 1.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 350 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 0.6980 chunk 166 optimal weight: 10.0000 chunk 151 optimal weight: 0.8980 chunk 161 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 chunk 70 optimal weight: 7.9990 chunk 126 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 146 optimal weight: 0.9990 chunk 152 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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** E 12 ASN E 162 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 15275 Z= 0.228 Angle : 1.026 22.330 20735 Z= 0.402 Chirality : 0.052 0.389 2265 Planarity : 0.005 0.077 2625 Dihedral : 19.793 179.878 2190 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.54 % Allowed : 13.57 % Favored : 84.89 % 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: 0.26 (0.20), residues: 1800 helix: -0.03 (0.19), residues: 770 sheet: -0.60 (0.32), residues: 235 loop : 0.94 (0.24), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 79 HIS 0.004 0.001 HIS A 371 PHE 0.014 0.001 PHE A 31 TYR 0.015 0.001 TYR D 166 ARG 0.005 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 149 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 125 time to evaluate : 1.719 Fit side-chains revert: symmetry clash REVERT: C 314 GLN cc_start: 0.7676 (OUTLIER) cc_final: 0.7431 (tt0) REVERT: A 314 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7801 (tp40) REVERT: E 269 MET cc_start: 0.8257 (ttm) cc_final: 0.8034 (ttm) REVERT: D 334 GLU cc_start: 0.6984 (OUTLIER) cc_final: 0.6688 (pt0) REVERT: B 178 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7967 (mt) outliers start: 24 outliers final: 15 residues processed: 144 average time/residue: 1.3701 time to fit residues: 217.7003 Evaluate side-chains 136 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 117 time to evaluate : 1.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 178 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 179 optimal weight: 0.0050 chunk 165 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 110 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 overall best weight: 2.0002 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 15275 Z= 0.317 Angle : 1.035 22.236 20735 Z= 0.409 Chirality : 0.053 0.388 2265 Planarity : 0.005 0.077 2625 Dihedral : 19.767 178.440 2190 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.22 % Allowed : 14.21 % 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: 0.18 (0.20), residues: 1800 helix: -0.04 (0.19), residues: 775 sheet: -0.65 (0.31), residues: 235 loop : 0.84 (0.24), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 79 HIS 0.005 0.001 HIS A 88 PHE 0.013 0.001 PHE A 31 TYR 0.013 0.001 TYR D 166 ARG 0.005 0.000 ARG E 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 135 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 116 time to evaluate : 1.844 Fit side-chains revert: symmetry clash REVERT: C 314 GLN cc_start: 0.7724 (OUTLIER) cc_final: 0.7480 (tt0) REVERT: A 314 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7852 (tp40) REVERT: E 269 MET cc_start: 0.8282 (ttm) cc_final: 0.8076 (ttm) REVERT: D 334 GLU cc_start: 0.6970 (OUTLIER) cc_final: 0.6669 (pt0) REVERT: B 178 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8051 (mt) outliers start: 19 outliers final: 12 residues processed: 133 average time/residue: 1.4982 time to fit residues: 218.9206 Evaluate side-chains 127 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 111 time to evaluate : 1.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 178 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 0.0980 chunk 43 optimal weight: 0.9990 chunk 131 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 143 optimal weight: 0.2980 chunk 59 optimal weight: 0.2980 chunk 146 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 125 optimal weight: 4.9990 overall best weight: 0.4782 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.097792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.083281 restraints weight = 24767.891| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.21 r_work: 0.2947 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 15275 Z= 0.317 Angle : 1.035 22.236 20735 Z= 0.409 Chirality : 0.053 0.388 2265 Planarity : 0.005 0.077 2625 Dihedral : 19.767 178.440 2190 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.03 % Allowed : 14.53 % Favored : 84.44 % 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: 0.18 (0.20), residues: 1800 helix: -0.04 (0.19), residues: 775 sheet: -0.65 (0.31), residues: 235 loop : 0.84 (0.24), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 79 HIS 0.005 0.001 HIS A 88 PHE 0.013 0.001 PHE A 31 TYR 0.013 0.001 TYR D 166 ARG 0.005 0.000 ARG E 147 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4611.62 seconds wall clock time: 84 minutes 18.17 seconds (5058.17 seconds total)