Starting phenix.real_space_refine (version: 1.21rc1) on Wed Apr 26 12:04:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7md2_23763/04_2023/7md2_23763_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7md2_23763/04_2023/7md2_23763.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7md2_23763/04_2023/7md2_23763.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7md2_23763/04_2023/7md2_23763.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7md2_23763/04_2023/7md2_23763_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7md2_23763/04_2023/7md2_23763_trim_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.002 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 22293 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians P 10 5.49 5 Mg 3 5.21 5 S 37 5.16 5 C 14870 2.51 5 N 4092 2.21 5 O 4462 1.98 5 H 23645 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 81": "OD1" <-> "OD2" Residue "A GLU 88": "OE1" <-> "OE2" Residue "A GLU 146": "OE1" <-> "OE2" Residue "A ASP 156": "OD1" <-> "OD2" Residue "A ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 167": "OE1" <-> "OE2" Residue "A ARG 173": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 196": "OD1" <-> "OD2" Residue "A TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 257": "OE1" <-> "OE2" Residue "A ASP 271": "OD1" <-> "OD2" Residue "A PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A GLU 316": "OE1" <-> "OE2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "A ASP 335": "OD1" <-> "OD2" Residue "A GLU 357": "OE1" <-> "OE2" Residue "A ARG 375": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 401": "OE1" <-> "OE2" Residue "A ASP 411": "OD1" <-> "OD2" Residue "A GLU 441": "OE1" <-> "OE2" Residue "A GLU 442": "OE1" <-> "OE2" Residue "A GLU 490": "OE1" <-> "OE2" Residue "B GLU 29": "OE1" <-> "OE2" Residue "B GLU 146": "OE1" <-> "OE2" Residue "B ASP 172": "OD1" <-> "OD2" Residue "B TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 299": "OD1" <-> "OD2" Residue "B GLU 316": "OE1" <-> "OE2" Residue "B ARG 422": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 424": "OE1" <-> "OE2" Residue "B GLU 465": "OE1" <-> "OE2" Residue "B PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 467": "OE1" <-> "OE2" Residue "C GLU 52": "OE1" <-> "OE2" Residue "C GLU 53": "OE1" <-> "OE2" Residue "C GLU 69": "OE1" <-> "OE2" Residue "C ARG 82": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 86": "OE1" <-> "OE2" Residue "C ASP 111": "OD1" <-> "OD2" Residue "C ASP 124": "OD1" <-> "OD2" Residue "C ARG 128": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 146": "OE1" <-> "OE2" Residue "C GLU 167": "OE1" <-> "OE2" Residue "C ASP 172": "OD1" <-> "OD2" Residue "C ARG 173": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 196": "OD1" <-> "OD2" Residue "C TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 223": "OE1" <-> "OE2" Residue "C GLU 257": "OE1" <-> "OE2" Residue "C ASP 261": "OD1" <-> "OD2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C GLU 316": "OE1" <-> "OE2" Residue "C GLU 318": "OE1" <-> "OE2" Residue "C PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 411": "OD1" <-> "OD2" Residue "C GLU 424": "OE1" <-> "OE2" Residue "C GLU 441": "OE1" <-> "OE2" Residue "C GLU 459": "OE1" <-> "OE2" Residue "C GLU 467": "OE1" <-> "OE2" Residue "C GLU 484": "OE1" <-> "OE2" Residue "C GLU 487": "OE1" <-> "OE2" Residue "C GLU 490": "OE1" <-> "OE2" Residue "C GLU 494": "OE1" <-> "OE2" Residue "C GLU 504": "OE1" <-> "OE2" Residue "C PHE 510": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 49": "OE1" <-> "OE2" Residue "D ASP 65": "OD1" <-> "OD2" Residue "D ARG 89": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ASP 120": "OD1" <-> "OD2" Residue "D ARG 149": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 200": "OE1" <-> "OE2" Residue "D ASP 256": "OD1" <-> "OD2" Residue "D ASP 288": "OD1" <-> "OD2" Residue "D GLU 294": "OE1" <-> "OE2" Residue "D ASP 315": "OD1" <-> "OD2" Residue "D ASP 316": "OD1" <-> "OD2" Residue "D ASP 352": "OD1" <-> "OD2" Residue "D ASP 359": "OD1" <-> "OD2" Residue "D GLU 366": "OE1" <-> "OE2" Residue "D ASP 369": "OD1" <-> "OD2" Residue "D GLU 395": "OE1" <-> "OE2" Residue "D ARG 412": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 424": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 433": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ASP 436": "OD1" <-> "OD2" Residue "D GLU 464": "OE1" <-> "OE2" Residue "D GLU 471": "OE1" <-> "OE2" Residue "E ASP 22": "OD1" <-> "OD2" Residue "E GLU 38": "OE1" <-> "OE2" Residue "E GLU 49": "OE1" <-> "OE2" Residue "E ASP 65": "OD1" <-> "OD2" Residue "E GLU 105": "OE1" <-> "OE2" Residue "E ASP 120": "OD1" <-> "OD2" Residue "E PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 126": "OE1" <-> "OE2" Residue "E GLU 135": "OE1" <-> "OE2" Residue "E GLU 189": "OE1" <-> "OE2" Residue "E GLU 193": "OE1" <-> "OE2" Residue "E ASP 196": "OD1" <-> "OD2" Residue "E GLU 200": "OE1" <-> "OE2" Residue "E GLU 203": "OE1" <-> "OE2" Residue "E GLU 210": "OE1" <-> "OE2" Residue "E GLU 212": "OE1" <-> "OE2" Residue "E GLU 224": "OE1" <-> "OE2" Residue "E GLU 246": "OE1" <-> "OE2" Residue "E GLU 267": "OE1" <-> "OE2" Residue "E ARG 337": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ASP 352": "OD1" <-> "OD2" Residue "E ASP 369": "OD1" <-> "OD2" Residue "E GLU 376": "OE1" <-> "OE2" Residue "E ASP 386": "OD1" <-> "OD2" Residue "E ASP 400": "OD1" <-> "OD2" Residue "E GLU 422": "OE1" <-> "OE2" Residue "F ASP 22": "OD1" <-> "OD2" Residue "F GLU 49": "OE1" <-> "OE2" Residue "F ASP 78": "OD1" <-> "OD2" Residue "F GLU 101": "OE1" <-> "OE2" Residue "F ASP 120": "OD1" <-> "OD2" Residue "F PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 126": "OE1" <-> "OE2" Residue "F GLU 132": "OE1" <-> "OE2" Residue "F GLU 210": "OE1" <-> "OE2" Residue "F GLU 247": "OE1" <-> "OE2" Residue "F ASP 256": "OD1" <-> "OD2" Residue "F PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 330": "OD1" <-> "OD2" Residue "F ASP 352": "OD1" <-> "OD2" Residue "F ASP 394": "OD1" <-> "OD2" Residue "F ASP 400": "OD1" <-> "OD2" Residue "F GLU 422": "OE1" <-> "OE2" Residue "F ASP 436": "OD1" <-> "OD2" Residue "G GLU 5": "OE1" <-> "OE2" Residue "G GLU 35": "OE1" <-> "OE2" Residue "G ASP 136": "OD1" <-> "OD2" Residue "G PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 269": "OD1" <-> "OD2" Residue "H TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 47119 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 7383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 7383 Classifications: {'peptide': 485} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 464} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 25 Chain: "B" Number of atoms: 6924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 6924 Classifications: {'peptide': 458} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 437} Chain breaks: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 8, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "C" Number of atoms: 7423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 7423 Classifications: {'peptide': 485} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 464} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "D" Number of atoms: 6996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 6996 Classifications: {'peptide': 469} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 445} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 11, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 56 Chain: "E" Number of atoms: 7078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 7078 Classifications: {'peptide': 469} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 445} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "F" Number of atoms: 7041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 7041 Classifications: {'peptide': 469} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 445} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 10} Unresolved non-hydrogen planarities: 44 Chain: "G" Number of atoms: 3493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 3493 Classifications: {'peptide': 232} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 224} Chain breaks: 3 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 48 Chain: "H" Number of atoms: 599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 599 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 81 Unusual residues: {'ZHD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 15.07, per 1000 atoms: 0.32 Number of scatterers: 47119 At special positions: 0 Unit cell: (130.81, 128.75, 145.23, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 37 16.00 P 10 15.00 Mg 3 11.99 O 4462 8.00 N 4092 7.00 C 14870 6.00 H 23645 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 30.78 Conformation dependent library (CDL) restraints added in 3.5 seconds 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5662 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 134 helices and 22 sheets defined 42.3% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.23 Creating SS restraints... Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 153 through 156 No H-bonds generated for 'chain 'A' and resid 153 through 156' Processing helix chain 'A' and resid 177 through 192 removed outlier: 3.873A pdb=" N GLN A 188 " --> pdb=" O THR A 184 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N LYS A 189 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ARG A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N TRP A 191 " --> pdb=" O ASN A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 224 Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 242 through 261 Proline residue: A 249 - end of helix removed outlier: 3.760A pdb=" N TRP A 258 " --> pdb=" O SER A 254 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N PHE A 259 " --> pdb=" O ILE A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 286 Processing helix chain 'A' and resid 293 through 295 No H-bonds generated for 'chain 'A' and resid 293 through 295' Processing helix chain 'A' and resid 300 through 310 removed outlier: 3.526A pdb=" N ARG A 306 " --> pdb=" O TYR A 302 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ARG A 310 " --> pdb=" O ARG A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 318 No H-bonds generated for 'chain 'A' and resid 316 through 318' Processing helix chain 'A' and resid 332 through 334 No H-bonds generated for 'chain 'A' and resid 332 through 334' Processing helix chain 'A' and resid 339 through 347 Processing helix chain 'A' and resid 356 through 359 No H-bonds generated for 'chain 'A' and resid 356 through 359' Processing helix chain 'A' and resid 377 through 379 No H-bonds generated for 'chain 'A' and resid 377 through 379' Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.673A pdb=" N VAL A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 408 removed outlier: 3.545A pdb=" N GLU A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N ALA A 404 " --> pdb=" O ARG A 400 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N PHE A 405 " --> pdb=" O GLU A 401 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N GLN A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N PHE A 408 " --> pdb=" O ALA A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 430 removed outlier: 4.261A pdb=" N THR A 419 " --> pdb=" O SER A 415 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU A 424 " --> pdb=" O LEU A 420 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG A 425 " --> pdb=" O VAL A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 451 Proline residue: A 445 - end of helix Processing helix chain 'A' and resid 454 through 457 removed outlier: 4.030A pdb=" N GLY A 457 " --> pdb=" O HIS A 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 454 through 457' Processing helix chain 'A' and resid 460 through 477 removed outlier: 3.807A pdb=" N ILE A 463 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N GLY A 464 " --> pdb=" O SER A 461 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU A 467 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER A 468 " --> pdb=" O GLU A 465 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU A 471 " --> pdb=" O SER A 468 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU A 474 " --> pdb=" O LEU A 471 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS A 475 " --> pdb=" O SER A 472 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN A 477 " --> pdb=" O LEU A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 488 Processing helix chain 'A' and resid 493 through 509 removed outlier: 3.653A pdb=" N ALA A 497 " --> pdb=" O LYS A 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 83 No H-bonds generated for 'chain 'B' and resid 81 through 83' Processing helix chain 'B' and resid 103 through 105 No H-bonds generated for 'chain 'B' and resid 103 through 105' Processing helix chain 'B' and resid 153 through 158 Processing helix chain 'B' and resid 177 through 192 removed outlier: 3.771A pdb=" N ALA B 181 " --> pdb=" O LYS B 177 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLN B 188 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N LYS B 189 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N ARG B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N TRP B 191 " --> pdb=" O ASN B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 224 Processing helix chain 'B' and resid 227 through 230 removed outlier: 3.782A pdb=" N TYR B 230 " --> pdb=" O ALA B 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 227 through 230' Processing helix chain 'B' and resid 242 through 261 Proline residue: B 249 - end of helix removed outlier: 3.784A pdb=" N TRP B 258 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE B 259 " --> pdb=" O ILE B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 287 Processing helix chain 'B' and resid 293 through 295 No H-bonds generated for 'chain 'B' and resid 293 through 295' Processing helix chain 'B' and resid 300 through 308 removed outlier: 3.641A pdb=" N ARG B 306 " --> pdb=" O TYR B 302 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU B 307 " --> pdb=" O LEU B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 334 No H-bonds generated for 'chain 'B' and resid 332 through 334' Processing helix chain 'B' and resid 339 through 347 Processing helix chain 'B' and resid 356 through 360 Processing helix chain 'B' and resid 377 through 379 No H-bonds generated for 'chain 'B' and resid 377 through 379' Processing helix chain 'B' and resid 383 through 389 Processing helix chain 'B' and resid 422 through 430 Processing helix chain 'B' and resid 440 through 451 Proline residue: B 445 - end of helix removed outlier: 3.646A pdb=" N GLY B 450 " --> pdb=" O LEU B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 457 removed outlier: 3.901A pdb=" N GLY B 457 " --> pdb=" O HIS B 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 454 through 457' Processing helix chain 'B' and resid 460 through 477 removed outlier: 4.546A pdb=" N GLY B 464 " --> pdb=" O SER B 461 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU B 467 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE B 470 " --> pdb=" O GLU B 467 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU B 471 " --> pdb=" O SER B 468 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER B 472 " --> pdb=" O SER B 469 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU B 474 " --> pdb=" O LEU B 471 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASN B 477 " --> pdb=" O LEU B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 487 Processing helix chain 'B' and resid 493 through 509 removed outlier: 4.074A pdb=" N ALA B 508 " --> pdb=" O GLU B 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 83 No H-bonds generated for 'chain 'C' and resid 81 through 83' Processing helix chain 'C' and resid 103 through 105 No H-bonds generated for 'chain 'C' and resid 103 through 105' Processing helix chain 'C' and resid 153 through 156 No H-bonds generated for 'chain 'C' and resid 153 through 156' Processing helix chain 'C' and resid 177 through 192 removed outlier: 3.944A pdb=" N GLN C 188 " --> pdb=" O THR C 184 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N LYS C 189 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N ARG C 190 " --> pdb=" O LEU C 186 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N TRP C 191 " --> pdb=" O ASN C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 224 Processing helix chain 'C' and resid 228 through 230 No H-bonds generated for 'chain 'C' and resid 228 through 230' Processing helix chain 'C' and resid 242 through 261 Proline residue: C 249 - end of helix removed outlier: 3.527A pdb=" N TRP C 258 " --> pdb=" O SER C 254 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE C 259 " --> pdb=" O ILE C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 286 Processing helix chain 'C' and resid 293 through 295 No H-bonds generated for 'chain 'C' and resid 293 through 295' Processing helix chain 'C' and resid 300 through 308 removed outlier: 3.621A pdb=" N ARG C 306 " --> pdb=" O TYR C 302 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU C 307 " --> pdb=" O LEU C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 318 No H-bonds generated for 'chain 'C' and resid 316 through 318' Processing helix chain 'C' and resid 332 through 334 No H-bonds generated for 'chain 'C' and resid 332 through 334' Processing helix chain 'C' and resid 339 through 347 removed outlier: 3.624A pdb=" N SER C 346 " --> pdb=" O THR C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 360 Processing helix chain 'C' and resid 377 through 380 Processing helix chain 'C' and resid 383 through 405 removed outlier: 3.819A pdb=" N VAL C 388 " --> pdb=" O ALA C 384 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N SER C 391 " --> pdb=" O GLN C 387 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N ALA C 404 " --> pdb=" O ARG C 400 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N PHE C 405 " --> pdb=" O GLU C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 429 Processing helix chain 'C' and resid 440 through 451 Proline residue: C 445 - end of helix Processing helix chain 'C' and resid 454 through 457 removed outlier: 3.820A pdb=" N GLY C 457 " --> pdb=" O HIS C 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 454 through 457' Processing helix chain 'C' and resid 463 through 477 removed outlier: 3.637A pdb=" N SER C 468 " --> pdb=" O GLY C 464 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU C 471 " --> pdb=" O GLU C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 488 Processing helix chain 'C' and resid 493 through 507 removed outlier: 3.727A pdb=" N SER C 498 " --> pdb=" O GLU C 494 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE C 506 " --> pdb=" O ALA C 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 91 No H-bonds generated for 'chain 'D' and resid 89 through 91' Processing helix chain 'D' and resid 124 through 126 No H-bonds generated for 'chain 'D' and resid 124 through 126' Processing helix chain 'D' and resid 139 through 144 Processing helix chain 'D' and resid 159 through 161 No H-bonds generated for 'chain 'D' and resid 159 through 161' Processing helix chain 'D' and resid 163 through 176 Processing helix chain 'D' and resid 191 through 204 Processing helix chain 'D' and resid 226 through 229 No H-bonds generated for 'chain 'D' and resid 226 through 229' Processing helix chain 'D' and resid 232 through 247 removed outlier: 3.759A pdb=" N ILE D 239 " --> pdb=" O THR D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 272 Processing helix chain 'D' and resid 285 through 295 removed outlier: 4.811A pdb=" N ARG D 295 " --> pdb=" O LEU D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 315 No H-bonds generated for 'chain 'D' and resid 313 through 315' Processing helix chain 'D' and resid 320 through 327 removed outlier: 3.803A pdb=" N ALA D 327 " --> pdb=" O ALA D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 340 No H-bonds generated for 'chain 'D' and resid 337 through 340' Processing helix chain 'D' and resid 360 through 363 No H-bonds generated for 'chain 'D' and resid 360 through 363' Processing helix chain 'D' and resid 365 through 383 removed outlier: 3.570A pdb=" N VAL D 370 " --> pdb=" O GLU D 366 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN D 379 " --> pdb=" O GLN D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 390 Processing helix chain 'D' and resid 398 through 413 Processing helix chain 'D' and resid 434 through 445 removed outlier: 3.557A pdb=" N SER D 440 " --> pdb=" O ASP D 436 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 457 Processing helix chain 'D' and resid 463 through 475 removed outlier: 4.205A pdb=" N ALA D 468 " --> pdb=" O GLU D 464 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 91 No H-bonds generated for 'chain 'E' and resid 89 through 91' Processing helix chain 'E' and resid 124 through 126 No H-bonds generated for 'chain 'E' and resid 124 through 126' Processing helix chain 'E' and resid 139 through 144 Processing helix chain 'E' and resid 163 through 177 Processing helix chain 'E' and resid 191 through 204 Processing helix chain 'E' and resid 226 through 229 No H-bonds generated for 'chain 'E' and resid 226 through 229' Processing helix chain 'E' and resid 232 through 245 Processing helix chain 'E' and resid 258 through 272 Processing helix chain 'E' and resid 285 through 295 removed outlier: 3.626A pdb=" N LEU E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ARG E 295 " --> pdb=" O LEU E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 315 No H-bonds generated for 'chain 'E' and resid 313 through 315' Processing helix chain 'E' and resid 320 through 326 Processing helix chain 'E' and resid 337 through 341 Processing helix chain 'E' and resid 365 through 384 removed outlier: 3.936A pdb=" N VAL E 370 " --> pdb=" O GLU E 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 390 No H-bonds generated for 'chain 'E' and resid 387 through 390' Processing helix chain 'E' and resid 393 through 395 No H-bonds generated for 'chain 'E' and resid 393 through 395' Processing helix chain 'E' and resid 398 through 413 Processing helix chain 'E' and resid 421 through 425 removed outlier: 3.795A pdb=" N THR E 425 " --> pdb=" O GLU E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 434 through 445 Processing helix chain 'E' and resid 454 through 457 Processing helix chain 'E' and resid 463 through 475 removed outlier: 3.734A pdb=" N ALA E 468 " --> pdb=" O GLU E 464 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 91 No H-bonds generated for 'chain 'F' and resid 89 through 91' Processing helix chain 'F' and resid 124 through 126 No H-bonds generated for 'chain 'F' and resid 124 through 126' Processing helix chain 'F' and resid 139 through 144 Processing helix chain 'F' and resid 163 through 174 Processing helix chain 'F' and resid 192 through 204 removed outlier: 3.914A pdb=" N LEU F 197 " --> pdb=" O GLU F 193 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU F 200 " --> pdb=" O ASP F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 229 No H-bonds generated for 'chain 'F' and resid 226 through 229' Processing helix chain 'F' and resid 232 through 245 Processing helix chain 'F' and resid 258 through 272 removed outlier: 3.538A pdb=" N GLU F 267 " --> pdb=" O ALA F 264 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ALA F 270 " --> pdb=" O GLU F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 283 through 295 removed outlier: 4.333A pdb=" N ALA F 286 " --> pdb=" O PRO F 283 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP F 288 " --> pdb=" O LEU F 285 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N MET F 289 " --> pdb=" O ALA F 286 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU F 291 " --> pdb=" O ASP F 288 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLU F 294 " --> pdb=" O LEU F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 315 No H-bonds generated for 'chain 'F' and resid 313 through 315' Processing helix chain 'F' and resid 320 through 328 removed outlier: 4.530A pdb=" N ALA F 327 " --> pdb=" O ALA F 323 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N HIS F 328 " --> pdb=" O THR F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 341 No H-bonds generated for 'chain 'F' and resid 338 through 341' Processing helix chain 'F' and resid 360 through 363 No H-bonds generated for 'chain 'F' and resid 360 through 363' Processing helix chain 'F' and resid 365 through 383 Processing helix chain 'F' and resid 385 through 390 Processing helix chain 'F' and resid 398 through 413 Processing helix chain 'F' and resid 422 through 425 No H-bonds generated for 'chain 'F' and resid 422 through 425' Processing helix chain 'F' and resid 434 through 445 Processing helix chain 'F' and resid 454 through 457 Processing helix chain 'F' and resid 463 through 474 Processing helix chain 'G' and resid 3 through 29 removed outlier: 3.530A pdb=" N MET G 8 " --> pdb=" O LYS G 4 " (cutoff:3.500A) Processing helix chain 'G' and resid 31 through 54 removed outlier: 3.905A pdb=" N ALA G 47 " --> pdb=" O LYS G 43 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU G 48 " --> pdb=" O MET G 44 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N PHE G 51 " --> pdb=" O ALA G 47 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N TYR G 52 " --> pdb=" O GLU G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 98 Processing helix chain 'G' and resid 112 through 121 removed outlier: 3.689A pdb=" N THR G 121 " --> pdb=" O GLN G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 153 Processing helix chain 'G' and resid 156 through 158 No H-bonds generated for 'chain 'G' and resid 156 through 158' Processing helix chain 'G' and resid 205 through 274 removed outlier: 3.800A pdb=" N ALA G 215 " --> pdb=" O GLU G 211 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N MET G 237 " --> pdb=" O ARG G 233 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE G 253 " --> pdb=" O ASN G 249 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASN G 256 " --> pdb=" O SER G 252 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 23 Processing helix chain 'H' and resid 32 through 38 removed outlier: 3.864A pdb=" N SER H 38 " --> pdb=" O VAL H 34 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 30 through 32 removed outlier: 6.682A pdb=" N GLY A 74 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N PHE A 44 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N VAL A 33 " --> pdb=" O PHE A 44 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 98 through 100 Processing sheet with id= C, first strand: chain 'A' and resid 351 through 353 removed outlier: 6.524A pdb=" N LEU A 168 " --> pdb=" O ILE A 352 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 231 through 236 removed outlier: 6.558A pdb=" N CYS A 203 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N VAL A 234 " --> pdb=" O CYS A 203 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N TYR A 205 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ALA A 236 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ALA A 207 " --> pdb=" O ALA A 236 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N SER A 322 " --> pdb=" O ALA A 266 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N ILE A 268 " --> pdb=" O SER A 322 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N THR A 324 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N TYR A 270 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LEU A 326 " --> pdb=" O TYR A 270 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 30 through 32 removed outlier: 6.933A pdb=" N GLY B 74 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N LEU B 68 " --> pdb=" O GLN B 72 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N GLN B 72 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N PHE B 44 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N VAL B 33 " --> pdb=" O PHE B 44 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 98 through 101 Processing sheet with id= G, first strand: chain 'B' and resid 351 through 354 removed outlier: 6.771A pdb=" N LEU B 168 " --> pdb=" O ILE B 352 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N LEU B 354 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE B 170 " --> pdb=" O LEU B 354 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 231 through 236 removed outlier: 6.597A pdb=" N CYS B 203 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N VAL B 234 " --> pdb=" O CYS B 203 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N TYR B 205 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ALA B 236 " --> pdb=" O TYR B 205 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ALA B 207 " --> pdb=" O ALA B 236 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N SER B 322 " --> pdb=" O ALA B 266 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N ILE B 268 " --> pdb=" O SER B 322 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N THR B 324 " --> pdb=" O ILE B 268 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N TYR B 270 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LEU B 326 " --> pdb=" O TYR B 270 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 30 through 32 removed outlier: 6.590A pdb=" N GLY C 74 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA C 35 " --> pdb=" O ARG C 42 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N PHE C 44 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N VAL C 33 " --> pdb=" O PHE C 44 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 98 through 101 Processing sheet with id= K, first strand: chain 'C' and resid 350 through 354 Processing sheet with id= L, first strand: chain 'C' and resid 231 through 236 removed outlier: 6.535A pdb=" N CYS C 203 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N VAL C 234 " --> pdb=" O CYS C 203 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N TYR C 205 " --> pdb=" O VAL C 234 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ALA C 236 " --> pdb=" O TYR C 205 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ALA C 207 " --> pdb=" O ALA C 236 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N SER C 322 " --> pdb=" O ALA C 266 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ILE C 268 " --> pdb=" O SER C 322 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N THR C 324 " --> pdb=" O ILE C 268 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N TYR C 270 " --> pdb=" O THR C 324 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU C 326 " --> pdb=" O TYR C 270 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 75 through 77 removed outlier: 6.448A pdb=" N ASP D 22 " --> pdb=" O THR D 14 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL D 16 " --> pdb=" O ILE D 20 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE D 20 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ILE D 62 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N VAL D 50 " --> pdb=" O ILE D 62 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 84 through 87 removed outlier: 4.620A pdb=" N LEU D 113 " --> pdb=" O VAL D 87 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 331 through 334 removed outlier: 3.636A pdb=" N ALA D 331 " --> pdb=" O LYS D 152 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N ILE D 153 " --> pdb=" O VAL D 304 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N SER D 306 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N LEU D 155 " --> pdb=" O SER D 306 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N GLN D 308 " --> pdb=" O LEU D 155 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL D 251 " --> pdb=" O THR D 305 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N VAL D 307 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU D 253 " --> pdb=" O VAL D 307 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ALA D 309 " --> pdb=" O LEU D 253 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE D 255 " --> pdb=" O ALA D 309 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ALA D 216 " --> pdb=" O PHE D 184 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N GLY D 186 " --> pdb=" O ALA D 216 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL D 218 " --> pdb=" O GLY D 186 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N GLY D 188 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N GLY D 220 " --> pdb=" O GLY D 188 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 75 through 77 removed outlier: 6.515A pdb=" N ASP E 22 " --> pdb=" O THR E 14 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL E 16 " --> pdb=" O ILE E 20 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE E 20 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ILE E 62 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N VAL E 50 " --> pdb=" O ILE E 62 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 84 through 86 Processing sheet with id= R, first strand: chain 'E' and resid 331 through 334 removed outlier: 8.500A pdb=" N ILE E 153 " --> pdb=" O VAL E 304 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N SER E 306 " --> pdb=" O ILE E 153 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N LEU E 155 " --> pdb=" O SER E 306 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N GLN E 308 " --> pdb=" O LEU E 155 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 75 through 77 removed outlier: 6.394A pdb=" N ASP F 22 " --> pdb=" O THR F 14 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N VAL F 16 " --> pdb=" O ILE F 20 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE F 20 " --> pdb=" O VAL F 16 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE F 62 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N VAL F 50 " --> pdb=" O ILE F 62 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 84 through 86 Processing sheet with id= U, first strand: chain 'F' and resid 331 through 335 removed outlier: 7.812A pdb=" N ILE F 153 " --> pdb=" O VAL F 304 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N SER F 306 " --> pdb=" O ILE F 153 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N LEU F 155 " --> pdb=" O SER F 306 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N GLN F 308 " --> pdb=" O LEU F 155 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N GLY F 157 " --> pdb=" O GLN F 308 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N VAL F 310 " --> pdb=" O GLY F 157 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL F 251 " --> pdb=" O THR F 305 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N VAL F 307 " --> pdb=" O VAL F 251 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU F 253 " --> pdb=" O VAL F 307 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N ALA F 309 " --> pdb=" O LEU F 253 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ILE F 255 " --> pdb=" O ALA F 309 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N TYR F 311 " --> pdb=" O ILE F 255 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N PHE F 181 " --> pdb=" O LEU F 252 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N PHE F 254 " --> pdb=" O PHE F 181 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL F 183 " --> pdb=" O PHE F 254 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N ASP F 256 " --> pdb=" O VAL F 183 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N THR F 185 " --> pdb=" O ASP F 256 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'G' and resid 126 through 130 removed outlier: 6.962A pdb=" N ILE G 107 " --> pdb=" O LYS G 127 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N SER G 129 " --> pdb=" O ILE G 107 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N THR G 109 " --> pdb=" O SER G 129 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ASN G 167 " --> pdb=" O ILE G 77 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE G 162 " --> pdb=" O ILE G 182 " (cutoff:3.500A) 896 hydrogen bonds defined for protein. 2538 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: 16.23 Time building geometry restraints manager: 32.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 23641 1.03 - 1.22: 5 1.22 - 1.42: 9422 1.42 - 1.61: 14340 1.61 - 1.81: 73 Bond restraints: 47481 Sorted by residual: bond pdb=" C4 ATP B 600 " pdb=" C5 ATP B 600 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.03e+01 bond pdb=" C4 ATP C 600 " pdb=" C5 ATP C 600 " ideal model delta sigma weight residual 1.388 1.455 -0.067 1.00e-02 1.00e+04 4.52e+01 bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.455 -0.067 1.00e-02 1.00e+04 4.46e+01 bond pdb=" C61 ZHD G 301 " pdb=" C64 ZHD G 301 " ideal model delta sigma weight residual 1.451 1.585 -0.134 2.00e-02 2.50e+03 4.46e+01 bond pdb=" C5 ATP B 600 " pdb=" C6 ATP B 600 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.33e+01 ... (remaining 47476 not shown) Histogram of bond angle deviations from ideal: 98.62 - 106.20: 626 106.20 - 113.79: 58622 113.79 - 121.37: 17721 121.37 - 128.96: 9065 128.96 - 136.54: 97 Bond angle restraints: 86131 Sorted by residual: angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 117.76 22.11 1.00e+00 1.00e+00 4.89e+02 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 118.06 21.81 1.00e+00 1.00e+00 4.76e+02 angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 120.15 19.72 1.00e+00 1.00e+00 3.89e+02 angle pdb=" PA ATP B 600 " pdb=" O3A ATP B 600 " pdb=" PB ATP B 600 " ideal model delta sigma weight residual 136.83 119.64 17.19 1.00e+00 1.00e+00 2.96e+02 angle pdb=" PA ATP A 600 " pdb=" O3A ATP A 600 " pdb=" PB ATP A 600 " ideal model delta sigma weight residual 136.83 120.68 16.15 1.00e+00 1.00e+00 2.61e+02 ... (remaining 86126 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 17288 17.94 - 35.88: 1038 35.88 - 53.83: 189 53.83 - 71.77: 57 71.77 - 89.71: 33 Dihedral angle restraints: 18605 sinusoidal: 8769 harmonic: 9836 Sorted by residual: dihedral pdb=" CA PHE F 219 " pdb=" C PHE F 219 " pdb=" N GLY F 220 " pdb=" CA GLY F 220 " ideal model delta harmonic sigma weight residual 180.00 151.05 28.95 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA ALA E 278 " pdb=" C ALA E 278 " pdb=" N VAL E 279 " pdb=" CA VAL E 279 " ideal model delta harmonic sigma weight residual -180.00 -151.69 -28.31 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA ALA D 278 " pdb=" C ALA D 278 " pdb=" N VAL D 279 " pdb=" CA VAL D 279 " ideal model delta harmonic sigma weight residual -180.00 -152.18 -27.82 0 5.00e+00 4.00e-02 3.10e+01 ... (remaining 18602 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 3381 0.076 - 0.152: 451 0.152 - 0.228: 9 0.228 - 0.304: 0 0.304 - 0.379: 1 Chirality restraints: 3842 Sorted by residual: chirality pdb=" C25 ZHD G 301 " pdb=" C24 ZHD G 301 " pdb=" C26 ZHD G 301 " pdb=" C27 ZHD G 301 " both_signs ideal model delta sigma weight residual False 2.33 2.71 -0.38 2.00e-01 2.50e+01 3.60e+00 chirality pdb=" C55 ZHD G 301 " pdb=" C43 ZHD G 301 " pdb=" C56 ZHD G 301 " pdb=" C57 ZHD G 301 " both_signs ideal model delta sigma weight residual False 2.61 2.82 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA PRO D 346 " pdb=" N PRO D 346 " pdb=" C PRO D 346 " pdb=" CB PRO D 346 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 9.76e-01 ... (remaining 3839 not shown) Planarity restraints: 7137 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER E 277 " 0.011 2.00e-02 2.50e+03 2.27e-02 5.15e+00 pdb=" C SER E 277 " -0.039 2.00e-02 2.50e+03 pdb=" O SER E 277 " 0.015 2.00e-02 2.50e+03 pdb=" N ALA E 278 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER D 277 " -0.010 2.00e-02 2.50e+03 2.09e-02 4.37e+00 pdb=" C SER D 277 " 0.036 2.00e-02 2.50e+03 pdb=" O SER D 277 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA D 278 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER F 277 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.25e+00 pdb=" C SER F 277 " -0.036 2.00e-02 2.50e+03 pdb=" O SER F 277 " 0.014 2.00e-02 2.50e+03 pdb=" N ALA F 278 " 0.012 2.00e-02 2.50e+03 ... (remaining 7134 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.11: 1228 2.11 - 2.73: 86552 2.73 - 3.35: 135868 3.35 - 3.98: 177812 3.98 - 4.60: 287215 Nonbonded interactions: 688675 Sorted by model distance: nonbonded pdb=" O ALA E 278 " pdb=" H GLY E 280 " model vdw 1.482 1.850 nonbonded pdb="HH22 ARG B 108 " pdb=" O GLY B 121 " model vdw 1.518 1.850 nonbonded pdb=" O GLY D 343 " pdb=" HH TYR D 458 " model vdw 1.527 1.850 nonbonded pdb=" OE1 GLN F 27 " pdb=" H GLU F 29 " model vdw 1.533 1.850 nonbonded pdb=" O ALA E 36 " pdb=" HG1 THR E 79 " model vdw 1.539 1.850 ... (remaining 688670 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 26 through 87 or (resid 88 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 89 through 177 or (resid \ 178 and (name N or name CA or name C or name O or name CB or name OG1 or name C \ G2 or name H or name HA or name HB or name HG21 or name HG22 or name HG23)) or r \ esid 179 through 194 or (resid 195 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 196 through 239 or (resid 240 and (nam \ e N or name CA or name C or name O or name CB or name H or name HA )) or resid 2 \ 41 through 356 or (resid 357 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 358 through 393 or (resid 421 and (name N or \ name CA or name C or name O or name CB or name CG1 or name CG2 or name HA or na \ me HB or name HG11 or name HG12 or name HG13 or name HG21 or name HG22 or name H \ G23)) or resid 422 through 458 or (resid 459 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 460 through 474 or (resid 47 \ 5 through 477 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 478 through 479 or (resid 480 and (name N or name CA or nam \ e C or name O or name CB or name H or name HA )) or resid 481 through 486 or (re \ sid 487 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 488 through 489 or (resid 490 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 491 or (resid 492 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 493 \ or (resid 494 and (name N or name CA or name C or name O or name CB or name H o \ r name HA )) or resid 495 through 497 or (resid 498 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 499 through 500 or (r \ esid 501 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 502 through 503 or (resid 504 through 505 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 506 through 508 \ or (resid 509 and (name N or name CA or name C or name O or name CB or name H o \ r name HA )) or resid 510 or resid 600 through 601)) selection = (chain 'B' and (resid 26 through 28 or (resid 29 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 30 through 68 or (resid \ 69 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 70 through 87 or (resid 88 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 89 through 133 or (resid 134 and (na \ me N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 135 through 171 or (resid 172 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 173 through 182 or (resid 183 and (name N o \ r name CA or name C or name O or name CB or name H or name HA )) or resid 184 th \ rough 356 or (resid 357 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 358 through 423 or (resid 424 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 425 through \ 499 or (resid 500 through 501 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 502 through 510 or resid 600 through 601)) selection = (chain 'C' and (resid 26 through 28 or (resid 29 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 30 through 37 or (resid \ 38 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 39 through 68 or (resid 69 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 70 through 133 or (resid 134 and (na \ me N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 135 through 171 or (resid 172 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 173 through 182 or (resid 183 and (name N o \ r name CA or name C or name O or name CB or name H or name HA )) or resid 184 th \ rough 194 or (resid 195 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 196 through 293 or (resid 294 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 295 through \ 393 or (resid 421 and (name N or name CA or name C or name O or name CB or name \ CG1 or name CG2 or name HA or name HB or name HG11 or name HG12 or name HG13 or \ name HG21 or name HG22 or name HG23)) or resid 422 through 423 or (resid 424 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or re \ sid 425 through 458 or (resid 459 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 460 through 474 or (resid 475 through 4 \ 77 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 478 through 479 or (resid 480 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 481 through 486 or (resid 487 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or re \ sid 488 through 489 or (resid 490 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 491 or (resid 492 and (name N or name C \ A or name C or name O or name CB or name H or name HA )) or resid 493 or (resid \ 494 and (name N or name CA or name C or name O or name CB or name H or name HA ) \ ) or resid 495 through 497 or (resid 498 and (name N or name CA or name C or nam \ e O or name CB or name H or name HA )) or resid 499 or (resid 500 through 501 an \ d (name N or name CA or name C or name O or name CB or name H or name HA )) or r \ esid 502 through 503 or (resid 504 through 505 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 506 through 510 or resid 6 \ 00 through 601)) } ncs_group { reference = (chain 'D' and (resid 8 through 25 or (resid 26 through 27 and (name N or name C \ A or name C or name O or name CB or name H or name HA )) or resid 28 through 104 \ or (resid 105 and (name N or name CA or name C or name O or name CB or name H o \ r name HA )) or resid 106 through 358 or (resid 359 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 360 through 372 or (r \ esid 373 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 374 through 393 or (resid 394 through 395 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 396 through 397 \ or (resid 398 and (name N or name CA or name C or name O or name CB or name H o \ r name HA )) or resid 399 through 404 or (resid 405 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 406 through 463 or (r \ esid 464 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 465 through 470 or (resid 471 through 472 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 473 through 476 \ )) selection = (chain 'E' and (resid 8 through 25 or (resid 26 through 27 and (name N or name C \ A or name C or name O or name CB or name H or name HA )) or resid 28 through 39 \ or (resid 40 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 41 through 42 or (resid 43 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 44 through 67 or (resid 68 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) o \ r resid 69 through 104 or (resid 105 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 106 through 111 or (resid 112 and (n \ ame N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 113 through 175 or (resid 176 and (name N or name CA or name C or name O or nam \ e CB or name H or name HA )) or resid 177 through 188 or (resid 189 and (name N \ or name CA or name C or name O or name CB or name H or name HA )) or resid 190 t \ hrough 202 or (resid 203 and (name N or name CA or name C or name O or name CB o \ r name H or name HA )) or resid 204 through 209 or (resid 210 and (name N or nam \ e CA or name C or name O or name CB or name H or name HA )) or resid 211 or (res \ id 212 and (name N or name CA or name C or name O or name CB or name H or name H \ A )) or resid 213 through 244 or (resid 245 through 247 and (name N or name CA o \ r name C or name O or name CB or name H or name HA )) or resid 248 through 336 o \ r (resid 337 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 338 through 372 or (resid 373 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 374 through 397 or (res \ id 398 and (name N or name CA or name C or name O or name CB or name H or name H \ A )) or resid 399 through 445 or (resid 446 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 447 through 470 or (resid 471 \ through 472 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 473 through 476)) selection = (chain 'F' and (resid 8 through 26 or (resid 27 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 28 through 55 or (resid 5 \ 6 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 57 through 67 or (resid 68 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 69 through 111 or (resid 112 and (nam \ e N or name CA or name C or name O or name CB or name H or name HA )) or resid 1 \ 13 through 175 or (resid 176 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 177 through 188 or (resid 189 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 190 thr \ ough 209 or (resid 210 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 211 or (resid 212 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 213 through 244 or (resid \ 245 through 247 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 248 through 336 or (resid 337 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 338 through 358 or \ (resid 359 and (name N or name CA or name C or name O or name CB or name H or na \ me HA )) or resid 360 through 393 or (resid 394 through 395 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 396 through 4 \ 45 or (resid 446 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 447 through 463 or (resid 464 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 465 through 471 or \ (resid 472 and (name N or name CA or name C or name O or name CB or name H or na \ me HA )) or resid 473 through 476)) } 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: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.310 Construct map_model_manager: 0.540 Extract box with map and model: 9.320 Check model and map are aligned: 0.680 Set scattering table: 0.360 Process input model: 115.030 Find NCS groups from input model: 1.850 Set up NCS constraints: 0.150 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: 0.020 Load rotamer database and sin/cos tables:2.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 132.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 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 : 0.009 0.134 23836 Z= 0.600 Angle : 0.798 22.114 32349 Z= 0.502 Chirality : 0.050 0.379 3842 Planarity : 0.004 0.046 4167 Dihedral : 14.017 89.709 8688 Min Nonbonded Distance : 1.726 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.78 % Favored : 97.99 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.13), residues: 3089 helix: -1.55 (0.12), residues: 1244 sheet: -0.42 (0.22), residues: 479 loop : -1.05 (0.16), residues: 1366 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 134 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue THR 178 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue LYS 475 is missing expected H atoms. Skipping. Residue SER 476 is missing expected H atoms. Skipping. Residue SER 492 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue SER 501 is missing expected H atoms. Skipping. Residue SER 505 is missing expected H atoms. Skipping. Residue THR 509 is missing expected H atoms. Skipping. Residue THR 178 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue THR 509 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 112 is missing expected H atoms. Skipping. Residue LYS 176 is missing expected H atoms. Skipping. Residue LYS 472 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 373 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue SER 40 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LYS 180 is missing expected H atoms. Skipping. Residue ILE 21 is missing expected H atoms. Skipping. Residue SER 23 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Evaluate side-chains 798 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 792 time to evaluate : 2.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 794 average time/residue: 0.9026 time to fit residues: 1024.8620 Evaluate side-chains 656 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 653 time to evaluate : 2.755 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.4650 time to fit residues: 6.1231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 1.9990 chunk 231 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 156 optimal weight: 0.7980 chunk 123 optimal weight: 0.8980 chunk 239 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 178 optimal weight: 0.9980 chunk 277 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN B 95 ASN C 95 ASN C 265 HIS C 433 ASN C 434 GLN C 452 ASN D 375 GLN D 451 ASN F 57 ASN F 127 GLN F 168 GLN F 172 ASN F 293 GLN F 308 GLN F 411 GLN G 88 HIS G 167 ASN G 216 ASN H 15 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 23836 Z= 0.243 Angle : 0.563 6.754 32349 Z= 0.293 Chirality : 0.043 0.159 3842 Planarity : 0.004 0.047 4167 Dihedral : 5.757 84.218 3363 Min Nonbonded Distance : 1.711 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.19 % Allowed : 1.36 % Favored : 98.45 % Rotamer Outliers : 1.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.57 (0.15), residues: 3089 helix: -0.23 (0.14), residues: 1251 sheet: -0.20 (0.23), residues: 476 loop : -0.40 (0.17), residues: 1362 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 134 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue THR 178 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue LYS 475 is missing expected H atoms. Skipping. Residue SER 476 is missing expected H atoms. Skipping. Residue SER 492 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue SER 501 is missing expected H atoms. Skipping. Residue SER 505 is missing expected H atoms. Skipping. Residue THR 509 is missing expected H atoms. Skipping. Residue THR 178 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue THR 509 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 112 is missing expected H atoms. Skipping. Residue LYS 176 is missing expected H atoms. Skipping. Residue LYS 472 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 373 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue SER 40 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LYS 180 is missing expected H atoms. Skipping. Residue ILE 21 is missing expected H atoms. Skipping. Residue SER 23 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Evaluate side-chains 716 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 684 time to evaluate : 2.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 20 residues processed: 695 average time/residue: 0.8848 time to fit residues: 891.5545 Evaluate side-chains 680 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 660 time to evaluate : 2.769 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.4730 time to fit residues: 20.7829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 154 optimal weight: 0.4980 chunk 86 optimal weight: 3.9990 chunk 231 optimal weight: 1.9990 chunk 189 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 278 optimal weight: 1.9990 chunk 300 optimal weight: 2.9990 chunk 247 optimal weight: 1.9990 chunk 276 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 223 optimal weight: 2.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN ** A 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 434 GLN B 26 ASN F 57 ASN F 293 GLN G 249 ASN G 265 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.044 23836 Z= 0.401 Angle : 0.585 6.552 32349 Z= 0.305 Chirality : 0.045 0.173 3842 Planarity : 0.005 0.082 4167 Dihedral : 5.605 84.255 3363 Min Nonbonded Distance : 1.714 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.01 % Favored : 97.80 % Rotamer Outliers : 1.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.15), residues: 3089 helix: 0.13 (0.14), residues: 1259 sheet: -0.24 (0.22), residues: 502 loop : -0.31 (0.17), residues: 1328 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 134 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue THR 178 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue LYS 475 is missing expected H atoms. Skipping. Residue SER 476 is missing expected H atoms. Skipping. Residue SER 492 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue SER 501 is missing expected H atoms. Skipping. Residue SER 505 is missing expected H atoms. Skipping. Residue THR 509 is missing expected H atoms. Skipping. Residue THR 178 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue THR 509 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 112 is missing expected H atoms. Skipping. Residue LYS 176 is missing expected H atoms. Skipping. Residue LYS 472 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 373 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue SER 40 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LYS 180 is missing expected H atoms. Skipping. Residue ILE 21 is missing expected H atoms. Skipping. Residue SER 23 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Evaluate side-chains 718 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 685 time to evaluate : 2.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 21 residues processed: 697 average time/residue: 0.8639 time to fit residues: 858.7136 Evaluate side-chains 687 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 666 time to evaluate : 2.750 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.5223 time to fit residues: 22.6216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 275 optimal weight: 0.7980 chunk 209 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 186 optimal weight: 2.9990 chunk 279 optimal weight: 1.9990 chunk 295 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 264 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 GLN A 149 GLN ** A 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 210 GLN D 249 GLN F 57 ASN F 168 GLN G 54 ASN G 98 HIS G 249 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 23836 Z= 0.357 Angle : 0.559 6.630 32349 Z= 0.291 Chirality : 0.044 0.165 3842 Planarity : 0.004 0.079 4167 Dihedral : 5.450 86.711 3363 Min Nonbonded Distance : 1.701 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.14 % Favored : 97.67 % Rotamer Outliers : 1.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.08 (0.15), residues: 3089 helix: 0.43 (0.15), residues: 1247 sheet: -0.20 (0.22), residues: 502 loop : -0.30 (0.17), residues: 1340 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 134 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue THR 178 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue LYS 475 is missing expected H atoms. Skipping. Residue SER 476 is missing expected H atoms. Skipping. Residue SER 492 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue SER 501 is missing expected H atoms. Skipping. Residue SER 505 is missing expected H atoms. Skipping. Residue THR 509 is missing expected H atoms. Skipping. Residue THR 178 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue THR 509 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 112 is missing expected H atoms. Skipping. Residue LYS 176 is missing expected H atoms. Skipping. Residue LYS 472 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 373 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue SER 40 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LYS 180 is missing expected H atoms. Skipping. Residue ILE 21 is missing expected H atoms. Skipping. Residue SER 23 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Evaluate side-chains 730 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 700 time to evaluate : 2.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 19 residues processed: 709 average time/residue: 0.8650 time to fit residues: 873.9017 Evaluate side-chains 707 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 688 time to evaluate : 2.737 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.4615 time to fit residues: 19.6820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 246 optimal weight: 0.9990 chunk 167 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 220 optimal weight: 0.0050 chunk 122 optimal weight: 3.9990 chunk 252 optimal weight: 1.9990 chunk 204 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 151 optimal weight: 0.3980 chunk 265 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.0800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 57 ASN G 54 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 23836 Z= 0.265 Angle : 0.525 6.227 32349 Z= 0.272 Chirality : 0.043 0.146 3842 Planarity : 0.004 0.072 4167 Dihedral : 5.239 85.688 3363 Min Nonbonded Distance : 1.730 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.14 % Favored : 97.67 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.15 (0.15), residues: 3089 helix: 0.70 (0.15), residues: 1248 sheet: -0.21 (0.22), residues: 513 loop : -0.20 (0.17), residues: 1328 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 134 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue THR 178 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue LYS 475 is missing expected H atoms. Skipping. Residue SER 476 is missing expected H atoms. Skipping. Residue SER 492 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue SER 501 is missing expected H atoms. Skipping. Residue SER 505 is missing expected H atoms. Skipping. Residue THR 509 is missing expected H atoms. Skipping. Residue THR 178 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue THR 509 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 112 is missing expected H atoms. Skipping. Residue LYS 176 is missing expected H atoms. Skipping. Residue LYS 472 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 373 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue SER 40 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LYS 180 is missing expected H atoms. Skipping. Residue ILE 21 is missing expected H atoms. Skipping. Residue SER 23 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Evaluate side-chains 716 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 701 time to evaluate : 2.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 705 average time/residue: 0.8625 time to fit residues: 870.9610 Evaluate side-chains 692 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 686 time to evaluate : 2.777 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.5364 time to fit residues: 8.8577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 99 optimal weight: 4.9990 chunk 266 optimal weight: 2.9990 chunk 58 optimal weight: 0.1980 chunk 173 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 296 optimal weight: 3.9990 chunk 245 optimal weight: 0.7980 chunk 137 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 155 optimal weight: 0.9980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN A 407 GLN C 210 GLN D 221 GLN F 57 ASN F 293 GLN F 308 GLN G 249 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 23836 Z= 0.248 Angle : 0.516 6.213 32349 Z= 0.267 Chirality : 0.042 0.147 3842 Planarity : 0.004 0.059 4167 Dihedral : 5.058 73.939 3363 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.14 % Favored : 97.67 % Rotamer Outliers : 1.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.32 (0.15), residues: 3089 helix: 0.89 (0.15), residues: 1249 sheet: -0.18 (0.22), residues: 513 loop : -0.14 (0.18), residues: 1327 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 134 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue THR 178 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue LYS 475 is missing expected H atoms. Skipping. Residue SER 476 is missing expected H atoms. Skipping. Residue SER 492 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue SER 501 is missing expected H atoms. Skipping. Residue SER 505 is missing expected H atoms. Skipping. Residue THR 509 is missing expected H atoms. Skipping. Residue THR 178 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue THR 509 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 112 is missing expected H atoms. Skipping. Residue LYS 176 is missing expected H atoms. Skipping. Residue LYS 472 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 373 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue SER 40 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LYS 180 is missing expected H atoms. Skipping. Residue ILE 21 is missing expected H atoms. Skipping. Residue SER 23 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Evaluate side-chains 720 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 694 time to evaluate : 2.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 17 residues processed: 701 average time/residue: 0.9007 time to fit residues: 910.9375 Evaluate side-chains 710 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 693 time to evaluate : 2.778 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 17 outliers final: 1 residues processed: 17 average time/residue: 0.4970 time to fit residues: 18.4100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 285 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 216 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 249 optimal weight: 0.9980 chunk 165 optimal weight: 2.9990 chunk 294 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 chunk 179 optimal weight: 0.7980 chunk 136 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN ** A 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN C 210 GLN C 276 GLN E 249 GLN F 57 ASN F 195 ASN F 379 GLN G 54 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.042 23836 Z= 0.369 Angle : 0.551 6.346 32349 Z= 0.286 Chirality : 0.044 0.166 3842 Planarity : 0.004 0.067 4167 Dihedral : 5.093 70.553 3363 Min Nonbonded Distance : 1.717 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.82 % Favored : 96.99 % Rotamer Outliers : 1.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 (0.15), residues: 3089 helix: 0.77 (0.15), residues: 1252 sheet: -0.19 (0.22), residues: 518 loop : -0.23 (0.18), residues: 1319 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 134 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue THR 178 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue LYS 475 is missing expected H atoms. Skipping. Residue SER 476 is missing expected H atoms. Skipping. Residue SER 492 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue SER 501 is missing expected H atoms. Skipping. Residue SER 505 is missing expected H atoms. Skipping. Residue THR 509 is missing expected H atoms. Skipping. Residue THR 178 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue THR 509 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 112 is missing expected H atoms. Skipping. Residue LYS 176 is missing expected H atoms. Skipping. Residue LYS 472 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 373 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue SER 40 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LYS 180 is missing expected H atoms. Skipping. Residue ILE 21 is missing expected H atoms. Skipping. Residue SER 23 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Evaluate side-chains 745 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 718 time to evaluate : 2.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 20 residues processed: 724 average time/residue: 0.8587 time to fit residues: 892.5150 Evaluate side-chains 718 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 698 time to evaluate : 2.814 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 20 outliers final: 1 residues processed: 20 average time/residue: 0.5185 time to fit residues: 21.3269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 182 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 187 optimal weight: 1.9990 chunk 200 optimal weight: 0.3980 chunk 145 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 231 optimal weight: 0.4980 chunk 268 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN C 210 GLN E 249 GLN F 57 ASN F 195 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 23836 Z= 0.192 Angle : 0.509 6.213 32349 Z= 0.261 Chirality : 0.042 0.166 3842 Planarity : 0.004 0.059 4167 Dihedral : 4.846 70.999 3363 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.19 % Allowed : 1.81 % Favored : 97.99 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.51 (0.15), residues: 3089 helix: 1.08 (0.15), residues: 1252 sheet: -0.07 (0.23), residues: 501 loop : -0.08 (0.18), residues: 1336 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 134 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue THR 178 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue LYS 475 is missing expected H atoms. Skipping. Residue SER 476 is missing expected H atoms. Skipping. Residue SER 492 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue SER 501 is missing expected H atoms. Skipping. Residue SER 505 is missing expected H atoms. Skipping. Residue THR 509 is missing expected H atoms. Skipping. Residue THR 178 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue THR 509 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 112 is missing expected H atoms. Skipping. Residue LYS 176 is missing expected H atoms. Skipping. Residue LYS 472 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 373 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue SER 40 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LYS 180 is missing expected H atoms. Skipping. Residue ILE 21 is missing expected H atoms. Skipping. Residue SER 23 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Evaluate side-chains 707 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 694 time to evaluate : 2.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 696 average time/residue: 0.8700 time to fit residues: 870.9351 Evaluate side-chains 698 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 692 time to evaluate : 2.754 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 6 average time/residue: 0.4762 time to fit residues: 8.8484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 282 optimal weight: 3.9990 chunk 257 optimal weight: 0.3980 chunk 274 optimal weight: 0.0870 chunk 165 optimal weight: 1.9990 chunk 119 optimal weight: 0.1980 chunk 215 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 248 optimal weight: 0.5980 chunk 259 optimal weight: 1.9990 chunk 273 optimal weight: 0.9990 chunk 180 optimal weight: 1.9990 overall best weight: 0.4560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 210 GLN E 172 ASN F 57 ASN F 195 ASN F 208 ASN G 54 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 23836 Z= 0.159 Angle : 0.498 6.564 32349 Z= 0.254 Chirality : 0.041 0.142 3842 Planarity : 0.004 0.069 4167 Dihedral : 4.633 71.636 3363 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.07 % Favored : 97.73 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.74 (0.16), residues: 3089 helix: 1.31 (0.15), residues: 1256 sheet: -0.04 (0.23), residues: 513 loop : 0.05 (0.18), residues: 1320 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 134 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue THR 178 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue LYS 475 is missing expected H atoms. Skipping. Residue SER 476 is missing expected H atoms. Skipping. Residue SER 492 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue SER 501 is missing expected H atoms. Skipping. Residue SER 505 is missing expected H atoms. Skipping. Residue THR 509 is missing expected H atoms. Skipping. Residue THR 178 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue THR 509 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 112 is missing expected H atoms. Skipping. Residue LYS 176 is missing expected H atoms. Skipping. Residue LYS 472 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 373 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue SER 40 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LYS 180 is missing expected H atoms. Skipping. Residue ILE 21 is missing expected H atoms. Skipping. Residue SER 23 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Evaluate side-chains 713 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 705 time to evaluate : 2.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 705 average time/residue: 0.9007 time to fit residues: 916.2649 Evaluate side-chains 693 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 688 time to evaluate : 3.218 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 5 average time/residue: 0.5551 time to fit residues: 8.5924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 290 optimal weight: 0.5980 chunk 177 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 202 optimal weight: 2.9990 chunk 304 optimal weight: 2.9990 chunk 280 optimal weight: 1.9990 chunk 242 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 187 optimal weight: 0.1980 chunk 148 optimal weight: 0.6980 chunk 192 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN C 210 GLN F 57 ASN F 195 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 23836 Z= 0.272 Angle : 0.525 6.244 32349 Z= 0.270 Chirality : 0.043 0.150 3842 Planarity : 0.004 0.109 4167 Dihedral : 4.717 69.921 3363 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.20 % Favored : 97.60 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.65 (0.15), residues: 3089 helix: 1.21 (0.15), residues: 1257 sheet: -0.05 (0.23), residues: 504 loop : 0.01 (0.18), residues: 1328 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 134 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue THR 178 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue LYS 475 is missing expected H atoms. Skipping. Residue SER 476 is missing expected H atoms. Skipping. Residue SER 492 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue SER 501 is missing expected H atoms. Skipping. Residue SER 505 is missing expected H atoms. Skipping. Residue THR 509 is missing expected H atoms. Skipping. Residue THR 178 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue THR 509 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 112 is missing expected H atoms. Skipping. Residue LYS 176 is missing expected H atoms. Skipping. Residue LYS 472 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 373 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue SER 40 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LYS 180 is missing expected H atoms. Skipping. Residue ILE 21 is missing expected H atoms. Skipping. Residue SER 23 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Evaluate side-chains 713 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 703 time to evaluate : 2.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 9 residues processed: 705 average time/residue: 0.9257 time to fit residues: 942.6438 Evaluate side-chains 715 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 706 time to evaluate : 2.783 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 9 average time/residue: 0.4622 time to fit residues: 11.2646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 223 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 243 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 chunk 249 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 213 optimal weight: 0.7980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN C 210 GLN D 173 ASN F 57 ASN F 195 ASN G 54 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.103635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.094421 restraints weight = 101755.376| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.87 r_work: 0.3130 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 23836 Z= 0.215 Angle : 0.512 6.213 32349 Z= 0.262 Chirality : 0.042 0.152 3842 Planarity : 0.004 0.073 4167 Dihedral : 4.645 70.147 3363 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.20 % Favored : 97.60 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.71 (0.16), residues: 3089 helix: 1.26 (0.15), residues: 1257 sheet: -0.02 (0.23), residues: 515 loop : 0.04 (0.18), residues: 1317 =============================================================================== Job complete usr+sys time: 13529.12 seconds wall clock time: 232 minutes 56.84 seconds (13976.84 seconds total)