Starting phenix.real_space_refine on Sat Feb 17 12:48:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7md2_23763/02_2024/7md2_23763_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7md2_23763/02_2024/7md2_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_23763/02_2024/7md2_23763.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7md2_23763/02_2024/7md2_23763.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7md2_23763/02_2024/7md2_23763_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7md2_23763/02_2024/7md2_23763_trim_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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-dev-5238/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: 16.37, per 1000 atoms: 0.35 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: 32.62 Conformation dependent library (CDL) restraints added in 3.9 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: 6.48 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: 14.70 Time building geometry restraints manager: 34.20 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: 20337 17.94 - 35.88: 1402 35.88 - 53.83: 418 53.83 - 71.77: 133 71.77 - 89.71: 34 Dihedral angle restraints: 22324 sinusoidal: 12488 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 22321 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: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.330 Construct map_model_manager: 0.540 Extract box with map and model: 8.280 Check model and map are aligned: 0.550 Set scattering table: 0.340 Process input model: 121.630 Find NCS groups from input model: 1.800 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 137.580 ------------------------------------------------------------------------------- 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 : 14.285 89.709 8916 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 % Allowed : 5.46 % Favored : 94.29 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 191 HIS 0.010 0.002 HIS C 478 PHE 0.024 0.002 PHE F 424 TYR 0.020 0.002 TYR E 198 ARG 0.009 0.001 ARG A 166 *********************** 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 : 2.782 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 REVERT: A 52 GLU cc_start: 0.6982 (tt0) cc_final: 0.6391 (mt-10) REVERT: A 53 GLU cc_start: 0.7980 (tt0) cc_final: 0.7346 (tt0) REVERT: A 66 LEU cc_start: 0.8249 (mt) cc_final: 0.8012 (mp) REVERT: A 129 SER cc_start: 0.7964 (m) cc_final: 0.7687 (t) REVERT: A 156 ASP cc_start: 0.7363 (m-30) cc_final: 0.7149 (m-30) REVERT: A 167 GLU cc_start: 0.7942 (tp30) cc_final: 0.7239 (tp30) REVERT: A 237 THR cc_start: 0.7180 (p) cc_final: 0.6951 (p) REVERT: A 342 THR cc_start: 0.8071 (m) cc_final: 0.7719 (p) REVERT: A 357 GLU cc_start: 0.7020 (tm-30) cc_final: 0.6383 (tm-30) REVERT: A 358 LEU cc_start: 0.8238 (mt) cc_final: 0.7899 (mt) REVERT: A 421 VAL cc_start: 0.7794 (t) cc_final: 0.7509 (p) REVERT: B 34 LEU cc_start: 0.8445 (mt) cc_final: 0.8145 (mt) REVERT: B 52 GLU cc_start: 0.7022 (mt-10) cc_final: 0.6759 (mt-10) REVERT: B 67 ASN cc_start: 0.8068 (p0) cc_final: 0.7708 (p0) REVERT: B 118 ASP cc_start: 0.7808 (p0) cc_final: 0.7606 (p0) REVERT: B 123 ILE cc_start: 0.8302 (mm) cc_final: 0.7980 (mt) REVERT: B 159 VAL cc_start: 0.8423 (m) cc_final: 0.7848 (t) REVERT: B 183 ASP cc_start: 0.6253 (m-30) cc_final: 0.6051 (m-30) REVERT: B 199 LYS cc_start: 0.8205 (mttm) cc_final: 0.7898 (mtmm) REVERT: B 211 LYS cc_start: 0.8189 (mtpt) cc_final: 0.7713 (mtmt) REVERT: B 257 GLU cc_start: 0.7073 (mt-10) cc_final: 0.6701 (mt-10) REVERT: B 261 ASP cc_start: 0.7312 (m-30) cc_final: 0.7025 (m-30) REVERT: B 331 THR cc_start: 0.8229 (p) cc_final: 0.7881 (p) REVERT: B 336 VAL cc_start: 0.8361 (m) cc_final: 0.8018 (t) REVERT: B 353 PHE cc_start: 0.7704 (t80) cc_final: 0.7385 (t80) REVERT: B 443 GLN cc_start: 0.7919 (mt0) cc_final: 0.7654 (mt0) REVERT: B 486 ARG cc_start: 0.8152 (ttp80) cc_final: 0.7878 (ttp80) REVERT: B 500 LYS cc_start: 0.6612 (ttmt) cc_final: 0.6089 (tppt) REVERT: C 32 ARG cc_start: 0.7335 (mmt180) cc_final: 0.7133 (mmt90) REVERT: C 52 GLU cc_start: 0.6927 (mt-10) cc_final: 0.6632 (mt-10) REVERT: C 81 ASP cc_start: 0.7458 (p0) cc_final: 0.7173 (p0) REVERT: C 93 THR cc_start: 0.8440 (m) cc_final: 0.8213 (p) REVERT: C 129 SER cc_start: 0.8448 (m) cc_final: 0.8053 (p) REVERT: C 142 ARG cc_start: 0.7619 (ttt90) cc_final: 0.7417 (ttt-90) REVERT: C 146 GLU cc_start: 0.8024 (pt0) cc_final: 0.7261 (pt0) REVERT: C 167 GLU cc_start: 0.7422 (tp30) cc_final: 0.6833 (mm-30) REVERT: C 228 MET cc_start: 0.7532 (mmm) cc_final: 0.7262 (mmt) REVERT: C 275 LYS cc_start: 0.7617 (mttp) cc_final: 0.7406 (mttp) REVERT: C 335 ASP cc_start: 0.6856 (t0) cc_final: 0.6234 (t0) REVERT: C 337 SER cc_start: 0.8278 (t) cc_final: 0.7770 (p) REVERT: C 386 LYS cc_start: 0.7892 (ttmt) cc_final: 0.7597 (ttmt) REVERT: C 393 LYS cc_start: 0.8230 (ttmt) cc_final: 0.7989 (ttmm) REVERT: C 424 GLU cc_start: 0.6838 (tp30) cc_final: 0.6331 (tp30) REVERT: C 431 LYS cc_start: 0.7507 (ptpt) cc_final: 0.7289 (mtpt) REVERT: C 480 GLU cc_start: 0.6913 (mm-30) cc_final: 0.6622 (mm-30) REVERT: D 64 MET cc_start: 0.8348 (mmm) cc_final: 0.7918 (mmt) REVERT: D 132 GLU cc_start: 0.7604 (tp30) cc_final: 0.7012 (tp30) REVERT: D 241 GLU cc_start: 0.7130 (mt-10) cc_final: 0.6852 (mt-10) REVERT: D 288 ASP cc_start: 0.6986 (m-30) cc_final: 0.6443 (m-30) REVERT: D 294 GLU cc_start: 0.7011 (mm-30) cc_final: 0.6755 (mm-30) REVERT: D 373 LYS cc_start: 0.7487 (tttm) cc_final: 0.7251 (mtpp) REVERT: D 390 ILE cc_start: 0.8294 (mt) cc_final: 0.8083 (mt) REVERT: E 30 LEU cc_start: 0.8032 (mp) cc_final: 0.7784 (mt) REVERT: E 54 LEU cc_start: 0.8301 (mt) cc_final: 0.8066 (mp) REVERT: E 196 ASP cc_start: 0.6982 (m-30) cc_final: 0.6596 (m-30) REVERT: E 281 TYR cc_start: 0.8275 (m-80) cc_final: 0.8000 (m-80) REVERT: E 289 MET cc_start: 0.8262 (tpp) cc_final: 0.7939 (tpt) REVERT: E 300 LYS cc_start: 0.7950 (pttt) cc_final: 0.7695 (pttt) REVERT: E 301 LYS cc_start: 0.8090 (mmtt) cc_final: 0.7794 (mmtt) REVERT: E 317 LEU cc_start: 0.8415 (mt) cc_final: 0.8124 (mm) REVERT: E 356 ARG cc_start: 0.7144 (mtp180) cc_final: 0.6921 (mtp180) REVERT: E 448 LYS cc_start: 0.8449 (mtpt) cc_final: 0.8194 (mtpt) REVERT: F 12 LYS cc_start: 0.8272 (mttm) cc_final: 0.8006 (mttm) REVERT: F 64 MET cc_start: 0.8131 (mmp) cc_final: 0.7921 (mmt) REVERT: F 90 GLU cc_start: 0.6490 (mm-30) cc_final: 0.6226 (mm-30) REVERT: F 178 HIS cc_start: 0.7207 (t70) cc_final: 0.6558 (t-90) REVERT: F 214 LYS cc_start: 0.7948 (pttt) cc_final: 0.7709 (pttp) REVERT: F 219 PHE cc_start: 0.8452 (m-80) cc_final: 0.8099 (m-80) REVERT: F 245 ASP cc_start: 0.7223 (m-30) cc_final: 0.6900 (m-30) REVERT: F 268 VAL cc_start: 0.8214 (m) cc_final: 0.7994 (t) REVERT: F 277 SER cc_start: 0.8060 (p) cc_final: 0.7859 (m) REVERT: F 467 VAL cc_start: 0.8035 (t) cc_final: 0.7814 (m) REVERT: G 19 ILE cc_start: 0.8264 (mp) cc_final: 0.8057 (mt) REVERT: G 24 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7859 (ttpp) REVERT: G 43 LYS cc_start: 0.8082 (ttmm) cc_final: 0.7105 (ttpt) REVERT: G 109 THR cc_start: 0.8070 (p) cc_final: 0.7788 (p) REVERT: G 114 ILE cc_start: 0.8441 (tp) cc_final: 0.8179 (tt) REVERT: G 123 PRO cc_start: 0.8395 (Cg_endo) cc_final: 0.8191 (Cg_exo) REVERT: G 154 MET cc_start: 0.6383 (mmm) cc_final: 0.6163 (mmm) REVERT: G 217 GLN cc_start: 0.7583 (mm110) cc_final: 0.7356 (mm110) REVERT: G 252 SER cc_start: 0.7764 (m) cc_final: 0.7366 (t) outliers start: 6 outliers final: 3 residues processed: 794 average time/residue: 0.9220 time to fit residues: 1050.8711 Evaluate side-chains 667 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 663 time to evaluate : 2.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain G residue 23 MET Chi-restraints excluded: chain G residue 24 LYS Chi-restraints excluded: chain G residue 80 ASP 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: 0.0020 chunk 128 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 156 optimal weight: 0.5980 chunk 123 optimal weight: 0.9980 chunk 239 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 145 optimal weight: 1.9990 chunk 178 optimal weight: 0.9980 chunk 277 optimal weight: 0.0040 overall best weight: 0.5000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 434 GLN B 95 ASN C 95 ASN C 433 ASN C 452 ASN D 375 GLN D 451 ASN F 57 ASN F 127 GLN F 168 GLN 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: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 23836 Z= 0.171 Angle : 0.539 6.786 32349 Z= 0.282 Chirality : 0.042 0.159 3842 Planarity : 0.004 0.047 4167 Dihedral : 7.561 86.933 3602 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.19 % Allowed : 1.26 % Favored : 98.54 % Rotamer: Outliers : 1.20 % Allowed : 11.71 % Favored : 87.09 % 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: -0.45 (0.15), residues: 3089 helix: -0.14 (0.14), residues: 1253 sheet: -0.19 (0.23), residues: 480 loop : -0.30 (0.17), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 191 HIS 0.004 0.001 HIS F 178 PHE 0.011 0.001 PHE C 466 TYR 0.012 0.001 TYR F 198 ARG 0.008 0.000 ARG E 192 *********************** 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 713 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 684 time to evaluate : 2.816 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: A 42 ARG cc_start: 0.6906 (mtp180) cc_final: 0.6556 (mtp-110) REVERT: A 52 GLU cc_start: 0.6897 (tt0) cc_final: 0.6574 (mt-10) REVERT: A 66 LEU cc_start: 0.8243 (mt) cc_final: 0.8020 (mp) REVERT: A 91 LYS cc_start: 0.8113 (mttt) cc_final: 0.7811 (mtpp) REVERT: A 129 SER cc_start: 0.8041 (m) cc_final: 0.7731 (t) REVERT: A 141 ARG cc_start: 0.8330 (mtt-85) cc_final: 0.8111 (mtt180) REVERT: A 167 GLU cc_start: 0.7952 (tp30) cc_final: 0.7359 (mm-30) REVERT: A 357 GLU cc_start: 0.7138 (tm-30) cc_final: 0.6513 (tm-30) REVERT: A 358 LEU cc_start: 0.8289 (mt) cc_final: 0.7775 (mt) REVERT: A 399 TYR cc_start: 0.7732 (t80) cc_final: 0.7283 (t80) REVERT: A 421 VAL cc_start: 0.7810 (t) cc_final: 0.7572 (p) REVERT: A 475 LYS cc_start: 0.8020 (ttmm) cc_final: 0.7564 (mttp) REVERT: B 34 LEU cc_start: 0.8420 (mt) cc_final: 0.8214 (mt) REVERT: B 67 ASN cc_start: 0.7932 (p0) cc_final: 0.7577 (p0) REVERT: B 69 GLU cc_start: 0.7005 (mt-10) cc_final: 0.6770 (mt-10) REVERT: B 91 LYS cc_start: 0.7992 (mttt) cc_final: 0.7732 (mtmm) REVERT: B 118 ASP cc_start: 0.7848 (p0) cc_final: 0.7609 (p0) REVERT: B 123 ILE cc_start: 0.8313 (mm) cc_final: 0.7994 (mt) REVERT: B 159 VAL cc_start: 0.8329 (m) cc_final: 0.8016 (p) REVERT: B 183 ASP cc_start: 0.6366 (m-30) cc_final: 0.6038 (m-30) REVERT: B 199 LYS cc_start: 0.8234 (mttm) cc_final: 0.7895 (mtmm) REVERT: B 257 GLU cc_start: 0.7120 (mt-10) cc_final: 0.6811 (mt-10) REVERT: B 261 ASP cc_start: 0.7331 (m-30) cc_final: 0.7067 (m-30) REVERT: B 336 VAL cc_start: 0.8356 (m) cc_final: 0.8068 (t) REVERT: B 353 PHE cc_start: 0.7720 (t80) cc_final: 0.7474 (t80) REVERT: C 29 GLU cc_start: 0.7223 (tt0) cc_final: 0.6985 (tt0) REVERT: C 52 GLU cc_start: 0.6765 (mt-10) cc_final: 0.6449 (mt-10) REVERT: C 93 THR cc_start: 0.8424 (m) cc_final: 0.8186 (p) REVERT: C 128 ARG cc_start: 0.7987 (mtp180) cc_final: 0.7701 (mtp180) REVERT: C 129 SER cc_start: 0.8470 (m) cc_final: 0.8101 (p) REVERT: C 146 GLU cc_start: 0.7955 (pt0) cc_final: 0.7442 (pt0) REVERT: C 167 GLU cc_start: 0.7427 (tp30) cc_final: 0.7056 (tp30) REVERT: C 228 MET cc_start: 0.7628 (mmm) cc_final: 0.7333 (mmt) REVERT: C 246 TYR cc_start: 0.8357 (OUTLIER) cc_final: 0.7858 (t80) REVERT: C 271 ASP cc_start: 0.7323 (t0) cc_final: 0.7087 (t70) REVERT: C 335 ASP cc_start: 0.6832 (t0) cc_final: 0.6294 (t0) REVERT: C 337 SER cc_start: 0.8213 (t) cc_final: 0.7716 (p) REVERT: C 361 LYS cc_start: 0.8296 (mttt) cc_final: 0.8086 (mttp) REVERT: C 393 LYS cc_start: 0.8294 (ttmt) cc_final: 0.8045 (ttmm) REVERT: C 424 GLU cc_start: 0.6853 (tp30) cc_final: 0.6365 (tp30) REVERT: C 446 LEU cc_start: 0.7913 (mt) cc_final: 0.7675 (mt) REVERT: D 12 LYS cc_start: 0.7959 (mtpp) cc_final: 0.7662 (mttm) REVERT: D 64 MET cc_start: 0.8333 (mmm) cc_final: 0.7892 (mmt) REVERT: D 267 GLU cc_start: 0.7121 (mt-10) cc_final: 0.6899 (mt-10) REVERT: D 288 ASP cc_start: 0.6941 (m-30) cc_final: 0.6397 (m-30) REVERT: D 365 GLN cc_start: 0.7505 (tp40) cc_final: 0.7161 (tp40) REVERT: D 435 LYS cc_start: 0.7905 (mptt) cc_final: 0.7671 (mmmt) REVERT: E 196 ASP cc_start: 0.7080 (m-30) cc_final: 0.6668 (m-30) REVERT: E 199 ARG cc_start: 0.7481 (ptm-80) cc_final: 0.7237 (ttp-110) REVERT: E 241 GLU cc_start: 0.7174 (mt-10) cc_final: 0.6673 (mt-10) REVERT: E 281 TYR cc_start: 0.8181 (m-80) cc_final: 0.7935 (m-80) REVERT: E 289 MET cc_start: 0.8307 (tpp) cc_final: 0.8098 (tpp) REVERT: E 300 LYS cc_start: 0.8000 (pttt) cc_final: 0.7739 (pttt) REVERT: E 301 LYS cc_start: 0.8058 (mmtt) cc_final: 0.7741 (mmtt) REVERT: E 448 LYS cc_start: 0.8419 (mtpt) cc_final: 0.8168 (mtpt) REVERT: F 75 LYS cc_start: 0.8116 (ttmt) cc_final: 0.7907 (ttpp) REVERT: F 90 GLU cc_start: 0.6567 (mm-30) cc_final: 0.6308 (mm-30) REVERT: F 214 LYS cc_start: 0.7944 (pttt) cc_final: 0.7732 (pttp) REVERT: F 245 ASP cc_start: 0.7259 (m-30) cc_final: 0.6894 (m-30) REVERT: F 268 VAL cc_start: 0.8155 (m) cc_final: 0.7908 (t) REVERT: F 277 SER cc_start: 0.8083 (p) cc_final: 0.7871 (m) REVERT: F 467 VAL cc_start: 0.8069 (t) cc_final: 0.7836 (m) REVERT: G 24 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7908 (ttpp) REVERT: G 43 LYS cc_start: 0.8046 (ttmm) cc_final: 0.7050 (tttt) REVERT: G 109 THR cc_start: 0.8120 (p) cc_final: 0.7870 (p) REVERT: G 131 ASN cc_start: 0.7745 (p0) cc_final: 0.7447 (p0) REVERT: G 249 ASN cc_start: 0.7940 (m-40) cc_final: 0.7692 (m-40) REVERT: H 43 PHE cc_start: 0.7264 (m-80) cc_final: 0.6826 (m-80) outliers start: 29 outliers final: 18 residues processed: 693 average time/residue: 0.8637 time to fit residues: 863.0501 Evaluate side-chains 680 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 660 time to evaluate : 2.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 220 GLN Chi-restraints excluded: chain C residue 246 TYR Chi-restraints excluded: chain D residue 397 SER Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain G residue 23 MET Chi-restraints excluded: chain G residue 24 LYS Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 220 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 154 optimal weight: 0.3980 chunk 86 optimal weight: 3.9990 chunk 231 optimal weight: 2.9990 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: 2.9990 chunk 276 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 223 optimal weight: 3.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN ** A 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 ASN C 265 HIS F 57 ASN F 172 ASN G 265 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 23836 Z= 0.477 Angle : 0.609 7.187 32349 Z= 0.320 Chirality : 0.047 0.192 3842 Planarity : 0.005 0.060 4167 Dihedral : 7.228 89.754 3600 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.17 % Favored : 97.64 % Rotamer: Outliers : 2.07 % Allowed : 12.75 % Favored : 85.18 % 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: -0.35 (0.15), residues: 3089 helix: 0.08 (0.14), residues: 1252 sheet: -0.25 (0.22), residues: 497 loop : -0.34 (0.17), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 258 HIS 0.010 0.002 HIS D 367 PHE 0.019 0.002 PHE F 424 TYR 0.015 0.002 TYR C 230 ARG 0.011 0.001 ARG B 82 *********************** 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 756 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 706 time to evaluate : 2.820 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: A 42 ARG cc_start: 0.6991 (mtp180) cc_final: 0.6698 (mtp180) REVERT: A 66 LEU cc_start: 0.8271 (mt) cc_final: 0.8061 (mp) REVERT: A 91 LYS cc_start: 0.8206 (mttt) cc_final: 0.7908 (mttp) REVERT: A 129 SER cc_start: 0.8093 (m) cc_final: 0.7766 (t) REVERT: A 167 GLU cc_start: 0.7905 (tp30) cc_final: 0.7421 (tp30) REVERT: A 357 GLU cc_start: 0.7280 (tm-30) cc_final: 0.6723 (tm-30) REVERT: A 358 LEU cc_start: 0.8385 (mt) cc_final: 0.7913 (mt) REVERT: B 67 ASN cc_start: 0.7975 (p0) cc_final: 0.7595 (p0) REVERT: B 69 GLU cc_start: 0.7170 (mt-10) cc_final: 0.6880 (mt-10) REVERT: B 91 LYS cc_start: 0.8019 (mttt) cc_final: 0.7808 (mtmm) REVERT: B 118 ASP cc_start: 0.7950 (p0) cc_final: 0.7733 (p0) REVERT: B 123 ILE cc_start: 0.8338 (mm) cc_final: 0.8037 (mt) REVERT: B 159 VAL cc_start: 0.8403 (m) cc_final: 0.8124 (p) REVERT: B 199 LYS cc_start: 0.8247 (mttm) cc_final: 0.7926 (mtmm) REVERT: B 257 GLU cc_start: 0.7215 (mt-10) cc_final: 0.6860 (mt-10) REVERT: B 261 ASP cc_start: 0.7474 (m-30) cc_final: 0.7152 (m-30) REVERT: B 336 VAL cc_start: 0.8377 (m) cc_final: 0.8070 (t) REVERT: B 353 PHE cc_start: 0.7777 (t80) cc_final: 0.7357 (t80) REVERT: C 52 GLU cc_start: 0.6883 (mt-10) cc_final: 0.6563 (mt-10) REVERT: C 93 THR cc_start: 0.8500 (m) cc_final: 0.8298 (p) REVERT: C 128 ARG cc_start: 0.7975 (mtp-110) cc_final: 0.7716 (mtp180) REVERT: C 129 SER cc_start: 0.8474 (m) cc_final: 0.8047 (p) REVERT: C 146 GLU cc_start: 0.7924 (pt0) cc_final: 0.7544 (pt0) REVERT: C 246 TYR cc_start: 0.8523 (OUTLIER) cc_final: 0.7980 (t80) REVERT: C 271 ASP cc_start: 0.7358 (t0) cc_final: 0.7145 (t70) REVERT: C 299 ASP cc_start: 0.7662 (p0) cc_final: 0.7451 (p0) REVERT: C 361 LYS cc_start: 0.8410 (mttt) cc_final: 0.8112 (mttt) REVERT: C 393 LYS cc_start: 0.8329 (ttmt) cc_final: 0.8064 (ttmm) REVERT: C 446 LEU cc_start: 0.7988 (mt) cc_final: 0.7730 (mt) REVERT: D 12 LYS cc_start: 0.7952 (mtpp) cc_final: 0.7666 (mttm) REVERT: D 38 GLU cc_start: 0.7250 (mt-10) cc_final: 0.7009 (mm-30) REVERT: D 64 MET cc_start: 0.8325 (mmm) cc_final: 0.7890 (mmt) REVERT: D 241 GLU cc_start: 0.7262 (mt-10) cc_final: 0.6943 (mt-10) REVERT: D 267 GLU cc_start: 0.7187 (mt-10) cc_final: 0.6882 (mt-10) REVERT: D 288 ASP cc_start: 0.7118 (m-30) cc_final: 0.6727 (m-30) REVERT: D 435 LYS cc_start: 0.7935 (mptt) cc_final: 0.7689 (mmmt) REVERT: E 196 ASP cc_start: 0.7152 (m-30) cc_final: 0.6672 (m-30) REVERT: E 301 LYS cc_start: 0.8055 (mmtt) cc_final: 0.7763 (mmtt) REVERT: E 448 LYS cc_start: 0.8471 (mtpt) cc_final: 0.8183 (mtpt) REVERT: F 89 ARG cc_start: 0.7667 (mtt-85) cc_final: 0.7440 (mtt90) REVERT: F 90 GLU cc_start: 0.6692 (mm-30) cc_final: 0.6453 (mm-30) REVERT: F 178 HIS cc_start: 0.7138 (t70) cc_final: 0.6736 (t70) REVERT: F 199 ARG cc_start: 0.7905 (ttp80) cc_final: 0.7454 (ttp-110) REVERT: F 245 ASP cc_start: 0.7302 (m-30) cc_final: 0.7018 (m-30) REVERT: F 250 ASP cc_start: 0.7054 (t0) cc_final: 0.6787 (t0) REVERT: F 412 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7895 (tpp-160) REVERT: G 5 GLU cc_start: 0.6863 (tm-30) cc_final: 0.6630 (tm-30) REVERT: G 23 MET cc_start: 0.7565 (OUTLIER) cc_final: 0.6917 (mpt) REVERT: G 32 SER cc_start: 0.8499 (t) cc_final: 0.8224 (p) REVERT: G 43 LYS cc_start: 0.8183 (ttmm) cc_final: 0.7167 (tttt) REVERT: G 109 THR cc_start: 0.8199 (p) cc_final: 0.7963 (p) REVERT: G 114 ILE cc_start: 0.8462 (tp) cc_final: 0.8167 (tt) REVERT: G 131 ASN cc_start: 0.7870 (p0) cc_final: 0.7592 (p0) REVERT: G 249 ASN cc_start: 0.7979 (m-40) cc_final: 0.7656 (m-40) REVERT: H 43 PHE cc_start: 0.7345 (m-80) cc_final: 0.7037 (m-80) outliers start: 50 outliers final: 35 residues processed: 724 average time/residue: 0.8885 time to fit residues: 930.8113 Evaluate side-chains 732 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 694 time to evaluate : 2.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 393 LYS Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 223 GLU Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 220 GLN Chi-restraints excluded: chain C residue 246 TYR Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 493 LYS Chi-restraints excluded: chain D residue 221 GLN Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 249 GLN Chi-restraints excluded: chain D residue 397 SER Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 471 GLU Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain F residue 412 ARG Chi-restraints excluded: chain F residue 452 ILE Chi-restraints excluded: chain G residue 23 MET Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 129 SER Chi-restraints excluded: chain H residue 33 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 275 optimal weight: 0.0980 chunk 209 optimal weight: 0.6980 chunk 144 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 186 optimal weight: 2.9990 chunk 279 optimal weight: 0.5980 chunk 295 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 264 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 GLN ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 ASN D 249 GLN F 57 ASN F 168 GLN G 54 ASN G 98 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 23836 Z= 0.222 Angle : 0.518 6.449 32349 Z= 0.270 Chirality : 0.042 0.154 3842 Planarity : 0.004 0.066 4167 Dihedral : 6.627 88.291 3594 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.19 % Allowed : 1.46 % Favored : 98.35 % Rotamer: Outliers : 1.61 % Allowed : 14.74 % Favored : 83.65 % 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: 0.06 (0.15), residues: 3089 helix: 0.50 (0.15), residues: 1255 sheet: -0.16 (0.23), residues: 497 loop : -0.15 (0.17), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 258 HIS 0.004 0.001 HIS D 367 PHE 0.013 0.001 PHE A 405 TYR 0.011 0.001 TYR C 230 ARG 0.008 0.000 ARG B 82 *********************** 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 722 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 683 time to evaluate : 2.996 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: A 42 ARG cc_start: 0.6969 (mtp180) cc_final: 0.6766 (mtm-85) REVERT: A 66 LEU cc_start: 0.8272 (mt) cc_final: 0.8055 (mp) REVERT: A 91 LYS cc_start: 0.8216 (mttt) cc_final: 0.7899 (mttp) REVERT: A 129 SER cc_start: 0.8063 (m) cc_final: 0.7740 (t) REVERT: A 167 GLU cc_start: 0.7916 (tp30) cc_final: 0.7629 (tp30) REVERT: A 357 GLU cc_start: 0.7263 (tm-30) cc_final: 0.6705 (tm-30) REVERT: A 358 LEU cc_start: 0.8363 (mt) cc_final: 0.7871 (mt) REVERT: A 373 VAL cc_start: 0.8718 (p) cc_final: 0.8261 (m) REVERT: A 475 LYS cc_start: 0.8118 (ttmm) cc_final: 0.7629 (mttp) REVERT: B 67 ASN cc_start: 0.7906 (p0) cc_final: 0.7534 (p0) REVERT: B 69 GLU cc_start: 0.7147 (mt-10) cc_final: 0.6841 (mt-10) REVERT: B 91 LYS cc_start: 0.8008 (mttt) cc_final: 0.7805 (mtmm) REVERT: B 118 ASP cc_start: 0.7951 (p0) cc_final: 0.7699 (p0) REVERT: B 123 ILE cc_start: 0.8340 (mm) cc_final: 0.8062 (mt) REVERT: B 159 VAL cc_start: 0.8412 (m) cc_final: 0.8122 (p) REVERT: B 199 LYS cc_start: 0.8245 (mttm) cc_final: 0.7932 (mtmm) REVERT: B 218 LEU cc_start: 0.8093 (tt) cc_final: 0.7839 (tt) REVERT: B 257 GLU cc_start: 0.7181 (mt-10) cc_final: 0.6865 (mt-10) REVERT: B 261 ASP cc_start: 0.7516 (m-30) cc_final: 0.7186 (m-30) REVERT: B 336 VAL cc_start: 0.8384 (m) cc_final: 0.8058 (t) REVERT: B 353 PHE cc_start: 0.7779 (t80) cc_final: 0.7475 (t80) REVERT: C 52 GLU cc_start: 0.6707 (mt-10) cc_final: 0.6361 (mt-10) REVERT: C 128 ARG cc_start: 0.7944 (mtp-110) cc_final: 0.7698 (mtp180) REVERT: C 129 SER cc_start: 0.8441 (m) cc_final: 0.8000 (p) REVERT: C 146 GLU cc_start: 0.7949 (pt0) cc_final: 0.7529 (pt0) REVERT: C 228 MET cc_start: 0.7875 (mmt) cc_final: 0.7670 (mmt) REVERT: C 246 TYR cc_start: 0.8495 (OUTLIER) cc_final: 0.7952 (t80) REVERT: C 271 ASP cc_start: 0.7378 (t0) cc_final: 0.7101 (t70) REVERT: C 299 ASP cc_start: 0.7663 (p0) cc_final: 0.7420 (p0) REVERT: C 337 SER cc_start: 0.8231 (t) cc_final: 0.7756 (p) REVERT: C 361 LYS cc_start: 0.8356 (mttt) cc_final: 0.8067 (mttp) REVERT: C 393 LYS cc_start: 0.8320 (ttmt) cc_final: 0.8055 (ttmm) REVERT: C 446 LEU cc_start: 0.7982 (mt) cc_final: 0.7708 (mt) REVERT: D 12 LYS cc_start: 0.7932 (mtpp) cc_final: 0.7641 (mttm) REVERT: D 38 GLU cc_start: 0.7258 (mt-10) cc_final: 0.6966 (mm-30) REVERT: D 64 MET cc_start: 0.8326 (mmm) cc_final: 0.7901 (mmt) REVERT: D 288 ASP cc_start: 0.7093 (m-30) cc_final: 0.6710 (m-30) REVERT: D 435 LYS cc_start: 0.7919 (mptt) cc_final: 0.7678 (mmmt) REVERT: E 192 ARG cc_start: 0.8061 (ptm160) cc_final: 0.7512 (ptm-80) REVERT: E 196 ASP cc_start: 0.7172 (m-30) cc_final: 0.6688 (m-30) REVERT: E 259 PHE cc_start: 0.8306 (t80) cc_final: 0.7873 (t80) REVERT: E 301 LYS cc_start: 0.8048 (mmtt) cc_final: 0.7738 (mmtt) REVERT: E 431 LEU cc_start: 0.6743 (OUTLIER) cc_final: 0.6538 (mp) REVERT: E 448 LYS cc_start: 0.8404 (mtpt) cc_final: 0.8096 (mtpt) REVERT: F 89 ARG cc_start: 0.7654 (mtt-85) cc_final: 0.7401 (mtt90) REVERT: F 90 GLU cc_start: 0.6615 (mm-30) cc_final: 0.6408 (mm-30) REVERT: F 199 ARG cc_start: 0.7918 (ttp80) cc_final: 0.7497 (ttp-110) REVERT: F 245 ASP cc_start: 0.7306 (m-30) cc_final: 0.6996 (m-30) REVERT: F 412 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.7844 (tpp-160) REVERT: G 23 MET cc_start: 0.7489 (OUTLIER) cc_final: 0.6966 (mpt) REVERT: G 43 LYS cc_start: 0.8153 (ttmm) cc_final: 0.7151 (tttt) REVERT: G 109 THR cc_start: 0.8190 (p) cc_final: 0.7970 (p) REVERT: G 114 ILE cc_start: 0.8438 (tp) cc_final: 0.8149 (tt) REVERT: G 131 ASN cc_start: 0.7849 (p0) cc_final: 0.7565 (p0) REVERT: G 224 GLN cc_start: 0.7717 (mm-40) cc_final: 0.7421 (mm-40) REVERT: G 249 ASN cc_start: 0.7919 (m-40) cc_final: 0.7571 (m110) REVERT: H 19 GLN cc_start: 0.8306 (mm-40) cc_final: 0.7999 (tp40) REVERT: H 43 PHE cc_start: 0.7257 (m-80) cc_final: 0.6943 (m-80) outliers start: 39 outliers final: 29 residues processed: 696 average time/residue: 0.8934 time to fit residues: 891.2809 Evaluate side-chains 720 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 687 time to evaluate : 3.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain C residue 220 GLN Chi-restraints excluded: chain C residue 246 TYR Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 493 LYS Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 249 GLN Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 376 GLU Chi-restraints excluded: chain D residue 397 SER Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain F residue 412 ARG Chi-restraints excluded: chain F residue 452 ILE Chi-restraints excluded: chain G residue 15 ASN Chi-restraints excluded: chain G residue 23 MET Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain H residue 33 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 246 optimal weight: 0.0870 chunk 167 optimal weight: 0.0270 chunk 4 optimal weight: 0.7980 chunk 220 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 252 optimal weight: 2.9990 chunk 204 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 151 optimal weight: 0.0980 chunk 265 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 57 ASN G 54 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 23836 Z= 0.180 Angle : 0.493 6.603 32349 Z= 0.256 Chirality : 0.042 0.143 3842 Planarity : 0.004 0.072 4167 Dihedral : 6.323 87.782 3594 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.19 % Allowed : 1.75 % Favored : 98.06 % Rotamer: Outliers : 1.70 % Allowed : 15.11 % Favored : 83.20 % 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: 0.42 (0.15), residues: 3089 helix: 0.89 (0.15), residues: 1249 sheet: -0.13 (0.23), residues: 507 loop : 0.02 (0.18), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 258 HIS 0.002 0.001 HIS F 178 PHE 0.009 0.001 PHE B 506 TYR 0.010 0.001 TYR C 230 ARG 0.009 0.000 ARG B 82 *********************** 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 737 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 696 time to evaluate : 2.847 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 REVERT: A 66 LEU cc_start: 0.8269 (mt) cc_final: 0.8045 (mp) REVERT: A 91 LYS cc_start: 0.8225 (mttt) cc_final: 0.7907 (mttp) REVERT: A 129 SER cc_start: 0.8068 (m) cc_final: 0.7732 (t) REVERT: A 167 GLU cc_start: 0.7930 (tp30) cc_final: 0.7604 (tp30) REVERT: A 373 VAL cc_start: 0.8721 (p) cc_final: 0.8276 (m) REVERT: A 475 LYS cc_start: 0.8114 (ttmm) cc_final: 0.7580 (mttp) REVERT: B 67 ASN cc_start: 0.7899 (p0) cc_final: 0.7527 (p0) REVERT: B 69 GLU cc_start: 0.7124 (mt-10) cc_final: 0.6836 (mt-10) REVERT: B 91 LYS cc_start: 0.8035 (mttt) cc_final: 0.7810 (mtmm) REVERT: B 118 ASP cc_start: 0.7951 (p0) cc_final: 0.7687 (p0) REVERT: B 123 ILE cc_start: 0.8343 (mm) cc_final: 0.8073 (mt) REVERT: B 159 VAL cc_start: 0.8394 (m) cc_final: 0.8120 (p) REVERT: B 199 LYS cc_start: 0.8240 (mttm) cc_final: 0.7919 (mtmm) REVERT: B 261 ASP cc_start: 0.7500 (m-30) cc_final: 0.7170 (m-30) REVERT: B 336 VAL cc_start: 0.8386 (m) cc_final: 0.8061 (t) REVERT: B 353 PHE cc_start: 0.7781 (t80) cc_final: 0.7450 (t80) REVERT: C 52 GLU cc_start: 0.6667 (mt-10) cc_final: 0.6281 (mt-10) REVERT: C 128 ARG cc_start: 0.7929 (mtp180) cc_final: 0.7692 (mtp180) REVERT: C 129 SER cc_start: 0.8440 (m) cc_final: 0.7988 (p) REVERT: C 133 VAL cc_start: 0.8745 (m) cc_final: 0.8512 (p) REVERT: C 146 GLU cc_start: 0.7926 (pt0) cc_final: 0.7661 (pt0) REVERT: C 228 MET cc_start: 0.7876 (mmt) cc_final: 0.7636 (mmt) REVERT: C 246 TYR cc_start: 0.8482 (OUTLIER) cc_final: 0.7959 (t80) REVERT: C 271 ASP cc_start: 0.7415 (t0) cc_final: 0.7094 (t70) REVERT: C 299 ASP cc_start: 0.7693 (p0) cc_final: 0.7408 (p0) REVERT: C 337 SER cc_start: 0.8225 (t) cc_final: 0.7751 (p) REVERT: C 361 LYS cc_start: 0.8351 (mttt) cc_final: 0.8108 (mttp) REVERT: C 393 LYS cc_start: 0.8312 (ttmt) cc_final: 0.8043 (ttmm) REVERT: C 446 LEU cc_start: 0.7983 (mt) cc_final: 0.7713 (mt) REVERT: D 12 LYS cc_start: 0.7835 (mtpp) cc_final: 0.7572 (mttm) REVERT: D 64 MET cc_start: 0.8329 (mmm) cc_final: 0.7926 (mmt) REVERT: D 74 GLU cc_start: 0.7544 (tt0) cc_final: 0.7312 (tt0) REVERT: D 241 GLU cc_start: 0.7235 (mt-10) cc_final: 0.6906 (mt-10) REVERT: D 267 GLU cc_start: 0.7179 (mt-10) cc_final: 0.6832 (mt-10) REVERT: D 288 ASP cc_start: 0.7111 (m-30) cc_final: 0.6713 (m-30) REVERT: D 365 GLN cc_start: 0.7763 (tp40) cc_final: 0.7424 (tp40) REVERT: D 435 LYS cc_start: 0.7954 (mptt) cc_final: 0.7690 (mmmt) REVERT: E 192 ARG cc_start: 0.8066 (ptm160) cc_final: 0.7518 (ptm-80) REVERT: E 196 ASP cc_start: 0.7182 (m-30) cc_final: 0.6712 (m-30) REVERT: E 259 PHE cc_start: 0.8337 (t80) cc_final: 0.7906 (t80) REVERT: E 301 LYS cc_start: 0.8045 (mmtt) cc_final: 0.7750 (mmtt) REVERT: E 431 LEU cc_start: 0.6735 (OUTLIER) cc_final: 0.6527 (mp) REVERT: E 448 LYS cc_start: 0.8405 (mtpt) cc_final: 0.8082 (mtpt) REVERT: F 196 ASP cc_start: 0.7182 (t70) cc_final: 0.6814 (t0) REVERT: F 199 ARG cc_start: 0.7920 (ttp80) cc_final: 0.7486 (ttp-110) REVERT: F 245 ASP cc_start: 0.7298 (m-30) cc_final: 0.6996 (m-30) REVERT: F 354 LYS cc_start: 0.7957 (OUTLIER) cc_final: 0.7500 (mttm) REVERT: F 412 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7803 (tpp-160) REVERT: G 43 LYS cc_start: 0.8134 (ttmm) cc_final: 0.7171 (ttpt) REVERT: G 109 THR cc_start: 0.8218 (p) cc_final: 0.7994 (p) REVERT: G 114 ILE cc_start: 0.8430 (tp) cc_final: 0.8139 (tt) REVERT: G 131 ASN cc_start: 0.7822 (p0) cc_final: 0.7551 (p0) REVERT: G 224 GLN cc_start: 0.7705 (mm-40) cc_final: 0.7479 (mm-40) REVERT: G 249 ASN cc_start: 0.7931 (m-40) cc_final: 0.7588 (m110) REVERT: H 43 PHE cc_start: 0.7243 (m-80) cc_final: 0.6954 (m-80) outliers start: 41 outliers final: 31 residues processed: 709 average time/residue: 0.8728 time to fit residues: 889.4546 Evaluate side-chains 727 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 692 time to evaluate : 2.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 443 GLN Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 220 GLN Chi-restraints excluded: chain C residue 246 TYR Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 493 LYS Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 397 SER Chi-restraints excluded: chain D residue 415 SER Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 132 GLU Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain F residue 354 LYS Chi-restraints excluded: chain F residue 412 ARG Chi-restraints excluded: chain F residue 452 ILE Chi-restraints excluded: chain G residue 15 ASN Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 33 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 99 optimal weight: 3.9990 chunk 266 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 173 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 296 optimal weight: 4.9990 chunk 245 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 GLN F 57 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 23836 Z= 0.459 Angle : 0.579 7.132 32349 Z= 0.302 Chirality : 0.046 0.183 3842 Planarity : 0.004 0.060 4167 Dihedral : 6.643 81.338 3591 Min Nonbonded Distance : 1.731 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.56 % Favored : 97.25 % Rotamer: Outliers : 2.19 % Allowed : 15.15 % Favored : 82.66 % 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: 0.10 (0.15), residues: 3089 helix: 0.62 (0.15), residues: 1254 sheet: -0.23 (0.22), residues: 517 loop : -0.19 (0.18), residues: 1318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 258 HIS 0.009 0.001 HIS D 367 PHE 0.016 0.002 PHE F 124 TYR 0.012 0.002 TYR F 198 ARG 0.007 0.001 ARG B 82 *********************** 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 772 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 719 time to evaluate : 2.973 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: A 66 LEU cc_start: 0.8291 (mt) cc_final: 0.8058 (mp) REVERT: A 91 LYS cc_start: 0.8226 (mttt) cc_final: 0.7907 (mttp) REVERT: A 129 SER cc_start: 0.8045 (m) cc_final: 0.7695 (t) REVERT: A 167 GLU cc_start: 0.7931 (tp30) cc_final: 0.7509 (tp30) REVERT: A 373 VAL cc_start: 0.8737 (p) cc_final: 0.8288 (m) REVERT: A 468 SER cc_start: 0.8375 (m) cc_final: 0.8099 (p) REVERT: A 475 LYS cc_start: 0.8044 (ttmm) cc_final: 0.7530 (mttm) REVERT: B 69 GLU cc_start: 0.7237 (mt-10) cc_final: 0.6867 (mt-10) REVERT: B 91 LYS cc_start: 0.8038 (mttt) cc_final: 0.7812 (mtmm) REVERT: B 118 ASP cc_start: 0.7986 (p0) cc_final: 0.7721 (p0) REVERT: B 123 ILE cc_start: 0.8368 (mm) cc_final: 0.8126 (mt) REVERT: B 159 VAL cc_start: 0.8436 (m) cc_final: 0.8149 (p) REVERT: B 199 LYS cc_start: 0.8238 (mttm) cc_final: 0.7953 (mtmm) REVERT: B 261 ASP cc_start: 0.7540 (m-30) cc_final: 0.7224 (m-30) REVERT: B 336 VAL cc_start: 0.8382 (m) cc_final: 0.8057 (t) REVERT: B 353 PHE cc_start: 0.7785 (t80) cc_final: 0.7535 (t80) REVERT: C 52 GLU cc_start: 0.6711 (mt-10) cc_final: 0.6329 (mt-10) REVERT: C 128 ARG cc_start: 0.7954 (mtp-110) cc_final: 0.7720 (mtp180) REVERT: C 129 SER cc_start: 0.8503 (m) cc_final: 0.8025 (p) REVERT: C 146 GLU cc_start: 0.7948 (pt0) cc_final: 0.7665 (pt0) REVERT: C 246 TYR cc_start: 0.8566 (OUTLIER) cc_final: 0.8043 (t80) REVERT: C 271 ASP cc_start: 0.7410 (t0) cc_final: 0.7129 (t70) REVERT: C 299 ASP cc_start: 0.7747 (p0) cc_final: 0.7463 (p0) REVERT: C 361 LYS cc_start: 0.8387 (mttt) cc_final: 0.8101 (mttp) REVERT: C 393 LYS cc_start: 0.8314 (ttmt) cc_final: 0.8042 (ttmm) REVERT: C 446 LEU cc_start: 0.8006 (mt) cc_final: 0.7757 (mt) REVERT: D 12 LYS cc_start: 0.7905 (mtpp) cc_final: 0.7631 (mttm) REVERT: D 241 GLU cc_start: 0.7291 (mt-10) cc_final: 0.6959 (mt-10) REVERT: D 267 GLU cc_start: 0.7205 (mt-10) cc_final: 0.6829 (mt-10) REVERT: D 288 ASP cc_start: 0.7186 (m-30) cc_final: 0.6867 (m-30) REVERT: D 435 LYS cc_start: 0.7963 (mptt) cc_final: 0.7725 (mmmt) REVERT: E 196 ASP cc_start: 0.7221 (m-30) cc_final: 0.6736 (m-30) REVERT: E 301 LYS cc_start: 0.8037 (mmtt) cc_final: 0.7736 (mmtt) REVERT: E 448 LYS cc_start: 0.8475 (mtpt) cc_final: 0.8135 (mtpt) REVERT: F 196 ASP cc_start: 0.7228 (t70) cc_final: 0.6888 (t0) REVERT: F 199 ARG cc_start: 0.7914 (ttp80) cc_final: 0.7615 (ttp-110) REVERT: F 245 ASP cc_start: 0.7309 (m-30) cc_final: 0.7023 (m-30) REVERT: F 291 LEU cc_start: 0.8460 (mt) cc_final: 0.8227 (mp) REVERT: F 382 LYS cc_start: 0.8251 (ttpt) cc_final: 0.8036 (ttpp) REVERT: F 412 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7893 (tpp-160) REVERT: G 5 GLU cc_start: 0.6903 (tm-30) cc_final: 0.6664 (tm-30) REVERT: G 43 LYS cc_start: 0.8222 (ttmm) cc_final: 0.7225 (ttpt) REVERT: G 90 GLN cc_start: 0.8183 (mt0) cc_final: 0.7920 (mt0) REVERT: G 109 THR cc_start: 0.8215 (p) cc_final: 0.7990 (p) REVERT: G 114 ILE cc_start: 0.8444 (tp) cc_final: 0.8170 (tt) REVERT: G 131 ASN cc_start: 0.7908 (p0) cc_final: 0.7620 (p0) REVERT: G 249 ASN cc_start: 0.7990 (m-40) cc_final: 0.7657 (m110) REVERT: H 43 PHE cc_start: 0.7271 (m-80) cc_final: 0.7065 (m-80) outliers start: 53 outliers final: 43 residues processed: 737 average time/residue: 0.8724 time to fit residues: 928.1497 Evaluate side-chains 758 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 713 time to evaluate : 2.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 220 GLN Chi-restraints excluded: chain C residue 246 TYR Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 493 LYS Chi-restraints excluded: chain D residue 221 GLN Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 397 SER Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 450 ASP Chi-restraints excluded: chain D residue 451 ASN Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 132 GLU Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain F residue 412 ARG Chi-restraints excluded: chain F residue 452 ILE Chi-restraints excluded: chain G residue 15 ASN Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 129 SER Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain H residue 33 SER 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: 0.3980 chunk 168 optimal weight: 0.7980 chunk 216 optimal weight: 3.9990 chunk 167 optimal weight: 0.5980 chunk 249 optimal weight: 2.9990 chunk 165 optimal weight: 2.9990 chunk 294 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 chunk 179 optimal weight: 1.9990 chunk 136 optimal weight: 0.0470 overall best weight: 0.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 57 ASN F 293 GLN F 308 GLN G 54 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 23836 Z= 0.210 Angle : 0.509 6.489 32349 Z= 0.264 Chirality : 0.042 0.145 3842 Planarity : 0.004 0.054 4167 Dihedral : 6.309 83.632 3591 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.19 % Allowed : 1.78 % Favored : 98.03 % Rotamer: Outliers : 1.86 % Allowed : 16.02 % Favored : 82.12 % 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: 0.44 (0.15), residues: 3089 helix: 0.96 (0.15), residues: 1244 sheet: -0.18 (0.23), residues: 518 loop : -0.00 (0.18), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 258 HIS 0.003 0.001 HIS D 367 PHE 0.012 0.001 PHE A 408 TYR 0.011 0.001 TYR F 449 ARG 0.007 0.000 ARG B 462 *********************** 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 748 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 703 time to evaluate : 2.836 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: A 66 LEU cc_start: 0.8283 (mt) cc_final: 0.8053 (mp) REVERT: A 91 LYS cc_start: 0.8211 (mttt) cc_final: 0.7898 (mttp) REVERT: A 129 SER cc_start: 0.8044 (m) cc_final: 0.7697 (t) REVERT: A 167 GLU cc_start: 0.7935 (tp30) cc_final: 0.7003 (mm-30) REVERT: A 283 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8081 (mp) REVERT: A 373 VAL cc_start: 0.8740 (p) cc_final: 0.8327 (m) REVERT: A 468 SER cc_start: 0.8399 (m) cc_final: 0.8133 (p) REVERT: A 475 LYS cc_start: 0.8041 (ttmm) cc_final: 0.7525 (mttm) REVERT: B 69 GLU cc_start: 0.7212 (mt-10) cc_final: 0.6883 (mt-10) REVERT: B 91 LYS cc_start: 0.8032 (mttt) cc_final: 0.7805 (mtmm) REVERT: B 118 ASP cc_start: 0.7972 (p0) cc_final: 0.7693 (p0) REVERT: B 123 ILE cc_start: 0.8368 (mm) cc_final: 0.8132 (mt) REVERT: B 159 VAL cc_start: 0.8421 (m) cc_final: 0.8165 (p) REVERT: B 183 ASP cc_start: 0.6869 (t0) cc_final: 0.6662 (t0) REVERT: B 199 LYS cc_start: 0.8223 (mttm) cc_final: 0.7977 (mtmm) REVERT: B 257 GLU cc_start: 0.7185 (mt-10) cc_final: 0.6883 (mt-10) REVERT: B 261 ASP cc_start: 0.7521 (m-30) cc_final: 0.7211 (m-30) REVERT: B 336 VAL cc_start: 0.8380 (m) cc_final: 0.8054 (t) REVERT: B 353 PHE cc_start: 0.7772 (t80) cc_final: 0.7486 (t80) REVERT: C 52 GLU cc_start: 0.6600 (mt-10) cc_final: 0.6203 (mt-10) REVERT: C 128 ARG cc_start: 0.7920 (mtp-110) cc_final: 0.7692 (mtp180) REVERT: C 129 SER cc_start: 0.8492 (m) cc_final: 0.8001 (p) REVERT: C 133 VAL cc_start: 0.8712 (m) cc_final: 0.8486 (p) REVERT: C 146 GLU cc_start: 0.7927 (pt0) cc_final: 0.7525 (mt-10) REVERT: C 246 TYR cc_start: 0.8529 (OUTLIER) cc_final: 0.8046 (t80) REVERT: C 299 ASP cc_start: 0.7670 (p0) cc_final: 0.7377 (p0) REVERT: C 361 LYS cc_start: 0.8348 (mttt) cc_final: 0.8068 (mttp) REVERT: C 393 LYS cc_start: 0.8307 (ttmt) cc_final: 0.8042 (ttmm) REVERT: C 446 LEU cc_start: 0.7994 (mt) cc_final: 0.7724 (mt) REVERT: D 12 LYS cc_start: 0.7810 (mtpp) cc_final: 0.7538 (mttm) REVERT: D 267 GLU cc_start: 0.7181 (mt-10) cc_final: 0.6819 (mt-10) REVERT: D 288 ASP cc_start: 0.7167 (m-30) cc_final: 0.6815 (m-30) REVERT: D 435 LYS cc_start: 0.8014 (mptt) cc_final: 0.7769 (mmmt) REVERT: E 192 ARG cc_start: 0.8092 (ptm160) cc_final: 0.7552 (ptm-80) REVERT: E 196 ASP cc_start: 0.7194 (m-30) cc_final: 0.6682 (m-30) REVERT: E 301 LYS cc_start: 0.8029 (mmtt) cc_final: 0.7721 (mmtt) REVERT: E 448 LYS cc_start: 0.8450 (mtpt) cc_final: 0.8099 (mtpt) REVERT: E 457 PHE cc_start: 0.7771 (m-80) cc_final: 0.7558 (m-80) REVERT: F 196 ASP cc_start: 0.7187 (t70) cc_final: 0.6856 (t0) REVERT: F 199 ARG cc_start: 0.7923 (ttp80) cc_final: 0.7652 (ttp-110) REVERT: F 215 VAL cc_start: 0.8380 (p) cc_final: 0.8057 (t) REVERT: F 245 ASP cc_start: 0.7292 (m-30) cc_final: 0.7017 (m-30) REVERT: F 247 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7195 (mm-30) REVERT: F 291 LEU cc_start: 0.8432 (mt) cc_final: 0.8187 (mp) REVERT: F 382 LYS cc_start: 0.8237 (ttpt) cc_final: 0.8010 (ttpp) REVERT: F 412 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7816 (tpp-160) REVERT: G 43 LYS cc_start: 0.8182 (ttmm) cc_final: 0.7166 (tttt) REVERT: G 90 GLN cc_start: 0.8128 (mt0) cc_final: 0.7922 (mt0) REVERT: G 109 THR cc_start: 0.8217 (p) cc_final: 0.8000 (p) REVERT: G 114 ILE cc_start: 0.8436 (tp) cc_final: 0.8104 (tt) REVERT: G 224 GLN cc_start: 0.7685 (mm-40) cc_final: 0.7269 (mm-40) REVERT: G 249 ASN cc_start: 0.7945 (m-40) cc_final: 0.7601 (m-40) REVERT: H 43 PHE cc_start: 0.7192 (m-80) cc_final: 0.6928 (m-10) outliers start: 45 outliers final: 35 residues processed: 719 average time/residue: 0.8626 time to fit residues: 886.8248 Evaluate side-chains 733 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 695 time to evaluate : 2.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 220 GLN Chi-restraints excluded: chain C residue 246 TYR Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 493 LYS Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 397 SER Chi-restraints excluded: chain D residue 415 SER Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 451 ASN Chi-restraints excluded: chain E residue 132 GLU Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain F residue 293 GLN Chi-restraints excluded: chain F residue 412 ARG Chi-restraints excluded: chain F residue 452 ILE Chi-restraints excluded: chain G residue 15 ASN Chi-restraints excluded: chain G residue 53 LYS Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 129 SER Chi-restraints excluded: chain H residue 33 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 182 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 176 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 chunk 57 optimal weight: 0.2980 chunk 187 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 231 optimal weight: 0.0870 chunk 268 optimal weight: 1.9990 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 GLN ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 57 ASN F 308 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 23836 Z= 0.212 Angle : 0.503 6.235 32349 Z= 0.260 Chirality : 0.042 0.144 3842 Planarity : 0.004 0.054 4167 Dihedral : 6.210 84.673 3591 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.10 % Favored : 97.70 % Rotamer: Outliers : 1.78 % Allowed : 16.02 % Favored : 82.20 % 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: 0.58 (0.16), residues: 3089 helix: 1.11 (0.15), residues: 1246 sheet: -0.12 (0.22), residues: 528 loop : 0.06 (0.18), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 258 HIS 0.004 0.001 HIS D 367 PHE 0.012 0.001 PHE A 466 TYR 0.012 0.001 TYR F 449 ARG 0.008 0.000 ARG B 462 *********************** 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 748 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 705 time to evaluate : 2.870 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: A 66 LEU cc_start: 0.8280 (mt) cc_final: 0.8050 (mp) REVERT: A 91 LYS cc_start: 0.8215 (mttt) cc_final: 0.7901 (mttp) REVERT: A 129 SER cc_start: 0.8045 (m) cc_final: 0.7697 (t) REVERT: A 167 GLU cc_start: 0.7944 (tp30) cc_final: 0.7030 (mm-30) REVERT: A 283 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8074 (mp) REVERT: A 373 VAL cc_start: 0.8758 (p) cc_final: 0.8346 (m) REVERT: A 468 SER cc_start: 0.8413 (m) cc_final: 0.8155 (p) REVERT: A 475 LYS cc_start: 0.8049 (ttmm) cc_final: 0.7517 (mttm) REVERT: B 69 GLU cc_start: 0.7203 (mt-10) cc_final: 0.6882 (mt-10) REVERT: B 91 LYS cc_start: 0.8034 (mttt) cc_final: 0.7803 (mtmm) REVERT: B 118 ASP cc_start: 0.7963 (p0) cc_final: 0.7678 (p0) REVERT: B 123 ILE cc_start: 0.8372 (mm) cc_final: 0.8137 (mt) REVERT: B 159 VAL cc_start: 0.8418 (m) cc_final: 0.8161 (p) REVERT: B 183 ASP cc_start: 0.6880 (t0) cc_final: 0.6652 (t0) REVERT: B 199 LYS cc_start: 0.8283 (mttm) cc_final: 0.7999 (mtmm) REVERT: B 261 ASP cc_start: 0.7520 (m-30) cc_final: 0.7211 (m-30) REVERT: B 336 VAL cc_start: 0.8377 (m) cc_final: 0.8045 (t) REVERT: B 353 PHE cc_start: 0.7775 (t80) cc_final: 0.7482 (t80) REVERT: C 52 GLU cc_start: 0.6580 (mt-10) cc_final: 0.6195 (mt-10) REVERT: C 128 ARG cc_start: 0.7912 (mtp-110) cc_final: 0.7688 (mtp180) REVERT: C 129 SER cc_start: 0.8473 (m) cc_final: 0.7979 (p) REVERT: C 133 VAL cc_start: 0.8700 (m) cc_final: 0.8481 (p) REVERT: C 146 GLU cc_start: 0.7925 (pt0) cc_final: 0.7541 (mt-10) REVERT: C 246 TYR cc_start: 0.8522 (OUTLIER) cc_final: 0.8045 (t80) REVERT: C 293 ARG cc_start: 0.8096 (ttp80) cc_final: 0.7776 (mtp180) REVERT: C 299 ASP cc_start: 0.7665 (p0) cc_final: 0.7369 (p0) REVERT: C 337 SER cc_start: 0.8201 (t) cc_final: 0.7837 (p) REVERT: C 361 LYS cc_start: 0.8346 (mttt) cc_final: 0.8065 (mttp) REVERT: C 393 LYS cc_start: 0.8307 (ttmt) cc_final: 0.8043 (ttmm) REVERT: C 446 LEU cc_start: 0.7983 (mt) cc_final: 0.7718 (mt) REVERT: D 12 LYS cc_start: 0.7805 (mtpp) cc_final: 0.7529 (mttm) REVERT: D 267 GLU cc_start: 0.7173 (mt-10) cc_final: 0.6796 (mt-10) REVERT: D 288 ASP cc_start: 0.7173 (m-30) cc_final: 0.6831 (m-30) REVERT: D 435 LYS cc_start: 0.8017 (mptt) cc_final: 0.7772 (mmmt) REVERT: E 192 ARG cc_start: 0.8101 (ptm160) cc_final: 0.7558 (ptm-80) REVERT: E 196 ASP cc_start: 0.7214 (m-30) cc_final: 0.6672 (m-30) REVERT: E 301 LYS cc_start: 0.8032 (mmtt) cc_final: 0.7715 (mmtt) REVERT: E 448 LYS cc_start: 0.8453 (mtpt) cc_final: 0.8098 (mtpt) REVERT: E 457 PHE cc_start: 0.7774 (m-80) cc_final: 0.7571 (m-80) REVERT: F 195 ASN cc_start: 0.8299 (t0) cc_final: 0.8062 (t0) REVERT: F 196 ASP cc_start: 0.7203 (t70) cc_final: 0.6885 (t0) REVERT: F 199 ARG cc_start: 0.7932 (ttp80) cc_final: 0.7653 (ttp-110) REVERT: F 215 VAL cc_start: 0.8381 (p) cc_final: 0.8057 (t) REVERT: F 245 ASP cc_start: 0.7292 (m-30) cc_final: 0.7012 (m-30) REVERT: F 281 TYR cc_start: 0.8197 (m-80) cc_final: 0.7996 (m-80) REVERT: F 291 LEU cc_start: 0.8455 (mt) cc_final: 0.8181 (mt) REVERT: F 382 LYS cc_start: 0.8221 (ttpt) cc_final: 0.8005 (ttpp) REVERT: F 412 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7794 (tpp-160) REVERT: G 2 THR cc_start: 0.8088 (t) cc_final: 0.7661 (p) REVERT: G 43 LYS cc_start: 0.8185 (ttmm) cc_final: 0.7167 (tttt) REVERT: G 90 GLN cc_start: 0.8128 (mt0) cc_final: 0.7918 (mt0) REVERT: G 114 ILE cc_start: 0.8302 (tp) cc_final: 0.8059 (tt) REVERT: H 43 PHE cc_start: 0.7131 (m-80) cc_final: 0.6927 (m-10) outliers start: 43 outliers final: 35 residues processed: 717 average time/residue: 0.9001 time to fit residues: 929.0517 Evaluate side-chains 741 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 703 time to evaluate : 2.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 220 GLN Chi-restraints excluded: chain C residue 246 TYR Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 493 LYS Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 397 SER Chi-restraints excluded: chain D residue 415 SER Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 451 ASN Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 459 MET Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain F residue 412 ARG Chi-restraints excluded: chain F residue 452 ILE Chi-restraints excluded: chain G residue 15 ASN Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain H residue 33 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 282 optimal weight: 2.9990 chunk 257 optimal weight: 2.9990 chunk 274 optimal weight: 0.9990 chunk 165 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 248 optimal weight: 1.9990 chunk 259 optimal weight: 0.6980 chunk 273 optimal weight: 0.4980 chunk 180 optimal weight: 1.9990 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 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 GLN E 249 GLN F 57 ASN F 293 GLN F 308 GLN G 54 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.3407 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= 0.249 Angle : 0.509 6.239 32349 Z= 0.263 Chirality : 0.042 0.149 3842 Planarity : 0.004 0.054 4167 Dihedral : 6.194 85.076 3591 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.43 % Favored : 97.38 % Rotamer: Outliers : 1.74 % Allowed : 16.39 % Favored : 81.87 % 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: 0.61 (0.16), residues: 3089 helix: 1.15 (0.15), residues: 1250 sheet: -0.13 (0.23), residues: 521 loop : 0.05 (0.18), residues: 1318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 258 HIS 0.005 0.001 HIS D 367 PHE 0.013 0.001 PHE A 466 TYR 0.012 0.001 TYR F 449 ARG 0.010 0.000 ARG B 462 *********************** 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 757 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 715 time to evaluate : 2.823 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: A 66 LEU cc_start: 0.8278 (mt) cc_final: 0.8049 (mp) REVERT: A 91 LYS cc_start: 0.8212 (mttt) cc_final: 0.7899 (mttp) REVERT: A 129 SER cc_start: 0.8049 (m) cc_final: 0.7704 (t) REVERT: A 167 GLU cc_start: 0.7959 (tp30) cc_final: 0.7608 (tp30) REVERT: A 283 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.8030 (mp) REVERT: A 373 VAL cc_start: 0.8800 (p) cc_final: 0.8368 (m) REVERT: A 468 SER cc_start: 0.8490 (m) cc_final: 0.8235 (p) REVERT: A 475 LYS cc_start: 0.8037 (ttmm) cc_final: 0.7475 (mttp) REVERT: B 69 GLU cc_start: 0.7223 (mt-10) cc_final: 0.6887 (mt-10) REVERT: B 91 LYS cc_start: 0.8032 (mttt) cc_final: 0.7806 (mtmm) REVERT: B 118 ASP cc_start: 0.7963 (p0) cc_final: 0.7686 (p0) REVERT: B 123 ILE cc_start: 0.8376 (mm) cc_final: 0.8152 (mt) REVERT: B 159 VAL cc_start: 0.8423 (m) cc_final: 0.8157 (p) REVERT: B 183 ASP cc_start: 0.6914 (t0) cc_final: 0.6696 (t0) REVERT: B 199 LYS cc_start: 0.8282 (mttm) cc_final: 0.7995 (mtmm) REVERT: B 261 ASP cc_start: 0.7522 (m-30) cc_final: 0.7217 (m-30) REVERT: B 336 VAL cc_start: 0.8370 (m) cc_final: 0.8044 (t) REVERT: B 353 PHE cc_start: 0.7773 (t80) cc_final: 0.7517 (t80) REVERT: C 52 GLU cc_start: 0.6578 (mt-10) cc_final: 0.6175 (mt-10) REVERT: C 129 SER cc_start: 0.8472 (m) cc_final: 0.7973 (p) REVERT: C 133 VAL cc_start: 0.8684 (m) cc_final: 0.8465 (p) REVERT: C 146 GLU cc_start: 0.7928 (pt0) cc_final: 0.7542 (mt-10) REVERT: C 246 TYR cc_start: 0.8539 (OUTLIER) cc_final: 0.8044 (t80) REVERT: C 293 ARG cc_start: 0.8087 (ttp80) cc_final: 0.7762 (mtp180) REVERT: C 299 ASP cc_start: 0.7675 (p0) cc_final: 0.7388 (p0) REVERT: C 337 SER cc_start: 0.8191 (t) cc_final: 0.7848 (p) REVERT: C 361 LYS cc_start: 0.8344 (mttt) cc_final: 0.8068 (mttp) REVERT: C 393 LYS cc_start: 0.8305 (ttmt) cc_final: 0.8042 (ttmm) REVERT: C 446 LEU cc_start: 0.7978 (mt) cc_final: 0.7712 (mt) REVERT: D 12 LYS cc_start: 0.7808 (mtpp) cc_final: 0.7527 (mttm) REVERT: D 147 TYR cc_start: 0.8503 (m-10) cc_final: 0.7957 (m-10) REVERT: D 267 GLU cc_start: 0.7173 (mt-10) cc_final: 0.6803 (mt-10) REVERT: D 288 ASP cc_start: 0.7191 (m-30) cc_final: 0.6857 (m-30) REVERT: D 435 LYS cc_start: 0.8017 (mptt) cc_final: 0.7777 (mmmt) REVERT: E 192 ARG cc_start: 0.8097 (ptm160) cc_final: 0.7554 (ptm-80) REVERT: E 196 ASP cc_start: 0.7204 (m-30) cc_final: 0.6689 (m-30) REVERT: E 301 LYS cc_start: 0.8033 (mmtt) cc_final: 0.7717 (mmtt) REVERT: E 448 LYS cc_start: 0.8473 (mtpt) cc_final: 0.8110 (mtpt) REVERT: E 457 PHE cc_start: 0.7778 (m-80) cc_final: 0.7566 (m-80) REVERT: F 195 ASN cc_start: 0.8321 (t0) cc_final: 0.8084 (t0) REVERT: F 196 ASP cc_start: 0.7206 (t70) cc_final: 0.6894 (t0) REVERT: F 199 ARG cc_start: 0.7930 (ttp80) cc_final: 0.7658 (ttp-110) REVERT: F 215 VAL cc_start: 0.8381 (p) cc_final: 0.8056 (t) REVERT: F 245 ASP cc_start: 0.7296 (m-30) cc_final: 0.7019 (m-30) REVERT: F 291 LEU cc_start: 0.8444 (mt) cc_final: 0.8168 (mt) REVERT: F 412 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7795 (tpp-160) REVERT: G 2 THR cc_start: 0.8065 (t) cc_final: 0.7676 (p) REVERT: G 43 LYS cc_start: 0.8193 (ttmm) cc_final: 0.7178 (tttt) REVERT: G 90 GLN cc_start: 0.8178 (mt0) cc_final: 0.7901 (mt0) REVERT: G 114 ILE cc_start: 0.8311 (tp) cc_final: 0.8072 (tt) outliers start: 42 outliers final: 34 residues processed: 727 average time/residue: 0.9226 time to fit residues: 968.3212 Evaluate side-chains 737 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 700 time to evaluate : 2.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 220 GLN Chi-restraints excluded: chain C residue 246 TYR Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 493 LYS Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 397 SER Chi-restraints excluded: chain D residue 415 SER Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 451 ASN Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 459 MET Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain F residue 293 GLN Chi-restraints excluded: chain F residue 412 ARG Chi-restraints excluded: chain F residue 452 ILE Chi-restraints excluded: chain G residue 15 ASN Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 33 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 290 optimal weight: 0.9980 chunk 177 optimal weight: 0.5980 chunk 137 optimal weight: 0.5980 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: 1.9990 chunk 187 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 57 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 23836 Z= 0.298 Angle : 0.523 6.268 32349 Z= 0.271 Chirality : 0.043 0.155 3842 Planarity : 0.004 0.054 4167 Dihedral : 6.228 84.385 3591 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.56 % Favored : 97.25 % Rotamer: Outliers : 1.70 % Allowed : 16.60 % Favored : 81.71 % 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: 0.56 (0.16), residues: 3089 helix: 1.10 (0.15), residues: 1251 sheet: -0.13 (0.23), residues: 521 loop : 0.01 (0.18), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 258 HIS 0.005 0.001 HIS D 367 PHE 0.013 0.001 PHE F 166 TYR 0.012 0.001 TYR F 449 ARG 0.010 0.001 ARG B 462 ********************** 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 745 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 704 time to evaluate : 2.851 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: A 66 LEU cc_start: 0.8284 (mt) cc_final: 0.8062 (mp) REVERT: A 91 LYS cc_start: 0.8212 (mttt) cc_final: 0.7905 (mttp) REVERT: A 129 SER cc_start: 0.8055 (m) cc_final: 0.7710 (t) REVERT: A 167 GLU cc_start: 0.7963 (tp30) cc_final: 0.7615 (tp30) REVERT: A 283 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.8036 (mp) REVERT: A 373 VAL cc_start: 0.8800 (p) cc_final: 0.8373 (m) REVERT: A 468 SER cc_start: 0.8496 (m) cc_final: 0.8243 (p) REVERT: A 475 LYS cc_start: 0.8036 (ttmm) cc_final: 0.7474 (mttp) REVERT: B 69 GLU cc_start: 0.7233 (mt-10) cc_final: 0.6900 (mt-10) REVERT: B 91 LYS cc_start: 0.8036 (mttt) cc_final: 0.7813 (mtmm) REVERT: B 118 ASP cc_start: 0.7972 (p0) cc_final: 0.7689 (p0) REVERT: B 123 ILE cc_start: 0.8381 (mm) cc_final: 0.8161 (mt) REVERT: B 132 GLN cc_start: 0.7719 (mm-40) cc_final: 0.7215 (mm-40) REVERT: B 159 VAL cc_start: 0.8430 (m) cc_final: 0.8158 (p) REVERT: B 182 LEU cc_start: 0.8193 (mt) cc_final: 0.7959 (mm) REVERT: B 199 LYS cc_start: 0.8285 (mttm) cc_final: 0.8001 (mtmm) REVERT: B 261 ASP cc_start: 0.7527 (m-30) cc_final: 0.7225 (m-30) REVERT: B 336 VAL cc_start: 0.8372 (m) cc_final: 0.8040 (t) REVERT: B 353 PHE cc_start: 0.7773 (t80) cc_final: 0.7510 (t80) REVERT: C 52 GLU cc_start: 0.6582 (mt-10) cc_final: 0.6190 (mt-10) REVERT: C 129 SER cc_start: 0.8451 (m) cc_final: 0.7991 (p) REVERT: C 133 VAL cc_start: 0.8682 (m) cc_final: 0.8467 (p) REVERT: C 146 GLU cc_start: 0.7947 (pt0) cc_final: 0.7567 (mt-10) REVERT: C 246 TYR cc_start: 0.8545 (OUTLIER) cc_final: 0.8046 (t80) REVERT: C 293 ARG cc_start: 0.8114 (ttp80) cc_final: 0.7766 (mtp180) REVERT: C 299 ASP cc_start: 0.7708 (p0) cc_final: 0.7421 (p0) REVERT: C 337 SER cc_start: 0.8196 (t) cc_final: 0.7856 (p) REVERT: C 361 LYS cc_start: 0.8328 (mttt) cc_final: 0.8070 (mttp) REVERT: C 393 LYS cc_start: 0.8308 (ttmt) cc_final: 0.8045 (ttmm) REVERT: C 446 LEU cc_start: 0.7975 (mt) cc_final: 0.7721 (mt) REVERT: D 12 LYS cc_start: 0.7871 (mtpp) cc_final: 0.7587 (mttm) REVERT: D 267 GLU cc_start: 0.7182 (mt-10) cc_final: 0.6812 (mt-10) REVERT: D 288 ASP cc_start: 0.7202 (m-30) cc_final: 0.6857 (m-30) REVERT: D 382 LYS cc_start: 0.8168 (tttt) cc_final: 0.7877 (ttmm) REVERT: D 435 LYS cc_start: 0.8017 (mptt) cc_final: 0.7777 (mmmt) REVERT: E 163 LYS cc_start: 0.7694 (ttpt) cc_final: 0.7460 (ttpp) REVERT: E 176 LYS cc_start: 0.8079 (mttm) cc_final: 0.7876 (mtpp) REVERT: E 192 ARG cc_start: 0.8091 (ptm160) cc_final: 0.7554 (ptm-80) REVERT: E 196 ASP cc_start: 0.7214 (m-30) cc_final: 0.6695 (m-30) REVERT: E 301 LYS cc_start: 0.8031 (mmtt) cc_final: 0.7718 (mmtt) REVERT: E 382 LYS cc_start: 0.8104 (tttp) cc_final: 0.7889 (ttmm) REVERT: E 448 LYS cc_start: 0.8478 (mtpt) cc_final: 0.8082 (mtpp) REVERT: E 454 GLU cc_start: 0.7680 (tt0) cc_final: 0.7420 (tt0) REVERT: E 457 PHE cc_start: 0.7773 (m-80) cc_final: 0.7554 (m-80) REVERT: F 195 ASN cc_start: 0.8327 (t0) cc_final: 0.8092 (t0) REVERT: F 196 ASP cc_start: 0.7210 (t70) cc_final: 0.6897 (t0) REVERT: F 199 ARG cc_start: 0.7964 (ttp80) cc_final: 0.7689 (ttp-110) REVERT: F 215 VAL cc_start: 0.8382 (p) cc_final: 0.8059 (t) REVERT: F 245 ASP cc_start: 0.7295 (m-30) cc_final: 0.7031 (m-30) REVERT: F 291 LEU cc_start: 0.8365 (mt) cc_final: 0.8111 (mt) REVERT: F 412 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7797 (tpp-160) REVERT: G 2 THR cc_start: 0.8071 (t) cc_final: 0.7685 (p) REVERT: G 43 LYS cc_start: 0.8211 (ttmm) cc_final: 0.7166 (tttt) REVERT: G 90 GLN cc_start: 0.8186 (mt0) cc_final: 0.7910 (mt0) REVERT: G 114 ILE cc_start: 0.8317 (tp) cc_final: 0.8078 (tt) outliers start: 41 outliers final: 36 residues processed: 718 average time/residue: 0.8985 time to fit residues: 924.1026 Evaluate side-chains 745 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 706 time to evaluate : 2.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 220 GLN Chi-restraints excluded: chain C residue 246 TYR Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 493 LYS Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 397 SER Chi-restraints excluded: chain D residue 415 SER Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 451 ASN Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 132 GLU Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 459 MET Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain F residue 412 ARG Chi-restraints excluded: chain F residue 452 ILE Chi-restraints excluded: chain G residue 15 ASN Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 129 SER Chi-restraints excluded: chain H residue 33 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 223 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 243 optimal weight: 0.6980 chunk 101 optimal weight: 0.6980 chunk 249 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 213 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 57 ASN G 54 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.103388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.094257 restraints weight = 101524.684| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.86 r_work: 0.3113 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 23836 Z= 0.198 Angle : 0.498 6.543 32349 Z= 0.256 Chirality : 0.042 0.142 3842 Planarity : 0.004 0.053 4167 Dihedral : 6.045 85.980 3591 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.19 % Allowed : 1.94 % Favored : 97.86 % Rotamer: Outliers : 1.61 % Allowed : 16.85 % Favored : 81.54 % 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: 0.75 (0.16), residues: 3089 helix: 1.28 (0.15), residues: 1252 sheet: -0.07 (0.23), residues: 517 loop : 0.11 (0.18), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 258 HIS 0.003 0.001 HIS D 367 PHE 0.010 0.001 PHE H 43 TYR 0.012 0.001 TYR F 449 ARG 0.010 0.000 ARG B 462 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14108.87 seconds wall clock time: 242 minutes 53.01 seconds (14573.01 seconds total)