Starting phenix.real_space_refine on Tue Feb 13 23:12:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c4e_16425/02_2024/8c4e_16425_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c4e_16425/02_2024/8c4e_16425.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c4e_16425/02_2024/8c4e_16425.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c4e_16425/02_2024/8c4e_16425.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c4e_16425/02_2024/8c4e_16425_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c4e_16425/02_2024/8c4e_16425_trim_updated.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 24 5.49 5 Mg 8 5.21 5 S 188 5.16 5 C 18152 2.51 5 N 4896 2.21 5 O 5528 1.98 5 H 28304 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 57": "OE1" <-> "OE2" Residue "A GLU 72": "OE1" <-> "OE2" Residue "A GLU 107": "OE1" <-> "OE2" Residue "A GLU 205": "OE1" <-> "OE2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 276": "OE1" <-> "OE2" Residue "A TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 361": "OE1" <-> "OE2" Residue "A GLU 364": "OE1" <-> "OE2" Residue "B ASP 25": "OD1" <-> "OD2" Residue "B PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 51": "OD1" <-> "OD2" Residue "B TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 72": "OE1" <-> "OE2" Residue "B ASP 80": "OD1" <-> "OD2" Residue "B GLU 99": "OE1" <-> "OE2" Residue "B GLU 207": "OE1" <-> "OE2" Residue "B PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 270": "OE1" <-> "OE2" Residue "B ASP 286": "OD1" <-> "OD2" Residue "B ASP 363": "OD1" <-> "OD2" Residue "C TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 83": "OE1" <-> "OE2" Residue "C GLU 99": "OE1" <-> "OE2" Residue "C GLU 100": "OE1" <-> "OE2" Residue "C TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 211": "OD1" <-> "OD2" Residue "C ASP 222": "OD1" <-> "OD2" Residue "C GLU 237": "OE1" <-> "OE2" Residue "C ASP 292": "OD1" <-> "OD2" Residue "C GLU 316": "OE1" <-> "OE2" Residue "C GLU 364": "OE1" <-> "OE2" Residue "D ASP 25": "OD1" <-> "OD2" Residue "D PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 72": "OE1" <-> "OE2" Residue "D TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 154": "OD1" <-> "OD2" Residue "D TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 187": "OD1" <-> "OD2" Residue "D GLU 205": "OE1" <-> "OE2" Residue "D ASP 211": "OD1" <-> "OD2" Residue "D ASP 286": "OD1" <-> "OD2" Residue "D ASP 288": "OD1" <-> "OD2" Residue "D GLU 364": "OE1" <-> "OE2" Residue "E ASP 25": "OD1" <-> "OD2" Residue "E TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 72": "OE1" <-> "OE2" Residue "E GLU 167": "OE1" <-> "OE2" Residue "E TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 292": "OD1" <-> "OD2" Residue "E GLU 316": "OE1" <-> "OE2" Residue "E GLU 361": "OE1" <-> "OE2" Residue "F ASP 24": "OD1" <-> "OD2" Residue "F PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 224": "OE1" <-> "OE2" Residue "F PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 270": "OE1" <-> "OE2" Residue "F ASP 286": "OD1" <-> "OD2" Residue "F GLU 364": "OE1" <-> "OE2" Residue "G TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 99": "OE1" <-> "OE2" Residue "G TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 237": "OE1" <-> "OE2" Residue "G GLU 241": "OE1" <-> "OE2" Residue "G PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 361": "OE1" <-> "OE2" Residue "H GLU 93": "OE1" <-> "OE2" Residue "H TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 167": "OE1" <-> "OE2" Residue "H TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 222": "OD1" <-> "OD2" Residue "H GLU 226": "OE1" <-> "OE2" Residue "H PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 286": "OD1" <-> "OD2" Residue "K ASP 541": "OD1" <-> "OD2" Residue "K PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ASP 569": "OD1" <-> "OD2" Residue "K GLU 608": "OE1" <-> "OE2" Residue "K ASP 640": "OD1" <-> "OD2" Residue "K GLU 663": "OE1" <-> "OE2" Residue "L GLU 544": "OE1" <-> "OE2" Residue "L ASP 579": "OD1" <-> "OD2" Residue "L GLU 608": "OE1" <-> "OE2" Residue "L GLU 621": "OE1" <-> "OE2" Residue "L GLU 629": "OE1" <-> "OE2" Residue "L GLU 638": "OE1" <-> "OE2" Residue "L ASP 640": "OD1" <-> "OD2" Residue "L GLU 663": "OE1" <-> "OE2" Residue "M ASP 541": "OD1" <-> "OD2" Residue "M GLU 544": "OE1" <-> "OE2" Residue "M PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ASP 569": "OD1" <-> "OD2" Residue "M GLU 608": "OE1" <-> "OE2" Residue "M GLU 617": "OE1" <-> "OE2" Residue "M GLU 638": "OE1" <-> "OE2" Residue "N ASP 541": "OD1" <-> "OD2" Residue "N ASP 557": "OD1" <-> "OD2" Residue "N GLU 574": "OE1" <-> "OE2" Residue "N GLU 598": "OE1" <-> "OE2" Residue "N GLU 608": "OE1" <-> "OE2" Residue "N GLU 621": "OE1" <-> "OE2" Residue "N PHE 626": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 57100 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 5751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5751 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 5751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5751 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 19, 'TRANS': 349} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 5751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5751 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 19, 'TRANS': 349} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 5751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5751 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 19, 'TRANS': 349} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 5751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5751 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 19, 'TRANS': 349} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 5751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5751 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 19, 'TRANS': 349} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 5751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5751 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 19, 'TRANS': 349} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 5751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5751 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 19, 'TRANS': 349} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 2707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2707 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 9, 'TRANS': 162} Chain: "L" Number of atoms: 2707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2707 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 9, 'TRANS': 162} Chain: "M" Number of atoms: 2707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2707 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 9, 'TRANS': 162} Chain: "N" Number of atoms: 2707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2707 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 9, 'TRANS': 162} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 19.36, per 1000 atoms: 0.34 Number of scatterers: 57100 At special positions: 0 Unit cell: (117.292, 97.468, 276.71, 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 188 16.00 P 24 15.00 Mg 8 11.99 O 5528 8.00 N 4896 7.00 C 18152 6.00 H 28304 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: 39.28 Conformation dependent library (CDL) restraints added in 4.9 seconds 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6760 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 201 helices and 37 sheets defined 45.3% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.74 Creating SS restraints... Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 79 through 91 Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 113 through 125 Processing helix chain 'A' and resid 137 through 144 Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 185 through 196 removed outlier: 3.538A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 216 Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 252 through 256 removed outlier: 3.650A pdb=" N ARG A 256 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 261 Processing helix chain 'A' and resid 264 through 267 Processing helix chain 'A' and resid 274 through 281 Processing helix chain 'A' and resid 290 through 294 Processing helix chain 'A' and resid 302 through 304 No H-bonds generated for 'chain 'A' and resid 302 through 304' Processing helix chain 'A' and resid 309 through 318 Processing helix chain 'A' and resid 335 through 348 removed outlier: 5.231A pdb=" N VAL A 339 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA A 347 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 365 Processing helix chain 'A' and resid 367 through 370 Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 79 through 91 Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 113 through 125 Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 182 through 194 removed outlier: 3.752A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 216 Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 252 through 261 removed outlier: 3.596A pdb=" N ARG B 256 " --> pdb=" O GLU B 253 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N CYS B 257 " --> pdb=" O ARG B 254 " (cutoff:3.500A) Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 274 through 283 Processing helix chain 'B' and resid 287 through 294 removed outlier: 3.519A pdb=" N ARG B 290 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N LYS B 291 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 304 No H-bonds generated for 'chain 'B' and resid 302 through 304' Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 338 through 348 Processing helix chain 'B' and resid 359 through 365 Processing helix chain 'B' and resid 367 through 373 removed outlier: 3.658A pdb=" N LYS B 373 " --> pdb=" O VAL B 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 79 through 91 Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 113 through 125 Processing helix chain 'C' and resid 137 through 144 Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 182 through 196 removed outlier: 3.904A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 252 through 261 removed outlier: 3.536A pdb=" N ARG C 256 " --> pdb=" O GLU C 253 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N CYS C 257 " --> pdb=" O ARG C 254 " (cutoff:3.500A) Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 264 through 267 Processing helix chain 'C' and resid 274 through 283 Processing helix chain 'C' and resid 290 through 294 Processing helix chain 'C' and resid 302 through 304 No H-bonds generated for 'chain 'C' and resid 302 through 304' Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 335 through 348 removed outlier: 5.255A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA C 347 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 352 No H-bonds generated for 'chain 'C' and resid 350 through 352' Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'C' and resid 367 through 373 removed outlier: 3.538A pdb=" N LYS C 373 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 60 Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'D' and resid 79 through 91 Processing helix chain 'D' and resid 98 through 100 No H-bonds generated for 'chain 'D' and resid 98 through 100' Processing helix chain 'D' and resid 113 through 125 Processing helix chain 'D' and resid 137 through 145 Processing helix chain 'D' and resid 172 through 174 No H-bonds generated for 'chain 'D' and resid 172 through 174' Processing helix chain 'D' and resid 182 through 196 removed outlier: 3.756A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ARG D 196 " --> pdb=" O ILE D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 216 Processing helix chain 'D' and resid 223 through 232 Processing helix chain 'D' and resid 252 through 261 removed outlier: 3.581A pdb=" N ARG D 256 " --> pdb=" O GLU D 253 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N CYS D 257 " --> pdb=" O ARG D 254 " (cutoff:3.500A) Proline residue: D 258 - end of helix Processing helix chain 'D' and resid 264 through 267 Processing helix chain 'D' and resid 274 through 283 Processing helix chain 'D' and resid 290 through 294 Processing helix chain 'D' and resid 302 through 304 No H-bonds generated for 'chain 'D' and resid 302 through 304' Processing helix chain 'D' and resid 309 through 320 Processing helix chain 'D' and resid 338 through 348 Processing helix chain 'D' and resid 350 through 352 No H-bonds generated for 'chain 'D' and resid 350 through 352' Processing helix chain 'D' and resid 359 through 365 Processing helix chain 'D' and resid 367 through 373 removed outlier: 3.500A pdb=" N LYS D 373 " --> pdb=" O VAL D 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 60 Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 79 through 91 Processing helix chain 'E' and resid 98 through 100 No H-bonds generated for 'chain 'E' and resid 98 through 100' Processing helix chain 'E' and resid 113 through 125 Processing helix chain 'E' and resid 137 through 144 Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 182 through 196 removed outlier: 4.157A pdb=" N GLU E 195 " --> pdb=" O LYS E 191 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ARG E 196 " --> pdb=" O ILE E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 216 Processing helix chain 'E' and resid 223 through 232 Processing helix chain 'E' and resid 252 through 261 removed outlier: 3.653A pdb=" N ARG E 256 " --> pdb=" O GLU E 253 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N CYS E 257 " --> pdb=" O ARG E 254 " (cutoff:3.500A) Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 264 through 267 Processing helix chain 'E' and resid 274 through 283 Processing helix chain 'E' and resid 290 through 294 Processing helix chain 'E' and resid 302 through 304 No H-bonds generated for 'chain 'E' and resid 302 through 304' Processing helix chain 'E' and resid 309 through 320 Processing helix chain 'E' and resid 338 through 348 Processing helix chain 'E' and resid 350 through 352 No H-bonds generated for 'chain 'E' and resid 350 through 352' Processing helix chain 'E' and resid 359 through 365 Processing helix chain 'E' and resid 367 through 373 removed outlier: 3.576A pdb=" N LYS E 373 " --> pdb=" O VAL E 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 60 Processing helix chain 'F' and resid 62 through 64 No H-bonds generated for 'chain 'F' and resid 62 through 64' Processing helix chain 'F' and resid 79 through 91 Processing helix chain 'F' and resid 98 through 100 No H-bonds generated for 'chain 'F' and resid 98 through 100' Processing helix chain 'F' and resid 113 through 125 Processing helix chain 'F' and resid 137 through 144 Processing helix chain 'F' and resid 172 through 174 No H-bonds generated for 'chain 'F' and resid 172 through 174' Processing helix chain 'F' and resid 182 through 196 removed outlier: 4.355A pdb=" N GLU F 195 " --> pdb=" O LYS F 191 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ARG F 196 " --> pdb=" O ILE F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 203 through 216 removed outlier: 3.533A pdb=" N LYS F 215 " --> pdb=" O ASP F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 223 through 232 Processing helix chain 'F' and resid 252 through 261 removed outlier: 3.652A pdb=" N ARG F 256 " --> pdb=" O GLU F 253 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N CYS F 257 " --> pdb=" O ARG F 254 " (cutoff:3.500A) Proline residue: F 258 - end of helix Processing helix chain 'F' and resid 264 through 267 Processing helix chain 'F' and resid 274 through 283 Processing helix chain 'F' and resid 290 through 294 Processing helix chain 'F' and resid 302 through 304 No H-bonds generated for 'chain 'F' and resid 302 through 304' Processing helix chain 'F' and resid 309 through 320 Processing helix chain 'F' and resid 338 through 348 Processing helix chain 'F' and resid 350 through 352 No H-bonds generated for 'chain 'F' and resid 350 through 352' Processing helix chain 'F' and resid 359 through 365 Processing helix chain 'F' and resid 367 through 373 removed outlier: 3.659A pdb=" N LYS F 373 " --> pdb=" O VAL F 370 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 60 Processing helix chain 'G' and resid 62 through 64 No H-bonds generated for 'chain 'G' and resid 62 through 64' Processing helix chain 'G' and resid 79 through 91 Processing helix chain 'G' and resid 98 through 100 No H-bonds generated for 'chain 'G' and resid 98 through 100' Processing helix chain 'G' and resid 113 through 125 Processing helix chain 'G' and resid 137 through 144 Processing helix chain 'G' and resid 172 through 174 No H-bonds generated for 'chain 'G' and resid 172 through 174' Processing helix chain 'G' and resid 182 through 196 removed outlier: 3.784A pdb=" N THR G 194 " --> pdb=" O MET G 190 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLU G 195 " --> pdb=" O LYS G 191 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ARG G 196 " --> pdb=" O ILE G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 203 through 216 Processing helix chain 'G' and resid 223 through 232 Processing helix chain 'G' and resid 252 through 261 removed outlier: 3.567A pdb=" N ARG G 256 " --> pdb=" O GLU G 253 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N CYS G 257 " --> pdb=" O ARG G 254 " (cutoff:3.500A) Proline residue: G 258 - end of helix Processing helix chain 'G' and resid 264 through 267 Processing helix chain 'G' and resid 274 through 283 Processing helix chain 'G' and resid 287 through 294 removed outlier: 3.566A pdb=" N ARG G 290 " --> pdb=" O ILE G 287 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N LYS G 291 " --> pdb=" O ASP G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 302 through 304 No H-bonds generated for 'chain 'G' and resid 302 through 304' Processing helix chain 'G' and resid 309 through 320 Processing helix chain 'G' and resid 338 through 348 Processing helix chain 'G' and resid 350 through 352 No H-bonds generated for 'chain 'G' and resid 350 through 352' Processing helix chain 'G' and resid 359 through 365 Processing helix chain 'G' and resid 367 through 373 removed outlier: 3.738A pdb=" N LYS G 373 " --> pdb=" O VAL G 370 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 60 Processing helix chain 'H' and resid 62 through 64 No H-bonds generated for 'chain 'H' and resid 62 through 64' Processing helix chain 'H' and resid 79 through 91 Processing helix chain 'H' and resid 98 through 100 No H-bonds generated for 'chain 'H' and resid 98 through 100' Processing helix chain 'H' and resid 113 through 125 Processing helix chain 'H' and resid 137 through 145 Processing helix chain 'H' and resid 172 through 174 No H-bonds generated for 'chain 'H' and resid 172 through 174' Processing helix chain 'H' and resid 182 through 196 removed outlier: 3.776A pdb=" N THR H 194 " --> pdb=" O MET H 190 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLU H 195 " --> pdb=" O LYS H 191 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ARG H 196 " --> pdb=" O ILE H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 203 through 216 Processing helix chain 'H' and resid 223 through 232 Processing helix chain 'H' and resid 252 through 256 removed outlier: 3.660A pdb=" N ARG H 256 " --> pdb=" O GLU H 253 " (cutoff:3.500A) Processing helix chain 'H' and resid 258 through 261 Processing helix chain 'H' and resid 264 through 267 Processing helix chain 'H' and resid 274 through 283 Processing helix chain 'H' and resid 287 through 294 removed outlier: 4.202A pdb=" N LYS H 291 " --> pdb=" O ILE H 287 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N ASP H 292 " --> pdb=" O ASP H 288 " (cutoff:3.500A) Processing helix chain 'H' and resid 302 through 304 No H-bonds generated for 'chain 'H' and resid 302 through 304' Processing helix chain 'H' and resid 309 through 320 Processing helix chain 'H' and resid 338 through 348 Processing helix chain 'H' and resid 351 through 354 removed outlier: 3.899A pdb=" N GLN H 354 " --> pdb=" O THR H 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 351 through 354' Processing helix chain 'H' and resid 359 through 365 Processing helix chain 'H' and resid 367 through 373 removed outlier: 3.856A pdb=" N LYS H 373 " --> pdb=" O VAL H 370 " (cutoff:3.500A) Processing helix chain 'K' and resid 526 through 528 No H-bonds generated for 'chain 'K' and resid 526 through 528' Processing helix chain 'K' and resid 532 through 536 Processing helix chain 'K' and resid 542 through 553 Processing helix chain 'K' and resid 562 through 575 Processing helix chain 'K' and resid 580 through 595 removed outlier: 3.601A pdb=" N GLN K 589 " --> pdb=" O ALA K 585 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ASP K 592 " --> pdb=" O ALA K 588 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE K 593 " --> pdb=" O GLN K 589 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ASP K 594 " --> pdb=" O CYS K 590 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N LYS K 595 " --> pdb=" O SER K 591 " (cutoff:3.500A) Processing helix chain 'K' and resid 597 through 612 Processing helix chain 'K' and resid 616 through 630 Processing helix chain 'K' and resid 636 through 638 No H-bonds generated for 'chain 'K' and resid 636 through 638' Processing helix chain 'K' and resid 641 through 650 Processing helix chain 'K' and resid 655 through 657 No H-bonds generated for 'chain 'K' and resid 655 through 657' Processing helix chain 'K' and resid 679 through 681 No H-bonds generated for 'chain 'K' and resid 679 through 681' Processing helix chain 'L' and resid 524 through 527 removed outlier: 3.995A pdb=" N SER L 527 " --> pdb=" O SER L 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 524 through 527' Processing helix chain 'L' and resid 532 through 536 removed outlier: 3.576A pdb=" N HIS L 536 " --> pdb=" O VAL L 532 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 532 through 536' Processing helix chain 'L' and resid 542 through 553 Processing helix chain 'L' and resid 562 through 575 Processing helix chain 'L' and resid 580 through 595 removed outlier: 4.300A pdb=" N ASP L 592 " --> pdb=" O ALA L 588 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE L 593 " --> pdb=" O GLN L 589 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ASP L 594 " --> pdb=" O CYS L 590 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N LYS L 595 " --> pdb=" O SER L 591 " (cutoff:3.500A) Processing helix chain 'L' and resid 597 through 612 Processing helix chain 'L' and resid 616 through 630 Processing helix chain 'L' and resid 636 through 638 No H-bonds generated for 'chain 'L' and resid 636 through 638' Processing helix chain 'L' and resid 641 through 650 Processing helix chain 'L' and resid 655 through 657 No H-bonds generated for 'chain 'L' and resid 655 through 657' Processing helix chain 'L' and resid 677 through 682 removed outlier: 3.698A pdb=" N LEU L 681 " --> pdb=" O THR L 677 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N HIS L 682 " --> pdb=" O VAL L 678 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 677 through 682' Processing helix chain 'M' and resid 526 through 528 No H-bonds generated for 'chain 'M' and resid 526 through 528' Processing helix chain 'M' and resid 532 through 536 Processing helix chain 'M' and resid 542 through 553 Processing helix chain 'M' and resid 562 through 575 Processing helix chain 'M' and resid 580 through 589 Processing helix chain 'M' and resid 593 through 595 No H-bonds generated for 'chain 'M' and resid 593 through 595' Processing helix chain 'M' and resid 597 through 611 Processing helix chain 'M' and resid 616 through 630 Processing helix chain 'M' and resid 636 through 638 No H-bonds generated for 'chain 'M' and resid 636 through 638' Processing helix chain 'M' and resid 641 through 650 Processing helix chain 'M' and resid 655 through 657 No H-bonds generated for 'chain 'M' and resid 655 through 657' Processing helix chain 'N' and resid 526 through 528 No H-bonds generated for 'chain 'N' and resid 526 through 528' Processing helix chain 'N' and resid 532 through 536 Processing helix chain 'N' and resid 542 through 553 Processing helix chain 'N' and resid 562 through 575 Processing helix chain 'N' and resid 580 through 595 removed outlier: 3.907A pdb=" N ASP N 592 " --> pdb=" O ALA N 588 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE N 593 " --> pdb=" O GLN N 589 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N ASP N 594 " --> pdb=" O CYS N 590 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N LYS N 595 " --> pdb=" O SER N 591 " (cutoff:3.500A) Processing helix chain 'N' and resid 597 through 611 Processing helix chain 'N' and resid 616 through 630 Processing helix chain 'N' and resid 636 through 638 No H-bonds generated for 'chain 'N' and resid 636 through 638' Processing helix chain 'N' and resid 641 through 650 Processing helix chain 'N' and resid 655 through 657 No H-bonds generated for 'chain 'N' and resid 655 through 657' Processing sheet with id= A, first strand: chain 'A' and resid 52 through 54 Processing sheet with id= B, first strand: chain 'A' and resid 103 through 107 Processing sheet with id= C, first strand: chain 'A' and resid 297 through 300 removed outlier: 6.399A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 238 through 241 Processing sheet with id= E, first strand: chain 'B' and resid 132 through 136 removed outlier: 6.579A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 35 through 38 Processing sheet with id= G, first strand: chain 'B' and resid 297 through 300 removed outlier: 6.321A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 238 through 241 Processing sheet with id= I, first strand: chain 'C' and resid 132 through 136 removed outlier: 6.679A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 35 through 38 Processing sheet with id= K, first strand: chain 'C' and resid 297 through 300 removed outlier: 6.449A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 238 through 241 Processing sheet with id= M, first strand: chain 'D' and resid 8 through 12 Processing sheet with id= N, first strand: chain 'D' and resid 35 through 38 Processing sheet with id= O, first strand: chain 'D' and resid 103 through 107 Processing sheet with id= P, first strand: chain 'D' and resid 297 through 300 removed outlier: 6.408A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 238 through 241 Processing sheet with id= R, first strand: chain 'E' and resid 8 through 12 Processing sheet with id= S, first strand: chain 'E' and resid 35 through 38 Processing sheet with id= T, first strand: chain 'E' and resid 103 through 107 Processing sheet with id= U, first strand: chain 'E' and resid 297 through 300 removed outlier: 6.434A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 238 through 241 Processing sheet with id= W, first strand: chain 'F' and resid 8 through 12 Processing sheet with id= X, first strand: chain 'F' and resid 35 through 38 Processing sheet with id= Y, first strand: chain 'F' and resid 103 through 107 Processing sheet with id= Z, first strand: chain 'F' and resid 297 through 300 removed outlier: 6.438A pdb=" N ILE F 151 " --> pdb=" O VAL F 298 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N SER F 300 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LEU F 153 " --> pdb=" O SER F 300 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'F' and resid 238 through 241 Processing sheet with id= AB, first strand: chain 'G' and resid 8 through 12 Processing sheet with id= AC, first strand: chain 'G' and resid 35 through 38 Processing sheet with id= AD, first strand: chain 'G' and resid 103 through 107 Processing sheet with id= AE, first strand: chain 'G' and resid 297 through 300 removed outlier: 6.302A pdb=" N ILE G 151 " --> pdb=" O VAL G 298 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N SER G 300 " --> pdb=" O ILE G 151 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LEU G 153 " --> pdb=" O SER G 300 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'G' and resid 238 through 241 Processing sheet with id= AG, first strand: chain 'H' and resid 8 through 12 Processing sheet with id= AH, first strand: chain 'H' and resid 35 through 38 Processing sheet with id= AI, first strand: chain 'H' and resid 103 through 107 Processing sheet with id= AJ, first strand: chain 'H' and resid 297 through 300 removed outlier: 6.381A pdb=" N ILE H 151 " --> pdb=" O VAL H 298 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N SER H 300 " --> pdb=" O ILE H 151 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LEU H 153 " --> pdb=" O SER H 300 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'H' and resid 238 through 241 1066 hydrogen bonds defined for protein. 2850 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: 19.75 Time building geometry restraints manager: 41.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 28260 1.03 - 1.23: 172 1.23 - 1.42: 11941 1.42 - 1.62: 17011 1.62 - 1.81: 332 Bond restraints: 57716 Sorted by residual: bond pdb=" O3 PO4 D 803 " pdb=" P PO4 D 803 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 8.90e+00 bond pdb=" O3 PO4 E 803 " pdb=" P PO4 E 803 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 8.90e+00 bond pdb=" O3 PO4 H 802 " pdb=" P PO4 H 802 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 8.88e+00 bond pdb=" O4 PO4 F 803 " pdb=" P PO4 F 803 " ideal model delta sigma weight residual 1.568 1.509 0.059 2.00e-02 2.50e+03 8.79e+00 bond pdb=" CE1 HIC F 73 " pdb=" NE2 HIC F 73 " ideal model delta sigma weight residual 1.347 1.406 -0.059 2.00e-02 2.50e+03 8.74e+00 ... (remaining 57711 not shown) Histogram of bond angle deviations from ideal: 98.32 - 105.93: 853 105.93 - 113.54: 69047 113.54 - 121.15: 22789 121.15 - 128.77: 11456 128.77 - 136.38: 223 Bond angle restraints: 104368 Sorted by residual: angle pdb=" N ILE A 282 " pdb=" CA ILE A 282 " pdb=" C ILE A 282 " ideal model delta sigma weight residual 110.21 104.07 6.14 1.13e+00 7.83e-01 2.95e+01 angle pdb=" C GLY B 42 " pdb=" N VAL B 43 " pdb=" CA VAL B 43 " ideal model delta sigma weight residual 121.70 130.34 -8.64 1.80e+00 3.09e-01 2.30e+01 angle pdb=" C GLY G 42 " pdb=" N VAL G 43 " pdb=" CA VAL G 43 " ideal model delta sigma weight residual 121.70 129.52 -7.82 1.80e+00 3.09e-01 1.89e+01 angle pdb=" C GLY C 42 " pdb=" N VAL C 43 " pdb=" CA VAL C 43 " ideal model delta sigma weight residual 121.70 129.36 -7.66 1.80e+00 3.09e-01 1.81e+01 angle pdb=" C GLY D 42 " pdb=" N VAL D 43 " pdb=" CA VAL D 43 " ideal model delta sigma weight residual 121.70 129.22 -7.52 1.80e+00 3.09e-01 1.74e+01 ... (remaining 104363 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.05: 25943 31.05 - 62.09: 1138 62.09 - 93.14: 87 93.14 - 124.18: 13 124.18 - 155.23: 11 Dihedral angle restraints: 27192 sinusoidal: 14972 harmonic: 12220 Sorted by residual: dihedral pdb=" CA VAL A 9 " pdb=" C VAL A 9 " pdb=" N CYS A 10 " pdb=" CA CYS A 10 " ideal model delta harmonic sigma weight residual -180.00 -145.81 -34.19 0 5.00e+00 4.00e-02 4.68e+01 dihedral pdb=" O2A ADP E 802 " pdb=" O3A ADP E 802 " pdb=" PA ADP E 802 " pdb=" PB ADP E 802 " ideal model delta sinusoidal sigma weight residual -60.00 95.23 -155.23 1 2.00e+01 2.50e-03 4.58e+01 dihedral pdb=" O2A ADP H 803 " pdb=" O3A ADP H 803 " pdb=" PA ADP H 803 " pdb=" PB ADP H 803 " ideal model delta sinusoidal sigma weight residual -60.00 94.38 -154.38 1 2.00e+01 2.50e-03 4.56e+01 ... (remaining 27189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2888 0.036 - 0.072: 1101 0.072 - 0.108: 331 0.108 - 0.144: 103 0.144 - 0.180: 5 Chirality restraints: 4428 Sorted by residual: chirality pdb=" CB ILE A 76 " pdb=" CA ILE A 76 " pdb=" CG1 ILE A 76 " pdb=" CG2 ILE A 76 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.14e-01 chirality pdb=" CB VAL A 201 " pdb=" CA VAL A 201 " pdb=" CG1 VAL A 201 " pdb=" CG2 VAL A 201 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.07e-01 chirality pdb=" CA ILE A 282 " pdb=" N ILE A 282 " pdb=" C ILE A 282 " pdb=" CB ILE A 282 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.40e-01 ... (remaining 4425 not shown) Planarity restraints: 8544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 28 " 0.157 9.50e-02 1.11e+02 5.26e-02 3.51e+00 pdb=" NE ARG F 28 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG F 28 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG F 28 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG F 28 " 0.001 2.00e-02 2.50e+03 pdb="HH11 ARG F 28 " -0.006 2.00e-02 2.50e+03 pdb="HH12 ARG F 28 " -0.001 2.00e-02 2.50e+03 pdb="HH21 ARG F 28 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG F 28 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN H 12 " -0.007 2.00e-02 2.50e+03 1.49e-02 2.22e+00 pdb=" C ASN H 12 " 0.026 2.00e-02 2.50e+03 pdb=" O ASN H 12 " -0.010 2.00e-02 2.50e+03 pdb=" N GLY H 13 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 128 " 0.005 2.00e-02 2.50e+03 1.15e-02 1.99e+00 pdb=" CG ASN E 128 " -0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN E 128 " 0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN E 128 " 0.003 2.00e-02 2.50e+03 pdb="HD21 ASN E 128 " 0.005 2.00e-02 2.50e+03 pdb="HD22 ASN E 128 " -0.001 2.00e-02 2.50e+03 ... (remaining 8541 not shown) Histogram of nonbonded interaction distances: 1.32 - 1.98: 652 1.98 - 2.63: 75325 2.63 - 3.29: 181123 3.29 - 3.94: 241308 3.94 - 4.60: 373475 Nonbonded interactions: 871883 Sorted by model distance: nonbonded pdb=" HZ2 LYS G 213 " pdb=" O2' ADP G 402 " model vdw 1.323 1.850 nonbonded pdb=" HZ1 LYS H 213 " pdb=" O2' ADP H 803 " model vdw 1.339 1.850 nonbonded pdb=" HZ1 LYS F 213 " pdb=" O2' ADP F 802 " model vdw 1.353 1.850 nonbonded pdb=" HZ1 LYS D 213 " pdb=" O2' ADP D 802 " model vdw 1.391 1.850 nonbonded pdb=" HZ2 LYS C 213 " pdb=" O2' ADP C 401 " model vdw 1.431 1.850 ... (remaining 871878 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 6 through 375) selection = (chain 'B' and resid 6 through 375) selection = (chain 'C' and resid 6 through 375) selection = (chain 'D' and resid 6 through 375) selection = (chain 'E' and resid 6 through 375) selection = (chain 'F' and resid 6 through 375) selection = (chain 'G' and resid 6 through 375) selection = (chain 'H' and resid 6 through 375) } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } 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: 7.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.640 Extract box with map and model: 26.520 Check model and map are aligned: 0.660 Set scattering table: 0.410 Process input model: 148.850 Find NCS groups from input model: 2.410 Set up NCS constraints: 0.250 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:9.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 197.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 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 : 0.005 0.060 29412 Z= 0.305 Angle : 0.657 8.641 39884 Z= 0.345 Chirality : 0.043 0.180 4428 Planarity : 0.004 0.069 5104 Dihedral : 16.878 155.228 10968 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.47 % Favored : 97.39 % Rotamer: Outliers : 1.13 % Allowed : 11.35 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 (0.14), residues: 3600 helix: 0.27 (0.13), residues: 1554 sheet: -0.15 (0.29), residues: 320 loop : 0.83 (0.16), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 340 HIS 0.005 0.001 HIS F 161 PHE 0.020 0.002 PHE B 266 TYR 0.017 0.001 TYR E 143 ARG 0.010 0.001 ARG F 28 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 305 time to evaluate : 3.606 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 105 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7807 (mp) REVERT: E 269 MET cc_start: 0.8696 (mtp) cc_final: 0.8429 (mtt) REVERT: H 132 MET cc_start: 0.8183 (tmt) cc_final: 0.7963 (OUTLIER) outliers start: 35 outliers final: 30 residues processed: 333 average time/residue: 2.5782 time to fit residues: 1007.5121 Evaluate side-chains 335 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 305 time to evaluate : 3.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 323 SER Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain L residue 516 SER Chi-restraints excluded: chain M residue 569 ASP Chi-restraints excluded: chain M residue 651 ILE Chi-restraints excluded: chain M residue 682 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 307 optimal weight: 2.9990 chunk 275 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 186 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 285 optimal weight: 3.9990 chunk 110 optimal weight: 0.4980 chunk 173 optimal weight: 0.7980 chunk 212 optimal weight: 1.9990 chunk 330 optimal weight: 0.6980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 ASN E 162 ASN M 625 GLN ** N 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.0418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 29412 Z= 0.248 Angle : 0.622 7.173 39884 Z= 0.313 Chirality : 0.045 0.169 4428 Planarity : 0.004 0.039 5104 Dihedral : 11.620 167.469 4116 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.53 % Favored : 97.39 % Rotamer: Outliers : 1.98 % Allowed : 10.77 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.72 (0.14), residues: 3600 helix: 0.51 (0.13), residues: 1568 sheet: -0.42 (0.27), residues: 360 loop : 0.93 (0.16), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 340 HIS 0.005 0.001 HIS D 161 PHE 0.017 0.002 PHE A 31 TYR 0.014 0.001 TYR E 143 ARG 0.005 0.000 ARG F 28 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 307 time to evaluate : 3.575 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 360 GLN cc_start: 0.7439 (tp40) cc_final: 0.7207 (tp-100) REVERT: A 364 GLU cc_start: 0.6621 (OUTLIER) cc_final: 0.6331 (mp0) REVERT: C 105 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7813 (mp) REVERT: D 191 LYS cc_start: 0.8753 (ttpp) cc_final: 0.8359 (ttmm) REVERT: E 269 MET cc_start: 0.8726 (mtp) cc_final: 0.8451 (mtt) REVERT: H 113 LYS cc_start: 0.6187 (OUTLIER) cc_final: 0.4768 (mptt) REVERT: L 589 GLN cc_start: 0.7427 (OUTLIER) cc_final: 0.6798 (mp10) REVERT: L 595 LYS cc_start: 0.6531 (ptpt) cc_final: 0.6254 (pttm) REVERT: N 679 ASP cc_start: 0.6534 (m-30) cc_final: 0.6213 (m-30) outliers start: 61 outliers final: 37 residues processed: 347 average time/residue: 2.7078 time to fit residues: 1096.2405 Evaluate side-chains 333 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 292 time to evaluate : 3.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 323 SER Chi-restraints excluded: chain E residue 354 GLN Chi-restraints excluded: chain F residue 116 ARG Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 257 CYS Chi-restraints excluded: chain L residue 527 SER Chi-restraints excluded: chain L residue 589 GLN Chi-restraints excluded: chain M residue 544 GLU Chi-restraints excluded: chain N residue 544 GLU Chi-restraints excluded: chain N residue 590 CYS Chi-restraints excluded: chain N residue 604 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 183 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 275 optimal weight: 3.9990 chunk 225 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 331 optimal weight: 2.9990 chunk 357 optimal weight: 1.9990 chunk 294 optimal weight: 3.9990 chunk 328 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 265 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 625 GLN M 625 GLN ** N 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.0662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 29412 Z= 0.340 Angle : 0.654 8.012 39884 Z= 0.329 Chirality : 0.046 0.192 4428 Planarity : 0.005 0.051 5104 Dihedral : 11.667 179.057 4101 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.86 % Favored : 97.06 % Rotamer: Outliers : 2.59 % Allowed : 10.51 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.14), residues: 3600 helix: 0.36 (0.13), residues: 1568 sheet: -0.47 (0.27), residues: 360 loop : 0.86 (0.16), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP E 340 HIS 0.005 0.001 HIS F 161 PHE 0.021 0.002 PHE A 31 TYR 0.014 0.002 TYR E 143 ARG 0.006 0.001 ARG F 28 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 297 time to evaluate : 3.593 Fit side-chains revert: symmetry clash REVERT: A 360 GLN cc_start: 0.7509 (tp40) cc_final: 0.7237 (tp-100) REVERT: B 47 MET cc_start: 0.3557 (OUTLIER) cc_final: 0.1968 (ptm) REVERT: C 105 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7836 (mp) REVERT: F 72 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7484 (mt-10) REVERT: H 113 LYS cc_start: 0.6133 (OUTLIER) cc_final: 0.4762 (mptt) REVERT: H 227 MET cc_start: 0.8530 (mmm) cc_final: 0.8306 (mmm) REVERT: N 679 ASP cc_start: 0.6666 (m-30) cc_final: 0.6388 (m-30) outliers start: 80 outliers final: 49 residues processed: 352 average time/residue: 2.6085 time to fit residues: 1077.4744 Evaluate side-chains 345 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 292 time to evaluate : 3.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 323 SER Chi-restraints excluded: chain E residue 360 GLN Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 116 ARG Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 257 CYS Chi-restraints excluded: chain L residue 527 SER Chi-restraints excluded: chain M residue 544 GLU Chi-restraints excluded: chain M residue 569 ASP Chi-restraints excluded: chain N residue 516 SER Chi-restraints excluded: chain N residue 544 GLU Chi-restraints excluded: chain N residue 566 ARG Chi-restraints excluded: chain N residue 578 ASN Chi-restraints excluded: chain N residue 590 CYS Chi-restraints excluded: chain N residue 604 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 327 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 222 optimal weight: 2.9990 chunk 332 optimal weight: 2.9990 chunk 351 optimal weight: 0.7980 chunk 173 optimal weight: 0.9980 chunk 314 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 128 ASN H 246 GLN M 625 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.0778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 29412 Z= 0.258 Angle : 0.616 7.644 39884 Z= 0.306 Chirality : 0.045 0.178 4428 Planarity : 0.004 0.048 5104 Dihedral : 11.394 179.124 4101 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.75 % Favored : 97.17 % Rotamer: Outliers : 2.43 % Allowed : 10.89 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.68 (0.14), residues: 3600 helix: 0.46 (0.13), residues: 1568 sheet: -0.49 (0.26), residues: 360 loop : 0.93 (0.16), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 340 HIS 0.006 0.001 HIS F 161 PHE 0.018 0.002 PHE A 31 TYR 0.013 0.001 TYR E 143 ARG 0.007 0.000 ARG F 28 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 302 time to evaluate : 3.715 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 360 GLN cc_start: 0.7553 (tp40) cc_final: 0.7324 (tp-100) REVERT: A 364 GLU cc_start: 0.6671 (OUTLIER) cc_final: 0.6400 (mp0) REVERT: C 105 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7875 (mp) REVERT: D 237 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7910 (mt-10) REVERT: F 72 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7453 (mt-10) REVERT: H 113 LYS cc_start: 0.6161 (OUTLIER) cc_final: 0.4800 (mptt) REVERT: L 657 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7102 (ttm110) REVERT: N 679 ASP cc_start: 0.6661 (m-30) cc_final: 0.6372 (m-30) outliers start: 75 outliers final: 50 residues processed: 352 average time/residue: 2.6745 time to fit residues: 1111.0364 Evaluate side-chains 347 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 292 time to evaluate : 3.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 323 SER Chi-restraints excluded: chain E residue 360 GLN Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 116 ARG Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 257 CYS Chi-restraints excluded: chain L residue 527 SER Chi-restraints excluded: chain L residue 589 GLN Chi-restraints excluded: chain L residue 657 ARG Chi-restraints excluded: chain M residue 544 GLU Chi-restraints excluded: chain M residue 569 ASP Chi-restraints excluded: chain M residue 682 HIS Chi-restraints excluded: chain N residue 516 SER Chi-restraints excluded: chain N residue 544 GLU Chi-restraints excluded: chain N residue 566 ARG Chi-restraints excluded: chain N residue 578 ASN Chi-restraints excluded: chain N residue 590 CYS Chi-restraints excluded: chain N residue 604 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 293 optimal weight: 2.9990 chunk 199 optimal weight: 0.4980 chunk 5 optimal weight: 3.9990 chunk 261 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 chunk 300 optimal weight: 2.9990 chunk 243 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 179 optimal weight: 1.9990 chunk 315 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 297 ASN G 121 GLN ** N 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.0874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 29412 Z= 0.293 Angle : 0.628 8.458 39884 Z= 0.313 Chirality : 0.045 0.183 4428 Planarity : 0.004 0.043 5104 Dihedral : 11.331 179.842 4099 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.86 % Favored : 97.06 % Rotamer: Outliers : 2.37 % Allowed : 11.22 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.66 (0.14), residues: 3600 helix: 0.44 (0.13), residues: 1568 sheet: -0.49 (0.26), residues: 360 loop : 0.92 (0.16), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 340 HIS 0.005 0.001 HIS F 161 PHE 0.019 0.002 PHE A 31 TYR 0.013 0.001 TYR E 143 ARG 0.006 0.000 ARG E 28 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 294 time to evaluate : 3.569 Fit side-chains revert: symmetry clash REVERT: C 105 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7889 (mp) REVERT: D 237 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7889 (mt-10) REVERT: E 178 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8151 (mp) REVERT: F 72 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7443 (mt-10) REVERT: G 147 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7871 (ptp-110) REVERT: H 113 LYS cc_start: 0.6104 (OUTLIER) cc_final: 0.4859 (mttt) REVERT: L 599 LEU cc_start: 0.6996 (OUTLIER) cc_final: 0.6677 (tt) REVERT: L 657 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7100 (ttm110) REVERT: N 679 ASP cc_start: 0.6699 (m-30) cc_final: 0.6432 (m-30) outliers start: 73 outliers final: 50 residues processed: 348 average time/residue: 2.6176 time to fit residues: 1067.5901 Evaluate side-chains 344 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 287 time to evaluate : 3.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 360 GLN Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 116 ARG Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 147 ARG Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 132 MET Chi-restraints excluded: chain H residue 257 CYS Chi-restraints excluded: chain L residue 527 SER Chi-restraints excluded: chain L residue 599 LEU Chi-restraints excluded: chain L residue 657 ARG Chi-restraints excluded: chain M residue 544 GLU Chi-restraints excluded: chain M residue 569 ASP Chi-restraints excluded: chain M residue 651 ILE Chi-restraints excluded: chain M residue 682 HIS Chi-restraints excluded: chain N residue 516 SER Chi-restraints excluded: chain N residue 544 GLU Chi-restraints excluded: chain N residue 566 ARG Chi-restraints excluded: chain N residue 578 ASN Chi-restraints excluded: chain N residue 590 CYS Chi-restraints excluded: chain N residue 604 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 118 optimal weight: 0.9980 chunk 316 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 206 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 352 optimal weight: 2.9990 chunk 292 optimal weight: 2.9990 chunk 163 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 128 ASN M 625 GLN ** N 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.0943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 29412 Z= 0.235 Angle : 0.603 7.888 39884 Z= 0.298 Chirality : 0.044 0.175 4428 Planarity : 0.004 0.045 5104 Dihedral : 10.944 178.257 4095 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.75 % Favored : 97.17 % Rotamer: Outliers : 2.20 % Allowed : 11.54 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 (0.14), residues: 3600 helix: 0.53 (0.13), residues: 1616 sheet: -0.46 (0.26), residues: 360 loop : 0.97 (0.16), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 340 HIS 0.006 0.001 HIS F 161 PHE 0.016 0.001 PHE A 31 TYR 0.013 0.001 TYR E 143 ARG 0.007 0.000 ARG E 28 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 303 time to evaluate : 3.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 360 GLN cc_start: 0.7465 (tp40) cc_final: 0.7212 (tp-100) REVERT: A 364 GLU cc_start: 0.6656 (OUTLIER) cc_final: 0.6321 (mp0) REVERT: C 105 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7990 (mp) REVERT: D 237 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7915 (mt-10) REVERT: E 25 ASP cc_start: 0.7489 (OUTLIER) cc_final: 0.7208 (t70) REVERT: F 72 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7425 (mt-10) REVERT: H 113 LYS cc_start: 0.6097 (OUTLIER) cc_final: 0.4851 (mttt) REVERT: L 599 LEU cc_start: 0.6943 (OUTLIER) cc_final: 0.6632 (tt) REVERT: L 657 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7091 (ttm110) REVERT: N 679 ASP cc_start: 0.6678 (m-30) cc_final: 0.6392 (m-30) outliers start: 68 outliers final: 50 residues processed: 351 average time/residue: 2.6419 time to fit residues: 1091.5158 Evaluate side-chains 354 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 297 time to evaluate : 3.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 323 SER Chi-restraints excluded: chain E residue 360 GLN Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 116 ARG Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 132 MET Chi-restraints excluded: chain H residue 257 CYS Chi-restraints excluded: chain L residue 527 SER Chi-restraints excluded: chain L residue 589 GLN Chi-restraints excluded: chain L residue 599 LEU Chi-restraints excluded: chain L residue 657 ARG Chi-restraints excluded: chain M residue 544 GLU Chi-restraints excluded: chain M residue 569 ASP Chi-restraints excluded: chain M residue 651 ILE Chi-restraints excluded: chain M residue 682 HIS Chi-restraints excluded: chain N residue 516 SER Chi-restraints excluded: chain N residue 566 ARG Chi-restraints excluded: chain N residue 578 ASN Chi-restraints excluded: chain N residue 590 CYS Chi-restraints excluded: chain N residue 604 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 339 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 200 optimal weight: 0.9990 chunk 257 optimal weight: 1.9990 chunk 199 optimal weight: 0.5980 chunk 296 optimal weight: 1.9990 chunk 196 optimal weight: 0.9990 chunk 350 optimal weight: 1.9990 chunk 219 optimal weight: 1.9990 chunk 213 optimal weight: 0.9990 chunk 161 optimal weight: 2.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 29412 Z= 0.201 Angle : 0.583 7.468 39884 Z= 0.286 Chirality : 0.043 0.166 4428 Planarity : 0.004 0.076 5104 Dihedral : 10.277 165.798 4095 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.75 % Favored : 97.17 % Rotamer: Outliers : 2.08 % Allowed : 11.80 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.14), residues: 3600 helix: 0.72 (0.13), residues: 1598 sheet: -0.43 (0.26), residues: 360 loop : 1.07 (0.16), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 340 HIS 0.005 0.001 HIS F 161 PHE 0.015 0.001 PHE A 31 TYR 0.013 0.001 TYR E 143 ARG 0.011 0.000 ARG G 95 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 310 time to evaluate : 3.803 Fit side-chains revert: symmetry clash REVERT: C 105 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7943 (mp) REVERT: C 167 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7743 (mp0) REVERT: D 237 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7908 (mt-10) REVERT: F 72 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7414 (mt-10) REVERT: G 147 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7862 (ptp-110) REVERT: H 113 LYS cc_start: 0.6047 (OUTLIER) cc_final: 0.4844 (mttt) REVERT: L 599 LEU cc_start: 0.6917 (OUTLIER) cc_final: 0.6600 (tt) REVERT: L 657 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7056 (ttm110) REVERT: N 679 ASP cc_start: 0.6675 (m-30) cc_final: 0.6398 (m-30) outliers start: 64 outliers final: 44 residues processed: 357 average time/residue: 2.7241 time to fit residues: 1159.0255 Evaluate side-chains 350 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 299 time to evaluate : 3.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 360 GLN Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 116 ARG Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 147 ARG Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 132 MET Chi-restraints excluded: chain H residue 257 CYS Chi-restraints excluded: chain L residue 527 SER Chi-restraints excluded: chain L residue 599 LEU Chi-restraints excluded: chain L residue 657 ARG Chi-restraints excluded: chain M residue 544 GLU Chi-restraints excluded: chain M residue 569 ASP Chi-restraints excluded: chain M residue 682 HIS Chi-restraints excluded: chain N residue 516 SER Chi-restraints excluded: chain N residue 566 ARG Chi-restraints excluded: chain N residue 578 ASN Chi-restraints excluded: chain N residue 590 CYS Chi-restraints excluded: chain N residue 594 ASP Chi-restraints excluded: chain N residue 604 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 217 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 chunk 209 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 223 optimal weight: 2.9990 chunk 239 optimal weight: 2.9990 chunk 173 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 chunk 275 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 128 ASN M 625 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 29412 Z= 0.210 Angle : 0.587 7.397 39884 Z= 0.288 Chirality : 0.043 0.176 4428 Planarity : 0.004 0.068 5104 Dihedral : 9.882 167.879 4094 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.72 % Favored : 97.19 % Rotamer: Outliers : 2.11 % Allowed : 11.96 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.98 (0.14), residues: 3600 helix: 0.75 (0.13), residues: 1598 sheet: -0.40 (0.26), residues: 360 loop : 1.08 (0.16), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 340 HIS 0.005 0.001 HIS F 161 PHE 0.015 0.001 PHE A 31 TYR 0.012 0.001 TYR E 143 ARG 0.008 0.000 ARG E 28 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 301 time to evaluate : 3.538 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 360 GLN cc_start: 0.7412 (tp40) cc_final: 0.7159 (tp-100) REVERT: C 105 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7940 (mp) REVERT: C 167 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7767 (mp0) REVERT: D 237 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7928 (mt-10) REVERT: F 72 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7421 (mt-10) REVERT: H 113 LYS cc_start: 0.6099 (OUTLIER) cc_final: 0.4831 (mttt) REVERT: L 599 LEU cc_start: 0.6911 (OUTLIER) cc_final: 0.6596 (tt) REVERT: L 657 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7058 (ttm110) REVERT: N 679 ASP cc_start: 0.6666 (m-30) cc_final: 0.6394 (m-30) outliers start: 65 outliers final: 49 residues processed: 348 average time/residue: 2.6240 time to fit residues: 1071.8963 Evaluate side-chains 354 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 299 time to evaluate : 3.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 323 SER Chi-restraints excluded: chain E residue 360 GLN Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 116 ARG Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 132 MET Chi-restraints excluded: chain H residue 257 CYS Chi-restraints excluded: chain L residue 527 SER Chi-restraints excluded: chain L residue 599 LEU Chi-restraints excluded: chain L residue 657 ARG Chi-restraints excluded: chain M residue 544 GLU Chi-restraints excluded: chain M residue 569 ASP Chi-restraints excluded: chain M residue 651 ILE Chi-restraints excluded: chain M residue 682 HIS Chi-restraints excluded: chain N residue 566 ARG Chi-restraints excluded: chain N residue 578 ASN Chi-restraints excluded: chain N residue 590 CYS Chi-restraints excluded: chain N residue 594 ASP Chi-restraints excluded: chain N residue 604 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 319 optimal weight: 0.9980 chunk 336 optimal weight: 4.9990 chunk 306 optimal weight: 2.9990 chunk 326 optimal weight: 3.9990 chunk 196 optimal weight: 1.9990 chunk 142 optimal weight: 0.8980 chunk 256 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 295 optimal weight: 0.0980 chunk 309 optimal weight: 0.9980 chunk 325 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 29412 Z= 0.214 Angle : 0.589 7.417 39884 Z= 0.289 Chirality : 0.043 0.185 4428 Planarity : 0.004 0.076 5104 Dihedral : 9.754 172.439 4094 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.72 % Favored : 97.19 % Rotamer: Outliers : 2.01 % Allowed : 12.13 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 1.00 (0.14), residues: 3600 helix: 0.76 (0.13), residues: 1598 sheet: -0.39 (0.26), residues: 360 loop : 1.08 (0.16), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 340 HIS 0.006 0.001 HIS N 596 PHE 0.015 0.001 PHE A 31 TYR 0.012 0.001 TYR E 143 ARG 0.010 0.000 ARG E 28 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 303 time to evaluate : 3.633 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 105 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.8004 (mp) REVERT: C 167 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7766 (mp0) REVERT: D 237 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7934 (mt-10) REVERT: F 72 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7421 (mt-10) REVERT: H 113 LYS cc_start: 0.6115 (OUTLIER) cc_final: 0.4828 (mttt) REVERT: L 599 LEU cc_start: 0.6907 (OUTLIER) cc_final: 0.6593 (tt) REVERT: L 657 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7059 (ttm110) REVERT: N 679 ASP cc_start: 0.6685 (m-30) cc_final: 0.6404 (m-30) outliers start: 62 outliers final: 48 residues processed: 349 average time/residue: 2.6268 time to fit residues: 1082.6885 Evaluate side-chains 354 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 300 time to evaluate : 3.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 323 SER Chi-restraints excluded: chain E residue 360 GLN Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 116 ARG Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 132 MET Chi-restraints excluded: chain H residue 257 CYS Chi-restraints excluded: chain L residue 527 SER Chi-restraints excluded: chain L residue 599 LEU Chi-restraints excluded: chain L residue 657 ARG Chi-restraints excluded: chain M residue 544 GLU Chi-restraints excluded: chain M residue 569 ASP Chi-restraints excluded: chain M residue 651 ILE Chi-restraints excluded: chain M residue 682 HIS Chi-restraints excluded: chain N residue 516 SER Chi-restraints excluded: chain N residue 566 ARG Chi-restraints excluded: chain N residue 578 ASN Chi-restraints excluded: chain N residue 590 CYS Chi-restraints excluded: chain N residue 594 ASP Chi-restraints excluded: chain N residue 604 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 214 optimal weight: 2.9990 chunk 345 optimal weight: 0.3980 chunk 211 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 240 optimal weight: 1.9990 chunk 362 optimal weight: 4.9990 chunk 333 optimal weight: 2.9990 chunk 288 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 223 optimal weight: 1.9990 chunk 177 optimal weight: 3.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 29412 Z= 0.318 Angle : 0.632 7.875 39884 Z= 0.313 Chirality : 0.046 0.199 4428 Planarity : 0.005 0.071 5104 Dihedral : 10.067 172.209 4094 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.81 % Favored : 97.11 % Rotamer: Outliers : 1.91 % Allowed : 12.19 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.77 (0.14), residues: 3600 helix: 0.56 (0.13), residues: 1616 sheet: -0.45 (0.26), residues: 360 loop : 0.96 (0.16), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 340 HIS 0.006 0.001 HIS F 161 PHE 0.021 0.002 PHE B 266 TYR 0.011 0.002 TYR H 143 ARG 0.012 0.001 ARG H 28 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 296 time to evaluate : 4.559 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 237 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7910 (mt-10) REVERT: E 178 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8105 (mp) REVERT: F 72 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7413 (mt-10) REVERT: G 147 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7906 (ptp-110) REVERT: H 113 LYS cc_start: 0.6002 (OUTLIER) cc_final: 0.4592 (mptt) REVERT: L 599 LEU cc_start: 0.6900 (OUTLIER) cc_final: 0.6584 (tt) REVERT: L 657 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7092 (ttm110) REVERT: N 679 ASP cc_start: 0.6688 (m-30) cc_final: 0.6451 (m-30) outliers start: 59 outliers final: 49 residues processed: 340 average time/residue: 2.5859 time to fit residues: 1031.9439 Evaluate side-chains 348 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 293 time to evaluate : 3.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 323 SER Chi-restraints excluded: chain E residue 360 GLN Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 116 ARG Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 147 ARG Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 257 CYS Chi-restraints excluded: chain L residue 527 SER Chi-restraints excluded: chain L residue 599 LEU Chi-restraints excluded: chain L residue 657 ARG Chi-restraints excluded: chain M residue 544 GLU Chi-restraints excluded: chain M residue 569 ASP Chi-restraints excluded: chain M residue 651 ILE Chi-restraints excluded: chain M residue 682 HIS Chi-restraints excluded: chain N residue 516 SER Chi-restraints excluded: chain N residue 566 ARG Chi-restraints excluded: chain N residue 578 ASN Chi-restraints excluded: chain N residue 590 CYS Chi-restraints excluded: chain N residue 594 ASP Chi-restraints excluded: chain N residue 604 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 229 optimal weight: 1.9990 chunk 307 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 266 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 289 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 296 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.107927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.092452 restraints weight = 102116.880| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 1.04 r_work: 0.2930 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 2.36 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 29412 Z= 0.233 Angle : 0.603 7.564 39884 Z= 0.297 Chirality : 0.044 0.190 4428 Planarity : 0.004 0.073 5104 Dihedral : 9.891 174.188 4092 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.64 % Favored : 97.28 % Rotamer: Outliers : 1.85 % Allowed : 12.29 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.91 (0.14), residues: 3600 helix: 0.68 (0.13), residues: 1598 sheet: -0.42 (0.26), residues: 360 loop : 1.05 (0.16), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 340 HIS 0.005 0.001 HIS F 161 PHE 0.015 0.001 PHE A 31 TYR 0.012 0.001 TYR E 143 ARG 0.011 0.000 ARG H 28 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16553.65 seconds wall clock time: 285 minutes 33.39 seconds (17133.39 seconds total)