Starting phenix.real_space_refine on Thu Mar 21 00:15:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f64_31472/03_2024/7f64_31472.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f64_31472/03_2024/7f64_31472.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f64_31472/03_2024/7f64_31472.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f64_31472/03_2024/7f64_31472.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f64_31472/03_2024/7f64_31472.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f64_31472/03_2024/7f64_31472.pdb" } resolution = 2.42 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= 1.000 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: 4 Type Number sf(0) Gaussians S 158 5.16 5 C 18274 2.51 5 N 4994 2.21 5 O 5326 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 19": "OD1" <-> "OD2" Residue "A PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 54": "OE1" <-> "OE2" Residue "A PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 82": "OE1" <-> "OE2" Residue "A ASP 113": "OD1" <-> "OD2" Residue "B ASP 19": "OD1" <-> "OD2" Residue "B GLU 32": "OE1" <-> "OE2" Residue "B GLU 70": "OE1" <-> "OE2" Residue "B GLU 82": "OE1" <-> "OE2" Residue "B GLU 95": "OE1" <-> "OE2" Residue "B ASP 121": "OD1" <-> "OD2" Residue "C GLU 13": "OE1" <-> "OE2" Residue "C GLU 20": "OE1" <-> "OE2" Residue "C GLU 32": "OE1" <-> "OE2" Residue "C GLU 75": "OE1" <-> "OE2" Residue "C ASP 121": "OD1" <-> "OD2" Residue "C PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 202": "OE1" <-> "OE2" Residue "C ASP 219": "OD1" <-> "OD2" Residue "C ASP 347": "OD1" <-> "OD2" Residue "D GLU 32": "OE1" <-> "OE2" Residue "D GLU 59": "OE1" <-> "OE2" Residue "D GLU 75": "OE1" <-> "OE2" Residue "D PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 143": "OE1" <-> "OE2" Residue "D GLU 149": "OE1" <-> "OE2" Residue "E GLU 44": "OE1" <-> "OE2" Residue "E GLU 49": "OE1" <-> "OE2" Residue "E GLU 116": "OE1" <-> "OE2" Residue "E ASP 125": "OD1" <-> "OD2" Residue "E ASP 175": "OD1" <-> "OD2" Residue "E ASP 177": "OD1" <-> "OD2" Residue "E GLU 227": "OE1" <-> "OE2" Residue "F GLU 44": "OE1" <-> "OE2" Residue "F GLU 50": "OE1" <-> "OE2" Residue "F ASP 100": "OD1" <-> "OD2" Residue "F ASP 111": "OD1" <-> "OD2" Residue "F PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 161": "OD1" <-> "OD2" Residue "F GLU 178": "OE1" <-> "OE2" Residue "F ASP 201": "OD1" <-> "OD2" Residue "F TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 217": "OE1" <-> "OE2" Residue "G PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 246": "OE1" <-> "OE2" Residue "H ASP 305": "OD1" <-> "OD2" Residue "H ASP 458": "OD1" <-> "OD2" Residue "I PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 199": "OD1" <-> "OD2" Residue "I PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 270": "OD1" <-> "OD2" Residue "I GLU 418": "OE1" <-> "OE2" Residue "I GLU 458": "OE1" <-> "OE2" Residue "J ASP 199": "OD1" <-> "OD2" Residue "J PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 358": "OE1" <-> "OE2" Residue "J PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 415": "OD1" <-> "OD2" Residue "J GLU 421": "OE1" <-> "OE2" Residue "J ASP 455": "OD1" <-> "OD2" Residue "J GLU 458": "OE1" <-> "OE2" Residue "K TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 45": "OE1" <-> "OE2" Residue "K PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 155": "OD1" <-> "OD2" Residue "K ASP 181": "OD1" <-> "OD2" Residue "L TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 42": "OE1" <-> "OE2" Residue "L PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 144": "OD1" <-> "OD2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 28752 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2268 Classifications: {'peptide': 292} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 9, 'TRANS': 282} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 2268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2268 Classifications: {'peptide': 292} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 9, 'TRANS': 282} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 2613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2613 Classifications: {'peptide': 333} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain breaks: 2 Chain: "D" Number of atoms: 2613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2613 Classifications: {'peptide': 333} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain breaks: 2 Chain: "E" Number of atoms: 1802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1802 Classifications: {'peptide': 242} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 9, 'TRANS': 232} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 146 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 8, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 93 Chain: "F" Number of atoms: 1802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1802 Classifications: {'peptide': 242} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 9, 'TRANS': 232} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 146 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 8, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 93 Chain: "G" Number of atoms: 2771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2771 Classifications: {'peptide': 356} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 337} Chain: "H" Number of atoms: 2771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2771 Classifications: {'peptide': 356} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 337} Chain: "I" Number of atoms: 3333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3333 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 407} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "J" Number of atoms: 3333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3333 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 407} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "K" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1589 Classifications: {'peptide': 197} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 188} Chain breaks: 1 Chain: "L" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1589 Classifications: {'peptide': 197} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 188} Chain breaks: 1 Time building chain proxies: 14.03, per 1000 atoms: 0.49 Number of scatterers: 28752 At special positions: 0 Unit cell: (152.536, 168.287, 181.551, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 158 16.00 O 5326 8.00 N 4994 7.00 C 18274 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.43 Conformation dependent library (CDL) restraints added in 5.4 seconds 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7012 Finding SS restraints... Secondary structure from input PDB file: 164 helices and 32 sheets defined 47.3% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.38 Creating SS restraints... Processing helix chain 'A' and resid 2 through 17 removed outlier: 3.571A pdb=" N ASP A 17 " --> pdb=" O GLN A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 36 Processing helix chain 'A' and resid 42 through 60 WARNING: missing atoms! Processing helix chain 'A' and resid 62 through 83 removed outlier: 3.735A pdb=" N SER A 66 " --> pdb=" O SER A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 116 removed outlier: 4.030A pdb=" N LYS A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ARG A 108 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ASN A 109 " --> pdb=" O SER A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 119 No H-bonds generated for 'chain 'A' and resid 117 through 119' Processing helix chain 'A' and resid 131 through 144 Processing helix chain 'A' and resid 159 through 171 removed outlier: 3.578A pdb=" N LYS A 163 " --> pdb=" O LEU A 159 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU A 171 " --> pdb=" O ALA A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 187 Processing helix chain 'A' and resid 211 through 222 removed outlier: 3.552A pdb=" N MET A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 Processing helix chain 'A' and resid 247 through 252 removed outlier: 3.726A pdb=" N LYS A 251 " --> pdb=" O PRO A 247 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR A 252 " --> pdb=" O ASP A 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 247 through 252' Processing helix chain 'A' and resid 277 through 281 Processing helix chain 'A' and resid 292 through 304 removed outlier: 4.133A pdb=" N VAL A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N SER A 297 " --> pdb=" O PRO A 293 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP A 298 " --> pdb=" O SER A 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 17 removed outlier: 3.785A pdb=" N ASP B 17 " --> pdb=" O GLN B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 36 removed outlier: 3.642A pdb=" N ARG B 36 " --> pdb=" O GLU B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 60 WARNING: missing atoms! Processing helix chain 'B' and resid 62 through 83 removed outlier: 3.773A pdb=" N SER B 66 " --> pdb=" O SER B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 106 removed outlier: 3.672A pdb=" N LEU B 106 " --> pdb=" O ARG B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 116 removed outlier: 3.547A pdb=" N LYS B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 119 No H-bonds generated for 'chain 'B' and resid 117 through 119' Processing helix chain 'B' and resid 131 through 144 Processing helix chain 'B' and resid 159 through 170 removed outlier: 3.507A pdb=" N LYS B 163 " --> pdb=" O LEU B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 187 Processing helix chain 'B' and resid 211 through 222 removed outlier: 3.640A pdb=" N MET B 215 " --> pdb=" O GLY B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 235 Processing helix chain 'B' and resid 247 through 252 removed outlier: 3.724A pdb=" N LYS B 251 " --> pdb=" O PRO B 247 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR B 252 " --> pdb=" O ASP B 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 247 through 252' Processing helix chain 'B' and resid 277 through 281 Processing helix chain 'B' and resid 292 through 304 removed outlier: 3.924A pdb=" N VAL B 296 " --> pdb=" O THR B 292 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER B 297 " --> pdb=" O PRO B 293 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP B 298 " --> pdb=" O SER B 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 24 Processing helix chain 'C' and resid 30 through 49 Processing helix chain 'C' and resid 53 through 72 removed outlier: 3.680A pdb=" N GLN C 72 " --> pdb=" O MET C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 98 removed outlier: 4.619A pdb=" N GLY C 79 " --> pdb=" O GLU C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 115 Processing helix chain 'C' and resid 128 through 146 removed outlier: 3.955A pdb=" N ASN C 132 " --> pdb=" O GLN C 128 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY C 146 " --> pdb=" O VAL C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 153 Processing helix chain 'C' and resid 171 through 182 Processing helix chain 'C' and resid 199 through 210 Processing helix chain 'C' and resid 218 through 220 No H-bonds generated for 'chain 'C' and resid 218 through 220' Processing helix chain 'C' and resid 221 through 226 Processing helix chain 'C' and resid 227 through 229 No H-bonds generated for 'chain 'C' and resid 227 through 229' Processing helix chain 'C' and resid 250 through 261 Processing helix chain 'C' and resid 270 through 274 Processing helix chain 'C' and resid 290 through 294 removed outlier: 3.502A pdb=" N GLU C 293 " --> pdb=" O ALA C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 304 removed outlier: 3.684A pdb=" N GLY C 300 " --> pdb=" O PHE C 297 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ASP C 301 " --> pdb=" O THR C 298 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N ILE C 302 " --> pdb=" O GLU C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 321 Processing helix chain 'C' and resid 332 through 334 No H-bonds generated for 'chain 'C' and resid 332 through 334' Processing helix chain 'C' and resid 335 through 344 removed outlier: 3.532A pdb=" N LEU C 339 " --> pdb=" O TYR C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 349 removed outlier: 3.597A pdb=" N HIS C 349 " --> pdb=" O PRO C 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 25 Processing helix chain 'D' and resid 30 through 49 Processing helix chain 'D' and resid 53 through 72 removed outlier: 3.599A pdb=" N LEU D 57 " --> pdb=" O ASN D 53 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN D 72 " --> pdb=" O MET D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 98 removed outlier: 4.365A pdb=" N GLY D 79 " --> pdb=" O GLU D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 115 Processing helix chain 'D' and resid 128 through 146 removed outlier: 3.625A pdb=" N GLY D 146 " --> pdb=" O VAL D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 153 Processing helix chain 'D' and resid 171 through 182 Processing helix chain 'D' and resid 199 through 210 removed outlier: 3.502A pdb=" N MET D 203 " --> pdb=" O GLN D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 220 No H-bonds generated for 'chain 'D' and resid 218 through 220' Processing helix chain 'D' and resid 221 through 227 removed outlier: 4.175A pdb=" N SER D 227 " --> pdb=" O PHE D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 261 Processing helix chain 'D' and resid 270 through 274 Processing helix chain 'D' and resid 290 through 294 removed outlier: 3.501A pdb=" N GLU D 293 " --> pdb=" O ALA D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 304 removed outlier: 3.913A pdb=" N GLY D 300 " --> pdb=" O PHE D 297 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ASP D 301 " --> pdb=" O THR D 298 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ILE D 302 " --> pdb=" O GLU D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 321 Processing helix chain 'D' and resid 332 through 334 No H-bonds generated for 'chain 'D' and resid 332 through 334' Processing helix chain 'D' and resid 335 through 344 Processing helix chain 'D' and resid 345 through 349 removed outlier: 3.848A pdb=" N HIS D 349 " --> pdb=" O PRO D 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 47 Processing helix chain 'E' and resid 62 through 68 Processing helix chain 'E' and resid 85 through 93 Processing helix chain 'E' and resid 94 through 97 Processing helix chain 'E' and resid 114 through 124 removed outlier: 4.584A pdb=" N LEU E 120 " --> pdb=" O GLU E 116 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N TYR E 124 " --> pdb=" O LEU E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 190 Processing helix chain 'E' and resid 208 through 218 removed outlier: 3.757A pdb=" N VAL E 212 " --> pdb=" O LYS E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 236 Processing helix chain 'E' and resid 277 through 279 No H-bonds generated for 'chain 'E' and resid 277 through 279' Processing helix chain 'E' and resid 280 through 293 removed outlier: 3.537A pdb=" N ALA E 284 " --> pdb=" O ALA E 280 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N CYS E 285 " --> pdb=" O CYS E 281 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG E 289 " --> pdb=" O CYS E 285 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N TRP E 290 " --> pdb=" O ARG E 286 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU E 293 " --> pdb=" O ARG E 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 47 removed outlier: 3.713A pdb=" N LEU F 40 " --> pdb=" O ILE F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 68 Processing helix chain 'F' and resid 85 through 93 removed outlier: 3.577A pdb=" N ILE F 93 " --> pdb=" O SER F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 97 Processing helix chain 'F' and resid 114 through 124 removed outlier: 4.492A pdb=" N LEU F 120 " --> pdb=" O GLU F 116 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TYR F 124 " --> pdb=" O LEU F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 190 Processing helix chain 'F' and resid 208 through 218 removed outlier: 3.716A pdb=" N VAL F 212 " --> pdb=" O LYS F 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 236 Processing helix chain 'F' and resid 277 through 279 No H-bonds generated for 'chain 'F' and resid 277 through 279' Processing helix chain 'F' and resid 280 through 292 removed outlier: 3.613A pdb=" N ARG F 289 " --> pdb=" O CYS F 285 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TRP F 290 " --> pdb=" O ARG F 286 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 181 Processing helix chain 'G' and resid 191 through 196 removed outlier: 4.012A pdb=" N GLN G 194 " --> pdb=" O SER G 191 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE G 195 " --> pdb=" O LEU G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 216 Processing helix chain 'G' and resid 221 through 240 Processing helix chain 'G' and resid 247 through 267 removed outlier: 4.121A pdb=" N VAL G 253 " --> pdb=" O SER G 249 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS G 257 " --> pdb=" O VAL G 253 " (cutoff:3.500A) Proline residue: G 258 - end of helix Processing helix chain 'G' and resid 270 through 286 Processing helix chain 'G' and resid 292 through 325 removed outlier: 4.101A pdb=" N LEU G 314 " --> pdb=" O GLU G 310 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ALA G 315 " --> pdb=" O LYS G 311 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLN G 325 " --> pdb=" O ARG G 321 " (cutoff:3.500A) Processing helix chain 'G' and resid 339 through 353 removed outlier: 3.575A pdb=" N GLY G 353 " --> pdb=" O ALA G 349 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 379 removed outlier: 3.820A pdb=" N THR G 372 " --> pdb=" O GLU G 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 390 through 395 removed outlier: 3.646A pdb=" N VAL G 394 " --> pdb=" O ALA G 390 " (cutoff:3.500A) Processing helix chain 'G' and resid 396 through 398 No H-bonds generated for 'chain 'G' and resid 396 through 398' Processing helix chain 'G' and resid 419 through 430 Processing helix chain 'G' and resid 439 through 443 Processing helix chain 'G' and resid 459 through 464 Processing helix chain 'G' and resid 475 through 479 Processing helix chain 'G' and resid 493 through 497 Processing helix chain 'G' and resid 508 through 510 No H-bonds generated for 'chain 'G' and resid 508 through 510' Processing helix chain 'G' and resid 511 through 521 Processing helix chain 'H' and resid 177 through 181 Processing helix chain 'H' and resid 191 through 196 removed outlier: 3.693A pdb=" N GLN H 194 " --> pdb=" O SER H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 216 Processing helix chain 'H' and resid 221 through 240 Processing helix chain 'H' and resid 247 through 267 removed outlier: 4.176A pdb=" N VAL H 253 " --> pdb=" O SER H 249 " (cutoff:3.500A) Proline residue: H 258 - end of helix Processing helix chain 'H' and resid 270 through 286 Processing helix chain 'H' and resid 292 through 325 removed outlier: 4.568A pdb=" N LEU H 314 " --> pdb=" O GLU H 310 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N ALA H 315 " --> pdb=" O LYS H 311 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLN H 325 " --> pdb=" O ARG H 321 " (cutoff:3.500A) Processing helix chain 'H' and resid 339 through 353 removed outlier: 3.517A pdb=" N GLY H 353 " --> pdb=" O ALA H 349 " (cutoff:3.500A) Processing helix chain 'H' and resid 368 through 379 removed outlier: 3.868A pdb=" N THR H 372 " --> pdb=" O GLU H 368 " (cutoff:3.500A) Processing helix chain 'H' and resid 390 through 395 removed outlier: 3.614A pdb=" N VAL H 394 " --> pdb=" O ALA H 390 " (cutoff:3.500A) Processing helix chain 'H' and resid 396 through 398 No H-bonds generated for 'chain 'H' and resid 396 through 398' Processing helix chain 'H' and resid 419 through 430 Processing helix chain 'H' and resid 439 through 443 Processing helix chain 'H' and resid 459 through 464 Processing helix chain 'H' and resid 475 through 479 Processing helix chain 'H' and resid 493 through 497 Processing helix chain 'H' and resid 508 through 510 No H-bonds generated for 'chain 'H' and resid 508 through 510' Processing helix chain 'H' and resid 511 through 521 removed outlier: 3.567A pdb=" N SER H 520 " --> pdb=" O LEU H 516 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER H 521 " --> pdb=" O ARG H 517 " (cutoff:3.500A) Processing helix chain 'I' and resid 58 through 62 removed outlier: 3.627A pdb=" N ASP I 62 " --> pdb=" O ILE I 59 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 68 Processing helix chain 'I' and resid 74 through 86 Processing helix chain 'I' and resid 98 through 108 removed outlier: 3.640A pdb=" N ILE I 102 " --> pdb=" O LYS I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 130 through 142 Processing helix chain 'I' and resid 161 through 175 Processing helix chain 'I' and resid 228 through 234 Processing helix chain 'I' and resid 253 through 263 removed outlier: 3.774A pdb=" N ALA I 257 " --> pdb=" O SER I 253 " (cutoff:3.500A) Processing helix chain 'I' and resid 268 through 279 removed outlier: 3.568A pdb=" N ASN I 279 " --> pdb=" O GLY I 275 " (cutoff:3.500A) Processing helix chain 'I' and resid 302 through 315 Processing helix chain 'I' and resid 330 through 334 removed outlier: 3.560A pdb=" N GLN I 333 " --> pdb=" O SER I 330 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER I 334 " --> pdb=" O THR I 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 330 through 334' Processing helix chain 'J' and resid 58 through 63 removed outlier: 4.258A pdb=" N ASP J 62 " --> pdb=" O PRO J 58 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN J 63 " --> pdb=" O ILE J 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 58 through 63' Processing helix chain 'J' and resid 64 through 68 Processing helix chain 'J' and resid 74 through 87 Processing helix chain 'J' and resid 98 through 109 removed outlier: 3.611A pdb=" N ILE J 102 " --> pdb=" O LYS J 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 110 through 113 Processing helix chain 'J' and resid 130 through 142 Processing helix chain 'J' and resid 161 through 175 Processing helix chain 'J' and resid 196 through 199 Processing helix chain 'J' and resid 228 through 234 Processing helix chain 'J' and resid 253 through 263 removed outlier: 3.662A pdb=" N ALA J 257 " --> pdb=" O SER J 253 " (cutoff:3.500A) Processing helix chain 'J' and resid 268 through 279 Processing helix chain 'J' and resid 302 through 315 Processing helix chain 'J' and resid 330 through 334 Processing helix chain 'K' and resid 1 through 3 No H-bonds generated for 'chain 'K' and resid 1 through 3' Processing helix chain 'K' and resid 61 through 66 Processing helix chain 'K' and resid 90 through 99 removed outlier: 4.187A pdb=" N ARG K 99 " --> pdb=" O SER K 95 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 119 removed outlier: 4.223A pdb=" N TRP K 119 " --> pdb=" O LYS K 115 " (cutoff:3.500A) Processing helix chain 'K' and resid 126 through 133 removed outlier: 3.836A pdb=" N SER K 130 " --> pdb=" O CYS K 126 " (cutoff:3.500A) Processing helix chain 'K' and resid 142 through 154 Processing helix chain 'K' and resid 158 through 177 Processing helix chain 'K' and resid 188 through 204 Processing helix chain 'L' and resid 1 through 3 No H-bonds generated for 'chain 'L' and resid 1 through 3' Processing helix chain 'L' and resid 61 through 66 Processing helix chain 'L' and resid 90 through 98 Processing helix chain 'L' and resid 112 through 118 Processing helix chain 'L' and resid 126 through 133 removed outlier: 3.860A pdb=" N SER L 130 " --> pdb=" O CYS L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 142 through 154 Processing helix chain 'L' and resid 158 through 178 Processing helix chain 'L' and resid 188 through 204 Processing sheet with id=AA1, first strand: chain 'A' and resid 175 through 178 removed outlier: 6.726A pdb=" N VAL A 150 " --> pdb=" O THR A 176 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N VAL A 178 " --> pdb=" O VAL A 150 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL A 152 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE A 125 " --> pdb=" O TYR A 151 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N THR A 153 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N THR A 124 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N ILE A 194 " --> pdb=" O THR A 124 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N LEU A 126 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N GLY A 196 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N VAL A 193 " --> pdb=" O TYR A 227 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N VAL A 229 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N VAL A 195 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N PHE A 226 " --> pdb=" O LEU A 283 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N PHE A 285 " --> pdb=" O PHE A 226 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL A 228 " --> pdb=" O PHE A 285 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 199 through 200 Processing sheet with id=AA3, first strand: chain 'B' and resid 175 through 178 removed outlier: 6.795A pdb=" N VAL B 150 " --> pdb=" O THR B 176 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N VAL B 178 " --> pdb=" O VAL B 150 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL B 152 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ILE B 125 " --> pdb=" O TYR B 151 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N THR B 153 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N THR B 127 " --> pdb=" O THR B 153 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N THR B 124 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE B 194 " --> pdb=" O THR B 124 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N LEU B 126 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VAL B 193 " --> pdb=" O TYR B 227 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N VAL B 229 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL B 195 " --> pdb=" O VAL B 229 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N PHE B 226 " --> pdb=" O LEU B 283 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N PHE B 285 " --> pdb=" O PHE B 226 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL B 228 " --> pdb=" O PHE B 285 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 199 through 200 Processing sheet with id=AA5, first strand: chain 'C' and resid 329 through 331 removed outlier: 6.709A pdb=" N LEU C 265 " --> pdb=" O LEU C 323 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ILE C 325 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL C 267 " --> pdb=" O ILE C 325 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL C 232 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N CYS C 268 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE C 234 " --> pdb=" O CYS C 268 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL C 164 " --> pdb=" O LYS C 231 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ILE C 233 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N MET C 166 " --> pdb=" O ILE C 233 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 238 through 239 Processing sheet with id=AA7, first strand: chain 'C' and resid 306 through 308 removed outlier: 6.430A pdb=" N ILE H 333 " --> pdb=" O VAL H 359 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N VAL H 361 " --> pdb=" O ILE H 333 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL H 335 " --> pdb=" O VAL H 361 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N VAL H 332 " --> pdb=" O LYS H 400 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N LEU H 402 " --> pdb=" O VAL H 332 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N LEU H 334 " --> pdb=" O LEU H 402 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N GLY H 404 " --> pdb=" O LEU H 334 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N TYR H 336 " --> pdb=" O GLY H 404 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N VAL H 401 " --> pdb=" O LEU H 435 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N CYS H 437 " --> pdb=" O VAL H 401 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU H 403 " --> pdb=" O CYS H 437 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL H 434 " --> pdb=" O LEU H 499 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ILE H 501 " --> pdb=" O VAL H 434 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL H 436 " --> pdb=" O ILE H 501 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 329 through 331 removed outlier: 6.202A pdb=" N VAL D 232 " --> pdb=" O ILE D 266 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N CYS D 268 " --> pdb=" O VAL D 232 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE D 234 " --> pdb=" O CYS D 268 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL D 164 " --> pdb=" O LYS D 231 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ILE D 233 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N MET D 166 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE D 165 " --> pdb=" O ILE D 190 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N ALA D 192 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N THR D 167 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N THR D 214 " --> pdb=" O ARG G 483 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 238 through 239 Processing sheet with id=AB1, first strand: chain 'D' and resid 306 through 308 removed outlier: 6.409A pdb=" N SER D 307 " --> pdb=" O TYR G 385 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N LEU G 387 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE G 333 " --> pdb=" O VAL G 359 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N VAL G 361 " --> pdb=" O ILE G 333 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL G 335 " --> pdb=" O VAL G 361 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N VAL G 332 " --> pdb=" O LYS G 400 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N LEU G 402 " --> pdb=" O VAL G 332 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N LEU G 334 " --> pdb=" O LEU G 402 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N GLY G 404 " --> pdb=" O LEU G 334 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N TYR G 336 " --> pdb=" O GLY G 404 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL G 401 " --> pdb=" O LEU G 435 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N CYS G 437 " --> pdb=" O VAL G 401 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU G 403 " --> pdb=" O CYS G 437 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL G 434 " --> pdb=" O LEU G 499 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ILE G 501 " --> pdb=" O VAL G 434 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL G 436 " --> pdb=" O ILE G 501 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 74 through 79 removed outlier: 3.675A pdb=" N VAL E 51 " --> pdb=" O ASP E 74 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ALA E 5 " --> pdb=" O GLU E 50 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N GLN E 4 " --> pdb=" O LEU E 102 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N LEU E 104 " --> pdb=" O GLN E 4 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL E 6 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER E 105 " --> pdb=" O HIS E 203 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N HIS E 203 " --> pdb=" O SER E 105 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LEU E 131 " --> pdb=" O ALA E 202 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU E 204 " --> pdb=" O ALA E 129 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA E 129 " --> pdb=" O LEU E 204 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 167 through 172 removed outlier: 4.172A pdb=" N VAL I 238 " --> pdb=" O PHE E 195 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ASP I 206 " --> pdb=" O VAL I 212 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N VAL I 212 " --> pdb=" O ASP I 206 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ILE I 287 " --> pdb=" O VAL I 212 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N MET I 181 " --> pdb=" O HIS I 288 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N HIS I 290 " --> pdb=" O MET I 181 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N MET I 183 " --> pdb=" O HIS I 290 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N THR I 292 " --> pdb=" O MET I 183 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N PHE I 185 " --> pdb=" O THR I 292 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N THR I 182 " --> pdb=" O ILE I 249 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ILE I 249 " --> pdb=" O THR I 182 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N ILE I 184 " --> pdb=" O CYS I 247 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N CYS I 247 " --> pdb=" O ILE I 184 " (cutoff:3.500A) removed outlier: 8.844A pdb=" N HIS I 248 " --> pdb=" O TYR I 152 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N TYR I 152 " --> pdb=" O HIS I 248 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 179 through 183 Processing sheet with id=AB5, first strand: chain 'F' and resid 75 through 79 removed outlier: 3.511A pdb=" N THR F 55 " --> pdb=" O ILE F 78 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N GLN F 4 " --> pdb=" O LEU F 102 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N LEU F 104 " --> pdb=" O GLN F 4 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N VAL F 6 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N SER F 105 " --> pdb=" O HIS F 203 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N HIS F 203 " --> pdb=" O SER F 105 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N LEU F 131 " --> pdb=" O ALA F 202 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU F 204 " --> pdb=" O ALA F 129 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ALA F 129 " --> pdb=" O LEU F 204 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 167 through 172 removed outlier: 6.348A pdb=" N GLY F 159 " --> pdb=" O LEU F 168 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N MET F 170 " --> pdb=" O PHE F 157 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N PHE F 157 " --> pdb=" O MET F 170 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N VAL J 238 " --> pdb=" O PHE F 195 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ASP J 206 " --> pdb=" O VAL J 212 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL J 212 " --> pdb=" O ASP J 206 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ILE J 287 " --> pdb=" O VAL J 212 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N THR J 182 " --> pdb=" O ILE J 249 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ILE J 249 " --> pdb=" O THR J 182 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ILE J 184 " --> pdb=" O CYS J 247 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N CYS J 247 " --> pdb=" O ILE J 184 " (cutoff:3.500A) removed outlier: 9.111A pdb=" N HIS J 248 " --> pdb=" O TYR J 152 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N TYR J 152 " --> pdb=" O HIS J 248 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N GLN J 44 " --> pdb=" O LEU J 149 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N VAL J 151 " --> pdb=" O GLN J 44 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N VAL J 46 " --> pdb=" O VAL J 151 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N THR J 91 " --> pdb=" O ARG J 121 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ILE J 123 " --> pdb=" O THR J 91 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N VAL J 93 " --> pdb=" O ILE J 123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 179 through 183 Processing sheet with id=AB8, first strand: chain 'G' and resid 407 through 408 Processing sheet with id=AB9, first strand: chain 'H' and resid 407 through 408 Processing sheet with id=AC1, first strand: chain 'I' and resid 155 through 157 Processing sheet with id=AC2, first strand: chain 'I' and resid 336 through 338 removed outlier: 6.204A pdb=" N LEU I 361 " --> pdb=" O ILE I 379 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N VAL I 378 " --> pdb=" O LEU I 396 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TYR I 395 " --> pdb=" O LEU I 413 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU I 412 " --> pdb=" O LEU I 431 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL I 430 " --> pdb=" O ILE I 449 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 355 through 356 removed outlier: 6.417A pdb=" N ILE I 355 " --> pdb=" O ILE I 374 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N PHE I 373 " --> pdb=" O LEU I 391 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N VAL I 390 " --> pdb=" O ILE I 408 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N GLN I 407 " --> pdb=" O LEU I 425 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N THR I 424 " --> pdb=" O LEU I 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'I' and resid 367 through 368 removed outlier: 6.525A pdb=" N VAL I 367 " --> pdb=" O ILE I 385 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N HIS I 384 " --> pdb=" O VAL I 402 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ARG I 401 " --> pdb=" O VAL I 419 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N GLU I 418 " --> pdb=" O VAL I 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'J' and resid 155 through 157 Processing sheet with id=AC6, first strand: chain 'J' and resid 336 through 338 removed outlier: 6.231A pdb=" N LEU J 361 " --> pdb=" O ILE J 379 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N VAL J 378 " --> pdb=" O LEU J 396 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N TYR J 395 " --> pdb=" O LEU J 413 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 355 through 356 removed outlier: 6.389A pdb=" N ILE J 355 " --> pdb=" O ILE J 374 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N GLN J 407 " --> pdb=" O LEU J 425 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N THR J 424 " --> pdb=" O LEU J 443 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 384 through 385 removed outlier: 6.494A pdb=" N HIS J 384 " --> pdb=" O VAL J 402 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ARG J 401 " --> pdb=" O VAL J 419 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N GLU J 418 " --> pdb=" O VAL J 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'K' and resid 5 through 13 removed outlier: 6.693A pdb=" N ASP K 8 " --> pdb=" O TYR K 30 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N TYR K 30 " --> pdb=" O ASP K 8 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL K 28 " --> pdb=" O PRO K 10 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ILE K 12 " --> pdb=" O SER K 26 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N SER K 26 " --> pdb=" O ILE K 12 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 38 through 41 Processing sheet with id=AD2, first strand: chain 'K' and resid 52 through 54 Processing sheet with id=AD3, first strand: chain 'L' and resid 5 through 13 removed outlier: 4.895A pdb=" N TYR L 5 " --> pdb=" O LYS L 32 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LYS L 32 " --> pdb=" O TYR L 5 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N PHE L 7 " --> pdb=" O TYR L 30 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 44 through 47 removed outlier: 9.088A pdb=" N TRP L 74 " --> pdb=" O VAL L 38 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N THR L 40 " --> pdb=" O TRP L 74 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 52 through 54 1284 hydrogen bonds defined for protein. 3582 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: 11.17 Time building geometry restraints manager: 12.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 9522 1.35 - 1.46: 6392 1.46 - 1.58: 13138 1.58 - 1.70: 0 1.70 - 1.82: 240 Bond restraints: 29292 Sorted by residual: bond pdb=" CB PRO H 243 " pdb=" CG PRO H 243 " ideal model delta sigma weight residual 1.492 1.562 -0.070 5.00e-02 4.00e+02 1.95e+00 bond pdb=" CB LYS I 176 " pdb=" CG LYS I 176 " ideal model delta sigma weight residual 1.520 1.560 -0.040 3.00e-02 1.11e+03 1.81e+00 bond pdb=" CG PRO B 157 " pdb=" CD PRO B 157 " ideal model delta sigma weight residual 1.503 1.545 -0.042 3.40e-02 8.65e+02 1.55e+00 bond pdb=" CB GLU C 64 " pdb=" CG GLU C 64 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.50e+00 bond pdb=" C PRO J 453 " pdb=" N PRO J 454 " ideal model delta sigma weight residual 1.334 1.362 -0.028 2.34e-02 1.83e+03 1.44e+00 ... (remaining 29287 not shown) Histogram of bond angle deviations from ideal: 98.09 - 105.27: 501 105.27 - 112.45: 15463 112.45 - 119.62: 9553 119.62 - 126.80: 13863 126.80 - 133.97: 320 Bond angle restraints: 39700 Sorted by residual: angle pdb=" CB LYS I 176 " pdb=" CG LYS I 176 " pdb=" CD LYS I 176 " ideal model delta sigma weight residual 111.30 120.11 -8.81 2.30e+00 1.89e-01 1.47e+01 angle pdb=" CB MET K 87 " pdb=" CG MET K 87 " pdb=" SD MET K 87 " ideal model delta sigma weight residual 112.70 123.62 -10.92 3.00e+00 1.11e-01 1.32e+01 angle pdb=" C GLU D 282 " pdb=" N ASP D 283 " pdb=" CA ASP D 283 " ideal model delta sigma weight residual 121.54 128.16 -6.62 1.91e+00 2.74e-01 1.20e+01 angle pdb=" CA LEU F 27 " pdb=" CB LEU F 27 " pdb=" CG LEU F 27 " ideal model delta sigma weight residual 116.30 127.20 -10.90 3.50e+00 8.16e-02 9.70e+00 angle pdb=" CA LEU B 171 " pdb=" CB LEU B 171 " pdb=" CG LEU B 171 " ideal model delta sigma weight residual 116.30 127.09 -10.79 3.50e+00 8.16e-02 9.50e+00 ... (remaining 39695 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.31: 15505 18.31 - 36.62: 1703 36.62 - 54.94: 471 54.94 - 73.25: 66 73.25 - 91.56: 39 Dihedral angle restraints: 17784 sinusoidal: 6990 harmonic: 10794 Sorted by residual: dihedral pdb=" CA THR J 432 " pdb=" C THR J 432 " pdb=" N SER J 433 " pdb=" CA SER J 433 " ideal model delta harmonic sigma weight residual 180.00 156.52 23.48 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA THR I 432 " pdb=" C THR I 432 " pdb=" N SER I 433 " pdb=" CA SER I 433 " ideal model delta harmonic sigma weight residual 180.00 158.73 21.27 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA LEU J 431 " pdb=" C LEU J 431 " pdb=" N THR J 432 " pdb=" CA THR J 432 " ideal model delta harmonic sigma weight residual 180.00 -159.73 -20.27 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 17781 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 3091 0.033 - 0.066: 991 0.066 - 0.098: 319 0.098 - 0.131: 217 0.131 - 0.164: 16 Chirality restraints: 4634 Sorted by residual: chirality pdb=" CA ILE L 123 " pdb=" N ILE L 123 " pdb=" C ILE L 123 " pdb=" CB ILE L 123 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.72e-01 chirality pdb=" CA ILE J 156 " pdb=" N ILE J 156 " pdb=" C ILE J 156 " pdb=" CB ILE J 156 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.44e-01 chirality pdb=" CA GLU C 64 " pdb=" N GLU C 64 " pdb=" C GLU C 64 " pdb=" CB GLU C 64 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.13e-01 ... (remaining 4631 not shown) Planarity restraints: 5072 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN B 156 " 0.055 5.00e-02 4.00e+02 8.21e-02 1.08e+01 pdb=" N PRO B 157 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO B 157 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 157 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU G 395 " -0.041 5.00e-02 4.00e+02 6.15e-02 6.06e+00 pdb=" N PRO G 396 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO G 396 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO G 396 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU H 395 " 0.040 5.00e-02 4.00e+02 6.09e-02 5.94e+00 pdb=" N PRO H 396 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO H 396 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO H 396 " 0.034 5.00e-02 4.00e+02 ... (remaining 5069 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 681 2.70 - 3.25: 27798 3.25 - 3.80: 46591 3.80 - 4.35: 61892 4.35 - 4.90: 101941 Nonbonded interactions: 238903 Sorted by model distance: nonbonded pdb=" OG SER J 51 " pdb=" OD1 ASP J 53 " model vdw 2.154 2.440 nonbonded pdb=" OG SER B 61 " pdb=" O LYS B 249 " model vdw 2.164 2.440 nonbonded pdb=" OG SER K 39 " pdb=" O PRO K 71 " model vdw 2.197 2.440 nonbonded pdb=" NZ LYS I 61 " pdb=" OD2 ASP I 455 " model vdw 2.221 2.520 nonbonded pdb=" OG SER A 61 " pdb=" O LYS A 249 " model vdw 2.221 2.440 ... (remaining 238898 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' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'L' } 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: 4.060 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: 0.030 Extract box with map and model: 14.370 Check model and map are aligned: 0.410 Set scattering table: 0.230 Process input model: 75.780 Find NCS groups from input model: 1.570 Set up NCS constraints: 0.210 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:15.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 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 : 0.003 0.070 29292 Z= 0.164 Angle : 0.533 10.920 39700 Z= 0.281 Chirality : 0.042 0.164 4634 Planarity : 0.004 0.082 5072 Dihedral : 16.817 91.561 10772 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.67 % Allowed : 21.82 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.14), residues: 3642 helix: 1.47 (0.14), residues: 1476 sheet: 0.12 (0.24), residues: 462 loop : 0.28 (0.16), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP L 119 HIS 0.007 0.001 HIS I 304 PHE 0.017 0.001 PHE L 190 TYR 0.011 0.001 TYR K 65 ARG 0.009 0.000 ARG F 194 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 327 time to evaluate : 3.366 Fit side-chains REVERT: B 91 LYS cc_start: 0.8367 (pttt) cc_final: 0.8083 (ptpp) REVERT: D 135 GLU cc_start: 0.7798 (tm-30) cc_final: 0.7436 (tt0) REVERT: E 173 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7343 (mp0) REVERT: F 222 THR cc_start: 0.7949 (OUTLIER) cc_final: 0.7684 (m) REVERT: J 433 SER cc_start: 0.7684 (OUTLIER) cc_final: 0.7445 (m) REVERT: K 93 MET cc_start: 0.7315 (ptm) cc_final: 0.4955 (mpt) REVERT: L 42 GLU cc_start: 0.6300 (mm-30) cc_final: 0.6096 (tm-30) REVERT: L 86 MET cc_start: 0.6346 (ptp) cc_final: 0.5496 (ptp) REVERT: L 87 MET cc_start: 0.6292 (ppp) cc_final: 0.5711 (tpt) outliers start: 84 outliers final: 58 residues processed: 405 average time/residue: 1.3967 time to fit residues: 660.8395 Evaluate side-chains 361 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 301 time to evaluate : 2.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain F residue 116 GLU Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 185 SER Chi-restraints excluded: chain F residue 188 GLN Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 260 SER Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain H residue 305 ASP Chi-restraints excluded: chain H residue 432 VAL Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 95 CYS Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 174 LEU Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 389 VAL Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 447 SER Chi-restraints excluded: chain J residue 62 ASP Chi-restraints excluded: chain J residue 95 CYS Chi-restraints excluded: chain J residue 256 VAL Chi-restraints excluded: chain J residue 265 ASP Chi-restraints excluded: chain J residue 318 VAL Chi-restraints excluded: chain J residue 324 GLU Chi-restraints excluded: chain J residue 332 THR Chi-restraints excluded: chain J residue 429 SER Chi-restraints excluded: chain J residue 433 SER Chi-restraints excluded: chain K residue 80 PHE Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 95 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 307 optimal weight: 6.9990 chunk 275 optimal weight: 6.9990 chunk 153 optimal weight: 20.0000 chunk 94 optimal weight: 6.9990 chunk 186 optimal weight: 1.9990 chunk 147 optimal weight: 0.9980 chunk 285 optimal weight: 7.9990 chunk 110 optimal weight: 1.9990 chunk 173 optimal weight: 0.0070 chunk 212 optimal weight: 0.9980 chunk 330 optimal weight: 3.9990 overall best weight: 1.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN A 222 GLN B 13 GLN D 199 GLN F 172 ASN G 265 GLN H 317 GLN H 347 GLN H 477 GLN ** I 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 145 GLN K 183 HIS L 145 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.0707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29292 Z= 0.213 Angle : 0.528 10.993 39700 Z= 0.274 Chirality : 0.043 0.170 4634 Planarity : 0.004 0.062 5072 Dihedral : 5.875 54.444 4080 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.37 % Allowed : 20.87 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.14), residues: 3642 helix: 1.70 (0.14), residues: 1486 sheet: 0.05 (0.24), residues: 460 loop : 0.33 (0.16), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 37 HIS 0.008 0.001 HIS J 304 PHE 0.018 0.001 PHE L 190 TYR 0.015 0.001 TYR K 65 ARG 0.006 0.000 ARG F 194 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 317 time to evaluate : 3.318 Fit side-chains REVERT: B 91 LYS cc_start: 0.8399 (pttt) cc_final: 0.8091 (ptpp) REVERT: B 121 ASP cc_start: 0.8036 (OUTLIER) cc_final: 0.7799 (t0) REVERT: B 244 GLN cc_start: 0.7944 (OUTLIER) cc_final: 0.7473 (tm-30) REVERT: C 124 PHE cc_start: 0.7536 (t80) cc_final: 0.7286 (m-80) REVERT: D 274 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8295 (mp) REVERT: E 188 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.8286 (tp40) REVERT: F 132 MET cc_start: 0.7848 (mtp) cc_final: 0.7509 (mtt) REVERT: H 344 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.7785 (ttt-90) REVERT: H 347 GLN cc_start: 0.7793 (OUTLIER) cc_final: 0.7177 (mp-120) REVERT: H 506 MET cc_start: 0.8622 (OUTLIER) cc_final: 0.8031 (mtp) REVERT: I 176 LYS cc_start: 0.8237 (tppt) cc_final: 0.7823 (mmmt) REVERT: I 222 ARG cc_start: 0.7700 (mpp80) cc_final: 0.7365 (mmm-85) REVERT: I 230 LEU cc_start: 0.7055 (OUTLIER) cc_final: 0.6532 (mt) REVERT: I 357 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7179 (tt0) REVERT: K 93 MET cc_start: 0.7434 (ptm) cc_final: 0.4973 (mpt) REVERT: K 155 ASP cc_start: 0.7880 (p0) cc_final: 0.7609 (p0) REVERT: L 86 MET cc_start: 0.6395 (ptp) cc_final: 0.6184 (ptp) REVERT: L 144 ASP cc_start: 0.7350 (OUTLIER) cc_final: 0.6461 (m-30) REVERT: L 187 TYR cc_start: 0.6422 (t80) cc_final: 0.6218 (t80) outliers start: 106 outliers final: 47 residues processed: 392 average time/residue: 1.4759 time to fit residues: 670.6904 Evaluate side-chains 352 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 295 time to evaluate : 3.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 244 GLN Chi-restraints excluded: chain C residue 148 MET Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 188 GLN Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 188 GLN Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain H residue 344 ARG Chi-restraints excluded: chain H residue 347 GLN Chi-restraints excluded: chain H residue 432 VAL Chi-restraints excluded: chain H residue 506 MET Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 95 CYS Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 230 LEU Chi-restraints excluded: chain I residue 357 GLU Chi-restraints excluded: chain I residue 389 VAL Chi-restraints excluded: chain I residue 435 VAL Chi-restraints excluded: chain J residue 62 ASP Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 179 SER Chi-restraints excluded: chain J residue 256 VAL Chi-restraints excluded: chain J residue 318 VAL Chi-restraints excluded: chain J residue 331 THR Chi-restraints excluded: chain J residue 400 VAL Chi-restraints excluded: chain K residue 80 PHE Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 195 SER Chi-restraints excluded: chain L residue 14 ILE Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 142 THR Chi-restraints excluded: chain L residue 144 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 183 optimal weight: 0.1980 chunk 102 optimal weight: 0.9990 chunk 275 optimal weight: 6.9990 chunk 225 optimal weight: 3.9990 chunk 91 optimal weight: 8.9990 chunk 331 optimal weight: 0.6980 chunk 357 optimal weight: 0.9990 chunk 294 optimal weight: 0.6980 chunk 328 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 265 optimal weight: 3.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN D 199 GLN G 265 GLN H 317 GLN H 347 GLN H 477 GLN ** I 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 183 HIS L 145 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.0806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 29292 Z= 0.159 Angle : 0.482 7.414 39700 Z= 0.251 Chirality : 0.042 0.158 4634 Planarity : 0.004 0.061 5072 Dihedral : 5.002 59.231 4032 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 4.16 % Allowed : 20.36 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.14), residues: 3642 helix: 1.93 (0.14), residues: 1476 sheet: -0.00 (0.21), residues: 648 loop : 0.31 (0.17), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 37 HIS 0.007 0.001 HIS J 304 PHE 0.019 0.001 PHE D 272 TYR 0.014 0.001 TYR K 65 ARG 0.007 0.000 ARG F 194 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 320 time to evaluate : 3.182 Fit side-chains REVERT: B 1 MET cc_start: 0.6111 (ttt) cc_final: 0.5759 (ttm) REVERT: B 32 GLU cc_start: 0.5895 (OUTLIER) cc_final: 0.4765 (tm-30) REVERT: B 91 LYS cc_start: 0.8371 (pttt) cc_final: 0.8064 (ptpp) REVERT: B 121 ASP cc_start: 0.8060 (OUTLIER) cc_final: 0.7807 (t0) REVERT: B 244 GLN cc_start: 0.7937 (OUTLIER) cc_final: 0.7470 (tm-30) REVERT: C 16 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6626 (mp0) REVERT: C 20 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7212 (mp0) REVERT: D 12 SER cc_start: 0.7861 (OUTLIER) cc_final: 0.7657 (t) REVERT: D 202 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7099 (mp0) REVERT: D 240 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8326 (mm) REVERT: E 188 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.8304 (tp40) REVERT: F 128 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7705 (pp) REVERT: H 344 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7551 (ttt-90) REVERT: H 368 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.8009 (mt-10) REVERT: H 506 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.8029 (mtp) REVERT: I 156 ILE cc_start: 0.8435 (OUTLIER) cc_final: 0.8174 (mm) REVERT: I 163 ARG cc_start: 0.7265 (OUTLIER) cc_final: 0.7037 (mtm180) REVERT: I 176 LYS cc_start: 0.8290 (tppt) cc_final: 0.7945 (mmmt) REVERT: I 222 ARG cc_start: 0.7705 (mpp80) cc_final: 0.7380 (mmm-85) REVERT: I 230 LEU cc_start: 0.7126 (OUTLIER) cc_final: 0.6620 (mt) REVERT: I 357 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7166 (tt0) REVERT: J 121 ARG cc_start: 0.6133 (OUTLIER) cc_final: 0.5739 (mtt-85) REVERT: J 199 ASP cc_start: 0.7505 (m-30) cc_final: 0.6880 (t0) REVERT: J 222 ARG cc_start: 0.7489 (OUTLIER) cc_final: 0.7208 (mtt-85) REVERT: K 93 MET cc_start: 0.7421 (ptm) cc_final: 0.5032 (mpt) REVERT: K 175 ARG cc_start: 0.7472 (OUTLIER) cc_final: 0.7112 (mpt-90) REVERT: L 86 MET cc_start: 0.6378 (ptp) cc_final: 0.6128 (ptp) REVERT: L 87 MET cc_start: 0.6434 (ppp) cc_final: 0.5831 (tpt) outliers start: 131 outliers final: 46 residues processed: 414 average time/residue: 1.4826 time to fit residues: 711.8911 Evaluate side-chains 357 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 291 time to evaluate : 3.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 244 GLN Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 135 GLU Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 106 CYS Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 188 GLN Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 116 GLU Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 188 GLN Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain H residue 305 ASP Chi-restraints excluded: chain H residue 344 ARG Chi-restraints excluded: chain H residue 368 GLU Chi-restraints excluded: chain H residue 432 VAL Chi-restraints excluded: chain H residue 506 MET Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 95 CYS Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 163 ARG Chi-restraints excluded: chain I residue 230 LEU Chi-restraints excluded: chain I residue 331 THR Chi-restraints excluded: chain I residue 357 GLU Chi-restraints excluded: chain I residue 389 VAL Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 435 VAL Chi-restraints excluded: chain J residue 62 ASP Chi-restraints excluded: chain J residue 121 ARG Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 222 ARG Chi-restraints excluded: chain J residue 256 VAL Chi-restraints excluded: chain J residue 318 VAL Chi-restraints excluded: chain J residue 400 VAL Chi-restraints excluded: chain K residue 80 PHE Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 175 ARG Chi-restraints excluded: chain K residue 195 SER Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 38 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 327 optimal weight: 7.9990 chunk 248 optimal weight: 3.9990 chunk 171 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 158 optimal weight: 1.9990 chunk 222 optimal weight: 3.9990 chunk 332 optimal weight: 3.9990 chunk 351 optimal weight: 2.9990 chunk 173 optimal weight: 4.9990 chunk 314 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 HIS D 199 GLN F 188 GLN G 265 GLN H 317 GLN H 347 GLN H 477 GLN ** I 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 290 HIS ** J 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 183 HIS L 91 GLN ** L 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 29292 Z= 0.411 Angle : 0.639 10.386 39700 Z= 0.333 Chirality : 0.049 0.188 4634 Planarity : 0.005 0.062 5072 Dihedral : 5.620 58.308 4025 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 4.76 % Allowed : 19.66 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.14), residues: 3642 helix: 1.40 (0.13), residues: 1488 sheet: -0.24 (0.23), residues: 486 loop : 0.09 (0.16), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 37 HIS 0.010 0.001 HIS J 168 PHE 0.021 0.002 PHE L 190 TYR 0.024 0.002 TYR B 304 ARG 0.007 0.001 ARG C 36 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 296 time to evaluate : 3.312 Fit side-chains revert: symmetry clash REVERT: A 5 GLU cc_start: 0.7519 (pt0) cc_final: 0.7278 (pt0) REVERT: B 1 MET cc_start: 0.6614 (ttt) cc_final: 0.6196 (ttm) REVERT: B 32 GLU cc_start: 0.5884 (OUTLIER) cc_final: 0.4596 (tm-30) REVERT: B 121 ASP cc_start: 0.8061 (OUTLIER) cc_final: 0.7782 (t0) REVERT: B 244 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.7490 (tm-30) REVERT: C 16 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6579 (mp0) REVERT: C 20 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7161 (mp0) REVERT: D 134 ILE cc_start: 0.8239 (OUTLIER) cc_final: 0.7846 (mp) REVERT: D 202 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7175 (mp0) REVERT: D 274 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8304 (mp) REVERT: E 188 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.8320 (tp40) REVERT: E 227 GLU cc_start: 0.7138 (mp0) cc_final: 0.6899 (mp0) REVERT: F 225 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7545 (ttm170) REVERT: G 445 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7584 (mp0) REVERT: H 344 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.7825 (ttt-90) REVERT: H 347 GLN cc_start: 0.7826 (OUTLIER) cc_final: 0.7266 (mp-120) REVERT: H 368 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.8047 (mt-10) REVERT: H 506 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.8044 (mtp) REVERT: I 163 ARG cc_start: 0.7377 (OUTLIER) cc_final: 0.7082 (mtm180) REVERT: I 176 LYS cc_start: 0.8325 (tppt) cc_final: 0.7986 (mmmt) REVERT: I 230 LEU cc_start: 0.7265 (OUTLIER) cc_final: 0.6650 (mt) REVERT: I 357 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7216 (tt0) REVERT: J 121 ARG cc_start: 0.6248 (OUTLIER) cc_final: 0.5825 (mtt-85) REVERT: J 222 ARG cc_start: 0.7454 (OUTLIER) cc_final: 0.7160 (mtt-85) REVERT: K 175 ARG cc_start: 0.7400 (OUTLIER) cc_final: 0.6965 (mpt-90) outliers start: 150 outliers final: 69 residues processed: 404 average time/residue: 1.4873 time to fit residues: 695.6865 Evaluate side-chains 370 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 281 time to evaluate : 3.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 244 GLN Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 197 PHE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 135 GLU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 188 GLN Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 116 GLU Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 177 ASP Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 188 GLN Chi-restraints excluded: chain F residue 225 ARG Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 511 SER Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 305 ASP Chi-restraints excluded: chain H residue 344 ARG Chi-restraints excluded: chain H residue 347 GLN Chi-restraints excluded: chain H residue 368 GLU Chi-restraints excluded: chain H residue 394 VAL Chi-restraints excluded: chain H residue 432 VAL Chi-restraints excluded: chain H residue 506 MET Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 95 CYS Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 163 ARG Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 230 LEU Chi-restraints excluded: chain I residue 357 GLU Chi-restraints excluded: chain I residue 389 VAL Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain J residue 51 SER Chi-restraints excluded: chain J residue 62 ASP Chi-restraints excluded: chain J residue 121 ARG Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 147 ASP Chi-restraints excluded: chain J residue 208 THR Chi-restraints excluded: chain J residue 222 ARG Chi-restraints excluded: chain J residue 256 VAL Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 318 VAL Chi-restraints excluded: chain J residue 331 THR Chi-restraints excluded: chain K residue 80 PHE Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 175 ARG Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 142 THR 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: 0.9990 chunk 5 optimal weight: 1.9990 chunk 261 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 300 optimal weight: 4.9990 chunk 243 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 179 optimal weight: 10.0000 chunk 315 optimal weight: 7.9990 chunk 88 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN C 199 GLN D 199 GLN E 172 ASN ** G 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 371 HIS H 317 GLN H 347 GLN H 477 GLN ** I 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 29292 Z= 0.302 Angle : 0.570 9.215 39700 Z= 0.297 Chirality : 0.046 0.173 4634 Planarity : 0.004 0.063 5072 Dihedral : 5.531 59.360 4025 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 4.57 % Allowed : 20.49 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.14), residues: 3642 helix: 1.47 (0.13), residues: 1488 sheet: -0.33 (0.22), residues: 500 loop : 0.09 (0.16), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 111 HIS 0.007 0.001 HIS I 304 PHE 0.022 0.002 PHE L 190 TYR 0.016 0.002 TYR E 210 ARG 0.007 0.000 ARG J 223 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 301 time to evaluate : 3.415 Fit side-chains REVERT: A 91 LYS cc_start: 0.8526 (mmpt) cc_final: 0.8183 (mmmt) REVERT: A 121 ASP cc_start: 0.8360 (OUTLIER) cc_final: 0.8088 (t0) REVERT: B 1 MET cc_start: 0.6545 (ttt) cc_final: 0.6169 (ttm) REVERT: B 32 GLU cc_start: 0.5953 (OUTLIER) cc_final: 0.4712 (tm-30) REVERT: B 92 ILE cc_start: 0.8127 (OUTLIER) cc_final: 0.7777 (mp) REVERT: B 121 ASP cc_start: 0.8073 (OUTLIER) cc_final: 0.7788 (t0) REVERT: B 244 GLN cc_start: 0.7993 (OUTLIER) cc_final: 0.7477 (tm-30) REVERT: C 16 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.6635 (mp0) REVERT: C 20 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7192 (mp0) REVERT: C 49 HIS cc_start: 0.7506 (OUTLIER) cc_final: 0.6848 (m-70) REVERT: D 139 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.7169 (mp0) REVERT: D 202 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7143 (mp0) REVERT: D 240 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8494 (mm) REVERT: D 274 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8278 (mp) REVERT: E 188 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.8333 (tp40) REVERT: F 155 ARG cc_start: 0.6477 (OUTLIER) cc_final: 0.6028 (ptt180) REVERT: F 194 ARG cc_start: 0.6860 (tpt90) cc_final: 0.6088 (tmt170) REVERT: F 225 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.7580 (ttm170) REVERT: H 344 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7825 (ttt-90) REVERT: H 347 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.6837 (mp-120) REVERT: H 506 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.8035 (mtp) REVERT: I 163 ARG cc_start: 0.7351 (OUTLIER) cc_final: 0.7066 (mtm180) REVERT: I 176 LYS cc_start: 0.8300 (tppt) cc_final: 0.8080 (mmmt) REVERT: I 230 LEU cc_start: 0.7248 (OUTLIER) cc_final: 0.6656 (mt) REVERT: I 357 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7217 (tt0) REVERT: J 121 ARG cc_start: 0.6222 (OUTLIER) cc_final: 0.5798 (mtt-85) REVERT: J 222 ARG cc_start: 0.7448 (OUTLIER) cc_final: 0.7158 (mtt-85) REVERT: K 93 MET cc_start: 0.7431 (ptm) cc_final: 0.5110 (mpt) REVERT: K 175 ARG cc_start: 0.7361 (OUTLIER) cc_final: 0.6825 (mpt-90) outliers start: 144 outliers final: 64 residues processed: 403 average time/residue: 1.5605 time to fit residues: 728.3063 Evaluate side-chains 373 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 285 time to evaluate : 3.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 244 GLN Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 49 HIS Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 197 PHE Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 135 GLU Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 106 CYS Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 188 GLN Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 116 GLU Chi-restraints excluded: chain F residue 155 ARG Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 177 ASP Chi-restraints excluded: chain F residue 188 GLN Chi-restraints excluded: chain F residue 225 ARG Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 351 THR Chi-restraints excluded: chain G residue 511 SER Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 305 ASP Chi-restraints excluded: chain H residue 344 ARG Chi-restraints excluded: chain H residue 347 GLN Chi-restraints excluded: chain H residue 368 GLU Chi-restraints excluded: chain H residue 394 VAL Chi-restraints excluded: chain H residue 432 VAL Chi-restraints excluded: chain H residue 506 MET Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 95 CYS Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 163 ARG Chi-restraints excluded: chain I residue 230 LEU Chi-restraints excluded: chain I residue 357 GLU Chi-restraints excluded: chain I residue 389 VAL Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain J residue 121 ARG Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 147 ASP Chi-restraints excluded: chain J residue 222 ARG Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 256 VAL Chi-restraints excluded: chain J residue 318 VAL Chi-restraints excluded: chain J residue 400 VAL Chi-restraints excluded: chain K residue 80 PHE Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 175 ARG Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 142 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 118 optimal weight: 0.8980 chunk 316 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 206 optimal weight: 0.2980 chunk 86 optimal weight: 0.7980 chunk 352 optimal weight: 1.9990 chunk 292 optimal weight: 4.9990 chunk 163 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 116 optimal weight: 0.0970 chunk 184 optimal weight: 10.0000 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 GLN C 199 GLN D 199 GLN E 172 ASN G 265 GLN H 317 GLN H 347 GLN H 477 GLN ** I 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 145 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 29292 Z= 0.153 Angle : 0.499 11.604 39700 Z= 0.257 Chirality : 0.042 0.161 4634 Planarity : 0.004 0.062 5072 Dihedral : 5.112 58.951 4023 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.49 % Allowed : 21.66 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.14), residues: 3642 helix: 1.90 (0.14), residues: 1474 sheet: -0.04 (0.22), residues: 566 loop : 0.13 (0.16), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 111 HIS 0.006 0.001 HIS J 304 PHE 0.021 0.001 PHE D 272 TYR 0.015 0.001 TYR K 65 ARG 0.007 0.000 ARG J 223 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 315 time to evaluate : 2.961 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.7494 (pt0) cc_final: 0.7239 (pt0) REVERT: A 91 LYS cc_start: 0.8473 (mmpt) cc_final: 0.8152 (mmmt) REVERT: B 1 MET cc_start: 0.6438 (ttt) cc_final: 0.6164 (ttm) REVERT: B 32 GLU cc_start: 0.5894 (OUTLIER) cc_final: 0.4726 (tm-30) REVERT: B 91 LYS cc_start: 0.8380 (pttt) cc_final: 0.7980 (pttm) REVERT: B 92 ILE cc_start: 0.8139 (OUTLIER) cc_final: 0.7768 (mp) REVERT: B 121 ASP cc_start: 0.8057 (OUTLIER) cc_final: 0.7769 (t0) REVERT: B 244 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7446 (tm-30) REVERT: C 16 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.6603 (mp0) REVERT: C 20 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7154 (mp0) REVERT: C 49 HIS cc_start: 0.7378 (OUTLIER) cc_final: 0.6733 (m-70) REVERT: D 135 GLU cc_start: 0.7677 (tt0) cc_final: 0.7390 (tm-30) REVERT: D 202 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.7089 (mp0) REVERT: D 240 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8295 (mm) REVERT: E 188 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.8299 (tp40) REVERT: F 155 ARG cc_start: 0.6496 (OUTLIER) cc_final: 0.6014 (ptt180) REVERT: F 225 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7562 (ttm170) REVERT: G 445 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7548 (mp0) REVERT: H 506 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.8028 (mtp) REVERT: I 156 ILE cc_start: 0.8505 (OUTLIER) cc_final: 0.8219 (mm) REVERT: I 163 ARG cc_start: 0.7278 (OUTLIER) cc_final: 0.7043 (mtm180) REVERT: I 176 LYS cc_start: 0.8276 (tppt) cc_final: 0.8040 (mmpt) REVERT: I 230 LEU cc_start: 0.7203 (OUTLIER) cc_final: 0.6642 (mt) REVERT: I 357 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7189 (tt0) REVERT: J 199 ASP cc_start: 0.7630 (m-30) cc_final: 0.7014 (t0) REVERT: K 93 MET cc_start: 0.7280 (ptm) cc_final: 0.5055 (mpp) REVERT: K 175 ARG cc_start: 0.7356 (OUTLIER) cc_final: 0.6929 (mpt-90) REVERT: L 80 PHE cc_start: 0.6583 (OUTLIER) cc_final: 0.5448 (m-80) REVERT: L 87 MET cc_start: 0.6405 (ppp) cc_final: 0.5825 (tpt) outliers start: 110 outliers final: 48 residues processed: 394 average time/residue: 1.5316 time to fit residues: 695.6198 Evaluate side-chains 363 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 296 time to evaluate : 3.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 170 HIS Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 244 GLN Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 49 HIS Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain E residue 106 CYS Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 188 GLN Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 116 GLU Chi-restraints excluded: chain F residue 155 ARG Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 188 GLN Chi-restraints excluded: chain F residue 225 ARG Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 305 ASP Chi-restraints excluded: chain H residue 368 GLU Chi-restraints excluded: chain H residue 432 VAL Chi-restraints excluded: chain H residue 506 MET Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 95 CYS Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 163 ARG Chi-restraints excluded: chain I residue 174 LEU Chi-restraints excluded: chain I residue 230 LEU Chi-restraints excluded: chain I residue 357 GLU Chi-restraints excluded: chain I residue 389 VAL Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain J residue 51 SER Chi-restraints excluded: chain J residue 62 ASP Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 147 ASP Chi-restraints excluded: chain J residue 256 VAL Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 318 VAL Chi-restraints excluded: chain J residue 324 GLU Chi-restraints excluded: chain K residue 80 PHE Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 175 ARG Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 80 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 339 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 200 optimal weight: 4.9990 chunk 257 optimal weight: 4.9990 chunk 199 optimal weight: 1.9990 chunk 296 optimal weight: 0.6980 chunk 196 optimal weight: 0.8980 chunk 350 optimal weight: 7.9990 chunk 219 optimal weight: 2.9990 chunk 213 optimal weight: 1.9990 chunk 161 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN D 199 GLN G 265 GLN H 347 GLN J 302 ASN ** L 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 29292 Z= 0.199 Angle : 0.521 10.512 39700 Z= 0.268 Chirality : 0.043 0.161 4634 Planarity : 0.004 0.063 5072 Dihedral : 5.063 57.052 4020 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.43 % Allowed : 22.01 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.14), residues: 3642 helix: 1.91 (0.14), residues: 1474 sheet: -0.06 (0.23), residues: 456 loop : 0.14 (0.16), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 111 HIS 0.006 0.001 HIS J 304 PHE 0.019 0.001 PHE F 266 TYR 0.013 0.001 TYR E 210 ARG 0.007 0.000 ARG J 223 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 304 time to evaluate : 3.634 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 LYS cc_start: 0.8497 (mmpt) cc_final: 0.8168 (mmmt) REVERT: A 121 ASP cc_start: 0.8304 (OUTLIER) cc_final: 0.8039 (t0) REVERT: B 1 MET cc_start: 0.6521 (ttt) cc_final: 0.6234 (ttm) REVERT: B 32 GLU cc_start: 0.5895 (OUTLIER) cc_final: 0.4705 (tm-30) REVERT: B 92 ILE cc_start: 0.8131 (OUTLIER) cc_final: 0.7763 (mp) REVERT: B 121 ASP cc_start: 0.8049 (OUTLIER) cc_final: 0.7756 (t0) REVERT: B 244 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.7452 (tm-30) REVERT: C 16 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.6616 (mp0) REVERT: C 20 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7157 (mp0) REVERT: C 49 HIS cc_start: 0.7423 (OUTLIER) cc_final: 0.6772 (m-70) REVERT: D 202 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7114 (mp0) REVERT: D 240 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8391 (mm) REVERT: D 293 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8055 (mm-30) REVERT: E 188 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.8303 (tp40) REVERT: E 227 GLU cc_start: 0.6865 (mp0) cc_final: 0.6523 (mp0) REVERT: F 128 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7664 (pp) REVERT: F 132 MET cc_start: 0.7891 (mtp) cc_final: 0.7586 (mtt) REVERT: F 155 ARG cc_start: 0.6507 (OUTLIER) cc_final: 0.5980 (ptt180) REVERT: F 225 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7553 (ttm170) REVERT: G 445 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7545 (mp0) REVERT: H 506 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8028 (mtp) REVERT: I 156 ILE cc_start: 0.8503 (OUTLIER) cc_final: 0.8217 (mm) REVERT: I 163 ARG cc_start: 0.7309 (OUTLIER) cc_final: 0.7070 (mtm180) REVERT: I 230 LEU cc_start: 0.7214 (OUTLIER) cc_final: 0.6646 (mt) REVERT: I 357 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7163 (tt0) REVERT: J 222 ARG cc_start: 0.7435 (OUTLIER) cc_final: 0.7140 (mtt-85) REVERT: K 93 MET cc_start: 0.7449 (ptm) cc_final: 0.5034 (mpp) REVERT: K 175 ARG cc_start: 0.7334 (OUTLIER) cc_final: 0.6895 (mpt-90) REVERT: L 80 PHE cc_start: 0.6585 (OUTLIER) cc_final: 0.5471 (m-80) REVERT: L 87 MET cc_start: 0.6409 (ppp) cc_final: 0.5822 (tpt) outliers start: 108 outliers final: 52 residues processed: 379 average time/residue: 1.5231 time to fit residues: 666.7613 Evaluate side-chains 369 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 294 time to evaluate : 3.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 244 GLN Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 49 HIS Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 135 GLU Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain E residue 106 CYS Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 188 GLN Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 116 GLU Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 155 ARG Chi-restraints excluded: chain F residue 188 GLN Chi-restraints excluded: chain F residue 225 ARG Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 305 ASP Chi-restraints excluded: chain H residue 368 GLU Chi-restraints excluded: chain H residue 432 VAL Chi-restraints excluded: chain H residue 506 MET Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 95 CYS Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 163 ARG Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 230 LEU Chi-restraints excluded: chain I residue 357 GLU Chi-restraints excluded: chain I residue 389 VAL Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain J residue 51 SER Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 208 THR Chi-restraints excluded: chain J residue 222 ARG Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 256 VAL Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 318 VAL Chi-restraints excluded: chain K residue 80 PHE Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 175 ARG Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 80 PHE Chi-restraints excluded: chain L residue 142 THR Chi-restraints excluded: chain L residue 160 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 217 optimal weight: 4.9990 chunk 140 optimal weight: 6.9990 chunk 209 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 67 optimal weight: 4.9990 chunk 223 optimal weight: 0.9980 chunk 239 optimal weight: 0.8980 chunk 173 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 275 optimal weight: 5.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 HIS D 199 GLN G 265 GLN H 347 GLN ** I 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 29292 Z= 0.409 Angle : 0.644 12.205 39700 Z= 0.333 Chirality : 0.049 0.199 4634 Planarity : 0.005 0.062 5072 Dihedral : 5.537 59.844 4020 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.84 % Allowed : 21.76 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.14), residues: 3642 helix: 1.41 (0.13), residues: 1488 sheet: -0.39 (0.22), residues: 500 loop : 0.03 (0.16), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP I 111 HIS 0.009 0.001 HIS J 168 PHE 0.027 0.002 PHE F 266 TYR 0.020 0.002 TYR B 304 ARG 0.008 0.001 ARG J 223 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 300 time to evaluate : 3.256 Fit side-chains revert: symmetry clash REVERT: A 14 MET cc_start: 0.7342 (ttp) cc_final: 0.7015 (ttp) REVERT: A 88 LYS cc_start: 0.8111 (mtmm) cc_final: 0.7903 (mtpp) REVERT: A 91 LYS cc_start: 0.8531 (mmpt) cc_final: 0.8179 (mmmt) REVERT: A 121 ASP cc_start: 0.8350 (OUTLIER) cc_final: 0.8076 (t0) REVERT: B 1 MET cc_start: 0.6760 (ttt) cc_final: 0.6413 (ttm) REVERT: B 32 GLU cc_start: 0.6029 (OUTLIER) cc_final: 0.4784 (tm-30) REVERT: B 92 ILE cc_start: 0.8143 (OUTLIER) cc_final: 0.7776 (mp) REVERT: B 121 ASP cc_start: 0.8046 (OUTLIER) cc_final: 0.7734 (t0) REVERT: B 244 GLN cc_start: 0.7988 (OUTLIER) cc_final: 0.7466 (tm-30) REVERT: C 16 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.6638 (mp0) REVERT: C 20 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7175 (mp0) REVERT: C 49 HIS cc_start: 0.7562 (OUTLIER) cc_final: 0.6924 (m-70) REVERT: D 202 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7174 (mp0) REVERT: D 240 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8571 (mm) REVERT: D 274 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8281 (mp) REVERT: E 188 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.8333 (tp40) REVERT: E 227 GLU cc_start: 0.6968 (mp0) cc_final: 0.6708 (mp0) REVERT: F 128 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7744 (pp) REVERT: F 155 ARG cc_start: 0.6623 (OUTLIER) cc_final: 0.6011 (ptt180) REVERT: F 194 ARG cc_start: 0.6820 (tpt90) cc_final: 0.6043 (tmt170) REVERT: F 225 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7624 (ttm170) REVERT: G 445 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7578 (mp0) REVERT: H 506 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.8039 (mtp) REVERT: I 163 ARG cc_start: 0.7383 (OUTLIER) cc_final: 0.7097 (mtm180) REVERT: I 230 LEU cc_start: 0.7296 (OUTLIER) cc_final: 0.6682 (mt) REVERT: I 276 LEU cc_start: 0.8700 (tp) cc_final: 0.8494 (tp) REVERT: I 357 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7236 (tt0) REVERT: J 121 ARG cc_start: 0.6259 (OUTLIER) cc_final: 0.5821 (mtt-85) REVERT: J 222 ARG cc_start: 0.7456 (OUTLIER) cc_final: 0.7161 (mtt-85) REVERT: J 428 ARG cc_start: 0.6769 (mmp-170) cc_final: 0.6514 (mmp-170) REVERT: K 93 MET cc_start: 0.7433 (ptm) cc_final: 0.5034 (mpt) REVERT: K 175 ARG cc_start: 0.7318 (OUTLIER) cc_final: 0.6762 (mpt-90) REVERT: L 80 PHE cc_start: 0.6579 (OUTLIER) cc_final: 0.5520 (m-80) outliers start: 121 outliers final: 62 residues processed: 385 average time/residue: 1.5181 time to fit residues: 675.1191 Evaluate side-chains 369 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 284 time to evaluate : 3.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 170 HIS Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 244 GLN Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 49 HIS Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 197 PHE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain D residue 135 GLU Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain E residue 106 CYS Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 188 GLN Chi-restraints excluded: chain E residue 209 LYS Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 116 GLU Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 155 ARG Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 188 GLN Chi-restraints excluded: chain F residue 225 ARG Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 305 ASP Chi-restraints excluded: chain H residue 368 GLU Chi-restraints excluded: chain H residue 394 VAL Chi-restraints excluded: chain H residue 432 VAL Chi-restraints excluded: chain H residue 506 MET Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 95 CYS Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 163 ARG Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 230 LEU Chi-restraints excluded: chain I residue 357 GLU Chi-restraints excluded: chain I residue 389 VAL Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain J residue 51 SER Chi-restraints excluded: chain J residue 121 ARG Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 147 ASP Chi-restraints excluded: chain J residue 208 THR Chi-restraints excluded: chain J residue 222 ARG Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 256 VAL Chi-restraints excluded: chain J residue 265 ASP Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 318 VAL Chi-restraints excluded: chain K residue 80 PHE Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 175 ARG Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 80 PHE Chi-restraints excluded: chain L residue 142 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 319 optimal weight: 1.9990 chunk 336 optimal weight: 7.9990 chunk 306 optimal weight: 0.2980 chunk 326 optimal weight: 2.9990 chunk 196 optimal weight: 0.9990 chunk 142 optimal weight: 6.9990 chunk 256 optimal weight: 0.3980 chunk 100 optimal weight: 0.0870 chunk 295 optimal weight: 3.9990 chunk 309 optimal weight: 1.9990 chunk 325 optimal weight: 3.9990 overall best weight: 0.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 GLN D 199 GLN ** G 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 347 GLN ** I 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 29292 Z= 0.179 Angle : 0.529 11.567 39700 Z= 0.269 Chirality : 0.043 0.167 4634 Planarity : 0.004 0.063 5072 Dihedral : 5.115 58.669 4020 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.99 % Allowed : 22.71 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.14), residues: 3642 helix: 1.83 (0.14), residues: 1474 sheet: -0.13 (0.23), residues: 456 loop : 0.10 (0.16), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 119 HIS 0.006 0.001 HIS I 304 PHE 0.024 0.001 PHE D 272 TYR 0.014 0.001 TYR K 65 ARG 0.008 0.000 ARG J 223 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 302 time to evaluate : 3.547 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 ASP cc_start: 0.7444 (t70) cc_final: 0.7238 (t0) REVERT: A 91 LYS cc_start: 0.8516 (mmpt) cc_final: 0.8196 (mmmt) REVERT: A 121 ASP cc_start: 0.8330 (OUTLIER) cc_final: 0.8062 (t0) REVERT: A 202 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8209 (tp30) REVERT: B 1 MET cc_start: 0.6510 (ttt) cc_final: 0.6189 (ttm) REVERT: B 32 GLU cc_start: 0.5948 (OUTLIER) cc_final: 0.4755 (tm-30) REVERT: B 92 ILE cc_start: 0.8136 (OUTLIER) cc_final: 0.7765 (mp) REVERT: B 121 ASP cc_start: 0.8050 (OUTLIER) cc_final: 0.7724 (t0) REVERT: B 244 GLN cc_start: 0.7964 (OUTLIER) cc_final: 0.7449 (tm-30) REVERT: C 16 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.6838 (mp0) REVERT: C 20 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7121 (mp0) REVERT: C 49 HIS cc_start: 0.7478 (OUTLIER) cc_final: 0.6858 (m-70) REVERT: D 59 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7843 (mt-10) REVERT: D 202 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.7092 (mp0) REVERT: D 240 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8331 (mm) REVERT: E 188 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.8308 (tp40) REVERT: F 128 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7700 (pp) REVERT: F 155 ARG cc_start: 0.6578 (OUTLIER) cc_final: 0.5996 (ptt180) REVERT: F 225 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7602 (ttm170) REVERT: G 171 LYS cc_start: 0.7974 (mtmm) cc_final: 0.7690 (mmpt) REVERT: H 506 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.8025 (mtp) REVERT: I 163 ARG cc_start: 0.7328 (OUTLIER) cc_final: 0.7107 (mtm180) REVERT: I 230 LEU cc_start: 0.7240 (OUTLIER) cc_final: 0.6642 (mt) REVERT: I 357 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7181 (tt0) REVERT: J 121 ARG cc_start: 0.6208 (OUTLIER) cc_final: 0.5785 (mtt-85) REVERT: J 222 ARG cc_start: 0.7457 (OUTLIER) cc_final: 0.7177 (mtt-85) REVERT: K 93 MET cc_start: 0.7424 (ptm) cc_final: 0.5034 (mpp) REVERT: K 175 ARG cc_start: 0.7322 (OUTLIER) cc_final: 0.6756 (mpt-90) REVERT: L 87 MET cc_start: 0.6462 (ppp) cc_final: 0.5856 (tpt) outliers start: 94 outliers final: 50 residues processed: 371 average time/residue: 1.5567 time to fit residues: 665.4734 Evaluate side-chains 351 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 279 time to evaluate : 3.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 170 HIS Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 244 GLN Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 49 HIS Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain E residue 106 CYS Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 188 GLN Chi-restraints excluded: chain E residue 209 LYS Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 155 ARG Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 188 GLN Chi-restraints excluded: chain F residue 225 ARG Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 305 ASP Chi-restraints excluded: chain H residue 368 GLU Chi-restraints excluded: chain H residue 432 VAL Chi-restraints excluded: chain H residue 506 MET Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 95 CYS Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 163 ARG Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 230 LEU Chi-restraints excluded: chain I residue 357 GLU Chi-restraints excluded: chain I residue 389 VAL Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain J residue 51 SER Chi-restraints excluded: chain J residue 95 CYS Chi-restraints excluded: chain J residue 121 ARG Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 147 ASP Chi-restraints excluded: chain J residue 208 THR Chi-restraints excluded: chain J residue 222 ARG Chi-restraints excluded: chain J residue 256 VAL Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 318 VAL Chi-restraints excluded: chain K residue 80 PHE Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 175 ARG Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 142 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 214 optimal weight: 3.9990 chunk 345 optimal weight: 0.7980 chunk 211 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 240 optimal weight: 0.5980 chunk 362 optimal weight: 7.9990 chunk 333 optimal weight: 0.7980 chunk 288 optimal weight: 0.6980 chunk 29 optimal weight: 7.9990 chunk 223 optimal weight: 2.9990 chunk 177 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 GLN ** G 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 347 GLN ** I 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 145 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 29292 Z= 0.161 Angle : 0.524 15.807 39700 Z= 0.263 Chirality : 0.042 0.160 4634 Planarity : 0.004 0.063 5072 Dihedral : 4.837 57.979 4020 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.41 % Allowed : 23.22 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.14), residues: 3642 helix: 1.98 (0.14), residues: 1474 sheet: 0.12 (0.24), residues: 442 loop : 0.12 (0.16), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 119 HIS 0.006 0.001 HIS I 304 PHE 0.018 0.001 PHE F 266 TYR 0.013 0.001 TYR K 65 ARG 0.007 0.000 ARG J 223 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 289 time to evaluate : 3.598 Fit side-chains revert: symmetry clash REVERT: A 91 LYS cc_start: 0.8501 (mmpt) cc_final: 0.8172 (mmmt) REVERT: B 1 MET cc_start: 0.6439 (ttt) cc_final: 0.6187 (ttm) REVERT: B 91 LYS cc_start: 0.8351 (pttt) cc_final: 0.8056 (ptpp) REVERT: B 92 ILE cc_start: 0.8111 (OUTLIER) cc_final: 0.7770 (mp) REVERT: B 121 ASP cc_start: 0.8010 (OUTLIER) cc_final: 0.7679 (t0) REVERT: B 244 GLN cc_start: 0.7958 (OUTLIER) cc_final: 0.7442 (tm-30) REVERT: C 16 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.6846 (mp0) REVERT: C 20 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7108 (mp0) REVERT: C 49 HIS cc_start: 0.7431 (OUTLIER) cc_final: 0.6828 (m-70) REVERT: D 240 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8300 (mm) REVERT: E 188 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.8268 (tp40) REVERT: E 227 GLU cc_start: 0.6885 (mp0) cc_final: 0.6588 (mp0) REVERT: F 128 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7640 (pp) REVERT: F 132 MET cc_start: 0.7774 (mtp) cc_final: 0.7484 (mtt) REVERT: F 155 ARG cc_start: 0.6555 (OUTLIER) cc_final: 0.5943 (ptt180) REVERT: F 225 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.7586 (ttm170) REVERT: G 171 LYS cc_start: 0.7971 (mtmm) cc_final: 0.7668 (mmpt) REVERT: G 348 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7472 (mt-10) REVERT: H 506 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.8035 (mtp) REVERT: I 163 ARG cc_start: 0.7292 (OUTLIER) cc_final: 0.7090 (mtm180) REVERT: I 230 LEU cc_start: 0.7190 (OUTLIER) cc_final: 0.6622 (mt) REVERT: I 357 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7141 (tt0) REVERT: J 175 GLU cc_start: 0.6186 (mp0) cc_final: 0.5553 (pt0) REVERT: J 222 ARG cc_start: 0.7419 (OUTLIER) cc_final: 0.7134 (mtt-85) REVERT: K 93 MET cc_start: 0.7302 (ptm) cc_final: 0.4986 (mpp) REVERT: K 175 ARG cc_start: 0.7363 (OUTLIER) cc_final: 0.7107 (mpt-90) REVERT: L 87 MET cc_start: 0.6529 (ppp) cc_final: 0.5896 (tpt) outliers start: 76 outliers final: 43 residues processed: 343 average time/residue: 1.5571 time to fit residues: 624.2689 Evaluate side-chains 346 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 286 time to evaluate : 3.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLN Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 170 HIS Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 244 GLN Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 49 HIS Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain E residue 106 CYS Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 188 GLN Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 155 ARG Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 225 ARG Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 511 SER Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 305 ASP Chi-restraints excluded: chain H residue 368 GLU Chi-restraints excluded: chain H residue 432 VAL Chi-restraints excluded: chain H residue 506 MET Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 163 ARG Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 230 LEU Chi-restraints excluded: chain I residue 357 GLU Chi-restraints excluded: chain I residue 389 VAL Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain J residue 95 CYS Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 208 THR Chi-restraints excluded: chain J residue 222 ARG Chi-restraints excluded: chain J residue 256 VAL Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 318 VAL Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 175 ARG Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 142 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 229 optimal weight: 0.8980 chunk 307 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 266 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 289 optimal weight: 6.9990 chunk 121 optimal weight: 2.9990 chunk 296 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 53 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN A 222 GLN ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 GLN ** G 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 347 GLN L 145 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.149529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.111023 restraints weight = 39357.684| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.14 r_work: 0.3359 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.125 29292 Z= 0.198 Angle : 0.645 59.200 39700 Z= 0.353 Chirality : 0.045 0.894 4634 Planarity : 0.004 0.062 5072 Dihedral : 4.689 58.004 4013 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.29 % Allowed : 23.38 % Favored : 74.33 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.14), residues: 3642 helix: 1.98 (0.14), residues: 1474 sheet: 0.13 (0.24), residues: 442 loop : 0.13 (0.16), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 119 HIS 0.005 0.001 HIS J 168 PHE 0.016 0.001 PHE C 272 TYR 0.019 0.001 TYR F 94 ARG 0.007 0.000 ARG J 223 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11579.57 seconds wall clock time: 205 minutes 18.54 seconds (12318.54 seconds total)