Starting phenix.real_space_refine on Tue Jul 23 11:31:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tqz_41566/07_2024/8tqz_41566.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tqz_41566/07_2024/8tqz_41566.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tqz_41566/07_2024/8tqz_41566.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tqz_41566/07_2024/8tqz_41566.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tqz_41566/07_2024/8tqz_41566.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tqz_41566/07_2024/8tqz_41566.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.043 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 121 5.16 5 C 14206 2.51 5 N 3912 2.21 5 O 4095 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 299": "OE1" <-> "OE2" Residue "H TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 50": "OD1" <-> "OD2" Residue "A TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 139": "OD1" <-> "OD2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A ASP 262": "OD1" <-> "OD2" Residue "A PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 32": "OE1" <-> "OE2" Residue "D GLU 145": "OE1" <-> "OE2" Residue "D GLU 149": "OE1" <-> "OE2" Residue "D TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 342": "OE1" <-> "OE2" Residue "E ASP 331": "OD1" <-> "OD2" Residue "E GLU 456": "OE1" <-> "OE2" Residue "I TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 62": "OD1" <-> "OD2" Residue "B ASP 199": "OD1" <-> "OD2" Residue "B ASP 206": "OD1" <-> "OD2" Residue "B ASP 392": "OD1" <-> "OD2" Residue "C ASP 48": "OD1" <-> "OD2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "C GLU 75": "OE1" <-> "OE2" Residue "C GLU 139": "OE1" <-> "OE2" Residue "C TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 342": "OE1" <-> "OE2" Residue "F TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 251": "OD1" <-> "OD2" Residue "F PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 469": "OE1" <-> "OE2" Residue "F TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 49": "OE1" <-> "OE2" Residue "J GLU 116": "OE1" <-> "OE2" Residue "J GLU 178": "OE1" <-> "OE2" Residue "J GLU 217": "OE1" <-> "OE2" Residue "J TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 22334 Number of models: 1 Model: "" Number of chains: 10 Chain: "G" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2039 Classifications: {'peptide': 266} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 9, 'TRANS': 256} Chain breaks: 3 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "H" Number of atoms: 2002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2002 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 9, 'TRANS': 250} Chain breaks: 3 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 3244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3244 Classifications: {'peptide': 414} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 395} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 2483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2483 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 303} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 1983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1983 Classifications: {'peptide': 256} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 245} Chain breaks: 2 Chain: "I" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 380 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain breaks: 3 Chain: "B" Number of atoms: 3239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3239 Classifications: {'peptide': 413} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 394} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2486 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 14, 'TRANS': 303} Chain breaks: 1 Chain: "F" Number of atoms: 2690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2690 Classifications: {'peptide': 346} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 328} Chain: "J" Number of atoms: 1788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1788 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 214} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Time building chain proxies: 12.97, per 1000 atoms: 0.58 Number of scatterers: 22334 At special positions: 0 Unit cell: (133.6, 177.02, 122.745, 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 121 16.00 O 4095 8.00 N 3912 7.00 C 14206 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: 9.10 Conformation dependent library (CDL) restraints added in 4.3 seconds 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5430 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 29 sheets defined 45.5% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.34 Creating SS restraints... Processing helix chain 'G' and resid 10 through 15 Processing helix chain 'G' and resid 21 through 35 removed outlier: 4.101A pdb=" N LYS G 35 " --> pdb=" O LEU G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 60 removed outlier: 3.553A pdb=" N ASN G 48 " --> pdb=" O GLY G 44 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL G 59 " --> pdb=" O THR G 55 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP G 60 " --> pdb=" O LEU G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 74 Processing helix chain 'G' and resid 75 through 77 No H-bonds generated for 'chain 'G' and resid 75 through 77' Processing helix chain 'G' and resid 90 through 116 removed outlier: 3.913A pdb=" N GLU G 95 " --> pdb=" O LYS G 91 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ARG G 96 " --> pdb=" O ILE G 92 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N GLY G 97 " --> pdb=" O MET G 93 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLU G 98 " --> pdb=" O ILE G 94 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU G 99 " --> pdb=" O GLU G 95 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG G 108 " --> pdb=" O ILE G 104 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ASN G 109 " --> pdb=" O SER G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 119 No H-bonds generated for 'chain 'G' and resid 117 through 119' Processing helix chain 'G' and resid 131 through 144 Processing helix chain 'G' and resid 160 through 170 removed outlier: 4.096A pdb=" N HIS G 170 " --> pdb=" O LYS G 166 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 211 No H-bonds generated for 'chain 'G' and resid 209 through 211' Processing helix chain 'G' and resid 212 through 222 Processing helix chain 'G' and resid 231 through 235 removed outlier: 3.863A pdb=" N LYS G 234 " --> pdb=" O GLU G 231 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N PHE G 235 " --> pdb=" O SER G 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 231 through 235' Processing helix chain 'G' and resid 247 through 252 removed outlier: 3.626A pdb=" N LYS G 251 " --> pdb=" O PRO G 247 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR G 252 " --> pdb=" O ASP G 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 247 through 252' Processing helix chain 'G' and resid 277 through 281 Processing helix chain 'G' and resid 295 through 303 removed outlier: 3.703A pdb=" N GLU G 299 " --> pdb=" O ALA G 295 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 17 removed outlier: 3.692A pdb=" N ASP H 17 " --> pdb=" O GLN H 13 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 35 removed outlier: 4.235A pdb=" N LYS H 35 " --> pdb=" O LEU H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 60 Processing helix chain 'H' and resid 62 through 76 removed outlier: 3.684A pdb=" N SER H 66 " --> pdb=" O SER H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 116 removed outlier: 4.489A pdb=" N PHE H 100 " --> pdb=" O ARG H 96 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU H 101 " --> pdb=" O GLY H 97 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU H 106 " --> pdb=" O ARG H 102 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ARG H 108 " --> pdb=" O ILE H 104 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ASN H 109 " --> pdb=" O SER H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 119 No H-bonds generated for 'chain 'H' and resid 117 through 119' Processing helix chain 'H' and resid 131 through 144 Processing helix chain 'H' and resid 160 through 170 removed outlier: 4.268A pdb=" N HIS H 170 " --> pdb=" O LYS H 166 " (cutoff:3.500A) Processing helix chain 'H' and resid 179 through 183 removed outlier: 3.876A pdb=" N VAL H 183 " --> pdb=" O ASP H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 186 through 190 Processing helix chain 'H' and resid 211 through 222 removed outlier: 3.841A pdb=" N MET H 215 " --> pdb=" O GLY H 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 242 through 246 removed outlier: 3.763A pdb=" N VAL H 246 " --> pdb=" O GLN H 243 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 252 Processing helix chain 'H' and resid 277 through 281 Processing helix chain 'H' and resid 292 through 294 No H-bonds generated for 'chain 'H' and resid 292 through 294' Processing helix chain 'H' and resid 295 through 304 removed outlier: 3.534A pdb=" N GLU H 299 " --> pdb=" O ALA H 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 68 Processing helix chain 'A' and resid 74 through 87 removed outlier: 3.526A pdb=" N TYR A 78 " --> pdb=" O ALA A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 108 removed outlier: 3.653A pdb=" N LYS A 108 " --> pdb=" O GLU A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 113 Processing helix chain 'A' and resid 130 through 142 removed outlier: 3.608A pdb=" N VAL A 138 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA A 140 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS A 141 " --> pdb=" O ASP A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 175 removed outlier: 3.652A pdb=" N GLU A 175 " --> pdb=" O ARG A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 233 Processing helix chain 'A' and resid 253 through 263 removed outlier: 3.545A pdb=" N ALA A 257 " --> pdb=" O SER A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 276 Processing helix chain 'A' and resid 302 through 315 Processing helix chain 'D' and resid 9 through 25 removed outlier: 3.694A pdb=" N GLY D 25 " --> pdb=" O THR D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 48 Processing helix chain 'D' and resid 53 through 72 removed outlier: 3.687A pdb=" N LEU D 57 " --> pdb=" O ASN D 53 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN D 72 " --> pdb=" O MET D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 98 Processing helix chain 'D' and resid 128 through 145 removed outlier: 3.869A pdb=" N ASN D 132 " --> pdb=" O GLN D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 153 removed outlier: 3.741A pdb=" N ASN D 150 " --> pdb=" O GLY D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 159 removed outlier: 3.932A pdb=" N HIS D 158 " --> pdb=" O GLN D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 181 removed outlier: 3.952A pdb=" N ALA D 181 " --> pdb=" O PHE D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 209 removed outlier: 3.730A pdb=" N MET D 203 " --> pdb=" O GLN D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 222 removed outlier: 3.838A pdb=" N ALA D 221 " --> pdb=" O THR D 218 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE D 222 " --> pdb=" O ASP D 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 218 through 222' Processing helix chain 'D' and resid 250 through 261 Processing helix chain 'D' and resid 270 through 274 removed outlier: 3.652A pdb=" N LYS D 273 " --> pdb=" O PRO D 270 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU D 274 " --> pdb=" O MET D 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 270 through 274' Processing helix chain 'D' and resid 296 through 305 removed outlier: 4.394A pdb=" N GLY D 300 " --> pdb=" O PHE D 297 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ASP D 301 " --> pdb=" O THR D 298 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ILE D 302 " --> pdb=" O GLU D 299 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU D 303 " --> pdb=" O GLY D 300 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU D 304 " --> pdb=" O ASP D 301 " (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 removed outlier: 3.591A pdb=" N LEU D 339 " --> pdb=" O TYR D 335 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU D 342 " --> pdb=" O ARG D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 349 removed outlier: 3.588A pdb=" N HIS D 349 " --> pdb=" O PRO D 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 238 removed outlier: 3.549A pdb=" N VAL E 236 " --> pdb=" O ALA E 232 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE E 237 " --> pdb=" O LEU E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 283 Processing helix chain 'E' and resid 294 through 312 Processing helix chain 'E' and resid 312 through 325 removed outlier: 4.354A pdb=" N GLN E 325 " --> pdb=" O ARG E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 353 removed outlier: 3.507A pdb=" N GLY E 353 " --> pdb=" O ALA E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 380 removed outlier: 4.069A pdb=" N THR E 372 " --> pdb=" O GLU E 368 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA E 379 " --> pdb=" O SER E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 390 through 395 Processing helix chain 'E' and resid 396 through 398 No H-bonds generated for 'chain 'E' and resid 396 through 398' Processing helix chain 'E' and resid 418 through 430 removed outlier: 4.360A pdb=" N GLN E 422 " --> pdb=" O VAL E 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 459 through 463 removed outlier: 3.852A pdb=" N ASP E 462 " --> pdb=" O ASP E 459 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU E 463 " --> pdb=" O PRO E 460 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 459 through 463' Processing helix chain 'E' and resid 493 through 497 Processing helix chain 'E' and resid 508 through 510 No H-bonds generated for 'chain 'E' and resid 508 through 510' Processing helix chain 'E' and resid 511 through 516 Processing helix chain 'I' and resid 184 through 190 Processing helix chain 'I' and resid 230 through 235 Processing helix chain 'B' and resid 74 through 87 Processing helix chain 'B' and resid 98 through 109 removed outlier: 3.633A pdb=" N ILE B 102 " --> pdb=" O LYS B 98 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS B 108 " --> pdb=" O GLU B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 113 Processing helix chain 'B' and resid 130 through 142 Processing helix chain 'B' and resid 163 through 175 removed outlier: 3.555A pdb=" N GLU B 175 " --> pdb=" O ARG B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 199 Processing helix chain 'B' and resid 228 through 234 Processing helix chain 'B' and resid 253 through 263 removed outlier: 4.111A pdb=" N ALA B 257 " --> pdb=" O SER B 253 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLN B 258 " --> pdb=" O PRO B 254 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN B 263 " --> pdb=" O LEU B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 277 removed outlier: 3.804A pdb=" N LEU B 277 " --> pdb=" O VAL B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 315 Processing helix chain 'B' and resid 330 through 334 removed outlier: 3.849A pdb=" N SER B 334 " --> pdb=" O THR B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 341 No H-bonds generated for 'chain 'B' and resid 339 through 341' Processing helix chain 'C' and resid 9 through 24 Processing helix chain 'C' and resid 30 through 48 Processing helix chain 'C' and resid 53 through 72 removed outlier: 3.702A pdb=" N LEU C 57 " --> pdb=" O ASN C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 98 Processing helix chain 'C' and resid 128 through 153 removed outlier: 4.422A pdb=" N MET C 148 " --> pdb=" O LEU C 144 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N GLU C 149 " --> pdb=" O GLU C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 182 Processing helix chain 'C' and resid 199 through 209 removed outlier: 3.579A pdb=" N MET C 203 " --> pdb=" O GLN C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 223 removed outlier: 3.592A pdb=" N ILE C 222 " --> pdb=" O ASP C 219 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N PHE C 223 " --> pdb=" O ALA C 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 219 through 223' Processing helix chain 'C' and resid 250 through 261 Processing helix chain 'C' and resid 270 through 274 removed outlier: 3.635A pdb=" N LYS C 273 " --> pdb=" O PRO C 270 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU C 274 " --> pdb=" O MET C 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 270 through 274' Processing helix chain 'C' and resid 296 through 304 removed outlier: 4.438A pdb=" N GLY C 300 " --> pdb=" O PHE C 297 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ASP C 301 " --> pdb=" O THR C 298 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ILE C 302 " --> pdb=" O GLU C 299 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU C 303 " --> pdb=" O GLY C 300 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU C 304 " --> pdb=" O ASP C 301 " (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: 3.784A pdb=" N GLU C 342 " --> pdb=" O ARG C 338 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU C 343 " --> pdb=" O LEU C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 349 Processing helix chain 'F' and resid 191 through 196 removed outlier: 4.144A pdb=" N GLN F 194 " --> pdb=" O SER F 191 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE F 195 " --> pdb=" O LEU F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 217 Processing helix chain 'F' and resid 221 through 239 removed outlier: 3.649A pdb=" N CYS F 226 " --> pdb=" O SER F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 267 removed outlier: 4.785A pdb=" N VAL F 253 " --> pdb=" O SER F 249 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N ASN F 254 " --> pdb=" O ARG F 250 " (cutoff:3.500A) Proline residue: F 258 - end of helix Processing helix chain 'F' and resid 270 through 286 Processing helix chain 'F' and resid 292 through 312 Processing helix chain 'F' and resid 312 through 325 removed outlier: 3.889A pdb=" N GLN F 317 " --> pdb=" O VAL F 313 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA F 318 " --> pdb=" O LEU F 314 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLN F 325 " --> pdb=" O ARG F 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 353 Processing helix chain 'F' and resid 368 through 379 removed outlier: 4.133A pdb=" N THR F 372 " --> pdb=" O GLU F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 390 through 395 removed outlier: 3.599A pdb=" N VAL F 394 " --> pdb=" O ALA F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 398 No H-bonds generated for 'chain 'F' and resid 396 through 398' Processing helix chain 'F' and resid 420 through 430 Processing helix chain 'F' and resid 439 through 443 removed outlier: 3.510A pdb=" N LYS F 442 " --> pdb=" O GLU F 439 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE F 443 " --> pdb=" O THR F 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 439 through 443' Processing helix chain 'F' and resid 459 through 464 Processing helix chain 'F' and resid 475 through 479 Processing helix chain 'F' and resid 493 through 497 Processing helix chain 'F' and resid 511 through 517 removed outlier: 3.806A pdb=" N VAL F 515 " --> pdb=" O SER F 511 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 33 removed outlier: 4.030A pdb=" N ASN J 32 " --> pdb=" O PRO J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 34 through 35 No H-bonds generated for 'chain 'J' and resid 34 through 35' Processing helix chain 'J' and resid 36 through 44 Processing helix chain 'J' and resid 86 through 93 Processing helix chain 'J' and resid 114 through 124 removed outlier: 4.243A pdb=" N LEU J 120 " --> pdb=" O GLU J 116 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE J 121 " --> pdb=" O VAL J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 190 Processing helix chain 'J' and resid 208 through 218 removed outlier: 3.727A pdb=" N VAL J 212 " --> pdb=" O LYS J 208 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU J 217 " --> pdb=" O ASP J 213 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASN J 218 " --> pdb=" O PHE J 214 " (cutoff:3.500A) Processing helix chain 'J' and resid 223 through 236 removed outlier: 4.984A pdb=" N ILE J 229 " --> pdb=" O ARG J 225 " (cutoff:3.500A) Proline residue: J 230 - end of helix Processing helix chain 'J' and resid 315 through 334 Proline residue: J 327 - end of helix removed outlier: 3.865A pdb=" N ALA J 332 " --> pdb=" O LYS J 328 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 175 through 178 removed outlier: 8.795A pdb=" N THR G 176 " --> pdb=" O PHE G 148 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL G 150 " --> pdb=" O THR G 176 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N VAL G 178 " --> pdb=" O VAL G 150 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N VAL G 152 " --> pdb=" O VAL G 178 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE G 194 " --> pdb=" O LEU G 126 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N VAL G 193 " --> pdb=" O TYR G 227 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N VAL G 229 " --> pdb=" O VAL G 193 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL G 195 " --> pdb=" O VAL G 229 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N PHE G 226 " --> pdb=" O LEU G 283 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N PHE G 285 " --> pdb=" O PHE G 226 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL G 228 " --> pdb=" O PHE G 285 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR G 286 " --> pdb=" O GLY G 289 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 199 through 200 Processing sheet with id=AA3, first strand: chain 'H' and resid 175 through 178 removed outlier: 6.509A pdb=" N VAL H 150 " --> pdb=" O THR H 176 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N VAL H 178 " --> pdb=" O VAL H 150 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL H 152 " --> pdb=" O VAL H 178 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N THR H 124 " --> pdb=" O LEU H 192 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ILE H 194 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N LEU H 126 " --> pdb=" O ILE H 194 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N GLY H 196 " --> pdb=" O LEU H 126 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL H 193 " --> pdb=" O TYR H 227 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N VAL H 229 " --> pdb=" O VAL H 193 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL H 195 " --> pdb=" O VAL H 229 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N PHE H 226 " --> pdb=" O LEU H 283 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N PHE H 285 " --> pdb=" O PHE H 226 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL H 228 " --> pdb=" O PHE H 285 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR H 286 " --> pdb=" O GLY H 289 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 119 through 124 removed outlier: 6.779A pdb=" N THR A 91 " --> pdb=" O ARG A 121 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ILE A 123 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N VAL A 93 " --> pdb=" O ILE A 123 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL A 48 " --> pdb=" O VAL A 151 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A 250 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N TYR A 152 " --> pdb=" O HIS A 248 " (cutoff:3.500A) removed outlier: 9.216A pdb=" N HIS A 248 " --> pdb=" O TYR A 152 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N CYS A 247 " --> pdb=" O LYS A 186 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N LYS A 186 " --> pdb=" O CYS A 247 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ILE A 249 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N GLN A 286 " --> pdb=" O SER A 179 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N MET A 181 " --> pdb=" O GLN A 286 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ILE A 287 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ARG A 211 " --> pdb=" O ASP A 206 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP A 206 " --> pdb=" O ARG A 211 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL A 202 " --> pdb=" O GLN A 216 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN A 216 " --> pdb=" O VAL A 202 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 119 through 124 removed outlier: 6.779A pdb=" N THR A 91 " --> pdb=" O ARG A 121 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ILE A 123 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N VAL A 93 " --> pdb=" O ILE A 123 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL A 48 " --> pdb=" O VAL A 151 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A 250 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N TYR A 152 " --> pdb=" O HIS A 248 " (cutoff:3.500A) removed outlier: 9.216A pdb=" N HIS A 248 " --> pdb=" O TYR A 152 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N CYS A 247 " --> pdb=" O LYS A 186 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N LYS A 186 " --> pdb=" O CYS A 247 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ILE A 249 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N GLN A 286 " --> pdb=" O SER A 179 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N MET A 181 " --> pdb=" O GLN A 286 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ILE A 287 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ARG A 211 " --> pdb=" O ASP A 206 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP A 206 " --> pdb=" O ARG A 211 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N VAL A 238 " --> pdb=" O PHE I 195 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE I 195 " --> pdb=" O VAL A 238 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL I 160 " --> pdb=" O ARG I 194 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N HIS I 196 " --> pdb=" O ILE I 158 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 155 through 157 Processing sheet with id=AA7, first strand: chain 'A' and resid 223 through 226 removed outlier: 3.814A pdb=" N PHE A 224 " --> pdb=" O ILE I 182 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU I 180 " --> pdb=" O PHE A 226 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 336 through 338 removed outlier: 3.616A pdb=" N ILE A 342 " --> pdb=" O SER A 338 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N LEU A 361 " --> pdb=" O ILE A 379 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N VAL A 378 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N TYR A 395 " --> pdb=" O LEU A 413 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL A 430 " --> pdb=" O ILE A 449 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 355 through 356 removed outlier: 6.228A pdb=" N ILE A 355 " --> pdb=" O ILE A 374 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N PHE A 373 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N VAL A 390 " --> pdb=" O ILE A 408 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLN A 407 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N THR A 424 " --> pdb=" O LEU A 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 384 through 385 removed outlier: 6.376A pdb=" N HIS A 384 " --> pdb=" O VAL A 402 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ARG A 401 " --> pdb=" O VAL A 419 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N GLU A 418 " --> pdb=" O VAL A 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 323 through 325 removed outlier: 3.829A pdb=" N LEU D 323 " --> pdb=" O LEU D 265 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N VAL D 232 " --> pdb=" O ILE D 266 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N CYS D 268 " --> pdb=" O VAL D 232 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE D 234 " --> pdb=" O CYS D 268 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ILE D 168 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE D 165 " --> pdb=" O ILE D 190 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N ALA D 192 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N THR D 167 " --> pdb=" O ALA D 192 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 238 through 239 removed outlier: 3.822A pdb=" N THR D 238 " --> pdb=" O ARG D 246 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA D 247 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 307 through 308 removed outlier: 6.042A pdb=" N SER D 307 " --> pdb=" O TYR E 385 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N LEU E 387 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N VAL E 332 " --> pdb=" O LYS E 400 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU E 402 " --> pdb=" O VAL E 332 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N LEU E 334 " --> pdb=" O LEU E 402 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL E 434 " --> pdb=" O LEU E 499 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N ILE E 501 " --> pdb=" O VAL E 434 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL E 436 " --> pdb=" O ILE E 501 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 407 through 408 Processing sheet with id=AB6, first strand: chain 'B' and resid 119 through 124 removed outlier: 3.556A pdb=" N PHE B 148 " --> pdb=" O CYS B 252 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER B 250 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N TYR B 152 " --> pdb=" O HIS B 248 " (cutoff:3.500A) removed outlier: 9.438A pdb=" N HIS B 248 " --> pdb=" O TYR B 152 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N CYS B 247 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N ILE B 184 " --> pdb=" O CYS B 247 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ILE B 249 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N THR B 182 " --> pdb=" O ILE B 249 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE B 251 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL B 180 " --> pdb=" O ILE B 251 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N GLN B 286 " --> pdb=" O SER B 179 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N MET B 181 " --> pdb=" O GLN B 286 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 155 through 157 Processing sheet with id=AB8, first strand: chain 'B' and resid 212 through 217 removed outlier: 6.554A pdb=" N ALA B 204 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N PHE B 215 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N VAL B 202 " --> pdb=" O PHE B 215 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 223 through 226 Processing sheet with id=AC1, first strand: chain 'B' and resid 336 through 337 removed outlier: 6.040A pdb=" N LEU B 361 " --> pdb=" O ILE B 379 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL B 378 " --> pdb=" O LEU B 396 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TYR B 395 " --> pdb=" O LEU B 413 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU B 412 " --> pdb=" O LEU B 431 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL B 430 " --> pdb=" O ILE B 449 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 355 through 356 removed outlier: 6.279A pdb=" N ILE B 355 " --> pdb=" O ILE B 374 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N PHE B 373 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N VAL B 390 " --> pdb=" O ILE B 408 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLN B 407 " --> pdb=" O LEU B 425 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N THR B 424 " --> pdb=" O LEU B 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'B' and resid 401 through 402 removed outlier: 6.776A pdb=" N ARG B 401 " --> pdb=" O VAL B 419 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 323 through 325 removed outlier: 6.737A pdb=" N LEU C 265 " --> pdb=" O LEU C 323 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ILE C 325 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL C 267 " --> pdb=" O ILE C 325 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL C 232 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N CYS C 268 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE C 234 " --> pdb=" O CYS C 268 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N VAL C 164 " --> pdb=" O LYS C 231 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ILE C 233 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N MET C 166 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE C 165 " --> pdb=" O ILE C 190 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N ALA C 192 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N THR C 167 " --> pdb=" O ALA C 192 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET C 217 " --> pdb=" O VAL C 191 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 238 through 239 removed outlier: 3.898A pdb=" N LEU C 245 " --> pdb=" O VAL C 316 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL C 316 " --> pdb=" O LEU C 245 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA C 247 " --> pdb=" O ASP C 314 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 306 through 308 removed outlier: 6.300A pdb=" N SER C 307 " --> pdb=" O TYR F 385 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N LEU F 387 " --> pdb=" O SER C 307 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N VAL F 332 " --> pdb=" O LYS F 400 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N LEU F 402 " --> pdb=" O VAL F 332 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LEU F 334 " --> pdb=" O LEU F 402 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N GLY F 404 " --> pdb=" O LEU F 334 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N TYR F 336 " --> pdb=" O GLY F 404 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL F 401 " --> pdb=" O LEU F 435 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N CYS F 437 " --> pdb=" O VAL F 401 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LEU F 403 " --> pdb=" O CYS F 437 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL F 434 " --> pdb=" O LEU F 499 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N ILE F 501 " --> pdb=" O VAL F 434 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL F 436 " --> pdb=" O ILE F 501 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 407 through 408 Processing sheet with id=AC8, first strand: chain 'J' and resid 52 through 55 removed outlier: 3.945A pdb=" N THR J 55 " --> pdb=" O ILE J 78 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 101 through 103 removed outlier: 3.540A pdb=" N VAL J 101 " --> pdb=" O LEU J 207 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 199 through 201 Processing sheet with id=AD2, first strand: chain 'J' and resid 167 through 170 removed outlier: 3.516A pdb=" N PHE J 169 " --> pdb=" O GLY J 159 " (cutoff:3.500A) 905 hydrogen bonds defined for protein. 2532 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: 8.21 Time building geometry restraints manager: 9.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7385 1.34 - 1.46: 4221 1.46 - 1.58: 10955 1.58 - 1.70: 1 1.70 - 1.82: 181 Bond restraints: 22743 Sorted by residual: bond pdb=" CB PRO J 79 " pdb=" CG PRO J 79 " ideal model delta sigma weight residual 1.492 1.626 -0.134 5.00e-02 4.00e+02 7.18e+00 bond pdb=" CB ASN F 190 " pdb=" CG ASN F 190 " ideal model delta sigma weight residual 1.516 1.551 -0.035 2.50e-02 1.60e+03 1.99e+00 bond pdb=" CB GLU J 178 " pdb=" CG GLU J 178 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.66e+00 bond pdb=" CG ARG A 163 " pdb=" CD ARG A 163 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.51e+00 bond pdb=" C PHE A 57 " pdb=" N PRO A 58 " ideal model delta sigma weight residual 1.336 1.351 -0.015 1.20e-02 6.94e+03 1.47e+00 ... (remaining 22738 not shown) Histogram of bond angle deviations from ideal: 98.34 - 105.47: 422 105.47 - 112.60: 12281 112.60 - 119.73: 7360 119.73 - 126.86: 10505 126.86 - 133.99: 262 Bond angle restraints: 30830 Sorted by residual: angle pdb=" CA PRO J 79 " pdb=" N PRO J 79 " pdb=" CD PRO J 79 " ideal model delta sigma weight residual 112.00 103.74 8.26 1.40e+00 5.10e-01 3.48e+01 angle pdb=" CA GLU C 75 " pdb=" CB GLU C 75 " pdb=" CG GLU C 75 " ideal model delta sigma weight residual 114.10 120.78 -6.68 2.00e+00 2.50e-01 1.12e+01 angle pdb=" CA GLN E 309 " pdb=" CB GLN E 309 " pdb=" CG GLN E 309 " ideal model delta sigma weight residual 114.10 120.70 -6.60 2.00e+00 2.50e-01 1.09e+01 angle pdb=" CA GLU J 178 " pdb=" CB GLU J 178 " pdb=" CG GLU J 178 " ideal model delta sigma weight residual 114.10 120.70 -6.60 2.00e+00 2.50e-01 1.09e+01 angle pdb=" N PRO J 79 " pdb=" CD PRO J 79 " pdb=" CG PRO J 79 " ideal model delta sigma weight residual 103.20 98.34 4.86 1.50e+00 4.44e-01 1.05e+01 ... (remaining 30825 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 11830 17.84 - 35.67: 1370 35.67 - 53.51: 482 53.51 - 71.34: 84 71.34 - 89.18: 34 Dihedral angle restraints: 13800 sinusoidal: 5459 harmonic: 8341 Sorted by residual: dihedral pdb=" CA PHE B 57 " pdb=" C PHE B 57 " pdb=" N PRO B 58 " pdb=" CA PRO B 58 " ideal model delta harmonic sigma weight residual 180.00 148.31 31.69 0 5.00e+00 4.00e-02 4.02e+01 dihedral pdb=" CA PRO A 453 " pdb=" C PRO A 453 " pdb=" N PRO A 454 " pdb=" CA PRO A 454 " ideal model delta harmonic sigma weight residual -180.00 -158.69 -21.31 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA PRO B 58 " pdb=" C PRO B 58 " pdb=" N ILE B 59 " pdb=" CA ILE B 59 " ideal model delta harmonic sigma weight residual -180.00 -161.55 -18.45 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 13797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3059 0.055 - 0.111: 512 0.111 - 0.166: 61 0.166 - 0.222: 3 0.222 - 0.277: 1 Chirality restraints: 3636 Sorted by residual: chirality pdb=" CB VAL B 238 " pdb=" CA VAL B 238 " pdb=" CG1 VAL B 238 " pdb=" CG2 VAL B 238 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CG LEU A 174 " pdb=" CB LEU A 174 " pdb=" CD1 LEU A 174 " pdb=" CD2 LEU A 174 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA PHE A 57 " pdb=" N PHE A 57 " pdb=" C PHE A 57 " pdb=" CB PHE A 57 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.59e-01 ... (remaining 3633 not shown) Planarity restraints: 3926 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 57 " -0.084 5.00e-02 4.00e+02 1.30e-01 2.70e+01 pdb=" N PRO B 58 " 0.225 5.00e-02 4.00e+02 pdb=" CA PRO B 58 " -0.072 5.00e-02 4.00e+02 pdb=" CD PRO B 58 " -0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE J 78 " 0.087 5.00e-02 4.00e+02 1.26e-01 2.53e+01 pdb=" N PRO J 79 " -0.217 5.00e-02 4.00e+02 pdb=" CA PRO J 79 " 0.065 5.00e-02 4.00e+02 pdb=" CD PRO J 79 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN F 190 " -0.012 2.00e-02 2.50e+03 2.36e-02 5.58e+00 pdb=" C ASN F 190 " 0.041 2.00e-02 2.50e+03 pdb=" O ASN F 190 " -0.016 2.00e-02 2.50e+03 pdb=" N SER F 191 " -0.013 2.00e-02 2.50e+03 ... (remaining 3923 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 220 2.62 - 3.19: 18479 3.19 - 3.76: 33897 3.76 - 4.33: 45134 4.33 - 4.90: 78110 Nonbonded interactions: 175840 Sorted by model distance: nonbonded pdb=" N GLY I 159 " pdb=" O PHE I 169 " model vdw 2.049 2.520 nonbonded pdb=" O PHE B 56 " pdb=" OG SER B 60 " model vdw 2.136 2.440 nonbonded pdb=" OH TYR F 240 " pdb=" OD1 ASP F 251 " model vdw 2.175 2.440 nonbonded pdb=" OG1 THR A 268 " pdb=" OD2 ASP A 271 " model vdw 2.226 2.440 nonbonded pdb=" N GLN D 128 " pdb=" OE1 GLN D 128 " model vdw 2.236 2.520 ... (remaining 175835 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 41 through 175 or (resid 176 and (name N or name CA or nam \ e C or name O or name CB )) or resid 177 through 233 or (resid 234 and (name N o \ r name CA or name C or name O or name CB )) or resid 235 through 346 or (resid 3 \ 47 and (name N or name CA or name C or name O or name CB )) or resid 348 through \ 458)) selection = (chain 'B' and (resid 41 through 218 or (resid 219 and (name N or name CA or nam \ e C or name O or name CB )) or resid 220 through 293 or (resid 294 and (name N o \ r name CA or name C or name O or name CB )) or resid 295 through 420 or (resid 4 \ 21 and (name N or name CA or name C or name O or name CB )) or resid 422 through \ 458)) } ncs_group { reference = (chain 'C' and (resid 8 through 279 or (resid 280 and (name N or name CA or name \ C or name O or name CB )) or resid 281 through 351)) selection = chain 'D' } ncs_group { reference = (chain 'G' and (resid 9 through 14 or (resid 15 through 16 and (name N or name C \ A or name C or name O or name CB )) or resid 17 through 31 or (resid 32 and (nam \ e N or name CA or name C or name O or name CB )) or resid 33 through 36 or resid \ 45 through 76 or resid 94 through 305)) selection = (chain 'H' and (resid 9 through 15 or (resid 16 and (name N or name CA or name C \ or name O or name CB )) or resid 17 through 58 or (resid 59 through 60 and (nam \ e N or name CA or name C or name O or name CB )) or resid 61 through 72 or (resi \ d 73 and (name N or name CA or name C or name O or name CB )) or resid 74 throug \ h 144 or (resid 145 and (name N or name CA or name C or name O or name CB )) or \ resid 146 through 305)) } 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: 4.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.890 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 62.470 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.090 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: 0.000 Load rotamer database and sin/cos tables:11.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 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 : 0.002 0.134 22743 Z= 0.145 Angle : 0.501 10.939 30830 Z= 0.254 Chirality : 0.042 0.277 3636 Planarity : 0.005 0.130 3926 Dihedral : 17.764 89.181 8370 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 4.50 % Allowed : 29.61 % Favored : 65.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.83 % 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: 1.08 (0.17), residues: 2803 helix: 1.83 (0.17), residues: 1076 sheet: 0.35 (0.29), residues: 405 loop : -0.02 (0.18), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 97 HIS 0.008 0.000 HIS A 352 PHE 0.039 0.001 PHE G 10 TYR 0.023 0.001 TYR F 173 ARG 0.019 0.000 ARG A 163 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 247 time to evaluate : 2.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 305 ASP cc_start: 0.8209 (m-30) cc_final: 0.8005 (p0) REVERT: C 338 ARG cc_start: 0.7744 (mmm160) cc_final: 0.7016 (tpm-80) REVERT: F 299 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7285 (mp0) REVERT: J 132 MET cc_start: 0.7871 (mtp) cc_final: 0.7343 (mmt) REVERT: J 227 GLU cc_start: 0.7062 (mt-10) cc_final: 0.6657 (mt-10) outliers start: 111 outliers final: 97 residues processed: 352 average time/residue: 0.9016 time to fit residues: 382.9425 Evaluate side-chains 330 residues out of total 2489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 232 time to evaluate : 2.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 43 GLN Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 159 LEU Chi-restraints excluded: chain G residue 166 LYS Chi-restraints excluded: chain G residue 169 CYS Chi-restraints excluded: chain G residue 170 HIS Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 297 SER Chi-restraints excluded: chain G residue 298 ASP Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 166 LYS Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 287 ASP Chi-restraints excluded: chain H residue 300 LEU Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 232 GLN Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 268 CYS Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 334 SER Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 97 TRP Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 184 LYS Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain F residue 299 GLU Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 100 ASP Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain J residue 107 ASP Chi-restraints excluded: chain J residue 220 SER Chi-restraints excluded: chain J residue 315 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 237 optimal weight: 0.5980 chunk 212 optimal weight: 5.9990 chunk 118 optimal weight: 7.9990 chunk 72 optimal weight: 4.9990 chunk 143 optimal weight: 10.0000 chunk 113 optimal weight: 4.9990 chunk 220 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 chunk 255 optimal weight: 3.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 156 GLN ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 HIS A 248 HIS A 258 GLN A 263 ASN A 341 ASN A 352 HIS A 359 ASN D 150 ASN ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 406 HIS I 190 HIS B 409 HIS B 416 ASN C 230 ASN F 486 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 22743 Z= 0.402 Angle : 0.649 9.438 30830 Z= 0.330 Chirality : 0.049 0.252 3636 Planarity : 0.005 0.096 3926 Dihedral : 7.685 85.198 3231 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 8.92 % Allowed : 24.46 % Favored : 66.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.83 % 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: 0.44 (0.17), residues: 2803 helix: 1.40 (0.17), residues: 1096 sheet: -0.09 (0.28), residues: 400 loop : -0.48 (0.18), residues: 1307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 97 HIS 0.010 0.001 HIS A 352 PHE 0.023 0.002 PHE B 56 TYR 0.018 0.002 TYR J 210 ARG 0.012 0.001 ARG A 163 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 231 time to evaluate : 2.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 181 MET cc_start: 0.8161 (OUTLIER) cc_final: 0.7776 (ttp) REVERT: A 324 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7066 (pp20) REVERT: D 186 LYS cc_start: 0.7908 (tmmt) cc_final: 0.7426 (tmtm) REVERT: D 203 MET cc_start: 0.8113 (OUTLIER) cc_final: 0.7237 (tpt) REVERT: D 226 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7834 (mmt) REVERT: E 234 GLN cc_start: 0.7871 (OUTLIER) cc_final: 0.7488 (pp30) REVERT: E 305 ASP cc_start: 0.8062 (m-30) cc_final: 0.7762 (p0) REVERT: E 325 GLN cc_start: 0.7944 (OUTLIER) cc_final: 0.7630 (pm20) REVERT: E 464 GLN cc_start: 0.7605 (mm-40) cc_final: 0.7380 (mm-40) REVERT: B 62 ASP cc_start: 0.7330 (p0) cc_final: 0.6958 (p0) REVERT: B 219 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.8133 (tm-30) REVERT: C 186 LYS cc_start: 0.8064 (tptp) cc_final: 0.7811 (tppt) REVERT: C 217 MET cc_start: 0.9085 (OUTLIER) cc_final: 0.8527 (ptt) REVERT: J 49 GLU cc_start: 0.8280 (tm-30) cc_final: 0.7358 (mm-30) REVERT: J 227 GLU cc_start: 0.6873 (mt-10) cc_final: 0.6506 (mt-10) REVERT: J 321 GLU cc_start: 0.8479 (tp30) cc_final: 0.8265 (tp30) outliers start: 220 outliers final: 115 residues processed: 417 average time/residue: 0.9415 time to fit residues: 468.9727 Evaluate side-chains 320 residues out of total 2489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 197 time to evaluate : 2.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 159 LEU Chi-restraints excluded: chain G residue 163 LYS Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 149 SER Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain H residue 155 SER Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain H residue 166 LYS Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 279 SER Chi-restraints excluded: chain H residue 298 ASP Chi-restraints excluded: chain H residue 300 LEU Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 232 GLN Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 203 MET Chi-restraints excluded: chain D residue 208 SER Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 268 CYS Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain E residue 234 GLN Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 325 GLN Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 454 SER Chi-restraints excluded: chain E residue 462 ASP Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 515 VAL Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 97 TRP Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 219 GLN Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 305 LYS Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 195 PHE Chi-restraints excluded: chain F residue 249 SER Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 340 SER Chi-restraints excluded: chain F residue 392 SER Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 399 SER Chi-restraints excluded: chain F residue 437 CYS Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 481 SER Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 55 THR Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 77 CYS Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 100 ASP Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 315 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 141 optimal weight: 3.9990 chunk 79 optimal weight: 0.0000 chunk 212 optimal weight: 3.9990 chunk 173 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 255 optimal weight: 5.9990 chunk 276 optimal weight: 5.9990 chunk 227 optimal weight: 0.5980 chunk 253 optimal weight: 2.9990 chunk 87 optimal weight: 0.0570 chunk 205 optimal weight: 0.9990 overall best weight: 0.5104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 48 ASN G 170 HIS H 13 GLN A 118 ASN ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 HIS A 359 ASN ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 378 HIS E 406 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 22743 Z= 0.146 Angle : 0.504 7.535 30830 Z= 0.256 Chirality : 0.043 0.275 3636 Planarity : 0.004 0.066 3926 Dihedral : 6.460 85.380 3168 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 6.37 % Allowed : 27.91 % Favored : 65.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.83 % 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: 0.77 (0.17), residues: 2803 helix: 1.68 (0.17), residues: 1105 sheet: 0.12 (0.29), residues: 382 loop : -0.32 (0.18), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 97 HIS 0.008 0.001 HIS E 378 PHE 0.018 0.001 PHE G 75 TYR 0.019 0.001 TYR F 173 ARG 0.010 0.000 ARG A 223 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 223 time to evaluate : 2.744 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 131 SER cc_start: 0.7951 (OUTLIER) cc_final: 0.7597 (p) REVERT: H 164 MET cc_start: 0.7627 (OUTLIER) cc_final: 0.6971 (tpt) REVERT: H 166 LYS cc_start: 0.7705 (OUTLIER) cc_final: 0.7479 (ttmm) REVERT: A 200 ASN cc_start: 0.7718 (OUTLIER) cc_final: 0.7496 (t0) REVERT: A 324 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.6947 (pp20) REVERT: D 186 LYS cc_start: 0.7868 (tmmt) cc_final: 0.7393 (tmtm) REVERT: E 234 GLN cc_start: 0.7892 (OUTLIER) cc_final: 0.7533 (pp30) REVERT: E 325 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7593 (pm20) REVERT: E 456 GLU cc_start: 0.6895 (OUTLIER) cc_final: 0.6684 (pt0) REVERT: E 464 GLN cc_start: 0.7418 (mm-40) cc_final: 0.7106 (mm-40) REVERT: B 61 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7280 (mtmm) REVERT: B 62 ASP cc_start: 0.7169 (p0) cc_final: 0.6874 (p0) REVERT: B 274 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7798 (ttp-110) REVERT: C 217 MET cc_start: 0.9088 (OUTLIER) cc_final: 0.8511 (ptt) REVERT: F 368 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8648 (mt-10) REVERT: J 49 GLU cc_start: 0.8165 (tm-30) cc_final: 0.7263 (mm-30) outliers start: 157 outliers final: 80 residues processed: 354 average time/residue: 0.9598 time to fit residues: 404.3707 Evaluate side-chains 301 residues out of total 2489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 209 time to evaluate : 2.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 93 MET Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 159 LEU Chi-restraints excluded: chain G residue 170 HIS Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 223 ASN Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 294 SER Chi-restraints excluded: chain G residue 298 ASP Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain G residue 302 LYS Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 164 MET Chi-restraints excluded: chain H residue 166 LYS Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 300 LEU Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 232 GLN Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain E residue 234 GLN Chi-restraints excluded: chain E residue 325 GLN Chi-restraints excluded: chain E residue 378 HIS Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 456 GLU Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 515 VAL Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 97 TRP Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 305 LYS Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 195 PHE Chi-restraints excluded: chain F residue 368 GLU Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 399 SER Chi-restraints excluded: chain F residue 458 ASP Chi-restraints excluded: chain F residue 481 SER Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 100 ASP Chi-restraints excluded: chain J residue 104 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 252 optimal weight: 0.6980 chunk 192 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 28 optimal weight: 8.9990 chunk 122 optimal weight: 0.9980 chunk 171 optimal weight: 0.8980 chunk 256 optimal weight: 0.9990 chunk 271 optimal weight: 0.0270 chunk 134 optimal weight: 4.9990 chunk 243 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 48 ASN G 170 HIS ** G 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 GLN H 156 GLN ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 HIS A 359 ASN ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 378 HIS E 406 HIS F 486 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22743 Z= 0.166 Angle : 0.507 8.771 30830 Z= 0.258 Chirality : 0.043 0.306 3636 Planarity : 0.004 0.097 3926 Dihedral : 6.122 85.888 3153 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 6.45 % Allowed : 28.64 % Favored : 64.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.83 % 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: 0.81 (0.17), residues: 2803 helix: 1.71 (0.17), residues: 1107 sheet: 0.10 (0.29), residues: 372 loop : -0.30 (0.18), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 97 HIS 0.014 0.001 HIS E 378 PHE 0.018 0.001 PHE G 75 TYR 0.020 0.001 TYR F 173 ARG 0.009 0.000 ARG J 324 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 219 time to evaluate : 2.534 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 ASN cc_start: 0.7820 (OUTLIER) cc_final: 0.7564 (t0) REVERT: A 324 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.6949 (pp20) REVERT: D 186 LYS cc_start: 0.7783 (tmmt) cc_final: 0.7295 (tmtm) REVERT: E 234 GLN cc_start: 0.7862 (OUTLIER) cc_final: 0.7544 (pp30) REVERT: E 305 ASP cc_start: 0.8115 (m-30) cc_final: 0.7818 (p0) REVERT: E 325 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7628 (pm20) REVERT: E 464 GLN cc_start: 0.7470 (mm-40) cc_final: 0.7157 (mm-40) REVERT: I 170 MET cc_start: 0.7606 (tpp) cc_final: 0.7319 (ttt) REVERT: I 187 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.6991 (mp) REVERT: B 61 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.7381 (mtmm) REVERT: B 62 ASP cc_start: 0.7158 (p0) cc_final: 0.6870 (p0) REVERT: C 186 LYS cc_start: 0.7986 (OUTLIER) cc_final: 0.7438 (tptp) REVERT: C 217 MET cc_start: 0.9048 (OUTLIER) cc_final: 0.8468 (ptt) REVERT: F 368 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.8622 (mt-10) REVERT: J 227 GLU cc_start: 0.6737 (mt-10) cc_final: 0.6405 (mt-10) outliers start: 159 outliers final: 87 residues processed: 351 average time/residue: 0.9117 time to fit residues: 382.6110 Evaluate side-chains 304 residues out of total 2489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 208 time to evaluate : 2.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 93 MET Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 170 HIS Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 223 ASN Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 294 SER Chi-restraints excluded: chain G residue 298 ASP Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 149 SER Chi-restraints excluded: chain H residue 292 THR Chi-restraints excluded: chain H residue 300 LEU Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 232 GLN Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain E residue 234 GLN Chi-restraints excluded: chain E residue 325 GLN Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 454 SER Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 515 VAL Chi-restraints excluded: chain I residue 187 LEU Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 97 TRP Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain C residue 49 HIS Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 186 LYS Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 305 LYS Chi-restraints excluded: chain C residue 340 MET Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 368 GLU Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 399 SER Chi-restraints excluded: chain F residue 437 CYS Chi-restraints excluded: chain F residue 458 ASP Chi-restraints excluded: chain F residue 481 SER Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 55 THR Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 77 CYS Chi-restraints excluded: chain J residue 100 ASP Chi-restraints excluded: chain J residue 311 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 226 optimal weight: 8.9990 chunk 154 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 202 optimal weight: 0.7980 chunk 112 optimal weight: 0.7980 chunk 231 optimal weight: 1.9990 chunk 187 optimal weight: 0.0470 chunk 0 optimal weight: 7.9990 chunk 138 optimal weight: 2.9990 chunk 243 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 overall best weight: 1.3282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 48 ASN G 170 HIS ** G 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 GLN ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 HIS A 359 ASN ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 406 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 22743 Z= 0.235 Angle : 0.541 9.080 30830 Z= 0.274 Chirality : 0.045 0.323 3636 Planarity : 0.004 0.098 3926 Dihedral : 5.991 86.903 3143 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 6.82 % Allowed : 28.11 % Favored : 65.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.83 % 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: 0.66 (0.17), residues: 2803 helix: 1.63 (0.17), residues: 1108 sheet: -0.15 (0.28), residues: 400 loop : -0.35 (0.18), residues: 1295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 97 HIS 0.008 0.001 HIS A 352 PHE 0.019 0.001 PHE G 75 TYR 0.022 0.001 TYR F 173 ARG 0.015 0.000 ARG A 223 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 218 time to evaluate : 2.667 Fit side-chains revert: symmetry clash REVERT: H 166 LYS cc_start: 0.7667 (ttmm) cc_final: 0.7343 (ttmp) REVERT: A 200 ASN cc_start: 0.7889 (OUTLIER) cc_final: 0.7625 (t0) REVERT: A 324 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7014 (pp20) REVERT: D 178 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7532 (mp) REVERT: D 186 LYS cc_start: 0.7773 (tmmt) cc_final: 0.7317 (tmtm) REVERT: D 203 MET cc_start: 0.8097 (OUTLIER) cc_final: 0.7064 (tpt) REVERT: E 234 GLN cc_start: 0.7867 (OUTLIER) cc_final: 0.7561 (pp30) REVERT: E 321 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.8092 (mtp180) REVERT: E 325 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.7626 (pm20) REVERT: E 347 GLN cc_start: 0.7717 (tt0) cc_final: 0.7044 (tp40) REVERT: E 464 GLN cc_start: 0.7538 (mm-40) cc_final: 0.7138 (mm-40) REVERT: I 170 MET cc_start: 0.7719 (tpp) cc_final: 0.7419 (ttt) REVERT: I 187 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.6993 (mp) REVERT: B 61 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.7856 (mttt) REVERT: B 62 ASP cc_start: 0.7139 (p0) cc_final: 0.6874 (p0) REVERT: B 274 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7763 (ttp-110) REVERT: C 186 LYS cc_start: 0.8007 (OUTLIER) cc_final: 0.7445 (tptp) REVERT: C 217 MET cc_start: 0.9110 (OUTLIER) cc_final: 0.8622 (ptt) REVERT: J 316 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7770 (tm) outliers start: 168 outliers final: 102 residues processed: 360 average time/residue: 0.9788 time to fit residues: 421.0247 Evaluate side-chains 324 residues out of total 2489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 209 time to evaluate : 2.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 121 ASP Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 159 LEU Chi-restraints excluded: chain G residue 169 CYS Chi-restraints excluded: chain G residue 170 HIS Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 223 ASN Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 294 SER Chi-restraints excluded: chain G residue 298 ASP Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 149 SER Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain H residue 155 SER Chi-restraints excluded: chain H residue 292 THR Chi-restraints excluded: chain H residue 298 ASP Chi-restraints excluded: chain H residue 300 LEU Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 203 MET Chi-restraints excluded: chain D residue 208 SER Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain E residue 234 GLN Chi-restraints excluded: chain E residue 321 ARG Chi-restraints excluded: chain E residue 325 GLN Chi-restraints excluded: chain E residue 340 SER Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 454 SER Chi-restraints excluded: chain E residue 462 ASP Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 515 VAL Chi-restraints excluded: chain I residue 187 LEU Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 97 TRP Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 186 LYS Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 305 LYS Chi-restraints excluded: chain C residue 340 MET Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 399 SER Chi-restraints excluded: chain F residue 437 CYS Chi-restraints excluded: chain F residue 481 SER Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 55 THR Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 77 CYS Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 100 ASP Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 128 LEU Chi-restraints excluded: chain J residue 311 SER Chi-restraints excluded: chain J residue 316 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 91 optimal weight: 0.0000 chunk 244 optimal weight: 0.7980 chunk 53 optimal weight: 7.9990 chunk 159 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 271 optimal weight: 0.0980 chunk 225 optimal weight: 6.9990 chunk 125 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 142 optimal weight: 8.9990 overall best weight: 0.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 48 ASN G 170 HIS ** G 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 GLN ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 ASN A 197 HIS A 352 HIS A 359 ASN E 406 HIS F 486 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22743 Z= 0.169 Angle : 0.521 8.598 30830 Z= 0.264 Chirality : 0.044 0.266 3636 Planarity : 0.004 0.099 3926 Dihedral : 5.557 56.232 3138 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 6.41 % Allowed : 28.76 % Favored : 64.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.83 % 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: 0.72 (0.17), residues: 2803 helix: 1.69 (0.17), residues: 1109 sheet: -0.10 (0.28), residues: 384 loop : -0.35 (0.18), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 97 HIS 0.007 0.001 HIS A 352 PHE 0.018 0.001 PHE G 75 TYR 0.018 0.001 TYR F 173 ARG 0.015 0.000 ARG A 145 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 225 time to evaluate : 2.572 Fit side-chains revert: symmetry clash REVERT: H 166 LYS cc_start: 0.7651 (ttmm) cc_final: 0.7322 (ttmp) REVERT: A 200 ASN cc_start: 0.7856 (OUTLIER) cc_final: 0.7602 (t0) REVERT: A 324 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7006 (pp20) REVERT: A 357 GLU cc_start: 0.7392 (tt0) cc_final: 0.7026 (tt0) REVERT: D 186 LYS cc_start: 0.7763 (tmmt) cc_final: 0.7259 (tmtm) REVERT: E 234 GLN cc_start: 0.7845 (OUTLIER) cc_final: 0.7545 (pp30) REVERT: E 305 ASP cc_start: 0.8113 (m-30) cc_final: 0.7850 (p0) REVERT: E 325 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.7625 (pm20) REVERT: E 347 GLN cc_start: 0.7682 (tt0) cc_final: 0.7048 (tp40) REVERT: E 464 GLN cc_start: 0.7560 (mm-40) cc_final: 0.7234 (mm-40) REVERT: I 170 MET cc_start: 0.7705 (tpp) cc_final: 0.7470 (ttt) REVERT: I 187 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.6991 (mp) REVERT: B 61 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.7913 (mttt) REVERT: B 62 ASP cc_start: 0.7111 (p0) cc_final: 0.6860 (p0) REVERT: C 186 LYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7421 (tptp) REVERT: C 217 MET cc_start: 0.9039 (OUTLIER) cc_final: 0.8423 (ptt) REVERT: J 104 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8267 (mp) REVERT: J 227 GLU cc_start: 0.6752 (mt-10) cc_final: 0.6484 (mt-10) outliers start: 158 outliers final: 101 residues processed: 358 average time/residue: 0.9573 time to fit residues: 409.2844 Evaluate side-chains 318 residues out of total 2489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 208 time to evaluate : 2.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 93 MET Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 121 ASP Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 159 LEU Chi-restraints excluded: chain G residue 169 CYS Chi-restraints excluded: chain G residue 170 HIS Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 223 ASN Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 294 SER Chi-restraints excluded: chain G residue 298 ASP Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 149 SER Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 292 THR Chi-restraints excluded: chain H residue 300 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 208 SER Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain E residue 234 GLN Chi-restraints excluded: chain E residue 325 GLN Chi-restraints excluded: chain E residue 340 SER Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 454 SER Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 515 VAL Chi-restraints excluded: chain I residue 187 LEU Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 97 TRP Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain C residue 49 HIS Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 186 LYS Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 305 LYS Chi-restraints excluded: chain C residue 340 MET Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 399 SER Chi-restraints excluded: chain F residue 437 CYS Chi-restraints excluded: chain F residue 458 ASP Chi-restraints excluded: chain F residue 481 SER Chi-restraints excluded: chain J residue 8 MET Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 77 CYS Chi-restraints excluded: chain J residue 100 ASP Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain J residue 311 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 262 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 154 optimal weight: 4.9990 chunk 198 optimal weight: 3.9990 chunk 153 optimal weight: 0.5980 chunk 228 optimal weight: 3.9990 chunk 151 optimal weight: 6.9990 chunk 270 optimal weight: 3.9990 chunk 169 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 125 optimal weight: 7.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 48 ASN G 170 HIS G 208 ASN H 156 GLN A 197 HIS A 200 ASN A 304 HIS A 352 HIS A 359 ASN E 406 HIS ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 22743 Z= 0.393 Angle : 0.643 10.470 30830 Z= 0.325 Chirality : 0.048 0.303 3636 Planarity : 0.005 0.110 3926 Dihedral : 5.979 59.914 3133 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 7.59 % Allowed : 27.51 % Favored : 64.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.83 % 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: 0.25 (0.16), residues: 2803 helix: 1.35 (0.16), residues: 1106 sheet: -0.45 (0.27), residues: 400 loop : -0.62 (0.17), residues: 1297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 97 HIS 0.009 0.001 HIS A 352 PHE 0.019 0.002 PHE G 75 TYR 0.021 0.002 TYR F 173 ARG 0.014 0.001 ARG A 145 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 207 time to evaluate : 2.632 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 166 LYS cc_start: 0.7687 (ttmm) cc_final: 0.7327 (ttmp) REVERT: A 57 PHE cc_start: 0.7197 (p90) cc_final: 0.6825 (p90) REVERT: A 305 MET cc_start: 0.8416 (tpp) cc_final: 0.8064 (mmm) REVERT: A 324 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7148 (pp20) REVERT: A 357 GLU cc_start: 0.7634 (tt0) cc_final: 0.7218 (tt0) REVERT: D 178 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7505 (mp) REVERT: D 186 LYS cc_start: 0.7858 (tmmt) cc_final: 0.7372 (tmtm) REVERT: E 234 GLN cc_start: 0.7834 (OUTLIER) cc_final: 0.7539 (pp30) REVERT: E 325 GLN cc_start: 0.7946 (OUTLIER) cc_final: 0.7679 (pm20) REVERT: E 347 GLN cc_start: 0.7808 (tt0) cc_final: 0.7154 (tp40) REVERT: E 362 ASP cc_start: 0.8395 (OUTLIER) cc_final: 0.8185 (t0) REVERT: E 463 LEU cc_start: 0.7066 (mt) cc_final: 0.6822 (mt) REVERT: E 464 GLN cc_start: 0.7821 (mm-40) cc_final: 0.7452 (mm-40) REVERT: E 509 CYS cc_start: 0.6938 (OUTLIER) cc_final: 0.6480 (t) REVERT: I 170 MET cc_start: 0.7852 (tpp) cc_final: 0.7647 (ttt) REVERT: I 187 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7048 (mp) REVERT: B 61 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8068 (mttt) REVERT: B 62 ASP cc_start: 0.7115 (p0) cc_final: 0.6863 (p0) REVERT: B 274 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7786 (ttp-110) REVERT: C 74 SER cc_start: 0.8618 (OUTLIER) cc_final: 0.8067 (m) REVERT: C 186 LYS cc_start: 0.8028 (OUTLIER) cc_final: 0.7466 (tptp) REVERT: J 104 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8315 (mp) outliers start: 187 outliers final: 111 residues processed: 364 average time/residue: 1.0044 time to fit residues: 441.5510 Evaluate side-chains 330 residues out of total 2489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 207 time to evaluate : 2.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 121 ASP Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 159 LEU Chi-restraints excluded: chain G residue 169 CYS Chi-restraints excluded: chain G residue 170 HIS Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 298 ASP Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 149 SER Chi-restraints excluded: chain H residue 155 SER Chi-restraints excluded: chain H residue 170 HIS Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 279 SER Chi-restraints excluded: chain H residue 292 THR Chi-restraints excluded: chain H residue 298 ASP Chi-restraints excluded: chain H residue 300 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 208 SER Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain E residue 234 GLN Chi-restraints excluded: chain E residue 325 GLN Chi-restraints excluded: chain E residue 340 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 362 ASP Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 454 SER Chi-restraints excluded: chain E residue 462 ASP Chi-restraints excluded: chain E residue 509 CYS Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 515 VAL Chi-restraints excluded: chain I residue 185 SER Chi-restraints excluded: chain I residue 187 LEU Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 97 TRP Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 186 LYS Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 305 LYS Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 340 SER Chi-restraints excluded: chain F residue 392 SER Chi-restraints excluded: chain F residue 399 SER Chi-restraints excluded: chain F residue 437 CYS Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 481 SER Chi-restraints excluded: chain J residue 8 MET Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 55 THR Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 77 CYS Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 100 ASP Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 311 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 167 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 161 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 172 optimal weight: 0.8980 chunk 184 optimal weight: 0.8980 chunk 133 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 212 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 48 ASN ** G 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 GLN A 197 HIS A 352 HIS A 359 ASN E 406 HIS ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 486 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22743 Z= 0.184 Angle : 0.553 9.335 30830 Z= 0.281 Chirality : 0.044 0.302 3636 Planarity : 0.005 0.102 3926 Dihedral : 5.748 58.791 3133 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 5.68 % Allowed : 29.45 % Favored : 64.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.83 % 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: 0.49 (0.17), residues: 2803 helix: 1.57 (0.16), residues: 1107 sheet: -0.33 (0.28), residues: 394 loop : -0.51 (0.18), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 97 HIS 0.010 0.001 HIS A 304 PHE 0.019 0.001 PHE G 75 TYR 0.023 0.001 TYR A 128 ARG 0.017 0.000 ARG A 223 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 210 time to evaluate : 2.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 166 LYS cc_start: 0.7646 (ttmm) cc_final: 0.7293 (ttmp) REVERT: A 57 PHE cc_start: 0.7217 (p90) cc_final: 0.6955 (p90) REVERT: A 200 ASN cc_start: 0.7976 (OUTLIER) cc_final: 0.7745 (t0) REVERT: A 305 MET cc_start: 0.8296 (tpp) cc_final: 0.7973 (mmm) REVERT: A 324 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7088 (pp20) REVERT: A 357 GLU cc_start: 0.7532 (tt0) cc_final: 0.7154 (tt0) REVERT: A 450 SER cc_start: 0.7677 (OUTLIER) cc_final: 0.7218 (p) REVERT: E 234 GLN cc_start: 0.7790 (OUTLIER) cc_final: 0.7508 (pp30) REVERT: E 347 GLN cc_start: 0.7706 (tt0) cc_final: 0.7040 (tp40) REVERT: E 463 LEU cc_start: 0.7011 (mt) cc_final: 0.6757 (mt) REVERT: E 464 GLN cc_start: 0.7697 (mm-40) cc_final: 0.7350 (mm-40) REVERT: I 187 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7049 (mp) REVERT: B 61 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.8002 (mttt) REVERT: B 62 ASP cc_start: 0.7081 (p0) cc_final: 0.6798 (p0) REVERT: B 274 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.7726 (ttp-110) REVERT: C 186 LYS cc_start: 0.7986 (OUTLIER) cc_final: 0.7440 (tptp) REVERT: C 217 MET cc_start: 0.9017 (OUTLIER) cc_final: 0.8274 (ptt) REVERT: J 104 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8302 (mp) REVERT: J 227 GLU cc_start: 0.6793 (mt-10) cc_final: 0.6522 (mt-10) REVERT: J 316 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7767 (tm) outliers start: 140 outliers final: 96 residues processed: 329 average time/residue: 0.9471 time to fit residues: 371.7440 Evaluate side-chains 309 residues out of total 2489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 202 time to evaluate : 2.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 121 ASP Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 169 CYS Chi-restraints excluded: chain G residue 170 HIS Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 298 ASP Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 149 SER Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain H residue 155 SER Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 292 THR Chi-restraints excluded: chain H residue 300 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 232 GLN Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 208 SER Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 228 ARG Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain E residue 234 GLN Chi-restraints excluded: chain E residue 340 SER Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 454 SER Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 515 VAL Chi-restraints excluded: chain I residue 187 LEU Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 97 TRP Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 186 LYS Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 305 LYS Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 392 SER Chi-restraints excluded: chain F residue 399 SER Chi-restraints excluded: chain F residue 437 CYS Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 481 SER Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 55 THR Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 77 CYS Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 100 ASP Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain J residue 311 SER Chi-restraints excluded: chain J residue 316 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 246 optimal weight: 0.9990 chunk 259 optimal weight: 6.9990 chunk 236 optimal weight: 6.9990 chunk 252 optimal weight: 0.9990 chunk 151 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 198 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 228 optimal weight: 2.9990 chunk 238 optimal weight: 3.9990 chunk 251 optimal weight: 0.0170 overall best weight: 1.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 48 ASN G 170 HIS H 13 GLN ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 HIS A 200 ASN A 352 HIS A 359 ASN A 376 ASN E 406 HIS ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 218 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22743 Z= 0.221 Angle : 0.567 8.506 30830 Z= 0.287 Chirality : 0.045 0.307 3636 Planarity : 0.005 0.113 3926 Dihedral : 5.707 59.902 3132 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 5.48 % Allowed : 29.86 % Favored : 64.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.83 % 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: 0.48 (0.17), residues: 2803 helix: 1.57 (0.16), residues: 1108 sheet: -0.37 (0.28), residues: 399 loop : -0.51 (0.18), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 97 HIS 0.009 0.001 HIS A 304 PHE 0.023 0.001 PHE G 75 TYR 0.024 0.001 TYR A 128 ARG 0.015 0.000 ARG A 223 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 206 time to evaluate : 2.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 166 LYS cc_start: 0.7652 (ttmm) cc_final: 0.7295 (ttmp) REVERT: A 305 MET cc_start: 0.8292 (tpp) cc_final: 0.7968 (mmm) REVERT: A 324 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7107 (pp20) REVERT: A 357 GLU cc_start: 0.7577 (tt0) cc_final: 0.7206 (tt0) REVERT: A 450 SER cc_start: 0.7704 (OUTLIER) cc_final: 0.7220 (p) REVERT: E 234 GLN cc_start: 0.7824 (OUTLIER) cc_final: 0.7482 (pp30) REVERT: E 347 GLN cc_start: 0.7714 (tt0) cc_final: 0.7053 (tp40) REVERT: E 463 LEU cc_start: 0.6998 (mt) cc_final: 0.6739 (mt) REVERT: E 464 GLN cc_start: 0.7794 (mm-40) cc_final: 0.7436 (mm-40) REVERT: I 187 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7042 (mp) REVERT: B 61 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.7983 (mttt) REVERT: B 62 ASP cc_start: 0.7079 (p0) cc_final: 0.6801 (p0) REVERT: B 274 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7735 (ttp-110) REVERT: C 58 MET cc_start: 0.8592 (mtm) cc_final: 0.8188 (mtm) REVERT: C 186 LYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7430 (tptp) REVERT: C 217 MET cc_start: 0.9002 (OUTLIER) cc_final: 0.8288 (ptt) REVERT: C 226 MET cc_start: 0.8036 (OUTLIER) cc_final: 0.7570 (mmt) REVERT: J 49 GLU cc_start: 0.8075 (tm-30) cc_final: 0.7020 (mm-30) REVERT: J 104 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8330 (mp) outliers start: 135 outliers final: 101 residues processed: 322 average time/residue: 1.0081 time to fit residues: 386.4278 Evaluate side-chains 309 residues out of total 2489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 198 time to evaluate : 2.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 121 ASP Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 169 CYS Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 298 ASP Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 149 SER Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain H residue 155 SER Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 292 THR Chi-restraints excluded: chain H residue 298 ASP Chi-restraints excluded: chain H residue 300 LEU Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 232 GLN Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 208 SER Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 228 ARG Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain E residue 234 GLN Chi-restraints excluded: chain E residue 340 SER Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 454 SER Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 515 VAL Chi-restraints excluded: chain I residue 187 LEU Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 97 TRP Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 186 LYS Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 226 MET Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 305 LYS Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 392 SER Chi-restraints excluded: chain F residue 399 SER Chi-restraints excluded: chain F residue 437 CYS Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 481 SER Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 55 THR Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 77 CYS Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 100 ASP Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain J residue 311 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 165 optimal weight: 0.6980 chunk 266 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 126 optimal weight: 10.0000 chunk 185 optimal weight: 5.9990 chunk 279 optimal weight: 3.9990 chunk 257 optimal weight: 0.0970 chunk 222 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 172 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 48 ASN G 170 HIS ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 HIS A 352 HIS A 359 ASN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 406 HIS ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 486 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 22743 Z= 0.238 Angle : 0.577 9.521 30830 Z= 0.293 Chirality : 0.045 0.324 3636 Planarity : 0.005 0.111 3926 Dihedral : 5.710 58.584 3132 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 5.07 % Allowed : 29.98 % Favored : 64.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.83 % 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: 0.46 (0.17), residues: 2803 helix: 1.57 (0.16), residues: 1102 sheet: -0.38 (0.28), residues: 399 loop : -0.52 (0.18), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 97 HIS 0.009 0.001 HIS A 304 PHE 0.020 0.001 PHE A 52 TYR 0.024 0.001 TYR A 128 ARG 0.014 0.000 ARG A 223 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 201 time to evaluate : 2.523 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 166 LYS cc_start: 0.7657 (ttmm) cc_final: 0.7294 (ttmp) REVERT: A 305 MET cc_start: 0.8294 (tpp) cc_final: 0.7969 (mmm) REVERT: A 324 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7167 (pp20) REVERT: A 357 GLU cc_start: 0.7600 (tt0) cc_final: 0.7208 (tt0) REVERT: A 450 SER cc_start: 0.7739 (OUTLIER) cc_final: 0.7273 (p) REVERT: E 234 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.7485 (pp30) REVERT: E 347 GLN cc_start: 0.7715 (tt0) cc_final: 0.7057 (tp40) REVERT: E 463 LEU cc_start: 0.7025 (mt) cc_final: 0.6762 (mt) REVERT: E 464 GLN cc_start: 0.7805 (mm-40) cc_final: 0.7448 (mm-40) REVERT: I 187 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7018 (mp) REVERT: B 61 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.8043 (mttt) REVERT: B 62 ASP cc_start: 0.7080 (p0) cc_final: 0.6802 (p0) REVERT: B 274 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7743 (ttp-110) REVERT: B 352 HIS cc_start: 0.7423 (t-90) cc_final: 0.7073 (m-70) REVERT: C 58 MET cc_start: 0.8575 (mtm) cc_final: 0.8158 (mtm) REVERT: C 186 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7447 (tptp) REVERT: J 104 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8304 (mp) REVERT: J 227 GLU cc_start: 0.6733 (mt-10) cc_final: 0.6458 (mt-10) outliers start: 125 outliers final: 102 residues processed: 313 average time/residue: 0.9940 time to fit residues: 372.4813 Evaluate side-chains 309 residues out of total 2489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 199 time to evaluate : 2.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 93 MET Chi-restraints excluded: chain G residue 121 ASP Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 169 CYS Chi-restraints excluded: chain G residue 170 HIS Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 298 ASP Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 149 SER Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain H residue 155 SER Chi-restraints excluded: chain H residue 170 HIS Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 292 THR Chi-restraints excluded: chain H residue 298 ASP Chi-restraints excluded: chain H residue 300 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 232 GLN Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 208 SER Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 228 ARG Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain E residue 234 GLN Chi-restraints excluded: chain E residue 340 SER Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 454 SER Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 515 VAL Chi-restraints excluded: chain I residue 185 SER Chi-restraints excluded: chain I residue 187 LEU Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 97 TRP Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 186 LYS Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 305 LYS Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 340 SER Chi-restraints excluded: chain F residue 392 SER Chi-restraints excluded: chain F residue 399 SER Chi-restraints excluded: chain F residue 437 CYS Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 481 SER Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 55 THR Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 77 CYS Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 100 ASP Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain J residue 311 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 177 optimal weight: 0.9980 chunk 237 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 205 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 61 optimal weight: 6.9990 chunk 223 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 229 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 41 optimal weight: 0.0670 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 48 ASN G 170 HIS A 197 HIS A 352 HIS A 359 ASN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 406 HIS ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 218 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.136060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.105077 restraints weight = 33426.239| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.33 r_work: 0.3444 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22743 Z= 0.174 Angle : 0.557 10.313 30830 Z= 0.281 Chirality : 0.044 0.310 3636 Planarity : 0.004 0.112 3926 Dihedral : 5.544 57.716 3130 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 4.67 % Allowed : 30.55 % Favored : 64.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.83 % 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: 0.59 (0.17), residues: 2803 helix: 1.67 (0.17), residues: 1102 sheet: -0.31 (0.28), residues: 389 loop : -0.45 (0.18), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 97 HIS 0.009 0.001 HIS A 304 PHE 0.019 0.001 PHE G 75 TYR 0.024 0.001 TYR A 128 ARG 0.014 0.000 ARG A 223 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7463.18 seconds wall clock time: 131 minutes 26.65 seconds (7886.65 seconds total)