Starting phenix.real_space_refine on Sat Feb 17 21:12:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdf_4816/02_2024/6rdf_4816.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdf_4816/02_2024/6rdf_4816.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdf_4816/02_2024/6rdf_4816.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdf_4816/02_2024/6rdf_4816.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdf_4816/02_2024/6rdf_4816.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdf_4816/02_2024/6rdf_4816.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 33 5.16 5 C 12734 2.51 5 N 3312 2.21 5 O 3775 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1 TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 28": "NH1" <-> "NH2" Residue "1 PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 58": "OE1" <-> "OE2" Residue "1 ASP 69": "OD1" <-> "OD2" Residue "1 ARG 150": "NH1" <-> "NH2" Residue "1 ASP 172": "OD1" <-> "OD2" Residue "1 ARG 182": "NH1" <-> "NH2" Residue "1 GLU 215": "OE1" <-> "OE2" Residue "1 GLU 229": "OE1" <-> "OE2" Residue "1 GLU 235": "OE1" <-> "OE2" Residue "1 ARG 259": "NH1" <-> "NH2" Residue "1 PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 329": "OE1" <-> "OE2" Residue "1 GLU 339": "OE1" <-> "OE2" Residue "1 GLU 341": "OE1" <-> "OE2" Residue "1 GLU 350": "OE1" <-> "OE2" Residue "1 ARG 359": "NH1" <-> "NH2" Residue "1 GLU 385": "OE1" <-> "OE2" Residue "1 ARG 387": "NH1" <-> "NH2" Residue "1 GLU 409": "OE1" <-> "OE2" Residue "1 GLU 414": "OE1" <-> "OE2" Residue "1 ARG 434": "NH1" <-> "NH2" Residue "1 PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 442": "OD1" <-> "OD2" Residue "1 GLU 457": "OE1" <-> "OE2" Residue "1 GLU 496": "OE1" <-> "OE2" Residue "1 ASP 508": "OD1" <-> "OD2" Residue "1 GLU 577": "OE1" <-> "OE2" Residue "1 ASP 578": "OD1" <-> "OD2" Residue "1 ARG 609": "NH1" <-> "NH2" Residue "1 ASP 613": "OD1" <-> "OD2" Residue "2 TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 45": "NH1" <-> "NH2" Residue "2 TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 86": "OE1" <-> "OE2" Residue "2 GLU 119": "OE1" <-> "OE2" Residue "2 TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 173": "NH1" <-> "NH2" Residue "2 ASP 189": "OD1" <-> "OD2" Residue "2 PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 246": "OE1" <-> "OE2" Residue "2 PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 316": "OD1" <-> "OD2" Residue "2 PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 346": "NH1" <-> "NH2" Residue "2 ASP 362": "OD1" <-> "OD2" Residue "2 TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 149": "NH1" <-> "NH2" Residue "3 ASP 154": "OD1" <-> "OD2" Residue "3 ASP 156": "OD1" <-> "OD2" Residue "3 PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 175": "OE1" <-> "OE2" Residue "3 PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 200": "OD1" <-> "OD2" Residue "3 ARG 213": "NH1" <-> "NH2" Residue "3 TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 233": "NH1" <-> "NH2" Residue "3 ARG 242": "NH1" <-> "NH2" Residue "3 ARG 257": "NH1" <-> "NH2" Residue "3 PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 45": "OD1" <-> "OD2" Residue "4 GLU 64": "OE1" <-> "OE2" Residue "4 ARG 84": "NH1" <-> "NH2" Residue "4 TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 176": "NH1" <-> "NH2" Residue "4 TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 193": "OE1" <-> "OE2" Residue "4 PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 214": "OD1" <-> "OD2" Residue "4 GLU 218": "OE1" <-> "OE2" Residue "4 GLU 225": "OE1" <-> "OE2" Residue "4 ASP 231": "OD1" <-> "OD2" Residue "4 ARG 232": "NH1" <-> "NH2" Residue "4 ARG 255": "NH1" <-> "NH2" Residue "4 GLU 266": "OE1" <-> "OE2" Residue "4 TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 36": "NH1" <-> "NH2" Residue "5 ARG 50": "NH1" <-> "NH2" Residue "5 TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 112": "NH1" <-> "NH2" Residue "5 PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 81": "NH1" <-> "NH2" Residue "7 TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 109": "OD1" <-> "OD2" Residue "7 PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 117": "OD1" <-> "OD2" Residue "7 GLU 125": "OE1" <-> "OE2" Residue "7 TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 164": "NH1" <-> "NH2" Residue "7 ARG 165": "NH1" <-> "NH2" Residue "7 ARG 166": "NH1" <-> "NH2" Residue "7 PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ARG 13": "NH1" <-> "NH2" Residue "8 TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ARG 65": "NH1" <-> "NH2" Residue "8 TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 12": "OE1" <-> "OE2" Residue "9 PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ARG 28": "NH1" <-> "NH2" Residue "9 ARG 40": "NH1" <-> "NH2" Residue "9 PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 74": "OE1" <-> "OE2" Residue "M ARG 115": "NH1" <-> "NH2" Residue "M GLU 124": "OE1" <-> "OE2" Residue "M ARG 145": "NH1" <-> "NH2" Residue "M PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 232": "NH1" <-> "NH2" Residue "M ARG 239": "NH1" <-> "NH2" Residue "M PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 313": "OD1" <-> "OD2" Residue "P GLU 151": "OE1" <-> "OE2" Residue "P TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 163": "OD1" <-> "OD2" Residue "P GLU 166": "OE1" <-> "OE2" Residue "P ASP 179": "OD1" <-> "OD2" Residue "P ASP 191": "OD1" <-> "OD2" Residue "P PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 206": "NH1" <-> "NH2" Residue "P PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 49": "NH1" <-> "NH2" Residue "T GLU 72": "OE1" <-> "OE2" Residue "T GLU 74": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19855 Number of models: 1 Model: "" Number of chains: 18 Chain: "0" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 607 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 8, 'TRANS': 72} Chain: "1" Number of atoms: 4661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4661 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 31, 'TRANS': 563} Chain: "2" Number of atoms: 3163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3163 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 17, 'TRANS': 423} Chain: "3" Number of atoms: 1874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1874 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 239} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 7 Chain: "4" Number of atoms: 2177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2177 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 9, 'TRANS': 280} Chain: "5" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 986 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "6" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 926 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "7" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1347 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 5, 'TRANS': 170} Chain: "8" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 692 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 7, 'TRANS': 80} Chain: "9" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 776 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 5, 'TRANS': 91} Chain: "M" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1640 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "P" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 646 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "T" Number of atoms: 330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 330 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 3, 'TRANS': 36} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "1" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "5" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "6" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Time building chain proxies: 11.15, per 1000 atoms: 0.56 Number of scatterers: 19855 At special positions: 0 Unit cell: (180.063, 117.936, 252.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 33 16.00 O 3775 8.00 N 3312 7.00 C 12734 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: 8.64 Conformation dependent library (CDL) restraints added in 4.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN M 600 " pdb="ZN ZN M 600 " - pdb=" NE2 HIS M 252 " pdb="ZN ZN M 600 " - pdb=" NE2 HIS M 248 " 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4918 Finding SS restraints... Secondary structure from input PDB file: 135 helices and 6 sheets defined 68.2% alpha, 2.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.77 Creating SS restraints... Processing helix chain '0' and resid 3 through 8 removed outlier: 3.689A pdb=" N PHE 0 7 " --> pdb=" O TYR 0 3 " (cutoff:3.500A) Processing helix chain '0' and resid 17 through 30 removed outlier: 3.522A pdb=" N VAL 0 26 " --> pdb=" O VAL 0 22 " (cutoff:3.500A) Processing helix chain '0' and resid 43 through 50 Processing helix chain '0' and resid 51 through 56 removed outlier: 3.727A pdb=" N GLN 0 56 " --> pdb=" O ILE 0 52 " (cutoff:3.500A) Processing helix chain '1' and resid 45 through 70 removed outlier: 3.608A pdb=" N LYS 1 68 " --> pdb=" O LEU 1 64 " (cutoff:3.500A) Processing helix chain '1' and resid 96 through 100 removed outlier: 3.620A pdb=" N THR 1 99 " --> pdb=" O ASP 1 96 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN 1 100 " --> pdb=" O PHE 1 97 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 96 through 100' Processing helix chain '1' and resid 106 through 142 removed outlier: 3.581A pdb=" N ALA 1 122 " --> pdb=" O ARG 1 118 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR 1 135 " --> pdb=" O ALA 1 131 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA 1 139 " --> pdb=" O THR 1 135 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA 1 140 " --> pdb=" O GLU 1 136 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA 1 142 " --> pdb=" O GLU 1 138 " (cutoff:3.500A) Processing helix chain '1' and resid 163 through 176 removed outlier: 3.671A pdb=" N THR 1 169 " --> pdb=" O GLU 1 165 " (cutoff:3.500A) Processing helix chain '1' and resid 190 through 199 removed outlier: 4.261A pdb=" N ALA 1 196 " --> pdb=" O GLY 1 192 " (cutoff:3.500A) Processing helix chain '1' and resid 206 through 208 No H-bonds generated for 'chain '1' and resid 206 through 208' Processing helix chain '1' and resid 209 through 224 removed outlier: 3.739A pdb=" N SER 1 214 " --> pdb=" O ALA 1 210 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU 1 215 " --> pdb=" O SER 1 211 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS 1 224 " --> pdb=" O SER 1 220 " (cutoff:3.500A) Processing helix chain '1' and resid 244 through 271 removed outlier: 3.814A pdb=" N ARG 1 259 " --> pdb=" O GLU 1 255 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS 1 266 " --> pdb=" O LYS 1 262 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL 1 270 " --> pdb=" O LYS 1 266 " (cutoff:3.500A) Processing helix chain '1' and resid 272 through 277 removed outlier: 3.603A pdb=" N ALA 1 275 " --> pdb=" O PRO 1 272 " (cutoff:3.500A) Processing helix chain '1' and resid 278 through 286 removed outlier: 3.726A pdb=" N PHE 1 282 " --> pdb=" O LEU 1 279 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ASP 1 283 " --> pdb=" O ASN 1 280 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA 1 284 " --> pdb=" O GLU 1 281 " (cutoff:3.500A) Processing helix chain '1' and resid 289 through 293 Processing helix chain '1' and resid 297 through 305 removed outlier: 3.790A pdb=" N ALA 1 303 " --> pdb=" O GLU 1 299 " (cutoff:3.500A) Processing helix chain '1' and resid 310 through 317 removed outlier: 3.755A pdb=" N SER 1 317 " --> pdb=" O GLN 1 313 " (cutoff:3.500A) Processing helix chain '1' and resid 318 through 322 Processing helix chain '1' and resid 323 through 327 removed outlier: 3.765A pdb=" N LYS 1 327 " --> pdb=" O PHE 1 324 " (cutoff:3.500A) Processing helix chain '1' and resid 330 through 334 removed outlier: 3.530A pdb=" N GLU 1 334 " --> pdb=" O ALA 1 331 " (cutoff:3.500A) Processing helix chain '1' and resid 338 through 351 Processing helix chain '1' and resid 353 through 362 removed outlier: 3.645A pdb=" N LEU 1 358 " --> pdb=" O PRO 1 354 " (cutoff:3.500A) Processing helix chain '1' and resid 363 through 367 removed outlier: 3.870A pdb=" N GLU 1 367 " --> pdb=" O PRO 1 364 " (cutoff:3.500A) Processing helix chain '1' and resid 375 through 388 removed outlier: 3.829A pdb=" N ARG 1 381 " --> pdb=" O SER 1 377 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL 1 382 " --> pdb=" O GLU 1 378 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU 1 385 " --> pdb=" O ARG 1 381 " (cutoff:3.500A) Processing helix chain '1' and resid 392 through 415 removed outlier: 3.628A pdb=" N LYS 1 396 " --> pdb=" O ARG 1 392 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU 1 401 " --> pdb=" O GLU 1 397 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU 1 415 " --> pdb=" O ALA 1 411 " (cutoff:3.500A) Processing helix chain '1' and resid 425 through 432 removed outlier: 3.760A pdb=" N PHE 1 429 " --> pdb=" O ASP 1 425 " (cutoff:3.500A) Processing helix chain '1' and resid 435 through 444 Processing helix chain '1' and resid 446 through 460 removed outlier: 3.693A pdb=" N LYS 1 451 " --> pdb=" O ALA 1 447 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA 1 460 " --> pdb=" O LYS 1 456 " (cutoff:3.500A) Processing helix chain '1' and resid 463 through 478 removed outlier: 3.744A pdb=" N THR 1 471 " --> pdb=" O ALA 1 467 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN 1 474 " --> pdb=" O VAL 1 470 " (cutoff:3.500A) Processing helix chain '1' and resid 479 through 483 removed outlier: 3.576A pdb=" N ILE 1 483 " --> pdb=" O PRO 1 480 " (cutoff:3.500A) Processing helix chain '1' and resid 485 through 490 Processing helix chain '1' and resid 490 through 495 Processing helix chain '1' and resid 497 through 516 removed outlier: 3.849A pdb=" N GLU 1 501 " --> pdb=" O LEU 1 497 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER 1 503 " --> pdb=" O GLU 1 499 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP 1 508 " --> pdb=" O ASP 1 504 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU 1 512 " --> pdb=" O ASP 1 508 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA 1 515 " --> pdb=" O ALA 1 511 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU 1 516 " --> pdb=" O LEU 1 512 " (cutoff:3.500A) Processing helix chain '1' and resid 518 through 536 removed outlier: 3.716A pdb=" N THR 1 526 " --> pdb=" O LEU 1 522 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N HIS 1 531 " --> pdb=" O GLN 1 527 " (cutoff:3.500A) Processing helix chain '1' and resid 541 through 549 removed outlier: 3.545A pdb=" N VAL 1 545 " --> pdb=" O PRO 1 541 " (cutoff:3.500A) Processing helix chain '1' and resid 549 through 562 Processing helix chain '1' and resid 566 through 574 Processing helix chain '1' and resid 576 through 588 Processing helix chain '1' and resid 589 through 591 No H-bonds generated for 'chain '1' and resid 589 through 591' Processing helix chain '1' and resid 592 through 606 removed outlier: 3.569A pdb=" N ARG 1 600 " --> pdb=" O ILE 1 596 " (cutoff:3.500A) Processing helix chain '2' and resid 7 through 17 removed outlier: 3.651A pdb=" N ILE 2 11 " --> pdb=" O ASP 2 7 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS 2 13 " --> pdb=" O PRO 2 9 " (cutoff:3.500A) Processing helix chain '2' and resid 25 through 39 removed outlier: 3.506A pdb=" N VAL 2 29 " --> pdb=" O SER 2 25 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU 2 39 " --> pdb=" O ALA 2 35 " (cutoff:3.500A) Processing helix chain '2' and resid 44 through 58 removed outlier: 3.692A pdb=" N TRP 2 48 " --> pdb=" O ASN 2 44 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY 2 56 " --> pdb=" O LEU 2 52 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA 2 58 " --> pdb=" O LYS 2 54 " (cutoff:3.500A) Processing helix chain '2' and resid 62 through 76 removed outlier: 3.871A pdb=" N THR 2 67 " --> pdb=" O ALA 2 63 " (cutoff:3.500A) Processing helix chain '2' and resid 80 through 86 Processing helix chain '2' and resid 87 through 94 Processing helix chain '2' and resid 99 through 113 removed outlier: 3.869A pdb=" N SER 2 104 " --> pdb=" O PRO 2 100 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ILE 2 105 " --> pdb=" O VAL 2 101 " (cutoff:3.500A) Processing helix chain '2' and resid 117 through 129 removed outlier: 3.634A pdb=" N ALA 2 126 " --> pdb=" O ASN 2 122 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL 2 128 " --> pdb=" O ALA 2 124 " (cutoff:3.500A) Processing helix chain '2' and resid 136 through 150 removed outlier: 3.947A pdb=" N ARG 2 142 " --> pdb=" O ALA 2 138 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N VAL 2 143 " --> pdb=" O GLU 2 139 " (cutoff:3.500A) Processing helix chain '2' and resid 154 through 168 removed outlier: 3.508A pdb=" N ALA 2 158 " --> pdb=" O ASP 2 154 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA 2 160 " --> pdb=" O ALA 2 156 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY 2 162 " --> pdb=" O ALA 2 158 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS 2 163 " --> pdb=" O LYS 2 159 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL 2 164 " --> pdb=" O ALA 2 160 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER 2 167 " --> pdb=" O LYS 2 163 " (cutoff:3.500A) Processing helix chain '2' and resid 171 through 186 removed outlier: 3.512A pdb=" N LYS 2 184 " --> pdb=" O TYR 2 180 " (cutoff:3.500A) Processing helix chain '2' and resid 189 through 198 removed outlier: 3.602A pdb=" N ASP 2 194 " --> pdb=" O LYS 2 190 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ALA 2 195 " --> pdb=" O ALA 2 191 " (cutoff:3.500A) Processing helix chain '2' and resid 207 through 220 Processing helix chain '2' and resid 227 through 232 Processing helix chain '2' and resid 240 through 254 removed outlier: 3.728A pdb=" N GLU 2 246 " --> pdb=" O ALA 2 242 " (cutoff:3.500A) Processing helix chain '2' and resid 258 through 276 removed outlier: 3.682A pdb=" N PHE 2 262 " --> pdb=" O ASP 2 258 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA 2 264 " --> pdb=" O GLU 2 260 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL 2 268 " --> pdb=" O ALA 2 264 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL 2 269 " --> pdb=" O LEU 2 265 " (cutoff:3.500A) Proline residue: 2 271 - end of helix Processing helix chain '2' and resid 281 through 295 removed outlier: 3.935A pdb=" N GLN 2 287 " --> pdb=" O SER 2 283 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU 2 288 " --> pdb=" O SER 2 284 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER 2 295 " --> pdb=" O ALA 2 291 " (cutoff:3.500A) Processing helix chain '2' and resid 300 through 321 removed outlier: 3.581A pdb=" N SER 2 305 " --> pdb=" O ALA 2 301 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE 2 306 " --> pdb=" O ALA 2 302 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY 2 312 " --> pdb=" O ALA 2 308 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA 2 314 " --> pdb=" O ALA 2 310 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA 2 318 " --> pdb=" O ALA 2 314 " (cutoff:3.500A) Processing helix chain '2' and resid 326 through 341 removed outlier: 3.634A pdb=" N ASP 2 332 " --> pdb=" O ALA 2 328 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE 2 341 " --> pdb=" O THR 2 337 " (cutoff:3.500A) Processing helix chain '2' and resid 345 through 354 removed outlier: 3.824A pdb=" N ALA 2 352 " --> pdb=" O GLU 2 348 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA 2 354 " --> pdb=" O ALA 2 350 " (cutoff:3.500A) Processing helix chain '2' and resid 397 through 408 removed outlier: 3.601A pdb=" N ARG 2 406 " --> pdb=" O TYR 2 402 " (cutoff:3.500A) Processing helix chain '2' and resid 418 through 422 Processing helix chain '2' and resid 426 through 442 removed outlier: 3.619A pdb=" N VAL 2 441 " --> pdb=" O ALA 2 437 " (cutoff:3.500A) Processing helix chain '3' and resid 78 through 87 Processing helix chain '3' and resid 91 through 99 removed outlier: 3.620A pdb=" N ASN 3 97 " --> pdb=" O GLU 3 93 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA 3 99 " --> pdb=" O LEU 3 95 " (cutoff:3.500A) Processing helix chain '3' and resid 102 through 113 removed outlier: 3.551A pdb=" N TRP 3 109 " --> pdb=" O PHE 3 105 " (cutoff:3.500A) Processing helix chain '3' and resid 117 through 122 Processing helix chain '3' and resid 124 through 129 Processing helix chain '3' and resid 131 through 135 Processing helix chain '3' and resid 136 through 150 removed outlier: 3.541A pdb=" N LYS 3 148 " --> pdb=" O THR 3 144 " (cutoff:3.500A) Processing helix chain '3' and resid 154 through 168 removed outlier: 4.105A pdb=" N GLY 3 160 " --> pdb=" O ASP 3 156 " (cutoff:3.500A) Processing helix chain '3' and resid 169 through 172 removed outlier: 3.586A pdb=" N PHE 3 172 " --> pdb=" O PHE 3 169 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 169 through 172' Processing helix chain '3' and resid 173 through 181 removed outlier: 3.803A pdb=" N GLN 3 179 " --> pdb=" O GLU 3 175 " (cutoff:3.500A) Processing helix chain '3' and resid 191 through 204 Processing helix chain '3' and resid 215 through 229 removed outlier: 3.575A pdb=" N LEU 3 219 " --> pdb=" O GLY 3 215 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR 3 221 " --> pdb=" O ASP 3 217 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASN 3 229 " --> pdb=" O TYR 3 225 " (cutoff:3.500A) Processing helix chain '3' and resid 233 through 241 removed outlier: 3.563A pdb=" N THR 3 239 " --> pdb=" O ASP 3 235 " (cutoff:3.500A) Processing helix chain '3' and resid 242 through 244 No H-bonds generated for 'chain '3' and resid 242 through 244' Processing helix chain '3' and resid 245 through 251 Processing helix chain '3' and resid 253 through 271 removed outlier: 3.513A pdb=" N LYS 3 258 " --> pdb=" O ALA 3 254 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP 3 259 " --> pdb=" O ALA 3 255 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE 3 271 " --> pdb=" O ALA 3 267 " (cutoff:3.500A) Processing helix chain '3' and resid 275 through 277 No H-bonds generated for 'chain '3' and resid 275 through 277' Processing helix chain '3' and resid 278 through 287 removed outlier: 3.816A pdb=" N ALA 3 285 " --> pdb=" O VAL 3 281 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL 3 287 " --> pdb=" O GLY 3 283 " (cutoff:3.500A) Processing helix chain '3' and resid 288 through 292 removed outlier: 4.101A pdb=" N GLU 3 291 " --> pdb=" O SER 3 288 " (cutoff:3.500A) Processing helix chain '3' and resid 295 through 309 removed outlier: 3.648A pdb=" N VAL 3 303 " --> pdb=" O GLU 3 299 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN 3 309 " --> pdb=" O VAL 3 305 " (cutoff:3.500A) Processing helix chain '4' and resid 9 through 14 removed outlier: 3.585A pdb=" N TYR 4 13 " --> pdb=" O LYS 4 9 " (cutoff:3.500A) Processing helix chain '4' and resid 19 through 35 removed outlier: 3.617A pdb=" N ALA 4 25 " --> pdb=" O GLU 4 21 " (cutoff:3.500A) Processing helix chain '4' and resid 47 through 68 removed outlier: 4.059A pdb=" N GLN 4 61 " --> pdb=" O TYR 4 57 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL 4 62 " --> pdb=" O LEU 4 58 " (cutoff:3.500A) Proline residue: 4 65 - end of helix removed outlier: 3.676A pdb=" N HIS 4 68 " --> pdb=" O GLU 4 64 " (cutoff:3.500A) Processing helix chain '4' and resid 79 through 96 Processing helix chain '4' and resid 100 through 113 Processing helix chain '4' and resid 118 through 126 removed outlier: 3.515A pdb=" N VAL 4 122 " --> pdb=" O THR 4 118 " (cutoff:3.500A) Processing helix chain '4' and resid 131 through 150 removed outlier: 3.810A pdb=" N VAL 4 141 " --> pdb=" O ALA 4 137 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLU 4 148 " --> pdb=" O SER 4 144 " (cutoff:3.500A) Processing helix chain '4' and resid 159 through 177 removed outlier: 3.654A pdb=" N LYS 4 163 " --> pdb=" O THR 4 159 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE 4 165 " --> pdb=" O GLY 4 161 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LYS 4 168 " --> pdb=" O LYS 4 164 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA 4 171 " --> pdb=" O ALA 4 167 " (cutoff:3.500A) Processing helix chain '4' and resid 179 through 189 removed outlier: 3.735A pdb=" N ALA 4 185 " --> pdb=" O ASP 4 181 " (cutoff:3.500A) Processing helix chain '4' and resid 192 through 234 removed outlier: 3.570A pdb=" N LYS 4 198 " --> pdb=" O ASP 4 194 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL 4 199 " --> pdb=" O ALA 4 195 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR 4 205 " --> pdb=" O LYS 4 201 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TRP 4 206 " --> pdb=" O GLU 4 202 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA 4 213 " --> pdb=" O SER 4 209 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA 4 217 " --> pdb=" O ALA 4 213 " (cutoff:3.500A) Processing helix chain '4' and resid 237 through 259 removed outlier: 4.192A pdb=" N ALA 4 259 " --> pdb=" O ARG 4 255 " (cutoff:3.500A) Processing helix chain '4' and resid 262 through 285 removed outlier: 3.502A pdb=" N GLU 4 284 " --> pdb=" O ALA 4 280 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA 4 285 " --> pdb=" O SER 4 281 " (cutoff:3.500A) Processing helix chain '5' and resid 7 through 29 removed outlier: 3.556A pdb=" N GLU 5 11 " --> pdb=" O SER 5 7 " (cutoff:3.500A) Processing helix chain '5' and resid 30 through 59 removed outlier: 3.731A pdb=" N GLU 5 37 " --> pdb=" O THR 5 33 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU 5 40 " --> pdb=" O ARG 5 36 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N HIS 5 41 " --> pdb=" O GLU 5 37 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N LYS 5 49 " --> pdb=" O ALA 5 45 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ARG 5 50 " --> pdb=" O ALA 5 46 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN 5 52 " --> pdb=" O ALA 5 48 " (cutoff:3.500A) Processing helix chain '5' and resid 63 through 67 Processing helix chain '5' and resid 72 through 81 Processing helix chain '5' and resid 88 through 106 removed outlier: 4.201A pdb=" N LEU 5 92 " --> pdb=" O PRO 5 88 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS 5 94 " --> pdb=" O GLU 5 90 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER 5 97 " --> pdb=" O GLU 5 93 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LYS 5 101 " --> pdb=" O SER 5 97 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL 5 102 " --> pdb=" O ALA 5 98 " (cutoff:3.500A) Processing helix chain '5' and resid 114 through 119 removed outlier: 3.666A pdb=" N LYS 5 119 " --> pdb=" O ILE 5 115 " (cutoff:3.500A) Processing helix chain '6' and resid 30 through 41 Processing helix chain '6' and resid 50 through 58 Processing helix chain '6' and resid 72 through 95 removed outlier: 3.545A pdb=" N LEU 6 79 " --> pdb=" O ALA 6 75 " (cutoff:3.500A) Processing helix chain '6' and resid 98 through 104 Processing helix chain '6' and resid 104 through 118 removed outlier: 3.775A pdb=" N TRP 6 112 " --> pdb=" O LEU 6 108 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU 6 113 " --> pdb=" O GLN 6 109 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER 6 118 " --> pdb=" O ILE 6 114 " (cutoff:3.500A) Processing helix chain '6' and resid 121 through 131 Processing helix chain '6' and resid 133 through 138 removed outlier: 3.872A pdb=" N SER 6 138 " --> pdb=" O PRO 6 134 " (cutoff:3.500A) Processing helix chain '7' and resid 83 through 105 removed outlier: 3.659A pdb=" N GLU 7 99 " --> pdb=" O SER 7 95 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU 7 103 " --> pdb=" O GLU 7 99 " (cutoff:3.500A) Processing helix chain '7' and resid 109 through 114 removed outlier: 3.816A pdb=" N THR 7 112 " --> pdb=" O ASP 7 109 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR 7 114 " --> pdb=" O THR 7 111 " (cutoff:3.500A) Processing helix chain '7' and resid 115 through 120 Processing helix chain '7' and resid 123 through 145 removed outlier: 3.577A pdb=" N PHE 7 130 " --> pdb=" O ASP 7 126 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR 7 137 " --> pdb=" O ALA 7 133 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR 7 138 " --> pdb=" O ALA 7 134 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS 7 139 " --> pdb=" O ASP 7 135 " (cutoff:3.500A) Processing helix chain '7' and resid 146 through 148 No H-bonds generated for 'chain '7' and resid 146 through 148' Processing helix chain '7' and resid 149 through 154 Processing helix chain '7' and resid 157 through 165 removed outlier: 3.651A pdb=" N ARG 7 164 " --> pdb=" O ASN 7 160 " (cutoff:3.500A) Processing helix chain '7' and resid 174 through 187 removed outlier: 3.539A pdb=" N ASN 7 184 " --> pdb=" O GLY 7 180 " (cutoff:3.500A) Processing helix chain '8' and resid 26 through 31 removed outlier: 3.929A pdb=" N SER 8 31 " --> pdb=" O PRO 8 27 " (cutoff:3.500A) Processing helix chain '8' and resid 32 through 39 removed outlier: 3.546A pdb=" N LYS 8 38 " --> pdb=" O THR 8 34 " (cutoff:3.500A) Processing helix chain '8' and resid 39 through 44 Processing helix chain '8' and resid 44 through 78 removed outlier: 3.835A pdb=" N ALA 8 76 " --> pdb=" O ALA 8 72 " (cutoff:3.500A) Processing helix chain '9' and resid 4 through 16 removed outlier: 3.631A pdb=" N LYS 9 9 " --> pdb=" O SER 9 5 " (cutoff:3.500A) Processing helix chain '9' and resid 33 through 55 removed outlier: 3.639A pdb=" N ALA 9 38 " --> pdb=" O GLY 9 34 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N VAL 9 42 " --> pdb=" O ALA 9 38 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN 9 50 " --> pdb=" O MET 9 46 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU 9 53 " --> pdb=" O VAL 9 49 " (cutoff:3.500A) Processing helix chain '9' and resid 76 through 80 removed outlier: 3.550A pdb=" N GLN 9 80 " --> pdb=" O TRP 9 77 " (cutoff:3.500A) Processing helix chain '9' and resid 82 through 95 removed outlier: 3.596A pdb=" N ALA 9 86 " --> pdb=" O ASP 9 82 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU 9 88 " --> pdb=" O ALA 9 84 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS 9 95 " --> pdb=" O LYS 9 91 " (cutoff:3.500A) Processing helix chain 'M' and resid 104 through 119 Processing helix chain 'M' and resid 134 through 144 Processing helix chain 'M' and resid 147 through 164 removed outlier: 3.605A pdb=" N THR M 153 " --> pdb=" O GLY M 149 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N CYS M 162 " --> pdb=" O THR M 158 " (cutoff:3.500A) Processing helix chain 'M' and resid 173 through 176 Processing helix chain 'M' and resid 177 through 198 removed outlier: 3.703A pdb=" N SER M 187 " --> pdb=" O GLY M 183 " (cutoff:3.500A) Processing helix chain 'M' and resid 221 through 265 removed outlier: 3.903A pdb=" N SER M 228 " --> pdb=" O LEU M 224 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG M 232 " --> pdb=" O SER M 228 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ALA M 233 " --> pdb=" O TYR M 229 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N VAL M 234 " --> pdb=" O THR M 230 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLY M 237 " --> pdb=" O ALA M 233 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY M 247 " --> pdb=" O ASN M 243 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N HIS M 248 " --> pdb=" O MET M 244 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU M 261 " --> pdb=" O MET M 257 " (cutoff:3.500A) Proline residue: M 262 - end of helix removed outlier: 3.542A pdb=" N LEU M 265 " --> pdb=" O LEU M 261 " (cutoff:3.500A) Processing helix chain 'M' and resid 270 through 308 removed outlier: 3.720A pdb=" N THR M 274 " --> pdb=" O MET M 270 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU M 280 " --> pdb=" O GLY M 276 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER M 296 " --> pdb=" O ALA M 292 " (cutoff:3.500A) Processing helix chain 'M' and resid 309 through 311 No H-bonds generated for 'chain 'M' and resid 309 through 311' Processing helix chain 'P' and resid 163 through 175 removed outlier: 3.823A pdb=" N VAL P 168 " --> pdb=" O LYS P 164 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS P 172 " --> pdb=" O VAL P 168 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS P 173 " --> pdb=" O GLU P 169 " (cutoff:3.500A) Processing helix chain 'P' and resid 210 through 229 removed outlier: 3.506A pdb=" N GLU P 216 " --> pdb=" O ALA P 212 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU P 227 " --> pdb=" O ASN P 223 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER P 228 " --> pdb=" O LYS P 224 " (cutoff:3.500A) Processing helix chain 'T' and resid 57 through 75 removed outlier: 3.535A pdb=" N ILE T 67 " --> pdb=" O SER T 63 " (cutoff:3.500A) Proline residue: T 68 - end of helix removed outlier: 4.182A pdb=" N GLU T 72 " --> pdb=" O PRO T 68 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TRP T 73 " --> pdb=" O ALA T 69 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU T 74 " --> pdb=" O VAL T 70 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS T 75 " --> pdb=" O LYS T 71 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '1' and resid 183 through 185 removed outlier: 4.423A pdb=" N VAL 1 226 " --> pdb=" O ALA 1 185 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '2' and resid 369 through 372 removed outlier: 7.237A pdb=" N LYS 2 376 " --> pdb=" O ALA 2 412 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ALA 2 414 " --> pdb=" O LYS 2 376 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU 2 378 " --> pdb=" O ALA 2 414 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N VAL 2 416 " --> pdb=" O LEU 2 378 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N GLN 2 380 " --> pdb=" O VAL 2 416 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '3' and resid 314 through 317 Processing sheet with id=AA4, first strand: chain '7' and resid 36 through 41 Processing sheet with id=AA5, first strand: chain 'P' and resid 151 through 152 Processing sheet with id=AA6, first strand: chain 'P' and resid 188 through 190 1072 hydrogen bonds defined for protein. 3135 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: 5.52 Time building geometry restraints manager: 9.14 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: 6225 1.34 - 1.45: 3244 1.45 - 1.57: 10715 1.57 - 1.69: 1 1.69 - 1.81: 54 Bond restraints: 20239 Sorted by residual: bond pdb=" N ILE M 227 " pdb=" CA ILE M 227 " ideal model delta sigma weight residual 1.463 1.494 -0.031 1.14e-02 7.69e+03 7.34e+00 bond pdb=" N ILE 3 101 " pdb=" CA ILE 3 101 " ideal model delta sigma weight residual 1.462 1.492 -0.030 1.18e-02 7.18e+03 6.49e+00 bond pdb=" N LYS 3 88 " pdb=" CA LYS 3 88 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.42e-02 4.96e+03 5.97e+00 bond pdb=" N THR M 226 " pdb=" CA THR M 226 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.20e-02 6.94e+03 5.40e+00 bond pdb=" CB THR M 153 " pdb=" CG2 THR M 153 " ideal model delta sigma weight residual 1.521 1.445 0.076 3.30e-02 9.18e+02 5.35e+00 ... (remaining 20234 not shown) Histogram of bond angle deviations from ideal: 95.78 - 103.44: 222 103.44 - 111.10: 7682 111.10 - 118.77: 8537 118.77 - 126.43: 10741 126.43 - 134.09: 287 Bond angle restraints: 27469 Sorted by residual: angle pdb=" C VAL 7 157 " pdb=" N VAL 7 158 " pdb=" CA VAL 7 158 " ideal model delta sigma weight residual 120.33 126.10 -5.77 8.00e-01 1.56e+00 5.20e+01 angle pdb=" N PRO 3 77 " pdb=" CA PRO 3 77 " pdb=" CB PRO 3 77 " ideal model delta sigma weight residual 103.00 110.34 -7.34 1.10e+00 8.26e-01 4.45e+01 angle pdb=" C PHE 2 222 " pdb=" N LYS 2 223 " pdb=" CA LYS 2 223 " ideal model delta sigma weight residual 121.54 132.70 -11.16 1.91e+00 2.74e-01 3.42e+01 angle pdb=" C GLU 2 225 " pdb=" N LYS 2 226 " pdb=" CA LYS 2 226 " ideal model delta sigma weight residual 121.54 132.48 -10.94 1.91e+00 2.74e-01 3.28e+01 angle pdb=" C VAL P 185 " pdb=" N MET P 186 " pdb=" CA MET P 186 " ideal model delta sigma weight residual 121.54 130.79 -9.25 1.91e+00 2.74e-01 2.34e+01 ... (remaining 27464 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.11: 11181 18.11 - 36.21: 830 36.21 - 54.32: 133 54.32 - 72.42: 27 72.42 - 90.53: 11 Dihedral angle restraints: 12182 sinusoidal: 4595 harmonic: 7587 Sorted by residual: dihedral pdb=" CA VAL P 185 " pdb=" C VAL P 185 " pdb=" N MET P 186 " pdb=" CA MET P 186 " ideal model delta harmonic sigma weight residual 180.00 141.76 38.24 0 5.00e+00 4.00e-02 5.85e+01 dihedral pdb=" CA MET P 186 " pdb=" C MET P 186 " pdb=" N GLN P 187 " pdb=" CA GLN P 187 " ideal model delta harmonic sigma weight residual 180.00 150.39 29.61 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA LYS 5 119 " pdb=" C LYS 5 119 " pdb=" N PRO 5 120 " pdb=" CA PRO 5 120 " ideal model delta harmonic sigma weight residual -180.00 -153.01 -26.99 0 5.00e+00 4.00e-02 2.91e+01 ... (remaining 12179 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 2751 0.077 - 0.155: 375 0.155 - 0.232: 35 0.232 - 0.309: 1 0.309 - 0.386: 1 Chirality restraints: 3163 Sorted by residual: chirality pdb=" CB ILE 3 90 " pdb=" CA ILE 3 90 " pdb=" CG1 ILE 3 90 " pdb=" CG2 ILE 3 90 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.39 2.00e-01 2.50e+01 3.73e+00 chirality pdb=" CB VAL 1 94 " pdb=" CA VAL 1 94 " pdb=" CG1 VAL 1 94 " pdb=" CG2 VAL 1 94 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA PRO 3 77 " pdb=" N PRO 3 77 " pdb=" C PRO 3 77 " pdb=" CB PRO 3 77 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 3160 not shown) Planarity restraints: 3505 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA 3 210 " 0.054 5.00e-02 4.00e+02 8.01e-02 1.03e+01 pdb=" N PRO 3 211 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO 3 211 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO 3 211 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU M 261 " 0.049 5.00e-02 4.00e+02 7.26e-02 8.43e+00 pdb=" N PRO M 262 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO M 262 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO M 262 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR 1 92 " 0.046 5.00e-02 4.00e+02 6.96e-02 7.75e+00 pdb=" N PRO 1 93 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO 1 93 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO 1 93 " 0.038 5.00e-02 4.00e+02 ... (remaining 3502 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3216 2.75 - 3.29: 18290 3.29 - 3.82: 32796 3.82 - 4.36: 41062 4.36 - 4.90: 68671 Nonbonded interactions: 164035 Sorted by model distance: nonbonded pdb=" CD2 LEU M 224 " pdb=" O HOH M 709 " model vdw 2.212 3.460 nonbonded pdb=" CG LEU M 224 " pdb=" O HOH M 709 " model vdw 2.218 3.470 nonbonded pdb=" OH TYR 5 62 " pdb=" O PHE 6 146 " model vdw 2.227 2.440 nonbonded pdb=" O THR 5 83 " pdb=" OH TYR 7 119 " model vdw 2.240 2.440 nonbonded pdb=" O LEU 1 315 " pdb=" OG SER 1 318 " model vdw 2.278 2.440 ... (remaining 164030 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 6.680 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: 24.800 Check model and map are aligned: 0.340 Set scattering table: 0.250 Process input model: 57.700 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 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 : 0.008 0.086 20239 Z= 0.502 Angle : 0.891 12.907 27469 Z= 0.499 Chirality : 0.054 0.386 3163 Planarity : 0.007 0.080 3505 Dihedral : 13.404 90.526 7264 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.67 % Favored : 95.17 % Rotamer: Outliers : 0.15 % Allowed : 5.48 % Favored : 94.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -6.00 (0.10), residues: 2569 helix: -4.55 (0.05), residues: 1682 sheet: -1.91 (0.65), residues: 52 loop : -2.21 (0.18), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP 9 73 HIS 0.011 0.002 HIS 4 233 PHE 0.022 0.002 PHE 3 115 TYR 0.025 0.003 TYR 4 211 ARG 0.004 0.001 ARG 1 387 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 376 time to evaluate : 2.257 Fit side-chains REVERT: 1 155 GLU cc_start: 0.7659 (tm-30) cc_final: 0.7268 (tm-30) REVERT: 1 346 GLN cc_start: 0.8224 (pp30) cc_final: 0.7692 (mp10) REVERT: 1 572 ASP cc_start: 0.7846 (m-30) cc_final: 0.7537 (m-30) REVERT: 1 586 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7794 (mm-30) REVERT: 1 613 ASP cc_start: 0.8118 (m-30) cc_final: 0.7825 (m-30) REVERT: 2 154 ASP cc_start: 0.6606 (t70) cc_final: 0.5922 (p0) REVERT: 2 197 LEU cc_start: 0.7848 (mt) cc_final: 0.7504 (mt) REVERT: 4 197 ASP cc_start: 0.8593 (t70) cc_final: 0.8357 (t0) REVERT: 4 255 ARG cc_start: 0.8122 (ttm170) cc_final: 0.7897 (mtp180) REVERT: 5 37 GLU cc_start: 0.8716 (pt0) cc_final: 0.8447 (pt0) REVERT: 6 37 LYS cc_start: 0.8712 (ttpp) cc_final: 0.8437 (ttmt) REVERT: 8 69 LYS cc_start: 0.8543 (mttt) cc_final: 0.6233 (tmtt) REVERT: 9 13 LYS cc_start: 0.6687 (mtmt) cc_final: 0.6138 (tttm) REVERT: 9 56 ASN cc_start: 0.8584 (p0) cc_final: 0.8247 (p0) REVERT: M 97 VAL cc_start: 0.9252 (t) cc_final: 0.9034 (m) REVERT: M 168 MET cc_start: 0.8101 (mmt) cc_final: 0.7818 (mmt) REVERT: M 230 THR cc_start: 0.9168 (t) cc_final: 0.8936 (m) REVERT: P 183 LYS cc_start: 0.8291 (ptmm) cc_final: 0.8005 (ptmt) REVERT: P 205 ARG cc_start: 0.7596 (ptt-90) cc_final: 0.3492 (mmp-170) REVERT: T 49 ARG cc_start: 0.8399 (mtp-110) cc_final: 0.7947 (mtp85) outliers start: 3 outliers final: 2 residues processed: 379 average time/residue: 0.4059 time to fit residues: 218.0766 Evaluate side-chains 244 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 242 time to evaluate : 2.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 102 LEU Chi-restraints excluded: chain 1 residue 227 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 215 optimal weight: 5.9990 chunk 193 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 199 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 121 optimal weight: 0.0270 chunk 148 optimal weight: 7.9990 chunk 231 optimal weight: 0.8980 overall best weight: 0.7442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 60 GLN 1 209 ASN 1 257 HIS 1 285 GLN 1 298 GLN 1 316 ASN 1 365 GLN 1 482 ASN 1 531 HIS 1 587 ASN 1 590 HIS 2 243 GLN 2 427 GLN 3 164 ASN 3 189 HIS 3 206 ASN 3 229 ASN 4 240 GLN 5 29 GLN 5 107 ASN 5 117 GLN 6 40 ASN 6 74 GLN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 60 GLN 7 86 HIS 7 91 ASN ** 7 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 123 HIS 7 170 HIS 7 184 ASN 8 26 HIS 8 29 GLN 8 78 HIS M 108 ASN M 163 ASN P 223 ASN T 78 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20239 Z= 0.189 Angle : 0.586 13.813 27469 Z= 0.310 Chirality : 0.040 0.182 3163 Planarity : 0.006 0.057 3505 Dihedral : 5.383 33.242 2749 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.01 % Favored : 95.87 % Rotamer: Outliers : 1.70 % Allowed : 8.29 % Favored : 90.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.30 (0.14), residues: 2569 helix: -2.33 (0.10), residues: 1690 sheet: -0.68 (0.80), residues: 44 loop : -1.49 (0.20), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP 9 73 HIS 0.006 0.001 HIS 4 233 PHE 0.013 0.001 PHE 3 115 TYR 0.026 0.002 TYR 4 211 ARG 0.005 0.000 ARG 1 387 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 281 time to evaluate : 2.217 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 49 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7251 (tt0) REVERT: 1 572 ASP cc_start: 0.7810 (m-30) cc_final: 0.7459 (m-30) REVERT: 1 586 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7495 (mm-30) REVERT: 1 613 ASP cc_start: 0.7939 (m-30) cc_final: 0.7582 (m-30) REVERT: 2 74 ASN cc_start: 0.8444 (t0) cc_final: 0.8176 (t0) REVERT: 2 154 ASP cc_start: 0.6910 (t70) cc_final: 0.5968 (p0) REVERT: 4 255 ARG cc_start: 0.8098 (ttm170) cc_final: 0.7881 (mtp-110) REVERT: 5 90 GLU cc_start: 0.7932 (tm-30) cc_final: 0.7713 (tm-30) REVERT: 6 37 LYS cc_start: 0.8717 (ttpp) cc_final: 0.8432 (ttmt) REVERT: 8 69 LYS cc_start: 0.8444 (mttt) cc_final: 0.6347 (tmtt) REVERT: 9 56 ASN cc_start: 0.8467 (p0) cc_final: 0.8100 (p0) REVERT: M 168 MET cc_start: 0.8003 (mmt) cc_final: 0.7735 (mmt) REVERT: M 230 THR cc_start: 0.9373 (t) cc_final: 0.9061 (m) REVERT: M 270 MET cc_start: 0.6925 (tmm) cc_final: 0.6485 (mmm) REVERT: M 324 LYS cc_start: 0.7701 (tppt) cc_final: 0.7195 (tptp) REVERT: P 183 LYS cc_start: 0.7841 (ptmm) cc_final: 0.7538 (ttpt) REVERT: P 205 ARG cc_start: 0.7582 (ptt-90) cc_final: 0.3541 (mmp-170) REVERT: T 49 ARG cc_start: 0.8376 (mtp-110) cc_final: 0.7957 (mtp85) outliers start: 35 outliers final: 23 residues processed: 308 average time/residue: 0.3531 time to fit residues: 161.5264 Evaluate side-chains 266 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 243 time to evaluate : 2.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 1 residue 223 GLU Chi-restraints excluded: chain 1 residue 227 VAL Chi-restraints excluded: chain 1 residue 261 LEU Chi-restraints excluded: chain 1 residue 608 ASP Chi-restraints excluded: chain 2 residue 238 ASP Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 2 residue 359 THR Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 416 VAL Chi-restraints excluded: chain 3 residue 117 SER Chi-restraints excluded: chain 3 residue 195 LEU Chi-restraints excluded: chain 4 residue 19 ASP Chi-restraints excluded: chain 4 residue 45 ASP Chi-restraints excluded: chain 4 residue 273 LYS Chi-restraints excluded: chain 5 residue 61 SER Chi-restraints excluded: chain 5 residue 97 SER Chi-restraints excluded: chain 6 residue 72 SER Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 9 residue 76 THR Chi-restraints excluded: chain M residue 280 LEU Chi-restraints excluded: chain P residue 184 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 128 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 192 optimal weight: 20.0000 chunk 157 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 231 optimal weight: 2.9990 chunk 250 optimal weight: 4.9990 chunk 206 optimal weight: 4.9990 chunk 230 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 186 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 380 GLN 5 59 ASN ** 7 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 20239 Z= 0.318 Angle : 0.602 15.930 27469 Z= 0.312 Chirality : 0.043 0.202 3163 Planarity : 0.005 0.055 3505 Dihedral : 5.070 29.318 2747 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.44 % Favored : 95.48 % Rotamer: Outliers : 2.13 % Allowed : 10.66 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.16), residues: 2569 helix: -1.05 (0.12), residues: 1691 sheet: -0.50 (0.77), residues: 50 loop : -1.19 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP 9 73 HIS 0.008 0.001 HIS 7 123 PHE 0.017 0.001 PHE M 275 TYR 0.025 0.002 TYR 4 211 ARG 0.004 0.000 ARG 1 387 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 245 time to evaluate : 2.581 Fit side-chains revert: symmetry clash REVERT: 1 49 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7226 (tt0) REVERT: 1 346 GLN cc_start: 0.8318 (pp30) cc_final: 0.7980 (mp10) REVERT: 1 613 ASP cc_start: 0.8066 (m-30) cc_final: 0.7739 (m-30) REVERT: 2 74 ASN cc_start: 0.8575 (t0) cc_final: 0.8324 (t0) REVERT: 2 154 ASP cc_start: 0.6926 (t70) cc_final: 0.5990 (p0) REVERT: 2 316 ASP cc_start: 0.6967 (m-30) cc_final: 0.6655 (m-30) REVERT: 5 1 MET cc_start: 0.6664 (ttm) cc_final: 0.6240 (ttm) REVERT: 8 69 LYS cc_start: 0.8503 (mttt) cc_final: 0.6384 (tmtt) REVERT: 9 56 ASN cc_start: 0.8467 (p0) cc_final: 0.7821 (p0) REVERT: M 168 MET cc_start: 0.8050 (mmt) cc_final: 0.7776 (mmt) REVERT: M 324 LYS cc_start: 0.7636 (tppt) cc_final: 0.7323 (tptp) REVERT: P 186 MET cc_start: 0.5413 (OUTLIER) cc_final: 0.4149 (mmm) REVERT: P 205 ARG cc_start: 0.7614 (ptt-90) cc_final: 0.3710 (mmp-170) outliers start: 44 outliers final: 32 residues processed: 281 average time/residue: 0.3419 time to fit residues: 145.5972 Evaluate side-chains 260 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 227 time to evaluate : 2.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 1 residue 227 VAL Chi-restraints excluded: chain 1 residue 261 LEU Chi-restraints excluded: chain 1 residue 383 ILE Chi-restraints excluded: chain 1 residue 463 SER Chi-restraints excluded: chain 1 residue 470 VAL Chi-restraints excluded: chain 1 residue 494 SER Chi-restraints excluded: chain 1 residue 608 ASP Chi-restraints excluded: chain 2 residue 209 ASP Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 2 residue 359 THR Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 416 VAL Chi-restraints excluded: chain 3 residue 117 SER Chi-restraints excluded: chain 3 residue 195 LEU Chi-restraints excluded: chain 4 residue 19 ASP Chi-restraints excluded: chain 4 residue 45 ASP Chi-restraints excluded: chain 4 residue 187 CYS Chi-restraints excluded: chain 4 residue 229 ILE Chi-restraints excluded: chain 4 residue 273 LYS Chi-restraints excluded: chain 5 residue 61 SER Chi-restraints excluded: chain 5 residue 65 VAL Chi-restraints excluded: chain 5 residue 97 SER Chi-restraints excluded: chain 5 residue 110 SER Chi-restraints excluded: chain 6 residue 72 SER Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 9 residue 76 THR Chi-restraints excluded: chain M residue 254 LEU Chi-restraints excluded: chain M residue 280 LEU Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain P residue 186 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 229 optimal weight: 0.9990 chunk 174 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 25 optimal weight: 7.9990 chunk 110 optimal weight: 8.9990 chunk 155 optimal weight: 0.5980 chunk 232 optimal weight: 0.8980 chunk 246 optimal weight: 5.9990 chunk 121 optimal weight: 0.6980 chunk 220 optimal weight: 0.5980 chunk 66 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 48 ASN 5 59 ASN ** 7 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 78 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20239 Z= 0.168 Angle : 0.527 14.639 27469 Z= 0.271 Chirality : 0.039 0.214 3163 Planarity : 0.004 0.049 3505 Dihedral : 4.692 28.766 2747 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.89 % Favored : 96.07 % Rotamer: Outliers : 1.84 % Allowed : 11.68 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.16), residues: 2569 helix: -0.21 (0.13), residues: 1695 sheet: -0.80 (0.85), residues: 40 loop : -0.92 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 9 73 HIS 0.005 0.001 HIS 4 233 PHE 0.010 0.001 PHE M 275 TYR 0.024 0.001 TYR 4 211 ARG 0.003 0.000 ARG 1 387 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 254 time to evaluate : 2.447 Fit side-chains REVERT: 1 49 GLU cc_start: 0.7505 (mt-10) cc_final: 0.7214 (tt0) REVERT: 1 346 GLN cc_start: 0.8337 (pp30) cc_final: 0.8098 (mp10) REVERT: 1 572 ASP cc_start: 0.7724 (m-30) cc_final: 0.7405 (m-30) REVERT: 1 586 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7507 (mm-30) REVERT: 1 613 ASP cc_start: 0.7949 (m-30) cc_final: 0.7597 (m-30) REVERT: 8 69 LYS cc_start: 0.8446 (mttt) cc_final: 0.6362 (tmtt) REVERT: 9 22 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7257 (mm-30) REVERT: M 168 MET cc_start: 0.7993 (mmt) cc_final: 0.7703 (mmt) REVERT: M 324 LYS cc_start: 0.7518 (tppt) cc_final: 0.7167 (tttm) REVERT: P 186 MET cc_start: 0.4932 (OUTLIER) cc_final: 0.3771 (mmm) REVERT: P 205 ARG cc_start: 0.7504 (ptt-90) cc_final: 0.3634 (mmp-170) outliers start: 38 outliers final: 22 residues processed: 284 average time/residue: 0.3276 time to fit residues: 143.3134 Evaluate side-chains 252 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 229 time to evaluate : 2.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 1 residue 227 VAL Chi-restraints excluded: chain 1 residue 608 ASP Chi-restraints excluded: chain 2 residue 238 ASP Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 416 VAL Chi-restraints excluded: chain 4 residue 19 ASP Chi-restraints excluded: chain 4 residue 45 ASP Chi-restraints excluded: chain 4 residue 187 CYS Chi-restraints excluded: chain 4 residue 273 LYS Chi-restraints excluded: chain 5 residue 80 VAL Chi-restraints excluded: chain 5 residue 110 SER Chi-restraints excluded: chain 6 residue 72 SER Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 9 residue 76 THR Chi-restraints excluded: chain M residue 254 LEU Chi-restraints excluded: chain M residue 280 LEU Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain P residue 186 MET Chi-restraints excluded: chain T residue 63 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 205 optimal weight: 3.9990 chunk 139 optimal weight: 0.8980 chunk 3 optimal weight: 0.0030 chunk 183 optimal weight: 0.4980 chunk 101 optimal weight: 0.0870 chunk 210 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 221 optimal weight: 6.9990 chunk 62 optimal weight: 0.9980 overall best weight: 0.4968 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 48 ASN 0 61 HIS 5 59 ASN 5 82 HIS ** 7 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 78 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 20239 Z= 0.146 Angle : 0.505 12.661 27469 Z= 0.259 Chirality : 0.039 0.226 3163 Planarity : 0.004 0.044 3505 Dihedral : 4.412 28.038 2747 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.97 % Favored : 95.99 % Rotamer: Outliers : 2.08 % Allowed : 12.22 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.17), residues: 2569 helix: 0.35 (0.13), residues: 1692 sheet: -0.54 (0.86), residues: 41 loop : -0.76 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 1 264 HIS 0.004 0.001 HIS 4 233 PHE 0.015 0.001 PHE P 182 TYR 0.023 0.001 TYR 4 211 ARG 0.003 0.000 ARG 1 387 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 254 time to evaluate : 2.516 Fit side-chains revert: symmetry clash REVERT: 1 572 ASP cc_start: 0.7733 (m-30) cc_final: 0.7429 (m-30) REVERT: 1 586 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7486 (mm-30) REVERT: 1 613 ASP cc_start: 0.7902 (m-30) cc_final: 0.7544 (m-30) REVERT: 5 37 GLU cc_start: 0.8577 (pt0) cc_final: 0.8270 (pt0) REVERT: 7 60 GLN cc_start: 0.7121 (tt0) cc_final: 0.6830 (tt0) REVERT: 8 69 LYS cc_start: 0.8411 (mttt) cc_final: 0.6344 (tmtt) REVERT: 9 22 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7091 (mm-30) REVERT: M 168 MET cc_start: 0.8007 (mmt) cc_final: 0.7733 (mmt) REVERT: M 270 MET cc_start: 0.6938 (tmm) cc_final: 0.6150 (mmm) REVERT: M 324 LYS cc_start: 0.7639 (tppt) cc_final: 0.7194 (tttm) REVERT: P 186 MET cc_start: 0.4960 (OUTLIER) cc_final: 0.4747 (mmm) REVERT: P 205 ARG cc_start: 0.7486 (ptt-90) cc_final: 0.3609 (mmp-170) outliers start: 43 outliers final: 27 residues processed: 285 average time/residue: 0.3410 time to fit residues: 149.7764 Evaluate side-chains 251 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 223 time to evaluate : 2.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 1 residue 226 VAL Chi-restraints excluded: chain 1 residue 383 ILE Chi-restraints excluded: chain 1 residue 494 SER Chi-restraints excluded: chain 1 residue 608 ASP Chi-restraints excluded: chain 2 residue 238 ASP Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 2 residue 268 VAL Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 416 VAL Chi-restraints excluded: chain 4 residue 19 ASP Chi-restraints excluded: chain 4 residue 45 ASP Chi-restraints excluded: chain 4 residue 187 CYS Chi-restraints excluded: chain 4 residue 273 LYS Chi-restraints excluded: chain 5 residue 97 SER Chi-restraints excluded: chain 5 residue 110 SER Chi-restraints excluded: chain 5 residue 112 ARG Chi-restraints excluded: chain 6 residue 72 SER Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 254 LEU Chi-restraints excluded: chain M residue 280 LEU Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain P residue 186 MET Chi-restraints excluded: chain T residue 63 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 82 optimal weight: 0.9990 chunk 221 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 246 optimal weight: 0.5980 chunk 204 optimal weight: 0.6980 chunk 114 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 129 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 59 ASN 7 91 ASN ** 7 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 29 GLN 8 78 HIS 9 35 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20239 Z= 0.180 Angle : 0.519 13.968 27469 Z= 0.266 Chirality : 0.040 0.254 3163 Planarity : 0.004 0.047 3505 Dihedral : 4.333 27.887 2746 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.93 % Favored : 95.99 % Rotamer: Outliers : 2.28 % Allowed : 12.65 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.17), residues: 2569 helix: 0.63 (0.13), residues: 1708 sheet: -0.16 (0.88), residues: 41 loop : -0.67 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP 9 73 HIS 0.005 0.001 HIS 4 233 PHE 0.017 0.001 PHE M 275 TYR 0.022 0.001 TYR 4 211 ARG 0.008 0.000 ARG T 49 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 236 time to evaluate : 2.410 Fit side-chains REVERT: 1 572 ASP cc_start: 0.7732 (m-30) cc_final: 0.7418 (m-30) REVERT: 1 613 ASP cc_start: 0.7953 (m-30) cc_final: 0.7595 (m-30) REVERT: 4 121 ASP cc_start: 0.7794 (t70) cc_final: 0.7068 (t70) REVERT: 8 69 LYS cc_start: 0.8408 (mttt) cc_final: 0.6361 (tmtt) REVERT: 9 22 GLU cc_start: 0.7529 (mm-30) cc_final: 0.7120 (mm-30) REVERT: M 168 MET cc_start: 0.8034 (mmt) cc_final: 0.7758 (mmt) REVERT: M 270 MET cc_start: 0.6829 (tmm) cc_final: 0.6102 (mmm) REVERT: M 324 LYS cc_start: 0.7657 (tppt) cc_final: 0.7213 (tttm) REVERT: P 186 MET cc_start: 0.5034 (OUTLIER) cc_final: 0.4744 (mmm) REVERT: P 205 ARG cc_start: 0.7513 (ptt-90) cc_final: 0.3682 (mmp-170) REVERT: T 49 ARG cc_start: 0.8197 (mtm-85) cc_final: 0.7933 (mtp85) outliers start: 47 outliers final: 32 residues processed: 275 average time/residue: 0.3323 time to fit residues: 139.1644 Evaluate side-chains 254 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 221 time to evaluate : 2.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 1 residue 204 VAL Chi-restraints excluded: chain 1 residue 383 ILE Chi-restraints excluded: chain 1 residue 470 VAL Chi-restraints excluded: chain 1 residue 494 SER Chi-restraints excluded: chain 1 residue 608 ASP Chi-restraints excluded: chain 2 residue 238 ASP Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 2 residue 359 THR Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 416 VAL Chi-restraints excluded: chain 4 residue 19 ASP Chi-restraints excluded: chain 4 residue 44 THR Chi-restraints excluded: chain 4 residue 45 ASP Chi-restraints excluded: chain 4 residue 187 CYS Chi-restraints excluded: chain 4 residue 260 LYS Chi-restraints excluded: chain 4 residue 273 LYS Chi-restraints excluded: chain 5 residue 59 ASN Chi-restraints excluded: chain 5 residue 65 VAL Chi-restraints excluded: chain 5 residue 97 SER Chi-restraints excluded: chain 5 residue 110 SER Chi-restraints excluded: chain 5 residue 112 ARG Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 254 LEU Chi-restraints excluded: chain M residue 280 LEU Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain P residue 186 MET Chi-restraints excluded: chain T residue 63 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 237 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 140 optimal weight: 0.5980 chunk 180 optimal weight: 0.9990 chunk 139 optimal weight: 0.9990 chunk 207 optimal weight: 0.9990 chunk 137 optimal weight: 0.8980 chunk 245 optimal weight: 5.9990 chunk 153 optimal weight: 7.9990 chunk 149 optimal weight: 5.9990 chunk 113 optimal weight: 0.6980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 59 ASN 7 24 GLN 7 91 ASN ** 7 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 78 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20239 Z= 0.179 Angle : 0.520 12.493 27469 Z= 0.265 Chirality : 0.040 0.262 3163 Planarity : 0.004 0.042 3505 Dihedral : 4.304 27.272 2746 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.89 % Favored : 96.07 % Rotamer: Outliers : 1.99 % Allowed : 13.38 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.17), residues: 2569 helix: 0.80 (0.13), residues: 1714 sheet: -0.54 (0.83), residues: 41 loop : -0.63 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP 9 73 HIS 0.005 0.001 HIS 4 233 PHE 0.010 0.001 PHE M 180 TYR 0.022 0.001 TYR 4 211 ARG 0.006 0.000 ARG T 49 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 232 time to evaluate : 2.371 Fit side-chains REVERT: 1 155 GLU cc_start: 0.7815 (tm-30) cc_final: 0.7489 (tm-30) REVERT: 1 572 ASP cc_start: 0.7710 (m-30) cc_final: 0.7396 (m-30) REVERT: 1 613 ASP cc_start: 0.7961 (m-30) cc_final: 0.7626 (m-30) REVERT: 8 69 LYS cc_start: 0.8396 (mttt) cc_final: 0.6336 (tmtt) REVERT: 9 22 GLU cc_start: 0.7499 (mm-30) cc_final: 0.7102 (mm-30) REVERT: M 168 MET cc_start: 0.8036 (mmt) cc_final: 0.7762 (mmt) REVERT: M 270 MET cc_start: 0.6811 (tmm) cc_final: 0.6109 (mmm) REVERT: M 324 LYS cc_start: 0.7663 (tppt) cc_final: 0.7219 (tttm) REVERT: P 186 MET cc_start: 0.4797 (OUTLIER) cc_final: 0.4525 (mmm) REVERT: P 205 ARG cc_start: 0.7501 (ptt-90) cc_final: 0.3677 (mmp-170) REVERT: T 49 ARG cc_start: 0.8183 (mtm-85) cc_final: 0.7933 (mtp85) outliers start: 41 outliers final: 33 residues processed: 263 average time/residue: 0.3340 time to fit residues: 132.8849 Evaluate side-chains 254 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 220 time to evaluate : 2.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 1 residue 204 VAL Chi-restraints excluded: chain 1 residue 383 ILE Chi-restraints excluded: chain 1 residue 470 VAL Chi-restraints excluded: chain 1 residue 494 SER Chi-restraints excluded: chain 1 residue 608 ASP Chi-restraints excluded: chain 2 residue 238 ASP Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 2 residue 359 THR Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 416 VAL Chi-restraints excluded: chain 4 residue 19 ASP Chi-restraints excluded: chain 4 residue 44 THR Chi-restraints excluded: chain 4 residue 45 ASP Chi-restraints excluded: chain 4 residue 187 CYS Chi-restraints excluded: chain 4 residue 260 LYS Chi-restraints excluded: chain 4 residue 273 LYS Chi-restraints excluded: chain 5 residue 65 VAL Chi-restraints excluded: chain 5 residue 80 VAL Chi-restraints excluded: chain 5 residue 97 SER Chi-restraints excluded: chain 5 residue 110 SER Chi-restraints excluded: chain 5 residue 112 ARG Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 254 LEU Chi-restraints excluded: chain M residue 280 LEU Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain P residue 186 MET Chi-restraints excluded: chain T residue 63 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 152 optimal weight: 7.9990 chunk 98 optimal weight: 4.9990 chunk 146 optimal weight: 0.0270 chunk 74 optimal weight: 0.7980 chunk 48 optimal weight: 0.1980 chunk 47 optimal weight: 0.1980 chunk 156 optimal weight: 1.9990 chunk 167 optimal weight: 0.8980 chunk 121 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 193 optimal weight: 0.8980 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 44 ASN 2 177 GLN 2 380 GLN 5 59 ASN ** 7 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 78 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 20239 Z= 0.139 Angle : 0.496 12.895 27469 Z= 0.253 Chirality : 0.038 0.268 3163 Planarity : 0.004 0.051 3505 Dihedral : 4.124 26.410 2746 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.66 % Favored : 96.30 % Rotamer: Outliers : 1.50 % Allowed : 13.52 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.17), residues: 2569 helix: 1.12 (0.13), residues: 1712 sheet: -0.82 (0.80), residues: 41 loop : -0.59 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP 9 73 HIS 0.004 0.001 HIS 4 233 PHE 0.019 0.001 PHE M 275 TYR 0.022 0.001 TYR 4 211 ARG 0.005 0.000 ARG T 49 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 257 time to evaluate : 2.481 Fit side-chains REVERT: 1 155 GLU cc_start: 0.7793 (tm-30) cc_final: 0.7461 (tm-30) REVERT: 1 195 LYS cc_start: 0.7766 (pttt) cc_final: 0.7496 (ttpp) REVERT: 1 219 LYS cc_start: 0.8074 (mttp) cc_final: 0.7623 (mmtm) REVERT: 1 572 ASP cc_start: 0.7711 (m-30) cc_final: 0.7391 (m-30) REVERT: 2 246 GLU cc_start: 0.7547 (mt-10) cc_final: 0.7315 (mm-30) REVERT: 4 54 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7616 (mt-10) REVERT: 4 121 ASP cc_start: 0.7762 (t70) cc_final: 0.7057 (t70) REVERT: 8 69 LYS cc_start: 0.8352 (mttt) cc_final: 0.6351 (tmtt) REVERT: 9 1 MET cc_start: 0.1887 (ptt) cc_final: -0.0564 (mpp) REVERT: M 168 MET cc_start: 0.8061 (mmt) cc_final: 0.7794 (mmt) REVERT: M 270 MET cc_start: 0.6954 (tmm) cc_final: 0.6114 (mmm) REVERT: M 324 LYS cc_start: 0.7713 (tppt) cc_final: 0.7224 (tttm) REVERT: P 205 ARG cc_start: 0.7522 (ptt-90) cc_final: 0.3608 (mmp-170) outliers start: 31 outliers final: 23 residues processed: 282 average time/residue: 0.3319 time to fit residues: 141.7695 Evaluate side-chains 254 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 231 time to evaluate : 2.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 1 residue 204 VAL Chi-restraints excluded: chain 1 residue 470 VAL Chi-restraints excluded: chain 2 residue 238 ASP Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 2 residue 359 THR Chi-restraints excluded: chain 2 residue 371 THR Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 416 VAL Chi-restraints excluded: chain 4 residue 44 THR Chi-restraints excluded: chain 4 residue 118 THR Chi-restraints excluded: chain 4 residue 187 CYS Chi-restraints excluded: chain 4 residue 260 LYS Chi-restraints excluded: chain 4 residue 273 LYS Chi-restraints excluded: chain 5 residue 59 ASN Chi-restraints excluded: chain 5 residue 65 VAL Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain M residue 254 LEU Chi-restraints excluded: chain M residue 280 LEU Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain T residue 63 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 223 optimal weight: 2.9990 chunk 235 optimal weight: 0.9990 chunk 214 optimal weight: 3.9990 chunk 229 optimal weight: 0.9980 chunk 137 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 179 optimal weight: 0.1980 chunk 70 optimal weight: 0.2980 chunk 206 optimal weight: 0.5980 chunk 216 optimal weight: 0.0870 chunk 228 optimal weight: 0.4980 overall best weight: 0.3358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 44 ASN 5 59 ASN 7 24 GLN ** 7 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 78 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20239 Z= 0.133 Angle : 0.506 12.037 27469 Z= 0.256 Chirality : 0.039 0.292 3163 Planarity : 0.004 0.050 3505 Dihedral : 4.083 25.423 2746 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.78 % Favored : 96.19 % Rotamer: Outliers : 1.36 % Allowed : 14.30 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.17), residues: 2569 helix: 1.32 (0.13), residues: 1703 sheet: -0.81 (0.87), residues: 35 loop : -0.52 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 9 73 HIS 0.006 0.001 HIS 0 82 PHE 0.015 0.001 PHE P 182 TYR 0.022 0.001 TYR 4 211 ARG 0.005 0.000 ARG T 49 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 243 time to evaluate : 2.514 Fit side-chains revert: symmetry clash REVERT: 1 155 GLU cc_start: 0.7762 (tm-30) cc_final: 0.7414 (tm-30) REVERT: 1 441 PHE cc_start: 0.7654 (m-80) cc_final: 0.7399 (m-10) REVERT: 1 572 ASP cc_start: 0.7673 (m-30) cc_final: 0.7361 (m-30) REVERT: 2 246 GLU cc_start: 0.7542 (mt-10) cc_final: 0.7320 (mm-30) REVERT: 4 54 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7618 (mt-10) REVERT: 8 69 LYS cc_start: 0.8329 (mttt) cc_final: 0.6509 (tmtt) REVERT: 9 1 MET cc_start: 0.1480 (ptt) cc_final: 0.0056 (mpp) REVERT: M 168 MET cc_start: 0.8054 (mmt) cc_final: 0.7818 (mmt) REVERT: M 270 MET cc_start: 0.6881 (tmm) cc_final: 0.6157 (mmm) REVERT: M 324 LYS cc_start: 0.7744 (tppt) cc_final: 0.7259 (tttm) REVERT: P 205 ARG cc_start: 0.7531 (ptt-90) cc_final: 0.3611 (mmp-170) outliers start: 28 outliers final: 24 residues processed: 266 average time/residue: 0.3302 time to fit residues: 135.2027 Evaluate side-chains 253 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 229 time to evaluate : 2.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 1 residue 204 VAL Chi-restraints excluded: chain 1 residue 470 VAL Chi-restraints excluded: chain 1 residue 494 SER Chi-restraints excluded: chain 2 residue 238 ASP Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 2 residue 371 THR Chi-restraints excluded: chain 2 residue 416 VAL Chi-restraints excluded: chain 3 residue 111 SER Chi-restraints excluded: chain 4 residue 19 ASP Chi-restraints excluded: chain 4 residue 44 THR Chi-restraints excluded: chain 4 residue 118 THR Chi-restraints excluded: chain 4 residue 187 CYS Chi-restraints excluded: chain 4 residue 260 LYS Chi-restraints excluded: chain 4 residue 273 LYS Chi-restraints excluded: chain 5 residue 59 ASN Chi-restraints excluded: chain 5 residue 65 VAL Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 254 LEU Chi-restraints excluded: chain M residue 280 LEU Chi-restraints excluded: chain P residue 184 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 150 optimal weight: 6.9990 chunk 242 optimal weight: 0.0370 chunk 147 optimal weight: 5.9990 chunk 114 optimal weight: 0.9990 chunk 168 optimal weight: 4.9990 chunk 254 optimal weight: 0.0030 chunk 233 optimal weight: 0.9990 chunk 202 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 156 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 overall best weight: 0.5870 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 44 ASN 4 111 GLN 5 59 ASN ** 7 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 78 HIS 9 35 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 20239 Z= 0.151 Angle : 0.514 12.952 27469 Z= 0.260 Chirality : 0.039 0.305 3163 Planarity : 0.004 0.053 3505 Dihedral : 4.077 23.018 2746 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.62 % Favored : 96.34 % Rotamer: Outliers : 1.21 % Allowed : 14.49 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.17), residues: 2569 helix: 1.42 (0.13), residues: 1710 sheet: -0.57 (0.75), residues: 52 loop : -0.53 (0.22), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 9 73 HIS 0.004 0.001 HIS 0 80 PHE 0.020 0.001 PHE M 275 TYR 0.025 0.001 TYR 7 101 ARG 0.009 0.000 ARG 1 453 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 237 time to evaluate : 2.482 Fit side-chains revert: symmetry clash REVERT: 1 155 GLU cc_start: 0.7766 (tm-30) cc_final: 0.7445 (tm-30) REVERT: 1 572 ASP cc_start: 0.7745 (m-30) cc_final: 0.7436 (m-30) REVERT: 8 69 LYS cc_start: 0.8342 (mttt) cc_final: 0.6509 (tmtt) REVERT: 9 1 MET cc_start: 0.1400 (ptt) cc_final: 0.0093 (mpp) REVERT: M 168 MET cc_start: 0.8073 (mmt) cc_final: 0.7833 (mmt) REVERT: M 324 LYS cc_start: 0.7768 (tppt) cc_final: 0.7265 (tttm) REVERT: P 205 ARG cc_start: 0.7555 (ptt-90) cc_final: 0.3610 (mmp-170) outliers start: 25 outliers final: 24 residues processed: 256 average time/residue: 0.3225 time to fit residues: 127.4651 Evaluate side-chains 254 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 230 time to evaluate : 2.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 1 residue 204 VAL Chi-restraints excluded: chain 1 residue 470 VAL Chi-restraints excluded: chain 1 residue 494 SER Chi-restraints excluded: chain 2 residue 238 ASP Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 2 residue 371 THR Chi-restraints excluded: chain 2 residue 416 VAL Chi-restraints excluded: chain 4 residue 19 ASP Chi-restraints excluded: chain 4 residue 118 THR Chi-restraints excluded: chain 4 residue 187 CYS Chi-restraints excluded: chain 4 residue 260 LYS Chi-restraints excluded: chain 4 residue 273 LYS Chi-restraints excluded: chain 5 residue 59 ASN Chi-restraints excluded: chain 5 residue 65 VAL Chi-restraints excluded: chain 5 residue 97 SER Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 254 LEU Chi-restraints excluded: chain M residue 280 LEU Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain T residue 63 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 160 optimal weight: 5.9990 chunk 215 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 186 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 202 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 208 optimal weight: 0.9980 chunk 25 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 44 ASN 4 68 HIS 4 111 GLN 4 150 ASN 5 59 ASN 7 24 GLN ** 7 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 78 HIS 9 35 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.129086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.103006 restraints weight = 28656.163| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 1.83 r_work: 0.2868 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 20239 Z= 0.288 Angle : 0.592 14.517 27469 Z= 0.299 Chirality : 0.043 0.309 3163 Planarity : 0.004 0.057 3505 Dihedral : 4.369 23.069 2746 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.24 % Favored : 95.68 % Rotamer: Outliers : 1.45 % Allowed : 14.64 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.17), residues: 2569 helix: 1.14 (0.13), residues: 1716 sheet: -0.62 (0.85), residues: 41 loop : -0.56 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP 9 73 HIS 0.007 0.001 HIS 7 123 PHE 0.021 0.001 PHE 9 11 TYR 0.023 0.002 TYR 7 101 ARG 0.009 0.001 ARG 1 453 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4830.95 seconds wall clock time: 88 minutes 42.34 seconds (5322.34 seconds total)