Starting phenix.real_space_refine (version: dev) on Fri Mar 17 17:11:39 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdd_4814/03_2023/6rdd_4814.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdd_4814/03_2023/6rdd_4814.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/6rdd_4814/03_2023/6rdd_4814.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdd_4814/03_2023/6rdd_4814.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdd_4814/03_2023/6rdd_4814.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdd_4814/03_2023/6rdd_4814.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.005 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 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 33": "OE1" <-> "OE2" Residue "1 GLU 49": "OE1" <-> "OE2" Residue "1 ASP 69": "OD1" <-> "OD2" Residue "1 ASP 96": "OD1" <-> "OD2" Residue "1 ARG 150": "NH1" <-> "NH2" Residue "1 GLU 165": "OE1" <-> "OE2" Residue "1 ASP 172": "OD1" <-> "OD2" Residue "1 ARG 182": "NH1" <-> "NH2" Residue "1 GLU 191": "OE1" <-> "OE2" Residue "1 ASP 199": "OD1" <-> "OD2" Residue "1 GLU 215": "OE1" <-> "OE2" Residue "1 GLU 229": "OE1" <-> "OE2" Residue "1 ARG 259": "NH1" <-> "NH2" Residue "1 GLU 299": "OE1" <-> "OE2" Residue "1 GLU 329": "OE1" <-> "OE2" Residue "1 GLU 350": "OE1" <-> "OE2" Residue "1 ASP 353": "OD1" <-> "OD2" Residue "1 ARG 359": "NH1" <-> "NH2" Residue "1 ASP 373": "OD1" <-> "OD2" Residue "1 GLU 378": "OE1" <-> "OE2" Residue "1 ARG 387": "NH1" <-> "NH2" Residue "1 GLU 409": "OE1" <-> "OE2" Residue "1 TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 422": "OD1" <-> "OD2" Residue "1 ARG 434": "NH1" <-> "NH2" Residue "1 ASP 479": "OD1" <-> "OD2" Residue "1 GLU 496": "OE1" <-> "OE2" Residue "1 GLU 513": "OE1" <-> "OE2" Residue "1 GLU 516": "OE1" <-> "OE2" Residue "1 ASP 539": "OD1" <-> "OD2" Residue "1 ASP 601": "OD1" <-> "OD2" Residue "1 ARG 609": "NH1" <-> "NH2" Residue "2 ASP 31": "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 134": "OE1" <-> "OE2" Residue "2 TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 154": "OD1" <-> "OD2" Residue "2 ASP 171": "OD1" <-> "OD2" Residue "2 ARG 173": "NH1" <-> "NH2" Residue "2 PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 260": "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 GLU 326": "OE1" <-> "OE2" Residue "2 ASP 332": "OD1" <-> "OD2" Residue "2 PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 346": "NH1" <-> "NH2" Residue "2 ASP 374": "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 ASP 119": "OD1" <-> "OD2" Residue "3 PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 126": "OE1" <-> "OE2" 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 184": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 GLU 276": "OE1" <-> "OE2" Residue "3 GLU 299": "OE1" <-> "OE2" Residue "3 GLU 308": "OE1" <-> "OE2" Residue "3 PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 10": "OE1" <-> "OE2" Residue "4 TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 102": "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 ASP 197": "OD1" <-> "OD2" Residue "4 GLU 202": "OE1" <-> "OE2" Residue "4 PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "5 GLU 6": "OE1" <-> "OE2" Residue "5 ARG 36": "NH1" <-> "NH2" Residue "5 ARG 50": "NH1" <-> "NH2" Residue "5 ARG 112": "NH1" <-> "NH2" Residue "6 PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 47": "OE1" <-> "OE2" 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 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 ASP 17": "OD1" <-> "OD2" 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 88": "OE1" <-> "OE2" Residue "M ARG 115": "NH1" <-> "NH2" Residue "M ASP 132": "OD1" <-> "OD2" 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 GLU 288": "OE1" <-> "OE2" Residue "M PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 166": "OE1" <-> "OE2" Residue "P ARG 206": "NH1" <-> "NH2" Residue "P PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 47": "OE1" <-> "OE2" Residue "T ARG 49": "NH1" <-> "NH2" Residue "T GLU 72": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/chem_data/mon_lib" Total number of atoms: 19856 Number of models: 1 Model: "" Number of chains: 19 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "6" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "8" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 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: 10.94, per 1000 atoms: 0.55 Number of scatterers: 19856 At special positions: 0 Unit cell: (180.063, 120.042, 249.561, 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 3776 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: 8.09 Conformation dependent library (CDL) restraints added in 3.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN M 600 " pdb="ZN ZN M 600 " - pdb=" NE2 HIS M 248 " pdb="ZN ZN M 600 " - pdb=" NE2 HIS M 252 " 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: 138 helices and 7 sheets defined 67.8% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain '0' and resid 17 through 30 removed outlier: 3.618A pdb=" N LEU 0 21 " --> pdb=" O GLY 0 17 " (cutoff:3.500A) Processing helix chain '0' and resid 43 through 50 Processing helix chain '0' and resid 51 through 56 Processing helix chain '1' and resid 45 through 73 removed outlier: 3.573A pdb=" N ASN 1 51 " --> pdb=" O VAL 1 47 " (cutoff:3.500A) Processing helix chain '1' and resid 96 through 100 removed outlier: 3.683A pdb=" N THR 1 99 " --> pdb=" O ASP 1 96 " (cutoff:3.500A) removed outlier: 3.785A 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 105 through 124 removed outlier: 4.450A pdb=" N LYS 1 109 " --> pdb=" O GLY 1 105 " (cutoff:3.500A) Processing helix chain '1' and resid 126 through 139 removed outlier: 3.982A pdb=" N THR 1 135 " --> pdb=" O ALA 1 131 " (cutoff:3.500A) Processing helix chain '1' and resid 163 through 176 removed outlier: 3.990A pdb=" N THR 1 169 " --> pdb=" O GLU 1 165 " (cutoff:3.500A) Processing helix chain '1' and resid 190 through 204 removed outlier: 4.414A pdb=" N ALA 1 196 " --> pdb=" O GLY 1 192 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL 1 197 " --> pdb=" O VAL 1 193 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP 1 199 " --> pdb=" O LYS 1 195 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE 1 200 " --> pdb=" O ALA 1 196 " (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: 3.609A pdb=" N VAL 1 213 " --> pdb=" O ASN 1 209 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU 1 221 " --> pdb=" O LEU 1 217 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LYS 1 224 " --> pdb=" O SER 1 220 " (cutoff:3.500A) Processing helix chain '1' and resid 241 through 271 removed outlier: 3.517A pdb=" N ALA 1 250 " --> pdb=" O ALA 1 246 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU 1 258 " --> pdb=" O ALA 1 254 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG 1 259 " --> pdb=" O GLU 1 255 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL 1 270 " --> pdb=" O LYS 1 266 " (cutoff:3.500A) Processing helix chain '1' and resid 272 through 277 removed outlier: 3.644A pdb=" N ALA 1 275 " --> pdb=" O PRO 1 272 " (cutoff:3.500A) Processing helix chain '1' and resid 282 through 286 Processing helix chain '1' and resid 289 through 293 Processing helix chain '1' and resid 297 through 305 Processing helix chain '1' and resid 310 through 316 removed outlier: 3.545A pdb=" N ASN 1 316 " --> pdb=" O ALA 1 312 " (cutoff:3.500A) Processing helix chain '1' and resid 323 through 327 removed outlier: 3.701A pdb=" N LYS 1 327 " --> pdb=" O PHE 1 324 " (cutoff:3.500A) Processing helix chain '1' and resid 330 through 334 Processing helix chain '1' and resid 338 through 351 removed outlier: 3.581A pdb=" N GLU 1 350 " --> pdb=" O GLN 1 346 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU 1 351 " --> pdb=" O LYS 1 347 " (cutoff:3.500A) Processing helix chain '1' and resid 353 through 362 removed outlier: 3.649A pdb=" N LEU 1 358 " --> pdb=" O PRO 1 354 " (cutoff:3.500A) Processing helix chain '1' and resid 363 through 367 removed outlier: 3.875A pdb=" N GLU 1 367 " --> pdb=" O PRO 1 364 " (cutoff:3.500A) Processing helix chain '1' and resid 375 through 388 removed outlier: 3.541A pdb=" N ARG 1 381 " --> pdb=" O SER 1 377 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL 1 382 " --> pdb=" O GLU 1 378 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS 1 386 " --> pdb=" O VAL 1 382 " (cutoff:3.500A) Processing helix chain '1' and resid 392 through 421 removed outlier: 3.531A pdb=" N LYS 1 396 " --> pdb=" O ARG 1 392 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU 1 401 " --> pdb=" O GLU 1 397 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N VAL 1 418 " --> pdb=" O GLU 1 414 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N ILE 1 419 " --> pdb=" O GLU 1 415 " (cutoff:3.500A) Processing helix chain '1' and resid 425 through 432 removed outlier: 3.953A pdb=" N PHE 1 429 " --> pdb=" O ASP 1 425 " (cutoff:3.500A) Processing helix chain '1' and resid 435 through 441 Processing helix chain '1' and resid 446 through 458 removed outlier: 3.646A pdb=" N ARG 1 453 " --> pdb=" O ALA 1 449 " (cutoff:3.500A) Processing helix chain '1' and resid 463 through 478 removed outlier: 3.658A pdb=" N TYR 1 468 " --> pdb=" O PRO 1 464 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN 1 474 " --> pdb=" O VAL 1 470 " (cutoff:3.500A) Processing helix chain '1' and resid 479 through 483 Processing helix chain '1' and resid 485 through 490 Processing helix chain '1' and resid 490 through 495 Processing helix chain '1' and resid 495 through 515 removed outlier: 3.889A pdb=" N GLU 1 501 " --> pdb=" O LEU 1 497 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA 1 511 " --> pdb=" O GLU 1 507 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU 1 512 " --> pdb=" O ASP 1 508 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA 1 515 " --> pdb=" O ALA 1 511 " (cutoff:3.500A) Processing helix chain '1' and resid 518 through 536 removed outlier: 3.657A pdb=" N THR 1 526 " --> pdb=" O LEU 1 522 " (cutoff:3.500A) Processing helix chain '1' and resid 541 through 549 removed outlier: 3.515A pdb=" N VAL 1 545 " --> pdb=" O PRO 1 541 " (cutoff:3.500A) Processing helix chain '1' and resid 549 through 562 removed outlier: 3.571A pdb=" N GLU 1 559 " --> pdb=" O LYS 1 555 " (cutoff:3.500A) Processing helix chain '1' and resid 566 through 574 Processing helix chain '1' and resid 577 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: 3.664A pdb=" N LYS 1 605 " --> pdb=" O ASP 1 601 " (cutoff:3.500A) Processing helix chain '1' and resid 610 through 614 Processing helix chain '2' and resid 8 through 17 removed outlier: 3.824A pdb=" N LYS 2 13 " --> pdb=" O PRO 2 9 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU 2 14 " --> pdb=" O ALA 2 10 " (cutoff:3.500A) Processing helix chain '2' and resid 25 through 38 Processing helix chain '2' and resid 44 through 58 removed outlier: 3.619A pdb=" N TRP 2 48 " --> pdb=" O ASN 2 44 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY 2 56 " --> pdb=" O LEU 2 52 " (cutoff:3.500A) Processing helix chain '2' and resid 62 through 76 removed outlier: 3.528A 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: 3.602A pdb=" N SER 2 104 " --> pdb=" O PRO 2 100 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE 2 105 " --> pdb=" O VAL 2 101 " (cutoff:3.500A) Processing helix chain '2' and resid 117 through 131 removed outlier: 3.559A pdb=" N VAL 2 127 " --> pdb=" O LYS 2 123 " (cutoff:3.500A) Processing helix chain '2' and resid 136 through 150 removed outlier: 3.555A pdb=" N ALA 2 141 " --> pdb=" O PRO 2 137 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL 2 143 " --> pdb=" O GLU 2 139 " (cutoff:3.500A) Processing helix chain '2' and resid 154 through 166 removed outlier: 3.659A pdb=" N ALA 2 158 " --> pdb=" O ASP 2 154 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL 2 164 " --> pdb=" O ALA 2 160 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA 2 166 " --> pdb=" O GLY 2 162 " (cutoff:3.500A) Processing helix chain '2' and resid 171 through 186 Processing helix chain '2' and resid 189 through 198 removed outlier: 3.856A pdb=" N ALA 2 195 " --> pdb=" O ALA 2 191 " (cutoff:3.500A) Processing helix chain '2' and resid 209 through 221 removed outlier: 3.534A pdb=" N LEU 2 220 " --> pdb=" O ALA 2 216 " (cutoff:3.500A) Processing helix chain '2' and resid 227 through 235 removed outlier: 3.823A pdb=" N ALA 2 234 " --> pdb=" O ASP 2 230 " (cutoff:3.500A) Processing helix chain '2' and resid 240 through 254 removed outlier: 3.702A pdb=" N GLU 2 246 " --> pdb=" O ALA 2 242 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY 2 250 " --> pdb=" O GLU 2 246 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER 2 254 " --> pdb=" O GLY 2 250 " (cutoff:3.500A) Processing helix chain '2' and resid 258 through 276 removed outlier: 3.568A pdb=" N VAL 2 268 " --> pdb=" O ALA 2 264 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL 2 269 " --> pdb=" O LEU 2 265 " (cutoff:3.500A) Proline residue: 2 271 - end of helix removed outlier: 3.504A pdb=" N GLU 2 274 " --> pdb=" O ALA 2 270 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS 2 275 " --> pdb=" O PRO 2 271 " (cutoff:3.500A) Processing helix chain '2' and resid 281 through 295 removed outlier: 3.534A pdb=" N SER 2 295 " --> pdb=" O ALA 2 291 " (cutoff:3.500A) Processing helix chain '2' and resid 300 through 321 removed outlier: 3.911A pdb=" N SER 2 305 " --> pdb=" O ALA 2 301 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE 2 306 " --> pdb=" O ALA 2 302 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLY 2 312 " --> pdb=" O ALA 2 308 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA 2 318 " --> pdb=" O ALA 2 314 " (cutoff:3.500A) Processing helix chain '2' and resid 326 through 339 Processing helix chain '2' and resid 345 through 353 removed outlier: 3.624A pdb=" N ALA 2 350 " --> pdb=" O ARG 2 346 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER 2 351 " --> pdb=" O PRO 2 347 " (cutoff:3.500A) Processing helix chain '2' and resid 396 through 408 removed outlier: 4.185A pdb=" N ALA 2 400 " --> pdb=" O LEU 2 396 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA 2 408 " --> pdb=" O LYS 2 404 " (cutoff:3.500A) Processing helix chain '2' and resid 418 through 422 Processing helix chain '2' and resid 426 through 440 removed outlier: 3.690A pdb=" N ALA 2 436 " --> pdb=" O GLN 2 432 " (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: 3.942A pdb=" N TRP 3 106 " --> pdb=" O ASP 3 102 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER 3 111 " --> pdb=" O SER 3 107 " (cutoff:3.500A) Processing helix chain '3' and resid 119 through 128 removed outlier: 3.960A pdb=" N LYS 3 123 " --> pdb=" O ASP 3 119 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA 3 127 " --> pdb=" O LYS 3 123 " (cutoff:3.500A) Processing helix chain '3' and resid 131 through 135 Processing helix chain '3' and resid 136 through 150 removed outlier: 3.520A pdb=" N VAL 3 145 " --> pdb=" O THR 3 141 " (cutoff:3.500A) Processing helix chain '3' and resid 154 through 166 removed outlier: 3.693A pdb=" N GLY 3 160 " --> pdb=" O ASP 3 156 " (cutoff:3.500A) Processing helix chain '3' and resid 168 through 172 removed outlier: 3.628A pdb=" N PHE 3 172 " --> pdb=" O PHE 3 169 " (cutoff:3.500A) Processing helix chain '3' and resid 173 through 185 removed outlier: 4.074A pdb=" N GLN 3 179 " --> pdb=" O GLU 3 175 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA 3 182 " --> pdb=" O LEU 3 178 " (cutoff:3.500A) Processing helix chain '3' and resid 191 through 204 removed outlier: 3.537A pdb=" N SER 3 201 " --> pdb=" O ASP 3 197 " (cutoff:3.500A) Processing helix chain '3' and resid 215 through 229 removed outlier: 3.624A pdb=" N LEU 3 219 " --> pdb=" O GLY 3 215 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THR 3 221 " --> pdb=" O ASP 3 217 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN 3 229 " --> pdb=" O TYR 3 225 " (cutoff:3.500A) Processing helix chain '3' and resid 233 through 241 removed outlier: 3.513A 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: 3.526A pdb=" N LYS 3 258 " --> pdb=" O ALA 3 254 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP 3 259 " --> pdb=" O ALA 3 255 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA 3 267 " --> pdb=" O SER 3 263 " (cutoff:3.500A) removed outlier: 3.688A 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: 3.888A pdb=" N ALA 3 285 " --> pdb=" O VAL 3 281 " (cutoff:3.500A) Processing helix chain '3' and resid 293 through 299 Processing helix chain '3' and resid 300 through 312 Processing helix chain '4' and resid 8 through 14 removed outlier: 3.649A pdb=" N TYR 4 13 " --> pdb=" O LYS 4 9 " (cutoff:3.500A) Processing helix chain '4' and resid 19 through 35 removed outlier: 3.903A pdb=" N ALA 4 25 " --> pdb=" O GLU 4 21 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER 4 28 " --> pdb=" O THR 4 24 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER 4 32 " --> pdb=" O SER 4 28 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR 4 34 " --> pdb=" O LEU 4 30 " (cutoff:3.500A) Processing helix chain '4' and resid 47 through 69 removed outlier: 3.580A pdb=" N ALA 4 51 " --> pdb=" O SER 4 47 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS 4 56 " --> pdb=" O GLN 4 52 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA 4 60 " --> pdb=" O LYS 4 56 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLN 4 61 " --> pdb=" O TYR 4 57 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL 4 62 " --> pdb=" O LEU 4 58 " (cutoff:3.500A) Proline residue: 4 65 - end of helix removed outlier: 3.675A 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: 3.502A pdb=" N ASN 4 124 " --> pdb=" O LYS 4 120 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR 4 126 " --> pdb=" O VAL 4 122 " (cutoff:3.500A) Processing helix chain '4' and resid 131 through 136 Processing helix chain '4' and resid 138 through 150 removed outlier: 3.540A pdb=" N ALA 4 147 " --> pdb=" O SER 4 143 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU 4 148 " --> pdb=" O SER 4 144 " (cutoff:3.500A) Processing helix chain '4' and resid 159 through 177 removed outlier: 3.808A pdb=" N LYS 4 168 " --> pdb=" O LYS 4 164 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS 4 170 " --> pdb=" O ALA 4 166 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA 4 171 " --> pdb=" O ALA 4 167 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER 4 175 " --> pdb=" O ALA 4 171 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY 4 177 " --> pdb=" O ALA 4 173 " (cutoff:3.500A) Processing helix chain '4' and resid 179 through 188 Processing helix chain '4' and resid 192 through 234 removed outlier: 3.564A pdb=" N LYS 4 198 " --> pdb=" O ASP 4 194 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL 4 199 " --> pdb=" O ALA 4 195 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU 4 202 " --> pdb=" O LYS 4 198 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N THR 4 205 " --> pdb=" O LYS 4 201 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TRP 4 206 " --> pdb=" O GLU 4 202 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA 4 213 " --> pdb=" O SER 4 209 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP 4 214 " --> pdb=" O ALA 4 210 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA 4 221 " --> pdb=" O ALA 4 217 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE 4 222 " --> pdb=" O GLU 4 218 " (cutoff:3.500A) Processing helix chain '4' and resid 237 through 259 removed outlier: 3.570A pdb=" N ALA 4 256 " --> pdb=" O LEU 4 252 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA 4 259 " --> pdb=" O ARG 4 255 " (cutoff:3.500A) Processing helix chain '4' and resid 262 through 283 Processing helix chain '5' and resid 7 through 29 removed outlier: 3.616A pdb=" N GLU 5 11 " --> pdb=" O SER 5 7 " (cutoff:3.500A) Processing helix chain '5' and resid 30 through 59 removed outlier: 3.614A pdb=" N ARG 5 36 " --> pdb=" O PRO 5 32 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU 5 37 " --> pdb=" O THR 5 33 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU 5 40 " --> pdb=" O ARG 5 36 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N HIS 5 41 " --> pdb=" O GLU 5 37 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N LYS 5 49 " --> pdb=" O ALA 5 45 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ARG 5 50 " --> pdb=" O ALA 5 46 " (cutoff:3.500A) removed outlier: 3.510A 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 73 through 81 removed outlier: 3.531A pdb=" N ASN 5 79 " --> pdb=" O GLN 5 75 " (cutoff:3.500A) Processing helix chain '5' and resid 88 through 106 removed outlier: 3.963A pdb=" N LEU 5 92 " --> pdb=" O PRO 5 88 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER 5 97 " --> pdb=" O GLU 5 93 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LYS 5 101 " --> pdb=" O SER 5 97 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL 5 102 " --> pdb=" O ALA 5 98 " (cutoff:3.500A) Processing helix chain '5' and resid 114 through 119 Processing helix chain '6' and resid 30 through 41 Processing helix chain '6' and resid 48 through 50 No H-bonds generated for 'chain '6' and resid 48 through 50' Processing helix chain '6' and resid 51 through 58 Processing helix chain '6' and resid 72 through 94 removed outlier: 3.548A pdb=" N ALA 6 78 " --> pdb=" O GLN 6 74 " (cutoff:3.500A) removed outlier: 3.532A 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 105 through 118 removed outlier: 3.683A pdb=" N TRP 6 112 " --> pdb=" O LEU 6 108 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER 6 117 " --> pdb=" O LEU 6 113 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER 6 118 " --> pdb=" O ILE 6 114 " (cutoff:3.500A) Processing helix chain '6' and resid 121 through 130 Processing helix chain '6' and resid 133 through 138 removed outlier: 4.006A pdb=" N SER 6 138 " --> pdb=" O PRO 6 134 " (cutoff:3.500A) Processing helix chain '7' and resid 63 through 68 removed outlier: 3.840A pdb=" N ARG 7 67 " --> pdb=" O ALA 7 63 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS 7 68 " --> pdb=" O ALA 7 64 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 63 through 68' Processing helix chain '7' and resid 69 through 72 removed outlier: 4.102A pdb=" N SER 7 72 " --> pdb=" O LEU 7 69 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 69 through 72' Processing helix chain '7' and resid 83 through 102 removed outlier: 3.506A pdb=" N TYR 7 92 " --> pdb=" O SER 7 88 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU 7 99 " --> pdb=" O SER 7 95 " (cutoff:3.500A) Processing helix chain '7' and resid 109 through 114 removed outlier: 3.836A pdb=" N THR 7 112 " --> pdb=" O ASP 7 109 " (cutoff:3.500A) removed outlier: 3.672A 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 124 through 145 removed outlier: 3.625A pdb=" N PHE 7 130 " --> pdb=" O ASP 7 126 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP 7 135 " --> pdb=" O TYR 7 131 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR 7 137 " --> pdb=" O ALA 7 133 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR 7 138 " --> pdb=" O ALA 7 134 " (cutoff:3.500A) Processing helix chain '7' and resid 146 through 149 Processing helix chain '7' and resid 150 through 155 removed outlier: 3.640A pdb=" N SER 7 155 " --> pdb=" O SER 7 151 " (cutoff:3.500A) Processing helix chain '7' and resid 157 through 163 Processing helix chain '7' and resid 174 through 187 removed outlier: 3.576A pdb=" N ASN 7 184 " --> pdb=" O GLY 7 180 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE 7 185 " --> pdb=" O ALA 7 181 " (cutoff:3.500A) Processing helix chain '8' and resid 26 through 31 removed outlier: 3.840A pdb=" N SER 8 31 " --> pdb=" O PRO 8 27 " (cutoff:3.500A) Processing helix chain '8' and resid 31 through 39 removed outlier: 3.556A pdb=" N TYR 8 35 " --> pdb=" O SER 8 31 " (cutoff:3.500A) Processing helix chain '8' and resid 39 through 78 removed outlier: 3.751A pdb=" N TRP 8 45 " --> pdb=" O ILE 8 41 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N TYR 8 46 " --> pdb=" O PRO 8 42 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N LEU 8 47 " --> pdb=" O ARG 8 43 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA 8 76 " --> pdb=" O ALA 8 72 " (cutoff:3.500A) Processing helix chain '9' and resid 5 through 17 Processing helix chain '9' and resid 36 through 55 removed outlier: 4.208A pdb=" N VAL 9 42 " --> pdb=" O ALA 9 38 " (cutoff:3.500A) Processing helix chain '9' and resid 82 through 97 removed outlier: 4.288A pdb=" N GLU 9 88 " --> pdb=" O ALA 9 84 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N MET 9 89 " --> pdb=" O LYS 9 85 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS 9 91 " --> pdb=" O LEU 9 87 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER 9 96 " --> pdb=" O GLU 9 92 " (cutoff:3.500A) Processing helix chain 'M' and resid 104 through 118 Processing helix chain 'M' and resid 134 through 145 Processing helix chain 'M' and resid 147 through 164 removed outlier: 3.653A pdb=" N THR M 153 " --> pdb=" O GLY M 149 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER M 161 " --> pdb=" O CYS M 157 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N CYS M 162 " --> pdb=" O THR M 158 " (cutoff:3.500A) Processing helix chain 'M' and resid 165 through 168 Processing helix chain 'M' and resid 173 through 176 Processing helix chain 'M' and resid 177 through 199 removed outlier: 3.581A pdb=" N SER M 187 " --> pdb=" O GLY M 183 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS M 199 " --> pdb=" O LEU M 195 " (cutoff:3.500A) Processing helix chain 'M' and resid 221 through 231 Processing helix chain 'M' and resid 231 through 265 removed outlier: 4.106A pdb=" N GLY M 237 " --> pdb=" O ALA M 233 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY M 247 " --> pdb=" O ASN M 243 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N HIS M 248 " --> pdb=" O MET M 244 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU M 250 " --> pdb=" O ALA M 246 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU M 261 " --> pdb=" O MET M 257 " (cutoff:3.500A) Proline residue: M 262 - end of helix Processing helix chain 'M' and resid 270 through 308 removed outlier: 3.678A pdb=" N VAL M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU M 280 " --> pdb=" O GLY M 276 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU M 290 " --> pdb=" O GLY M 286 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER M 296 " --> pdb=" O ALA M 292 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER M 300 " --> pdb=" O SER M 296 " (cutoff:3.500A) Processing helix chain 'P' and resid 163 through 175 removed outlier: 3.773A pdb=" N VAL P 168 " --> pdb=" O LYS P 164 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU P 170 " --> pdb=" O GLU P 166 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS P 172 " --> pdb=" O VAL P 168 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS P 173 " --> pdb=" O GLU P 169 " (cutoff:3.500A) Processing helix chain 'P' and resid 210 through 226 removed outlier: 3.871A pdb=" N GLU P 216 " --> pdb=" O ALA P 212 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASN P 219 " --> pdb=" O VAL P 215 " (cutoff:3.500A) Processing helix chain 'T' and resid 57 through 67 removed outlier: 3.652A pdb=" N ILE T 67 " --> pdb=" O SER T 63 " (cutoff:3.500A) Processing helix chain 'T' and resid 67 through 75 removed outlier: 3.668A pdb=" N GLU T 72 " --> pdb=" O PRO T 68 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N TRP T 73 " --> pdb=" O ALA T 69 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU T 74 " --> pdb=" O VAL T 70 " (cutoff:3.500A) removed outlier: 3.687A 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 184 Processing sheet with id=AA2, first strand: chain '2' and resid 369 through 372 removed outlier: 8.110A pdb=" N ALA 2 414 " --> pdb=" O LYS 2 376 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU 2 378 " --> pdb=" O ALA 2 414 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N VAL 2 416 " --> pdb=" O LEU 2 378 " (cutoff:3.500A) removed outlier: 6.544A 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 '7' and resid 36 through 41 Processing sheet with id=AA6, first strand: chain 'P' and resid 151 through 152 Processing sheet with id=AA7, first strand: chain 'P' and resid 188 through 190 1059 hydrogen bonds defined for protein. 3087 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: 6.02 Time building geometry restraints manager: 8.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5210 1.33 - 1.45: 3678 1.45 - 1.57: 11297 1.57 - 1.69: 0 1.69 - 1.81: 54 Bond restraints: 20239 Sorted by residual: bond pdb=" N THR M 200 " pdb=" CA THR M 200 " ideal model delta sigma weight residual 1.457 1.485 -0.029 6.40e-03 2.44e+04 2.04e+01 bond pdb=" CB THR M 153 " pdb=" CG2 THR M 153 " ideal model delta sigma weight residual 1.521 1.418 0.103 3.30e-02 9.18e+02 9.65e+00 bond pdb=" N ILE 3 101 " pdb=" CA ILE 3 101 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.25e-02 6.40e+03 7.12e+00 bond pdb=" CB PRO 4 65 " pdb=" CG PRO 4 65 " ideal model delta sigma weight residual 1.492 1.360 0.132 5.00e-02 4.00e+02 6.99e+00 bond pdb=" CG1 ILE 5 34 " pdb=" CD1 ILE 5 34 " ideal model delta sigma weight residual 1.513 1.414 0.099 3.90e-02 6.57e+02 6.49e+00 ... (remaining 20234 not shown) Histogram of bond angle deviations from ideal: 94.62 - 102.52: 70 102.52 - 110.42: 5775 110.42 - 118.32: 9733 118.32 - 126.22: 11597 126.22 - 134.12: 294 Bond angle restraints: 27469 Sorted by residual: 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 THR M 200 " pdb=" CA THR M 200 " pdb=" CB THR M 200 " ideal model delta sigma weight residual 117.07 107.48 9.59 1.44e+00 4.82e-01 4.43e+01 angle pdb=" C VAL 7 157 " pdb=" N VAL 7 158 " pdb=" CA VAL 7 158 " ideal model delta sigma weight residual 120.33 125.36 -5.03 8.00e-01 1.56e+00 3.96e+01 angle pdb=" N ILE 8 11 " pdb=" CA ILE 8 11 " pdb=" C ILE 8 11 " ideal model delta sigma weight residual 111.62 107.68 3.94 7.90e-01 1.60e+00 2.48e+01 angle pdb=" C VAL P 185 " pdb=" N MET P 186 " pdb=" CA MET P 186 " ideal model delta sigma weight residual 121.54 130.69 -9.15 1.91e+00 2.74e-01 2.29e+01 ... (remaining 27464 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 11104 17.59 - 35.17: 866 35.17 - 52.76: 167 52.76 - 70.34: 30 70.34 - 87.93: 15 Dihedral angle restraints: 12182 sinusoidal: 4595 harmonic: 7587 Sorted by residual: 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 180.00 140.10 39.90 0 5.00e+00 4.00e-02 6.37e+01 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 180.00 144.47 35.53 0 5.00e+00 4.00e-02 5.05e+01 dihedral pdb=" CA SER 4 47 " pdb=" C SER 4 47 " pdb=" N GLU 4 48 " pdb=" CA GLU 4 48 " ideal model delta harmonic sigma weight residual -180.00 -148.99 -31.01 0 5.00e+00 4.00e-02 3.85e+01 ... (remaining 12179 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 2594 0.077 - 0.155: 514 0.155 - 0.232: 51 0.232 - 0.309: 3 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 ILE P 200 " pdb=" CA ILE P 200 " pdb=" CG1 ILE P 200 " pdb=" CG2 ILE P 200 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.11e+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 -2.35 -0.27 2.00e-01 2.50e+01 1.88e+00 ... (remaining 3160 not shown) Planarity restraints: 3505 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR 1 92 " 0.048 5.00e-02 4.00e+02 7.27e-02 8.46e+00 pdb=" N PRO 1 93 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO 1 93 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO 1 93 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU M 135 " 0.046 5.00e-02 4.00e+02 6.91e-02 7.65e+00 pdb=" N PRO M 136 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO M 136 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO M 136 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA 3 210 " 0.045 5.00e-02 4.00e+02 6.68e-02 7.13e+00 pdb=" N PRO 3 211 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO 3 211 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO 3 211 " 0.038 5.00e-02 4.00e+02 ... (remaining 3502 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 470 2.68 - 3.24: 18793 3.24 - 3.79: 31442 3.79 - 4.35: 43455 4.35 - 4.90: 71365 Nonbonded interactions: 165525 Sorted by model distance: nonbonded pdb="ZN ZN M 600 " pdb=" O HOH M 715 " model vdw 2.126 2.230 nonbonded pdb=" O GLY M 183 " pdb=" OG SER M 187 " model vdw 2.234 2.440 nonbonded pdb=" O THR 5 83 " pdb=" OH TYR 7 119 " model vdw 2.248 2.440 nonbonded pdb=" OH TYR 5 62 " pdb=" O PHE 6 146 " model vdw 2.250 2.440 nonbonded pdb=" OH TYR 6 126 " pdb=" O HOH 6 201 " model vdw 2.263 2.440 ... (remaining 165520 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 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 3776 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 6.350 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: 0.010 Extract box with map and model: 25.060 Check model and map are aligned: 0.260 Process input model: 54.490 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.180 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 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 : 0.012 0.132 20239 Z= 0.782 Angle : 1.028 13.598 27469 Z= 0.565 Chirality : 0.062 0.386 3163 Planarity : 0.008 0.073 3505 Dihedral : 13.794 87.928 7264 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.94 % Favored : 94.78 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -5.88 (0.11), residues: 2569 helix: -4.52 (0.05), residues: 1675 sheet: -2.05 (0.58), residues: 70 loop : -2.02 (0.18), residues: 824 *********************** 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 333 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 329 time to evaluate : 2.056 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 333 average time/residue: 0.3817 time to fit residues: 187.4551 Evaluate side-chains 238 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 237 time to evaluate : 2.293 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1808 time to fit residues: 3.4842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 107 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 103 optimal weight: 0.2980 chunk 199 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 chunk 148 optimal weight: 0.8980 chunk 231 optimal weight: 0.7980 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 44 ASN 0 48 ASN 1 65 GLN 1 100 GLN 1 285 GLN 1 298 GLN 1 316 ASN ** 1 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 423 ASN 1 430 GLN 1 482 ASN 1 587 ASN 1 590 HIS 2 122 ASN 2 243 GLN 2 289 HIS 2 380 GLN 2 427 GLN 3 189 HIS 3 206 ASN 4 135 ASN 4 240 GLN 5 107 ASN 6 40 ASN 7 86 HIS 7 98 ASN 7 123 HIS 7 170 HIS 7 184 ASN 8 26 HIS 9 23 GLN ** 9 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 120 GLN M 163 ASN P 223 ASN T 64 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 20239 Z= 0.187 Angle : 0.592 13.331 27469 Z= 0.313 Chirality : 0.040 0.232 3163 Planarity : 0.006 0.059 3505 Dihedral : 5.471 35.647 2746 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.74 % Favored : 96.19 % Rotamer Outliers : 1.65 % 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: -3.31 (0.14), residues: 2569 helix: -2.31 (0.10), residues: 1681 sheet: -1.26 (0.65), residues: 64 loop : -1.54 (0.19), residues: 824 *********************** 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 307 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 273 time to evaluate : 2.249 Fit side-chains revert: symmetry clash outliers start: 34 outliers final: 16 residues processed: 292 average time/residue: 0.3434 time to fit residues: 152.0913 Evaluate side-chains 244 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 228 time to evaluate : 2.412 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2075 time to fit residues: 9.0103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 128 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 192 optimal weight: 7.9990 chunk 157 optimal weight: 0.6980 chunk 63 optimal weight: 5.9990 chunk 231 optimal weight: 0.9980 chunk 250 optimal weight: 0.9990 chunk 206 optimal weight: 4.9990 chunk 230 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 186 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 44 ASN 0 48 ASN ** 1 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 153 ASN 3 229 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 20239 Z= 0.202 Angle : 0.559 13.378 27469 Z= 0.287 Chirality : 0.040 0.177 3163 Planarity : 0.005 0.051 3505 Dihedral : 4.909 32.056 2746 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.17 % Favored : 95.76 % Rotamer Outliers : 1.41 % 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: -1.65 (0.16), residues: 2569 helix: -0.89 (0.12), residues: 1686 sheet: -0.87 (0.72), residues: 51 loop : -1.21 (0.20), residues: 832 *********************** 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 279 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 250 time to evaluate : 2.236 Fit side-chains outliers start: 29 outliers final: 13 residues processed: 267 average time/residue: 0.3567 time to fit residues: 143.5318 Evaluate side-chains 231 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 218 time to evaluate : 2.360 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1835 time to fit residues: 7.4627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 229 optimal weight: 3.9990 chunk 174 optimal weight: 0.8980 chunk 120 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 chunk 155 optimal weight: 0.7980 chunk 232 optimal weight: 0.0050 chunk 246 optimal weight: 0.6980 chunk 121 optimal weight: 0.8980 chunk 220 optimal weight: 7.9990 chunk 66 optimal weight: 0.0980 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 44 ASN 0 48 ASN ** 1 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 562 ASN 2 153 ASN 4 111 GLN 6 74 GLN P 223 ASN T 64 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 20239 Z= 0.147 Angle : 0.516 12.242 27469 Z= 0.263 Chirality : 0.039 0.146 3163 Planarity : 0.004 0.053 3505 Dihedral : 4.575 31.559 2746 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.93 % Favored : 95.99 % Rotamer Outliers : 1.50 % 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: -0.73 (0.16), residues: 2569 helix: -0.10 (0.13), residues: 1679 sheet: -0.53 (0.72), residues: 58 loop : -1.05 (0.20), residues: 832 *********************** 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 273 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 242 time to evaluate : 2.380 Fit side-chains outliers start: 31 outliers final: 14 residues processed: 266 average time/residue: 0.3816 time to fit residues: 154.8033 Evaluate side-chains 239 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 225 time to evaluate : 2.463 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1927 time to fit residues: 8.2933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 205 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 101 optimal weight: 0.1980 chunk 210 optimal weight: 0.7980 chunk 170 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 chunk 221 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 44 ASN 0 48 ASN ** 1 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 52 GLN 4 111 GLN 5 59 ASN T 64 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2487 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= 0.206 Angle : 0.539 13.181 27469 Z= 0.272 Chirality : 0.040 0.146 3163 Planarity : 0.004 0.052 3505 Dihedral : 4.504 31.105 2746 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.01 % Favored : 95.91 % Rotamer Outliers : 1.16 % 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: -0.31 (0.17), residues: 2569 helix: 0.23 (0.13), residues: 1684 sheet: -0.39 (0.73), residues: 63 loop : -0.88 (0.21), residues: 822 *********************** 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 258 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 234 time to evaluate : 2.172 Fit side-chains outliers start: 24 outliers final: 14 residues processed: 248 average time/residue: 0.3429 time to fit residues: 127.5683 Evaluate side-chains 241 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 227 time to evaluate : 2.081 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1791 time to fit residues: 7.4951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 82 optimal weight: 7.9990 chunk 221 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 144 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 246 optimal weight: 10.0000 chunk 204 optimal weight: 0.6980 chunk 114 optimal weight: 5.9990 chunk 20 optimal weight: 0.0570 chunk 81 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 44 ASN 0 48 ASN ** 1 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 111 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 20239 Z= 0.159 Angle : 0.519 11.891 27469 Z= 0.261 Chirality : 0.039 0.176 3163 Planarity : 0.004 0.049 3505 Dihedral : 4.362 29.123 2746 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.85 % Favored : 96.07 % Rotamer Outliers : 0.48 % 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: 0.08 (0.17), residues: 2569 helix: 0.54 (0.13), residues: 1691 sheet: -0.25 (0.74), residues: 62 loop : -0.77 (0.21), residues: 816 *********************** 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 252 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 242 time to evaluate : 2.402 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 248 average time/residue: 0.3519 time to fit residues: 132.8342 Evaluate side-chains 229 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 225 time to evaluate : 2.272 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1770 time to fit residues: 4.4402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 237 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 140 optimal weight: 0.6980 chunk 180 optimal weight: 0.0980 chunk 139 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 137 optimal weight: 0.9990 chunk 245 optimal weight: 8.9990 chunk 153 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 chunk 113 optimal weight: 0.4980 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 44 ASN 0 48 ASN ** 1 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 531 HIS 4 111 GLN 6 74 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 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 0.029 20239 Z= 0.161 Angle : 0.516 12.001 27469 Z= 0.259 Chirality : 0.039 0.159 3163 Planarity : 0.004 0.048 3505 Dihedral : 4.275 28.676 2746 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.78 % Favored : 96.15 % Rotamer Outliers : 0.63 % 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: 0.35 (0.17), residues: 2569 helix: 0.76 (0.13), residues: 1698 sheet: -0.18 (0.74), residues: 62 loop : -0.69 (0.22), residues: 809 *********************** 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 246 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 233 time to evaluate : 2.348 Fit side-chains outliers start: 13 outliers final: 6 residues processed: 241 average time/residue: 0.3487 time to fit residues: 127.7538 Evaluate side-chains 232 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 226 time to evaluate : 2.251 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1798 time to fit residues: 5.0341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 152 optimal weight: 0.8980 chunk 98 optimal weight: 0.7980 chunk 146 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 48 optimal weight: 0.0000 chunk 47 optimal weight: 0.4980 chunk 156 optimal weight: 0.8980 chunk 167 optimal weight: 0.7980 chunk 121 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 193 optimal weight: 0.4980 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 44 ASN ** 1 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 111 GLN T 64 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 20239 Z= 0.146 Angle : 0.509 12.203 27469 Z= 0.255 Chirality : 0.039 0.156 3163 Planarity : 0.004 0.048 3505 Dihedral : 4.188 25.399 2746 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.85 % Favored : 96.11 % Rotamer Outliers : 0.29 % 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: 0.60 (0.17), residues: 2569 helix: 0.98 (0.13), residues: 1700 sheet: -0.01 (0.76), residues: 56 loop : -0.68 (0.22), residues: 813 *********************** 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 250 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 244 time to evaluate : 2.808 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 247 average time/residue: 0.3532 time to fit residues: 133.4227 Evaluate side-chains 229 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 226 time to evaluate : 2.411 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1954 time to fit residues: 4.0981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 223 optimal weight: 0.7980 chunk 235 optimal weight: 0.5980 chunk 214 optimal weight: 0.0050 chunk 229 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 179 optimal weight: 3.9990 chunk 70 optimal weight: 0.5980 chunk 206 optimal weight: 0.8980 chunk 216 optimal weight: 6.9990 chunk 228 optimal weight: 0.0570 overall best weight: 0.4112 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 44 ASN ** 1 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 111 GLN 5 82 HIS 6 74 GLN T 64 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 20239 Z= 0.134 Angle : 0.519 18.896 27469 Z= 0.255 Chirality : 0.038 0.148 3163 Planarity : 0.004 0.049 3505 Dihedral : 4.087 20.376 2746 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.54 % Favored : 96.42 % Rotamer Outliers : 0.29 % 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: 0.85 (0.17), residues: 2569 helix: 1.17 (0.13), residues: 1708 sheet: 0.13 (0.78), residues: 56 loop : -0.60 (0.22), residues: 805 *********************** 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 245 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 239 time to evaluate : 2.346 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 243 average time/residue: 0.3589 time to fit residues: 131.7204 Evaluate side-chains 234 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 231 time to evaluate : 2.275 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1831 time to fit residues: 3.9393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 150 optimal weight: 0.5980 chunk 242 optimal weight: 1.9990 chunk 147 optimal weight: 0.7980 chunk 114 optimal weight: 5.9990 chunk 168 optimal weight: 2.9990 chunk 254 optimal weight: 0.3980 chunk 233 optimal weight: 5.9990 chunk 202 optimal weight: 0.0000 chunk 21 optimal weight: 1.9990 chunk 156 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 44 ASN ** 1 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 111 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 20239 Z= 0.150 Angle : 0.528 17.264 27469 Z= 0.259 Chirality : 0.039 0.145 3163 Planarity : 0.004 0.048 3505 Dihedral : 4.078 20.550 2746 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.74 % Favored : 96.22 % Rotamer Outliers : 0.05 % 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: 0.95 (0.17), residues: 2569 helix: 1.25 (0.13), residues: 1701 sheet: -0.17 (0.68), residues: 70 loop : -0.54 (0.22), residues: 798 ********************** 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 244 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 243 time to evaluate : 2.317 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 243 average time/residue: 0.3621 time to fit residues: 133.7115 Evaluate side-chains 239 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 238 time to evaluate : 2.332 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1866 time to fit residues: 3.5748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 160 optimal weight: 7.9990 chunk 215 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 chunk 186 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 56 optimal weight: 1.9990 chunk 202 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 chunk 208 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 44 ASN ** 1 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 430 GLN 4 111 GLN 6 74 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.132286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.105169 restraints weight = 27719.056| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.20 r_work: 0.2777 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 20239 Z= 0.220 Angle : 0.563 16.389 27469 Z= 0.277 Chirality : 0.041 0.144 3163 Planarity : 0.004 0.047 3505 Dihedral : 4.229 21.369 2746 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.78 % Favored : 96.15 % Rotamer Outliers : 0.29 % 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: 0.83 (0.17), residues: 2569 helix: 1.16 (0.13), residues: 1704 sheet: -0.22 (0.69), residues: 69 loop : -0.58 (0.22), residues: 796 Sorry: There was an error with writing 6rdd_4814_real_space_refined_001.pdb. [Errno 28] No space left on device