Starting phenix.real_space_refine on Sat Feb 17 21:14:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdd_4814/02_2024/6rdd_4814.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdd_4814/02_2024/6rdd_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_4814/02_2024/6rdd_4814.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdd_4814/02_2024/6rdd_4814.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdd_4814/02_2024/6rdd_4814.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdd_4814/02_2024/6rdd_4814.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= 0.005 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 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. 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-5238/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: 10.51, per 1000 atoms: 0.53 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: 8.31 Conformation dependent library (CDL) restraints added in 3.8 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: 2.01 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: 6.25 Time building geometry restraints manager: 8.81 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 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: 5.770 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: 24.550 Check model and map are aligned: 0.290 Set scattering table: 0.180 Process input model: 56.760 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.080 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 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 % Allowed : 6.64 % Favored : 93.17 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP 7 107 HIS 0.014 0.002 HIS 4 233 PHE 0.029 0.003 PHE 3 121 TYR 0.034 0.003 TYR 4 211 ARG 0.007 0.001 ARG P 206 *********************** 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 : 2.328 Fit side-chains revert: symmetry clash REVERT: 0 40 LYS cc_start: 0.8947 (ttpt) cc_final: 0.7786 (tppt) REVERT: 1 101 ASN cc_start: 0.8172 (t0) cc_final: 0.7938 (t0) REVERT: 1 242 LYS cc_start: 0.8249 (tttt) cc_final: 0.8018 (mmtm) REVERT: 1 504 ASP cc_start: 0.7889 (t0) cc_final: 0.7532 (t0) REVERT: 2 68 ASN cc_start: 0.8857 (m110) cc_final: 0.8270 (m110) REVERT: 2 74 ASN cc_start: 0.9047 (t0) cc_final: 0.8818 (t0) REVERT: 2 346 ARG cc_start: 0.7549 (mtm-85) cc_final: 0.7265 (mtt180) REVERT: 4 117 GLU cc_start: 0.7559 (pm20) cc_final: 0.7316 (pm20) REVERT: 4 121 ASP cc_start: 0.8323 (t70) cc_final: 0.8119 (t0) REVERT: 4 255 ARG cc_start: 0.8307 (ttm170) cc_final: 0.8021 (ttm170) REVERT: 7 135 ASP cc_start: 0.8515 (m-30) cc_final: 0.8129 (m-30) REVERT: 7 160 ASN cc_start: 0.8866 (m-40) cc_final: 0.8665 (m-40) REVERT: 8 33 TYR cc_start: 0.9103 (t80) cc_final: 0.8844 (t80) REVERT: 8 38 LYS cc_start: 0.8983 (mttt) cc_final: 0.8676 (mtpp) REVERT: 9 12 GLU cc_start: 0.8137 (tt0) cc_final: 0.7925 (tt0) REVERT: M 140 ASP cc_start: 0.8381 (t70) cc_final: 0.8069 (t70) outliers start: 4 outliers final: 1 residues processed: 333 average time/residue: 0.3637 time to fit residues: 177.5380 Evaluate side-chains 241 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 240 time to evaluate : 2.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 144 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: 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: 0.7980 chunk 77 optimal weight: 0.6980 chunk 121 optimal weight: 1.9990 chunk 148 optimal weight: 0.8980 chunk 231 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 1 101 ASN 1 285 GLN 1 298 GLN 1 316 ASN ** 1 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 423 ASN 1 482 ASN 1 587 ASN 1 590 HIS 2 68 ASN 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: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1663 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= 0.190 Angle : 0.594 13.183 27469 Z= 0.314 Chirality : 0.041 0.259 3163 Planarity : 0.006 0.059 3505 Dihedral : 5.512 35.782 2747 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.74 % Favored : 96.19 % Rotamer: Outliers : 1.70 % Allowed : 10.08 % Favored : 88.22 % 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: -3.33 (0.14), residues: 2569 helix: -2.31 (0.10), residues: 1685 sheet: -1.45 (0.68), residues: 52 loop : -1.55 (0.19), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP 4 206 HIS 0.005 0.001 HIS 4 233 PHE 0.017 0.001 PHE 9 6 TYR 0.025 0.001 TYR 4 211 ARG 0.005 0.000 ARG 1 609 *********************** 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 315 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 280 time to evaluate : 2.288 Fit side-chains revert: symmetry clash REVERT: 0 40 LYS cc_start: 0.8899 (ttpt) cc_final: 0.7721 (tppt) REVERT: 1 69 ASP cc_start: 0.7432 (m-30) cc_final: 0.6852 (m-30) REVERT: 1 194 LYS cc_start: 0.7036 (ttpp) cc_final: 0.6573 (ttmt) REVERT: 1 456 LYS cc_start: 0.7932 (tmmt) cc_final: 0.7704 (tptt) REVERT: 2 68 ASN cc_start: 0.8787 (m-40) cc_final: 0.8227 (m110) REVERT: 2 74 ASN cc_start: 0.8942 (t0) cc_final: 0.8714 (t0) REVERT: 8 38 LYS cc_start: 0.8794 (mttt) cc_final: 0.8574 (mtpp) REVERT: 9 12 GLU cc_start: 0.8155 (tt0) cc_final: 0.7920 (tt0) outliers start: 35 outliers final: 17 residues processed: 300 average time/residue: 0.3374 time to fit residues: 153.2659 Evaluate side-chains 251 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 234 time to evaluate : 2.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 1 residue 29 SER Chi-restraints excluded: chain 1 residue 42 SER Chi-restraints excluded: chain 1 residue 310 THR Chi-restraints excluded: chain 1 residue 356 VAL Chi-restraints excluded: chain 1 residue 367 GLU Chi-restraints excluded: chain 1 residue 578 ASP Chi-restraints excluded: chain 2 residue 155 VAL Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 422 GLU Chi-restraints excluded: chain 3 residue 303 VAL Chi-restraints excluded: chain 4 residue 45 ASP Chi-restraints excluded: chain 4 residue 77 SER Chi-restraints excluded: chain 6 residue 52 LYS Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 9 residue 3 VAL Chi-restraints excluded: chain 9 residue 92 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 128 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 192 optimal weight: 5.9990 chunk 157 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 231 optimal weight: 0.9990 chunk 250 optimal weight: 0.7980 chunk 206 optimal weight: 4.9990 chunk 230 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 186 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 44 ASN 0 48 ASN ** 1 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 153 ASN 3 229 ASN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20239 Z= 0.205 Angle : 0.556 13.268 27469 Z= 0.287 Chirality : 0.041 0.204 3163 Planarity : 0.004 0.052 3505 Dihedral : 4.980 32.381 2747 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.17 % Favored : 95.76 % Rotamer: Outliers : 2.04 % Allowed : 11.29 % Favored : 86.67 % 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: -1.73 (0.16), residues: 2569 helix: -0.95 (0.12), residues: 1682 sheet: -0.88 (0.71), residues: 51 loop : -1.24 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP 9 73 HIS 0.006 0.001 HIS 4 233 PHE 0.014 0.001 PHE 1 529 TYR 0.026 0.001 TYR 4 211 ARG 0.006 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 288 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 246 time to evaluate : 2.402 Fit side-chains revert: symmetry clash REVERT: 0 40 LYS cc_start: 0.8910 (ttpt) cc_final: 0.7756 (tppt) REVERT: 1 69 ASP cc_start: 0.7232 (m-30) cc_final: 0.6460 (m-30) REVERT: 1 101 ASN cc_start: 0.8130 (t0) cc_final: 0.7899 (t0) REVERT: 1 456 LYS cc_start: 0.8029 (tmmt) cc_final: 0.7825 (tptt) REVERT: 2 68 ASN cc_start: 0.8763 (m-40) cc_final: 0.8192 (m110) REVERT: 8 38 LYS cc_start: 0.8795 (mttt) cc_final: 0.8531 (mtpp) REVERT: 9 12 GLU cc_start: 0.8216 (tt0) cc_final: 0.7973 (tt0) REVERT: 9 88 GLU cc_start: 0.7086 (mp0) cc_final: 0.6869 (mp0) REVERT: P 186 MET cc_start: 0.5722 (tpp) cc_final: 0.5502 (tpp) outliers start: 42 outliers final: 27 residues processed: 272 average time/residue: 0.3472 time to fit residues: 141.4033 Evaluate side-chains 255 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 228 time to evaluate : 2.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 0 residue 43 SER Chi-restraints excluded: chain 0 residue 82 HIS Chi-restraints excluded: chain 1 residue 42 SER Chi-restraints excluded: chain 1 residue 92 TYR Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 310 THR Chi-restraints excluded: chain 1 residue 356 VAL Chi-restraints excluded: chain 1 residue 501 GLU Chi-restraints excluded: chain 1 residue 578 ASP Chi-restraints excluded: chain 2 residue 41 VAL Chi-restraints excluded: chain 2 residue 155 VAL Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 422 GLU Chi-restraints excluded: chain 3 residue 303 VAL Chi-restraints excluded: chain 4 residue 77 SER Chi-restraints excluded: chain 6 residue 52 LYS Chi-restraints excluded: chain 6 residue 84 SER Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 8 residue 6 VAL Chi-restraints excluded: chain 8 residue 77 ILE Chi-restraints excluded: chain 9 residue 3 VAL Chi-restraints excluded: chain 9 residue 7 LEU Chi-restraints excluded: chain 9 residue 65 THR Chi-restraints excluded: chain 9 residue 92 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 229 optimal weight: 2.9990 chunk 174 optimal weight: 3.9990 chunk 120 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 110 optimal weight: 5.9990 chunk 155 optimal weight: 0.7980 chunk 232 optimal weight: 0.0770 chunk 246 optimal weight: 2.9990 chunk 121 optimal weight: 0.7980 chunk 220 optimal weight: 0.0170 chunk 66 optimal weight: 0.4980 overall best weight: 0.4376 ------------------------------------------------------------------------------- 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 P 223 ASN T 64 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 20239 Z= 0.139 Angle : 0.506 11.684 27469 Z= 0.258 Chirality : 0.038 0.167 3163 Planarity : 0.004 0.047 3505 Dihedral : 4.571 28.850 2747 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.97 % Favored : 95.95 % Rotamer: Outliers : 2.04 % Allowed : 12.17 % Favored : 85.80 % 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: -0.70 (0.16), residues: 2569 helix: -0.07 (0.13), residues: 1677 sheet: -0.43 (0.77), residues: 51 loop : -1.04 (0.20), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP 9 73 HIS 0.005 0.001 HIS 4 233 PHE 0.014 0.001 PHE 1 529 TYR 0.025 0.001 TYR 4 211 ARG 0.004 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 299 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 257 time to evaluate : 2.151 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 40 LYS cc_start: 0.8965 (ttpt) cc_final: 0.7761 (tppt) REVERT: 1 69 ASP cc_start: 0.7187 (m-30) cc_final: 0.6344 (m-30) REVERT: 8 38 LYS cc_start: 0.8833 (mttt) cc_final: 0.8569 (mtpp) REVERT: 9 13 LYS cc_start: 0.7213 (tttm) cc_final: 0.6639 (mmmt) REVERT: M 154 THR cc_start: 0.8759 (m) cc_final: 0.8475 (m) outliers start: 42 outliers final: 26 residues processed: 282 average time/residue: 0.3320 time to fit residues: 141.2849 Evaluate side-chains 267 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 241 time to evaluate : 2.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 0 residue 43 SER Chi-restraints excluded: chain 1 residue 92 TYR Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 277 VAL Chi-restraints excluded: chain 1 residue 310 THR Chi-restraints excluded: chain 1 residue 367 GLU Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 501 GLU Chi-restraints excluded: chain 1 residue 512 LEU Chi-restraints excluded: chain 2 residue 41 VAL Chi-restraints excluded: chain 2 residue 370 ILE Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 422 GLU Chi-restraints excluded: chain 3 residue 303 VAL Chi-restraints excluded: chain 3 residue 319 GLN Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 77 ILE Chi-restraints excluded: chain 9 residue 7 LEU Chi-restraints excluded: chain 9 residue 65 THR Chi-restraints excluded: chain 9 residue 92 GLU Chi-restraints excluded: chain M residue 148 ILE Chi-restraints excluded: chain M residue 261 LEU Chi-restraints excluded: chain M residue 323 VAL 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: 3.9990 chunk 3 optimal weight: 0.0060 chunk 183 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 210 optimal weight: 0.8980 chunk 170 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 221 optimal weight: 0.0870 chunk 62 optimal weight: 3.9990 overall best weight: 0.7576 ------------------------------------------------------------------------------- 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 5 59 ASN T 64 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 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 0.046 20239 Z= 0.182 Angle : 0.523 13.238 27469 Z= 0.264 Chirality : 0.039 0.142 3163 Planarity : 0.004 0.049 3505 Dihedral : 4.476 31.477 2747 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.81 % Favored : 96.11 % Rotamer: Outliers : 2.33 % Allowed : 12.99 % Favored : 84.68 % 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: -0.24 (0.17), residues: 2569 helix: 0.27 (0.13), residues: 1695 sheet: -0.30 (0.78), residues: 51 loop : -0.84 (0.21), residues: 823 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 0.029 0.001 PHE 3 115 TYR 0.025 0.001 TYR 4 211 ARG 0.003 0.000 ARG 2 187 *********************** 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 296 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 248 time to evaluate : 2.439 Fit side-chains revert: symmetry clash REVERT: 0 40 LYS cc_start: 0.8952 (ttpt) cc_final: 0.7767 (tppt) REVERT: 1 69 ASP cc_start: 0.7233 (m-30) cc_final: 0.6374 (m-30) REVERT: 2 16 ASP cc_start: 0.8163 (t70) cc_final: 0.7741 (t0) REVERT: 2 68 ASN cc_start: 0.8738 (m-40) cc_final: 0.8223 (m110) REVERT: 2 139 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7174 (mp0) REVERT: 4 229 ILE cc_start: 0.8842 (tt) cc_final: 0.8431 (pt) REVERT: 5 111 LYS cc_start: 0.8514 (ttmm) cc_final: 0.8269 (mmtm) REVERT: 6 52 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.8055 (mmtt) REVERT: 7 187 LEU cc_start: 0.7893 (mt) cc_final: 0.7630 (mt) REVERT: 8 38 LYS cc_start: 0.8865 (mttt) cc_final: 0.8600 (mtpp) REVERT: 9 13 LYS cc_start: 0.7267 (tttm) cc_final: 0.6724 (mmmt) REVERT: 9 82 ASP cc_start: 0.8033 (OUTLIER) cc_final: 0.7800 (p0) REVERT: 9 88 GLU cc_start: 0.6935 (mp0) cc_final: 0.6705 (mp0) outliers start: 48 outliers final: 29 residues processed: 277 average time/residue: 0.3569 time to fit residues: 152.3112 Evaluate side-chains 272 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 240 time to evaluate : 2.414 ------------------------------------------------------------------------------- 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 82 HIS Chi-restraints excluded: chain 1 residue 92 TYR Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 277 VAL Chi-restraints excluded: chain 1 residue 283 ASP Chi-restraints excluded: chain 1 residue 310 THR Chi-restraints excluded: chain 1 residue 367 GLU Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 2 residue 41 VAL Chi-restraints excluded: chain 2 residue 97 SER Chi-restraints excluded: chain 2 residue 139 GLU Chi-restraints excluded: chain 2 residue 370 ILE Chi-restraints excluded: chain 2 residue 422 GLU Chi-restraints excluded: chain 3 residue 303 VAL Chi-restraints excluded: chain 4 residue 77 SER Chi-restraints excluded: chain 4 residue 141 VAL Chi-restraints excluded: chain 4 residue 181 ASP Chi-restraints excluded: chain 5 residue 59 ASN Chi-restraints excluded: chain 5 residue 106 LEU Chi-restraints excluded: chain 6 residue 52 LYS Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 84 SER Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 8 residue 6 VAL Chi-restraints excluded: chain 8 residue 77 ILE Chi-restraints excluded: chain 9 residue 65 THR Chi-restraints excluded: chain 9 residue 82 ASP Chi-restraints excluded: chain 9 residue 92 GLU Chi-restraints excluded: chain M residue 323 VAL Chi-restraints excluded: chain P residue 184 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 82 optimal weight: 9.9990 chunk 221 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 chunk 144 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 246 optimal weight: 7.9990 chunk 204 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 chunk 20 optimal weight: 0.3980 chunk 81 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 T 64 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20239 Z= 0.237 Angle : 0.547 12.944 27469 Z= 0.275 Chirality : 0.041 0.166 3163 Planarity : 0.004 0.051 3505 Dihedral : 4.478 30.655 2746 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.01 % Favored : 95.91 % Rotamer: Outliers : 2.23 % Allowed : 13.57 % Favored : 84.20 % 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: -0.06 (0.17), residues: 2569 helix: 0.42 (0.13), residues: 1694 sheet: -0.26 (0.80), residues: 51 loop : -0.79 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 9 73 HIS 0.006 0.001 HIS 4 233 PHE 0.024 0.001 PHE 3 115 TYR 0.025 0.001 TYR 4 211 ARG 0.003 0.000 ARG 1 387 *********************** 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 288 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 242 time to evaluate : 2.380 Fit side-chains revert: symmetry clash REVERT: 0 40 LYS cc_start: 0.8956 (ttpt) cc_final: 0.7776 (tppt) REVERT: 1 69 ASP cc_start: 0.7213 (m-30) cc_final: 0.6325 (m-30) REVERT: 1 456 LYS cc_start: 0.7961 (tttt) cc_final: 0.7655 (tptt) REVERT: 2 16 ASP cc_start: 0.8220 (t70) cc_final: 0.7797 (t0) REVERT: 2 68 ASN cc_start: 0.8755 (m-40) cc_final: 0.8236 (m110) REVERT: 2 139 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7177 (mp0) REVERT: 3 297 LEU cc_start: 0.8469 (mt) cc_final: 0.8073 (mt) REVERT: 5 111 LYS cc_start: 0.8562 (ttmm) cc_final: 0.8317 (mmtm) REVERT: 6 52 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.8088 (mmtt) REVERT: 7 187 LEU cc_start: 0.7994 (mt) cc_final: 0.7711 (mt) REVERT: 8 38 LYS cc_start: 0.8863 (mttt) cc_final: 0.8605 (mtpp) REVERT: 9 82 ASP cc_start: 0.8105 (OUTLIER) cc_final: 0.7742 (p0) outliers start: 46 outliers final: 36 residues processed: 272 average time/residue: 0.3442 time to fit residues: 141.3234 Evaluate side-chains 272 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 233 time to evaluate : 2.423 ------------------------------------------------------------------------------- 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 43 SER Chi-restraints excluded: chain 0 residue 82 HIS Chi-restraints excluded: chain 1 residue 92 TYR Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 277 VAL Chi-restraints excluded: chain 1 residue 283 ASP Chi-restraints excluded: chain 1 residue 310 THR Chi-restraints excluded: chain 1 residue 367 GLU Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 2 residue 41 VAL Chi-restraints excluded: chain 2 residue 97 SER Chi-restraints excluded: chain 2 residue 139 GLU Chi-restraints excluded: chain 2 residue 370 ILE Chi-restraints excluded: chain 2 residue 422 GLU Chi-restraints excluded: chain 3 residue 303 VAL Chi-restraints excluded: chain 4 residue 21 GLU Chi-restraints excluded: chain 4 residue 77 SER Chi-restraints excluded: chain 4 residue 122 VAL Chi-restraints excluded: chain 4 residue 141 VAL Chi-restraints excluded: chain 4 residue 181 ASP Chi-restraints excluded: chain 5 residue 26 LEU Chi-restraints excluded: chain 5 residue 106 LEU Chi-restraints excluded: chain 6 residue 52 LYS Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 84 SER Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 8 residue 6 VAL Chi-restraints excluded: chain 8 residue 77 ILE Chi-restraints excluded: chain 9 residue 65 THR Chi-restraints excluded: chain 9 residue 82 ASP Chi-restraints excluded: chain 9 residue 92 GLU Chi-restraints excluded: chain M residue 290 LEU Chi-restraints excluded: chain M residue 323 VAL Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain T residue 67 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 237 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 140 optimal weight: 0.8980 chunk 180 optimal weight: 5.9990 chunk 139 optimal weight: 0.9980 chunk 207 optimal weight: 0.8980 chunk 137 optimal weight: 0.8980 chunk 245 optimal weight: 0.8980 chunk 153 optimal weight: 0.5980 chunk 149 optimal weight: 3.9990 chunk 113 optimal weight: 0.0050 overall best weight: 0.6594 ------------------------------------------------------------------------------- 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: 0.8156 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20239 Z= 0.163 Angle : 0.513 11.460 27469 Z= 0.258 Chirality : 0.039 0.141 3163 Planarity : 0.004 0.049 3505 Dihedral : 4.324 28.738 2746 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.93 % Favored : 95.99 % Rotamer: Outliers : 2.38 % Allowed : 13.38 % Favored : 84.25 % 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: 0.32 (0.17), residues: 2569 helix: 0.72 (0.13), residues: 1689 sheet: -0.66 (0.89), residues: 41 loop : -0.61 (0.21), residues: 839 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 0.021 0.001 PHE 3 115 TYR 0.024 0.001 TYR 4 211 ARG 0.002 0.000 ARG 1 387 *********************** 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 301 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 252 time to evaluate : 2.366 Fit side-chains revert: symmetry clash REVERT: 0 40 LYS cc_start: 0.8940 (ttpt) cc_final: 0.7791 (tppt) REVERT: 1 69 ASP cc_start: 0.7205 (m-30) cc_final: 0.6358 (m-30) REVERT: 1 456 LYS cc_start: 0.7932 (tttt) cc_final: 0.7616 (tptt) REVERT: 2 16 ASP cc_start: 0.8188 (t70) cc_final: 0.7741 (t0) REVERT: 2 68 ASN cc_start: 0.8726 (m-40) cc_final: 0.8214 (m110) REVERT: 2 139 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7143 (mp0) REVERT: 3 297 LEU cc_start: 0.8449 (mt) cc_final: 0.8059 (mt) REVERT: 3 319 GLN cc_start: 0.7369 (OUTLIER) cc_final: 0.7055 (mm-40) REVERT: 4 229 ILE cc_start: 0.8742 (tt) cc_final: 0.8454 (pt) REVERT: 6 52 LYS cc_start: 0.8388 (OUTLIER) cc_final: 0.8077 (mmtt) REVERT: 7 187 LEU cc_start: 0.7877 (mt) cc_final: 0.7627 (mt) REVERT: 8 38 LYS cc_start: 0.8854 (mttt) cc_final: 0.8587 (mtpp) outliers start: 49 outliers final: 38 residues processed: 281 average time/residue: 0.3396 time to fit residues: 144.2947 Evaluate side-chains 280 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 239 time to evaluate : 2.270 ------------------------------------------------------------------------------- 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 43 SER Chi-restraints excluded: chain 0 residue 82 HIS Chi-restraints excluded: chain 1 residue 92 TYR Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 277 VAL Chi-restraints excluded: chain 1 residue 310 THR Chi-restraints excluded: chain 1 residue 367 GLU Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 512 LEU Chi-restraints excluded: chain 2 residue 41 VAL Chi-restraints excluded: chain 2 residue 97 SER Chi-restraints excluded: chain 2 residue 139 GLU Chi-restraints excluded: chain 2 residue 370 ILE Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 422 GLU Chi-restraints excluded: chain 3 residue 303 VAL Chi-restraints excluded: chain 3 residue 319 GLN Chi-restraints excluded: chain 4 residue 77 SER Chi-restraints excluded: chain 4 residue 122 VAL Chi-restraints excluded: chain 4 residue 141 VAL Chi-restraints excluded: chain 4 residue 181 ASP Chi-restraints excluded: chain 5 residue 106 LEU Chi-restraints excluded: chain 6 residue 52 LYS Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 84 SER Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 6 VAL Chi-restraints excluded: chain 8 residue 9 LYS Chi-restraints excluded: chain 8 residue 77 ILE Chi-restraints excluded: chain 9 residue 3 VAL Chi-restraints excluded: chain 9 residue 65 THR Chi-restraints excluded: chain 9 residue 92 GLU Chi-restraints excluded: chain M residue 148 ILE Chi-restraints excluded: chain M residue 261 LEU Chi-restraints excluded: chain M residue 290 LEU Chi-restraints excluded: chain M residue 296 SER Chi-restraints excluded: chain M residue 323 VAL Chi-restraints excluded: chain P residue 184 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 152 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 146 optimal weight: 3.9990 chunk 74 optimal weight: 0.4980 chunk 48 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 chunk 167 optimal weight: 0.5980 chunk 121 optimal weight: 0.9980 chunk 22 optimal weight: 0.0370 chunk 193 optimal weight: 4.9990 overall best weight: 0.6260 ------------------------------------------------------------------------------- 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 9 80 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2756 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= 0.158 Angle : 0.511 12.215 27469 Z= 0.255 Chirality : 0.039 0.140 3163 Planarity : 0.004 0.049 3505 Dihedral : 4.244 27.939 2746 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.85 % Favored : 96.07 % Rotamer: Outliers : 2.08 % Allowed : 14.06 % Favored : 83.86 % 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: 0.56 (0.17), residues: 2569 helix: 0.92 (0.13), residues: 1699 sheet: -0.62 (0.89), residues: 41 loop : -0.57 (0.21), residues: 829 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 0.020 0.001 PHE 3 115 TYR 0.024 0.001 TYR 4 211 ARG 0.002 0.000 ARG 3 149 *********************** 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 298 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 255 time to evaluate : 2.422 Fit side-chains revert: symmetry clash REVERT: 0 40 LYS cc_start: 0.8930 (ttpt) cc_final: 0.7788 (tppt) REVERT: 1 69 ASP cc_start: 0.7197 (m-30) cc_final: 0.6360 (m-30) REVERT: 1 456 LYS cc_start: 0.7904 (tttt) cc_final: 0.7587 (tptt) REVERT: 2 16 ASP cc_start: 0.8183 (t70) cc_final: 0.7727 (t0) REVERT: 2 68 ASN cc_start: 0.8744 (m-40) cc_final: 0.8219 (m110) REVERT: 2 139 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7033 (mp0) REVERT: 3 297 LEU cc_start: 0.8443 (mt) cc_final: 0.8070 (mt) REVERT: 3 319 GLN cc_start: 0.7344 (OUTLIER) cc_final: 0.7071 (mm110) REVERT: 4 229 ILE cc_start: 0.8761 (tt) cc_final: 0.8469 (pt) REVERT: 6 52 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.8083 (mmtt) REVERT: 7 187 LEU cc_start: 0.7861 (mt) cc_final: 0.7610 (mt) REVERT: 8 38 LYS cc_start: 0.8839 (mttt) cc_final: 0.8570 (mtpp) REVERT: 9 13 LYS cc_start: 0.7256 (tttm) cc_final: 0.6708 (mmmt) REVERT: 9 88 GLU cc_start: 0.6967 (mp0) cc_final: 0.6763 (mp0) outliers start: 43 outliers final: 36 residues processed: 283 average time/residue: 0.3319 time to fit residues: 143.9992 Evaluate side-chains 285 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 246 time to evaluate : 2.397 ------------------------------------------------------------------------------- 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 82 HIS Chi-restraints excluded: chain 1 residue 92 TYR Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 256 VAL Chi-restraints excluded: chain 1 residue 277 VAL Chi-restraints excluded: chain 1 residue 310 THR Chi-restraints excluded: chain 1 residue 367 GLU Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 2 residue 41 VAL Chi-restraints excluded: chain 2 residue 97 SER Chi-restraints excluded: chain 2 residue 139 GLU Chi-restraints excluded: chain 2 residue 370 ILE Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 422 GLU Chi-restraints excluded: chain 3 residue 303 VAL Chi-restraints excluded: chain 3 residue 319 GLN Chi-restraints excluded: chain 4 residue 77 SER Chi-restraints excluded: chain 4 residue 122 VAL Chi-restraints excluded: chain 4 residue 141 VAL Chi-restraints excluded: chain 4 residue 181 ASP Chi-restraints excluded: chain 4 residue 204 PHE Chi-restraints excluded: chain 5 residue 89 VAL Chi-restraints excluded: chain 5 residue 106 LEU Chi-restraints excluded: chain 6 residue 52 LYS Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 84 SER Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 6 VAL Chi-restraints excluded: chain 8 residue 77 ILE Chi-restraints excluded: chain 9 residue 3 VAL Chi-restraints excluded: chain 9 residue 65 THR Chi-restraints excluded: chain 9 residue 92 GLU Chi-restraints excluded: chain M residue 261 LEU Chi-restraints excluded: chain M residue 290 LEU Chi-restraints excluded: chain M residue 296 SER Chi-restraints excluded: chain M residue 323 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 223 optimal weight: 0.9980 chunk 235 optimal weight: 0.6980 chunk 214 optimal weight: 0.7980 chunk 229 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 179 optimal weight: 0.0000 chunk 70 optimal weight: 0.4980 chunk 206 optimal weight: 0.9990 chunk 216 optimal weight: 6.9990 chunk 228 optimal weight: 1.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- 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: 0.8144 moved from start: 0.2834 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= 0.154 Angle : 0.510 12.097 27469 Z= 0.255 Chirality : 0.039 0.169 3163 Planarity : 0.004 0.049 3505 Dihedral : 4.185 23.647 2746 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.93 % Favored : 96.03 % Rotamer: Outliers : 2.28 % Allowed : 14.06 % Favored : 83.66 % 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: 1.10 (0.13), residues: 1701 sheet: -0.61 (0.87), residues: 41 loop : -0.54 (0.21), residues: 827 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 0.018 0.001 PHE 3 115 TYR 0.024 0.001 TYR 4 211 ARG 0.002 0.000 ARG 1 387 *********************** 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 302 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 255 time to evaluate : 2.489 Fit side-chains revert: symmetry clash REVERT: 0 40 LYS cc_start: 0.8919 (ttpt) cc_final: 0.7779 (tppt) REVERT: 1 69 ASP cc_start: 0.7184 (m-30) cc_final: 0.6355 (m-30) REVERT: 1 101 ASN cc_start: 0.8024 (t0) cc_final: 0.7750 (t0) REVERT: 1 456 LYS cc_start: 0.7887 (tttt) cc_final: 0.7566 (tptt) REVERT: 2 16 ASP cc_start: 0.8167 (t70) cc_final: 0.7710 (t0) REVERT: 2 68 ASN cc_start: 0.8735 (m-40) cc_final: 0.8217 (m110) REVERT: 2 139 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.6991 (mp0) REVERT: 3 297 LEU cc_start: 0.8457 (mt) cc_final: 0.8084 (mt) REVERT: 3 319 GLN cc_start: 0.7306 (OUTLIER) cc_final: 0.7042 (mm110) REVERT: 4 229 ILE cc_start: 0.8750 (tt) cc_final: 0.8484 (pt) REVERT: 5 90 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7796 (tm-30) REVERT: 6 52 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.8063 (mmtp) REVERT: 7 187 LEU cc_start: 0.7850 (mt) cc_final: 0.7607 (mt) REVERT: 8 38 LYS cc_start: 0.8831 (mttt) cc_final: 0.8559 (mtpp) REVERT: 9 13 LYS cc_start: 0.7179 (tttm) cc_final: 0.6628 (mmmt) REVERT: M 154 THR cc_start: 0.8771 (m) cc_final: 0.8533 (m) outliers start: 47 outliers final: 41 residues processed: 285 average time/residue: 0.3363 time to fit residues: 146.3132 Evaluate side-chains 289 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 245 time to evaluate : 2.314 ------------------------------------------------------------------------------- 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 82 HIS Chi-restraints excluded: chain 1 residue 92 TYR Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 256 VAL Chi-restraints excluded: chain 1 residue 277 VAL Chi-restraints excluded: chain 1 residue 310 THR Chi-restraints excluded: chain 1 residue 367 GLU Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 512 LEU Chi-restraints excluded: chain 2 residue 41 VAL Chi-restraints excluded: chain 2 residue 97 SER Chi-restraints excluded: chain 2 residue 139 GLU Chi-restraints excluded: chain 2 residue 370 ILE Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 422 GLU Chi-restraints excluded: chain 3 residue 121 PHE Chi-restraints excluded: chain 3 residue 303 VAL Chi-restraints excluded: chain 3 residue 319 GLN Chi-restraints excluded: chain 4 residue 77 SER Chi-restraints excluded: chain 4 residue 122 VAL Chi-restraints excluded: chain 4 residue 141 VAL Chi-restraints excluded: chain 4 residue 181 ASP Chi-restraints excluded: chain 4 residue 204 PHE Chi-restraints excluded: chain 5 residue 26 LEU Chi-restraints excluded: chain 5 residue 89 VAL Chi-restraints excluded: chain 5 residue 106 LEU Chi-restraints excluded: chain 6 residue 52 LYS Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 84 SER Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 8 residue 6 VAL Chi-restraints excluded: chain 8 residue 77 ILE Chi-restraints excluded: chain 9 residue 3 VAL Chi-restraints excluded: chain 9 residue 65 THR Chi-restraints excluded: chain 9 residue 92 GLU Chi-restraints excluded: chain M residue 261 LEU Chi-restraints excluded: chain M residue 290 LEU Chi-restraints excluded: chain M residue 296 SER Chi-restraints excluded: chain M residue 323 VAL Chi-restraints excluded: chain P residue 195 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 150 optimal weight: 1.9990 chunk 242 optimal weight: 2.9990 chunk 147 optimal weight: 6.9990 chunk 114 optimal weight: 5.9990 chunk 168 optimal weight: 2.9990 chunk 254 optimal weight: 3.9990 chunk 233 optimal weight: 3.9990 chunk 202 optimal weight: 0.7980 chunk 21 optimal weight: 0.3980 chunk 156 optimal weight: 3.9990 chunk 124 optimal weight: 0.6980 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 95 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 20239 Z= 0.261 Angle : 0.563 13.612 27469 Z= 0.282 Chirality : 0.041 0.174 3163 Planarity : 0.004 0.049 3505 Dihedral : 4.366 22.336 2746 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.28 % Favored : 95.64 % Rotamer: Outliers : 2.18 % Allowed : 14.40 % Favored : 83.42 % 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: 0.61 (0.17), residues: 2569 helix: 1.00 (0.13), residues: 1689 sheet: 0.14 (0.77), residues: 56 loop : -0.68 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 3 109 HIS 0.007 0.001 HIS 4 233 PHE 0.020 0.001 PHE 3 115 TYR 0.023 0.001 TYR 4 211 ARG 0.002 0.000 ARG 1 387 ********************** 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 286 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 241 time to evaluate : 2.524 Fit side-chains revert: symmetry clash REVERT: 0 40 LYS cc_start: 0.8944 (ttpt) cc_final: 0.7811 (tppt) REVERT: 1 69 ASP cc_start: 0.7194 (m-30) cc_final: 0.6315 (m-30) REVERT: 1 456 LYS cc_start: 0.7931 (tttt) cc_final: 0.7610 (tptt) REVERT: 2 139 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7047 (mp0) REVERT: 3 297 LEU cc_start: 0.8483 (mt) cc_final: 0.8090 (mt) REVERT: 3 319 GLN cc_start: 0.7426 (OUTLIER) cc_final: 0.7213 (mm110) REVERT: 4 229 ILE cc_start: 0.8875 (tt) cc_final: 0.8494 (pt) REVERT: 5 90 GLU cc_start: 0.7962 (tm-30) cc_final: 0.7740 (tm-30) REVERT: 6 52 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8118 (mmtp) REVERT: 7 187 LEU cc_start: 0.7949 (mt) cc_final: 0.7633 (mt) REVERT: 8 38 LYS cc_start: 0.8858 (mttt) cc_final: 0.8600 (mtpp) outliers start: 45 outliers final: 39 residues processed: 275 average time/residue: 0.3311 time to fit residues: 138.4645 Evaluate side-chains 275 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 233 time to evaluate : 2.265 ------------------------------------------------------------------------------- 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 82 HIS Chi-restraints excluded: chain 1 residue 92 TYR Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 256 VAL Chi-restraints excluded: chain 1 residue 277 VAL Chi-restraints excluded: chain 1 residue 310 THR Chi-restraints excluded: chain 1 residue 367 GLU Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 512 LEU Chi-restraints excluded: chain 2 residue 41 VAL Chi-restraints excluded: chain 2 residue 139 GLU Chi-restraints excluded: chain 2 residue 370 ILE Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 422 GLU Chi-restraints excluded: chain 3 residue 121 PHE Chi-restraints excluded: chain 3 residue 303 VAL Chi-restraints excluded: chain 3 residue 319 GLN Chi-restraints excluded: chain 4 residue 77 SER Chi-restraints excluded: chain 4 residue 122 VAL Chi-restraints excluded: chain 4 residue 141 VAL Chi-restraints excluded: chain 4 residue 181 ASP Chi-restraints excluded: chain 5 residue 26 LEU Chi-restraints excluded: chain 5 residue 89 VAL Chi-restraints excluded: chain 5 residue 106 LEU Chi-restraints excluded: chain 6 residue 52 LYS Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 84 SER Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 8 residue 6 VAL Chi-restraints excluded: chain 8 residue 77 ILE Chi-restraints excluded: chain 9 residue 3 VAL Chi-restraints excluded: chain 9 residue 65 THR Chi-restraints excluded: chain 9 residue 92 GLU Chi-restraints excluded: chain M residue 261 LEU Chi-restraints excluded: chain M residue 290 LEU Chi-restraints excluded: chain M residue 296 SER Chi-restraints excluded: chain M residue 323 VAL Chi-restraints excluded: chain P residue 195 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 160 optimal weight: 0.9980 chunk 215 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 186 optimal weight: 0.5980 chunk 29 optimal weight: 8.9990 chunk 56 optimal weight: 3.9990 chunk 202 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 208 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.132071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.105046 restraints weight = 27661.765| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.16 r_work: 0.2784 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20239 Z= 0.195 Angle : 0.536 12.983 27469 Z= 0.267 Chirality : 0.040 0.155 3163 Planarity : 0.004 0.049 3505 Dihedral : 4.303 24.491 2746 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.01 % Favored : 95.91 % Rotamer: Outliers : 2.18 % Allowed : 14.74 % Favored : 83.08 % 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: 1696 sheet: 0.10 (0.73), residues: 62 loop : -0.62 (0.22), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP 9 73 HIS 0.006 0.001 HIS 4 233 PHE 0.014 0.001 PHE 1 200 TYR 0.024 0.001 TYR 4 211 ARG 0.002 0.000 ARG 1 387 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4852.16 seconds wall clock time: 89 minutes 17.13 seconds (5357.13 seconds total)