Starting phenix.real_space_refine on Sun Dec 17 00:40:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h38_34455/12_2023/8h38_34455.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h38_34455/12_2023/8h38_34455.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h38_34455/12_2023/8h38_34455.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h38_34455/12_2023/8h38_34455.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h38_34455/12_2023/8h38_34455.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h38_34455/12_2023/8h38_34455.pdb" } resolution = 4.25 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 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 4 6.06 5 S 245 5.16 5 C 23674 2.51 5 N 6367 2.21 5 O 7016 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 179": "OE1" <-> "OE2" Residue "A TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 466": "OD1" <-> "OD2" Residue "B GLU 27": "OE1" <-> "OE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 46": "OD1" <-> "OD2" Residue "B GLU 133": "OE1" <-> "OE2" Residue "B ASP 183": "OD1" <-> "OD2" Residue "B GLU 267": "OE1" <-> "OE2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 412": "OD1" <-> "OD2" Residue "C PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 163": "OD1" <-> "OD2" Residue "C GLU 284": "OE1" <-> "OE2" Residue "D GLU 55": "OE1" <-> "OE2" Residue "D GLU 100": "OE1" <-> "OE2" Residue "D TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 104": "OE1" <-> "OE2" Residue "E TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 122": "OE1" <-> "OE2" Residue "E TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 197": "OD1" <-> "OD2" Residue "E TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 234": "OD1" <-> "OD2" Residue "E GLU 271": "OE1" <-> "OE2" Residue "E GLU 277": "OE1" <-> "OE2" Residue "F PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 213": "OE1" <-> "OE2" Residue "F PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 157": "OE1" <-> "OE2" Residue "I PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 215": "OE1" <-> "OE2" Residue "L GLU 278": "OE1" <-> "OE2" Residue "L PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 429": "OE1" <-> "OE2" Residue "L ASP 760": "OD1" <-> "OD2" Residue "L TYR 766": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 66": "OE1" <-> "OE2" Residue "M TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 12": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 37306 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3296 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 11, 'TRANS': 400} Chain breaks: 2 Chain: "B" Number of atoms: 3430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3430 Classifications: {'peptide': 420} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 407} Chain: "C" Number of atoms: 3235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3235 Classifications: {'peptide': 407} Link IDs: {'PTRANS': 13, 'TRANS': 393} Chain: "D" Number of atoms: 3251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3251 Classifications: {'peptide': 406} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 396} Chain: "E" Number of atoms: 2452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2452 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 10, 'TRANS': 298} Chain: "F" Number of atoms: 2279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2279 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 10, 'TRANS': 277} Chain: "G" Number of atoms: 1692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1692 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 4, 'TRANS': 209} Chain: "H" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1411 Classifications: {'peptide': 177} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 165} Chain breaks: 1 Chain: "I" Number of atoms: 4505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4505 Classifications: {'peptide': 557} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 535} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 5866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 720, 5866 Classifications: {'peptide': 720} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 17, 'TRANS': 702} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "M" Number of atoms: 4557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 564, 4557 Classifications: {'peptide': 564} Link IDs: {'PTRANS': 22, 'TRANS': 541} Chain breaks: 2 Chain: "R" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 737 Classifications: {'peptide': 89} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain: "N" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 591 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 72} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 36171 SG CYS R 42 101.009 98.525 55.565 1.00135.97 S ATOM 36190 SG CYS R 45 102.148 95.106 54.339 1.00137.74 S ATOM 36485 SG CYS R 83 98.573 95.602 55.722 1.00118.07 S ATOM 36414 SG CYS R 75 101.155 109.936 61.737 1.00115.91 S ATOM 36581 SG CYS R 94 100.344 106.504 63.224 1.00129.19 S ATOM 36257 SG CYS R 53 96.883 93.650 52.414 1.00143.05 S ATOM 36280 SG CYS R 56 94.584 92.901 49.482 1.00146.03 S ATOM 36364 SG CYS R 68 96.443 96.034 49.713 1.00133.77 S Time building chain proxies: 18.87, per 1000 atoms: 0.51 Number of scatterers: 37306 At special positions: 0 Unit cell: (156.6, 202.536, 183.744, 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 4 29.99 S 245 16.00 O 7016 8.00 N 6367 7.00 C 23674 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: 15.23 Conformation dependent library (CDL) restraints added in 7.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E 401 " pdb="ZN ZN E 401 " - pdb=" NE2 HIS E 140 " pdb=" ZN R4001 " pdb="ZN ZN R4001 " - pdb=" ND1 HIS R 80 " pdb="ZN ZN R4001 " - pdb=" SG CYS R 42 " pdb="ZN ZN R4001 " - pdb=" SG CYS R 45 " pdb="ZN ZN R4001 " - pdb=" SG CYS R 83 " pdb=" ZN R4002 " pdb="ZN ZN R4002 " - pdb=" ND1 HIS R 77 " pdb="ZN ZN R4002 " - pdb=" SG CYS R 75 " pdb="ZN ZN R4002 " - pdb=" SG CYS R 94 " pdb=" ZN R4003 " pdb="ZN ZN R4003 " - pdb=" ND1 HIS R 82 " pdb="ZN ZN R4003 " - pdb=" SG CYS R 53 " pdb="ZN ZN R4003 " - pdb=" SG CYS R 56 " pdb="ZN ZN R4003 " - pdb=" SG CYS R 68 " Number of angles added : 6 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8890 Finding SS restraints... Secondary structure from input PDB file: 193 helices and 28 sheets defined 60.7% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.84 Creating SS restraints... Processing helix chain 'A' and resid 83 through 91 removed outlier: 3.791A pdb=" N TYR A 91 " --> pdb=" O TYR A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 107 Processing helix chain 'A' and resid 110 through 123 Processing helix chain 'A' and resid 128 through 146 removed outlier: 3.719A pdb=" N GLU A 132 " --> pdb=" O VAL A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 192 Processing helix chain 'A' and resid 193 through 212 Processing helix chain 'A' and resid 213 through 225 Processing helix chain 'A' and resid 230 through 248 removed outlier: 3.651A pdb=" N TYR A 247 " --> pdb=" O LYS A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 264 removed outlier: 3.541A pdb=" N THR A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 296 removed outlier: 4.269A pdb=" N LYS A 284 " --> pdb=" O ALA A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 308 Processing helix chain 'A' and resid 310 through 314 Processing helix chain 'A' and resid 321 through 337 Processing helix chain 'A' and resid 338 through 350 removed outlier: 3.730A pdb=" N SER A 350 " --> pdb=" O VAL A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 359 Processing helix chain 'A' and resid 359 through 371 Processing helix chain 'A' and resid 373 through 389 removed outlier: 3.616A pdb=" N ASP A 386 " --> pdb=" O ASP A 382 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ASN A 387 " --> pdb=" O GLU A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 415 removed outlier: 4.015A pdb=" N ARG A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N THR A 400 " --> pdb=" O PRO A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 428 Processing helix chain 'A' and resid 432 through 447 Processing helix chain 'A' and resid 466 through 498 removed outlier: 3.760A pdb=" N THR A 470 " --> pdb=" O ASP A 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.520A pdb=" N ASN B 34 " --> pdb=" O VAL B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 62 removed outlier: 4.116A pdb=" N GLY B 62 " --> pdb=" O LEU B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 82 Processing helix chain 'B' and resid 85 through 100 removed outlier: 3.903A pdb=" N ARG B 100 " --> pdb=" O LEU B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 120 Processing helix chain 'B' and resid 124 through 142 removed outlier: 3.783A pdb=" N ALA B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 162 removed outlier: 3.509A pdb=" N ARG B 162 " --> pdb=" O LEU B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 178 removed outlier: 3.998A pdb=" N LYS B 170 " --> pdb=" O GLY B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 209 removed outlier: 3.738A pdb=" N GLU B 196 " --> pdb=" O THR B 192 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA B 207 " --> pdb=" O GLN B 203 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN B 208 " --> pdb=" O MET B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 225 removed outlier: 3.800A pdb=" N HIS B 223 " --> pdb=" O GLU B 219 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE B 224 " --> pdb=" O GLN B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 249 Processing helix chain 'B' and resid 250 through 269 removed outlier: 3.614A pdb=" N ALA B 254 " --> pdb=" O GLU B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 287 Processing helix chain 'B' and resid 300 through 304 Processing helix chain 'B' and resid 305 through 321 removed outlier: 4.408A pdb=" N ALA B 310 " --> pdb=" O PRO B 306 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N MET B 311 " --> pdb=" O GLU B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 333 Processing helix chain 'B' and resid 333 through 338 removed outlier: 3.909A pdb=" N MET B 338 " --> pdb=" O HIS B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 367 removed outlier: 4.393A pdb=" N GLU B 348 " --> pdb=" O ARG B 344 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N GLU B 349 " --> pdb=" O GLU B 345 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LYS B 364 " --> pdb=" O ILE B 360 " (cutoff:3.500A) Proline residue: B 365 - end of helix Processing helix chain 'B' and resid 371 through 379 Processing helix chain 'B' and resid 381 through 395 Processing helix chain 'B' and resid 420 through 443 Processing helix chain 'C' and resid 3 through 18 Processing helix chain 'C' and resid 20 through 29 Processing helix chain 'C' and resid 32 through 38 Processing helix chain 'C' and resid 41 through 49 Processing helix chain 'C' and resid 52 through 68 Processing helix chain 'C' and resid 73 through 87 Processing helix chain 'C' and resid 96 through 115 removed outlier: 3.548A pdb=" N PHE C 100 " --> pdb=" O ALA C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 132 removed outlier: 3.578A pdb=" N ILE C 123 " --> pdb=" O ARG C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 153 removed outlier: 3.652A pdb=" N ASP C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 163 removed outlier: 3.830A pdb=" N TYR C 161 " --> pdb=" O PRO C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 195 removed outlier: 3.854A pdb=" N PHE C 181 " --> pdb=" O ASP C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 210 Processing helix chain 'C' and resid 217 through 235 Processing helix chain 'C' and resid 248 through 257 removed outlier: 3.737A pdb=" N LYS C 254 " --> pdb=" O GLY C 250 " (cutoff:3.500A) Proline residue: C 255 - end of helix Processing helix chain 'C' and resid 257 through 270 Processing helix chain 'C' and resid 271 through 282 Processing helix chain 'C' and resid 292 through 313 removed outlier: 3.575A pdb=" N LYS C 296 " --> pdb=" O MET C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 327 Processing helix chain 'C' and resid 330 through 344 Processing helix chain 'C' and resid 369 through 400 removed outlier: 3.822A pdb=" N LEU C 373 " --> pdb=" O ASN C 369 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN C 400 " --> pdb=" O GLU C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 408 removed outlier: 3.840A pdb=" N VAL C 404 " --> pdb=" O ASN C 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 14 removed outlier: 3.572A pdb=" N ASN D 14 " --> pdb=" O ALA D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 36 removed outlier: 3.503A pdb=" N LEU D 36 " --> pdb=" O LYS D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 54 removed outlier: 3.619A pdb=" N GLN D 41 " --> pdb=" O SER D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 73 Processing helix chain 'D' and resid 74 through 76 No H-bonds generated for 'chain 'D' and resid 74 through 76' Processing helix chain 'D' and resid 79 through 81 No H-bonds generated for 'chain 'D' and resid 79 through 81' Processing helix chain 'D' and resid 82 through 92 Processing helix chain 'D' and resid 100 through 117 Processing helix chain 'D' and resid 119 through 129 removed outlier: 3.539A pdb=" N ALA D 123 " --> pdb=" O ASP D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 158 removed outlier: 3.691A pdb=" N ASP D 158 " --> pdb=" O LEU D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 176 removed outlier: 3.581A pdb=" N ALA D 166 " --> pdb=" O VAL D 162 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG D 170 " --> pdb=" O ALA D 166 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN D 176 " --> pdb=" O SER D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 198 Processing helix chain 'D' and resid 200 through 213 removed outlier: 3.707A pdb=" N TYR D 213 " --> pdb=" O ASN D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 236 Processing helix chain 'D' and resid 239 through 250 Processing helix chain 'D' and resid 252 through 258 removed outlier: 3.745A pdb=" N GLN D 256 " --> pdb=" O ASP D 252 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU D 258 " --> pdb=" O ARG D 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 252 through 258' Processing helix chain 'D' and resid 260 through 270 Processing helix chain 'D' and resid 277 through 286 removed outlier: 3.636A pdb=" N PHE D 281 " --> pdb=" O GLN D 277 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N MET D 286 " --> pdb=" O ALA D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 315 removed outlier: 3.594A pdb=" N LEU D 315 " --> pdb=" O SER D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 329 Processing helix chain 'D' and resid 331 through 345 Processing helix chain 'D' and resid 366 through 392 Processing helix chain 'D' and resid 392 through 406 Processing helix chain 'E' and resid 26 through 30 Processing helix chain 'E' and resid 32 through 43 Processing helix chain 'E' and resid 44 through 48 Processing helix chain 'E' and resid 58 through 72 Processing helix chain 'E' and resid 112 through 128 removed outlier: 3.937A pdb=" N TYR E 116 " --> pdb=" O ALA E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 162 Processing helix chain 'E' and resid 172 through 179 Processing helix chain 'E' and resid 207 through 218 removed outlier: 4.664A pdb=" N GLU E 212 " --> pdb=" O LEU E 208 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ASP E 213 " --> pdb=" O ASN E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 247 removed outlier: 3.651A pdb=" N VAL E 247 " --> pdb=" O ASN E 243 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 257 Processing helix chain 'E' and resid 258 through 284 removed outlier: 4.482A pdb=" N THR E 262 " --> pdb=" O ASN E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 289 through 330 removed outlier: 3.740A pdb=" N ASP E 293 " --> pdb=" O LEU E 289 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN E 330 " --> pdb=" O LYS E 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 62 removed outlier: 3.607A pdb=" N ILE F 48 " --> pdb=" O HIS F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 114 Processing helix chain 'F' and resid 134 through 144 removed outlier: 3.512A pdb=" N GLN F 141 " --> pdb=" O HIS F 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 209 Processing helix chain 'F' and resid 217 through 248 Processing helix chain 'F' and resid 254 through 265 Processing helix chain 'F' and resid 272 through 313 removed outlier: 3.565A pdb=" N VAL F 311 " --> pdb=" O ASN F 307 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N TYR F 313 " --> pdb=" O PHE F 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 20 Processing helix chain 'G' and resid 24 through 37 Processing helix chain 'G' and resid 43 through 48 Processing helix chain 'G' and resid 49 through 58 removed outlier: 3.626A pdb=" N GLN G 53 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU G 57 " --> pdb=" O GLN G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 73 Processing helix chain 'G' and resid 74 through 81 Processing helix chain 'G' and resid 89 through 108 removed outlier: 3.568A pdb=" N ARG G 107 " --> pdb=" O SER G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 120 removed outlier: 3.652A pdb=" N LEU G 120 " --> pdb=" O LEU G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 138 Processing helix chain 'G' and resid 165 through 220 removed outlier: 4.333A pdb=" N ASN G 169 " --> pdb=" O LYS G 165 " (cutoff:3.500A) Processing helix chain 'H' and resid 11 through 26 Processing helix chain 'H' and resid 33 through 47 Processing helix chain 'H' and resid 49 through 60 Processing helix chain 'H' and resid 61 through 68 removed outlier: 3.633A pdb=" N LYS H 65 " --> pdb=" O PRO H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 84 removed outlier: 3.811A pdb=" N GLY H 72 " --> pdb=" O ASN H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 96 removed outlier: 3.769A pdb=" N HIS H 96 " --> pdb=" O THR H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 124 Processing helix chain 'H' and resid 130 through 138 Processing helix chain 'H' and resid 140 through 150 removed outlier: 3.528A pdb=" N ALA H 144 " --> pdb=" O PRO H 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 192 through 209 removed outlier: 3.759A pdb=" N ASN H 209 " --> pdb=" O ALA H 205 " (cutoff:3.500A) Processing helix chain 'I' and resid 13 through 27 removed outlier: 3.731A pdb=" N LEU I 17 " --> pdb=" O TYR I 13 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 53 removed outlier: 3.581A pdb=" N LEU I 49 " --> pdb=" O HIS I 45 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 62 removed outlier: 3.529A pdb=" N SER I 62 " --> pdb=" O ALA I 58 " (cutoff:3.500A) Processing helix chain 'I' and resid 78 through 92 Processing helix chain 'I' and resid 100 through 112 Processing helix chain 'I' and resid 113 through 127 Processing helix chain 'I' and resid 132 through 143 Processing helix chain 'I' and resid 145 through 164 removed outlier: 3.673A pdb=" N THR I 161 " --> pdb=" O GLU I 157 " (cutoff:3.500A) Processing helix chain 'I' and resid 166 through 170 Processing helix chain 'I' and resid 173 through 183 Processing helix chain 'I' and resid 191 through 203 removed outlier: 3.817A pdb=" N ARG I 195 " --> pdb=" O GLU I 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 217 removed outlier: 3.873A pdb=" N TYR I 212 " --> pdb=" O SER I 208 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER I 214 " --> pdb=" O SER I 210 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N SER I 215 " --> pdb=" O GLN I 211 " (cutoff:3.500A) Processing helix chain 'I' and resid 218 through 220 No H-bonds generated for 'chain 'I' and resid 218 through 220' Processing helix chain 'I' and resid 221 through 225 Processing helix chain 'I' and resid 228 through 236 removed outlier: 4.117A pdb=" N GLN I 235 " --> pdb=" O ARG I 231 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY I 236 " --> pdb=" O ALA I 232 " (cutoff:3.500A) Processing helix chain 'I' and resid 242 through 250 Processing helix chain 'L' and resid 26 through 46 removed outlier: 3.634A pdb=" N VAL L 30 " --> pdb=" O ASP L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 53 through 67 removed outlier: 4.091A pdb=" N LEU L 57 " --> pdb=" O SER L 53 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N HIS L 67 " --> pdb=" O THR L 63 " (cutoff:3.500A) Processing helix chain 'L' and resid 69 through 88 Processing helix chain 'L' and resid 88 through 96 Processing helix chain 'L' and resid 100 through 135 removed outlier: 4.246A pdb=" N MET L 118 " --> pdb=" O THR L 114 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TYR L 125 " --> pdb=" O ASP L 121 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N MET L 126 " --> pdb=" O ILE L 122 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL L 129 " --> pdb=" O TYR L 125 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLN L 132 " --> pdb=" O ARG L 128 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN L 133 " --> pdb=" O VAL L 129 " (cutoff:3.500A) Processing helix chain 'L' and resid 138 through 151 Processing helix chain 'L' and resid 156 through 175 removed outlier: 3.717A pdb=" N GLY L 175 " --> pdb=" O ARG L 171 " (cutoff:3.500A) Processing helix chain 'L' and resid 180 through 195 removed outlier: 3.928A pdb=" N LEU L 195 " --> pdb=" O MET L 191 " (cutoff:3.500A) Processing helix chain 'L' and resid 199 through 228 removed outlier: 3.650A pdb=" N GLU L 203 " --> pdb=" O SER L 199 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA L 207 " --> pdb=" O GLU L 203 " (cutoff:3.500A) Proline residue: L 208 - end of helix removed outlier: 3.889A pdb=" N ALA L 226 " --> pdb=" O GLN L 222 " (cutoff:3.500A) Processing helix chain 'L' and resid 232 through 252 Processing helix chain 'L' and resid 257 through 280 removed outlier: 3.589A pdb=" N LYS L 262 " --> pdb=" O GLU L 258 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL L 263 " --> pdb=" O PRO L 259 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU L 278 " --> pdb=" O LYS L 274 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET L 279 " --> pdb=" O THR L 275 " (cutoff:3.500A) Processing helix chain 'L' and resid 284 through 290 Processing helix chain 'L' and resid 292 through 304 Processing helix chain 'L' and resid 308 through 329 removed outlier: 4.004A pdb=" N THR L 312 " --> pdb=" O ASN L 308 " (cutoff:3.500A) Processing helix chain 'L' and resid 337 through 359 Processing helix chain 'L' and resid 363 through 378 removed outlier: 3.647A pdb=" N LEU L 378 " --> pdb=" O PHE L 374 " (cutoff:3.500A) Processing helix chain 'L' and resid 384 through 398 removed outlier: 3.612A pdb=" N LYS L 398 " --> pdb=" O ASP L 394 " (cutoff:3.500A) Processing helix chain 'L' and resid 404 through 421 removed outlier: 3.606A pdb=" N MET L 416 " --> pdb=" O LEU L 412 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL L 417 " --> pdb=" O ASP L 413 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU L 418 " --> pdb=" O LYS L 414 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE L 421 " --> pdb=" O VAL L 417 " (cutoff:3.500A) Processing helix chain 'L' and resid 424 through 441 removed outlier: 3.677A pdb=" N PHE L 428 " --> pdb=" O GLU L 424 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU L 436 " --> pdb=" O TYR L 432 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA L 437 " --> pdb=" O LYS L 433 " (cutoff:3.500A) Processing helix chain 'L' and resid 448 through 462 Processing helix chain 'L' and resid 464 through 494 removed outlier: 4.007A pdb=" N LYS L 469 " --> pdb=" O GLN L 465 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU L 470 " --> pdb=" O PHE L 466 " (cutoff:3.500A) Processing helix chain 'L' and resid 525 through 542 Processing helix chain 'L' and resid 598 through 608 Processing helix chain 'L' and resid 612 through 619 Processing helix chain 'L' and resid 625 through 632 Processing helix chain 'L' and resid 664 through 668 Processing helix chain 'L' and resid 687 through 714 removed outlier: 3.706A pdb=" N THR L 691 " --> pdb=" O GLU L 687 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU L 702 " --> pdb=" O ASP L 698 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS L 712 " --> pdb=" O VAL L 708 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER L 713 " --> pdb=" O ARG L 709 " (cutoff:3.500A) Processing helix chain 'L' and resid 721 through 726 Processing helix chain 'L' and resid 727 through 730 Processing helix chain 'L' and resid 737 through 744 removed outlier: 3.852A pdb=" N ILE L 741 " --> pdb=" O SER L 737 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS L 743 " --> pdb=" O VAL L 739 " (cutoff:3.500A) Processing helix chain 'L' and resid 746 through 751 removed outlier: 3.530A pdb=" N ILE L 749 " --> pdb=" O GLU L 746 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLU L 750 " --> pdb=" O GLY L 747 " (cutoff:3.500A) Processing helix chain 'M' and resid 10 through 27 Processing helix chain 'M' and resid 45 through 53 removed outlier: 3.660A pdb=" N ALA M 50 " --> pdb=" O LYS M 46 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N CYS M 52 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing helix chain 'M' and resid 56 through 61 Processing helix chain 'M' and resid 64 through 68 Processing helix chain 'M' and resid 78 through 92 Processing helix chain 'M' and resid 100 through 112 Processing helix chain 'M' and resid 113 through 128 Processing helix chain 'M' and resid 132 through 143 Processing helix chain 'M' and resid 145 through 164 removed outlier: 3.535A pdb=" N HIS M 158 " --> pdb=" O ARG M 154 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR M 161 " --> pdb=" O GLU M 157 " (cutoff:3.500A) Processing helix chain 'M' and resid 166 through 170 Processing helix chain 'M' and resid 173 through 183 Processing helix chain 'M' and resid 191 through 204 removed outlier: 3.744A pdb=" N ARG M 195 " --> pdb=" O GLU M 191 " (cutoff:3.500A) Processing helix chain 'M' and resid 205 through 208 removed outlier: 5.803A pdb=" N SER M 208 " --> pdb=" O ASN M 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 205 through 208' Processing helix chain 'M' and resid 209 through 217 removed outlier: 3.849A pdb=" N SER M 214 " --> pdb=" O SER M 210 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N SER M 215 " --> pdb=" O GLN M 211 " (cutoff:3.500A) Processing helix chain 'M' and resid 218 through 220 No H-bonds generated for 'chain 'M' and resid 218 through 220' Processing helix chain 'M' and resid 230 through 237 Processing helix chain 'M' and resid 244 through 250 removed outlier: 3.524A pdb=" N TYR M 250 " --> pdb=" O VAL M 246 " (cutoff:3.500A) Processing helix chain 'R' and resid 53 through 58 Processing helix chain 'R' and resid 81 through 88 Processing helix chain 'N' and resid 22 through 34 removed outlier: 3.955A pdb=" N ILE N 26 " --> pdb=" O LYS N 22 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS N 27 " --> pdb=" O VAL N 23 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU N 28 " --> pdb=" O GLU N 24 " (cutoff:3.500A) Processing helix chain 'N' and resid 56 through 60 Processing sheet with id=AA1, first strand: chain 'B' and resid 402 through 403 removed outlier: 5.678A pdb=" N ILE B 402 " --> pdb=" O TYR A 417 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER A 419 " --> pdb=" O ILE B 402 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL A 418 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N LEU C 315 " --> pdb=" O ALA A 451 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N VAL A 453 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N LEU C 317 " --> pdb=" O VAL A 453 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N LEU C 315 " --> pdb=" O PHE C 360 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N THR H 126 " --> pdb=" O ALA C 349 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N ILE C 351 " --> pdb=" O THR H 126 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N ILE H 128 " --> pdb=" O ILE C 351 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 369 through 370 removed outlier: 3.802A pdb=" N ILE B 369 " --> pdb=" O LEU B 409 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 358 through 359 removed outlier: 6.574A pdb=" N LYS G 144 " --> pdb=" O VAL G 154 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N VAL G 154 " --> pdb=" O LYS G 144 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ASP G 146 " --> pdb=" O LEU G 152 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N LEU G 152 " --> pdb=" O ASP G 146 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 221 through 223 removed outlier: 4.292A pdb=" N ASN E 182 " --> pdb=" O ASP E 171 " (cutoff:3.500A) removed outlier: 9.950A pdb=" N VAL E 166 " --> pdb=" O ASN E 132 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ILE E 134 " --> pdb=" O VAL E 166 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N VAL E 168 " --> pdb=" O ILE E 134 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N TRP E 136 " --> pdb=" O VAL E 168 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N ILE E 170 " --> pdb=" O TRP E 136 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA E 138 " --> pdb=" O ILE E 170 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN E 132 " --> pdb=" O GLY E 83 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N MET E 81 " --> pdb=" O ILE E 134 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N TRP E 136 " --> pdb=" O GLY E 79 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLY E 79 " --> pdb=" O TRP E 136 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LEU E 80 " --> pdb=" O SER E 95 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER E 95 " --> pdb=" O LEU E 80 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU E 82 " --> pdb=" O MET E 93 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TYR E 54 " --> pdb=" O MET E 90 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N ILE E 92 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LYS E 56 " --> pdb=" O ILE E 92 " (cutoff:3.500A) removed outlier: 8.564A pdb=" N ASP E 94 " --> pdb=" O LYS E 56 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N CYS E 55 " --> pdb=" O SER E 227 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 178 through 186 removed outlier: 4.535A pdb=" N VAL F 167 " --> pdb=" O LEU F 186 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU F 72 " --> pdb=" O LEU F 122 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N TRP F 124 " --> pdb=" O GLY F 70 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLY F 70 " --> pdb=" O TRP F 124 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LYS F 75 " --> pdb=" O VAL F 83 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N VAL F 83 " --> pdb=" O LYS F 75 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N GLU F 77 " --> pdb=" O ILE F 81 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ILE F 81 " --> pdb=" O GLU F 77 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N SER F 40 " --> pdb=" O ILE F 81 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N VAL F 83 " --> pdb=" O SER F 40 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ALA F 42 " --> pdb=" O VAL F 83 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ASN F 85 " --> pdb=" O ALA F 42 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL F 41 " --> pdb=" O THR F 189 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 91 through 94 Processing sheet with id=AA7, first strand: chain 'I' and resid 40 through 44 removed outlier: 3.605A pdb=" N ILE I 33 " --> pdb=" O CYS I 44 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL I 72 " --> pdb=" O VAL I 34 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 580 through 586 removed outlier: 3.537A pdb=" N ARG I 580 " --> pdb=" O ILE I 272 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU I 266 " --> pdb=" O LEU I 586 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N ILE I 270 " --> pdb=" O TYR I 288 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N TYR I 288 " --> pdb=" O ILE I 270 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ILE I 272 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL I 286 " --> pdb=" O ILE I 272 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER I 285 " --> pdb=" O LEU I 298 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLU I 592 " --> pdb=" O LYS I 297 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 309 through 312 removed outlier: 3.713A pdb=" N GLY I 309 " --> pdb=" O ALA I 321 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA I 321 " --> pdb=" O GLY I 309 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL I 311 " --> pdb=" O TYR I 319 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR I 319 " --> pdb=" O VAL I 311 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N ILE I 318 " --> pdb=" O PHE I 353 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 374 through 378 removed outlier: 3.710A pdb=" N SER I 374 " --> pdb=" O ILE I 385 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU I 408 " --> pdb=" O ASP I 403 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 423 through 427 removed outlier: 3.564A pdb=" N TYR I 440 " --> pdb=" O VAL I 433 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER I 448 " --> pdb=" O PHE I 443 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 463 through 467 removed outlier: 4.174A pdb=" N SER I 463 " --> pdb=" O ILE I 474 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE I 474 " --> pdb=" O SER I 463 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP I 503 " --> pdb=" O GLU I 508 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU I 508 " --> pdb=" O ASP I 503 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 527 through 530 removed outlier: 3.549A pdb=" N VAL I 528 " --> pdb=" O CYS I 535 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N CYS I 535 " --> pdb=" O VAL I 528 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N LEU I 534 " --> pdb=" O TYR I 554 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET I 538 " --> pdb=" O VAL I 550 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL I 550 " --> pdb=" O MET I 538 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU I 540 " --> pdb=" O LYS I 548 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS I 548 " --> pdb=" O GLU I 540 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N TYR I 549 " --> pdb=" O HIS I 566 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N HIS I 566 " --> pdb=" O TYR I 549 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N THR I 551 " --> pdb=" O ARG I 564 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG I 564 " --> pdb=" O THR I 551 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 502 through 503 removed outlier: 3.503A pdb=" N ASP L 502 " --> pdb=" O LYS R 25 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASP L 558 " --> pdb=" O LYS R 25 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 506 through 509 removed outlier: 5.962A pdb=" N ARG L 506 " --> pdb=" O ALA R 31 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N TRP R 33 " --> pdb=" O ARG L 506 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU L 508 " --> pdb=" O TRP R 33 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU R 32 " --> pdb=" O THR L 549 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ALA R 34 " --> pdb=" O GLN L 547 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N GLN L 547 " --> pdb=" O ALA R 34 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 645 through 646 Processing sheet with id=AB8, first strand: chain 'M' and resid 40 through 44 removed outlier: 3.705A pdb=" N ILE M 33 " --> pdb=" O CYS M 44 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL M 72 " --> pdb=" O VAL M 34 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 295 through 297 removed outlier: 3.519A pdb=" N GLU M 266 " --> pdb=" O LEU M 586 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU M 586 " --> pdb=" O GLU M 266 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'M' and resid 274 through 275 Processing sheet with id=AC2, first strand: chain 'M' and resid 309 through 312 removed outlier: 3.602A pdb=" N GLY M 309 " --> pdb=" O ALA M 321 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA M 321 " --> pdb=" O GLY M 309 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL M 311 " --> pdb=" O TYR M 319 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N ILE M 318 " --> pdb=" O PHE M 353 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N PHE M 350 " --> pdb=" O LYS M 363 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N THR M 359 " --> pdb=" O ASP M 354 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'M' and resid 324 through 325 Processing sheet with id=AC4, first strand: chain 'M' and resid 374 through 378 removed outlier: 3.816A pdb=" N SER M 374 " --> pdb=" O ILE M 385 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU M 400 " --> pdb=" O ALA M 384 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'M' and resid 423 through 427 removed outlier: 3.608A pdb=" N VAL M 433 " --> pdb=" O TYR M 440 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR M 440 " --> pdb=" O VAL M 433 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER M 448 " --> pdb=" O PHE M 443 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 463 through 467 removed outlier: 3.909A pdb=" N SER M 463 " --> pdb=" O ILE M 474 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA M 465 " --> pdb=" O PHE M 472 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE M 472 " --> pdb=" O ALA M 465 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU M 508 " --> pdb=" O ASP M 503 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 527 through 530 removed outlier: 4.752A pdb=" N LEU M 534 " --> pdb=" O TYR M 554 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL M 550 " --> pdb=" O MET M 538 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N TYR M 549 " --> pdb=" O HIS M 566 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N HIS M 566 " --> pdb=" O TYR M 549 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N THR M 551 " --> pdb=" O ARG M 564 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG M 564 " --> pdb=" O THR M 551 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG M 560 " --> pdb=" O ASP M 555 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'R' and resid 78 through 80 Processing sheet with id=AC9, first strand: chain 'N' and resid 13 through 16 removed outlier: 8.844A pdb=" N LEU N 67 " --> pdb=" O LEU N 2 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LYS N 4 " --> pdb=" O LEU N 67 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 44 through 45 2146 hydrogen bonds defined for protein. 6282 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: 13.36 Time building geometry restraints manager: 16.37 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: 7466 1.33 - 1.45: 8734 1.45 - 1.57: 21425 1.57 - 1.69: 1 1.69 - 1.81: 390 Bond restraints: 38016 Sorted by residual: bond pdb=" C CYS F 264 " pdb=" O CYS F 264 " ideal model delta sigma weight residual 1.237 1.315 -0.078 1.17e-02 7.31e+03 4.43e+01 bond pdb=" N TYR A 75 " pdb=" CA TYR A 75 " ideal model delta sigma weight residual 1.458 1.486 -0.028 6.30e-03 2.52e+04 1.94e+01 bond pdb=" C HIS F 254 " pdb=" O HIS F 254 " ideal model delta sigma weight residual 1.235 1.285 -0.049 1.26e-02 6.30e+03 1.53e+01 bond pdb=" N LYS B 364 " pdb=" CA LYS B 364 " ideal model delta sigma weight residual 1.462 1.492 -0.030 7.70e-03 1.69e+04 1.50e+01 bond pdb=" N ILE N 36 " pdb=" CA ILE N 36 " ideal model delta sigma weight residual 1.461 1.494 -0.034 9.10e-03 1.21e+04 1.37e+01 ... (remaining 38011 not shown) Histogram of bond angle deviations from ideal: 98.86 - 105.97: 675 105.97 - 113.07: 20591 113.07 - 120.18: 13620 120.18 - 127.28: 16151 127.28 - 134.39: 329 Bond angle restraints: 51366 Sorted by residual: angle pdb=" C THR C 245 " pdb=" CA THR C 245 " pdb=" CB THR C 245 " ideal model delta sigma weight residual 115.79 107.29 8.50 1.19e+00 7.06e-01 5.10e+01 angle pdb=" C SER E 95 " pdb=" N PHE E 96 " pdb=" CA PHE E 96 " ideal model delta sigma weight residual 121.94 113.00 8.94 1.76e+00 3.23e-01 2.58e+01 angle pdb=" N LYS E 125 " pdb=" CA LYS E 125 " pdb=" C LYS E 125 " ideal model delta sigma weight residual 111.71 105.93 5.78 1.15e+00 7.56e-01 2.53e+01 angle pdb=" N PRO F 268 " pdb=" CA PRO F 268 " pdb=" CB PRO F 268 " ideal model delta sigma weight residual 102.35 105.89 -3.54 7.10e-01 1.98e+00 2.49e+01 angle pdb=" C PRO M 254 " pdb=" N LYS M 255 " pdb=" CA LYS M 255 " ideal model delta sigma weight residual 122.74 129.47 -6.73 1.44e+00 4.82e-01 2.18e+01 ... (remaining 51361 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.06: 21372 18.06 - 36.11: 1427 36.11 - 54.17: 262 54.17 - 72.22: 92 72.22 - 90.28: 22 Dihedral angle restraints: 23175 sinusoidal: 9471 harmonic: 13704 Sorted by residual: dihedral pdb=" C ASP L 685 " pdb=" N ASP L 685 " pdb=" CA ASP L 685 " pdb=" CB ASP L 685 " ideal model delta harmonic sigma weight residual -122.60 -137.93 15.33 0 2.50e+00 1.60e-01 3.76e+01 dihedral pdb=" CA LYS M 255 " pdb=" C LYS M 255 " pdb=" N PHE M 256 " pdb=" CA PHE M 256 " ideal model delta harmonic sigma weight residual 180.00 150.74 29.26 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" N ASP L 685 " pdb=" C ASP L 685 " pdb=" CA ASP L 685 " pdb=" CB ASP L 685 " ideal model delta harmonic sigma weight residual 122.80 137.33 -14.53 0 2.50e+00 1.60e-01 3.38e+01 ... (remaining 23172 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 5529 0.107 - 0.214: 206 0.214 - 0.321: 12 0.321 - 0.428: 1 0.428 - 0.535: 1 Chirality restraints: 5749 Sorted by residual: chirality pdb=" CA ASP L 685 " pdb=" N ASP L 685 " pdb=" C ASP L 685 " pdb=" CB ASP L 685 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.15e+00 chirality pdb=" CA TYR E 143 " pdb=" N TYR E 143 " pdb=" C TYR E 143 " pdb=" CB TYR E 143 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.40e+00 chirality pdb=" CA GLU E 115 " pdb=" N GLU E 115 " pdb=" C GLU E 115 " pdb=" CB GLU E 115 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.42e+00 ... (remaining 5746 not shown) Planarity restraints: 6583 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET D 286 " 0.085 5.00e-02 4.00e+02 1.30e-01 2.68e+01 pdb=" N PRO D 287 " -0.224 5.00e-02 4.00e+02 pdb=" CA PRO D 287 " 0.071 5.00e-02 4.00e+02 pdb=" CD PRO D 287 " 0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 226 " 0.023 2.00e-02 2.50e+03 4.48e-02 2.01e+01 pdb=" C VAL E 226 " -0.078 2.00e-02 2.50e+03 pdb=" O VAL E 226 " 0.029 2.00e-02 2.50e+03 pdb=" N SER E 227 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS C 254 " 0.054 5.00e-02 4.00e+02 8.32e-02 1.11e+01 pdb=" N PRO C 255 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO C 255 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 255 " 0.046 5.00e-02 4.00e+02 ... (remaining 6580 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 248 2.57 - 3.15: 30671 3.15 - 3.73: 60853 3.73 - 4.32: 80961 4.32 - 4.90: 131742 Nonbonded interactions: 304475 Sorted by model distance: nonbonded pdb=" OD2 ASP E 151 " pdb="ZN ZN E 401 " model vdw 1.986 2.230 nonbonded pdb=" OG SER I 275 " pdb=" O ASP I 574 " model vdw 2.210 2.440 nonbonded pdb=" OG SER M 389 " pdb=" OG1 THR M 398 " model vdw 2.217 2.440 nonbonded pdb=" O GLY L 463 " pdb=" OG1 THR L 467 " model vdw 2.219 2.440 nonbonded pdb=" O PRO C 255 " pdb=" ND2 ASN M 544 " model vdw 2.224 2.520 ... (remaining 304470 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'I' and resid 7 through 598) selection = (chain 'M' and ((resid 7 and (name N or name CA or name C or name O or name CB ) \ ) or resid 8 through 325 or resid 344 through 477 or resid 496 through 598)) } 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 group one per residue 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: 0.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 4.590 Check model and map are aligned: 0.550 Set scattering table: 0.350 Process input model: 100.680 Find NCS groups from input model: 1.430 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4957 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 : 0.004 0.099 38016 Z= 0.264 Angle : 0.696 10.225 51366 Z= 0.450 Chirality : 0.046 0.535 5749 Planarity : 0.004 0.130 6583 Dihedral : 13.050 90.279 14285 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.67 % Allowed : 6.48 % Favored : 92.84 % Rotamer: Outliers : 2.22 % Allowed : 1.56 % Favored : 96.23 % Cbeta Deviations : 0.04 % 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: -0.18 (0.13), residues: 4597 helix: 1.18 (0.10), residues: 2607 sheet: -1.05 (0.24), residues: 430 loop : -2.11 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 246 HIS 0.007 0.001 HIS E 49 PHE 0.025 0.001 PHE M 160 TYR 0.021 0.001 TYR E 143 ARG 0.004 0.000 ARG B 105 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1414 residues out of total 4113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 1323 time to evaluate : 4.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 91 outliers final: 35 residues processed: 1394 average time/residue: 0.5521 time to fit residues: 1199.2363 Evaluate side-chains 991 residues out of total 4113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 956 time to evaluate : 4.353 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.5303 time to fit residues: 35.8232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 385 optimal weight: 30.0000 chunk 346 optimal weight: 2.9990 chunk 192 optimal weight: 0.7980 chunk 118 optimal weight: 0.0970 chunk 233 optimal weight: 0.8980 chunk 185 optimal weight: 0.7980 chunk 358 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 217 optimal weight: 0.9990 chunk 266 optimal weight: 5.9990 chunk 415 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 ASN A 397 HIS A 423 HIS A 483 GLN ** A 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 ASN B 90 ASN B 124 GLN B 208 GLN ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 GLN B 319 GLN B 333 ASN B 357 GLN B 435 ASN ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 HIS C 261 HIS C 361 HIS ** C 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 ASN D 86 HIS D 109 HIS D 138 GLN ** D 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 176 ASN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 354 GLN D 383 ASN ** D 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 406 GLN ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 220 HIS F 224 GLN ** F 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 232 HIS F 253 ASN G 65 GLN G 93 GLN G 169 ASN ** H 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 69 GLN I 83 GLN ** I 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 306 HIS I 324 GLN I 357 GLN ** I 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 160 HIS ** L 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 553 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 606 ASN L 617 GLN L 618 GLN M 28 GLN M 76 ASN ** M 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 150 GLN M 187 ASN M 219 GLN M 230 GLN M 235 GLN ** R 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 76 ASN R 98 ASN ** N 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5205 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 38016 Z= 0.220 Angle : 0.702 13.662 51366 Z= 0.362 Chirality : 0.045 0.297 5749 Planarity : 0.005 0.125 6583 Dihedral : 4.479 33.543 5047 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 19.29 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.31 % Favored : 93.32 % Rotamer: Outliers : 0.29 % Allowed : 4.92 % Favored : 94.79 % 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: -0.26 (0.12), residues: 4597 helix: 1.00 (0.10), residues: 2658 sheet: -0.96 (0.24), residues: 437 loop : -2.06 (0.16), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP A 166 HIS 0.013 0.002 HIS D 109 PHE 0.046 0.002 PHE F 112 TYR 0.026 0.002 TYR M 351 ARG 0.008 0.001 ARG B 238 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1116 residues out of total 4113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 1104 time to evaluate : 3.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 3 residues processed: 1113 average time/residue: 0.3935 time to fit residues: 688.6383 Evaluate side-chains 915 residues out of total 4113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 912 time to evaluate : 2.573 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2125 time to fit residues: 4.9012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 230 optimal weight: 0.7980 chunk 128 optimal weight: 1.9990 chunk 345 optimal weight: 0.5980 chunk 282 optimal weight: 0.0470 chunk 114 optimal weight: 0.7980 chunk 415 optimal weight: 5.9990 chunk 449 optimal weight: 0.9980 chunk 370 optimal weight: 0.9990 chunk 412 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 333 optimal weight: 1.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 187 ASN ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 483 GLN A 501 HIS ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 304 ASN B 313 ASN ** B 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 GLN ** C 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 383 ASN D 403 GLN ** E 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 50 ASN F 232 HIS G 93 GLN ** H 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 187 ASN I 306 HIS I 358 ASN ** L 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 28 GLN ** M 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 420 GLN ** R 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5245 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 38016 Z= 0.219 Angle : 0.678 9.720 51366 Z= 0.349 Chirality : 0.044 0.306 5749 Planarity : 0.005 0.123 6583 Dihedral : 4.572 30.417 5047 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 20.21 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.24 % Favored : 93.37 % Rotamer: Outliers : 0.19 % Allowed : 3.07 % Favored : 96.74 % 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: -0.24 (0.12), residues: 4597 helix: 0.98 (0.10), residues: 2660 sheet: -0.93 (0.23), residues: 448 loop : -2.00 (0.16), residues: 1489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 370 HIS 0.012 0.001 HIS B 346 PHE 0.030 0.002 PHE F 112 TYR 0.038 0.002 TYR F 105 ARG 0.012 0.001 ARG M 7 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1080 residues out of total 4113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1072 time to evaluate : 4.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 410 optimal weight: 5.9990 chunk 312 optimal weight: 2.9990 chunk 215 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 198 optimal weight: 9.9990 chunk 279 optimal weight: 4.9990 chunk 417 optimal weight: 0.6980 chunk 441 optimal weight: 6.9990 chunk 217 optimal weight: 2.9990 chunk 395 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: