Starting phenix.real_space_refine on Fri Aug 9 09:47:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6usf_20863/08_2024/6usf_20863.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6usf_20863/08_2024/6usf_20863.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6usf_20863/08_2024/6usf_20863.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6usf_20863/08_2024/6usf_20863.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6usf_20863/08_2024/6usf_20863.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6usf_20863/08_2024/6usf_20863.cif" } resolution = 3.87 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3066 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 117 5.16 5 C 14903 2.51 5 N 3726 2.21 5 O 4276 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 7": "NH1" <-> "NH2" Residue "A GLU 12": "OE1" <-> "OE2" Residue "A GLU 247": "OE1" <-> "OE2" Residue "A GLU 268": "OE1" <-> "OE2" Residue "A GLU 434": "OE1" <-> "OE2" Residue "B GLU 73": "OE1" <-> "OE2" Residue "B GLU 336": "OE1" <-> "OE2" Residue "C PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 316": "OE1" <-> "OE2" Residue "D ARG 7": "NH1" <-> "NH2" Residue "D GLU 11": "OE1" <-> "OE2" Residue "E TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 157": "OE1" <-> "OE2" Residue "E GLU 189": "OE1" <-> "OE2" Residue "H TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 163": "OE1" <-> "OE2" Residue "L GLU 197": "OE1" <-> "OE2" Residue "L PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 108": "OE1" <-> "OE2" Residue "K TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 163": "OE1" <-> "OE2" Residue "M GLU 167": "OE1" <-> "OE2" Residue "M GLU 197": "OE1" <-> "OE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 23022 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 3764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3764 Classifications: {'peptide': 464} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 441} Chain breaks: 2 Chain: "B" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2917 Classifications: {'peptide': 358} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 337} Chain breaks: 1 Chain: "C" Number of atoms: 2908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2908 Classifications: {'peptide': 357} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 336} Chain breaks: 1 Chain: "D" Number of atoms: 3764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3764 Classifications: {'peptide': 464} Link IDs: {'PTRANS': 22, 'TRANS': 441} Chain breaks: 2 Chain: "E" Number of atoms: 2908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2908 Classifications: {'peptide': 357} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 336} Chain breaks: 1 Chain: "H" Number of atoms: 1655 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 219, 1649 Classifications: {'peptide': 219} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 205} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 219, 1649 Classifications: {'peptide': 219} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 205} Chain breaks: 1 bond proxies already assigned to first conformer: 1689 Chain: "L" Number of atoms: 1602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1602 Classifications: {'peptide': 209} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 198} Chain breaks: 1 Chain: "K" Number of atoms: 1700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1700 Classifications: {'peptide': 227} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 213} Chain: "M" Number of atoms: 1627 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 213, 1626 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 202} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 213, 1626 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 202} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 1658 Chain: "F" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 1, 'QMR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 1, 'QMR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'BMA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 16.45, per 1000 atoms: 0.71 Number of scatterers: 23022 At special positions: 0 Unit cell: (214.968, 145.517, 177.486, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 117 16.00 O 4276 8.00 N 3726 7.00 C 14903 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 149 " distance=2.05 Simple disulfide: pdb=" SG CYS A 199 " - pdb=" SG CYS A 200 " distance=2.65 Simple disulfide: pdb=" SG CYS B 130 " - pdb=" SG CYS B 144 " distance=2.05 Simple disulfide: pdb=" SG CYS C 130 " - pdb=" SG CYS C 144 " distance=2.06 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 149 " distance=2.04 Simple disulfide: pdb=" SG CYS D 199 " - pdb=" SG CYS D 200 " distance=2.05 Simple disulfide: pdb=" SG CYS E 130 " - pdb=" SG CYS E 144 " distance=2.05 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.05 Simple disulfide: pdb=" SG CYS H 154 " - pdb=" SG CYS H 210 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.46 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 196 " distance=2.04 Simple disulfide: pdb=" SG CYS K 25 " - pdb=" SG CYS K 99 " distance=2.04 Simple disulfide: pdb=" SG CYS K 154 " - pdb=" SG CYS K 210 " distance=2.03 Simple disulfide: pdb=" SG CYS M 24 " - pdb=" SG CYS M 89 " distance=2.04 Simple disulfide: pdb=" SG CYS M 136 " - pdb=" SG CYS M 196 " distance=2.07 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 Atom "HETATM22965 O5 NAG B 401 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " BMA F 2 " " NAG F 1 " - " NAG B 401 " " NAG G 1 " - " BMA G 2 " " NAG G 1 " - " NAG C 401 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA E 403 " NAG-ASN " NAG A 501 " - " ASN A 148 " " NAG B 401 " - " ASN B 143 " " NAG C 401 " - " ASN C 143 " " NAG D 501 " - " ASN D 148 " " NAG I 1 " - " ASN E 143 " Time building additional restraints: 9.64 Conformation dependent library (CDL) restraints added in 5.0 seconds 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5498 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 40 sheets defined 28.9% alpha, 30.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.45 Creating SS restraints... Processing helix chain 'A' and resid 6 through 19 removed outlier: 3.820A pdb=" N ALA A 10 " --> pdb=" O THR A 6 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N PHE A 19 " --> pdb=" O LEU A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 224 Processing helix chain 'A' and resid 224 through 232 removed outlier: 3.687A pdb=" N CYS A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 241 removed outlier: 4.233A pdb=" N VAL A 236 " --> pdb=" O CYS A 233 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LEU A 237 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N VAL A 238 " --> pdb=" O THR A 235 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE A 239 " --> pdb=" O VAL A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 267 Processing helix chain 'A' and resid 278 through 306 removed outlier: 3.641A pdb=" N TYR A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N HIS A 306 " --> pdb=" O LEU A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 326 removed outlier: 3.793A pdb=" N VAL A 321 " --> pdb=" O TRP A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 355 removed outlier: 4.096A pdb=" N THR A 351 " --> pdb=" O ASP A 347 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASN A 353 " --> pdb=" O TRP A 349 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN A 355 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 361 removed outlier: 3.724A pdb=" N ILE A 359 " --> pdb=" O ASN A 355 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS A 361 " --> pdb=" O LYS A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.634A pdb=" N VAL A 368 " --> pdb=" O ASN A 364 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 382 removed outlier: 3.589A pdb=" N LEU A 380 " --> pdb=" O ARG A 376 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASP A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 407 removed outlier: 3.656A pdb=" N PHE A 403 " --> pdb=" O GLU A 399 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE A 407 " --> pdb=" O PHE A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 413 through 422 removed outlier: 3.720A pdb=" N LYS A 419 " --> pdb=" O ASP A 415 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU A 420 " --> pdb=" O ASP A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 430 Processing helix chain 'A' and resid 440 through 444 removed outlier: 3.947A pdb=" N ILE A 444 " --> pdb=" O ASN A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 478 removed outlier: 3.712A pdb=" N VAL A 456 " --> pdb=" O TYR A 452 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP A 458 " --> pdb=" O ALA A 454 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N PHE A 461 " --> pdb=" O ILE A 457 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N TRP A 463 " --> pdb=" O ARG A 459 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ILE A 467 " --> pdb=" O TRP A 463 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL A 468 " --> pdb=" O MET A 464 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR A 473 " --> pdb=" O CYS A 469 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE A 477 " --> pdb=" O THR A 473 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 12 removed outlier: 3.510A pdb=" N LEU B 12 " --> pdb=" O VAL B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 217 removed outlier: 3.518A pdb=" N THR B 213 " --> pdb=" O PRO B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 225 Processing helix chain 'B' and resid 229 through 233 Processing helix chain 'B' and resid 234 through 238 removed outlier: 3.788A pdb=" N CYS B 237 " --> pdb=" O PRO B 234 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY B 238 " --> pdb=" O SER B 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 234 through 238' Processing helix chain 'B' and resid 240 through 262 Processing helix chain 'B' and resid 270 through 298 removed outlier: 3.557A pdb=" N LYS B 274 " --> pdb=" O PRO B 270 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N HIS B 298 " --> pdb=" O LEU B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 315 removed outlier: 4.316A pdb=" N LYS B 311 " --> pdb=" O ALA B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 321 Processing helix chain 'B' and resid 337 through 352 removed outlier: 3.679A pdb=" N VAL B 344 " --> pdb=" O TYR B 340 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE B 345 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP B 346 " --> pdb=" O ALA B 342 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ARG B 347 " --> pdb=" O MET B 343 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TRP B 351 " --> pdb=" O ARG B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 360 Processing helix chain 'B' and resid 361 through 363 No H-bonds generated for 'chain 'B' and resid 361 through 363' Processing helix chain 'C' and resid 3 through 12 Processing helix chain 'C' and resid 209 through 217 removed outlier: 3.637A pdb=" N THR C 213 " --> pdb=" O PRO C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 225 Processing helix chain 'C' and resid 239 through 262 removed outlier: 3.840A pdb=" N LEU C 243 " --> pdb=" O GLU C 239 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL C 262 " --> pdb=" O ILE C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 298 removed outlier: 4.017A pdb=" N HIS C 298 " --> pdb=" O LEU C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 315 Processing helix chain 'C' and resid 317 through 321 Processing helix chain 'C' and resid 337 through 342 removed outlier: 3.670A pdb=" N ALA C 342 " --> pdb=" O TRP C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 352 removed outlier: 3.798A pdb=" N TRP C 351 " --> pdb=" O ARG C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 361 removed outlier: 3.602A pdb=" N VAL C 358 " --> pdb=" O VAL C 354 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE C 359 " --> pdb=" O PHE C 355 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR C 361 " --> pdb=" O CYS C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 365 Processing helix chain 'D' and resid 6 through 19 removed outlier: 3.924A pdb=" N ALA D 10 " --> pdb=" O THR D 6 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N PHE D 19 " --> pdb=" O LEU D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 224 Processing helix chain 'D' and resid 224 through 232 removed outlier: 3.528A pdb=" N CYS D 228 " --> pdb=" O LEU D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 235 No H-bonds generated for 'chain 'D' and resid 233 through 235' Processing helix chain 'D' and resid 247 through 270 removed outlier: 4.198A pdb=" N LEU D 251 " --> pdb=" O GLU D 247 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N GLU D 268 " --> pdb=" O LEU D 264 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ILE D 269 " --> pdb=" O LEU D 265 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE D 270 " --> pdb=" O ILE D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 306 removed outlier: 3.567A pdb=" N GLU D 282 " --> pdb=" O PRO D 278 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TYR D 283 " --> pdb=" O LEU D 279 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N HIS D 306 " --> pdb=" O LEU D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 326 removed outlier: 3.509A pdb=" N VAL D 321 " --> pdb=" O TRP D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 353 removed outlier: 3.595A pdb=" N ASN D 348 " --> pdb=" O ASP D 344 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR D 351 " --> pdb=" O ASP D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 384 removed outlier: 3.901A pdb=" N ALA D 371 " --> pdb=" O GLN D 367 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA D 379 " --> pdb=" O MET D 375 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASP D 381 " --> pdb=" O ALA D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 391 removed outlier: 3.641A pdb=" N GLU D 391 " --> pdb=" O PRO D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 405 Processing helix chain 'D' and resid 407 through 413 Processing helix chain 'D' and resid 415 through 420 removed outlier: 4.582A pdb=" N LYS D 419 " --> pdb=" O ASP D 415 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LEU D 420 " --> pdb=" O ASP D 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 415 through 420' Processing helix chain 'D' and resid 425 through 433 removed outlier: 3.802A pdb=" N ALA D 429 " --> pdb=" O LYS D 425 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLN D 430 " --> pdb=" O VAL D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 442 removed outlier: 3.567A pdb=" N ASN D 441 " --> pdb=" O LYS D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 478 removed outlier: 3.685A pdb=" N VAL D 456 " --> pdb=" O TYR D 452 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ASP D 458 " --> pdb=" O ALA D 454 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE D 460 " --> pdb=" O VAL D 456 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N PHE D 461 " --> pdb=" O ILE D 457 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU D 462 " --> pdb=" O ASP D 458 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE D 466 " --> pdb=" O LEU D 462 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ILE D 467 " --> pdb=" O TRP D 463 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR D 473 " --> pdb=" O CYS D 469 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL D 474 " --> pdb=" O LEU D 470 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU D 478 " --> pdb=" O VAL D 474 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 12 Processing helix chain 'E' and resid 209 through 225 removed outlier: 3.714A pdb=" N THR E 213 " --> pdb=" O PRO E 209 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N ILE E 218 " --> pdb=" O ILE E 214 " (cutoff:3.500A) Proline residue: E 219 - end of helix Processing helix chain 'E' and resid 234 through 238 removed outlier: 3.654A pdb=" N CYS E 237 " --> pdb=" O PRO E 234 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY E 238 " --> pdb=" O SER E 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 234 through 238' Processing helix chain 'E' and resid 239 through 262 removed outlier: 4.134A pdb=" N LEU E 243 " --> pdb=" O GLU E 239 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL E 262 " --> pdb=" O ILE E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 298 removed outlier: 3.601A pdb=" N LYS E 274 " --> pdb=" O PRO E 270 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR E 275 " --> pdb=" O LEU E 271 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N HIS E 298 " --> pdb=" O LEU E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 315 Processing helix chain 'E' and resid 317 through 321 Processing helix chain 'E' and resid 340 through 358 removed outlier: 3.649A pdb=" N VAL E 344 " --> pdb=" O TYR E 340 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ASP E 346 " --> pdb=" O ALA E 342 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG E 347 " --> pdb=" O MET E 343 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N TRP E 351 " --> pdb=" O ARG E 347 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE E 352 " --> pdb=" O LEU E 348 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N VAL E 356 " --> pdb=" O ILE E 352 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 112 removed outlier: 3.716A pdb=" N TRP H 111 " --> pdb=" O GLY H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 170 through 172 No H-bonds generated for 'chain 'H' and resid 170 through 172' Processing helix chain 'H' and resid 201 through 203 No H-bonds generated for 'chain 'H' and resid 201 through 203' Processing helix chain 'L' and resid 94 through 98 removed outlier: 4.206A pdb=" N VAL L 98 " --> pdb=" O TYR L 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 130 removed outlier: 3.697A pdb=" N SER L 129 " --> pdb=" O SER L 125 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY L 130 " --> pdb=" O GLN L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 185 through 190 Processing helix chain 'K' and resid 90 through 94 removed outlier: 3.854A pdb=" N ASP K 93 " --> pdb=" O ARG K 90 " (cutoff:3.500A) Processing helix chain 'K' and resid 107 through 112 Processing helix chain 'K' and resid 170 through 172 No H-bonds generated for 'chain 'K' and resid 170 through 172' Processing helix chain 'K' and resid 201 through 203 No H-bonds generated for 'chain 'K' and resid 201 through 203' Processing helix chain 'M' and resid 123 through 128 Processing helix chain 'M' and resid 185 through 190 Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 40 removed outlier: 3.579A pdb=" N VAL A 166 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 44 through 51 removed outlier: 7.330A pdb=" N ALA A 45 " --> pdb=" O TRP A 62 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N TRP A 62 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N LEU A 47 " --> pdb=" O ASN A 60 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ASN A 60 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP A 49 " --> pdb=" O THR A 58 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 65 through 68 removed outlier: 4.529A pdb=" N ARG A 122 " --> pdb=" O PHE A 118 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 97 through 99 removed outlier: 4.169A pdb=" N SER A 155 " --> pdb=" O PRO A 205 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ARG A 214 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ILE A 185 " --> pdb=" O ARG A 214 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 79 through 83 removed outlier: 3.735A pdb=" N SER B 113 " --> pdb=" O SER B 117 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N SER B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 79 through 83 removed outlier: 3.735A pdb=" N SER B 113 " --> pdb=" O SER B 117 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N SER B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ASN B 55 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N LEU B 42 " --> pdb=" O ASN B 55 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N TRP B 57 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ALA B 40 " --> pdb=" O TRP B 57 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N THR B 59 " --> pdb=" O SER B 38 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N SER B 38 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N GLU B 61 " --> pdb=" O MET B 36 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N MET B 36 " --> pdb=" O GLU B 61 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N GLU B 63 " --> pdb=" O GLN B 34 " (cutoff:3.500A) removed outlier: 9.571A pdb=" N GLN B 34 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N VAL B 31 " --> pdb=" O ASP B 159 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N VAL B 161 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL B 33 " --> pdb=" O VAL B 161 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 92 through 94 removed outlier: 3.645A pdb=" N ARG B 149 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N SER B 150 " --> pdb=" O VAL B 197 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N VAL B 197 " --> pdb=" O SER B 150 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA B 182 " --> pdb=" O ILE B 204 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ARG B 206 " --> pdb=" O ILE B 180 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N ILE B 180 " --> pdb=" O ARG B 206 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 92 through 94 removed outlier: 3.645A pdb=" N ARG B 149 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N SER B 150 " --> pdb=" O VAL B 197 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N VAL B 197 " --> pdb=" O SER B 150 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 79 through 82 removed outlier: 3.583A pdb=" N SER C 113 " --> pdb=" O SER C 117 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N SER C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 79 through 82 removed outlier: 3.583A pdb=" N SER C 113 " --> pdb=" O SER C 117 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N SER C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ILE C 51 " --> pdb=" O SER C 44 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N SER C 44 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N THR C 53 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N LEU C 42 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ASN C 55 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLU C 63 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N THR C 32 " --> pdb=" O GLU C 63 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N VAL C 31 " --> pdb=" O ASP C 159 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N VAL C 161 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N VAL C 33 " --> pdb=" O VAL C 161 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 92 through 94 removed outlier: 4.918A pdb=" N SER C 150 " --> pdb=" O VAL C 197 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N VAL C 197 " --> pdb=" O SER C 150 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE C 204 " --> pdb=" O VAL C 181 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 92 through 94 removed outlier: 4.918A pdb=" N SER C 150 " --> pdb=" O VAL C 197 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N VAL C 197 " --> pdb=" O SER C 150 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 36 through 40 removed outlier: 3.551A pdb=" N ASP D 164 " --> pdb=" O VAL D 36 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 44 through 51 removed outlier: 7.330A pdb=" N ALA D 45 " --> pdb=" O TRP D 62 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N TRP D 62 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N LEU D 47 " --> pdb=" O ASN D 60 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ASN D 60 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP D 49 " --> pdb=" O THR D 58 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 65 through 68 Processing sheet with id=AB7, first strand: chain 'D' and resid 97 through 99 removed outlier: 4.379A pdb=" N SER D 155 " --> pdb=" O PRO D 205 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N TYR D 204 " --> pdb=" O THR D 194 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N THR D 194 " --> pdb=" O TYR D 204 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ASP D 206 " --> pdb=" O TYR D 192 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N TYR D 192 " --> pdb=" O ASP D 206 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N THR D 208 " --> pdb=" O GLY D 190 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N GLY D 190 " --> pdb=" O THR D 208 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ALA D 210 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA D 188 " --> pdb=" O ALA D 210 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL D 212 " --> pdb=" O VAL D 186 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 80 through 82 Processing sheet with id=AB9, first strand: chain 'E' and resid 80 through 82 removed outlier: 6.733A pdb=" N ASN E 55 " --> pdb=" O LEU E 42 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N LEU E 42 " --> pdb=" O ASN E 55 " (cutoff:3.500A) removed outlier: 8.541A pdb=" N TRP E 57 " --> pdb=" O ALA E 40 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ALA E 40 " --> pdb=" O TRP E 57 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N THR E 59 " --> pdb=" O SER E 38 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N SER E 38 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N GLU E 61 " --> pdb=" O MET E 36 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N MET E 36 " --> pdb=" O GLU E 61 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N GLU E 63 " --> pdb=" O GLN E 34 " (cutoff:3.500A) removed outlier: 9.359A pdb=" N GLN E 34 " --> pdb=" O GLU E 63 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL E 31 " --> pdb=" O ASP E 159 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N VAL E 161 " --> pdb=" O VAL E 31 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL E 33 " --> pdb=" O VAL E 161 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 92 through 93 removed outlier: 3.637A pdb=" N ARG E 149 " --> pdb=" O VAL E 93 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N SER E 150 " --> pdb=" O VAL E 197 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N VAL E 197 " --> pdb=" O SER E 150 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA E 182 " --> pdb=" O ILE E 204 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ARG E 206 " --> pdb=" O ILE E 180 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ILE E 180 " --> pdb=" O ARG E 206 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 92 through 93 removed outlier: 3.637A pdb=" N ARG E 149 " --> pdb=" O VAL E 93 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N SER E 150 " --> pdb=" O VAL E 197 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N VAL E 197 " --> pdb=" O SER E 150 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 6 through 10 Processing sheet with id=AC4, first strand: chain 'H' and resid 61 through 63 removed outlier: 4.937A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 134 through 138 removed outlier: 6.399A pdb=" N TYR H 190 " --> pdb=" O ASP H 158 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 134 through 138 removed outlier: 6.399A pdb=" N TYR H 190 " --> pdb=" O ASP H 158 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER H 191 " --> pdb=" O VAL H 183 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 165 through 168 removed outlier: 4.393A pdb=" N TYR H 208 " --> pdb=" O VAL H 225 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 5 through 8 Processing sheet with id=AC9, first strand: chain 'L' and resid 36 through 38 removed outlier: 6.351A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 85 through 87 Processing sheet with id=AD2, first strand: chain 'L' and resid 116 through 120 removed outlier: 5.233A pdb=" N SER L 133 " --> pdb=" O LEU L 183 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N LEU L 183 " --> pdb=" O SER L 133 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N VAL L 135 " --> pdb=" O LEU L 181 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N LEU L 181 " --> pdb=" O VAL L 135 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N LEU L 137 " --> pdb=" O SER L 179 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N SER L 179 " --> pdb=" O LEU L 137 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ASN L 139 " --> pdb=" O LEU L 177 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N LEU L 177 " --> pdb=" O ASN L 139 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 147 through 152 Processing sheet with id=AD4, first strand: chain 'K' and resid 6 through 10 Processing sheet with id=AD5, first strand: chain 'K' and resid 14 through 15 removed outlier: 3.978A pdb=" N VAL K 15 " --> pdb=" O THR K 124 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE K 37 " --> pdb=" O TYR K 53 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N TYR K 53 " --> pdb=" O ILE K 37 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N TRP K 39 " --> pdb=" O VAL K 51 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 134 through 138 removed outlier: 6.206A pdb=" N TYR K 190 " --> pdb=" O ASP K 158 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 134 through 138 removed outlier: 6.206A pdb=" N TYR K 190 " --> pdb=" O ASP K 158 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER K 191 " --> pdb=" O VAL K 183 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL K 183 " --> pdb=" O SER K 191 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 164 through 168 removed outlier: 4.413A pdb=" N TYR K 208 " --> pdb=" O VAL K 225 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'M' and resid 5 through 8 Processing sheet with id=AE1, first strand: chain 'M' and resid 34 through 39 Processing sheet with id=AE2, first strand: chain 'M' and resid 34 through 39 Processing sheet with id=AE3, first strand: chain 'M' and resid 116 through 120 removed outlier: 6.057A pdb=" N TYR M 175 " --> pdb=" O ASN M 140 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 146 through 152 941 hydrogen bonds defined for protein. 2627 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.94 Time building geometry restraints manager: 10.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6599 1.34 - 1.47: 6548 1.47 - 1.59: 10287 1.59 - 1.72: 8 1.72 - 1.85: 178 Bond restraints: 23620 Sorted by residual: bond pdb=" N PRO A 480 " pdb=" CA PRO A 480 " ideal model delta sigma weight residual 1.473 1.707 -0.233 1.32e-02 5.74e+03 3.12e+02 bond pdb=" C04 QMR D 502 " pdb=" C05 QMR D 502 " ideal model delta sigma weight residual 1.536 1.240 0.296 2.00e-02 2.50e+03 2.19e+02 bond pdb=" C05 QMR D 502 " pdb=" C06 QMR D 502 " ideal model delta sigma weight residual 1.536 1.241 0.295 2.00e-02 2.50e+03 2.18e+02 bond pdb=" C04 QMR A 502 " pdb=" C05 QMR A 502 " ideal model delta sigma weight residual 1.536 1.243 0.293 2.00e-02 2.50e+03 2.15e+02 bond pdb=" C05 QMR A 502 " pdb=" C06 QMR A 502 " ideal model delta sigma weight residual 1.536 1.245 0.291 2.00e-02 2.50e+03 2.11e+02 ... (remaining 23615 not shown) Histogram of bond angle deviations from ideal: 93.33 - 103.31: 313 103.31 - 113.28: 13177 113.28 - 123.26: 17021 123.26 - 133.24: 1592 133.24 - 143.21: 102 Bond angle restraints: 32205 Sorted by residual: angle pdb=" N CYS A 200 " pdb=" CA CYS A 200 " pdb=" C CYS A 200 " ideal model delta sigma weight residual 109.96 143.21 -33.25 1.49e+00 4.50e-01 4.98e+02 angle pdb=" C PRO A 479 " pdb=" N PRO A 480 " pdb=" CA PRO A 480 " ideal model delta sigma weight residual 118.97 139.03 -20.06 1.04e+00 9.25e-01 3.72e+02 angle pdb=" C ALA B 307 " pdb=" N PRO B 308 " pdb=" CA PRO B 308 " ideal model delta sigma weight residual 118.97 137.39 -18.42 1.04e+00 9.25e-01 3.14e+02 angle pdb=" C LEU H 138 " pdb=" N ALA H 139 " pdb=" CA ALA H 139 " ideal model delta sigma weight residual 120.49 138.84 -18.35 1.42e+00 4.96e-01 1.67e+02 angle pdb=" N CYS A 200 " pdb=" CA CYS A 200 " pdb=" CB CYS A 200 " ideal model delta sigma weight residual 109.51 93.33 16.18 1.58e+00 4.01e-01 1.05e+02 ... (remaining 32200 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.35: 12693 20.35 - 40.70: 1290 40.70 - 61.05: 170 61.05 - 81.40: 45 81.40 - 101.75: 15 Dihedral angle restraints: 14213 sinusoidal: 5745 harmonic: 8468 Sorted by residual: dihedral pdb=" CB CYS M 136 " pdb=" SG CYS M 136 " pdb=" SG CYS M 196 " pdb=" CB CYS M 196 " ideal model delta sinusoidal sigma weight residual -86.00 -5.32 -80.68 1 1.00e+01 1.00e-02 8.04e+01 dihedral pdb=" CB CYS E 130 " pdb=" SG CYS E 130 " pdb=" SG CYS E 144 " pdb=" CB CYS E 144 " ideal model delta sinusoidal sigma weight residual 93.00 18.56 74.44 1 1.00e+01 1.00e-02 7.03e+01 dihedral pdb=" CB CYS A 135 " pdb=" SG CYS A 135 " pdb=" SG CYS A 149 " pdb=" CB CYS A 149 " ideal model delta sinusoidal sigma weight residual 93.00 32.04 60.96 1 1.00e+01 1.00e-02 4.94e+01 ... (remaining 14210 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.659: 3737 0.659 - 1.317: 2 1.317 - 1.976: 1 1.976 - 2.634: 1 2.634 - 3.293: 1 Chirality restraints: 3742 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " pdb=" O4 NAG B 401 " both_signs ideal model delta sigma weight residual False -2.40 0.89 -3.29 2.00e-02 2.50e+03 2.71e+04 chirality pdb=" C1 BMA G 2 " pdb=" O4 NAG G 1 " pdb=" C2 BMA G 2 " pdb=" O5 BMA G 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.72 -0.68 2.00e-02 2.50e+03 1.17e+03 chirality pdb=" C1 BMA F 2 " pdb=" O4 NAG F 1 " pdb=" C2 BMA F 2 " pdb=" O5 BMA F 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-02 2.50e+03 4.43e+02 ... (remaining 3739 not shown) Planarity restraints: 3983 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 143 " -0.166 2.00e-02 2.50e+03 1.96e-01 4.82e+02 pdb=" CG ASN B 143 " 0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN B 143 " 0.029 2.00e-02 2.50e+03 pdb=" ND2 ASN B 143 " 0.332 2.00e-02 2.50e+03 pdb=" C1 NAG B 401 " -0.230 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 143 " 0.141 2.00e-02 2.50e+03 1.48e-01 2.75e+02 pdb=" CG ASN C 143 " -0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN C 143 " -0.061 2.00e-02 2.50e+03 pdb=" ND2 ASN C 143 " -0.233 2.00e-02 2.50e+03 pdb=" C1 NAG C 401 " 0.177 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS B 304 " -0.032 2.00e-02 2.50e+03 6.69e-02 4.48e+01 pdb=" C HIS B 304 " 0.116 2.00e-02 2.50e+03 pdb=" O HIS B 304 " -0.044 2.00e-02 2.50e+03 pdb=" N THR B 305 " -0.039 2.00e-02 2.50e+03 ... (remaining 3980 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 255 2.58 - 3.16: 16203 3.16 - 3.74: 34098 3.74 - 4.32: 44974 4.32 - 4.90: 74873 Nonbonded interactions: 170403 Sorted by model distance: nonbonded pdb=" O PRO M 81 " pdb=" CD1 ILE M 108 " model vdw 2.004 3.460 nonbonded pdb=" O VAL B 197 " pdb=" OD1 ASP B 198 " model vdw 2.021 3.040 nonbonded pdb=" O GLN M 39 " pdb=" CB ALA M 85 " model vdw 2.048 3.460 nonbonded pdb=" CB SER E 84 " pdb=" O SER E 108 " model vdw 2.085 3.440 nonbonded pdb=" CB ASN D 102 " pdb=" CE1 PHE D 107 " model vdw 2.156 3.740 ... (remaining 170398 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = (chain 'B' and (resid 2 through 325 or resid 333 through 365)) selection = (chain 'C' and resid 2 through 365) selection = (chain 'E' and resid 2 through 365) } ncs_group { reference = (chain 'F' and resid 1) selection = (chain 'G' and resid 1) selection = (chain 'I' and resid 1) } ncs_group { reference = (chain 'H' and (resid 3 through 184 or resid 186 through 229)) selection = (chain 'K' and (resid 3 through 122 or resid 131 through 184 or resid 186 throug \ h 229)) } ncs_group { reference = (chain 'L' and (resid 2 through 23 or resid 25 through 214)) selection = (chain 'M' and (resid 2 through 23 or resid 25 through 108 or resid 113 through \ 214)) } 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=0.50 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: 3.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.190 Construct map_model_manager: 0.020 Extract box with map and model: 1.100 Check model and map are aligned: 0.190 Set scattering table: 0.250 Process input model: 69.300 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.140 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:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 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 : 0.014 0.296 23620 Z= 0.917 Angle : 1.546 33.255 32205 Z= 0.878 Chirality : 0.109 3.293 3742 Planarity : 0.011 0.109 3978 Dihedral : 16.343 101.747 8669 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 0.08 % Allowed : 13.81 % Favored : 86.11 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 9.33 % 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: -4.48 (0.13), residues: 2834 helix: -4.66 (0.08), residues: 710 sheet: -1.38 (0.18), residues: 819 loop : -2.98 (0.14), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.004 TRP H 110 HIS 0.010 0.002 HIS K 38 PHE 0.045 0.004 PHE A 322 TYR 0.042 0.004 TYR B 340 ARG 0.010 0.001 ARG C 207 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 284 time to evaluate : 2.884 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: A 350 GLU cc_start: 0.9219 (mt-10) cc_final: 0.8849 (mp0) REVERT: B 77 MET cc_start: 0.8751 (mtp) cc_final: 0.8302 (ttm) REVERT: B 324 MET cc_start: 0.6545 (ptp) cc_final: 0.6111 (ptt) REVERT: B 325 GLN cc_start: 0.6353 (mm110) cc_final: 0.6147 (tp40) REVERT: D 240 TYR cc_start: 0.8500 (t80) cc_final: 0.7894 (t80) REVERT: D 310 ARG cc_start: 0.6596 (tpt170) cc_final: 0.6266 (tpt90) REVERT: D 413 GLN cc_start: 0.8050 (mt0) cc_final: 0.7436 (mp10) REVERT: D 470 LEU cc_start: 0.8649 (tp) cc_final: 0.8375 (tp) REVERT: E 36 MET cc_start: 0.8320 (ppp) cc_final: 0.8028 (ppp) REVERT: H 23 LEU cc_start: 0.6835 (mt) cc_final: 0.6267 (mt) REVERT: H 73 ILE cc_start: 0.8409 (mt) cc_final: 0.8151 (mt) REVERT: H 108 GLU cc_start: 0.8462 (tt0) cc_final: 0.8209 (tm-30) REVERT: H 119 GLN cc_start: 0.8017 (pm20) cc_final: 0.6644 (mm110) REVERT: L 47 LEU cc_start: 0.7425 (tp) cc_final: 0.5418 (tt) REVERT: K 35 PHE cc_start: 0.7692 (m-80) cc_final: 0.7396 (m-80) REVERT: K 81 THR cc_start: 0.6921 (m) cc_final: 0.6631 (p) REVERT: K 83 TYR cc_start: 0.6443 (m-80) cc_final: 0.5998 (m-80) REVERT: M 87 TYR cc_start: 0.5856 (m-80) cc_final: 0.5307 (m-80) REVERT: M 92 TYR cc_start: 0.7867 (p90) cc_final: 0.7446 (p90) outliers start: 2 outliers final: 2 residues processed: 286 average time/residue: 0.3326 time to fit residues: 150.3445 Evaluate side-chains 206 residues out of total 2583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 204 time to evaluate : 2.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain E residue 86 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 237 optimal weight: 10.0000 chunk 212 optimal weight: 7.9990 chunk 118 optimal weight: 0.5980 chunk 72 optimal weight: 0.9980 chunk 143 optimal weight: 1.9990 chunk 113 optimal weight: 0.0070 chunk 220 optimal weight: 10.0000 chunk 85 optimal weight: 0.9990 chunk 133 optimal weight: 0.8980 chunk 163 optimal weight: 0.6980 chunk 255 optimal weight: 5.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 HIS A 405 HIS A 435 GLN B 97 ASN C 26 ASN C 109 ASN C 304 HIS D 119 HIS D 430 GLN D 445 GLN L 91 GLN M 90 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 23620 Z= 0.225 Angle : 0.729 11.224 32205 Z= 0.379 Chirality : 0.046 0.318 3742 Planarity : 0.006 0.084 3978 Dihedral : 8.125 59.153 3343 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.32 % Allowed : 16.75 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.33 % 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: -2.99 (0.14), residues: 2834 helix: -2.47 (0.15), residues: 752 sheet: -0.97 (0.18), residues: 809 loop : -2.28 (0.15), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP H 110 HIS 0.008 0.001 HIS A 119 PHE 0.023 0.002 PHE B 359 TYR 0.024 0.002 TYR K 53 ARG 0.012 0.001 ARG H 22 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 247 time to evaluate : 2.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 TRP cc_start: 0.7587 (t-100) cc_final: 0.6466 (t-100) REVERT: A 350 GLU cc_start: 0.9282 (mt-10) cc_final: 0.8785 (mp0) REVERT: A 392 ASP cc_start: 0.8280 (p0) cc_final: 0.7766 (t70) REVERT: B 77 MET cc_start: 0.8652 (mtp) cc_final: 0.8255 (ttm) REVERT: B 324 MET cc_start: 0.6199 (ptp) cc_final: 0.5936 (ptt) REVERT: B 343 MET cc_start: 0.7953 (tpp) cc_final: 0.7540 (tpp) REVERT: C 21 ILE cc_start: 0.8735 (pt) cc_final: 0.8413 (mt) REVERT: D 11 GLU cc_start: 0.8152 (tt0) cc_final: 0.7951 (mt-10) REVERT: D 163 ILE cc_start: 0.9356 (mt) cc_final: 0.9131 (mt) REVERT: D 310 ARG cc_start: 0.6524 (tpt170) cc_final: 0.6309 (tpt90) REVERT: D 481 TRP cc_start: 0.5832 (t-100) cc_final: 0.5604 (t-100) REVERT: E 36 MET cc_start: 0.8320 (ppp) cc_final: 0.8007 (ppp) REVERT: E 37 VAL cc_start: 0.9533 (OUTLIER) cc_final: 0.9312 (p) REVERT: E 95 TYR cc_start: 0.8923 (OUTLIER) cc_final: 0.8010 (m-80) REVERT: H 61 THR cc_start: 0.8177 (p) cc_final: 0.7702 (p) REVERT: H 108 GLU cc_start: 0.8402 (tt0) cc_final: 0.8043 (tm-30) REVERT: H 112 LYS cc_start: 0.8252 (mttt) cc_final: 0.7851 (mttt) REVERT: H 119 GLN cc_start: 0.8057 (pm20) cc_final: 0.6285 (mm110) REVERT: L 86 THR cc_start: 0.6377 (m) cc_final: 0.5639 (t) REVERT: L 88 TYR cc_start: 0.6541 (m-10) cc_final: 0.6118 (m-10) REVERT: K 81 THR cc_start: 0.6765 (m) cc_final: 0.6392 (p) REVERT: K 83 TYR cc_start: 0.6120 (m-80) cc_final: 0.5839 (m-80) outliers start: 60 outliers final: 29 residues processed: 293 average time/residue: 0.2791 time to fit residues: 132.8632 Evaluate side-chains 236 residues out of total 2583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 205 time to evaluate : 2.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 135 LYS Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain C residue 85 LYS Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 405 HIS Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 343 MET Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain K residue 8 VAL Chi-restraints excluded: chain M residue 34 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 141 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 212 optimal weight: 4.9990 chunk 173 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 255 optimal weight: 40.0000 chunk 276 optimal weight: 2.9990 chunk 227 optimal weight: 4.9990 chunk 253 optimal weight: 10.0000 chunk 87 optimal weight: 0.5980 chunk 205 optimal weight: 4.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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: