Starting phenix.real_space_refine on Wed Nov 15 16:45:07 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dgf_27422/11_2023/8dgf_27422_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dgf_27422/11_2023/8dgf_27422.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dgf_27422/11_2023/8dgf_27422.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dgf_27422/11_2023/8dgf_27422.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dgf_27422/11_2023/8dgf_27422_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dgf_27422/11_2023/8dgf_27422_updated.pdb" } resolution = 2.9 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= 0.003 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 4 5.21 5 S 234 5.16 5 C 41812 2.51 5 N 10676 2.21 5 O 12220 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 58": "OE1" <-> "OE2" Residue "A ASP 77": "OD1" <-> "OD2" Residue "A TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 185": "OE1" <-> "OE2" Residue "A ASP 211": "OD1" <-> "OD2" Residue "A GLU 248": "OE1" <-> "OE2" Residue "A ASP 308": "OD1" <-> "OD2" Residue "A ASP 375": "OD1" <-> "OD2" Residue "A PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 629": "OD1" <-> "OD2" Residue "A GLU 715": "OE1" <-> "OE2" Residue "A GLU 742": "OE1" <-> "OE2" Residue "A TYR 860": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 980": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1000": "OD1" <-> "OD2" Residue "A GLU 1027": "OE1" <-> "OE2" Residue "A GLU 1073": "OE1" <-> "OE2" Residue "A GLU 1096": "OE1" <-> "OE2" Residue "A PHE 1133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1143": "OD1" <-> "OD2" Residue "A TYR 1171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1316": "OD1" <-> "OD2" Residue "A PHE 1398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1464": "OE1" <-> "OE2" Residue "B GLU 15": "OE1" <-> "OE2" Residue "B GLU 32": "OE1" <-> "OE2" Residue "B GLU 83": "OE1" <-> "OE2" Residue "B TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 102": "OE1" <-> "OE2" Residue "B ASP 138": "OD1" <-> "OD2" Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 185": "OE1" <-> "OE2" Residue "B GLU 196": "OE1" <-> "OE2" Residue "B ASP 205": "OD1" <-> "OD2" Residue "B GLU 221": "OE1" <-> "OE2" Residue "B GLU 234": "OE1" <-> "OE2" Residue "B TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 363": "OE1" <-> "OE2" Residue "B GLU 496": "OE1" <-> "OE2" Residue "B GLU 534": "OE1" <-> "OE2" Residue "B ASP 552": "OD1" <-> "OD2" Residue "B TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 702": "OE1" <-> "OE2" Residue "B TYR 734": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 940": "OD1" <-> "OD2" Residue "B TYR 980": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 991": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1003": "OE1" <-> "OE2" Residue "B TYR 1015": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1059": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1131": "OE1" <-> "OE2" Residue "B PHE 1133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1166": "OD1" <-> "OD2" Residue "B TYR 1263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1360": "OE1" <-> "OE2" Residue "B GLU 1464": "OE1" <-> "OE2" Residue "B GLU 1518": "OE1" <-> "OE2" Residue "C GLU 58": "OE1" <-> "OE2" Residue "C ASP 77": "OD1" <-> "OD2" Residue "C TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 185": "OE1" <-> "OE2" Residue "C GLU 196": "OE1" <-> "OE2" Residue "C ASP 211": "OD1" <-> "OD2" Residue "C GLU 234": "OE1" <-> "OE2" Residue "C GLU 248": "OE1" <-> "OE2" Residue "C ASP 308": "OD1" <-> "OD2" Residue "C ASP 335": "OD1" <-> "OD2" Residue "C ASP 375": "OD1" <-> "OD2" Residue "C GLU 474": "OE1" <-> "OE2" Residue "C PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 980": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1000": "OD1" <-> "OD2" Residue "C GLU 1027": "OE1" <-> "OE2" Residue "C GLU 1073": "OE1" <-> "OE2" Residue "C GLU 1096": "OE1" <-> "OE2" Residue "C PHE 1133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1143": "OD1" <-> "OD2" Residue "C TYR 1171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1178": "OE1" <-> "OE2" Residue "C TYR 1263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1316": "OD1" <-> "OD2" Residue "C PHE 1398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 32": "OE1" <-> "OE2" Residue "D GLU 83": "OE1" <-> "OE2" Residue "D TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 102": "OE1" <-> "OE2" Residue "D ASP 138": "OD1" <-> "OD2" Residue "D GLU 147": "OE1" <-> "OE2" Residue "D PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 185": "OE1" <-> "OE2" Residue "D ASP 205": "OD1" <-> "OD2" Residue "D GLU 221": "OE1" <-> "OE2" Residue "D TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 363": "OE1" <-> "OE2" Residue "D GLU 496": "OE1" <-> "OE2" Residue "D PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 702": "OE1" <-> "OE2" Residue "D TYR 734": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 940": "OD1" <-> "OD2" Residue "D TYR 980": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1003": "OE1" <-> "OE2" Residue "D TYR 1015": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1059": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1131": "OE1" <-> "OE2" Residue "D ASP 1143": "OD1" <-> "OD2" Residue "D TYR 1171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1360": "OE1" <-> "OE2" Residue "D TYR 1445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1464": "OE1" <-> "OE2" Residue "D GLU 1518": "OE1" <-> "OE2" Residue "E PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 151": "OE1" <-> "OE2" Residue "E ASP 184": "OD1" <-> "OD2" Residue "E TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 260": "OD1" <-> "OD2" Residue "E PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 333": "OE1" <-> "OE2" Residue "E TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 373": "OE1" <-> "OE2" Residue "F PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 151": "OE1" <-> "OE2" Residue "F ASP 194": "OD1" <-> "OD2" Residue "F ASP 208": "OD1" <-> "OD2" Residue "F PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 395": "OE1" <-> "OE2" Residue "G PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 151": "OE1" <-> "OE2" Residue "G PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 333": "OE1" <-> "OE2" Residue "G GLU 382": "OE1" <-> "OE2" Residue "H PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 151": "OE1" <-> "OE2" Residue "H ASP 194": "OD1" <-> "OD2" Residue "H ASP 208": "OD1" <-> "OD2" Residue "H ASP 233": "OD1" <-> "OD2" Residue "H PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 326": "OD1" <-> "OD2" Residue "H ASP 383": "OD1" <-> "OD2" Residue "H GLU 395": "OE1" <-> "OE2" Residue "H GLU 423": "OE1" <-> "OE2" Time to flip residues: 0.22s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 64958 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 12805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1541, 12805 Classifications: {'peptide': 1541} Link IDs: {'PTRANS': 44, 'TRANS': 1496} Chain breaks: 4 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 12756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1534, 12756 Classifications: {'peptide': 1534} Link IDs: {'PTRANS': 44, 'TRANS': 1489} Chain breaks: 4 Chain: "C" Number of atoms: 12805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1541, 12805 Classifications: {'peptide': 1541} Link IDs: {'PTRANS': 44, 'TRANS': 1496} Chain breaks: 4 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 12756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1534, 12756 Classifications: {'peptide': 1534} Link IDs: {'PTRANS': 44, 'TRANS': 1489} Chain breaks: 4 Chain: "E" Number of atoms: 3427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3427 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 19, 'TRANS': 418} Chain breaks: 1 Chain: "F" Number of atoms: 3427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3427 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 19, 'TRANS': 418} Chain breaks: 1 Chain: "G" Number of atoms: 3427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3427 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 19, 'TRANS': 418} Chain breaks: 1 Chain: "H" Number of atoms: 3427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3427 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 19, 'TRANS': 418} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 25.66, per 1000 atoms: 0.40 Number of scatterers: 64958 At special positions: 0 Unit cell: (255.487, 261.694, 196.529, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 234 16.00 P 12 15.00 Mg 4 11.99 O 12220 8.00 N 10676 7.00 C 41812 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A1439 " - pdb=" SG CYS A1490 " distance=2.05 Simple disulfide: pdb=" SG CYS B1439 " - pdb=" SG CYS B1490 " distance=2.05 Simple disulfide: pdb=" SG CYS C1439 " - pdb=" SG CYS C1490 " distance=2.05 Simple disulfide: pdb=" SG CYS D1439 " - pdb=" SG CYS D1490 " distance=2.05 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: 18.34 Conformation dependent library (CDL) restraints added in 8.5 seconds 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15148 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 438 helices and 42 sheets defined 59.9% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 14.14 Creating SS restraints... Processing helix chain 'A' and resid 6 through 12 Processing helix chain 'A' and resid 17 through 32 Processing helix chain 'A' and resid 39 through 42 No H-bonds generated for 'chain 'A' and resid 39 through 42' Processing helix chain 'A' and resid 45 through 47 No H-bonds generated for 'chain 'A' and resid 45 through 47' Processing helix chain 'A' and resid 71 through 88 removed outlier: 3.602A pdb=" N ASN A 74 " --> pdb=" O LEU A 71 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LYS A 75 " --> pdb=" O SER A 72 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N ALA A 76 " --> pdb=" O ASP A 73 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU A 83 " --> pdb=" O GLU A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 143 Processing helix chain 'A' and resid 153 through 156 No H-bonds generated for 'chain 'A' and resid 153 through 156' Processing helix chain 'A' and resid 159 through 162 No H-bonds generated for 'chain 'A' and resid 159 through 162' Processing helix chain 'A' and resid 166 through 173 removed outlier: 4.085A pdb=" N HIS A 171 " --> pdb=" O LYS A 167 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE A 172 " --> pdb=" O ILE A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 193 Processing helix chain 'A' and resid 213 through 225 removed outlier: 3.542A pdb=" N VAL A 224 " --> pdb=" O HIS A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 249 removed outlier: 3.685A pdb=" N ILE A 243 " --> pdb=" O LYS A 239 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA A 249 " --> pdb=" O LYS A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 264 removed outlier: 3.774A pdb=" N PHE A 264 " --> pdb=" O ALA A 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 261 through 264' Processing helix chain 'A' and resid 269 through 273 Processing helix chain 'A' and resid 278 through 285 removed outlier: 4.086A pdb=" N HIS A 285 " --> pdb=" O PHE A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 308 through 319 Processing helix chain 'A' and resid 330 through 342 removed outlier: 3.657A pdb=" N LEU A 333 " --> pdb=" O ASN A 330 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ALA A 334 " --> pdb=" O ASN A 331 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASP A 342 " --> pdb=" O ALA A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 368 Processing helix chain 'A' and resid 376 through 379 No H-bonds generated for 'chain 'A' and resid 376 through 379' Processing helix chain 'A' and resid 385 through 393 removed outlier: 3.628A pdb=" N ARG A 393 " --> pdb=" O SER A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 413 Processing helix chain 'A' and resid 419 through 435 Processing helix chain 'A' and resid 448 through 454 Processing helix chain 'A' and resid 470 through 486 Processing helix chain 'A' and resid 491 through 497 Processing helix chain 'A' and resid 502 through 517 Processing helix chain 'A' and resid 521 through 532 Proline residue: A 525 - end of helix removed outlier: 3.730A pdb=" N CYS A 532 " --> pdb=" O GLU A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 550 Processing helix chain 'A' and resid 554 through 560 removed outlier: 3.928A pdb=" N PHE A 558 " --> pdb=" O SER A 554 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN A 559 " --> pdb=" O SER A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 567 Processing helix chain 'A' and resid 571 through 583 Processing helix chain 'A' and resid 589 through 595 Processing helix chain 'A' and resid 616 through 626 Processing helix chain 'A' and resid 628 through 631 No H-bonds generated for 'chain 'A' and resid 628 through 631' Processing helix chain 'A' and resid 636 through 638 No H-bonds generated for 'chain 'A' and resid 636 through 638' Processing helix chain 'A' and resid 640 through 647 Processing helix chain 'A' and resid 654 through 672 Processing helix chain 'A' and resid 686 through 693 removed outlier: 3.750A pdb=" N GLY A 693 " --> pdb=" O THR A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 711 Processing helix chain 'A' and resid 721 through 729 Processing helix chain 'A' and resid 731 through 739 Proline residue: A 735 - end of helix Processing helix chain 'A' and resid 741 through 752 removed outlier: 3.657A pdb=" N GLN A 746 " --> pdb=" O GLU A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 772 Processing helix chain 'A' and resid 776 through 781 removed outlier: 3.909A pdb=" N HIS A 779 " --> pdb=" O ARG A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 797 removed outlier: 3.990A pdb=" N LEU A 795 " --> pdb=" O TYR A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 818 Processing helix chain 'A' and resid 821 through 823 No H-bonds generated for 'chain 'A' and resid 821 through 823' Processing helix chain 'A' and resid 846 through 852 removed outlier: 3.870A pdb=" N SER A 851 " --> pdb=" O ARG A 847 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N TYR A 852 " --> pdb=" O LEU A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 876 Processing helix chain 'A' and resid 882 through 895 removed outlier: 3.569A pdb=" N ASN A 895 " --> pdb=" O PHE A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 899 through 911 removed outlier: 3.766A pdb=" N VAL A 904 " --> pdb=" O SER A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 925 removed outlier: 4.040A pdb=" N VAL A 922 " --> pdb=" O ASN A 918 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLN A 925 " --> pdb=" O LYS A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 947 removed outlier: 3.681A pdb=" N PHE A 932 " --> pdb=" O PHE A 929 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASP A 933 " --> pdb=" O PHE A 930 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N HIS A 943 " --> pdb=" O ASP A 940 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N LYS A 944 " --> pdb=" O ARG A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 973 removed outlier: 3.783A pdb=" N ASP A 967 " --> pdb=" O LEU A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 978 Processing helix chain 'A' and resid 981 through 989 removed outlier: 4.144A pdb=" N GLN A 989 " --> pdb=" O ALA A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1018 removed outlier: 3.930A pdb=" N GLN A1018 " --> pdb=" O LYS A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1022 through 1024 No H-bonds generated for 'chain 'A' and resid 1022 through 1024' Processing helix chain 'A' and resid 1027 through 1037 Processing helix chain 'A' and resid 1041 through 1043 No H-bonds generated for 'chain 'A' and resid 1041 through 1043' Processing helix chain 'A' and resid 1065 through 1095 removed outlier: 3.777A pdb=" N LYS A1083 " --> pdb=" O SER A1079 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N TYR A1084 " --> pdb=" O GLU A1080 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N VAL A1085 " --> pdb=" O HIS A1081 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N THR A1086 " --> pdb=" O MET A1082 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N LEU A1087 " --> pdb=" O LYS A1083 " (cutoff:3.500A) Processing helix chain 'A' and resid 1099 through 1103 Processing helix chain 'A' and resid 1111 through 1126 Processing helix chain 'A' and resid 1131 through 1137 removed outlier: 3.839A pdb=" N LEU A1136 " --> pdb=" O ASP A1132 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1151 Processing helix chain 'A' and resid 1158 through 1176 removed outlier: 3.783A pdb=" N LYS A1173 " --> pdb=" O LEU A1169 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU A1174 " --> pdb=" O ALA A1170 " (cutoff:3.500A) Proline residue: A1175 - end of helix Processing helix chain 'A' and resid 1188 through 1201 removed outlier: 3.958A pdb=" N ALA A1194 " --> pdb=" O SER A1190 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU A1195 " --> pdb=" O ALA A1191 " (cutoff:3.500A) Proline residue: A1196 - end of helix Processing helix chain 'A' and resid 1203 through 1217 removed outlier: 3.709A pdb=" N ARG A1206 " --> pdb=" O PRO A1203 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N GLU A1207 " --> pdb=" O MET A1204 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A1213 " --> pdb=" O LYS A1210 " (cutoff:3.500A) Processing helix chain 'A' and resid 1230 through 1240 Proline residue: A1234 - end of helix removed outlier: 3.707A pdb=" N HIS A1239 " --> pdb=" O MET A1236 " (cutoff:3.500A) Processing helix chain 'A' and resid 1246 through 1276 Proline residue: A1261 - end of helix removed outlier: 3.648A pdb=" N VAL A1264 " --> pdb=" O LYS A1260 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ILE A1265 " --> pdb=" O PRO A1261 " (cutoff:3.500A) Processing helix chain 'A' and resid 1287 through 1294 Processing helix chain 'A' and resid 1296 through 1304 Processing helix chain 'A' and resid 1320 through 1329 removed outlier: 4.018A pdb=" N LEU A1329 " --> pdb=" O THR A1325 " (cutoff:3.500A) Processing helix chain 'A' and resid 1337 through 1354 removed outlier: 3.543A pdb=" N LEU A1345 " --> pdb=" O LYS A1341 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS A1348 " --> pdb=" O SER A1344 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N SER A1353 " --> pdb=" O ARG A1349 " (cutoff:3.500A) Processing helix chain 'A' and resid 1359 through 1361 No H-bonds generated for 'chain 'A' and resid 1359 through 1361' Processing helix chain 'A' and resid 1365 through 1380 removed outlier: 3.766A pdb=" N ARG A1374 " --> pdb=" O SER A1370 " (cutoff:3.500A) Processing helix chain 'A' and resid 1387 through 1390 No H-bonds generated for 'chain 'A' and resid 1387 through 1390' Processing helix chain 'A' and resid 1392 through 1396 Processing helix chain 'A' and resid 1402 through 1418 removed outlier: 3.563A pdb=" N LEU A1407 " --> pdb=" O ILE A1404 " (cutoff:3.500A) Processing helix chain 'A' and resid 1421 through 1430 Processing helix chain 'A' and resid 1432 through 1441 removed outlier: 3.712A pdb=" N LYS A1440 " --> pdb=" O VAL A1436 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ASP A1441 " --> pdb=" O THR A1437 " (cutoff:3.500A) Processing helix chain 'A' and resid 1448 through 1455 Processing helix chain 'A' and resid 1474 through 1486 removed outlier: 3.586A pdb=" N GLN A1478 " --> pdb=" O SER A1475 " (cutoff:3.500A) Processing helix chain 'A' and resid 1491 through 1502 removed outlier: 3.634A pdb=" N ASN A1502 " --> pdb=" O ALA A1498 " (cutoff:3.500A) Processing helix chain 'A' and resid 1506 through 1522 removed outlier: 5.714A pdb=" N ASN A1510 " --> pdb=" O CYS A1507 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE A1513 " --> pdb=" O ASN A1510 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A1516 " --> pdb=" O ILE A1513 " (cutoff:3.500A) Processing helix chain 'A' and resid 1524 through 1527 Processing helix chain 'A' and resid 1535 through 1556 removed outlier: 3.649A pdb=" N ASN A1548 " --> pdb=" O ARG A1544 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN A1549 " --> pdb=" O ARG A1545 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLU A1552 " --> pdb=" O ASN A1548 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ARG A1553 " --> pdb=" O ASN A1549 " (cutoff:3.500A) Processing helix chain 'A' and resid 1558 through 1573 removed outlier: 3.987A pdb=" N ILE A1567 " --> pdb=" O GLU A1563 " (cutoff:3.500A) Processing helix chain 'A' and resid 1577 through 1586 Processing helix chain 'B' and resid 6 through 12 Processing helix chain 'B' and resid 17 through 32 removed outlier: 3.584A pdb=" N TRP B 23 " --> pdb=" O GLY B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 88 removed outlier: 4.040A pdb=" N LYS B 75 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ALA B 76 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE B 79 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS B 86 " --> pdb=" O GLU B 83 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS B 87 " --> pdb=" O LYS B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 144 Processing helix chain 'B' and resid 153 through 155 No H-bonds generated for 'chain 'B' and resid 153 through 155' Processing helix chain 'B' and resid 159 through 162 No H-bonds generated for 'chain 'B' and resid 159 through 162' Processing helix chain 'B' and resid 166 through 173 removed outlier: 3.876A pdb=" N HIS B 171 " --> pdb=" O LYS B 167 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N PHE B 172 " --> pdb=" O ILE B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 196 removed outlier: 4.001A pdb=" N LEU B 183 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N LYS B 186 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU B 194 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR B 195 " --> pdb=" O ASN B 192 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU B 196 " --> pdb=" O VAL B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 225 removed outlier: 3.623A pdb=" N GLU B 217 " --> pdb=" O ARG B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 250 removed outlier: 3.604A pdb=" N ILE B 243 " --> pdb=" O LYS B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 264 removed outlier: 3.684A pdb=" N PHE B 264 " --> pdb=" O ALA B 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 261 through 264' Processing helix chain 'B' and resid 269 through 272 Processing helix chain 'B' and resid 278 through 285 removed outlier: 3.976A pdb=" N HIS B 285 " --> pdb=" O PHE B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 303 removed outlier: 3.588A pdb=" N LEU B 302 " --> pdb=" O GLU B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 319 Processing helix chain 'B' and resid 330 through 344 removed outlier: 5.004A pdb=" N ALA B 334 " --> pdb=" O ASN B 331 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP B 335 " --> pdb=" O TYR B 332 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU B 336 " --> pdb=" O LEU B 333 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ALA B 339 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE B 340 " --> pdb=" O ASN B 337 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE B 343 " --> pdb=" O PHE B 340 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TYR B 344 " --> pdb=" O ILE B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 368 Processing helix chain 'B' and resid 376 through 383 removed outlier: 3.787A pdb=" N LYS B 383 " --> pdb=" O LEU B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 393 Processing helix chain 'B' and resid 402 through 413 Processing helix chain 'B' and resid 419 through 435 removed outlier: 3.505A pdb=" N ARG B 432 " --> pdb=" O THR B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 454 Processing helix chain 'B' and resid 470 through 486 Processing helix chain 'B' and resid 491 through 497 Processing helix chain 'B' and resid 502 through 515 Processing helix chain 'B' and resid 522 through 531 removed outlier: 3.800A pdb=" N PHE B 526 " --> pdb=" O SER B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 549 Processing helix chain 'B' and resid 554 through 560 removed outlier: 3.723A pdb=" N PHE B 558 " --> pdb=" O SER B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 567 Processing helix chain 'B' and resid 571 through 583 removed outlier: 3.594A pdb=" N THR B 577 " --> pdb=" O LEU B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 595 Processing helix chain 'B' and resid 616 through 626 Processing helix chain 'B' and resid 628 through 631 No H-bonds generated for 'chain 'B' and resid 628 through 631' Processing helix chain 'B' and resid 633 through 638 removed outlier: 3.873A pdb=" N ILE B 636 " --> pdb=" O ILE B 633 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ASN B 637 " --> pdb=" O ARG B 634 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N PHE B 638 " --> pdb=" O ASN B 635 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 633 through 638' Processing helix chain 'B' and resid 640 through 647 Processing helix chain 'B' and resid 654 through 672 Processing helix chain 'B' and resid 686 through 696 removed outlier: 3.714A pdb=" N GLY B 693 " --> pdb=" O THR B 689 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N ALA B 695 " --> pdb=" O LEU B 691 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N MET B 696 " --> pdb=" O HIS B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 698 through 711 Processing helix chain 'B' and resid 721 through 729 Processing helix chain 'B' and resid 731 through 739 Proline residue: B 735 - end of helix Processing helix chain 'B' and resid 741 through 752 removed outlier: 3.731A pdb=" N GLN B 746 " --> pdb=" O GLU B 742 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 772 Processing helix chain 'B' and resid 776 through 781 removed outlier: 4.345A pdb=" N HIS B 779 " --> pdb=" O ARG B 776 " (cutoff:3.500A) Processing helix chain 'B' and resid 790 through 797 removed outlier: 3.933A pdb=" N LEU B 795 " --> pdb=" O TYR B 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 799 through 818 Processing helix chain 'B' and resid 846 through 849 No H-bonds generated for 'chain 'B' and resid 846 through 849' Processing helix chain 'B' and resid 860 through 876 Processing helix chain 'B' and resid 882 through 895 removed outlier: 3.556A pdb=" N ASN B 895 " --> pdb=" O PHE B 891 " (cutoff:3.500A) Processing helix chain 'B' and resid 899 through 911 removed outlier: 3.788A pdb=" N VAL B 904 " --> pdb=" O SER B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 917 through 925 removed outlier: 4.010A pdb=" N VAL B 922 " --> pdb=" O ASN B 918 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLN B 925 " --> pdb=" O LYS B 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 927 through 947 removed outlier: 3.683A pdb=" N PHE B 932 " --> pdb=" O PHE B 929 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP B 933 " --> pdb=" O PHE B 930 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N HIS B 943 " --> pdb=" O ASP B 940 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LYS B 944 " --> pdb=" O ARG B 941 " (cutoff:3.500A) Processing helix chain 'B' and resid 962 through 973 removed outlier: 3.749A pdb=" N ASP B 967 " --> pdb=" O LEU B 963 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP B 973 " --> pdb=" O ILE B 969 " (cutoff:3.500A) Processing helix chain 'B' and resid 975 through 978 Processing helix chain 'B' and resid 981 through 989 removed outlier: 4.152A pdb=" N GLN B 989 " --> pdb=" O ALA B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 998 through 1018 removed outlier: 4.014A pdb=" N GLN B1018 " --> pdb=" O LYS B1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1024 No H-bonds generated for 'chain 'B' and resid 1022 through 1024' Processing helix chain 'B' and resid 1027 through 1038 Processing helix chain 'B' and resid 1041 through 1043 No H-bonds generated for 'chain 'B' and resid 1041 through 1043' Processing helix chain 'B' and resid 1065 through 1081 removed outlier: 3.697A pdb=" N TYR B1070 " --> pdb=" O LYS B1066 " (cutoff:3.500A) Processing helix chain 'B' and resid 1085 through 1095 Processing helix chain 'B' and resid 1099 through 1103 Processing helix chain 'B' and resid 1111 through 1126 Processing helix chain 'B' and resid 1131 through 1137 removed outlier: 3.934A pdb=" N LEU B1136 " --> pdb=" O ASP B1132 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1151 Processing helix chain 'B' and resid 1158 through 1176 removed outlier: 3.852A pdb=" N LYS B1173 " --> pdb=" O LEU B1169 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU B1174 " --> pdb=" O ALA B1170 " (cutoff:3.500A) Proline residue: B1175 - end of helix Processing helix chain 'B' and resid 1188 through 1201 removed outlier: 3.904A pdb=" N ALA B1194 " --> pdb=" O SER B1190 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU B1195 " --> pdb=" O ALA B1191 " (cutoff:3.500A) Proline residue: B1196 - end of helix Processing helix chain 'B' and resid 1203 through 1217 removed outlier: 3.662A pdb=" N ARG B1206 " --> pdb=" O PRO B1203 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N GLU B1207 " --> pdb=" O MET B1204 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B1213 " --> pdb=" O LYS B1210 " (cutoff:3.500A) Processing helix chain 'B' and resid 1230 through 1240 Proline residue: B1234 - end of helix removed outlier: 3.734A pdb=" N HIS B1239 " --> pdb=" O MET B1236 " (cutoff:3.500A) Processing helix chain 'B' and resid 1246 through 1276 Proline residue: B1261 - end of helix removed outlier: 3.636A pdb=" N VAL B1264 " --> pdb=" O LYS B1260 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE B1265 " --> pdb=" O PRO B1261 " (cutoff:3.500A) Processing helix chain 'B' and resid 1287 through 1294 Processing helix chain 'B' and resid 1296 through 1304 Processing helix chain 'B' and resid 1309 through 1311 No H-bonds generated for 'chain 'B' and resid 1309 through 1311' Processing helix chain 'B' and resid 1315 through 1317 No H-bonds generated for 'chain 'B' and resid 1315 through 1317' Processing helix chain 'B' and resid 1320 through 1329 removed outlier: 4.027A pdb=" N LEU B1329 " --> pdb=" O THR B1325 " (cutoff:3.500A) Processing helix chain 'B' and resid 1337 through 1354 removed outlier: 3.583A pdb=" N LEU B1345 " --> pdb=" O LYS B1341 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS B1348 " --> pdb=" O SER B1344 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER B1353 " --> pdb=" O ARG B1349 " (cutoff:3.500A) Processing helix chain 'B' and resid 1359 through 1361 No H-bonds generated for 'chain 'B' and resid 1359 through 1361' Processing helix chain 'B' and resid 1365 through 1380 removed outlier: 3.770A pdb=" N ARG B1374 " --> pdb=" O SER B1370 " (cutoff:3.500A) Processing helix chain 'B' and resid 1387 through 1390 No H-bonds generated for 'chain 'B' and resid 1387 through 1390' Processing helix chain 'B' and resid 1392 through 1396 Processing helix chain 'B' and resid 1402 through 1418 removed outlier: 3.676A pdb=" N LEU B1407 " --> pdb=" O ILE B1404 " (cutoff:3.500A) Processing helix chain 'B' and resid 1421 through 1430 Processing helix chain 'B' and resid 1432 through 1441 removed outlier: 3.776A pdb=" N LYS B1440 " --> pdb=" O VAL B1436 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASP B1441 " --> pdb=" O THR B1437 " (cutoff:3.500A) Processing helix chain 'B' and resid 1448 through 1455 Processing helix chain 'B' and resid 1474 through 1486 removed outlier: 3.710A pdb=" N GLN B1478 " --> pdb=" O SER B1475 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N CYS B1481 " --> pdb=" O GLN B1478 " (cutoff:3.500A) Processing helix chain 'B' and resid 1491 through 1502 removed outlier: 3.714A pdb=" N ASN B1502 " --> pdb=" O ALA B1498 " (cutoff:3.500A) Processing helix chain 'B' and resid 1506 through 1522 removed outlier: 5.696A pdb=" N ASN B1510 " --> pdb=" O CYS B1507 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE B1513 " --> pdb=" O ASN B1510 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU B1516 " --> pdb=" O ILE B1513 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU B1520 " --> pdb=" O SER B1517 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL B1522 " --> pdb=" O ILE B1519 " (cutoff:3.500A) Processing helix chain 'B' and resid 1524 through 1527 Processing helix chain 'B' and resid 1535 through 1555 removed outlier: 3.640A pdb=" N ASN B1549 " --> pdb=" O ARG B1545 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N GLU B1552 " --> pdb=" O ASN B1548 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ARG B1553 " --> pdb=" O ASN B1549 " (cutoff:3.500A) Processing helix chain 'B' and resid 1558 through 1573 removed outlier: 3.916A pdb=" N ILE B1567 " --> pdb=" O GLU B1563 " (cutoff:3.500A) Processing helix chain 'B' and resid 1577 through 1586 Processing helix chain 'C' and resid 6 through 12 Processing helix chain 'C' and resid 17 through 32 Processing helix chain 'C' and resid 39 through 42 No H-bonds generated for 'chain 'C' and resid 39 through 42' Processing helix chain 'C' and resid 45 through 47 No H-bonds generated for 'chain 'C' and resid 45 through 47' Processing helix chain 'C' and resid 71 through 88 removed outlier: 3.590A pdb=" N ASN C 74 " --> pdb=" O LEU C 71 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LYS C 75 " --> pdb=" O SER C 72 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N ALA C 76 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 143 Processing helix chain 'C' and resid 153 through 156 No H-bonds generated for 'chain 'C' and resid 153 through 156' Processing helix chain 'C' and resid 159 through 162 No H-bonds generated for 'chain 'C' and resid 159 through 162' Processing helix chain 'C' and resid 166 through 173 removed outlier: 4.073A pdb=" N HIS C 171 " --> pdb=" O LYS C 167 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N PHE C 172 " --> pdb=" O ILE C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 193 Processing helix chain 'C' and resid 213 through 225 removed outlier: 3.634A pdb=" N VAL C 224 " --> pdb=" O HIS C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 249 removed outlier: 3.690A pdb=" N ILE C 243 " --> pdb=" O LYS C 239 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA C 249 " --> pdb=" O LYS C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 264 removed outlier: 3.759A pdb=" N PHE C 264 " --> pdb=" O ALA C 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 261 through 264' Processing helix chain 'C' and resid 269 through 272 Processing helix chain 'C' and resid 278 through 285 removed outlier: 4.105A pdb=" N HIS C 285 " --> pdb=" O PHE C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 303 Processing helix chain 'C' and resid 308 through 319 Processing helix chain 'C' and resid 330 through 342 removed outlier: 3.656A pdb=" N LEU C 333 " --> pdb=" O ASN C 330 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N ALA C 334 " --> pdb=" O ASN C 331 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP C 342 " --> pdb=" O ALA C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 368 Processing helix chain 'C' and resid 376 through 379 No H-bonds generated for 'chain 'C' and resid 376 through 379' Processing helix chain 'C' and resid 385 through 393 removed outlier: 3.669A pdb=" N ARG C 393 " --> pdb=" O SER C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 413 Processing helix chain 'C' and resid 419 through 435 Processing helix chain 'C' and resid 448 through 454 Processing helix chain 'C' and resid 470 through 486 Processing helix chain 'C' and resid 491 through 497 Processing helix chain 'C' and resid 502 through 517 Processing helix chain 'C' and resid 521 through 532 Proline residue: C 525 - end of helix removed outlier: 3.742A pdb=" N CYS C 532 " --> pdb=" O GLU C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 550 Processing helix chain 'C' and resid 554 through 560 removed outlier: 3.932A pdb=" N PHE C 558 " --> pdb=" O SER C 554 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN C 559 " --> pdb=" O SER C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 567 Processing helix chain 'C' and resid 571 through 583 Processing helix chain 'C' and resid 589 through 595 Processing helix chain 'C' and resid 616 through 626 Processing helix chain 'C' and resid 628 through 631 No H-bonds generated for 'chain 'C' and resid 628 through 631' Processing helix chain 'C' and resid 636 through 638 No H-bonds generated for 'chain 'C' and resid 636 through 638' Processing helix chain 'C' and resid 640 through 647 Processing helix chain 'C' and resid 654 through 672 Processing helix chain 'C' and resid 686 through 693 removed outlier: 3.766A pdb=" N GLY C 693 " --> pdb=" O THR C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 698 through 711 Processing helix chain 'C' and resid 721 through 729 Processing helix chain 'C' and resid 731 through 739 Proline residue: C 735 - end of helix Processing helix chain 'C' and resid 741 through 752 removed outlier: 3.708A pdb=" N GLN C 746 " --> pdb=" O GLU C 742 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 772 Processing helix chain 'C' and resid 776 through 781 removed outlier: 4.192A pdb=" N HIS C 779 " --> pdb=" O ARG C 776 " (cutoff:3.500A) Processing helix chain 'C' and resid 790 through 797 removed outlier: 3.984A pdb=" N LEU C 795 " --> pdb=" O TYR C 792 " (cutoff:3.500A) Processing helix chain 'C' and resid 799 through 818 Processing helix chain 'C' and resid 821 through 823 No H-bonds generated for 'chain 'C' and resid 821 through 823' Processing helix chain 'C' and resid 846 through 852 removed outlier: 3.905A pdb=" N SER C 851 " --> pdb=" O ARG C 847 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N TYR C 852 " --> pdb=" O LEU C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 860 through 876 Processing helix chain 'C' and resid 882 through 895 removed outlier: 3.570A pdb=" N ASN C 895 " --> pdb=" O PHE C 891 " (cutoff:3.500A) Processing helix chain 'C' and resid 899 through 911 removed outlier: 3.779A pdb=" N VAL C 904 " --> pdb=" O SER C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 917 through 925 removed outlier: 4.058A pdb=" N VAL C 922 " --> pdb=" O ASN C 918 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLN C 925 " --> pdb=" O LYS C 921 " (cutoff:3.500A) Processing helix chain 'C' and resid 928 through 947 removed outlier: 3.707A pdb=" N PHE C 932 " --> pdb=" O PHE C 929 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP C 933 " --> pdb=" O PHE C 930 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N HIS C 943 " --> pdb=" O ASP C 940 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N LYS C 944 " --> pdb=" O ARG C 941 " (cutoff:3.500A) Processing helix chain 'C' and resid 962 through 973 removed outlier: 3.802A pdb=" N ASP C 967 " --> pdb=" O LEU C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 975 through 978 Processing helix chain 'C' and resid 981 through 989 removed outlier: 4.147A pdb=" N GLN C 989 " --> pdb=" O ALA C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 998 through 1018 removed outlier: 3.934A pdb=" N GLN C1018 " --> pdb=" O LYS C1014 " (cutoff:3.500A) Processing helix chain 'C' and resid 1022 through 1024 No H-bonds generated for 'chain 'C' and resid 1022 through 1024' Processing helix chain 'C' and resid 1027 through 1037 Processing helix chain 'C' and resid 1041 through 1043 No H-bonds generated for 'chain 'C' and resid 1041 through 1043' Processing helix chain 'C' and resid 1065 through 1095 removed outlier: 3.759A pdb=" N LYS C1083 " --> pdb=" O SER C1079 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N TYR C1084 " --> pdb=" O GLU C1080 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N VAL C1085 " --> pdb=" O HIS C1081 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N THR C1086 " --> pdb=" O MET C1082 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N LEU C1087 " --> pdb=" O LYS C1083 " (cutoff:3.500A) Processing helix chain 'C' and resid 1099 through 1103 Processing helix chain 'C' and resid 1111 through 1126 Processing helix chain 'C' and resid 1131 through 1137 removed outlier: 3.819A pdb=" N LEU C1136 " --> pdb=" O ASP C1132 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1151 Processing helix chain 'C' and resid 1158 through 1176 removed outlier: 3.791A pdb=" N LYS C1173 " --> pdb=" O LEU C1169 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU C1174 " --> pdb=" O ALA C1170 " (cutoff:3.500A) Proline residue: C1175 - end of helix Processing helix chain 'C' and resid 1188 through 1201 removed outlier: 3.959A pdb=" N ALA C1194 " --> pdb=" O SER C1190 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU C1195 " --> pdb=" O ALA C1191 " (cutoff:3.500A) Proline residue: C1196 - end of helix Processing helix chain 'C' and resid 1203 through 1217 removed outlier: 3.689A pdb=" N ARG C1206 " --> pdb=" O PRO C1203 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLU C1207 " --> pdb=" O MET C1204 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU C1213 " --> pdb=" O LYS C1210 " (cutoff:3.500A) Processing helix chain 'C' and resid 1230 through 1240 Proline residue: C1234 - end of helix removed outlier: 3.707A pdb=" N HIS C1239 " --> pdb=" O MET C1236 " (cutoff:3.500A) Processing helix chain 'C' and resid 1246 through 1276 Proline residue: C1261 - end of helix removed outlier: 3.647A pdb=" N VAL C1264 " --> pdb=" O LYS C1260 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ILE C1265 " --> pdb=" O PRO C1261 " (cutoff:3.500A) Processing helix chain 'C' and resid 1287 through 1294 Processing helix chain 'C' and resid 1296 through 1304 Processing helix chain 'C' and resid 1320 through 1329 removed outlier: 4.037A pdb=" N LEU C1329 " --> pdb=" O THR C1325 " (cutoff:3.500A) Processing helix chain 'C' and resid 1337 through 1354 removed outlier: 3.549A pdb=" N LEU C1345 " --> pdb=" O LYS C1341 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS C1348 " --> pdb=" O SER C1344 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER C1353 " --> pdb=" O ARG C1349 " (cutoff:3.500A) Processing helix chain 'C' and resid 1359 through 1361 No H-bonds generated for 'chain 'C' and resid 1359 through 1361' Processing helix chain 'C' and resid 1365 through 1380 removed outlier: 3.781A pdb=" N ARG C1374 " --> pdb=" O SER C1370 " (cutoff:3.500A) Processing helix chain 'C' and resid 1387 through 1390 No H-bonds generated for 'chain 'C' and resid 1387 through 1390' Processing helix chain 'C' and resid 1392 through 1396 Processing helix chain 'C' and resid 1402 through 1418 removed outlier: 3.587A pdb=" N LEU C1407 " --> pdb=" O ILE C1404 " (cutoff:3.500A) Processing helix chain 'C' and resid 1421 through 1430 Processing helix chain 'C' and resid 1432 through 1441 removed outlier: 3.730A pdb=" N LYS C1440 " --> pdb=" O VAL C1436 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ASP C1441 " --> pdb=" O THR C1437 " (cutoff:3.500A) Processing helix chain 'C' and resid 1448 through 1455 Processing helix chain 'C' and resid 1474 through 1486 removed outlier: 3.577A pdb=" N GLN C1478 " --> pdb=" O SER C1475 " (cutoff:3.500A) Processing helix chain 'C' and resid 1491 through 1502 removed outlier: 3.642A pdb=" N ASN C1502 " --> pdb=" O ALA C1498 " (cutoff:3.500A) Processing helix chain 'C' and resid 1506 through 1522 removed outlier: 5.694A pdb=" N ASN C1510 " --> pdb=" O CYS C1507 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE C1513 " --> pdb=" O ASN C1510 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU C1516 " --> pdb=" O ILE C1513 " (cutoff:3.500A) Processing helix chain 'C' and resid 1524 through 1527 Processing helix chain 'C' and resid 1535 through 1556 removed outlier: 3.668A pdb=" N ASN C1548 " --> pdb=" O ARG C1544 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN C1549 " --> pdb=" O ARG C1545 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N GLU C1552 " --> pdb=" O ASN C1548 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ARG C1553 " --> pdb=" O ASN C1549 " (cutoff:3.500A) Processing helix chain 'C' and resid 1558 through 1573 removed outlier: 4.005A pdb=" N ILE C1567 " --> pdb=" O GLU C1563 " (cutoff:3.500A) Processing helix chain 'C' and resid 1577 through 1586 Processing helix chain 'D' and resid 6 through 12 Processing helix chain 'D' and resid 17 through 32 removed outlier: 3.557A pdb=" N TRP D 23 " --> pdb=" O GLY D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 88 removed outlier: 4.064A pdb=" N LYS D 75 " --> pdb=" O SER D 72 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ALA D 76 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE D 79 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS D 86 " --> pdb=" O GLU D 83 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS D 87 " --> pdb=" O LYS D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 144 Processing helix chain 'D' and resid 153 through 156 No H-bonds generated for 'chain 'D' and resid 153 through 156' Processing helix chain 'D' and resid 159 through 162 No H-bonds generated for 'chain 'D' and resid 159 through 162' Processing helix chain 'D' and resid 166 through 173 removed outlier: 3.880A pdb=" N HIS D 171 " --> pdb=" O LYS D 167 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE D 172 " --> pdb=" O ILE D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 196 removed outlier: 4.014A pdb=" N LEU D 183 " --> pdb=" O PHE D 180 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N LYS D 186 " --> pdb=" O LEU D 183 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU D 194 " --> pdb=" O GLU D 191 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR D 195 " --> pdb=" O ASN D 192 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU D 196 " --> pdb=" O VAL D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 225 removed outlier: 3.626A pdb=" N GLU D 217 " --> pdb=" O ARG D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 253 removed outlier: 3.619A pdb=" N ILE D 243 " --> pdb=" O LYS D 239 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N GLN D 252 " --> pdb=" O GLU D 248 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N TYR D 253 " --> pdb=" O ALA D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 264 removed outlier: 3.694A pdb=" N PHE D 264 " --> pdb=" O ALA D 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 261 through 264' Processing helix chain 'D' and resid 269 through 272 Processing helix chain 'D' and resid 278 through 285 removed outlier: 3.981A pdb=" N HIS D 285 " --> pdb=" O PHE D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 303 removed outlier: 3.566A pdb=" N LEU D 302 " --> pdb=" O GLU D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 319 Processing helix chain 'D' and resid 330 through 344 removed outlier: 5.260A pdb=" N ALA D 334 " --> pdb=" O ASN D 331 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP D 335 " --> pdb=" O TYR D 332 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU D 336 " --> pdb=" O LEU D 333 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ALA D 339 " --> pdb=" O LEU D 336 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE D 340 " --> pdb=" O ASN D 337 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE D 343 " --> pdb=" O PHE D 340 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TYR D 344 " --> pdb=" O ILE D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 368 Processing helix chain 'D' and resid 376 through 383 removed outlier: 3.790A pdb=" N LYS D 383 " --> pdb=" O LEU D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 393 Processing helix chain 'D' and resid 402 through 413 Processing helix chain 'D' and resid 419 through 435 Processing helix chain 'D' and resid 448 through 454 Processing helix chain 'D' and resid 470 through 486 Processing helix chain 'D' and resid 491 through 498 Processing helix chain 'D' and resid 502 through 515 Processing helix chain 'D' and resid 522 through 531 removed outlier: 3.780A pdb=" N PHE D 526 " --> pdb=" O SER D 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 549 Processing helix chain 'D' and resid 554 through 560 removed outlier: 3.655A pdb=" N PHE D 558 " --> pdb=" O SER D 554 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 567 Processing helix chain 'D' and resid 571 through 583 removed outlier: 3.600A pdb=" N THR D 577 " --> pdb=" O LEU D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 589 through 594 Processing helix chain 'D' and resid 616 through 626 Processing helix chain 'D' and resid 628 through 631 No H-bonds generated for 'chain 'D' and resid 628 through 631' Processing helix chain 'D' and resid 636 through 638 No H-bonds generated for 'chain 'D' and resid 636 through 638' Processing helix chain 'D' and resid 640 through 647 Processing helix chain 'D' and resid 654 through 672 Processing helix chain 'D' and resid 686 through 696 removed outlier: 3.694A pdb=" N GLY D 693 " --> pdb=" O THR D 689 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ALA D 695 " --> pdb=" O LEU D 691 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N MET D 696 " --> pdb=" O HIS D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 698 through 711 Processing helix chain 'D' and resid 721 through 729 Processing helix chain 'D' and resid 731 through 739 Proline residue: D 735 - end of helix Processing helix chain 'D' and resid 741 through 752 removed outlier: 3.725A pdb=" N GLN D 746 " --> pdb=" O GLU D 742 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 772 Processing helix chain 'D' and resid 776 through 781 removed outlier: 4.315A pdb=" N HIS D 779 " --> pdb=" O ARG D 776 " (cutoff:3.500A) Processing helix chain 'D' and resid 790 through 797 removed outlier: 3.908A pdb=" N LEU D 795 " --> pdb=" O TYR D 792 " (cutoff:3.500A) Processing helix chain 'D' and resid 799 through 818 Processing helix chain 'D' and resid 846 through 849 No H-bonds generated for 'chain 'D' and resid 846 through 849' Processing helix chain 'D' and resid 860 through 876 Processing helix chain 'D' and resid 882 through 895 removed outlier: 3.545A pdb=" N ASN D 895 " --> pdb=" O PHE D 891 " (cutoff:3.500A) Processing helix chain 'D' and resid 899 through 911 removed outlier: 3.823A pdb=" N VAL D 904 " --> pdb=" O SER D 900 " (cutoff:3.500A) Processing helix chain 'D' and resid 917 through 925 removed outlier: 3.994A pdb=" N VAL D 922 " --> pdb=" O ASN D 918 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLN D 925 " --> pdb=" O LYS D 921 " (cutoff:3.500A) Processing helix chain 'D' and resid 927 through 947 removed outlier: 3.685A pdb=" N PHE D 932 " --> pdb=" O PHE D 929 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASP D 933 " --> pdb=" O PHE D 930 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG D 941 " --> pdb=" O VAL D 938 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N HIS D 943 " --> pdb=" O ASP D 940 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N LYS D 944 " --> pdb=" O ARG D 941 " (cutoff:3.500A) Processing helix chain 'D' and resid 962 through 973 removed outlier: 3.743A pdb=" N ASP D 967 " --> pdb=" O LEU D 963 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP D 973 " --> pdb=" O ILE D 969 " (cutoff:3.500A) Processing helix chain 'D' and resid 975 through 978 Processing helix chain 'D' and resid 981 through 989 removed outlier: 4.159A pdb=" N GLN D 989 " --> pdb=" O ALA D 985 " (cutoff:3.500A) Processing helix chain 'D' and resid 998 through 1018 removed outlier: 4.084A pdb=" N GLN D1018 " --> pdb=" O LYS D1014 " (cutoff:3.500A) Processing helix chain 'D' and resid 1022 through 1024 No H-bonds generated for 'chain 'D' and resid 1022 through 1024' Processing helix chain 'D' and resid 1027 through 1038 Processing helix chain 'D' and resid 1041 through 1043 No H-bonds generated for 'chain 'D' and resid 1041 through 1043' Processing helix chain 'D' and resid 1065 through 1081 removed outlier: 3.645A pdb=" N TYR D1070 " --> pdb=" O LYS D1066 " (cutoff:3.500A) Processing helix chain 'D' and resid 1085 through 1095 Processing helix chain 'D' and resid 1099 through 1103 Processing helix chain 'D' and resid 1111 through 1126 Processing helix chain 'D' and resid 1131 through 1137 removed outlier: 3.927A pdb=" N LEU D1136 " --> pdb=" O ASP D1132 " (cutoff:3.500A) Processing helix chain 'D' and resid 1140 through 1151 Processing helix chain 'D' and resid 1158 through 1176 removed outlier: 3.848A pdb=" N LYS D1173 " --> pdb=" O LEU D1169 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU D1174 " --> pdb=" O ALA D1170 " (cutoff:3.500A) Proline residue: D1175 - end of helix Processing helix chain 'D' and resid 1188 through 1201 removed outlier: 3.891A pdb=" N ALA D1194 " --> pdb=" O SER D1190 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU D1195 " --> pdb=" O ALA D1191 " (cutoff:3.500A) Proline residue: D1196 - end of helix Processing helix chain 'D' and resid 1203 through 1217 removed outlier: 3.658A pdb=" N ARG D1206 " --> pdb=" O PRO D1203 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N GLU D1207 " --> pdb=" O MET D1204 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU D1213 " --> pdb=" O LYS D1210 " (cutoff:3.500A) Processing helix chain 'D' and resid 1230 through 1240 Proline residue: D1234 - end of helix removed outlier: 3.749A pdb=" N HIS D1239 " --> pdb=" O MET D1236 " (cutoff:3.500A) Processing helix chain 'D' and resid 1246 through 1276 Proline residue: D1261 - end of helix removed outlier: 3.596A pdb=" N VAL D1264 " --> pdb=" O LYS D1260 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE D1265 " --> pdb=" O PRO D1261 " (cutoff:3.500A) Processing helix chain 'D' and resid 1287 through 1294 Processing helix chain 'D' and resid 1296 through 1304 Processing helix chain 'D' and resid 1309 through 1311 No H-bonds generated for 'chain 'D' and resid 1309 through 1311' Processing helix chain 'D' and resid 1315 through 1317 No H-bonds generated for 'chain 'D' and resid 1315 through 1317' Processing helix chain 'D' and resid 1320 through 1329 removed outlier: 4.028A pdb=" N LEU D1329 " --> pdb=" O THR D1325 " (cutoff:3.500A) Processing helix chain 'D' and resid 1337 through 1354 removed outlier: 3.576A pdb=" N LEU D1345 " --> pdb=" O LYS D1341 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS D1348 " --> pdb=" O SER D1344 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER D1353 " --> pdb=" O ARG D1349 " (cutoff:3.500A) Processing helix chain 'D' and resid 1359 through 1361 No H-bonds generated for 'chain 'D' and resid 1359 through 1361' Processing helix chain 'D' and resid 1365 through 1380 removed outlier: 3.778A pdb=" N ARG D1374 " --> pdb=" O SER D1370 " (cutoff:3.500A) Processing helix chain 'D' and resid 1387 through 1390 No H-bonds generated for 'chain 'D' and resid 1387 through 1390' Processing helix chain 'D' and resid 1392 through 1396 Processing helix chain 'D' and resid 1402 through 1418 removed outlier: 3.657A pdb=" N LEU D1407 " --> pdb=" O ILE D1404 " (cutoff:3.500A) Processing helix chain 'D' and resid 1421 through 1430 Processing helix chain 'D' and resid 1432 through 1441 removed outlier: 3.765A pdb=" N LYS D1440 " --> pdb=" O VAL D1436 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ASP D1441 " --> pdb=" O THR D1437 " (cutoff:3.500A) Processing helix chain 'D' and resid 1448 through 1455 Processing helix chain 'D' and resid 1474 through 1486 removed outlier: 3.713A pdb=" N GLN D1478 " --> pdb=" O SER D1475 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N CYS D1481 " --> pdb=" O GLN D1478 " (cutoff:3.500A) Processing helix chain 'D' and resid 1491 through 1502 removed outlier: 3.692A pdb=" N ASN D1502 " --> pdb=" O ALA D1498 " (cutoff:3.500A) Processing helix chain 'D' and resid 1506 through 1522 removed outlier: 5.703A pdb=" N ASN D1510 " --> pdb=" O CYS D1507 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE D1513 " --> pdb=" O ASN D1510 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU D1516 " --> pdb=" O ILE D1513 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU D1520 " --> pdb=" O SER D1517 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL D1522 " --> pdb=" O ILE D1519 " (cutoff:3.500A) Processing helix chain 'D' and resid 1524 through 1527 Processing helix chain 'D' and resid 1535 through 1555 removed outlier: 3.583A pdb=" N ASN D1548 " --> pdb=" O ARG D1544 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN D1549 " --> pdb=" O ARG D1545 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N GLU D1552 " --> pdb=" O ASN D1548 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ARG D1553 " --> pdb=" O ASN D1549 " (cutoff:3.500A) Processing helix chain 'D' and resid 1558 through 1573 removed outlier: 3.901A pdb=" N ILE D1567 " --> pdb=" O GLU D1563 " (cutoff:3.500A) Processing helix chain 'D' and resid 1577 through 1586 Processing helix chain 'E' and resid 9 through 11 No H-bonds generated for 'chain 'E' and resid 9 through 11' Processing helix chain 'E' and resid 15 through 38 removed outlier: 4.447A pdb=" N ASN E 24 " --> pdb=" O ASP E 20 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ASP E 25 " --> pdb=" O ALA E 21 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ARG E 26 " --> pdb=" O LEU E 22 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASN E 27 " --> pdb=" O LYS E 23 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N SER E 28 " --> pdb=" O ASN E 24 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N TYR E 29 " --> pdb=" O ASP E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 44 No H-bonds generated for 'chain 'E' and resid 42 through 44' Processing helix chain 'E' and resid 63 through 78 removed outlier: 3.573A pdb=" N LEU E 77 " --> pdb=" O SER E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 100 removed outlier: 3.680A pdb=" N GLN E 97 " --> pdb=" O PHE E 93 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ALA E 100 " --> pdb=" O LYS E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 125 Processing helix chain 'E' and resid 128 through 142 Processing helix chain 'E' and resid 164 through 166 No H-bonds generated for 'chain 'E' and resid 164 through 166' Processing helix chain 'E' and resid 188 through 190 No H-bonds generated for 'chain 'E' and resid 188 through 190' Processing helix chain 'E' and resid 193 through 199 removed outlier: 4.088A pdb=" N MET E 199 " --> pdb=" O VAL E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 248 No H-bonds generated for 'chain 'E' and resid 246 through 248' Processing helix chain 'E' and resid 269 through 291 removed outlier: 3.654A pdb=" N LEU E 273 " --> pdb=" O GLU E 270 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N GLY E 274 " --> pdb=" O GLU E 271 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG E 277 " --> pdb=" O GLY E 274 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLU E 280 " --> pdb=" O ARG E 277 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU E 284 " --> pdb=" O ASN E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 312 Processing helix chain 'E' and resid 324 through 326 No H-bonds generated for 'chain 'E' and resid 324 through 326' Processing helix chain 'E' and resid 338 through 355 Processing helix chain 'E' and resid 376 through 380 Processing helix chain 'E' and resid 383 through 395 removed outlier: 4.159A pdb=" N GLY E 387 " --> pdb=" O ASP E 383 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N VAL E 388 " --> pdb=" O THR E 384 " (cutoff:3.500A) Processing helix chain 'E' and resid 397 through 410 Processing helix chain 'E' and resid 434 through 440 Processing helix chain 'E' and resid 443 through 451 Processing helix chain 'F' and resid 9 through 13 removed outlier: 4.556A pdb=" N ASN F 13 " --> pdb=" O PHE F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 38 removed outlier: 4.586A pdb=" N ASN F 24 " --> pdb=" O ASP F 20 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ASP F 25 " --> pdb=" O ALA F 21 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ARG F 26 " --> pdb=" O LEU F 22 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASN F 27 " --> pdb=" O LYS F 23 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N SER F 28 " --> pdb=" O ASN F 24 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N TYR F 29 " --> pdb=" O ASP F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 44 No H-bonds generated for 'chain 'F' and resid 42 through 44' Processing helix chain 'F' and resid 63 through 78 Processing helix chain 'F' and resid 92 through 100 removed outlier: 3.646A pdb=" N GLN F 97 " --> pdb=" O PHE F 93 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N ALA F 100 " --> pdb=" O LYS F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 125 removed outlier: 3.574A pdb=" N GLY F 111 " --> pdb=" O LYS F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 142 Processing helix chain 'F' and resid 164 through 166 No H-bonds generated for 'chain 'F' and resid 164 through 166' Processing helix chain 'F' and resid 188 through 190 No H-bonds generated for 'chain 'F' and resid 188 through 190' Processing helix chain 'F' and resid 193 through 199 removed outlier: 3.621A pdb=" N MET F 199 " --> pdb=" O VAL F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 248 No H-bonds generated for 'chain 'F' and resid 246 through 248' Processing helix chain 'F' and resid 269 through 291 removed outlier: 3.708A pdb=" N LEU F 273 " --> pdb=" O GLU F 270 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N GLY F 274 " --> pdb=" O GLU F 271 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG F 277 " --> pdb=" O GLY F 274 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLU F 280 " --> pdb=" O ARG F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 312 Processing helix chain 'F' and resid 338 through 355 Processing helix chain 'F' and resid 376 through 381 removed outlier: 3.733A pdb=" N LEU F 381 " --> pdb=" O ALA F 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 395 removed outlier: 3.702A pdb=" N GLY F 387 " --> pdb=" O ASP F 383 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL F 388 " --> pdb=" O THR F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 410 Processing helix chain 'F' and resid 434 through 440 removed outlier: 3.673A pdb=" N ASP F 438 " --> pdb=" O GLY F 434 " (cutoff:3.500A) Processing helix chain 'F' and resid 443 through 451 Processing helix chain 'G' and resid 9 through 11 No H-bonds generated for 'chain 'G' and resid 9 through 11' Processing helix chain 'G' and resid 15 through 38 removed outlier: 4.444A pdb=" N ASN G 24 " --> pdb=" O ASP G 20 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ASP G 25 " --> pdb=" O ALA G 21 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ARG G 26 " --> pdb=" O LEU G 22 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ASN G 27 " --> pdb=" O LYS G 23 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N SER G 28 " --> pdb=" O ASN G 24 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N TYR G 29 " --> pdb=" O ASP G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 44 No H-bonds generated for 'chain 'G' and resid 42 through 44' Processing helix chain 'G' and resid 63 through 78 removed outlier: 3.614A pdb=" N LEU G 77 " --> pdb=" O SER G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 100 removed outlier: 3.712A pdb=" N GLN G 97 " --> pdb=" O PHE G 93 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N ALA G 100 " --> pdb=" O LYS G 96 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 125 Processing helix chain 'G' and resid 128 through 142 Processing helix chain 'G' and resid 164 through 166 No H-bonds generated for 'chain 'G' and resid 164 through 166' Processing helix chain 'G' and resid 188 through 190 No H-bonds generated for 'chain 'G' and resid 188 through 190' Processing helix chain 'G' and resid 193 through 198 Processing helix chain 'G' and resid 246 through 248 No H-bonds generated for 'chain 'G' and resid 246 through 248' Processing helix chain 'G' and resid 269 through 291 removed outlier: 3.635A pdb=" N LEU G 273 " --> pdb=" O GLU G 270 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N GLY G 274 " --> pdb=" O GLU G 271 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG G 277 " --> pdb=" O GLY G 274 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLU G 280 " --> pdb=" O ARG G 277 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU G 284 " --> pdb=" O ASN G 281 " (cutoff:3.500A) Processing helix chain 'G' and resid 308 through 312 Processing helix chain 'G' and resid 324 through 326 No H-bonds generated for 'chain 'G' and resid 324 through 326' Processing helix chain 'G' and resid 338 through 355 Processing helix chain 'G' and resid 376 through 380 Processing helix chain 'G' and resid 383 through 395 removed outlier: 4.022A pdb=" N GLY G 387 " --> pdb=" O ASP G 383 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N VAL G 388 " --> pdb=" O THR G 384 " (cutoff:3.500A) Processing helix chain 'G' and resid 397 through 410 Processing helix chain 'G' and resid 434 through 440 Processing helix chain 'G' and resid 443 through 452 Processing helix chain 'H' and resid 9 through 11 No H-bonds generated for 'chain 'H' and resid 9 through 11' Processing helix chain 'H' and resid 15 through 38 removed outlier: 4.606A pdb=" N ASN H 24 " --> pdb=" O ASP H 20 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ASP H 25 " --> pdb=" O ALA H 21 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ARG H 26 " --> pdb=" O LEU H 22 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ASN H 27 " --> pdb=" O LYS H 23 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N SER H 28 " --> pdb=" O ASN H 24 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N TYR H 29 " --> pdb=" O ASP H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 44 No H-bonds generated for 'chain 'H' and resid 42 through 44' Processing helix chain 'H' and resid 63 through 78 Processing helix chain 'H' and resid 92 through 100 removed outlier: 3.655A pdb=" N GLN H 97 " --> pdb=" O PHE H 93 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N ALA H 100 " --> pdb=" O LYS H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 125 removed outlier: 3.561A pdb=" N GLY H 111 " --> pdb=" O LYS H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 142 Processing helix chain 'H' and resid 164 through 166 No H-bonds generated for 'chain 'H' and resid 164 through 166' Processing helix chain 'H' and resid 188 through 190 No H-bonds generated for 'chain 'H' and resid 188 through 190' Processing helix chain 'H' and resid 193 through 198 Processing helix chain 'H' and resid 246 through 248 No H-bonds generated for 'chain 'H' and resid 246 through 248' Processing helix chain 'H' and resid 269 through 291 removed outlier: 3.699A pdb=" N LEU H 273 " --> pdb=" O GLU H 270 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N GLY H 274 " --> pdb=" O GLU H 271 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG H 277 " --> pdb=" O GLY H 274 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU H 280 " --> pdb=" O ARG H 277 " (cutoff:3.500A) Processing helix chain 'H' and resid 308 through 312 Processing helix chain 'H' and resid 338 through 355 Processing helix chain 'H' and resid 376 through 381 removed outlier: 3.726A pdb=" N LEU H 381 " --> pdb=" O ALA H 378 " (cutoff:3.500A) Processing helix chain 'H' and resid 383 through 395 removed outlier: 4.033A pdb=" N VAL H 388 " --> pdb=" O THR H 384 " (cutoff:3.500A) Processing helix chain 'H' and resid 397 through 410 Processing helix chain 'H' and resid 434 through 439 removed outlier: 3.720A pdb=" N ASP H 438 " --> pdb=" O GLY H 434 " (cutoff:3.500A) Processing helix chain 'H' and resid 443 through 452 Processing sheet with id= A, first strand: chain 'A' and resid 53 through 55 removed outlier: 6.418A pdb=" N LYS A 94 " --> pdb=" O GLY A 61 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N GLN A 63 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ILE A 96 " --> pdb=" O GLN A 63 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N LYS A 65 " --> pdb=" O ILE A 96 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TYR A 98 " --> pdb=" O LYS A 65 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N GLU A 147 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N PHE A 97 " --> pdb=" O GLU A 147 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL A 149 " --> pdb=" O PHE A 97 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N THR A 99 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ARG A 151 " --> pdb=" O THR A 99 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 201 through 203 Processing sheet with id= C, first strand: chain 'A' and resid 349 through 352 removed outlier: 6.611A pdb=" N VAL A 324 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N VAL A 231 " --> pdb=" O VAL A 324 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N PHE A 326 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N VAL A 294 " --> pdb=" O PRO A 255 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N TYR A 257 " --> pdb=" O VAL A 294 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ASP A 296 " --> pdb=" O TYR A 257 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N PHE A 259 " --> pdb=" O ASP A 296 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 458 through 461 Processing sheet with id= E, first strand: chain 'A' and resid 585 through 587 Processing sheet with id= F, first strand: chain 'A' and resid 1044 through 1051 Processing sheet with id= G, first strand: chain 'A' and resid 828 through 835 removed outlier: 6.827A pdb=" N LYS A 838 " --> pdb=" O ILE A 834 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 53 through 55 removed outlier: 6.454A pdb=" N LYS B 94 " --> pdb=" O GLY B 61 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N GLN B 63 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ILE B 96 " --> pdb=" O GLN B 63 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N LYS B 65 " --> pdb=" O ILE B 96 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N TYR B 98 " --> pdb=" O LYS B 65 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLU B 147 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N PHE B 97 " --> pdb=" O GLU B 147 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL B 149 " --> pdb=" O PHE B 97 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N THR B 99 " --> pdb=" O VAL B 149 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ARG B 151 " --> pdb=" O THR B 99 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 201 through 203 Processing sheet with id= J, first strand: chain 'B' and resid 349 through 352 removed outlier: 6.652A pdb=" N VAL B 324 " --> pdb=" O VAL B 229 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N VAL B 231 " --> pdb=" O VAL B 324 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N PHE B 326 " --> pdb=" O VAL B 231 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N GLY B 233 " --> pdb=" O PHE B 326 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N THR B 328 " --> pdb=" O GLY B 233 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N VAL B 294 " --> pdb=" O PRO B 255 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N TYR B 257 " --> pdb=" O VAL B 294 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ASP B 296 " --> pdb=" O TYR B 257 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N PHE B 259 " --> pdb=" O ASP B 296 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 458 through 461 Processing sheet with id= L, first strand: chain 'B' and resid 585 through 587 Processing sheet with id= M, first strand: chain 'B' and resid 1044 through 1051 Processing sheet with id= N, first strand: chain 'B' and resid 828 through 835 removed outlier: 6.772A pdb=" N LYS B 838 " --> pdb=" O ILE B 834 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 53 through 55 removed outlier: 6.395A pdb=" N LYS C 94 " --> pdb=" O GLY C 61 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N GLN C 63 " --> pdb=" O LYS C 94 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ILE C 96 " --> pdb=" O GLN C 63 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N LYS C 65 " --> pdb=" O ILE C 96 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TYR C 98 " --> pdb=" O LYS C 65 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLU C 147 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N PHE C 97 " --> pdb=" O GLU C 147 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL C 149 " --> pdb=" O PHE C 97 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N THR C 99 " --> pdb=" O VAL C 149 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ARG C 151 " --> pdb=" O THR C 99 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 201 through 203 Processing sheet with id= Q, first strand: chain 'C' and resid 349 through 352 removed outlier: 6.619A pdb=" N VAL C 324 " --> pdb=" O VAL C 229 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N VAL C 231 " --> pdb=" O VAL C 324 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N PHE C 326 " --> pdb=" O VAL C 231 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N VAL C 294 " --> pdb=" O PRO C 255 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N TYR C 257 " --> pdb=" O VAL C 294 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ASP C 296 " --> pdb=" O TYR C 257 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N PHE C 259 " --> pdb=" O ASP C 296 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 458 through 461 Processing sheet with id= S, first strand: chain 'C' and resid 585 through 587 Processing sheet with id= T, first strand: chain 'C' and resid 1044 through 1051 Processing sheet with id= U, first strand: chain 'C' and resid 828 through 835 removed outlier: 6.827A pdb=" N LYS C 838 " --> pdb=" O ILE C 834 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 53 through 55 removed outlier: 6.456A pdb=" N LYS D 94 " --> pdb=" O GLY D 61 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N GLN D 63 " --> pdb=" O LYS D 94 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ILE D 96 " --> pdb=" O GLN D 63 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N LYS D 65 " --> pdb=" O ILE D 96 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N TYR D 98 " --> pdb=" O LYS D 65 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N GLU D 147 " --> pdb=" O ILE D 95 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N PHE D 97 " --> pdb=" O GLU D 147 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N VAL D 149 " --> pdb=" O PHE D 97 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N THR D 99 " --> pdb=" O VAL D 149 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ARG D 151 " --> pdb=" O THR D 99 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 201 through 203 Processing sheet with id= X, first strand: chain 'D' and resid 349 through 352 removed outlier: 6.638A pdb=" N VAL D 324 " --> pdb=" O VAL D 229 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N VAL D 231 " --> pdb=" O VAL D 324 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N PHE D 326 " --> pdb=" O VAL D 231 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N GLY D 233 " --> pdb=" O PHE D 326 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N THR D 328 " --> pdb=" O GLY D 233 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N VAL D 294 " --> pdb=" O PRO D 255 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TYR D 257 " --> pdb=" O VAL D 294 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N ASP D 296 " --> pdb=" O TYR D 257 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N PHE D 259 " --> pdb=" O ASP D 296 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 458 through 461 Processing sheet with id= Z, first strand: chain 'D' and resid 585 through 587 Processing sheet with id= AA, first strand: chain 'D' and resid 1044 through 1051 Processing sheet with id= AB, first strand: chain 'D' and resid 828 through 835 removed outlier: 6.773A pdb=" N LYS D 838 " --> pdb=" O ILE D 834 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'E' and resid 86 through 90 Processing sheet with id= AD, first strand: chain 'E' and resid 251 through 255 Processing sheet with id= AE, first strand: chain 'E' and resid 242 through 245 removed outlier: 3.531A pdb=" N THR E 186 " --> pdb=" O ILE E 211 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N LEU E 178 " --> pdb=" O LEU E 219 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLN E 170 " --> pdb=" O LEU E 178 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ILE E 180 " --> pdb=" O VAL E 168 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL E 168 " --> pdb=" O ILE E 180 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'E' and resid 298 through 300 Processing sheet with id= AG, first strand: chain 'F' and resid 251 through 255 Processing sheet with id= AH, first strand: chain 'F' and resid 242 through 245 removed outlier: 3.567A pdb=" N THR F 186 " --> pdb=" O ILE F 211 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N LEU F 178 " --> pdb=" O LEU F 219 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLN F 170 " --> pdb=" O LEU F 178 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ILE F 180 " --> pdb=" O VAL F 168 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL F 168 " --> pdb=" O ILE F 180 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'F' and resid 298 through 300 Processing sheet with id= AJ, first strand: chain 'G' and resid 86 through 90 Processing sheet with id= AK, first strand: chain 'G' and resid 251 through 255 Processing sheet with id= AL, first strand: chain 'G' and resid 242 through 245 removed outlier: 8.021A pdb=" N LEU G 178 " --> pdb=" O LEU G 219 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLN G 170 " --> pdb=" O LEU G 178 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ILE G 180 " --> pdb=" O VAL G 168 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL G 168 " --> pdb=" O ILE G 180 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'G' and resid 298 through 300 Processing sheet with id= AN, first strand: chain 'H' and resid 251 through 255 Processing sheet with id= AO, first strand: chain 'H' and resid 242 through 245 removed outlier: 3.529A pdb=" N THR H 186 " --> pdb=" O ILE H 211 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N LEU H 178 " --> pdb=" O LEU H 219 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLN H 170 " --> pdb=" O LEU H 178 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ILE H 180 " --> pdb=" O VAL H 168 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL H 168 " --> pdb=" O ILE H 180 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'H' and resid 298 through 300 2961 hydrogen bonds defined for protein. 7299 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: 28.45 Time building geometry restraints manager: 20.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.44 - 0.77: 1 0.77 - 1.09: 1 1.09 - 1.41: 27692 1.41 - 1.73: 38334 1.73 - 2.06: 366 Warning: very small bond lengths. Bond restraints: 66394 Sorted by residual: bond pdb=" CG PRO E 324 " pdb=" CD PRO E 324 " ideal model delta sigma weight residual 1.503 0.445 1.058 3.40e-02 8.65e+02 9.68e+02 bond pdb=" CG PRO G 454 " pdb=" CD PRO G 454 " ideal model delta sigma weight residual 1.503 0.852 0.651 3.40e-02 8.65e+02 3.67e+02 bond pdb=" C PHE E 80 " pdb=" O PHE E 80 " ideal model delta sigma weight residual 1.235 1.288 -0.053 4.70e-03 4.53e+04 1.29e+02 bond pdb=" CB PRO E 324 " pdb=" CG PRO E 324 " ideal model delta sigma weight residual 1.492 2.056 -0.564 5.00e-02 4.00e+02 1.27e+02 bond pdb=" CG PRO F 324 " pdb=" CD PRO F 324 " ideal model delta sigma weight residual 1.503 1.124 0.379 3.40e-02 8.65e+02 1.24e+02 ... (remaining 66389 not shown) Histogram of bond angle deviations from ideal: 0.07 - 28.54: 1 28.54 - 57.02: 0 57.02 - 85.49: 3 85.49 - 113.96: 36875 113.96 - 142.43: 52909 Bond angle restraints: 89788 Sorted by residual: angle pdb=" CB PRO E 324 " pdb=" CG PRO E 324 " pdb=" CD PRO E 324 " ideal model delta sigma weight residual 106.10 0.07 106.03 3.20e+00 9.77e-02 1.10e+03 angle pdb=" N PRO G 454 " pdb=" CD PRO G 454 " pdb=" CG PRO G 454 " ideal model delta sigma weight residual 103.20 72.77 30.43 1.50e+00 4.44e-01 4.12e+02 angle pdb=" CA PRO E 324 " pdb=" N PRO E 324 " pdb=" CD PRO E 324 " ideal model delta sigma weight residual 112.00 90.20 21.80 1.40e+00 5.10e-01 2.42e+02 angle pdb=" CA PRO G 454 " pdb=" CB PRO G 454 " pdb=" CG PRO G 454 " ideal model delta sigma weight residual 104.50 82.49 22.01 1.90e+00 2.77e-01 1.34e+02 angle pdb=" N PRO F 324 " pdb=" CD PRO F 324 " pdb=" CG PRO F 324 " ideal model delta sigma weight residual 103.20 85.88 17.32 1.50e+00 4.44e-01 1.33e+02 ... (remaining 89783 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 36513 17.99 - 35.99: 2603 35.99 - 53.98: 570 53.98 - 71.97: 146 71.97 - 89.97: 88 Dihedral angle restraints: 39920 sinusoidal: 16506 harmonic: 23414 Sorted by residual: dihedral pdb=" CA ASP A 445 " pdb=" C ASP A 445 " pdb=" N THR A 446 " pdb=" CA THR A 446 " ideal model delta harmonic sigma weight residual 180.00 -150.15 -29.85 0 5.00e+00 4.00e-02 3.56e+01 dihedral pdb=" CA ASP C 445 " pdb=" C ASP C 445 " pdb=" N THR C 446 " pdb=" CA THR C 446 " ideal model delta harmonic sigma weight residual -180.00 -150.19 -29.81 0 5.00e+00 4.00e-02 3.55e+01 dihedral pdb=" CA LEU H 330 " pdb=" C LEU H 330 " pdb=" N GLN H 331 " pdb=" CA GLN H 331 " ideal model delta harmonic sigma weight residual -180.00 -153.07 -26.93 0 5.00e+00 4.00e-02 2.90e+01 ... (remaining 39917 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 8118 0.076 - 0.152: 1554 0.152 - 0.228: 145 0.228 - 0.304: 20 0.304 - 0.379: 5 Chirality restraints: 9842 Sorted by residual: chirality pdb=" CG LEU H 398 " pdb=" CB LEU H 398 " pdb=" CD1 LEU H 398 " pdb=" CD2 LEU H 398 " both_signs ideal model delta sigma weight residual False -2.59 -2.97 0.38 2.00e-01 2.50e+01 3.60e+00 chirality pdb=" CG LEU G 398 " pdb=" CB LEU G 398 " pdb=" CD1 LEU G 398 " pdb=" CD2 LEU G 398 " both_signs ideal model delta sigma weight residual False -2.59 -2.92 0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" CG LEU E 398 " pdb=" CB LEU E 398 " pdb=" CD1 LEU E 398 " pdb=" CD2 LEU E 398 " both_signs ideal model delta sigma weight residual False -2.59 -2.91 0.32 2.00e-01 2.50e+01 2.53e+00 ... (remaining 9839 not shown) Planarity restraints: 11402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG F 323 " -0.094 5.00e-02 4.00e+02 1.32e-01 2.77e+01 pdb=" N PRO F 324 " 0.227 5.00e-02 4.00e+02 pdb=" CA PRO F 324 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO F 324 " -0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP A1143 " -0.026 2.00e-02 2.50e+03 5.24e-02 2.75e+01 pdb=" CG ASP A1143 " 0.091 2.00e-02 2.50e+03 pdb=" OD1 ASP A1143 " -0.033 2.00e-02 2.50e+03 pdb=" OD2 ASP A1143 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP C1143 " -0.026 2.00e-02 2.50e+03 5.17e-02 2.67e+01 pdb=" CG ASP C1143 " 0.089 2.00e-02 2.50e+03 pdb=" OD1 ASP C1143 " -0.032 2.00e-02 2.50e+03 pdb=" OD2 ASP C1143 " -0.031 2.00e-02 2.50e+03 ... (remaining 11399 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 333 2.65 - 3.21: 58440 3.21 - 3.78: 91966 3.78 - 4.34: 133017 4.34 - 4.90: 216479 Nonbonded interactions: 500235 Sorted by model distance: nonbonded pdb=" O2B ATP B1601 " pdb="MG MG B1602 " model vdw 2.088 2.170 nonbonded pdb=" O2B ATP D1601 " pdb="MG MG D1602 " model vdw 2.091 2.170 nonbonded pdb=" OG1 THR C1026 " pdb=" OE1 GLU C1027 " model vdw 2.127 2.440 nonbonded pdb=" O1G ATP A1601 " pdb="MG MG A1602 " model vdw 2.128 2.170 nonbonded pdb=" O1G ATP C1601 " pdb="MG MG C1602 " model vdw 2.130 2.170 ... (remaining 500230 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 'A' and (resid 2 through 103 or resid 130 through 1587 or resid 1601 thro \ ugh 1602)) selection = chain 'B' selection = (chain 'C' and (resid 2 through 103 or resid 130 through 1587 or resid 1601 thro \ ugh 1602)) selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 12.480 Check model and map are aligned: 0.740 Set scattering table: 0.470 Process input model: 135.440 Find NCS groups from input model: 4.020 Set up NCS constraints: 0.370 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: 0.030 Load rotamer database and sin/cos tables:11.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 167.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5479 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 : 0.009 1.058 66394 Z= 0.646 Angle : 1.207 106.028 89788 Z= 0.651 Chirality : 0.060 0.379 9842 Planarity : 0.009 0.132 11402 Dihedral : 14.260 89.966 24760 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 1.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.53 % Allowed : 8.87 % Favored : 90.60 % 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: -0.06 (0.09), residues: 7844 helix: 0.01 (0.07), residues: 4658 sheet: 0.00 (0.20), residues: 624 loop : 0.21 (0.12), residues: 2562 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 991 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 953 time to evaluate : 6.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 3 residues processed: 983 average time/residue: 1.4368 time to fit residues: 1830.9686 Evaluate side-chains 394 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 391 time to evaluate : 5.477 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 7.9957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 663 optimal weight: 7.9990 chunk 595 optimal weight: 7.9990 chunk 330 optimal weight: 0.9980 chunk 203 optimal weight: 2.9990 chunk 401 optimal weight: 6.9990 chunk 318 optimal weight: 5.9990 chunk 616 optimal weight: 40.0000 chunk 238 optimal weight: 7.9990 chunk 374 optimal weight: 3.9990 chunk 458 optimal weight: 0.9990 chunk 713 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 627 ASN A 987 HIS ** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1533 ASN B 139 GLN B 648 GLN ** B 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1272 HIS ** C 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 987 HIS ** C1321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 ASN E 144 ASN E 281 ASN ** E 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 413 GLN ** G 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 70 ASN G 144 ASN G 281 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5518 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 66394 Z= 0.213 Angle : 0.611 11.032 89788 Z= 0.326 Chirality : 0.043 0.259 9842 Planarity : 0.005 0.057 11402 Dihedral : 5.340 38.512 8624 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.86 % Allowed : 11.98 % Favored : 85.15 % 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: 0.44 (0.09), residues: 7844 helix: 0.55 (0.07), residues: 4620 sheet: -0.02 (0.19), residues: 690 loop : 0.18 (0.13), residues: 2534 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 496 time to evaluate : 5.489 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 outliers start: 205 outliers final: 37 residues processed: 649 average time/residue: 1.4090 time to fit residues: 1208.3791 Evaluate side-chains 405 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 368 time to evaluate : 5.539 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 33 residues processed: 4 average time/residue: 1.3783 time to fit residues: 15.2937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 396 optimal weight: 30.0000 chunk 221 optimal weight: 7.9990 chunk 594 optimal weight: 0.1980 chunk 486 optimal weight: 8.9990 chunk 196 optimal weight: 1.9990 chunk 715 optimal weight: 30.0000 chunk 772 optimal weight: 5.9990 chunk 636 optimal weight: 20.0000 chunk 709 optimal weight: 20.0000 chunk 243 optimal weight: 10.0000 chunk 573 optimal weight: 30.0000 overall best weight: 5.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN A 276 HIS A 521 GLN ** A 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1533 ASN ** B 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 ASN C 276 HIS ** C 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 647 ASN ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 559 ASN ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 ASN E 157 ASN ** E 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 101 GLN G 121 ASN ** G 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5585 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 66394 Z= 0.328 Angle : 0.676 12.095 89788 Z= 0.354 Chirality : 0.045 0.291 9842 Planarity : 0.005 0.056 11402 Dihedral : 5.329 50.546 8624 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.25 % Allowed : 13.16 % Favored : 83.59 % 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: 0.06 (0.09), residues: 7844 helix: 0.32 (0.07), residues: 4652 sheet: -0.07 (0.19), residues: 662 loop : -0.19 (0.12), residues: 2530 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 402 time to evaluate : 5.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 233 outliers final: 77 residues processed: 586 average time/residue: 1.4023 time to fit residues: 1080.9654 Evaluate side-chains 427 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 350 time to evaluate : 5.622 Switching outliers to nearest non-outliers outliers start: 77 outliers final: 68 residues processed: 9 average time/residue: 1.3932 time to fit residues: 24.6557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 706 optimal weight: 20.0000 chunk 537 optimal weight: 1.9990 chunk 371 optimal weight: 6.9990 chunk 79 optimal weight: 30.0000 chunk 341 optimal weight: 1.9990 chunk 480 optimal weight: 6.9990 chunk 717 optimal weight: 5.9990 chunk 759 optimal weight: 20.0000 chunk 374 optimal weight: 8.9990 chunk 680 optimal weight: 20.0000 chunk 204 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN ** A 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 987 HIS ** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1533 ASN ** B 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 ASN ** C 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 987 HIS C1137 ASN ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 648 GLN D 692 HIS ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 GLN ** E 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 69 ASN G 407 GLN H 70 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5577 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 66394 Z= 0.240 Angle : 0.576 11.238 89788 Z= 0.302 Chirality : 0.042 0.215 9842 Planarity : 0.005 0.057 11402 Dihedral : 5.047 49.214 8624 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.81 % Allowed : 14.29 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.09), residues: 7844 helix: 0.44 (0.08), residues: 4648 sheet: -0.02 (0.20), residues: 662 loop : -0.31 (0.12), residues: 2534 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 410 time to evaluate : 5.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 201 outliers final: 97 residues processed: 577 average time/residue: 1.3726 time to fit residues: 1057.3845 Evaluate side-chains 428 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 331 time to evaluate : 5.533 Switching outliers to nearest non-outliers outliers start: 97 outliers final: 85 residues processed: 14 average time/residue: 1.0293 time to fit residues: 28.4992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 632 optimal weight: 0.6980 chunk 431 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 565 optimal weight: 3.9990 chunk 313 optimal weight: 1.9990 chunk 648 optimal weight: 3.9990 chunk 525 optimal weight: 0.0970 chunk 0 optimal weight: 8.9990 chunk 387 optimal weight: 6.9990 chunk 681 optimal weight: 7.9990 chunk 191 optimal weight: 3.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1137 ASN A1297 HIS A1533 ASN ** B 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 627 ASN C 716 HIS C1297 HIS ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 83 GLN ** G 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5565 moved from start: 0.4037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 66394 Z= 0.177 Angle : 0.525 15.949 89788 Z= 0.274 Chirality : 0.040 0.235 9842 Planarity : 0.004 0.049 11402 Dihedral : 4.816 47.312 8624 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.77 % Allowed : 14.93 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.10), residues: 7844 helix: 0.60 (0.08), residues: 4666 sheet: 0.09 (0.20), residues: 658 loop : -0.25 (0.12), residues: 2520 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 382 time to evaluate : 5.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 198 outliers final: 101 residues processed: 550 average time/residue: 1.3463 time to fit residues: 986.0746 Evaluate side-chains 448 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 347 time to evaluate : 5.455 Switching outliers to nearest non-outliers outliers start: 101 outliers final: 93 residues processed: 9 average time/residue: 0.9984 time to fit residues: 20.7385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 255 optimal weight: 0.8980 chunk 684 optimal weight: 6.9990 chunk 150 optimal weight: 1.9990 chunk 446 optimal weight: 20.0000 chunk 187 optimal weight: 3.9990 chunk 760 optimal weight: 7.9990 chunk 631 optimal weight: 5.9990 chunk 352 optimal weight: 0.7980 chunk 63 optimal weight: 10.0000 chunk 251 optimal weight: 2.9990 chunk 399 optimal weight: 5.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 637 ASN ** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1533 ASN ** B 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1137 ASN ** C 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 779 HIS ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 925 GLN E 69 ASN ** E 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 83 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5565 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 66394 Z= 0.172 Angle : 0.517 16.613 89788 Z= 0.269 Chirality : 0.040 0.213 9842 Planarity : 0.004 0.048 11402 Dihedral : 4.689 50.323 8624 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.74 % Allowed : 15.42 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.10), residues: 7844 helix: 0.69 (0.08), residues: 4666 sheet: 0.15 (0.20), residues: 666 loop : -0.23 (0.13), residues: 2512 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 376 time to evaluate : 5.511 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 outliers start: 196 outliers final: 112 residues processed: 550 average time/residue: 1.3261 time to fit residues: 987.4914 Evaluate side-chains 453 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 341 time to evaluate : 5.499 Switching outliers to nearest non-outliers outliers start: 112 outliers final: 106 residues processed: 6 average time/residue: 0.7895 time to fit residues: 15.4745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 733 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 433 optimal weight: 2.9990 chunk 555 optimal weight: 4.9990 chunk 430 optimal weight: 8.9990 chunk 640 optimal weight: 6.9990 chunk 424 optimal weight: 9.9990 chunk 757 optimal weight: 7.9990 chunk 474 optimal weight: 0.6980 chunk 461 optimal weight: 0.0000 chunk 349 optimal weight: 4.9990 overall best weight: 2.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1533 ASN ** B 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 925 GLN B1110 ASN ** C 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 637 ASN ** C 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1137 ASN E 407 GLN ** E 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5577 moved from start: 0.4460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 66394 Z= 0.197 Angle : 0.539 12.492 89788 Z= 0.279 Chirality : 0.040 0.215 9842 Planarity : 0.004 0.097 11402 Dihedral : 4.722 54.459 8624 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.71 % Allowed : 15.87 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.10), residues: 7844 helix: 0.67 (0.08), residues: 4658 sheet: 0.07 (0.20), residues: 666 loop : -0.27 (0.13), residues: 2520 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 370 time to evaluate : 5.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 194 outliers final: 115 residues processed: 539 average time/residue: 1.2857 time to fit residues: 940.6180 Evaluate side-chains 459 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 344 time to evaluate : 5.507 Switching outliers to nearest non-outliers outliers start: 115 outliers final: 108 residues processed: 7 average time/residue: 0.6266 time to fit residues: 15.4773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 468 optimal weight: 0.2980 chunk 302 optimal weight: 4.9990 chunk 452 optimal weight: 20.0000 chunk 228 optimal weight: 6.9990 chunk 148 optimal weight: 10.0000 chunk 146 optimal weight: 1.9990 chunk 481 optimal weight: 5.9990 chunk 516 optimal weight: 30.0000 chunk 374 optimal weight: 8.9990 chunk 70 optimal weight: 0.8980 chunk 595 optimal weight: 10.0000 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 987 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1533 ASN ** B 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1559 GLN ** C 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1562 GLN ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1110 ASN E 83 GLN ** E 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5580 moved from start: 0.4676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 66394 Z= 0.199 Angle : 0.534 11.680 89788 Z= 0.278 Chirality : 0.040 0.218 9842 Planarity : 0.004 0.056 11402 Dihedral : 4.670 48.099 8624 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.72 % Allowed : 16.34 % Favored : 80.94 % 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: 0.37 (0.10), residues: 7844 helix: 0.66 (0.08), residues: 4664 sheet: 0.11 (0.21), residues: 642 loop : -0.30 (0.13), residues: 2538 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 363 time to evaluate : 5.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 195 outliers final: 115 residues processed: 535 average time/residue: 1.2919 time to fit residues: 933.0485 Evaluate side-chains 462 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 347 time to evaluate : 5.457 Switching outliers to nearest non-outliers outliers start: 115 outliers final: 110 residues processed: 5 average time/residue: 0.9267 time to fit residues: 14.7264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 689 optimal weight: 0.2980 chunk 725 optimal weight: 20.0000 chunk 662 optimal weight: 3.9990 chunk 705 optimal weight: 0.3980 chunk 424 optimal weight: 6.9990 chunk 307 optimal weight: 2.9990 chunk 554 optimal weight: 3.9990 chunk 216 optimal weight: 5.9990 chunk 637 optimal weight: 20.0000 chunk 667 optimal weight: 5.9990 chunk 703 optimal weight: 7.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 987 HIS ** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1533 ASN ** B 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1559 GLN ** E 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 407 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5573 moved from start: 0.4825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 66394 Z= 0.179 Angle : 0.527 10.766 89788 Z= 0.272 Chirality : 0.040 0.199 9842 Planarity : 0.004 0.067 11402 Dihedral : 4.593 47.012 8624 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.16 % Allowed : 17.19 % Favored : 80.64 % 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: 0.45 (0.10), residues: 7844 helix: 0.74 (0.08), residues: 4650 sheet: 0.16 (0.21), residues: 638 loop : -0.28 (0.12), residues: 2556 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 369 time to evaluate : 5.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 155 outliers final: 117 residues processed: 510 average time/residue: 1.3218 time to fit residues: 915.6216 Evaluate side-chains 463 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 346 time to evaluate : 5.502 Switching outliers to nearest non-outliers outliers start: 117 outliers final: 113 residues processed: 4 average time/residue: 1.0132 time to fit residues: 13.9207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 463 optimal weight: 0.8980 chunk 746 optimal weight: 0.7980 chunk 455 optimal weight: 0.0970 chunk 354 optimal weight: 6.9990 chunk 518 optimal weight: 20.0000 chunk 783 optimal weight: 0.2980 chunk 720 optimal weight: 10.0000 chunk 623 optimal weight: 0.2980 chunk 64 optimal weight: 7.9990 chunk 481 optimal weight: 0.8980 chunk 382 optimal weight: 0.6980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 627 ASN ** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1533 ASN ** B 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 594 GLN ** B 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 788 GLN ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 637 ASN D 648 GLN ** E 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5527 moved from start: 0.4902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 66394 Z= 0.126 Angle : 0.496 13.255 89788 Z= 0.253 Chirality : 0.039 0.195 9842 Planarity : 0.004 0.080 11402 Dihedral : 4.252 38.317 8624 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.77 % Allowed : 17.68 % Favored : 80.54 % 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: 0.71 (0.10), residues: 7844 helix: 0.93 (0.08), residues: 4622 sheet: 0.34 (0.21), residues: 634 loop : -0.14 (0.13), residues: 2588 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 369 time to evaluate : 5.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 127 outliers final: 105 residues processed: 492 average time/residue: 1.3144 time to fit residues: 876.0939 Evaluate side-chains 435 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 330 time to evaluate : 5.641 Switching outliers to nearest non-outliers outliers start: 105 outliers final: 104 residues processed: 1 average time/residue: 1.4483 time to fit residues: 10.1793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 495 optimal weight: 0.9980 chunk 664 optimal weight: 1.9990 chunk 191 optimal weight: 4.9990 chunk 574 optimal weight: 0.1980 chunk 92 optimal weight: 9.9990 chunk 173 optimal weight: 9.9990 chunk 624 optimal weight: 5.9990 chunk 261 optimal weight: 7.9990 chunk 641 optimal weight: 0.8980 chunk 79 optimal weight: 10.0000 chunk 115 optimal weight: 8.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1533 ASN ** B 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1533 ASN ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4929 r_free = 0.4929 target = 0.253020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4820 r_free = 0.4820 target = 0.241583 restraints weight = 113335.292| |-----------------------------------------------------------------------------| r_work (start): 0.4818 rms_B_bonded: 0.97 r_work: 0.4520 rms_B_bonded: 1.12 restraints_weight: 0.5000 r_work: 0.4489 rms_B_bonded: 1.49 restraints_weight: 0.2500 r_work: 0.4457 rms_B_bonded: 2.04 restraints_weight: 0.1250 r_work (final): 0.4457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5908 moved from start: 0.4967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 66394 Z= 0.161 Angle : 0.515 12.323 89788 Z= 0.263 Chirality : 0.039 0.184 9842 Planarity : 0.004 0.067 11402 Dihedral : 4.311 42.171 8624 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.75 % Allowed : 17.93 % Favored : 80.32 % 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: 0.67 (0.10), residues: 7844 helix: 0.91 (0.08), residues: 4638 sheet: 0.24 (0.21), residues: 650 loop : -0.18 (0.13), residues: 2556 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18229.60 seconds wall clock time: 318 minutes 48.63 seconds (19128.63 seconds total)