Starting phenix.real_space_refine on Sat Dec 9 17:59:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6q_33025/12_2023/7x6q_33025.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6q_33025/12_2023/7x6q_33025.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6q_33025/12_2023/7x6q_33025.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6q_33025/12_2023/7x6q_33025.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6q_33025/12_2023/7x6q_33025.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6q_33025/12_2023/7x6q_33025.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 4 Type Number sf(0) Gaussians S 396 5.16 5 C 40432 2.51 5 N 11248 2.21 5 O 12396 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 66": "OD1" <-> "OD2" Residue "B PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 254": "OE1" <-> "OE2" Residue "H TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 491": "OD1" <-> "OD2" Residue "J TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 498": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 66": "OD1" <-> "OD2" Residue "L PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 329": "OE1" <-> "OE2" Residue "M TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 491": "OD1" <-> "OD2" Residue "a TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ASP 144": "OD1" <-> "OD2" Residue "z PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 64472 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 4077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4077 Classifications: {'peptide': 537} Link IDs: {'PTRANS': 14, 'TRANS': 522} Chain: "B" Number of atoms: 3937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3937 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 10, 'TRANS': 512} Chain: "E" Number of atoms: 4126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 4126 Classifications: {'peptide': 535} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 515} Chain: "G" Number of atoms: 4094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4094 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "H" Number of atoms: 4037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4037 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 16, 'TRANS': 509} Chain: "I" Number of atoms: 3935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3935 Classifications: {'peptide': 521} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 505} Chain: "J" Number of atoms: 4008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4008 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 511} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 4022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4022 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 14, 'TRANS': 510} Chain: "L" Number of atoms: 3937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3937 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 10, 'TRANS': 512} Chain: "M" Number of atoms: 3935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3935 Classifications: {'peptide': 521} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 505} Chain: "N" Number of atoms: 4094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4094 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "O" Number of atoms: 4037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4037 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 16, 'TRANS': 509} Chain: "P" Number of atoms: 4008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4008 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 511} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "a" Number of atoms: 4077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4077 Classifications: {'peptide': 537} Link IDs: {'PTRANS': 14, 'TRANS': 522} Chain: "e" Number of atoms: 4126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 4126 Classifications: {'peptide': 535} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 515} Chain: "z" Number of atoms: 4022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4022 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 14, 'TRANS': 510} Time building chain proxies: 25.61, per 1000 atoms: 0.40 Number of scatterers: 64472 At special positions: 0 Unit cell: (181.56, 186.01, 181.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 396 16.00 O 12396 8.00 N 11248 7.00 C 40432 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 19.63 Conformation dependent library (CDL) restraints added in 9.3 seconds 16816 Ramachandran restraints generated. 8408 Oldfield, 0 Emsley, 8408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15736 Finding SS restraints... Secondary structure from input PDB file: 359 helices and 96 sheets defined 54.4% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.85 Creating SS restraints... Processing helix chain 'A' and resid 14 through 33 removed outlier: 3.649A pdb=" N VAL A 22 " --> pdb=" O ARG A 18 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE A 31 " --> pdb=" O SER A 27 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 36 No H-bonds generated for 'chain 'A' and resid 34 through 36' Processing helix chain 'A' and resid 57 through 65 Processing helix chain 'A' and resid 69 through 86 removed outlier: 4.050A pdb=" N LEU A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 109 removed outlier: 3.514A pdb=" N ILE A 95 " --> pdb=" O THR A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 135 Processing helix chain 'A' and resid 139 through 144 removed outlier: 4.471A pdb=" N LEU A 143 " --> pdb=" O ASN A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 157 removed outlier: 4.150A pdb=" N LEU A 148 " --> pdb=" O GLY A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 178 removed outlier: 3.576A pdb=" N MET A 171 " --> pdb=" O PHE A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 195 Processing helix chain 'A' and resid 204 through 208 removed outlier: 3.716A pdb=" N SER A 208 " --> pdb=" O GLN A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 258 No H-bonds generated for 'chain 'A' and resid 256 through 258' Processing helix chain 'A' and resid 259 through 280 removed outlier: 3.922A pdb=" N GLU A 267 " --> pdb=" O ILE A 263 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N SER A 268 " --> pdb=" O ARG A 264 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N THR A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ARG A 274 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS A 277 " --> pdb=" O GLU A 273 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU A 279 " --> pdb=" O ILE A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.932A pdb=" N LYS A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N TYR A 299 " --> pdb=" O MET A 295 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE A 300 " --> pdb=" O CYS A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 324 Processing helix chain 'A' and resid 341 through 345 removed outlier: 4.034A pdb=" N LEU A 345 " --> pdb=" O ALA A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 405 removed outlier: 3.555A pdb=" N GLU A 387 " --> pdb=" O PHE A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 427 removed outlier: 4.347A pdb=" N GLU A 424 " --> pdb=" O SER A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 445 removed outlier: 3.697A pdb=" N LEU A 445 " --> pdb=" O PHE A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 456 Processing helix chain 'A' and resid 460 through 477 removed outlier: 3.572A pdb=" N ALA A 465 " --> pdb=" O THR A 461 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLN A 475 " --> pdb=" O HIS A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 507 through 525 removed outlier: 3.877A pdb=" N SER A 513 " --> pdb=" O VAL A 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 40 removed outlier: 3.994A pdb=" N LEU B 26 " --> pdb=" O GLU B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 43 No H-bonds generated for 'chain 'B' and resid 41 through 43' Processing helix chain 'B' and resid 66 through 72 Processing helix chain 'B' and resid 81 through 95 Processing helix chain 'B' and resid 98 through 119 Processing helix chain 'B' and resid 122 through 144 removed outlier: 3.507A pdb=" N SER B 144 " --> pdb=" O ALA B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 168 removed outlier: 3.862A pdb=" N PHE B 155 " --> pdb=" O ASP B 151 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLN B 157 " --> pdb=" O VAL B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 189 removed outlier: 5.076A pdb=" N LYS B 181 " --> pdb=" O ASP B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 212 Processing helix chain 'B' and resid 260 through 284 removed outlier: 4.140A pdb=" N VAL B 264 " --> pdb=" O SER B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 307 removed outlier: 3.725A pdb=" N ALA B 307 " --> pdb=" O LEU B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 328 Processing helix chain 'B' and resid 337 through 341 removed outlier: 3.575A pdb=" N VAL B 341 " --> pdb=" O PRO B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 401 Processing helix chain 'B' and resid 411 through 426 Processing helix chain 'B' and resid 429 through 455 removed outlier: 3.714A pdb=" N VAL B 434 " --> pdb=" O GLY B 430 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N ALA B 435 " --> pdb=" O LYS B 431 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU B 446 " --> pdb=" O ALA B 442 " (cutoff:3.500A) Proline residue: B 447 - end of helix Processing helix chain 'B' and resid 457 through 469 removed outlier: 4.195A pdb=" N ALA B 463 " --> pdb=" O ALA B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 492 Processing helix chain 'B' and resid 497 through 516 removed outlier: 3.691A pdb=" N ALA B 508 " --> pdb=" O LEU B 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 23 Processing helix chain 'E' and resid 29 through 47 removed outlier: 3.701A pdb=" N THR E 45 " --> pdb=" O ALA E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 50 No H-bonds generated for 'chain 'E' and resid 48 through 50' Processing helix chain 'E' and resid 71 through 77 Processing helix chain 'E' and resid 83 through 100 removed outlier: 3.846A pdb=" N LEU E 88 " --> pdb=" O GLN E 84 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL E 90 " --> pdb=" O ALA E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 124 removed outlier: 3.529A pdb=" N GLU E 119 " --> pdb=" O LEU E 115 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLN E 120 " --> pdb=" O GLU E 116 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU E 121 " --> pdb=" O GLU E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 147 removed outlier: 3.766A pdb=" N GLU E 136 " --> pdb=" O ALA E 132 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL E 141 " --> pdb=" O GLN E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 172 Processing helix chain 'E' and resid 176 through 180 Processing helix chain 'E' and resid 181 through 193 Processing helix chain 'E' and resid 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'E' and resid 216 through 220 Processing helix chain 'E' and resid 268 through 292 removed outlier: 3.765A pdb=" N ILE E 287 " --> pdb=" O PHE E 283 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE E 290 " --> pdb=" O MET E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 315 removed outlier: 3.681A pdb=" N HIS E 310 " --> pdb=" O ASP E 306 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 335 Processing helix chain 'E' and resid 347 through 351 Processing helix chain 'E' and resid 389 through 413 removed outlier: 3.544A pdb=" N ILE E 393 " --> pdb=" O ASN E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 421 through 436 removed outlier: 4.044A pdb=" N ASP E 436 " --> pdb=" O SER E 432 " (cutoff:3.500A) Processing helix chain 'E' and resid 442 through 453 Processing helix chain 'E' and resid 454 through 464 Processing helix chain 'E' and resid 467 through 482 removed outlier: 3.818A pdb=" N GLU E 474 " --> pdb=" O GLN E 470 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL E 480 " --> pdb=" O ARG E 476 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU E 482 " --> pdb=" O ARG E 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 503 Processing helix chain 'E' and resid 508 through 527 removed outlier: 3.603A pdb=" N ILE E 525 " --> pdb=" O MET E 521 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 24 Processing helix chain 'G' and resid 24 through 35 Processing helix chain 'G' and resid 62 through 68 Processing helix chain 'G' and resid 76 through 91 removed outlier: 3.823A pdb=" N MET G 80 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU G 89 " --> pdb=" O ARG G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 114 removed outlier: 3.831A pdb=" N HIS G 111 " --> pdb=" O SER G 107 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE G 112 " --> pdb=" O VAL G 108 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU G 114 " --> pdb=" O GLU G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 140 removed outlier: 3.524A pdb=" N ASP G 131 " --> pdb=" O ARG G 127 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP G 132 " --> pdb=" O LYS G 128 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 160 Processing helix chain 'G' and resid 163 through 167 removed outlier: 4.072A pdb=" N ARG G 167 " --> pdb=" O ALA G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 183 removed outlier: 4.755A pdb=" N ASN G 174 " --> pdb=" O SER G 170 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 212 Processing helix chain 'G' and resid 260 through 282 removed outlier: 4.172A pdb=" N PHE G 264 " --> pdb=" O ARG G 260 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N THR G 265 " --> pdb=" O GLU G 261 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE G 275 " --> pdb=" O GLU G 271 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE G 282 " --> pdb=" O LEU G 278 " (cutoff:3.500A) Processing helix chain 'G' and resid 297 through 307 Processing helix chain 'G' and resid 316 through 328 removed outlier: 3.863A pdb=" N ARG G 325 " --> pdb=" O ASN G 321 " (cutoff:3.500A) Processing helix chain 'G' and resid 334 through 338 removed outlier: 3.671A pdb=" N LEU G 338 " --> pdb=" O PRO G 335 " (cutoff:3.500A) Processing helix chain 'G' and resid 339 through 343 Processing helix chain 'G' and resid 380 through 404 removed outlier: 3.764A pdb=" N GLN G 396 " --> pdb=" O GLN G 392 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N CYS G 398 " --> pdb=" O ALA G 394 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG G 399 " --> pdb=" O MET G 395 " (cutoff:3.500A) Processing helix chain 'G' and resid 412 through 427 removed outlier: 3.596A pdb=" N LYS G 427 " --> pdb=" O THR G 423 " (cutoff:3.500A) Processing helix chain 'G' and resid 433 through 444 removed outlier: 3.627A pdb=" N ALA G 441 " --> pdb=" O TYR G 437 " (cutoff:3.500A) Processing helix chain 'G' and resid 445 through 455 removed outlier: 3.722A pdb=" N CYS G 455 " --> pdb=" O LEU G 451 " (cutoff:3.500A) Processing helix chain 'G' and resid 460 through 470 Processing helix chain 'G' and resid 490 through 494 Processing helix chain 'G' and resid 499 through 517 Processing helix chain 'H' and resid 18 through 33 Processing helix chain 'H' and resid 34 through 40 removed outlier: 3.582A pdb=" N ARG H 37 " --> pdb=" O GLU H 34 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N THR H 38 " --> pdb=" O ALA H 35 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU H 40 " --> pdb=" O ARG H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 66 Processing helix chain 'H' and resid 67 through 69 No H-bonds generated for 'chain 'H' and resid 67 through 69' Processing helix chain 'H' and resid 77 through 90 removed outlier: 4.108A pdb=" N ALA H 83 " --> pdb=" O LEU H 79 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA H 88 " --> pdb=" O LYS H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 113 removed outlier: 3.688A pdb=" N LEU H 105 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL H 108 " --> pdb=" O PHE H 104 " (cutoff:3.500A) Proline residue: H 110 - end of helix removed outlier: 3.804A pdb=" N GLU H 113 " --> pdb=" O LYS H 109 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 140 removed outlier: 3.830A pdb=" N ILE H 121 " --> pdb=" O HIS H 117 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG H 123 " --> pdb=" O GLN H 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 163 Processing helix chain 'H' and resid 171 through 184 removed outlier: 3.811A pdb=" N LYS H 177 " --> pdb=" O ALA H 173 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N MET H 178 " --> pdb=" O PHE H 174 " (cutoff:3.500A) Processing helix chain 'H' and resid 191 through 193 No H-bonds generated for 'chain 'H' and resid 191 through 193' Processing helix chain 'H' and resid 204 through 208 Processing helix chain 'H' and resid 259 through 282 removed outlier: 3.582A pdb=" N TRP H 271 " --> pdb=" O VAL H 267 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU H 274 " --> pdb=" O GLU H 270 " (cutoff:3.500A) Processing helix chain 'H' and resid 296 through 306 Processing helix chain 'H' and resid 315 through 327 Processing helix chain 'H' and resid 352 through 356 removed outlier: 3.835A pdb=" N GLU H 356 " --> pdb=" O ILE H 353 " (cutoff:3.500A) Processing helix chain 'H' and resid 378 through 402 removed outlier: 3.831A pdb=" N LYS H 401 " --> pdb=" O ARG H 397 " (cutoff:3.500A) Processing helix chain 'H' and resid 410 through 425 Processing helix chain 'H' and resid 426 through 427 No H-bonds generated for 'chain 'H' and resid 426 through 427' Processing helix chain 'H' and resid 428 through 430 No H-bonds generated for 'chain 'H' and resid 428 through 430' Processing helix chain 'H' and resid 431 through 442 removed outlier: 3.604A pdb=" N GLY H 436 " --> pdb=" O GLN H 432 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA H 437 " --> pdb=" O LEU H 433 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU H 442 " --> pdb=" O TYR H 438 " (cutoff:3.500A) Processing helix chain 'H' and resid 443 through 452 removed outlier: 3.585A pdb=" N CYS H 450 " --> pdb=" O PRO H 446 " (cutoff:3.500A) Processing helix chain 'H' and resid 456 through 469 Processing helix chain 'H' and resid 496 through 515 Processing helix chain 'I' and resid 29 through 46 removed outlier: 5.089A pdb=" N PHE I 35 " --> pdb=" O ALA I 31 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE I 38 " --> pdb=" O ARG I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 52 removed outlier: 4.898A pdb=" N THR I 50 " --> pdb=" O ALA I 47 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU I 52 " --> pdb=" O ARG I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 73 through 82 removed outlier: 3.781A pdb=" N GLN I 80 " --> pdb=" O THR I 76 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN I 82 " --> pdb=" O LEU I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 89 through 102 removed outlier: 3.509A pdb=" N GLU I 93 " --> pdb=" O ARG I 89 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN I 98 " --> pdb=" O LEU I 94 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 120 removed outlier: 3.612A pdb=" N ILE I 111 " --> pdb=" O THR I 107 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N CYS I 120 " --> pdb=" O LEU I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 125 removed outlier: 3.788A pdb=" N GLN I 125 " --> pdb=" O THR I 121 " (cutoff:3.500A) Processing helix chain 'I' and resid 129 through 152 Processing helix chain 'I' and resid 159 through 172 Processing helix chain 'I' and resid 176 through 178 No H-bonds generated for 'chain 'I' and resid 176 through 178' Processing helix chain 'I' and resid 179 through 193 Proline residue: I 185 - end of helix removed outlier: 3.718A pdb=" N VAL I 191 " --> pdb=" O SER I 187 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS I 193 " --> pdb=" O ASN I 189 " (cutoff:3.500A) Processing helix chain 'I' and resid 204 through 206 No H-bonds generated for 'chain 'I' and resid 204 through 206' Processing helix chain 'I' and resid 217 through 221 Processing helix chain 'I' and resid 268 through 294 removed outlier: 3.756A pdb=" N MET I 272 " --> pdb=" O ASP I 268 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ASP I 273 " --> pdb=" O TYR I 269 " (cutoff:3.500A) Processing helix chain 'I' and resid 310 through 320 Processing helix chain 'I' and resid 332 through 341 Processing helix chain 'I' and resid 347 through 351 Processing helix chain 'I' and resid 352 through 356 Processing helix chain 'I' and resid 394 through 418 removed outlier: 3.522A pdb=" N ILE I 412 " --> pdb=" O ALA I 408 " (cutoff:3.500A) Processing helix chain 'I' and resid 426 through 441 Processing helix chain 'I' and resid 447 through 457 removed outlier: 4.158A pdb=" N ARG I 452 " --> pdb=" O SER I 448 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA I 453 " --> pdb=" O TYR I 449 " (cutoff:3.500A) Processing helix chain 'I' and resid 459 through 469 Processing helix chain 'I' and resid 472 through 487 removed outlier: 3.766A pdb=" N THR I 478 " --> pdb=" O ILE I 474 " (cutoff:3.500A) Processing helix chain 'I' and resid 504 through 507 Processing helix chain 'I' and resid 512 through 530 removed outlier: 3.796A pdb=" N LEU I 519 " --> pdb=" O SER I 515 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER I 528 " --> pdb=" O GLU I 524 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 45 removed outlier: 3.556A pdb=" N LEU J 39 " --> pdb=" O ALA J 35 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N THR J 45 " --> pdb=" O GLN J 41 " (cutoff:3.500A) Processing helix chain 'J' and resid 68 through 73 Processing helix chain 'J' and resid 82 through 97 removed outlier: 4.098A pdb=" N ILE J 86 " --> pdb=" O ALA J 82 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER J 90 " --> pdb=" O ILE J 86 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N HIS J 91 " --> pdb=" O VAL J 87 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N MET J 92 " --> pdb=" O MET J 88 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN J 93 " --> pdb=" O ALA J 89 " (cutoff:3.500A) Processing helix chain 'J' and resid 101 through 120 removed outlier: 4.344A pdb=" N LEU J 105 " --> pdb=" O THR J 101 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU J 118 " --> pdb=" O LEU J 114 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG J 120 " --> pdb=" O GLU J 116 " (cutoff:3.500A) Processing helix chain 'J' and resid 124 through 143 removed outlier: 4.293A pdb=" N GLU J 130 " --> pdb=" O SER J 126 " (cutoff:3.500A) Processing helix chain 'J' and resid 144 through 146 No H-bonds generated for 'chain 'J' and resid 144 through 146' Processing helix chain 'J' and resid 156 through 164 Processing helix chain 'J' and resid 164 through 170 Processing helix chain 'J' and resid 172 through 176 removed outlier: 3.733A pdb=" N GLU J 176 " --> pdb=" O TYR J 173 " (cutoff:3.500A) Processing helix chain 'J' and resid 177 through 190 removed outlier: 3.780A pdb=" N ILE J 190 " --> pdb=" O ALA J 186 " (cutoff:3.500A) Processing helix chain 'J' and resid 198 through 200 No H-bonds generated for 'chain 'J' and resid 198 through 200' Processing helix chain 'J' and resid 211 through 215 Processing helix chain 'J' and resid 261 through 267 Processing helix chain 'J' and resid 267 through 285 removed outlier: 3.756A pdb=" N GLY J 271 " --> pdb=" O ASN J 267 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU J 272 " --> pdb=" O PHE J 268 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ILE J 283 " --> pdb=" O GLN J 279 " (cutoff:3.500A) Processing helix chain 'J' and resid 298 through 308 Processing helix chain 'J' and resid 317 through 329 Processing helix chain 'J' and resid 381 through 405 Processing helix chain 'J' and resid 413 through 429 removed outlier: 3.583A pdb=" N THR J 429 " --> pdb=" O SER J 425 " (cutoff:3.500A) Processing helix chain 'J' and resid 434 through 456 removed outlier: 3.754A pdb=" N PHE J 445 " --> pdb=" O PHE J 441 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ILE J 448 " --> pdb=" O ALA J 444 " (cutoff:3.500A) Proline residue: J 449 - end of helix Processing helix chain 'J' and resid 459 through 470 Processing helix chain 'J' and resid 501 through 520 Processing helix chain 'K' and resid 3 through 8 Processing helix chain 'K' and resid 15 through 35 removed outlier: 4.414A pdb=" N LEU K 20 " --> pdb=" O ALA K 16 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ALA K 21 " --> pdb=" O GLN K 17 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL K 33 " --> pdb=" O GLY K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 36 through 38 No H-bonds generated for 'chain 'K' and resid 36 through 38' Processing helix chain 'K' and resid 59 through 66 Processing helix chain 'K' and resid 73 through 88 removed outlier: 3.622A pdb=" N LYS K 79 " --> pdb=" O SER K 75 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN K 84 " --> pdb=" O VAL K 80 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ASP K 85 " --> pdb=" O ALA K 81 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ASP K 86 " --> pdb=" O THR K 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 91 through 111 removed outlier: 3.558A pdb=" N ALA K 106 " --> pdb=" O LEU K 102 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP K 107 " --> pdb=" O LEU K 103 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU K 108 " --> pdb=" O LYS K 104 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TYR K 109 " --> pdb=" O GLN K 105 " (cutoff:3.500A) Processing helix chain 'K' and resid 115 through 137 removed outlier: 4.184A pdb=" N ILE K 119 " --> pdb=" O HIS K 115 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU K 136 " --> pdb=" O GLN K 132 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL K 137 " --> pdb=" O PHE K 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 144 through 157 Processing helix chain 'K' and resid 158 through 160 No H-bonds generated for 'chain 'K' and resid 158 through 160' Processing helix chain 'K' and resid 164 through 178 removed outlier: 4.688A pdb=" N GLU K 170 " --> pdb=" O ASP K 166 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA K 171 " --> pdb=" O VAL K 167 " (cutoff:3.500A) Processing helix chain 'K' and resid 187 through 189 No H-bonds generated for 'chain 'K' and resid 187 through 189' Processing helix chain 'K' and resid 200 through 204 removed outlier: 3.729A pdb=" N THR K 204 " --> pdb=" O GLU K 201 " (cutoff:3.500A) Processing helix chain 'K' and resid 252 through 264 removed outlier: 3.673A pdb=" N ARG K 264 " --> pdb=" O VAL K 260 " (cutoff:3.500A) Processing helix chain 'K' and resid 264 through 279 removed outlier: 3.875A pdb=" N LYS K 273 " --> pdb=" O ASP K 269 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE K 274 " --> pdb=" O ARG K 270 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU K 276 " --> pdb=" O LYS K 272 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU K 277 " --> pdb=" O LYS K 273 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LYS K 278 " --> pdb=" O ILE K 274 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ARG K 279 " --> pdb=" O ILE K 275 " (cutoff:3.500A) Processing helix chain 'K' and resid 298 through 308 removed outlier: 3.981A pdb=" N GLU K 308 " --> pdb=" O ALA K 304 " (cutoff:3.500A) Processing helix chain 'K' and resid 319 through 329 removed outlier: 3.773A pdb=" N THR K 325 " --> pdb=" O MET K 321 " (cutoff:3.500A) Processing helix chain 'K' and resid 340 through 344 Processing helix chain 'K' and resid 380 through 404 Processing helix chain 'K' and resid 412 through 425 removed outlier: 4.158A pdb=" N ALA K 417 " --> pdb=" O ALA K 413 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N HIS K 425 " --> pdb=" O ALA K 421 " (cutoff:3.500A) Processing helix chain 'K' and resid 426 through 430 removed outlier: 3.664A pdb=" N VAL K 429 " --> pdb=" O LYS K 426 " (cutoff:3.500A) Processing helix chain 'K' and resid 431 through 432 No H-bonds generated for 'chain 'K' and resid 431 through 432' Processing helix chain 'K' and resid 433 through 444 Processing helix chain 'K' and resid 445 through 455 Processing helix chain 'K' and resid 458 through 472 Processing helix chain 'K' and resid 489 through 493 Processing helix chain 'K' and resid 497 through 517 removed outlier: 3.556A pdb=" N CYS K 508 " --> pdb=" O LEU K 504 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N THR K 509 " --> pdb=" O LEU K 505 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU K 517 " --> pdb=" O THR K 513 " (cutoff:3.500A) Processing helix chain 'L' and resid 23 through 41 removed outlier: 4.015A pdb=" N ILE L 35 " --> pdb=" O GLY L 31 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLY L 36 " --> pdb=" O ALA L 32 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP L 37 " --> pdb=" O ILE L 33 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N SER L 41 " --> pdb=" O ASP L 37 " (cutoff:3.500A) Processing helix chain 'L' and resid 66 through 72 Processing helix chain 'L' and resid 80 through 95 removed outlier: 4.362A pdb=" N LEU L 84 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 98 through 119 Processing helix chain 'L' and resid 122 through 144 Processing helix chain 'L' and resid 151 through 168 removed outlier: 4.095A pdb=" N GLN L 157 " --> pdb=" O VAL L 153 " (cutoff:3.500A) Processing helix chain 'L' and resid 175 through 189 removed outlier: 5.257A pdb=" N LYS L 181 " --> pdb=" O ASP L 177 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA L 186 " --> pdb=" O LEU L 182 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL L 187 " --> pdb=" O ALA L 183 " (cutoff:3.500A) Processing helix chain 'L' and resid 208 through 212 Processing helix chain 'L' and resid 260 through 284 removed outlier: 4.050A pdb=" N VAL L 264 " --> pdb=" O SER L 260 " (cutoff:3.500A) Processing helix chain 'L' and resid 297 through 307 Processing helix chain 'L' and resid 318 through 328 Processing helix chain 'L' and resid 337 through 341 Processing helix chain 'L' and resid 379 through 401 removed outlier: 3.619A pdb=" N GLN L 399 " --> pdb=" O CYS L 395 " (cutoff:3.500A) Processing helix chain 'L' and resid 411 through 426 Processing helix chain 'L' and resid 429 through 455 removed outlier: 4.987A pdb=" N ALA L 435 " --> pdb=" O LYS L 431 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU L 446 " --> pdb=" O ALA L 442 " (cutoff:3.500A) Proline residue: L 447 - end of helix Processing helix chain 'L' and resid 457 through 471 removed outlier: 3.866A pdb=" N ALA L 463 " --> pdb=" O ALA L 459 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU L 471 " --> pdb=" O ALA L 467 " (cutoff:3.500A) Processing helix chain 'L' and resid 488 through 492 Processing helix chain 'L' and resid 497 through 516 removed outlier: 3.869A pdb=" N VAL L 513 " --> pdb=" O GLU L 509 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE L 514 " --> pdb=" O ALA L 510 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 46 removed outlier: 3.639A pdb=" N ILE M 33 " --> pdb=" O LYS M 29 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N PHE M 35 " --> pdb=" O ALA M 31 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ILE M 38 " --> pdb=" O ARG M 34 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL M 44 " --> pdb=" O ALA M 40 " (cutoff:3.500A) Processing helix chain 'M' and resid 48 through 52 removed outlier: 3.805A pdb=" N LEU M 52 " --> pdb=" O ARG M 49 " (cutoff:3.500A) Processing helix chain 'M' and resid 73 through 82 removed outlier: 3.759A pdb=" N GLN M 80 " --> pdb=" O THR M 76 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN M 82 " --> pdb=" O LEU M 78 " (cutoff:3.500A) Processing helix chain 'M' and resid 88 through 102 removed outlier: 3.913A pdb=" N VAL M 92 " --> pdb=" O ALA M 88 " (cutoff:3.500A) Processing helix chain 'M' and resid 107 through 120 removed outlier: 3.570A pdb=" N ILE M 111 " --> pdb=" O THR M 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 120 through 125 Processing helix chain 'M' and resid 129 through 150 removed outlier: 3.890A pdb=" N GLU M 146 " --> pdb=" O GLU M 142 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP M 150 " --> pdb=" O GLU M 146 " (cutoff:3.500A) Processing helix chain 'M' and resid 159 through 172 removed outlier: 3.661A pdb=" N LEU M 171 " --> pdb=" O ALA M 167 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 178 No H-bonds generated for 'chain 'M' and resid 176 through 178' Processing helix chain 'M' and resid 179 through 193 Proline residue: M 185 - end of helix removed outlier: 3.810A pdb=" N VAL M 191 " --> pdb=" O SER M 187 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS M 193 " --> pdb=" O ASN M 189 " (cutoff:3.500A) Processing helix chain 'M' and resid 204 through 206 No H-bonds generated for 'chain 'M' and resid 204 through 206' Processing helix chain 'M' and resid 217 through 221 Processing helix chain 'M' and resid 270 through 294 removed outlier: 3.592A pdb=" N GLU M 278 " --> pdb=" O ARG M 274 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY M 294 " --> pdb=" O ILE M 290 " (cutoff:3.500A) Processing helix chain 'M' and resid 310 through 320 Processing helix chain 'M' and resid 332 through 340 Processing helix chain 'M' and resid 347 through 351 Processing helix chain 'M' and resid 352 through 356 Processing helix chain 'M' and resid 394 through 418 removed outlier: 3.643A pdb=" N VAL M 411 " --> pdb=" O ASP M 407 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE M 412 " --> pdb=" O ALA M 408 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG M 413 " --> pdb=" O LEU M 409 " (cutoff:3.500A) Processing helix chain 'M' and resid 426 through 441 Processing helix chain 'M' and resid 442 through 443 No H-bonds generated for 'chain 'M' and resid 442 through 443' Processing helix chain 'M' and resid 444 through 445 No H-bonds generated for 'chain 'M' and resid 444 through 445' Processing helix chain 'M' and resid 446 through 458 removed outlier: 4.536A pdb=" N ARG M 452 " --> pdb=" O SER M 448 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA M 453 " --> pdb=" O TYR M 449 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N MET M 458 " --> pdb=" O PHE M 454 " (cutoff:3.500A) Processing helix chain 'M' and resid 459 through 469 Processing helix chain 'M' and resid 472 through 487 removed outlier: 3.614A pdb=" N THR M 478 " --> pdb=" O ILE M 474 " (cutoff:3.500A) Processing helix chain 'M' and resid 504 through 507 Processing helix chain 'M' and resid 512 through 530 removed outlier: 3.645A pdb=" N LEU M 519 " --> pdb=" O SER M 515 " (cutoff:3.500A) Processing helix chain 'N' and resid 19 through 35 removed outlier: 4.089A pdb=" N ILE N 27 " --> pdb=" O GLN N 23 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASP N 35 " --> pdb=" O LYS N 31 " (cutoff:3.500A) Processing helix chain 'N' and resid 36 through 38 No H-bonds generated for 'chain 'N' and resid 36 through 38' Processing helix chain 'N' and resid 62 through 69 removed outlier: 3.823A pdb=" N GLU N 69 " --> pdb=" O ALA N 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 76 through 91 removed outlier: 3.843A pdb=" N MET N 80 " --> pdb=" O ALA N 76 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU N 89 " --> pdb=" O ARG N 85 " (cutoff:3.500A) Processing helix chain 'N' and resid 95 through 114 removed outlier: 3.509A pdb=" N ILE N 99 " --> pdb=" O THR N 95 " (cutoff:3.500A) Processing helix chain 'N' and resid 118 through 140 removed outlier: 4.016A pdb=" N ASP N 131 " --> pdb=" O ARG N 127 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP N 132 " --> pdb=" O LYS N 128 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS N 139 " --> pdb=" O SER N 135 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE N 140 " --> pdb=" O THR N 136 " (cutoff:3.500A) Processing helix chain 'N' and resid 148 through 161 removed outlier: 3.522A pdb=" N SER N 159 " --> pdb=" O ILE N 155 " (cutoff:3.500A) Processing helix chain 'N' and resid 165 through 167 No H-bonds generated for 'chain 'N' and resid 165 through 167' Processing helix chain 'N' and resid 168 through 182 removed outlier: 4.737A pdb=" N ASN N 174 " --> pdb=" O SER N 170 " (cutoff:3.500A) Processing helix chain 'N' and resid 208 through 212 Processing helix chain 'N' and resid 262 through 282 removed outlier: 3.566A pdb=" N ILE N 275 " --> pdb=" O GLU N 271 " (cutoff:3.500A) Processing helix chain 'N' and resid 297 through 307 Processing helix chain 'N' and resid 316 through 328 removed outlier: 3.631A pdb=" N ARG N 322 " --> pdb=" O THR N 318 " (cutoff:3.500A) Processing helix chain 'N' and resid 334 through 338 Processing helix chain 'N' and resid 339 through 343 Processing helix chain 'N' and resid 380 through 404 Processing helix chain 'N' and resid 412 through 427 removed outlier: 3.547A pdb=" N LYS N 427 " --> pdb=" O THR N 423 " (cutoff:3.500A) Processing helix chain 'N' and resid 433 through 445 removed outlier: 3.674A pdb=" N VAL N 440 " --> pdb=" O PRO N 436 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA N 441 " --> pdb=" O TYR N 437 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU N 445 " --> pdb=" O ALA N 441 " (cutoff:3.500A) Processing helix chain 'N' and resid 445 through 454 Processing helix chain 'N' and resid 460 through 470 Processing helix chain 'N' and resid 490 through 494 Processing helix chain 'N' and resid 499 through 517 Processing helix chain 'O' and resid 18 through 33 Processing helix chain 'O' and resid 34 through 36 No H-bonds generated for 'chain 'O' and resid 34 through 36' Processing helix chain 'O' and resid 61 through 66 Processing helix chain 'O' and resid 67 through 69 No H-bonds generated for 'chain 'O' and resid 67 through 69' Processing helix chain 'O' and resid 77 through 90 removed outlier: 4.651A pdb=" N ALA O 83 " --> pdb=" O LEU O 79 " (cutoff:3.500A) Processing helix chain 'O' and resid 93 through 113 removed outlier: 3.911A pdb=" N VAL O 97 " --> pdb=" O GLY O 93 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR O 98 " --> pdb=" O THR O 94 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL O 108 " --> pdb=" O PHE O 104 " (cutoff:3.500A) Proline residue: O 110 - end of helix removed outlier: 3.939A pdb=" N GLU O 113 " --> pdb=" O LYS O 109 " (cutoff:3.500A) Processing helix chain 'O' and resid 117 through 140 removed outlier: 3.693A pdb=" N ILE O 121 " --> pdb=" O HIS O 117 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS O 137 " --> pdb=" O VAL O 133 " (cutoff:3.500A) Processing helix chain 'O' and resid 148 through 163 removed outlier: 3.661A pdb=" N THR O 161 " --> pdb=" O LYS O 157 " (cutoff:3.500A) Processing helix chain 'O' and resid 171 through 185 removed outlier: 3.862A pdb=" N MET O 178 " --> pdb=" O PHE O 174 " (cutoff:3.500A) Processing helix chain 'O' and resid 191 through 193 No H-bonds generated for 'chain 'O' and resid 191 through 193' Processing helix chain 'O' and resid 204 through 208 Processing helix chain 'O' and resid 259 through 282 removed outlier: 3.530A pdb=" N LEU O 274 " --> pdb=" O GLU O 270 " (cutoff:3.500A) Processing helix chain 'O' and resid 296 through 306 Processing helix chain 'O' and resid 315 through 327 Processing helix chain 'O' and resid 333 through 337 removed outlier: 4.063A pdb=" N ALA O 336 " --> pdb=" O SER O 333 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU O 337 " --> pdb=" O VAL O 334 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 333 through 337' Processing helix chain 'O' and resid 378 through 402 removed outlier: 3.543A pdb=" N LYS O 401 " --> pdb=" O ARG O 397 " (cutoff:3.500A) Processing helix chain 'O' and resid 410 through 425 Processing helix chain 'O' and resid 429 through 433 Processing helix chain 'O' and resid 434 through 442 removed outlier: 3.797A pdb=" N LEU O 442 " --> pdb=" O TYR O 438 " (cutoff:3.500A) Processing helix chain 'O' and resid 443 through 452 removed outlier: 3.525A pdb=" N ASN O 452 " --> pdb=" O GLN O 448 " (cutoff:3.500A) Processing helix chain 'O' and resid 456 through 468 Processing helix chain 'O' and resid 496 through 514 Processing helix chain 'P' and resid 28 through 45 removed outlier: 4.165A pdb=" N THR P 45 " --> pdb=" O GLN P 41 " (cutoff:3.500A) Processing helix chain 'P' and resid 68 through 73 Processing helix chain 'P' and resid 80 through 97 removed outlier: 3.960A pdb=" N MET P 85 " --> pdb=" O PRO P 81 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE P 86 " --> pdb=" O ALA P 82 " (cutoff:3.500A) Processing helix chain 'P' and resid 101 through 120 removed outlier: 4.000A pdb=" N LEU P 105 " --> pdb=" O THR P 101 " (cutoff:3.500A) Processing helix chain 'P' and resid 124 through 143 removed outlier: 4.596A pdb=" N GLU P 130 " --> pdb=" O SER P 126 " (cutoff:3.500A) Processing helix chain 'P' and resid 144 through 147 removed outlier: 4.022A pdb=" N VAL P 147 " --> pdb=" O PRO P 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 144 through 147' Processing helix chain 'P' and resid 156 through 164 removed outlier: 3.687A pdb=" N SER P 162 " --> pdb=" O ASP P 158 " (cutoff:3.500A) Processing helix chain 'P' and resid 164 through 170 removed outlier: 3.731A pdb=" N SER P 170 " --> pdb=" O THR P 166 " (cutoff:3.500A) Processing helix chain 'P' and resid 177 through 190 removed outlier: 3.689A pdb=" N SER P 189 " --> pdb=" O GLN P 185 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE P 190 " --> pdb=" O ALA P 186 " (cutoff:3.500A) Processing helix chain 'P' and resid 198 through 200 No H-bonds generated for 'chain 'P' and resid 198 through 200' Processing helix chain 'P' and resid 211 through 215 Processing helix chain 'P' and resid 261 through 285 removed outlier: 4.452A pdb=" N SER P 269 " --> pdb=" O LEU P 265 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LYS P 270 " --> pdb=" O MET P 266 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ILE P 283 " --> pdb=" O GLN P 279 " (cutoff:3.500A) Processing helix chain 'P' and resid 298 through 308 Processing helix chain 'P' and resid 317 through 329 Processing helix chain 'P' and resid 381 through 405 Processing helix chain 'P' and resid 413 through 429 removed outlier: 3.662A pdb=" N THR P 429 " --> pdb=" O SER P 425 " (cutoff:3.500A) Processing helix chain 'P' and resid 434 through 456 removed outlier: 3.803A pdb=" N PHE P 445 " --> pdb=" O PHE P 441 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU P 446 " --> pdb=" O ALA P 442 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ILE P 448 " --> pdb=" O ALA P 444 " (cutoff:3.500A) Proline residue: P 449 - end of helix Processing helix chain 'P' and resid 459 through 470 Processing helix chain 'P' and resid 491 through 496 Processing helix chain 'P' and resid 500 through 520 removed outlier: 3.620A pdb=" N LYS P 509 " --> pdb=" O TYR P 505 " (cutoff:3.500A) Processing helix chain 'a' and resid 14 through 33 removed outlier: 3.576A pdb=" N ARG a 18 " --> pdb=" O GLY a 14 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL a 22 " --> pdb=" O ARG a 18 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ILE a 31 " --> pdb=" O SER a 27 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL a 32 " --> pdb=" O ILE a 28 " (cutoff:3.500A) Processing helix chain 'a' and resid 34 through 36 No H-bonds generated for 'chain 'a' and resid 34 through 36' Processing helix chain 'a' and resid 57 through 65 Processing helix chain 'a' and resid 69 through 86 removed outlier: 3.916A pdb=" N VAL a 74 " --> pdb=" O PRO a 70 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU a 75 " --> pdb=" O ALA a 71 " (cutoff:3.500A) Processing helix chain 'a' and resid 91 through 109 Processing helix chain 'a' and resid 113 through 134 Processing helix chain 'a' and resid 139 through 144 removed outlier: 4.470A pdb=" N LEU a 143 " --> pdb=" O ASN a 139 " (cutoff:3.500A) Processing helix chain 'a' and resid 144 through 157 removed outlier: 4.146A pdb=" N LEU a 148 " --> pdb=" O GLY a 144 " (cutoff:3.500A) Processing helix chain 'a' and resid 166 through 178 Processing helix chain 'a' and resid 191 through 195 Processing helix chain 'a' and resid 204 through 208 Processing helix chain 'a' and resid 256 through 258 No H-bonds generated for 'chain 'a' and resid 256 through 258' Processing helix chain 'a' and resid 259 through 278 removed outlier: 3.880A pdb=" N GLU a 267 " --> pdb=" O ILE a 263 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N SER a 268 " --> pdb=" O ARG a 264 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N THR a 271 " --> pdb=" O GLU a 267 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN a 276 " --> pdb=" O LYS a 272 " (cutoff:3.500A) Processing helix chain 'a' and resid 293 through 303 removed outlier: 3.943A pdb=" N LYS a 298 " --> pdb=" O ASP a 294 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TYR a 299 " --> pdb=" O MET a 295 " (cutoff:3.500A) Processing helix chain 'a' and resid 312 through 324 removed outlier: 3.825A pdb=" N ARG a 318 " --> pdb=" O ARG a 314 " (cutoff:3.500A) Processing helix chain 'a' and resid 341 through 345 removed outlier: 4.100A pdb=" N LEU a 345 " --> pdb=" O ALA a 342 " (cutoff:3.500A) Processing helix chain 'a' and resid 381 through 405 Processing helix chain 'a' and resid 413 through 430 removed outlier: 3.634A pdb=" N ILE a 421 " --> pdb=" O ALA a 417 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLU a 424 " --> pdb=" O SER a 420 " (cutoff:3.500A) Processing helix chain 'a' and resid 434 through 445 removed outlier: 3.623A pdb=" N LEU a 445 " --> pdb=" O PHE a 441 " (cutoff:3.500A) Processing helix chain 'a' and resid 446 through 456 Processing helix chain 'a' and resid 459 through 477 removed outlier: 3.907A pdb=" N ALA a 465 " --> pdb=" O THR a 461 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA a 474 " --> pdb=" O PHE a 470 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN a 475 " --> pdb=" O HIS a 471 " (cutoff:3.500A) Processing helix chain 'a' and resid 498 through 502 Processing helix chain 'a' and resid 507 through 524 removed outlier: 3.992A pdb=" N SER a 513 " --> pdb=" O VAL a 509 " (cutoff:3.500A) Processing helix chain 'a' and resid 525 through 527 No H-bonds generated for 'chain 'a' and resid 525 through 527' Processing helix chain 'e' and resid 19 through 23 removed outlier: 3.689A pdb=" N LYS e 23 " --> pdb=" O GLN e 20 " (cutoff:3.500A) Processing helix chain 'e' and resid 29 through 48 removed outlier: 4.562A pdb=" N THR e 48 " --> pdb=" O ASN e 44 " (cutoff:3.500A) Processing helix chain 'e' and resid 71 through 78 Processing helix chain 'e' and resid 83 through 100 removed outlier: 3.819A pdb=" N LEU e 88 " --> pdb=" O GLN e 84 " (cutoff:3.500A) Processing helix chain 'e' and resid 105 through 124 removed outlier: 3.580A pdb=" N GLU e 119 " --> pdb=" O LEU e 115 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLN e 120 " --> pdb=" O GLU e 116 " (cutoff:3.500A) Processing helix chain 'e' and resid 127 through 147 removed outlier: 3.965A pdb=" N VAL e 141 " --> pdb=" O GLN e 137 " (cutoff:3.500A) Processing helix chain 'e' and resid 160 through 172 Processing helix chain 'e' and resid 176 through 180 Processing helix chain 'e' and resid 181 through 193 Processing helix chain 'e' and resid 203 through 205 No H-bonds generated for 'chain 'e' and resid 203 through 205' Processing helix chain 'e' and resid 216 through 220 Processing helix chain 'e' and resid 268 through 292 removed outlier: 3.549A pdb=" N LYS e 282 " --> pdb=" O TYR e 278 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N PHE e 283 " --> pdb=" O GLU e 279 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N GLU e 284 " --> pdb=" O LYS e 280 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU e 285 " --> pdb=" O GLU e 281 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET e 286 " --> pdb=" O LYS e 282 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE e 287 " --> pdb=" O PHE e 283 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ILE e 290 " --> pdb=" O MET e 286 " (cutoff:3.500A) Processing helix chain 'e' and resid 305 through 315 removed outlier: 3.590A pdb=" N HIS e 310 " --> pdb=" O ASP e 306 " (cutoff:3.500A) Processing helix chain 'e' and resid 324 through 336 Processing helix chain 'e' and resid 347 through 351 Processing helix chain 'e' and resid 389 through 413 removed outlier: 3.551A pdb=" N ILE e 393 " --> pdb=" O ASN e 389 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG e 398 " --> pdb=" O GLU e 394 " (cutoff:3.500A) Processing helix chain 'e' and resid 421 through 436 removed outlier: 3.869A pdb=" N ASP e 436 " --> pdb=" O SER e 432 " (cutoff:3.500A) Processing helix chain 'e' and resid 442 through 454 removed outlier: 3.852A pdb=" N GLU e 454 " --> pdb=" O ALA e 450 " (cutoff:3.500A) Processing helix chain 'e' and resid 454 through 464 Processing helix chain 'e' and resid 467 through 482 removed outlier: 3.529A pdb=" N VAL e 480 " --> pdb=" O ARG e 476 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU e 482 " --> pdb=" O ARG e 478 " (cutoff:3.500A) Processing helix chain 'e' and resid 498 through 503 Processing helix chain 'e' and resid 508 through 527 removed outlier: 3.565A pdb=" N ILE e 525 " --> pdb=" O MET e 521 " (cutoff:3.500A) Processing helix chain 'z' and resid 3 through 8 Processing helix chain 'z' and resid 15 through 35 removed outlier: 3.558A pdb=" N LEU z 20 " --> pdb=" O ALA z 16 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA z 21 " --> pdb=" O GLN z 17 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL z 33 " --> pdb=" O GLY z 29 " (cutoff:3.500A) Processing helix chain 'z' and resid 36 through 38 No H-bonds generated for 'chain 'z' and resid 36 through 38' Processing helix chain 'z' and resid 59 through 66 Processing helix chain 'z' and resid 73 through 88 removed outlier: 3.669A pdb=" N GLN z 84 " --> pdb=" O VAL z 80 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ASP z 85 " --> pdb=" O ALA z 81 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASP z 86 " --> pdb=" O THR z 82 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE z 87 " --> pdb=" O ALA z 83 " (cutoff:3.500A) Processing helix chain 'z' and resid 91 through 111 removed outlier: 3.841A pdb=" N ALA z 106 " --> pdb=" O LEU z 102 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASP z 107 " --> pdb=" O LEU z 103 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LEU z 108 " --> pdb=" O LYS z 104 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N TYR z 109 " --> pdb=" O GLN z 105 " (cutoff:3.500A) Processing helix chain 'z' and resid 115 through 137 removed outlier: 4.138A pdb=" N ILE z 119 " --> pdb=" O HIS z 115 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU z 136 " --> pdb=" O GLN z 132 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL z 137 " --> pdb=" O PHE z 133 " (cutoff:3.500A) Processing helix chain 'z' and resid 144 through 157 Processing helix chain 'z' and resid 164 through 178 removed outlier: 4.245A pdb=" N GLU z 170 " --> pdb=" O ASP z 166 " (cutoff:3.500A) Processing helix chain 'z' and resid 187 through 189 No H-bonds generated for 'chain 'z' and resid 187 through 189' Processing helix chain 'z' and resid 200 through 204 Processing helix chain 'z' and resid 252 through 264 removed outlier: 4.023A pdb=" N ARG z 264 " --> pdb=" O VAL z 260 " (cutoff:3.500A) Processing helix chain 'z' and resid 264 through 280 removed outlier: 3.838A pdb=" N ARG z 270 " --> pdb=" O PHE z 266 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LEU z 277 " --> pdb=" O LYS z 273 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LYS z 278 " --> pdb=" O ILE z 274 " (cutoff:3.500A) Processing helix chain 'z' and resid 298 through 308 removed outlier: 3.733A pdb=" N GLU z 308 " --> pdb=" O ALA z 304 " (cutoff:3.500A) Processing helix chain 'z' and resid 319 through 329 removed outlier: 3.855A pdb=" N THR z 325 " --> pdb=" O MET z 321 " (cutoff:3.500A) Processing helix chain 'z' and resid 340 through 344 Processing helix chain 'z' and resid 380 through 404 removed outlier: 3.795A pdb=" N ARG z 396 " --> pdb=" O ARG z 392 " (cutoff:3.500A) Processing helix chain 'z' and resid 412 through 425 removed outlier: 4.129A pdb=" N ALA z 417 " --> pdb=" O ALA z 413 " (cutoff:3.500A) Processing helix chain 'z' and resid 426 through 429 Processing helix chain 'z' and resid 433 through 444 Processing helix chain 'z' and resid 445 through 455 Processing helix chain 'z' and resid 458 through 472 removed outlier: 3.605A pdb=" N THR z 462 " --> pdb=" O ASP z 458 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU z 463 " --> pdb=" O LEU z 459 " (cutoff:3.500A) Processing helix chain 'z' and resid 489 through 493 Processing helix chain 'z' and resid 497 through 516 removed outlier: 3.986A pdb=" N THR z 509 " --> pdb=" O LEU z 505 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.322A pdb=" N ASP A 529 " --> pdb=" O MET I 60 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N GLN I 62 " --> pdb=" O ASP A 529 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE A 531 " --> pdb=" O GLN I 62 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 55 removed outlier: 6.473A pdb=" N ASP A 42 " --> pdb=" O ILE G 519 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASP G 521 " --> pdb=" O ASP A 42 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 196 through 201 removed outlier: 6.210A pdb=" N ASN A 196 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N LEU A 377 " --> pdb=" O ASN A 196 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU A 198 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N GLY A 379 " --> pdb=" O LEU A 198 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ALA A 200 " --> pdb=" O GLY A 379 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLU A 350 " --> pdb=" O LYS A 365 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLU A 350 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL A 230 " --> pdb=" O GLU A 350 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL A 352 " --> pdb=" O ARG A 228 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ARG A 228 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ILE A 286 " --> pdb=" O VAL A 308 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 264 through 266 removed outlier: 9.092A pdb=" N GLN I 263 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VAL B 256 " --> pdb=" O GLN I 263 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N VAL I 265 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL B 258 " --> pdb=" O VAL I 265 " (cutoff:3.500A) removed outlier: 9.289A pdb=" N ASP G 255 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL A 252 " --> pdb=" O ASP G 255 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 408 through 410 Processing sheet with id=AA6, first strand: chain 'A' and resid 486 through 488 Processing sheet with id=AA7, first strand: chain 'B' and resid 17 through 20 removed outlier: 6.446A pdb=" N ASP E 56 " --> pdb=" O VAL B 517 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ASN B 519 " --> pdb=" O ASP E 56 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 62 through 64 removed outlier: 6.326A pdb=" N ASP B 49 " --> pdb=" O ILE I 532 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP I 534 " --> pdb=" O ASP B 49 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU B 53 " --> pdb=" O VAL I 536 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 199 through 205 removed outlier: 6.494A pdb=" N HIS B 200 " --> pdb=" O ILE B 373 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N LEU B 375 " --> pdb=" O HIS B 200 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ILE B 202 " --> pdb=" O LEU B 375 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N GLY B 377 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LYS B 204 " --> pdb=" O GLY B 377 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR B 372 " --> pdb=" O ASP B 215 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR B 213 " --> pdb=" O VAL B 374 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 218 through 220 Processing sheet with id=AB2, first strand: chain 'B' and resid 310 through 313 Processing sheet with id=AB3, first strand: chain 'B' and resid 406 through 408 Processing sheet with id=AB4, first strand: chain 'B' and resid 476 through 479 removed outlier: 3.514A pdb=" N THR B 484 " --> pdb=" O ASP B 479 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 207 through 211 Processing sheet with id=AB6, first strand: chain 'E' and resid 240 through 241 Processing sheet with id=AB7, first strand: chain 'E' and resid 319 through 320 removed outlier: 6.922A pdb=" N ALA E 298 " --> pdb=" O VAL E 320 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N LYS E 245 " --> pdb=" O LEU E 297 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N ILE E 299 " --> pdb=" O LYS E 245 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ALA E 247 " --> pdb=" O ILE E 299 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 416 through 418 Processing sheet with id=AB9, first strand: chain 'E' and resid 528 through 532 removed outlier: 4.567A pdb=" N ILE E 528 " --> pdb=" O ASP H 46 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N LEU H 48 " --> pdb=" O ILE E 528 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ASP E 530 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N VAL H 50 " --> pdb=" O ASP E 530 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ARG E 532 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 57 through 60 removed outlier: 6.201A pdb=" N MET G 49 " --> pdb=" O MET K 522 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 142 through 143 Processing sheet with id=AC3, first strand: chain 'G' and resid 199 through 205 removed outlier: 4.266A pdb=" N GLY G 378 " --> pdb=" O ILE G 204 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR G 373 " --> pdb=" O LEU G 215 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 218 through 220 Processing sheet with id=AC5, first strand: chain 'G' and resid 310 through 312 removed outlier: 9.186A pdb=" N VAL G 332 " --> pdb=" O ILE G 238 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU G 240 " --> pdb=" O VAL G 332 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 478 through 480 removed outlier: 3.502A pdb=" N GLY G 479 " --> pdb=" O VAL G 488 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL G 488 " --> pdb=" O GLY G 479 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'H' and resid 14 through 17 removed outlier: 6.028A pdb=" N ASN J 53 " --> pdb=" O VAL H 516 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU H 518 " --> pdb=" O ASN J 53 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 195 through 201 removed outlier: 6.672A pdb=" N GLY H 196 " --> pdb=" O PHE H 372 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N LEU H 374 " --> pdb=" O GLY H 196 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LYS H 198 " --> pdb=" O LEU H 374 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N GLY H 376 " --> pdb=" O LYS H 198 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL H 200 " --> pdb=" O GLY H 376 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 215 through 216 Processing sheet with id=AD1, first strand: chain 'H' and resid 309 through 311 removed outlier: 6.433A pdb=" N VAL H 289 " --> pdb=" O ALA H 311 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LYS H 236 " --> pdb=" O VAL H 288 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N SER H 290 " --> pdb=" O LYS H 236 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ALA H 238 " --> pdb=" O SER H 290 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N GLN H 331 " --> pdb=" O ILE H 237 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU H 239 " --> pdb=" O GLN H 331 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'H' and resid 309 through 311 removed outlier: 6.433A pdb=" N VAL H 289 " --> pdb=" O ALA H 311 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LYS H 236 " --> pdb=" O VAL H 288 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N SER H 290 " --> pdb=" O LYS H 236 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ALA H 238 " --> pdb=" O SER H 290 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 253 through 255 Processing sheet with id=AD4, first strand: chain 'H' and resid 405 through 407 Processing sheet with id=AD5, first strand: chain 'H' and resid 475 through 477 Processing sheet with id=AD6, first strand: chain 'I' and resid 153 through 154 Processing sheet with id=AD7, first strand: chain 'I' and resid 208 through 212 removed outlier: 6.214A pdb=" N LYS I 209 " --> pdb=" O ILE I 388 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N VAL I 390 " --> pdb=" O LYS I 209 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL I 211 " --> pdb=" O VAL I 390 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'I' and resid 227 through 229 removed outlier: 3.569A pdb=" N LEU I 373 " --> pdb=" O VAL I 365 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU I 361 " --> pdb=" O GLU I 242 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N GLU I 242 " --> pdb=" O LEU I 361 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLU I 363 " --> pdb=" O ARG I 240 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ARG I 240 " --> pdb=" O GLU I 363 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N VAL I 297 " --> pdb=" O LYS I 243 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N LYS I 245 " --> pdb=" O VAL I 297 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N LEU I 299 " --> pdb=" O LYS I 245 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLY I 247 " --> pdb=" O LEU I 299 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N GLN I 301 " --> pdb=" O GLY I 247 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ILE I 249 " --> pdb=" O GLN I 301 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 227 through 229 removed outlier: 3.569A pdb=" N LEU I 373 " --> pdb=" O VAL I 365 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU I 361 " --> pdb=" O GLU I 242 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N GLU I 242 " --> pdb=" O LEU I 361 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLU I 363 " --> pdb=" O ARG I 240 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ARG I 240 " --> pdb=" O GLU I 363 " (cutoff:3.500A) removed outlier: 9.313A pdb=" N VAL I 345 " --> pdb=" O ILE I 246 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N LEU I 248 " --> pdb=" O VAL I 345 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 491 through 494 Processing sheet with id=AE2, first strand: chain 'J' and resid 21 through 23 Processing sheet with id=AE3, first strand: chain 'J' and resid 149 through 150 removed outlier: 3.551A pdb=" N CYS J 149 " --> pdb=" O LEU J 408 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 202 through 208 removed outlier: 6.604A pdb=" N ARG J 203 " --> pdb=" O ILE J 375 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N LEU J 377 " --> pdb=" O ARG J 203 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N CYS J 205 " --> pdb=" O LEU J 377 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N GLY J 379 " --> pdb=" O CYS J 205 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ILE J 207 " --> pdb=" O GLY J 379 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 220 through 223 Processing sheet with id=AE6, first strand: chain 'J' and resid 311 through 314 removed outlier: 9.230A pdb=" N LEU J 333 " --> pdb=" O ILE J 239 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N VAL J 241 " --> pdb=" O LEU J 333 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 311 through 314 Processing sheet with id=AE8, first strand: chain 'K' and resid 191 through 195 Processing sheet with id=AE9, first strand: chain 'K' and resid 210 through 212 removed outlier: 6.826A pdb=" N GLY K 348 " --> pdb=" O ASP K 227 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N VAL K 290 " --> pdb=" O ASP K 227 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N TYR K 229 " --> pdb=" O VAL K 290 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 477 through 478 Processing sheet with id=AF2, first strand: chain 'L' and resid 17 through 20 removed outlier: 4.399A pdb=" N VAL L 517 " --> pdb=" O ASP e 56 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N MET e 58 " --> pdb=" O VAL L 517 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ASN L 519 " --> pdb=" O MET e 58 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N VAL e 60 " --> pdb=" O ASN L 519 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE L 521 " --> pdb=" O VAL e 60 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 62 through 64 removed outlier: 7.017A pdb=" N ASP L 49 " --> pdb=" O ASP M 534 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N VAL M 536 " --> pdb=" O ASP L 49 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ILE L 51 " --> pdb=" O VAL M 536 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 199 through 205 removed outlier: 6.344A pdb=" N HIS L 200 " --> pdb=" O ILE L 373 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N LEU L 375 " --> pdb=" O HIS L 200 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ILE L 202 " --> pdb=" O LEU L 375 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N GLY L 377 " --> pdb=" O ILE L 202 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LYS L 204 " --> pdb=" O GLY L 377 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR L 372 " --> pdb=" O ASP L 215 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 218 through 220 Processing sheet with id=AF6, first strand: chain 'L' and resid 310 through 313 removed outlier: 6.746A pdb=" N PHE L 290 " --> pdb=" O ILE L 312 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'N' and resid 255 through 256 removed outlier: 8.915A pdb=" N GLN M 263 " --> pdb=" O SER L 254 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VAL L 256 " --> pdb=" O GLN M 263 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N VAL M 265 " --> pdb=" O VAL L 256 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL L 258 " --> pdb=" O VAL M 265 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'L' and resid 406 through 408 Processing sheet with id=AF9, first strand: chain 'L' and resid 476 through 479 Processing sheet with id=AG1, first strand: chain 'M' and resid 68 through 71 Processing sheet with id=AG2, first strand: chain 'M' and resid 153 through 154 Processing sheet with id=AG3, first strand: chain 'M' and resid 208 through 212 removed outlier: 6.242A pdb=" N LYS M 209 " --> pdb=" O ILE M 388 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N VAL M 390 " --> pdb=" O LYS M 209 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL M 211 " --> pdb=" O VAL M 390 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'M' and resid 227 through 229 removed outlier: 3.617A pdb=" N LEU M 373 " --> pdb=" O VAL M 365 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N GLU M 360 " --> pdb=" O LYS M 243 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'M' and resid 323 through 328 removed outlier: 3.678A pdb=" N ASP M 327 " --> pdb=" O ILE M 300 " (cutoff:3.500A) removed outlier: 9.535A pdb=" N VAL M 345 " --> pdb=" O ILE M 246 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N LEU M 248 " --> pdb=" O VAL M 345 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'M' and resid 491 through 494 Processing sheet with id=AG7, first strand: chain 'N' and resid 15 through 18 removed outlier: 4.439A pdb=" N ILE N 519 " --> pdb=" O ASP a 42 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N MET a 44 " --> pdb=" O ILE N 519 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ASP N 521 " --> pdb=" O MET a 44 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N VAL a 46 " --> pdb=" O ASP N 521 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N VAL N 523 " --> pdb=" O VAL a 46 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'N' and resid 57 through 60 removed outlier: 6.352A pdb=" N MET N 49 " --> pdb=" O MET z 522 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'N' and resid 142 through 143 Processing sheet with id=AH1, first strand: chain 'N' and resid 184 through 185 Processing sheet with id=AH2, first strand: chain 'N' and resid 199 through 205 removed outlier: 3.533A pdb=" N ARG N 200 " --> pdb=" O CYS N 372 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLY N 378 " --> pdb=" O ILE N 204 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR N 373 " --> pdb=" O LEU N 215 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'N' and resid 218 through 220 Processing sheet with id=AH4, first strand: chain 'N' and resid 310 through 312 removed outlier: 9.383A pdb=" N VAL N 332 " --> pdb=" O ILE N 238 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LEU N 240 " --> pdb=" O VAL N 332 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'N' and resid 478 through 480 removed outlier: 3.589A pdb=" N VAL N 488 " --> pdb=" O GLY N 479 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'O' and resid 14 through 17 removed outlier: 6.024A pdb=" N ASN P 53 " --> pdb=" O VAL O 516 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU O 518 " --> pdb=" O ASN P 53 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'O' and resid 56 through 59 removed outlier: 7.658A pdb=" N ASP O 46 " --> pdb=" O ASP e 529 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ILE e 531 " --> pdb=" O ASP O 46 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N LEU O 48 " --> pdb=" O ILE e 531 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'O' and resid 195 through 201 removed outlier: 6.488A pdb=" N GLY O 196 " --> pdb=" O PHE O 372 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N LEU O 374 " --> pdb=" O GLY O 196 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LYS O 198 " --> pdb=" O LEU O 374 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N GLY O 376 " --> pdb=" O LYS O 198 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL O 200 " --> pdb=" O GLY O 376 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'O' and resid 215 through 216 removed outlier: 3.553A pdb=" N GLU O 349 " --> pdb=" O PHE O 360 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'O' and resid 309 through 311 removed outlier: 5.994A pdb=" N LYS O 236 " --> pdb=" O VAL O 288 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N SER O 290 " --> pdb=" O LYS O 236 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ALA O 238 " --> pdb=" O SER O 290 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N GLN O 331 " --> pdb=" O ILE O 237 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU O 239 " --> pdb=" O GLN O 331 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'O' and resid 309 through 311 removed outlier: 5.994A pdb=" N LYS O 236 " --> pdb=" O VAL O 288 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N SER O 290 " --> pdb=" O LYS O 236 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ALA O 238 " --> pdb=" O SER O 290 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'O' and resid 253 through 255 Processing sheet with id=AI4, first strand: chain 'O' and resid 405 through 407 Processing sheet with id=AI5, first strand: chain 'O' and resid 475 through 477 Processing sheet with id=AI6, first strand: chain 'P' and resid 21 through 23 Processing sheet with id=AI7, first strand: chain 'P' and resid 149 through 150 Processing sheet with id=AI8, first strand: chain 'P' and resid 202 through 208 removed outlier: 6.658A pdb=" N ARG P 203 " --> pdb=" O ILE P 375 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N LEU P 377 " --> pdb=" O ARG P 203 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N CYS P 205 " --> pdb=" O LEU P 377 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N GLY P 379 " --> pdb=" O CYS P 205 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE P 207 " --> pdb=" O GLY P 379 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'P' and resid 220 through 223 Processing sheet with id=AJ1, first strand: chain 'P' and resid 311 through 314 removed outlier: 9.485A pdb=" N LEU P 333 " --> pdb=" O ILE P 239 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N VAL P 241 " --> pdb=" O LEU P 333 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'P' and resid 311 through 314 Processing sheet with id=AJ3, first strand: chain 'a' and resid 181 through 183 Processing sheet with id=AJ4, first strand: chain 'a' and resid 196 through 201 removed outlier: 6.236A pdb=" N ASN a 196 " --> pdb=" O ILE a 375 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N LEU a 377 " --> pdb=" O ASN a 196 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU a 198 " --> pdb=" O LEU a 377 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N GLY a 379 " --> pdb=" O LEU a 198 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ALA a 200 " --> pdb=" O GLY a 379 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE a 362 " --> pdb=" O LEU a 216 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU a 350 " --> pdb=" O LYS a 365 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N GLU a 350 " --> pdb=" O VAL a 230 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N VAL a 230 " --> pdb=" O GLU a 350 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL a 352 " --> pdb=" O ARG a 228 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ARG a 228 " --> pdb=" O VAL a 352 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'a' and resid 408 through 410 Processing sheet with id=AJ6, first strand: chain 'a' and resid 486 through 488 Processing sheet with id=AJ7, first strand: chain 'e' and resid 207 through 213 removed outlier: 6.494A pdb=" N LYS e 208 " --> pdb=" O ILE e 383 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ILE e 385 " --> pdb=" O LYS e 208 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLU e 210 " --> pdb=" O ILE e 385 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N GLY e 387 " --> pdb=" O GLU e 210 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N LYS e 212 " --> pdb=" O GLY e 387 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'e' and resid 226 through 228 Processing sheet with id=AJ9, first strand: chain 'e' and resid 319 through 320 removed outlier: 6.592A pdb=" N ALA e 298 " --> pdb=" O VAL e 320 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N LYS e 245 " --> pdb=" O LEU e 297 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ILE e 299 " --> pdb=" O LYS e 245 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ALA e 247 " --> pdb=" O ILE e 299 " (cutoff:3.500A) removed outlier: 8.630A pdb=" N VAL e 340 " --> pdb=" O ILE e 246 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ILE e 248 " --> pdb=" O VAL e 340 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ9 Processing sheet with id=AK1, first strand: chain 'e' and resid 319 through 320 removed outlier: 6.592A pdb=" N ALA e 298 " --> pdb=" O VAL e 320 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N LYS e 245 " --> pdb=" O LEU e 297 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ILE e 299 " --> pdb=" O LYS e 245 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ALA e 247 " --> pdb=" O ILE e 299 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'e' and resid 416 through 418 Processing sheet with id=AK3, first strand: chain 'z' and resid 139 through 140 Processing sheet with id=AK4, first strand: chain 'z' and resid 191 through 195 removed outlier: 6.799A pdb=" N GLU z 192 " --> pdb=" O LEU z 374 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ILE z 376 " --> pdb=" O GLU z 192 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N MET z 194 " --> pdb=" O ILE z 376 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'z' and resid 210 through 212 removed outlier: 6.355A pdb=" N HIS z 346 " --> pdb=" O TYR z 229 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N TYR z 229 " --> pdb=" O HIS z 346 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLY z 348 " --> pdb=" O ASP z 227 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N VAL z 290 " --> pdb=" O ASP z 227 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N TYR z 229 " --> pdb=" O VAL z 290 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'z' and resid 477 through 478 3456 hydrogen bonds defined for protein. 9852 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: 28.43 Time building geometry restraints manager: 21.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.10 - 1.24: 11134 1.24 - 1.38: 12415 1.38 - 1.52: 31107 1.52 - 1.67: 9908 1.67 - 1.81: 656 Bond restraints: 65220 Sorted by residual: bond pdb=" CA THR O 94 " pdb=" C THR O 94 " ideal model delta sigma weight residual 1.524 1.367 0.157 7.00e-03 2.04e+04 5.03e+02 bond pdb=" CA THR M 106 " pdb=" C THR M 106 " ideal model delta sigma weight residual 1.521 1.360 0.162 1.29e-02 6.01e+03 1.57e+02 bond pdb=" CA ASP A 88 " pdb=" C ASP A 88 " ideal model delta sigma weight residual 1.533 1.415 0.119 9.60e-03 1.09e+04 1.53e+02 bond pdb=" N THR O 94 " pdb=" CA THR O 94 " ideal model delta sigma weight residual 1.459 1.343 0.116 1.06e-02 8.90e+03 1.19e+02 bond pdb=" CA ASN P 102 " pdb=" C ASN P 102 " ideal model delta sigma weight residual 1.523 1.376 0.147 1.37e-02 5.33e+03 1.15e+02 ... (remaining 65215 not shown) Histogram of bond angle deviations from ideal: 100.55 - 107.22: 1678 107.22 - 113.88: 38592 113.88 - 120.55: 25314 120.55 - 127.22: 21963 127.22 - 133.89: 449 Bond angle restraints: 87996 Sorted by residual: angle pdb=" C GLY O 93 " pdb=" N THR O 94 " pdb=" CA THR O 94 " ideal model delta sigma weight residual 122.44 108.33 14.11 1.19e+00 7.06e-01 1.41e+02 angle pdb=" C GLY M 105 " pdb=" N THR M 106 " pdb=" CA THR M 106 " ideal model delta sigma weight residual 122.26 105.07 17.19 1.59e+00 3.96e-01 1.17e+02 angle pdb=" C LEU K 114 " pdb=" N HIS K 115 " pdb=" CA HIS K 115 " ideal model delta sigma weight residual 120.67 131.81 -11.14 1.34e+00 5.57e-01 6.91e+01 angle pdb=" O GLY A 87 " pdb=" C GLY A 87 " pdb=" N ASP A 88 " ideal model delta sigma weight residual 122.65 114.13 8.52 1.13e+00 7.83e-01 5.69e+01 angle pdb=" C LEU z 114 " pdb=" N HIS z 115 " pdb=" CA HIS z 115 " ideal model delta sigma weight residual 120.49 131.16 -10.67 1.42e+00 4.96e-01 5.65e+01 ... (remaining 87991 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 39404 17.93 - 35.86: 760 35.86 - 53.79: 199 53.79 - 71.73: 96 71.73 - 89.66: 43 Dihedral angle restraints: 40502 sinusoidal: 16210 harmonic: 24292 Sorted by residual: dihedral pdb=" CA ASP J 499 " pdb=" C ASP J 499 " pdb=" N THR J 500 " pdb=" CA THR J 500 " ideal model delta harmonic sigma weight residual 180.00 146.51 33.49 0 5.00e+00 4.00e-02 4.49e+01 dihedral pdb=" CA ILE L 249 " pdb=" C ILE L 249 " pdb=" N LYS L 250 " pdb=" CA LYS L 250 " ideal model delta harmonic sigma weight residual 180.00 148.73 31.27 0 5.00e+00 4.00e-02 3.91e+01 dihedral pdb=" CA ILE B 249 " pdb=" C ILE B 249 " pdb=" N LYS B 250 " pdb=" CA LYS B 250 " ideal model delta harmonic sigma weight residual 180.00 149.97 30.03 0 5.00e+00 4.00e-02 3.61e+01 ... (remaining 40499 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 9712 0.118 - 0.237: 810 0.237 - 0.355: 2 0.355 - 0.473: 2 0.473 - 0.592: 2 Chirality restraints: 10528 Sorted by residual: chirality pdb=" CA THR M 106 " pdb=" N THR M 106 " pdb=" C THR M 106 " pdb=" CB THR M 106 " both_signs ideal model delta sigma weight residual False 2.53 1.93 0.59 2.00e-01 2.50e+01 8.75e+00 chirality pdb=" CA THR O 94 " pdb=" N THR O 94 " pdb=" C THR O 94 " pdb=" CB THR O 94 " both_signs ideal model delta sigma weight residual False 2.53 2.04 0.49 2.00e-01 2.50e+01 5.92e+00 chirality pdb=" CA THR I 106 " pdb=" N THR I 106 " pdb=" C THR I 106 " pdb=" CB THR I 106 " both_signs ideal model delta sigma weight residual False 2.53 2.10 0.42 2.00e-01 2.50e+01 4.48e+00 ... (remaining 10525 not shown) Planarity restraints: 11312 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY O 93 " 0.039 2.00e-02 2.50e+03 8.10e-02 6.55e+01 pdb=" C GLY O 93 " -0.140 2.00e-02 2.50e+03 pdb=" O GLY O 93 " 0.054 2.00e-02 2.50e+03 pdb=" N THR O 94 " 0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY M 105 " 0.033 2.00e-02 2.50e+03 6.83e-02 4.66e+01 pdb=" C GLY M 105 " -0.118 2.00e-02 2.50e+03 pdb=" O GLY M 105 " 0.045 2.00e-02 2.50e+03 pdb=" N THR M 106 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR P 101 " 0.031 2.00e-02 2.50e+03 6.09e-02 3.71e+01 pdb=" C THR P 101 " -0.105 2.00e-02 2.50e+03 pdb=" O THR P 101 " 0.039 2.00e-02 2.50e+03 pdb=" N ASN P 102 " 0.036 2.00e-02 2.50e+03 ... (remaining 11309 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3626 2.74 - 3.28: 65938 3.28 - 3.82: 98429 3.82 - 4.36: 125563 4.36 - 4.90: 208858 Nonbonded interactions: 502414 Sorted by model distance: nonbonded pdb=" OG1 THR a 55 " pdb=" OD1 ASP a 57 " model vdw 2.197 2.440 nonbonded pdb=" O ASP N 242 " pdb=" OD1 ASP N 242 " model vdw 2.258 3.040 nonbonded pdb=" N GLU J 343 " pdb=" OE1 GLU J 343 " model vdw 2.266 2.520 nonbonded pdb=" OD2 ASP G 298 " pdb=" NZ LYS K 295 " model vdw 2.302 2.520 nonbonded pdb=" NZ LYS G 48 " pdb=" OE1 GLU K 520 " model vdw 2.319 2.520 ... (remaining 502409 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' selection = chain 'a' } ncs_group { reference = chain 'B' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'e' } ncs_group { reference = chain 'G' selection = chain 'N' } ncs_group { reference = chain 'H' selection = chain 'O' } ncs_group { reference = chain 'I' selection = chain 'M' } ncs_group { reference = chain 'J' selection = chain 'P' } ncs_group { reference = chain 'K' selection = chain 'z' } Set up NCS constraints Number of NCS constrained groups: 8 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'a' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'L' } pdb_interpretation.ncs_group { reference = chain 'E' selection = chain 'e' } pdb_interpretation.ncs_group { reference = chain 'G' selection = chain 'N' } pdb_interpretation.ncs_group { reference = chain 'H' selection = chain 'O' } pdb_interpretation.ncs_group { reference = chain 'I' selection = chain 'M' } pdb_interpretation.ncs_group { reference = chain 'J' selection = chain 'P' } pdb_interpretation.ncs_group { reference = chain 'K' selection = chain 'z' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 11.920 Check model and map are aligned: 0.730 Set scattering table: 0.450 Process input model: 136.780 Find NCS groups from input model: 5.570 Set up NCS constraints: 0.350 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.020 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 160.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 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 0.162 65220 Z= 0.615 Angle : 0.729 17.190 87996 Z= 0.489 Chirality : 0.059 0.592 10528 Planarity : 0.003 0.081 11312 Dihedral : 9.961 89.657 24766 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 0.93 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.16 % Favored : 96.68 % Rotamer: Outliers : 0.01 % Allowed : 0.38 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.09), residues: 8408 helix: -0.38 (0.07), residues: 4020 sheet: 0.08 (0.16), residues: 990 loop : -0.83 (0.11), residues: 3398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 130 HIS 0.003 0.000 HIS B 122 PHE 0.007 0.000 PHE H 381 TYR 0.004 0.000 TYR J 304 ARG 0.002 0.000 ARG J 378 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16816 Ramachandran restraints generated. 8408 Oldfield, 0 Emsley, 8408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16816 Ramachandran restraints generated. 8408 Oldfield, 0 Emsley, 8408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.1905 time to fit residues: 39.7884 Evaluate side-chains 64 residues out of total 448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.368 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5286 Evaluate side-chains 163 residues out of total 416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 0.357 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.1749 time to fit residues: 33.6243 Evaluate side-chains 65 residues out of total 416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.352 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4792 Evaluate side-chains 182 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.1736 time to fit residues: 37.1427 Evaluate side-chains 59 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.384 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5121 Evaluate side-chains 185 residues out of total 457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 0.370 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.1721 time to fit residues: 37.3094 Evaluate side-chains 78 residues out of total 457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.367 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5064 Evaluate side-chains 179 residues out of total 433 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.1667 time to fit residues: 35.0807 Evaluate side-chains 86 residues out of total 433 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.354 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4799 Evaluate side-chains 181 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.1660 time to fit residues: 35.1629 Evaluate side-chains 74 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.356 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4794 Evaluate side-chains 174 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 0.366 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.1829 time to fit residues: 37.0435 Evaluate side-chains 73 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.348 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4656 Evaluate side-chains 167 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 0.356 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.1572 time to fit residues: 31.1513 Evaluate side-chains 74 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.358 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 836 random chunks: chunk 705 optimal weight: 2.9990 chunk 633 optimal weight: 0.8980 chunk 351 optimal weight: 4.9990 chunk 216 optimal weight: 1.9990 chunk 427 optimal weight: 2.9990 chunk 338 optimal weight: 8.9990 chunk 655 optimal weight: 0.0570 chunk 253 optimal weight: 0.9990 chunk 398 optimal weight: 0.9990 chunk 487 optimal weight: 3.9990 chunk 759 optimal weight: 6.9990 overall best weight: 0.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 455 ASN ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 ASN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 174 HIS B 391 HIS B 498 GLN Total number of N/Q/H flips: 3 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 53 ASN E 145 HIS E 310 HIS E 520 GLN Total number of N/Q/H flips: 4 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 12 GLN G 118 HIS ** G 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 392 GLN ** G 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 30 GLN H 86 GLN H 390 HIS H 501 ASN Total number of N/Q/H flips: 4 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 91 HIS J 513 ASN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 84 GLN ** K 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 334 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.6308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 65220 Z= 0.236 Angle : 0.689 11.208 87996 Z= 0.371 Chirality : 0.045 0.261 10528 Planarity : 0.005 0.067 11312 Dihedral : 4.474 31.754 8966 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.19 % Favored : 96.74 % Rotamer: Outliers : 0.23 % Allowed : 3.64 % Favored : 96.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.21 (0.09), residues: 8408 helix: 1.06 (0.08), residues: 4118 sheet: 0.17 (0.16), residues: 994 loop : -1.00 (0.10), residues: 3296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP H 271 HIS 0.014 0.002 HIS e 310 PHE 0.028 0.002 PHE B 335 TYR 0.034 0.002 TYR M 269 ARG 0.023 0.001 ARG a 122 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16710 Ramachandran restraints generated. 8355 Oldfield, 0 Emsley, 8355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16710 Ramachandran restraints generated. 8355 Oldfield, 0 Emsley, 8355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.1514 time to fit residues: 18.3640 Evaluate side-chains 52 residues out of total 448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.372 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5030 Evaluate side-chains 86 residues out of total 416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.344 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.1207 time to fit residues: 13.1972 Evaluate side-chains 56 residues out of total 416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.347 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4691 Evaluate side-chains 98 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 96 time to evaluate : 0.368 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 96 average time/residue: 0.1103 time to fit residues: 13.8618 Evaluate side-chains 57 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.369 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5042 Evaluate side-chains 105 residues out of total 457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 102 time to evaluate : 0.378 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 104 average time/residue: 0.1301 time to fit residues: 16.8609 Evaluate side-chains 64 residues out of total 457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.371 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5039 Evaluate side-chains 109 residues out of total 433 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 107 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 108 average time/residue: 0.1094 time to fit residues: 15.1372 Evaluate side-chains 71 residues out of total 433 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.352 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4789 Evaluate side-chains 98 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.0894 time to fit residues: 11.8071 Evaluate side-chains 61 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.355 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4769 Evaluate side-chains 93 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.347 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.0932 time to fit residues: 11.5722 Evaluate side-chains 54 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.349 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4672 Evaluate side-chains 94 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 93 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 93 average time/residue: 0.1483 time to fit residues: 16.8103 Evaluate side-chains 56 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.358 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 836 random chunks: chunk 421 optimal weight: 0.1980 chunk 235 optimal weight: 0.0570 chunk 631 optimal weight: 5.9990 chunk 516 optimal weight: 6.9990 chunk 209 optimal weight: 3.9990 chunk 760 optimal weight: 8.9990 chunk 821 optimal weight: 0.1980 chunk 677 optimal weight: 10.0000 chunk 754 optimal weight: 20.0000 chunk 259 optimal weight: 30.0000 chunk 610 optimal weight: 5.9990 overall best weight: 2.0902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 251 GLN A 393 HIS ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 391 HIS B 498 GLN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 111 HIS G 115 GLN ** G 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 420 HIS Total number of N/Q/H flips: 3 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 390 HIS Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 453 GLN K 506 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.6754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.281 65220 Z= 0.464 Angle : 1.109 32.885 87996 Z= 0.573 Chirality : 0.060 0.621 10528 Planarity : 0.013 0.390 11312 Dihedral : 5.145 96.251 8966 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.04 % Favored : 95.93 % Rotamer: Outliers : 0.63 % Allowed : 2.93 % Favored : 96.45 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.48 (0.09), residues: 8408 helix: 0.38 (0.08), residues: 4120 sheet: -0.06 (0.16), residues: 1016 loop : -1.22 (0.10), residues: 3272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.110 0.004 TRP A 485 HIS 0.075 0.002 HIS A 471 PHE 0.076 0.004 PHE a 516 TYR 0.144 0.006 TYR A 426 ARG 0.119 0.003 ARG a 130 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16710 Ramachandran restraints generated. 8355 Oldfield, 0 Emsley, 8355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16710 Ramachandran restraints generated. 8355 Oldfield, 0 Emsley, 8355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 85 time to evaluate : 0.365 Fit side-chains outliers start: 17 outliers final: 3 residues processed: 96 average time/residue: 0.1465 time to fit residues: 17.2277 Evaluate side-chains 63 residues out of total 448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 60 time to evaluate : 0.365 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0453 time to fit residues: 0.7195 Evaluate side-chains 76 residues out of total 416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 75 time to evaluate : 0.344 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 75 average time/residue: 0.1206 time to fit residues: 11.4795 Evaluate side-chains 53 residues out of total 416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.353 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4673 Evaluate side-chains 81 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 79 time to evaluate : 0.366 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 80 average time/residue: 0.1128 time to fit residues: 11.7740 Evaluate side-chains 52 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.372 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5046 Evaluate side-chains 87 residues out of total 457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 86 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 87 average time/residue: 0.1315 time to fit residues: 14.3805 Evaluate side-chains 62 residues out of total 457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 61 time to evaluate : 0.371 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0531 time to fit residues: 0.5961 Evaluate side-chains 99 residues out of total 433 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 98 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 98 average time/residue: 0.1017 time to fit residues: 13.0298 Evaluate side-chains 70 residues out of total 433 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.360 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4796 Evaluate side-chains 75 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.0898 time to fit residues: 9.2278 Evaluate side-chains 53 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.377 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4771 Evaluate side-chains 80 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.345 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1119 time to fit residues: 11.5231 Evaluate side-chains 50 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.349 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4693 Evaluate side-chains 77 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1233 time to fit residues: 12.0631 Evaluate side-chains 52 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.362 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 675, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 771, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.5221 > 50: distance: 0 - 26: 5.399 distance: 2 - 3: 21.057 distance: 3 - 4: 24.435 distance: 3 - 6: 23.924 distance: 4 - 5: 3.130 distance: 4 - 11: 13.442 distance: 5 - 32: 25.000 distance: 6 - 7: 23.298 distance: 7 - 8: 41.975 distance: 8 - 9: 19.591 distance: 9 - 10: 21.487 distance: 11 - 12: 8.819 distance: 12 - 13: 18.360 distance: 12 - 15: 18.023 distance: 13 - 14: 17.697 distance: 13 - 18: 6.738 distance: 14 - 41: 37.023 distance: 15 - 16: 28.617 distance: 15 - 17: 36.116 distance: 18 - 19: 9.249 distance: 19 - 20: 26.079 distance: 19 - 22: 13.444 distance: 20 - 21: 23.221 distance: 20 - 26: 24.161 distance: 21 - 49: 30.422 distance: 22 - 23: 11.221 distance: 23 - 24: 16.669 distance: 23 - 25: 16.445 distance: 26 - 27: 11.799 distance: 27 - 28: 3.261 distance: 27 - 30: 10.167 distance: 28 - 29: 26.381 distance: 28 - 32: 7.991 distance: 29 - 54: 24.484 distance: 30 - 31: 23.816 distance: 32 - 33: 12.876 distance: 33 - 34: 7.773 distance: 33 - 36: 17.460 distance: 34 - 41: 25.748 distance: 35 - 62: 14.165 distance: 36 - 37: 14.105 distance: 37 - 38: 12.933 distance: 38 - 39: 26.800 distance: 38 - 40: 18.934 distance: 41 - 42: 20.118 distance: 42 - 43: 8.537 distance: 42 - 45: 15.672 distance: 43 - 44: 27.802 distance: 43 - 49: 20.593 distance: 44 - 70: 39.299 distance: 45 - 46: 22.836 distance: 46 - 47: 38.153 distance: 46 - 48: 38.473 distance: 49 - 50: 8.483 distance: 50 - 51: 11.625 distance: 50 - 53: 9.977 distance: 51 - 52: 10.513 distance: 51 - 54: 3.184 distance: 55 - 56: 3.854 distance: 55 - 58: 12.336 distance: 56 - 57: 11.360 distance: 56 - 62: 12.725 distance: 58 - 59: 12.086 distance: 59 - 60: 43.246 distance: 59 - 61: 27.870 distance: 62 - 63: 6.864 distance: 63 - 64: 6.591 distance: 63 - 66: 4.360 distance: 64 - 65: 22.811 distance: 64 - 70: 9.736 distance: 66 - 67: 11.144 distance: 67 - 68: 12.817 distance: 67 - 69: 12.381 distance: 70 - 71: 6.377 distance: 71 - 72: 11.018