Starting phenix.real_space_refine on Thu Sep 26 00:15:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e11_8952/09_2024/6e11_8952.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e11_8952/09_2024/6e11_8952.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e11_8952/09_2024/6e11_8952.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e11_8952/09_2024/6e11_8952.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e11_8952/09_2024/6e11_8952.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e11_8952/09_2024/6e11_8952.cif" } resolution = 4.23 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 36 5.49 5 S 151 5.16 5 C 36554 2.51 5 N 9632 2.21 5 O 11028 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 57401 Number of models: 1 Model: "" Number of chains: 34 Chain: "i" Number of atoms: 230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 230 Classifications: {'peptide': 46} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'TRANS': 45} Chain breaks: 1 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'UNK:plan-1': 46} Unresolved non-hydrogen planarities: 46 Chain: "j" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 275 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'TRANS': 54} Chain breaks: 1 Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'UNK:plan-1': 55} Unresolved non-hydrogen planarities: 55 Chain: "k" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 300 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'TRANS': 59} Chain breaks: 1 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 180 Unresolved non-hydrogen dihedrals: 60 Planarities with less than four sites: {'UNK:plan-1': 60} Unresolved non-hydrogen planarities: 60 Chain: "1" Number of atoms: 5752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 717, 5752 Classifications: {'peptide': 717} Link IDs: {'PTRANS': 22, 'TRANS': 694} Chain: "2" Number of atoms: 5752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 717, 5752 Classifications: {'peptide': 717} Link IDs: {'PTRANS': 22, 'TRANS': 694} Chain: "3" Number of atoms: 5752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 717, 5752 Classifications: {'peptide': 717} Link IDs: {'PTRANS': 22, 'TRANS': 694} Chain: "4" Number of atoms: 5752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 717, 5752 Classifications: {'peptide': 717} Link IDs: {'PTRANS': 22, 'TRANS': 694} Chain: "5" Number of atoms: 5744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 716, 5744 Classifications: {'peptide': 716} Link IDs: {'PTRANS': 22, 'TRANS': 693} Chain: "C" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1715 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain: "6" Number of atoms: 5744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 716, 5744 Classifications: {'peptide': 716} Link IDs: {'PTRANS': 22, 'TRANS': 693} Chain: "D" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1715 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain: "0" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 30 Classifications: {'peptide': 6} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'TRANS': 5} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'UNK:plan-1': 6} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1724 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 8, 'TRANS': 201} Chain: "d" Number of atoms: 1286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1286 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain breaks: 1 Chain: "c" Number of atoms: 1286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1286 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain breaks: 1 Chain: "b" Number of atoms: 1286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1286 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain breaks: 1 Chain: "B" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1715 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain: "a" Number of atoms: 1286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1286 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain breaks: 1 Chain: "A" Number of atoms: 1571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1571 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 8, 'TRANS': 182} Chain: "g" Number of atoms: 1286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1286 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain breaks: 1 Chain: "G" Number of atoms: 1571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1571 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 8, 'TRANS': 182} Chain: "f" Number of atoms: 1286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1286 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain breaks: 1 Chain: "F" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1715 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain: "e" Number of atoms: 1286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1286 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain breaks: 1 Chain: "n" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 180 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'TRANS': 35} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'UNK:plan-1': 36} Unresolved non-hydrogen planarities: 36 Chain: "h" Number of atoms: 235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 235 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'TRANS': 46} Chain breaks: 1 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'UNK:plan-1': 47} Unresolved non-hydrogen planarities: 47 Chain: "l" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 265 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'TRANS': 52} Chain breaks: 1 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 159 Unresolved non-hydrogen dihedrals: 53 Planarities with less than four sites: {'UNK:plan-1': 53} Unresolved non-hydrogen planarities: 53 Chain: "m" Number of atoms: 290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 290 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'TRANS': 57} Chain breaks: 1 Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 174 Unresolved non-hydrogen dihedrals: 58 Planarities with less than four sites: {'UNK:plan-1': 58} Unresolved non-hydrogen planarities: 58 Chain: "1" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 93 Unusual residues: {'AGS': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "2" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "5" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "6" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 26.88, per 1000 atoms: 0.47 Number of scatterers: 57401 At special positions: 0 Unit cell: (196.56, 187.2, 192.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 151 16.00 P 36 15.00 O 11028 8.00 N 9632 7.00 C 36554 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 140 " distance=2.03 Simple disulfide: pdb=" SG CYS D 113 " - pdb=" SG CYS D 140 " distance=2.03 Simple disulfide: pdb=" SG CYS E 113 " - pdb=" SG CYS E 140 " distance=2.03 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 140 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 140 " distance=2.03 Simple disulfide: pdb=" SG CYS G 113 " - pdb=" SG CYS G 140 " distance=2.03 Simple disulfide: pdb=" SG CYS F 113 " - pdb=" SG CYS F 140 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM57114 O3A AGS 11003 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=11, symmetry=0 Number of additional bonds: simple=11, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.93 Conformation dependent library (CDL) restraints added in 6.3 seconds 13546 Ramachandran restraints generated. 6773 Oldfield, 0 Emsley, 6773 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13690 Finding SS restraints... Secondary structure from input PDB file: 341 helices and 33 sheets defined 62.7% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.16 Creating SS restraints... Processing helix chain 'i' and resid 1 through 29 Processing helix chain 'i' and resid 995 through 1003 removed outlier: 3.884A pdb=" N UNK i1003 " --> pdb=" O UNK i 999 " (cutoff:3.500A) Processing helix chain 'j' and resid 2 through 32 Processing helix chain 'j' and resid 994 through 1003 Processing helix chain 'k' and resid 0 through 33 Processing helix chain 'k' and resid 994 through 1004 Processing helix chain '1' and resid 197 through 203 removed outlier: 4.255A pdb=" N VAL 1 201 " --> pdb=" O MET 1 197 " (cutoff:3.500A) Processing helix chain '1' and resid 212 through 224 removed outlier: 3.537A pdb=" N ARG 1 217 " --> pdb=" O ASP 1 213 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA 1 218 " --> pdb=" O GLU 1 214 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER 1 222 " --> pdb=" O ALA 1 218 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU 1 224 " --> pdb=" O ILE 1 220 " (cutoff:3.500A) Processing helix chain '1' and resid 241 through 254 removed outlier: 4.209A pdb=" N VAL 1 245 " --> pdb=" O LYS 1 241 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL 1 249 " --> pdb=" O VAL 1 245 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TYR 1 250 " --> pdb=" O GLU 1 246 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS 1 254 " --> pdb=" O TYR 1 250 " (cutoff:3.500A) Processing helix chain '1' and resid 258 through 262 removed outlier: 3.523A pdb=" N GLN 1 262 " --> pdb=" O LYS 1 259 " (cutoff:3.500A) Processing helix chain '1' and resid 271 through 276 removed outlier: 4.604A pdb=" N THR 1 275 " --> pdb=" O PHE 1 271 " (cutoff:3.500A) Processing helix chain '1' and resid 280 through 283 Processing helix chain '1' and resid 284 through 297 removed outlier: 3.536A pdb=" N MET 1 288 " --> pdb=" O PHE 1 284 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLU 1 294 " --> pdb=" O ASN 1 290 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASN 1 297 " --> pdb=" O LYS 1 293 " (cutoff:3.500A) Processing helix chain '1' and resid 308 through 312 Processing helix chain '1' and resid 345 through 355 removed outlier: 4.327A pdb=" N LYS 1 350 " --> pdb=" O ALA 1 346 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N PHE 1 351 " --> pdb=" O GLU 1 347 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE 1 352 " --> pdb=" O TYR 1 348 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N CYS 1 355 " --> pdb=" O PHE 1 351 " (cutoff:3.500A) Processing helix chain '1' and resid 372 through 382 removed outlier: 3.676A pdb=" N LYS 1 377 " --> pdb=" O ASP 1 373 " (cutoff:3.500A) Processing helix chain '1' and resid 382 through 390 removed outlier: 3.569A pdb=" N TYR 1 386 " --> pdb=" O LEU 1 382 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU 1 387 " --> pdb=" O LYS 1 383 " (cutoff:3.500A) Processing helix chain '1' and resid 395 through 410 removed outlier: 3.758A pdb=" N LEU 1 399 " --> pdb=" O THR 1 395 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL 1 400 " --> pdb=" O ASP 1 396 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA 1 403 " --> pdb=" O LEU 1 399 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE 1 405 " --> pdb=" O ALA 1 401 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N SER 1 406 " --> pdb=" O ALA 1 402 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG 1 408 " --> pdb=" O LYS 1 404 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE 1 409 " --> pdb=" O ILE 1 405 " (cutoff:3.500A) Processing helix chain '1' and resid 414 through 426 removed outlier: 3.728A pdb=" N LEU 1 422 " --> pdb=" O LYS 1 418 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LEU 1 423 " --> pdb=" O ALA 1 419 " (cutoff:3.500A) Processing helix chain '1' and resid 426 through 435 removed outlier: 4.262A pdb=" N VAL 1 432 " --> pdb=" O SER 1 428 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN 1 433 " --> pdb=" O PHE 1 429 " (cutoff:3.500A) Processing helix chain '1' and resid 438 through 452 removed outlier: 3.676A pdb=" N ASP 1 442 " --> pdb=" O PRO 1 438 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASP 1 447 " --> pdb=" O VAL 1 443 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ILE 1 448 " --> pdb=" O THR 1 444 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLU 1 449 " --> pdb=" O GLU 1 445 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU 1 451 " --> pdb=" O ASP 1 447 " (cutoff:3.500A) Processing helix chain '1' and resid 453 through 456 Processing helix chain '1' and resid 464 through 467 removed outlier: 3.933A pdb=" N LYS 1 467 " --> pdb=" O LYS 1 464 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 464 through 467' Processing helix chain '1' and resid 468 through 505 removed outlier: 3.502A pdb=" N LYS 1 472 " --> pdb=" O LYS 1 468 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ILE 1 474 " --> pdb=" O TYR 1 470 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LYS 1 475 " --> pdb=" O ASN 1 471 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU 1 482 " --> pdb=" O GLU 1 478 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLN 1 483 " --> pdb=" O GLU 1 479 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS 1 486 " --> pdb=" O GLU 1 482 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR 1 487 " --> pdb=" O GLN 1 483 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR 1 488 " --> pdb=" O LEU 1 484 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU 1 489 " --> pdb=" O LYS 1 485 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLU 1 503 " --> pdb=" O LYS 1 499 " (cutoff:3.500A) Processing helix chain '1' and resid 506 through 514 removed outlier: 4.206A pdb=" N ASP 1 510 " --> pdb=" O LYS 1 506 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU 1 514 " --> pdb=" O ASP 1 510 " (cutoff:3.500A) Processing helix chain '1' and resid 530 through 541 removed outlier: 3.771A pdb=" N LYS 1 534 " --> pdb=" O GLN 1 530 " (cutoff:3.500A) Processing helix chain '1' and resid 542 through 552 removed outlier: 3.539A pdb=" N THR 1 547 " --> pdb=" O LEU 1 543 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL 1 551 " --> pdb=" O THR 1 547 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLU 1 552 " --> pdb=" O VAL 1 548 " (cutoff:3.500A) Processing helix chain '1' and resid 565 through 577 removed outlier: 3.679A pdb=" N ILE 1 572 " --> pdb=" O HIS 1 568 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR 1 573 " --> pdb=" O VAL 1 569 " (cutoff:3.500A) Processing helix chain '1' and resid 590 through 600 removed outlier: 4.097A pdb=" N LYS 1 594 " --> pdb=" O LYS 1 590 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N TYR 1 596 " --> pdb=" O ALA 1 592 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ASN 1 597 " --> pdb=" O LEU 1 593 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER 1 598 " --> pdb=" O LYS 1 594 " (cutoff:3.500A) Processing helix chain '1' and resid 606 through 621 removed outlier: 3.643A pdb=" N SER 1 612 " --> pdb=" O ASP 1 608 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL 1 617 " --> pdb=" O LEU 1 613 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL 1 618 " --> pdb=" O SER 1 614 " (cutoff:3.500A) Processing helix chain '1' and resid 645 through 654 removed outlier: 3.826A pdb=" N ALA 1 652 " --> pdb=" O ALA 1 648 " (cutoff:3.500A) Processing helix chain '1' and resid 666 through 670 Processing helix chain '1' and resid 673 through 675 No H-bonds generated for 'chain '1' and resid 673 through 675' Processing helix chain '1' and resid 676 through 681 removed outlier: 3.683A pdb=" N THR 1 680 " --> pdb=" O VAL 1 676 " (cutoff:3.500A) Processing helix chain '1' and resid 693 through 702 removed outlier: 3.681A pdb=" N ALA 1 698 " --> pdb=" O GLN 1 694 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL 1 699 " --> pdb=" O LEU 1 695 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG 1 700 " --> pdb=" O THR 1 696 " (cutoff:3.500A) Processing helix chain '1' and resid 711 through 715 removed outlier: 3.689A pdb=" N LYS 1 714 " --> pdb=" O GLU 1 711 " (cutoff:3.500A) Processing helix chain '1' and resid 719 through 727 removed outlier: 3.512A pdb=" N LEU 1 724 " --> pdb=" O PHE 1 720 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N GLN 1 725 " --> pdb=" O LYS 1 721 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE 1 726 " --> pdb=" O VAL 1 722 " (cutoff:3.500A) Processing helix chain '1' and resid 765 through 769 removed outlier: 4.021A pdb=" N ASN 1 768 " --> pdb=" O ASP 1 765 " (cutoff:3.500A) Processing helix chain '1' and resid 773 through 792 removed outlier: 3.552A pdb=" N SER 1 784 " --> pdb=" O ASP 1 780 " (cutoff:3.500A) Processing helix chain '1' and resid 795 through 801 removed outlier: 3.992A pdb=" N ASN 1 799 " --> pdb=" O PRO 1 795 " (cutoff:3.500A) Processing helix chain '1' and resid 811 through 830 removed outlier: 4.220A pdb=" N LYS 1 817 " --> pdb=" O LYS 1 813 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL 1 819 " --> pdb=" O LEU 1 815 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA 1 820 " --> pdb=" O HIS 1 816 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ARG 1 822 " --> pdb=" O ILE 1 818 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE 1 823 " --> pdb=" O VAL 1 819 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS 1 824 " --> pdb=" O ALA 1 820 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU 1 827 " --> pdb=" O PHE 1 823 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LYS 1 828 " --> pdb=" O LYS 1 824 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG 1 829 " --> pdb=" O LYS 1 825 " (cutoff:3.500A) Processing helix chain '1' and resid 841 through 849 removed outlier: 4.029A pdb=" N ASP 1 845 " --> pdb=" O GLU 1 841 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N TYR 1 846 " --> pdb=" O LYS 1 842 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE 1 847 " --> pdb=" O ALA 1 843 " (cutoff:3.500A) Processing helix chain '1' and resid 859 through 869 removed outlier: 3.941A pdb=" N ILE 1 863 " --> pdb=" O ARG 1 859 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL 1 868 " --> pdb=" O PHE 1 864 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE 1 869 " --> pdb=" O ILE 1 865 " (cutoff:3.500A) Processing helix chain '1' and resid 872 through 879 removed outlier: 3.519A pdb=" N LEU 1 878 " --> pdb=" O ALA 1 874 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS 1 879 " --> pdb=" O ILE 1 875 " (cutoff:3.500A) Processing helix chain '2' and resid 197 through 203 removed outlier: 3.735A pdb=" N VAL 2 201 " --> pdb=" O MET 2 197 " (cutoff:3.500A) Processing helix chain '2' and resid 212 through 224 Processing helix chain '2' and resid 241 through 254 removed outlier: 3.587A pdb=" N VAL 2 249 " --> pdb=" O VAL 2 245 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR 2 250 " --> pdb=" O GLU 2 246 " (cutoff:3.500A) Processing helix chain '2' and resid 258 through 262 Processing helix chain '2' and resid 284 through 296 removed outlier: 3.740A pdb=" N MET 2 288 " --> pdb=" O PHE 2 284 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU 2 294 " --> pdb=" O ASN 2 290 " (cutoff:3.500A) Processing helix chain '2' and resid 309 through 315 removed outlier: 3.738A pdb=" N LEU 2 313 " --> pdb=" O ILE 2 309 " (cutoff:3.500A) Processing helix chain '2' and resid 328 through 334 removed outlier: 3.951A pdb=" N LEU 2 332 " --> pdb=" O LEU 2 328 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER 2 333 " --> pdb=" O LYS 2 329 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS 2 334 " --> pdb=" O PRO 2 330 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 328 through 334' Processing helix chain '2' and resid 344 through 353 removed outlier: 4.102A pdb=" N LYS 2 350 " --> pdb=" O ALA 2 346 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N PHE 2 351 " --> pdb=" O GLU 2 347 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE 2 352 " --> pdb=" O TYR 2 348 " (cutoff:3.500A) Processing helix chain '2' and resid 371 through 373 No H-bonds generated for 'chain '2' and resid 371 through 373' Processing helix chain '2' and resid 374 through 382 Processing helix chain '2' and resid 383 through 391 removed outlier: 4.298A pdb=" N PHE 2 389 " --> pdb=" O LYS 2 385 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N TYR 2 390 " --> pdb=" O TYR 2 386 " (cutoff:3.500A) Processing helix chain '2' and resid 396 through 409 removed outlier: 3.847A pdb=" N VAL 2 400 " --> pdb=" O ASP 2 396 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA 2 401 " --> pdb=" O LYS 2 397 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER 2 406 " --> pdb=" O ALA 2 402 " (cutoff:3.500A) Processing helix chain '2' and resid 414 through 435 removed outlier: 3.536A pdb=" N ALA 2 419 " --> pdb=" O LEU 2 415 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE 2 420 " --> pdb=" O PRO 2 416 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU 2 423 " --> pdb=" O ALA 2 419 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU 2 430 " --> pdb=" O ALA 2 426 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL 2 432 " --> pdb=" O SER 2 428 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN 2 433 " --> pdb=" O PHE 2 429 " (cutoff:3.500A) Processing helix chain '2' and resid 438 through 459 removed outlier: 3.559A pdb=" N ASP 2 442 " --> pdb=" O PRO 2 438 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG 2 446 " --> pdb=" O ASP 2 442 " (cutoff:3.500A) Processing helix chain '2' and resid 465 through 514 removed outlier: 4.215A pdb=" N LYS 2 469 " --> pdb=" O VAL 2 465 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE 2 474 " --> pdb=" O TYR 2 470 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N LYS 2 475 " --> pdb=" O ASN 2 471 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU 2 476 " --> pdb=" O LYS 2 472 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE 2 477 " --> pdb=" O LEU 2 473 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLU 2 478 " --> pdb=" O ILE 2 474 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU 2 479 " --> pdb=" O LYS 2 475 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS 2 486 " --> pdb=" O GLU 2 482 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU 2 489 " --> pdb=" O LYS 2 485 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU 2 498 " --> pdb=" O THR 2 494 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP 2 510 " --> pdb=" O LYS 2 506 " (cutoff:3.500A) Processing helix chain '2' and resid 526 through 541 removed outlier: 3.913A pdb=" N GLN 2 530 " --> pdb=" O PRO 2 526 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS 2 534 " --> pdb=" O GLN 2 530 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA 2 536 " --> pdb=" O SER 2 532 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS 2 539 " --> pdb=" O GLU 2 535 " (cutoff:3.500A) Processing helix chain '2' and resid 542 through 554 removed outlier: 3.523A pdb=" N VAL 2 551 " --> pdb=" O THR 2 547 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU 2 552 " --> pdb=" O VAL 2 548 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ALA 2 553 " --> pdb=" O ALA 2 549 " (cutoff:3.500A) Processing helix chain '2' and resid 565 through 577 removed outlier: 3.798A pdb=" N VAL 2 569 " --> pdb=" O TYR 2 565 " (cutoff:3.500A) Processing helix chain '2' and resid 591 through 593 No H-bonds generated for 'chain '2' and resid 591 through 593' Processing helix chain '2' and resid 594 through 603 Processing helix chain '2' and resid 606 through 622 removed outlier: 3.989A pdb=" N ILE 2 610 " --> pdb=" O ASN 2 606 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER 2 612 " --> pdb=" O ASP 2 608 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA 2 620 " --> pdb=" O ALA 2 616 " (cutoff:3.500A) Processing helix chain '2' and resid 645 through 655 removed outlier: 4.010A pdb=" N LYS 2 649 " --> pdb=" O THR 2 645 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ALA 2 652 " --> pdb=" O ALA 2 648 " (cutoff:3.500A) Processing helix chain '2' and resid 668 through 672 removed outlier: 4.070A pdb=" N THR 2 671 " --> pdb=" O SER 2 668 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLU 2 672 " --> pdb=" O GLU 2 669 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 668 through 672' Processing helix chain '2' and resid 676 through 681 removed outlier: 4.069A pdb=" N THR 2 680 " --> pdb=" O VAL 2 676 " (cutoff:3.500A) Processing helix chain '2' and resid 693 through 702 removed outlier: 3.814A pdb=" N GLU 2 697 " --> pdb=" O GLY 2 693 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA 2 698 " --> pdb=" O GLN 2 694 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL 2 699 " --> pdb=" O LEU 2 695 " (cutoff:3.500A) Processing helix chain '2' and resid 711 through 715 removed outlier: 3.610A pdb=" N LYS 2 714 " --> pdb=" O GLU 2 711 " (cutoff:3.500A) Processing helix chain '2' and resid 716 through 727 removed outlier: 3.710A pdb=" N VAL 2 722 " --> pdb=" O ASP 2 718 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLN 2 725 " --> pdb=" O LYS 2 721 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE 2 726 " --> pdb=" O VAL 2 722 " (cutoff:3.500A) Processing helix chain '2' and resid 773 through 790 Processing helix chain '2' and resid 795 through 801 removed outlier: 3.530A pdb=" N ASN 2 799 " --> pdb=" O PRO 2 795 " (cutoff:3.500A) Processing helix chain '2' and resid 811 through 828 removed outlier: 3.557A pdb=" N LEU 2 815 " --> pdb=" O ASN 2 811 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LYS 2 817 " --> pdb=" O LYS 2 813 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA 2 820 " --> pdb=" O HIS 2 816 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE 2 823 " --> pdb=" O VAL 2 819 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS 2 824 " --> pdb=" O ALA 2 820 " (cutoff:3.500A) Processing helix chain '2' and resid 840 through 850 removed outlier: 4.827A pdb=" N TYR 2 846 " --> pdb=" O LYS 2 842 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE 2 847 " --> pdb=" O ALA 2 843 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN 2 850 " --> pdb=" O TYR 2 846 " (cutoff:3.500A) Processing helix chain '2' and resid 858 through 868 removed outlier: 3.842A pdb=" N LEU 2 862 " --> pdb=" O ALA 2 858 " (cutoff:3.500A) Processing helix chain '2' and resid 870 through 879 removed outlier: 3.589A pdb=" N ALA 2 874 " --> pdb=" O MET 2 870 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N MET 2 876 " --> pdb=" O LYS 2 872 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR 2 877 " --> pdb=" O PHE 2 873 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU 2 878 " --> pdb=" O ALA 2 874 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LYS 2 879 " --> pdb=" O ILE 2 875 " (cutoff:3.500A) Processing helix chain '3' and resid 198 through 203 removed outlier: 3.571A pdb=" N ARG 3 202 " --> pdb=" O ASN 3 198 " (cutoff:3.500A) Processing helix chain '3' and resid 212 through 224 removed outlier: 3.941A pdb=" N ALA 3 218 " --> pdb=" O GLU 3 214 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER 3 222 " --> pdb=" O ALA 3 218 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU 3 224 " --> pdb=" O ILE 3 220 " (cutoff:3.500A) Processing helix chain '3' and resid 242 through 254 removed outlier: 3.559A pdb=" N VAL 3 249 " --> pdb=" O VAL 3 245 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS 3 254 " --> pdb=" O TYR 3 250 " (cutoff:3.500A) Processing helix chain '3' and resid 258 through 262 removed outlier: 3.710A pdb=" N GLN 3 262 " --> pdb=" O LYS 3 259 " (cutoff:3.500A) Processing helix chain '3' and resid 283 through 298 removed outlier: 4.123A pdb=" N ARG 3 287 " --> pdb=" O GLU 3 283 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N MET 3 288 " --> pdb=" O PHE 3 284 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU 3 294 " --> pdb=" O ASN 3 290 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASN 3 297 " --> pdb=" O LYS 3 293 " (cutoff:3.500A) Processing helix chain '3' and resid 308 through 314 removed outlier: 4.008A pdb=" N GLY 3 314 " --> pdb=" O LEU 3 311 " (cutoff:3.500A) Processing helix chain '3' and resid 322 through 327 Processing helix chain '3' and resid 344 through 353 removed outlier: 3.745A pdb=" N ARG 3 349 " --> pdb=" O ILE 3 345 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N LYS 3 350 " --> pdb=" O ALA 3 346 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N PHE 3 351 " --> pdb=" O GLU 3 347 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE 3 352 " --> pdb=" O TYR 3 348 " (cutoff:3.500A) Processing helix chain '3' and resid 372 through 381 removed outlier: 3.540A pdb=" N LYS 3 377 " --> pdb=" O ASP 3 373 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER 3 381 " --> pdb=" O LYS 3 377 " (cutoff:3.500A) Processing helix chain '3' and resid 382 through 388 Processing helix chain '3' and resid 395 through 408 removed outlier: 3.552A pdb=" N LEU 3 399 " --> pdb=" O THR 3 395 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N SER 3 406 " --> pdb=" O ALA 3 402 " (cutoff:3.500A) Processing helix chain '3' and resid 416 through 435 removed outlier: 3.509A pdb=" N LEU 3 422 " --> pdb=" O LYS 3 418 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU 3 423 " --> pdb=" O ALA 3 419 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N CYS 3 427 " --> pdb=" O LEU 3 423 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N SER 3 428 " --> pdb=" O ASN 3 424 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN 3 433 " --> pdb=" O PHE 3 429 " (cutoff:3.500A) Processing helix chain '3' and resid 438 through 458 removed outlier: 3.506A pdb=" N VAL 3 443 " --> pdb=" O ARG 3 439 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE 3 448 " --> pdb=" O THR 3 444 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU 3 449 " --> pdb=" O GLU 3 445 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR 3 453 " --> pdb=" O GLU 3 449 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER 3 456 " --> pdb=" O SER 3 452 " (cutoff:3.500A) Processing helix chain '3' and resid 465 through 516 removed outlier: 4.140A pdb=" N LYS 3 469 " --> pdb=" O VAL 3 465 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LYS 3 475 " --> pdb=" O ASN 3 471 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N GLU 3 482 " --> pdb=" O GLU 3 478 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLU 3 489 " --> pdb=" O LYS 3 485 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG 3 497 " --> pdb=" O ILE 3 493 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS 3 499 " --> pdb=" O GLY 3 495 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU 3 503 " --> pdb=" O LYS 3 499 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS 3 512 " --> pdb=" O LEU 3 508 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU 3 513 " --> pdb=" O ASN 3 509 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU 3 514 " --> pdb=" O ASP 3 510 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR 3 515 " --> pdb=" O LEU 3 511 " (cutoff:3.500A) Processing helix chain '3' and resid 526 through 541 removed outlier: 3.527A pdb=" N LEU 3 533 " --> pdb=" O LEU 3 529 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS 3 534 " --> pdb=" O GLN 3 530 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN 3 538 " --> pdb=" O LYS 3 534 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS 3 539 " --> pdb=" O GLU 3 535 " (cutoff:3.500A) Processing helix chain '3' and resid 542 through 554 removed outlier: 3.668A pdb=" N THR 3 547 " --> pdb=" O LEU 3 543 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU 3 552 " --> pdb=" O VAL 3 548 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA 3 553 " --> pdb=" O ALA 3 549 " (cutoff:3.500A) Processing helix chain '3' and resid 565 through 577 removed outlier: 3.619A pdb=" N VAL 3 569 " --> pdb=" O TYR 3 565 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE 3 572 " --> pdb=" O HIS 3 568 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU 3 574 " --> pdb=" O SER 3 570 " (cutoff:3.500A) Processing helix chain '3' and resid 590 through 593 Processing helix chain '3' and resid 594 through 603 removed outlier: 3.630A pdb=" N SER 3 602 " --> pdb=" O SER 3 598 " (cutoff:3.500A) Processing helix chain '3' and resid 606 through 622 removed outlier: 3.711A pdb=" N ALA 3 616 " --> pdb=" O SER 3 612 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL 3 617 " --> pdb=" O LEU 3 613 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR 3 622 " --> pdb=" O VAL 3 618 " (cutoff:3.500A) Processing helix chain '3' and resid 647 through 655 Processing helix chain '3' and resid 666 through 671 removed outlier: 3.886A pdb=" N THR 3 671 " --> pdb=" O SER 3 668 " (cutoff:3.500A) Processing helix chain '3' and resid 672 through 679 removed outlier: 3.954A pdb=" N VAL 3 676 " --> pdb=" O ALA 3 673 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N SER 3 677 " --> pdb=" O HIS 3 674 " (cutoff:3.500A) Processing helix chain '3' and resid 697 through 702 Processing helix chain '3' and resid 716 through 729 removed outlier: 3.914A pdb=" N PHE 3 720 " --> pdb=" O HIS 3 716 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS 3 721 " --> pdb=" O ALA 3 717 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL 3 722 " --> pdb=" O ASP 3 718 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLN 3 725 " --> pdb=" O LYS 3 721 " (cutoff:3.500A) Processing helix chain '3' and resid 765 through 769 removed outlier: 3.875A pdb=" N ASN 3 768 " --> pdb=" O ASP 3 765 " (cutoff:3.500A) Processing helix chain '3' and resid 774 through 793 removed outlier: 3.847A pdb=" N GLU 3 779 " --> pdb=" O LYS 3 775 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ASP 3 780 " --> pdb=" O ARG 3 776 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER 3 784 " --> pdb=" O ASP 3 780 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS 3 791 " --> pdb=" O LYS 3 787 " (cutoff:3.500A) Processing helix chain '3' and resid 811 through 831 removed outlier: 4.209A pdb=" N LYS 3 817 " --> pdb=" O LYS 3 813 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS 3 824 " --> pdb=" O ALA 3 820 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS 3 828 " --> pdb=" O LYS 3 824 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG 3 829 " --> pdb=" O LYS 3 825 " (cutoff:3.500A) Processing helix chain '3' and resid 840 through 852 removed outlier: 3.771A pdb=" N ASP 3 845 " --> pdb=" O GLU 3 841 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR 3 846 " --> pdb=" O LYS 3 842 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN 3 850 " --> pdb=" O TYR 3 846 " (cutoff:3.500A) Processing helix chain '3' and resid 859 through 868 removed outlier: 3.681A pdb=" N ILE 3 865 " --> pdb=" O THR 3 861 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU 3 866 " --> pdb=" O LEU 3 862 " (cutoff:3.500A) Processing helix chain '3' and resid 870 through 879 removed outlier: 3.716A pdb=" N ALA 3 874 " --> pdb=" O MET 3 870 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS 3 879 " --> pdb=" O ILE 3 875 " (cutoff:3.500A) Processing helix chain '4' and resid 197 through 203 Processing helix chain '4' and resid 212 through 221 removed outlier: 4.262A pdb=" N ALA 4 218 " --> pdb=" O GLU 4 214 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE 4 219 " --> pdb=" O GLU 4 215 " (cutoff:3.500A) Processing helix chain '4' and resid 241 through 254 removed outlier: 3.590A pdb=" N VAL 4 245 " --> pdb=" O LYS 4 241 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL 4 249 " --> pdb=" O VAL 4 245 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG 4 251 " --> pdb=" O GLY 4 247 " (cutoff:3.500A) Processing helix chain '4' and resid 258 through 262 removed outlier: 3.704A pdb=" N GLN 4 262 " --> pdb=" O LYS 4 259 " (cutoff:3.500A) Processing helix chain '4' and resid 280 through 297 removed outlier: 3.582A pdb=" N PHE 4 284 " --> pdb=" O TYR 4 280 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLU 4 285 " --> pdb=" O ARG 4 281 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG 4 287 " --> pdb=" O GLU 4 283 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N MET 4 288 " --> pdb=" O PHE 4 284 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU 4 294 " --> pdb=" O ASN 4 290 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN 4 297 " --> pdb=" O LYS 4 293 " (cutoff:3.500A) Processing helix chain '4' and resid 308 through 312 Processing helix chain '4' and resid 345 through 355 removed outlier: 3.758A pdb=" N ARG 4 349 " --> pdb=" O ILE 4 345 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N LYS 4 350 " --> pdb=" O ALA 4 346 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N PHE 4 351 " --> pdb=" O GLU 4 347 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE 4 352 " --> pdb=" O TYR 4 348 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N CYS 4 355 " --> pdb=" O PHE 4 351 " (cutoff:3.500A) Processing helix chain '4' and resid 372 through 381 removed outlier: 4.018A pdb=" N LYS 4 377 " --> pdb=" O ASP 4 373 " (cutoff:3.500A) Processing helix chain '4' and resid 382 through 391 removed outlier: 3.794A pdb=" N TYR 4 386 " --> pdb=" O LEU 4 382 " (cutoff:3.500A) Processing helix chain '4' and resid 395 through 409 removed outlier: 4.129A pdb=" N SER 4 406 " --> pdb=" O ALA 4 402 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG 4 408 " --> pdb=" O LYS 4 404 " (cutoff:3.500A) Processing helix chain '4' and resid 414 through 436 removed outlier: 3.620A pdb=" N LEU 4 422 " --> pdb=" O LYS 4 418 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU 4 423 " --> pdb=" O ALA 4 419 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU 4 430 " --> pdb=" O ALA 4 426 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL 4 432 " --> pdb=" O SER 4 428 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLN 4 433 " --> pdb=" O PHE 4 429 " (cutoff:3.500A) Processing helix chain '4' and resid 438 through 458 removed outlier: 3.632A pdb=" N ASP 4 442 " --> pdb=" O PRO 4 438 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL 4 443 " --> pdb=" O ARG 4 439 " (cutoff:3.500A) Processing helix chain '4' and resid 465 through 468 Processing helix chain '4' and resid 469 through 502 removed outlier: 5.130A pdb=" N LYS 4 475 " --> pdb=" O ASN 4 471 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLU 4 482 " --> pdb=" O GLU 4 478 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLU 4 489 " --> pdb=" O LYS 4 485 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG 4 497 " --> pdb=" O ILE 4 493 " (cutoff:3.500A) Processing helix chain '4' and resid 503 through 516 removed outlier: 3.828A pdb=" N LYS 4 512 " --> pdb=" O LEU 4 508 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLU 4 513 " --> pdb=" O ASN 4 509 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU 4 514 " --> pdb=" O ASP 4 510 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N THR 4 515 " --> pdb=" O LEU 4 511 " (cutoff:3.500A) Processing helix chain '4' and resid 531 through 541 removed outlier: 3.513A pdb=" N GLN 4 538 " --> pdb=" O LYS 4 534 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LYS 4 539 " --> pdb=" O GLU 4 535 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N TYR 4 540 " --> pdb=" O ALA 4 536 " (cutoff:3.500A) Processing helix chain '4' and resid 542 through 552 removed outlier: 3.529A pdb=" N VAL 4 551 " --> pdb=" O THR 4 547 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLU 4 552 " --> pdb=" O VAL 4 548 " (cutoff:3.500A) Processing helix chain '4' and resid 565 through 577 removed outlier: 3.610A pdb=" N VAL 4 569 " --> pdb=" O TYR 4 565 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR 4 571 " --> pdb=" O GLU 4 567 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ILE 4 572 " --> pdb=" O HIS 4 568 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU 4 574 " --> pdb=" O SER 4 570 " (cutoff:3.500A) Processing helix chain '4' and resid 593 through 603 removed outlier: 4.562A pdb=" N ASN 4 597 " --> pdb=" O LEU 4 593 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER 4 602 " --> pdb=" O SER 4 598 " (cutoff:3.500A) Processing helix chain '4' and resid 606 through 622 removed outlier: 3.756A pdb=" N VAL 4 617 " --> pdb=" O LEU 4 613 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR 4 622 " --> pdb=" O VAL 4 618 " (cutoff:3.500A) Processing helix chain '4' and resid 646 through 654 removed outlier: 3.820A pdb=" N ALA 4 652 " --> pdb=" O ALA 4 648 " (cutoff:3.500A) Processing helix chain '4' and resid 666 through 670 removed outlier: 3.641A pdb=" N PHE 4 670 " --> pdb=" O MET 4 667 " (cutoff:3.500A) Processing helix chain '4' and resid 673 through 675 No H-bonds generated for 'chain '4' and resid 673 through 675' Processing helix chain '4' and resid 676 through 681 removed outlier: 3.802A pdb=" N THR 4 680 " --> pdb=" O VAL 4 676 " (cutoff:3.500A) Processing helix chain '4' and resid 693 through 702 removed outlier: 3.614A pdb=" N ARG 4 700 " --> pdb=" O THR 4 696 " (cutoff:3.500A) Processing helix chain '4' and resid 716 through 727 removed outlier: 3.559A pdb=" N PHE 4 720 " --> pdb=" O HIS 4 716 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS 4 721 " --> pdb=" O ALA 4 717 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU 4 723 " --> pdb=" O VAL 4 719 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLN 4 725 " --> pdb=" O LYS 4 721 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE 4 726 " --> pdb=" O VAL 4 722 " (cutoff:3.500A) Processing helix chain '4' and resid 773 through 793 removed outlier: 4.391A pdb=" N LEU 4 783 " --> pdb=" O GLU 4 779 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE 4 786 " --> pdb=" O ARG 4 782 " (cutoff:3.500A) Processing helix chain '4' and resid 795 through 801 Processing helix chain '4' and resid 811 through 819 removed outlier: 3.617A pdb=" N HIS 4 816 " --> pdb=" O LYS 4 812 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N LYS 4 817 " --> pdb=" O LYS 4 813 " (cutoff:3.500A) Processing helix chain '4' and resid 819 through 829 removed outlier: 3.574A pdb=" N PHE 4 823 " --> pdb=" O VAL 4 819 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS 4 824 " --> pdb=" O ALA 4 820 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS 4 825 " --> pdb=" O LEU 4 821 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS 4 828 " --> pdb=" O LYS 4 824 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG 4 829 " --> pdb=" O LYS 4 825 " (cutoff:3.500A) Processing helix chain '4' and resid 840 through 852 removed outlier: 3.679A pdb=" N GLN 4 850 " --> pdb=" O TYR 4 846 " (cutoff:3.500A) Processing helix chain '4' and resid 858 through 868 removed outlier: 3.694A pdb=" N GLU 4 866 " --> pdb=" O LEU 4 862 " (cutoff:3.500A) Processing helix chain '4' and resid 868 through 879 removed outlier: 4.150A pdb=" N LYS 4 872 " --> pdb=" O VAL 4 868 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE 4 873 " --> pdb=" O ILE 4 869 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA 4 874 " --> pdb=" O MET 4 870 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS 4 879 " --> pdb=" O ILE 4 875 " (cutoff:3.500A) Processing helix chain '5' and resid 197 through 204 removed outlier: 3.697A pdb=" N VAL 5 201 " --> pdb=" O MET 5 197 " (cutoff:3.500A) Processing helix chain '5' and resid 212 through 224 removed outlier: 4.054A pdb=" N ALA 5 218 " --> pdb=" O GLU 5 214 " (cutoff:3.500A) Processing helix chain '5' and resid 241 through 251 removed outlier: 3.822A pdb=" N VAL 5 245 " --> pdb=" O LYS 5 241 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL 5 249 " --> pdb=" O VAL 5 245 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TYR 5 250 " --> pdb=" O GLU 5 246 " (cutoff:3.500A) Processing helix chain '5' and resid 258 through 262 removed outlier: 3.705A pdb=" N GLN 5 262 " --> pdb=" O LYS 5 259 " (cutoff:3.500A) Processing helix chain '5' and resid 270 through 275 removed outlier: 3.704A pdb=" N PHE 5 274 " --> pdb=" O ASN 5 270 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR 5 275 " --> pdb=" O PHE 5 271 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 270 through 275' Processing helix chain '5' and resid 283 through 292 removed outlier: 3.627A pdb=" N ARG 5 287 " --> pdb=" O GLU 5 283 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASN 5 290 " --> pdb=" O THR 5 286 " (cutoff:3.500A) Processing helix chain '5' and resid 293 through 296 removed outlier: 3.704A pdb=" N LYS 5 296 " --> pdb=" O LYS 5 293 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 293 through 296' Processing helix chain '5' and resid 308 through 315 removed outlier: 3.856A pdb=" N LEU 5 312 " --> pdb=" O GLU 5 308 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA 5 315 " --> pdb=" O LEU 5 311 " (cutoff:3.500A) Processing helix chain '5' and resid 345 through 353 removed outlier: 3.916A pdb=" N LYS 5 350 " --> pdb=" O ALA 5 346 " (cutoff:3.500A) Processing helix chain '5' and resid 371 through 382 removed outlier: 3.556A pdb=" N VAL 5 376 " --> pdb=" O VAL 5 372 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LYS 5 377 " --> pdb=" O ASP 5 373 " (cutoff:3.500A) Processing helix chain '5' and resid 383 through 388 Processing helix chain '5' and resid 395 through 408 removed outlier: 4.155A pdb=" N SER 5 406 " --> pdb=" O ALA 5 402 " (cutoff:3.500A) Processing helix chain '5' and resid 414 through 435 removed outlier: 3.773A pdb=" N LYS 5 418 " --> pdb=" O TYR 5 414 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU 5 430 " --> pdb=" O ALA 5 426 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN 5 431 " --> pdb=" O CYS 5 427 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL 5 432 " --> pdb=" O SER 5 428 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLN 5 433 " --> pdb=" O PHE 5 429 " (cutoff:3.500A) Processing helix chain '5' and resid 438 through 458 removed outlier: 3.956A pdb=" N ASP 5 442 " --> pdb=" O PRO 5 438 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL 5 443 " --> pdb=" O ARG 5 439 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU 5 449 " --> pdb=" O GLU 5 445 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU 5 451 " --> pdb=" O ASP 5 447 " (cutoff:3.500A) Processing helix chain '5' and resid 466 through 515 removed outlier: 3.698A pdb=" N ASN 5 471 " --> pdb=" O LYS 5 467 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N LYS 5 475 " --> pdb=" O ASN 5 471 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLU 5 482 " --> pdb=" O GLU 5 478 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN 5 483 " --> pdb=" O GLU 5 479 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLU 5 489 " --> pdb=" O LYS 5 485 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU 5 498 " --> pdb=" O THR 5 494 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS 5 499 " --> pdb=" O GLY 5 495 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE 5 504 " --> pdb=" O ARG 5 500 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS 5 506 " --> pdb=" O LYS 5 502 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LYS 5 507 " --> pdb=" O GLU 5 503 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN 5 509 " --> pdb=" O GLU 5 505 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU 5 513 " --> pdb=" O ASN 5 509 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU 5 514 " --> pdb=" O ASP 5 510 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR 5 515 " --> pdb=" O LEU 5 511 " (cutoff:3.500A) Processing helix chain '5' and resid 519 through 523 removed outlier: 4.396A pdb=" N ASN 5 522 " --> pdb=" O VAL 5 519 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LYS 5 523 " --> pdb=" O TYR 5 520 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 519 through 523' Processing helix chain '5' and resid 526 through 540 removed outlier: 3.593A pdb=" N LYS 5 534 " --> pdb=" O GLN 5 530 " (cutoff:3.500A) Processing helix chain '5' and resid 542 through 553 removed outlier: 3.959A pdb=" N GLU 5 552 " --> pdb=" O VAL 5 548 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA 5 553 " --> pdb=" O ALA 5 549 " (cutoff:3.500A) Processing helix chain '5' and resid 566 through 577 removed outlier: 4.650A pdb=" N ILE 5 572 " --> pdb=" O HIS 5 568 " (cutoff:3.500A) Processing helix chain '5' and resid 594 through 603 removed outlier: 3.734A pdb=" N SER 5 600 " --> pdb=" O TYR 5 596 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS 5 601 " --> pdb=" O ASN 5 597 " (cutoff:3.500A) Processing helix chain '5' and resid 606 through 622 removed outlier: 3.663A pdb=" N ILE 5 610 " --> pdb=" O ASN 5 606 " (cutoff:3.500A) Processing helix chain '5' and resid 646 through 655 Processing helix chain '5' and resid 666 through 670 removed outlier: 4.032A pdb=" N GLU 5 669 " --> pdb=" O ASN 5 666 " (cutoff:3.500A) Processing helix chain '5' and resid 676 through 681 removed outlier: 4.552A pdb=" N THR 5 680 " --> pdb=" O VAL 5 676 " (cutoff:3.500A) Processing helix chain '5' and resid 695 through 702 Processing helix chain '5' and resid 716 through 729 removed outlier: 4.088A pdb=" N PHE 5 720 " --> pdb=" O HIS 5 716 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS 5 721 " --> pdb=" O ALA 5 717 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL 5 722 " --> pdb=" O ASP 5 718 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLN 5 725 " --> pdb=" O LYS 5 721 " (cutoff:3.500A) Processing helix chain '5' and resid 774 through 793 removed outlier: 3.546A pdb=" N ILE 5 786 " --> pdb=" O ARG 5 782 " (cutoff:3.500A) Processing helix chain '5' and resid 795 through 800 Processing helix chain '5' and resid 811 through 828 removed outlier: 3.660A pdb=" N HIS 5 816 " --> pdb=" O LYS 5 812 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LYS 5 817 " --> pdb=" O LYS 5 813 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ALA 5 820 " --> pdb=" O HIS 5 816 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS 5 824 " --> pdb=" O ALA 5 820 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS 5 828 " --> pdb=" O LYS 5 824 " (cutoff:3.500A) Processing helix chain '5' and resid 840 through 852 removed outlier: 3.508A pdb=" N ASP 5 845 " --> pdb=" O GLU 5 841 " (cutoff:3.500A) Processing helix chain '5' and resid 858 through 868 removed outlier: 3.864A pdb=" N LEU 5 862 " --> pdb=" O ALA 5 858 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL 5 868 " --> pdb=" O PHE 5 864 " (cutoff:3.500A) Processing helix chain '5' and resid 870 through 879 removed outlier: 3.643A pdb=" N MET 5 876 " --> pdb=" O LYS 5 872 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 57 removed outlier: 3.902A pdb=" N ALA C 33 " --> pdb=" O GLY C 29 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N THR C 34 " --> pdb=" O ASP C 30 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR C 39 " --> pdb=" O SER C 35 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP C 43 " --> pdb=" O THR C 39 " (cutoff:3.500A) Proline residue: C 44 - end of helix removed outlier: 3.682A pdb=" N LYS C 50 " --> pdb=" O SER C 46 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP C 51 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLU C 54 " --> pdb=" O LYS C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 73 removed outlier: 3.631A pdb=" N LYS C 67 " --> pdb=" O LYS C 63 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS C 70 " --> pdb=" O HIS C 66 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG C 73 " --> pdb=" O LYS C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 94 removed outlier: 4.197A pdb=" N TRP C 80 " --> pdb=" O LYS C 76 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N MET C 83 " --> pdb=" O ARG C 79 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU C 87 " --> pdb=" O MET C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 119 removed outlier: 3.989A pdb=" N ILE C 109 " --> pdb=" O ALA C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 148 removed outlier: 4.120A pdb=" N PHE C 132 " --> pdb=" O LYS C 128 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS C 134 " --> pdb=" O LEU C 130 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASN C 138 " --> pdb=" O HIS C 134 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS C 147 " --> pdb=" O ASN C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 164 removed outlier: 3.774A pdb=" N GLN C 161 " --> pdb=" O ALA C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 170 removed outlier: 3.668A pdb=" N ARG C 169 " --> pdb=" O GLN C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 182 removed outlier: 3.616A pdb=" N LYS C 178 " --> pdb=" O GLU C 174 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE C 179 " --> pdb=" O PRO C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 189 Processing helix chain 'C' and resid 198 through 201 Processing helix chain 'C' and resid 202 through 220 removed outlier: 3.527A pdb=" N SER C 208 " --> pdb=" O LYS C 204 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU C 211 " --> pdb=" O SER C 207 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS C 215 " --> pdb=" O GLU C 211 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N SER C 216 " --> pdb=" O GLU C 212 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS C 220 " --> pdb=" O SER C 216 " (cutoff:3.500A) Processing helix chain '6' and resid 212 through 224 removed outlier: 3.623A pdb=" N ILE 6 216 " --> pdb=" O ARG 6 212 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG 6 217 " --> pdb=" O ASP 6 213 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ALA 6 218 " --> pdb=" O GLU 6 214 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ILE 6 219 " --> pdb=" O GLU 6 215 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU 6 221 " --> pdb=" O ARG 6 217 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N SER 6 222 " --> pdb=" O ALA 6 218 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU 6 223 " --> pdb=" O ILE 6 219 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU 6 224 " --> pdb=" O ILE 6 220 " (cutoff:3.500A) Processing helix chain '6' and resid 236 through 240 removed outlier: 3.577A pdb=" N GLY 6 240 " --> pdb=" O PRO 6 237 " (cutoff:3.500A) Processing helix chain '6' and resid 241 through 250 removed outlier: 4.678A pdb=" N VAL 6 245 " --> pdb=" O LYS 6 241 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY 6 247 " --> pdb=" O THR 6 243 " (cutoff:3.500A) Processing helix chain '6' and resid 250 through 255 removed outlier: 4.251A pdb=" N LYS 6 254 " --> pdb=" O TYR 6 250 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY 6 255 " --> pdb=" O ARG 6 251 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 250 through 255' Processing helix chain '6' and resid 258 through 262 removed outlier: 4.223A pdb=" N GLN 6 262 " --> pdb=" O LYS 6 259 " (cutoff:3.500A) Processing helix chain '6' and resid 272 through 277 removed outlier: 4.112A pdb=" N SER 6 276 " --> pdb=" O LYS 6 273 " (cutoff:3.500A) Processing helix chain '6' and resid 283 through 293 removed outlier: 3.826A pdb=" N ARG 6 287 " --> pdb=" O GLU 6 283 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS 6 289 " --> pdb=" O GLU 6 285 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASN 6 290 " --> pdb=" O THR 6 286 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ILE 6 291 " --> pdb=" O ARG 6 287 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS 6 293 " --> pdb=" O LYS 6 289 " (cutoff:3.500A) Processing helix chain '6' and resid 309 through 315 removed outlier: 3.778A pdb=" N LEU 6 313 " --> pdb=" O ILE 6 309 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY 6 314 " --> pdb=" O HIS 6 310 " (cutoff:3.500A) Processing helix chain '6' and resid 327 through 334 removed outlier: 3.558A pdb=" N VAL 6 331 " --> pdb=" O LEU 6 327 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER 6 333 " --> pdb=" O LYS 6 329 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS 6 334 " --> pdb=" O PRO 6 330 " (cutoff:3.500A) Processing helix chain '6' and resid 344 through 351 removed outlier: 3.959A pdb=" N ARG 6 349 " --> pdb=" O ILE 6 345 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LYS 6 350 " --> pdb=" O ALA 6 346 " (cutoff:3.500A) Processing helix chain '6' and resid 351 through 356 removed outlier: 3.534A pdb=" N SER 6 356 " --> pdb=" O ILE 6 352 " (cutoff:3.500A) Processing helix chain '6' and resid 375 through 391 removed outlier: 4.062A pdb=" N SER 6 381 " --> pdb=" O LYS 6 377 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N LEU 6 382 " --> pdb=" O ILE 6 378 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS 6 383 " --> pdb=" O LEU 6 379 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER 6 384 " --> pdb=" O ARG 6 380 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LYS 6 385 " --> pdb=" O SER 6 381 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR 6 386 " --> pdb=" O LEU 6 382 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ASN 6 388 " --> pdb=" O SER 6 384 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N PHE 6 389 " --> pdb=" O LYS 6 385 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR 6 390 " --> pdb=" O TYR 6 386 " (cutoff:3.500A) Processing helix chain '6' and resid 395 through 410 removed outlier: 4.151A pdb=" N ALA 6 403 " --> pdb=" O LEU 6 399 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER 6 406 " --> pdb=" O ALA 6 402 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG 6 408 " --> pdb=" O LYS 6 404 " (cutoff:3.500A) Processing helix chain '6' and resid 414 through 435 removed outlier: 4.067A pdb=" N ALA 6 419 " --> pdb=" O LEU 6 415 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE 6 420 " --> pdb=" O PRO 6 416 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASP 6 421 " --> pdb=" O ASP 6 417 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU 6 422 " --> pdb=" O LYS 6 418 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU 6 423 " --> pdb=" O ALA 6 419 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ASN 6 424 " --> pdb=" O ILE 6 420 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LYS 6 425 " --> pdb=" O ASP 6 421 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA 6 426 " --> pdb=" O LEU 6 422 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N CYS 6 427 " --> pdb=" O LEU 6 423 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N SER 6 428 " --> pdb=" O ASN 6 424 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE 6 429 " --> pdb=" O LYS 6 425 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU 6 430 " --> pdb=" O ALA 6 426 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN 6 431 " --> pdb=" O CYS 6 427 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL 6 432 " --> pdb=" O SER 6 428 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLN 6 433 " --> pdb=" O PHE 6 429 " (cutoff:3.500A) Processing helix chain '6' and resid 438 through 456 removed outlier: 3.647A pdb=" N GLU 6 445 " --> pdb=" O ILE 6 441 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ARG 6 446 " --> pdb=" O ASP 6 442 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASP 6 447 " --> pdb=" O VAL 6 443 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LEU 6 451 " --> pdb=" O ASP 6 447 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER 6 452 " --> pdb=" O ILE 6 448 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU 6 454 " --> pdb=" O ARG 6 450 " (cutoff:3.500A) Processing helix chain '6' and resid 465 through 508 removed outlier: 3.832A pdb=" N LYS 6 469 " --> pdb=" O VAL 6 465 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR 6 470 " --> pdb=" O SER 6 466 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN 6 471 " --> pdb=" O LYS 6 467 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N LYS 6 475 " --> pdb=" O ASN 6 471 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN 6 483 " --> pdb=" O GLU 6 479 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS 6 486 " --> pdb=" O GLU 6 482 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR 6 488 " --> pdb=" O LEU 6 484 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLU 6 489 " --> pdb=" O LYS 6 485 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ARG 6 497 " --> pdb=" O ILE 6 493 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N LEU 6 498 " --> pdb=" O THR 6 494 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N LYS 6 499 " --> pdb=" O GLY 6 495 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG 6 500 " --> pdb=" O GLU 6 496 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE 6 504 " --> pdb=" O ARG 6 500 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N GLU 6 505 " --> pdb=" O LYS 6 501 " (cutoff:3.500A) Processing helix chain '6' and resid 509 through 515 removed outlier: 4.360A pdb=" N GLU 6 513 " --> pdb=" O ASN 6 509 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU 6 514 " --> pdb=" O ASP 6 510 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR 6 515 " --> pdb=" O LEU 6 511 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 509 through 515' Processing helix chain '6' and resid 526 through 536 removed outlier: 4.173A pdb=" N SER 6 532 " --> pdb=" O GLU 6 528 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N LEU 6 533 " --> pdb=" O LEU 6 529 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LYS 6 534 " --> pdb=" O GLN 6 530 " (cutoff:3.500A) Processing helix chain '6' and resid 537 through 542 removed outlier: 5.085A pdb=" N TYR 6 540 " --> pdb=" O GLN 6 537 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU 6 542 " --> pdb=" O LYS 6 539 " (cutoff:3.500A) Processing helix chain '6' and resid 543 through 554 removed outlier: 3.658A pdb=" N THR 6 547 " --> pdb=" O LEU 6 543 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL 6 548 " --> pdb=" O TYR 6 544 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA 6 549 " --> pdb=" O LYS 6 545 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL 6 551 " --> pdb=" O THR 6 547 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLU 6 552 " --> pdb=" O VAL 6 548 " (cutoff:3.500A) Processing helix chain '6' and resid 565 through 577 removed outlier: 3.817A pdb=" N VAL 6 569 " --> pdb=" O TYR 6 565 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER 6 570 " --> pdb=" O GLN 6 566 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE 6 572 " --> pdb=" O HIS 6 568 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG 6 575 " --> pdb=" O TYR 6 571 " (cutoff:3.500A) Processing helix chain '6' and resid 590 through 593 removed outlier: 3.735A pdb=" N LEU 6 593 " --> pdb=" O LYS 6 590 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 590 through 593' Processing helix chain '6' and resid 594 through 603 removed outlier: 3.701A pdb=" N SER 6 598 " --> pdb=" O LYS 6 594 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS 6 601 " --> pdb=" O ASN 6 597 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N SER 6 602 " --> pdb=" O SER 6 598 " (cutoff:3.500A) Processing helix chain '6' and resid 606 through 616 removed outlier: 4.030A pdb=" N ILE 6 610 " --> pdb=" O ASN 6 606 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER 6 612 " --> pdb=" O ASP 6 608 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP 6 615 " --> pdb=" O LYS 6 611 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA 6 616 " --> pdb=" O SER 6 612 " (cutoff:3.500A) Processing helix chain '6' and resid 617 through 622 Processing helix chain '6' and resid 645 through 655 Processing helix chain '6' and resid 658 through 660 No H-bonds generated for 'chain '6' and resid 658 through 660' Processing helix chain '6' and resid 666 through 670 removed outlier: 3.672A pdb=" N GLU 6 669 " --> pdb=" O ASN 6 666 " (cutoff:3.500A) Processing helix chain '6' and resid 672 through 675 Processing helix chain '6' and resid 676 through 681 Processing helix chain '6' and resid 693 through 702 removed outlier: 4.459A pdb=" N VAL 6 699 " --> pdb=" O LEU 6 695 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG 6 700 " --> pdb=" O THR 6 696 " (cutoff:3.500A) Processing helix chain '6' and resid 719 through 728 removed outlier: 3.678A pdb=" N LEU 6 723 " --> pdb=" O VAL 6 719 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN 6 725 " --> pdb=" O LYS 6 721 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU 6 727 " --> pdb=" O LEU 6 723 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLY 6 728 " --> pdb=" O LEU 6 724 " (cutoff:3.500A) Processing helix chain '6' and resid 759 through 764 removed outlier: 3.627A pdb=" N PHE 6 763 " --> pdb=" O LYS 6 759 " (cutoff:3.500A) Processing helix chain '6' and resid 773 through 792 Processing helix chain '6' and resid 795 through 801 Processing helix chain '6' and resid 814 through 828 removed outlier: 3.753A pdb=" N VAL 6 819 " --> pdb=" O LEU 6 815 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ALA 6 820 " --> pdb=" O HIS 6 816 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG 6 822 " --> pdb=" O ILE 6 818 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE 6 823 " --> pdb=" O VAL 6 819 " (cutoff:3.500A) Processing helix chain '6' and resid 840 through 852 removed outlier: 3.882A pdb=" N ILE 6 844 " --> pdb=" O SER 6 840 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR 6 846 " --> pdb=" O LYS 6 842 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE 6 848 " --> pdb=" O ILE 6 844 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR 6 852 " --> pdb=" O ILE 6 848 " (cutoff:3.500A) Processing helix chain '6' and resid 858 through 867 removed outlier: 3.793A pdb=" N LEU 6 862 " --> pdb=" O ALA 6 858 " (cutoff:3.500A) Processing helix chain '6' and resid 870 through 879 removed outlier: 3.704A pdb=" N MET 6 876 " --> pdb=" O LYS 6 872 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 57 removed outlier: 3.902A pdb=" N ALA D 33 " --> pdb=" O GLY D 29 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR D 34 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR D 39 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE D 41 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP D 43 " --> pdb=" O THR D 39 " (cutoff:3.500A) Proline residue: D 44 - end of helix removed outlier: 3.682A pdb=" N LYS D 50 " --> pdb=" O SER D 46 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP D 51 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLU D 54 " --> pdb=" O LYS D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 73 removed outlier: 3.631A pdb=" N LYS D 67 " --> pdb=" O LYS D 63 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS D 70 " --> pdb=" O HIS D 66 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG D 73 " --> pdb=" O LYS D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 94 removed outlier: 4.197A pdb=" N TRP D 80 " --> pdb=" O LYS D 76 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N MET D 83 " --> pdb=" O ARG D 79 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU D 87 " --> pdb=" O MET D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 119 removed outlier: 3.988A pdb=" N ILE D 109 " --> pdb=" O ALA D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 148 removed outlier: 4.119A pdb=" N PHE D 132 " --> pdb=" O LYS D 128 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS D 134 " --> pdb=" O LEU D 130 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASN D 138 " --> pdb=" O HIS D 134 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS D 147 " --> pdb=" O ASN D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 164 removed outlier: 3.603A pdb=" N GLN D 161 " --> pdb=" O ALA D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 170 removed outlier: 3.666A pdb=" N ARG D 169 " --> pdb=" O GLN D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 182 removed outlier: 3.615A pdb=" N LYS D 178 " --> pdb=" O GLU D 174 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE D 179 " --> pdb=" O PRO D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 189 Processing helix chain 'D' and resid 198 through 201 Processing helix chain 'D' and resid 202 through 218 removed outlier: 3.527A pdb=" N SER D 208 " --> pdb=" O LYS D 204 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU D 211 " --> pdb=" O SER D 207 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS D 215 " --> pdb=" O GLU D 211 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N SER D 216 " --> pdb=" O GLU D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 221 No H-bonds generated for 'chain 'D' and resid 219 through 221' Processing helix chain 'E' and resid 29 through 57 removed outlier: 3.901A pdb=" N ALA E 33 " --> pdb=" O GLY E 29 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N THR E 34 " --> pdb=" O ASP E 30 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR E 39 " --> pdb=" O SER E 35 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE E 41 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP E 43 " --> pdb=" O THR E 39 " (cutoff:3.500A) Proline residue: E 44 - end of helix removed outlier: 3.681A pdb=" N LYS E 50 " --> pdb=" O SER E 46 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP E 51 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLU E 54 " --> pdb=" O LYS E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 73 removed outlier: 3.631A pdb=" N LYS E 67 " --> pdb=" O LYS E 63 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS E 70 " --> pdb=" O HIS E 66 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG E 73 " --> pdb=" O LYS E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 94 removed outlier: 4.197A pdb=" N TRP E 80 " --> pdb=" O LYS E 76 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N MET E 83 " --> pdb=" O ARG E 79 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU E 87 " --> pdb=" O MET E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 119 removed outlier: 3.990A pdb=" N ILE E 109 " --> pdb=" O ALA E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 148 removed outlier: 4.119A pdb=" N PHE E 132 " --> pdb=" O LYS E 128 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS E 134 " --> pdb=" O LEU E 130 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASN E 138 " --> pdb=" O HIS E 134 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS E 147 " --> pdb=" O ASN E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 164 removed outlier: 3.775A pdb=" N GLN E 161 " --> pdb=" O ALA E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 170 removed outlier: 3.667A pdb=" N ARG E 169 " --> pdb=" O GLN E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 182 removed outlier: 3.615A pdb=" N LYS E 178 " --> pdb=" O GLU E 174 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE E 179 " --> pdb=" O PRO E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 189 Processing helix chain 'E' and resid 198 through 201 Processing helix chain 'E' and resid 202 through 219 removed outlier: 3.527A pdb=" N SER E 208 " --> pdb=" O LYS E 204 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU E 211 " --> pdb=" O SER E 207 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS E 215 " --> pdb=" O GLU E 211 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N SER E 216 " --> pdb=" O GLU E 212 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU E 218 " --> pdb=" O LEU E 214 " (cutoff:3.500A) Processing helix chain 'd' and resid 670 through 680 removed outlier: 3.689A pdb=" N LYS d 674 " --> pdb=" O LYS d 670 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU d 675 " --> pdb=" O ASP d 671 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N GLU d 678 " --> pdb=" O LYS d 674 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLY d 679 " --> pdb=" O LEU d 675 " (cutoff:3.500A) Processing helix chain 'd' and resid 687 through 696 removed outlier: 4.074A pdb=" N LYS d 693 " --> pdb=" O ASN d 689 " (cutoff:3.500A) Processing helix chain 'd' and resid 726 through 733 Processing helix chain 'd' and resid 743 through 757 removed outlier: 3.728A pdb=" N ASP d 747 " --> pdb=" O SER d 743 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS d 752 " --> pdb=" O TYR d 748 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LYS d 757 " --> pdb=" O LYS d 753 " (cutoff:3.500A) Processing helix chain 'd' and resid 761 through 777 removed outlier: 3.509A pdb=" N GLY d 766 " --> pdb=" O GLU d 762 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N PHE d 767 " --> pdb=" O ASP d 763 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N ALA d 770 " --> pdb=" O GLY d 766 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N TYR d 771 " --> pdb=" O PHE d 767 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS d 772 " --> pdb=" O TYR d 768 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN d 776 " --> pdb=" O LYS d 772 " (cutoff:3.500A) Processing helix chain 'd' and resid 806 through 816 Processing helix chain 'c' and resid 670 through 680 removed outlier: 3.688A pdb=" N LYS c 674 " --> pdb=" O LYS c 670 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU c 675 " --> pdb=" O ASP c 671 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N GLU c 678 " --> pdb=" O LYS c 674 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLY c 679 " --> pdb=" O LEU c 675 " (cutoff:3.500A) Processing helix chain 'c' and resid 687 through 696 removed outlier: 4.074A pdb=" N LYS c 693 " --> pdb=" O ASN c 689 " (cutoff:3.500A) Processing helix chain 'c' and resid 726 through 733 Processing helix chain 'c' and resid 744 through 757 removed outlier: 3.598A pdb=" N LYS c 750 " --> pdb=" O ILE c 746 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N LYS c 757 " --> pdb=" O LYS c 753 " (cutoff:3.500A) Processing helix chain 'c' and resid 764 through 777 removed outlier: 3.520A pdb=" N TYR c 771 " --> pdb=" O PHE c 767 " (cutoff:3.500A) Processing helix chain 'c' and resid 806 through 816 Processing helix chain 'b' and resid 670 through 680 removed outlier: 3.688A pdb=" N LYS b 674 " --> pdb=" O LYS b 670 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU b 675 " --> pdb=" O ASP b 671 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N GLU b 678 " --> pdb=" O LYS b 674 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLY b 679 " --> pdb=" O LEU b 675 " (cutoff:3.500A) Processing helix chain 'b' and resid 687 through 696 removed outlier: 4.074A pdb=" N LYS b 693 " --> pdb=" O ASN b 689 " (cutoff:3.500A) Processing helix chain 'b' and resid 726 through 733 Processing helix chain 'b' and resid 744 through 757 removed outlier: 3.581A pdb=" N LYS b 750 " --> pdb=" O ILE b 746 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LYS b 757 " --> pdb=" O LYS b 753 " (cutoff:3.500A) Processing helix chain 'b' and resid 761 through 777 removed outlier: 3.508A pdb=" N GLY b 766 " --> pdb=" O GLU b 762 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N PHE b 767 " --> pdb=" O ASP b 763 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N ALA b 770 " --> pdb=" O GLY b 766 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N TYR b 771 " --> pdb=" O PHE b 767 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS b 772 " --> pdb=" O TYR b 768 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN b 776 " --> pdb=" O LYS b 772 " (cutoff:3.500A) Processing helix chain 'b' and resid 806 through 816 Processing helix chain 'B' and resid 29 through 57 removed outlier: 3.900A pdb=" N ALA B 33 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N THR B 34 " --> pdb=" O ASP B 30 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR B 39 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP B 43 " --> pdb=" O THR B 39 " (cutoff:3.500A) Proline residue: B 44 - end of helix removed outlier: 3.682A pdb=" N LYS B 50 " --> pdb=" O SER B 46 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP B 51 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLU B 54 " --> pdb=" O LYS B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 73 removed outlier: 3.630A pdb=" N LYS B 67 " --> pdb=" O LYS B 63 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS B 70 " --> pdb=" O HIS B 66 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG B 73 " --> pdb=" O LYS B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 94 removed outlier: 4.197A pdb=" N TRP B 80 " --> pdb=" O LYS B 76 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N MET B 83 " --> pdb=" O ARG B 79 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU B 87 " --> pdb=" O MET B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 119 removed outlier: 3.989A pdb=" N ILE B 109 " --> pdb=" O ALA B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 148 removed outlier: 4.118A pdb=" N PHE B 132 " --> pdb=" O LYS B 128 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS B 134 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASN B 138 " --> pdb=" O HIS B 134 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS B 147 " --> pdb=" O ASN B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 164 removed outlier: 3.773A pdb=" N GLN B 161 " --> pdb=" O ALA B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 170 removed outlier: 3.667A pdb=" N ARG B 169 " --> pdb=" O GLN B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 182 removed outlier: 3.615A pdb=" N LYS B 178 " --> pdb=" O GLU B 174 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE B 179 " --> pdb=" O PRO B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 189 Processing helix chain 'B' and resid 198 through 201 Processing helix chain 'B' and resid 202 through 219 removed outlier: 3.527A pdb=" N SER B 208 " --> pdb=" O LYS B 204 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU B 211 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS B 213 " --> pdb=" O TYR B 209 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS B 215 " --> pdb=" O GLU B 211 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N SER B 216 " --> pdb=" O GLU B 212 " (cutoff:3.500A) Processing helix chain 'a' and resid 670 through 680 removed outlier: 3.687A pdb=" N LYS a 674 " --> pdb=" O LYS a 670 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU a 675 " --> pdb=" O ASP a 671 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N GLU a 678 " --> pdb=" O LYS a 674 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY a 679 " --> pdb=" O LEU a 675 " (cutoff:3.500A) Processing helix chain 'a' and resid 687 through 696 removed outlier: 4.073A pdb=" N LYS a 693 " --> pdb=" O ASN a 689 " (cutoff:3.500A) Processing helix chain 'a' and resid 726 through 733 Processing helix chain 'a' and resid 744 through 757 removed outlier: 4.585A pdb=" N LYS a 757 " --> pdb=" O LYS a 753 " (cutoff:3.500A) Processing helix chain 'a' and resid 761 through 777 removed outlier: 3.509A pdb=" N GLY a 766 " --> pdb=" O GLU a 762 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N PHE a 767 " --> pdb=" O ASP a 763 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ALA a 770 " --> pdb=" O GLY a 766 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N TYR a 771 " --> pdb=" O PHE a 767 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LYS a 772 " --> pdb=" O TYR a 768 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN a 776 " --> pdb=" O LYS a 772 " (cutoff:3.500A) Processing helix chain 'a' and resid 806 through 816 Processing helix chain 'A' and resid 29 through 57 removed outlier: 3.902A pdb=" N ALA A 33 " --> pdb=" O GLY A 29 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N THR A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR A 39 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP A 43 " --> pdb=" O THR A 39 " (cutoff:3.500A) Proline residue: A 44 - end of helix removed outlier: 3.683A pdb=" N LYS A 50 " --> pdb=" O SER A 46 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLU A 54 " --> pdb=" O LYS A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 73 removed outlier: 3.631A pdb=" N LYS A 67 " --> pdb=" O LYS A 63 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS A 70 " --> pdb=" O HIS A 66 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG A 73 " --> pdb=" O LYS A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 94 removed outlier: 4.197A pdb=" N TRP A 80 " --> pdb=" O LYS A 76 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N MET A 83 " --> pdb=" O ARG A 79 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU A 87 " --> pdb=" O MET A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 119 removed outlier: 3.989A pdb=" N ILE A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 148 removed outlier: 4.120A pdb=" N PHE A 132 " --> pdb=" O LYS A 128 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS A 134 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASN A 138 " --> pdb=" O HIS A 134 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS A 147 " --> pdb=" O ASN A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 164 removed outlier: 3.774A pdb=" N GLN A 161 " --> pdb=" O ALA A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 170 removed outlier: 3.666A pdb=" N ARG A 169 " --> pdb=" O GLN A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 182 removed outlier: 3.615A pdb=" N LYS A 178 " --> pdb=" O GLU A 174 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE A 179 " --> pdb=" O PRO A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 189 Processing helix chain 'A' and resid 198 through 201 Processing helix chain 'A' and resid 202 through 214 removed outlier: 3.528A pdb=" N SER A 208 " --> pdb=" O LYS A 204 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU A 211 " --> pdb=" O SER A 207 " (cutoff:3.500A) Processing helix chain 'g' and resid 670 through 680 removed outlier: 3.688A pdb=" N LYS g 674 " --> pdb=" O LYS g 670 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU g 675 " --> pdb=" O ASP g 671 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N GLU g 678 " --> pdb=" O LYS g 674 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLY g 679 " --> pdb=" O LEU g 675 " (cutoff:3.500A) Processing helix chain 'g' and resid 687 through 696 removed outlier: 4.072A pdb=" N LYS g 693 " --> pdb=" O ASN g 689 " (cutoff:3.500A) Processing helix chain 'g' and resid 726 through 733 Processing helix chain 'g' and resid 743 through 757 removed outlier: 3.710A pdb=" N ASP g 747 " --> pdb=" O SER g 743 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR g 748 " --> pdb=" O LYS g 744 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS g 752 " --> pdb=" O TYR g 748 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N LYS g 757 " --> pdb=" O LYS g 753 " (cutoff:3.500A) Processing helix chain 'g' and resid 761 through 766 removed outlier: 3.508A pdb=" N GLY g 766 " --> pdb=" O GLU g 762 " (cutoff:3.500A) Processing helix chain 'g' and resid 769 through 777 removed outlier: 3.806A pdb=" N GLN g 773 " --> pdb=" O ASP g 769 " (cutoff:3.500A) Processing helix chain 'g' and resid 806 through 816 Processing helix chain 'G' and resid 29 through 57 removed outlier: 3.902A pdb=" N ALA G 33 " --> pdb=" O GLY G 29 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N THR G 34 " --> pdb=" O ASP G 30 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR G 39 " --> pdb=" O SER G 35 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE G 41 " --> pdb=" O LEU G 37 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP G 43 " --> pdb=" O THR G 39 " (cutoff:3.500A) Proline residue: G 44 - end of helix removed outlier: 3.682A pdb=" N LYS G 50 " --> pdb=" O SER G 46 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP G 51 " --> pdb=" O LEU G 47 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU G 54 " --> pdb=" O LYS G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 73 removed outlier: 3.630A pdb=" N LYS G 67 " --> pdb=" O LYS G 63 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS G 70 " --> pdb=" O HIS G 66 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG G 73 " --> pdb=" O LYS G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 94 removed outlier: 4.197A pdb=" N TRP G 80 " --> pdb=" O LYS G 76 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N MET G 83 " --> pdb=" O ARG G 79 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU G 87 " --> pdb=" O MET G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 119 removed outlier: 3.989A pdb=" N ILE G 109 " --> pdb=" O ALA G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 128 through 148 removed outlier: 4.119A pdb=" N PHE G 132 " --> pdb=" O LYS G 128 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS G 134 " --> pdb=" O LEU G 130 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASN G 138 " --> pdb=" O HIS G 134 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS G 147 " --> pdb=" O ASN G 143 " (cutoff:3.500A) Processing helix chain 'G' and resid 154 through 164 removed outlier: 3.774A pdb=" N GLN G 161 " --> pdb=" O ALA G 157 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 170 removed outlier: 3.667A pdb=" N ARG G 169 " --> pdb=" O GLN G 166 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 182 removed outlier: 3.615A pdb=" N LYS G 178 " --> pdb=" O GLU G 174 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE G 179 " --> pdb=" O PRO G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 189 Processing helix chain 'G' and resid 198 through 201 Processing helix chain 'G' and resid 202 through 214 removed outlier: 3.527A pdb=" N SER G 208 " --> pdb=" O LYS G 204 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU G 211 " --> pdb=" O SER G 207 " (cutoff:3.500A) Processing helix chain 'f' and resid 670 through 680 removed outlier: 3.689A pdb=" N LYS f 674 " --> pdb=" O LYS f 670 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU f 675 " --> pdb=" O ASP f 671 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N GLU f 678 " --> pdb=" O LYS f 674 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLY f 679 " --> pdb=" O LEU f 675 " (cutoff:3.500A) Processing helix chain 'f' and resid 687 through 696 removed outlier: 4.073A pdb=" N LYS f 693 " --> pdb=" O ASN f 689 " (cutoff:3.500A) Processing helix chain 'f' and resid 726 through 733 Processing helix chain 'f' and resid 744 through 757 removed outlier: 4.585A pdb=" N LYS f 757 " --> pdb=" O LYS f 753 " (cutoff:3.500A) Processing helix chain 'f' and resid 761 through 766 removed outlier: 3.509A pdb=" N GLY f 766 " --> pdb=" O GLU f 762 " (cutoff:3.500A) Processing helix chain 'f' and resid 768 through 777 removed outlier: 4.105A pdb=" N LYS f 772 " --> pdb=" O TYR f 768 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN f 773 " --> pdb=" O ASP f 769 " (cutoff:3.500A) Processing helix chain 'f' and resid 806 through 816 Processing helix chain 'F' and resid 29 through 57 removed outlier: 3.902A pdb=" N ALA F 33 " --> pdb=" O GLY F 29 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N THR F 34 " --> pdb=" O ASP F 30 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR F 39 " --> pdb=" O SER F 35 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE F 41 " --> pdb=" O LEU F 37 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP F 43 " --> pdb=" O THR F 39 " (cutoff:3.500A) Proline residue: F 44 - end of helix removed outlier: 3.682A pdb=" N LYS F 50 " --> pdb=" O SER F 46 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP F 51 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLU F 54 " --> pdb=" O LYS F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 73 removed outlier: 3.630A pdb=" N LYS F 67 " --> pdb=" O LYS F 63 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS F 70 " --> pdb=" O HIS F 66 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG F 73 " --> pdb=" O LYS F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 94 removed outlier: 4.197A pdb=" N TRP F 80 " --> pdb=" O LYS F 76 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N MET F 83 " --> pdb=" O ARG F 79 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU F 87 " --> pdb=" O MET F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 119 removed outlier: 3.989A pdb=" N ILE F 109 " --> pdb=" O ALA F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 148 removed outlier: 4.120A pdb=" N PHE F 132 " --> pdb=" O LYS F 128 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS F 134 " --> pdb=" O LEU F 130 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASN F 138 " --> pdb=" O HIS F 134 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS F 147 " --> pdb=" O ASN F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 154 through 164 removed outlier: 3.774A pdb=" N GLN F 161 " --> pdb=" O ALA F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 170 removed outlier: 3.666A pdb=" N ARG F 169 " --> pdb=" O GLN F 166 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 182 removed outlier: 3.615A pdb=" N LYS F 178 " --> pdb=" O GLU F 174 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE F 179 " --> pdb=" O PRO F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 189 Processing helix chain 'F' and resid 198 through 201 Processing helix chain 'F' and resid 202 through 221 removed outlier: 3.528A pdb=" N SER F 208 " --> pdb=" O LYS F 204 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU F 212 " --> pdb=" O SER F 208 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET F 217 " --> pdb=" O LYS F 213 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS F 221 " --> pdb=" O MET F 217 " (cutoff:3.500A) Processing helix chain 'e' and resid 670 through 680 removed outlier: 3.689A pdb=" N LYS e 674 " --> pdb=" O LYS e 670 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU e 675 " --> pdb=" O ASP e 671 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N GLU e 678 " --> pdb=" O LYS e 674 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLY e 679 " --> pdb=" O LEU e 675 " (cutoff:3.500A) Processing helix chain 'e' and resid 687 through 696 removed outlier: 4.074A pdb=" N LYS e 693 " --> pdb=" O ASN e 689 " (cutoff:3.500A) Processing helix chain 'e' and resid 726 through 733 Processing helix chain 'e' and resid 744 through 757 removed outlier: 3.886A pdb=" N LYS e 750 " --> pdb=" O ILE e 746 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS e 752 " --> pdb=" O TYR e 748 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LYS e 757 " --> pdb=" O LYS e 753 " (cutoff:3.500A) Processing helix chain 'e' and resid 761 through 777 removed outlier: 3.509A pdb=" N GLY e 766 " --> pdb=" O GLU e 762 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N PHE e 767 " --> pdb=" O ASP e 763 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ALA e 770 " --> pdb=" O GLY e 766 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N TYR e 771 " --> pdb=" O PHE e 767 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS e 772 " --> pdb=" O TYR e 768 " (cutoff:3.500A) Processing helix chain 'e' and resid 806 through 816 Processing helix chain 'n' and resid -3 through 31 Processing helix chain 'h' and resid -1 through 28 Processing helix chain 'h' and resid 994 through 1003 Processing helix chain 'l' and resid 0 through 33 removed outlier: 3.515A pdb=" N UNK l 30 " --> pdb=" O UNK l 26 " (cutoff:3.500A) Processing helix chain 'l' and resid 994 through 1003 Processing helix chain 'm' and resid -2 through 31 Processing helix chain 'm' and resid 995 through 1003 Processing sheet with id=AA1, first strand: chain '1' and resid 195 through 196 removed outlier: 6.284A pdb=" N ILE 1 267 " --> pdb=" O PHE 1 305 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU 1 304 " --> pdb=" O ILE 1 340 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N ALA 1 342 " --> pdb=" O LEU 1 304 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N THR 1 343 " --> pdb=" O PRO 1 231 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N LEU 1 233 " --> pdb=" O THR 1 343 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N VAL 1 232 " --> pdb=" O ILE 1 365 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL 1 367 " --> pdb=" O VAL 1 232 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL 1 234 " --> pdb=" O VAL 1 367 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '1' and resid 662 through 663 removed outlier: 6.220A pdb=" N VAL 1 707 " --> pdb=" O ILE 1 748 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N THR 1 750 " --> pdb=" O VAL 1 707 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N LEU 1 635 " --> pdb=" O GLY 1 805 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '1' and resid 838 through 839 removed outlier: 4.648A pdb=" N ILE 1 901 " --> pdb=" O PHE 1 889 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '2' and resid 195 through 196 removed outlier: 3.516A pdb=" N LEU 2 269 " --> pdb=" O PHE 2 305 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '2' and resid 231 through 235 removed outlier: 5.781A pdb=" N VAL 2 232 " --> pdb=" O ILE 2 365 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N VAL 2 367 " --> pdb=" O VAL 2 232 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL 2 234 " --> pdb=" O VAL 2 367 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain '2' and resid 662 through 663 removed outlier: 6.852A pdb=" N SER 2 705 " --> pdb=" O ILE 2 746 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N ILE 2 748 " --> pdb=" O SER 2 705 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL 2 707 " --> pdb=" O ILE 2 748 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N THR 2 750 " --> pdb=" O VAL 2 707 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N THR 2 633 " --> pdb=" O LYS 2 803 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N GLY 2 805 " --> pdb=" O THR 2 633 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N LEU 2 635 " --> pdb=" O GLY 2 805 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '2' and resid 836 through 839 removed outlier: 6.403A pdb=" N ASN 2 898 " --> pdb=" O ASP B 231 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ASP B 233 " --> pdb=" O ASN 2 898 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL 2 900 " --> pdb=" O ASP B 233 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '3' and resid 341 through 342 removed outlier: 6.399A pdb=" N VAL 3 232 " --> pdb=" O ILE 3 365 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '3' and resid 265 through 268 removed outlier: 5.988A pdb=" N THR 3 265 " --> pdb=" O ILE 3 303 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N PHE 3 305 " --> pdb=" O THR 3 265 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ILE 3 267 " --> pdb=" O PHE 3 305 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain '3' and resid 393 through 394 removed outlier: 8.193A pdb=" N ASN 3 393 " --> pdb=" O VAL 3 564 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain '3' and resid 634 through 637 removed outlier: 5.972A pdb=" N VAL 3 707 " --> pdb=" O ILE 3 748 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N THR 3 750 " --> pdb=" O VAL 3 707 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N PHE 3 709 " --> pdb=" O THR 3 750 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE 3 663 " --> pdb=" O LEU 3 708 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '3' and resid 836 through 839 removed outlier: 6.268A pdb=" N GLN 3 836 " --> pdb=" O VAL 3 888 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N VAL 3 890 " --> pdb=" O GLN 3 836 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N SER 3 838 " --> pdb=" O VAL 3 890 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP 3 891 " --> pdb=" O LEU 3 899 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU 3 899 " --> pdb=" O ASP 3 891 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N VAL 3 900 " --> pdb=" O ASP C 233 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '4' and resid 195 through 196 removed outlier: 6.106A pdb=" N ILE 4 267 " --> pdb=" O PHE 4 305 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU 4 304 " --> pdb=" O ILE 4 340 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N ALA 4 342 " --> pdb=" O LEU 4 304 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '4' and resid 393 through 394 removed outlier: 7.514A pdb=" N ASN 4 393 " --> pdb=" O VAL 4 564 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain '4' and resid 747 through 751 removed outlier: 6.842A pdb=" N THR 4 633 " --> pdb=" O LYS 4 803 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N GLY 4 805 " --> pdb=" O THR 4 633 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N LEU 4 635 " --> pdb=" O GLY 4 805 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain '4' and resid 731 through 732 removed outlier: 3.593A pdb=" N ILE 4 732 " --> pdb=" O ILE 4 740 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '4' and resid 835 through 839 removed outlier: 3.586A pdb=" N ASP 4 891 " --> pdb=" O LEU 4 899 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU 4 899 " --> pdb=" O ASP 4 891 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain '5' and resid 341 through 344 removed outlier: 6.029A pdb=" N LEU 5 233 " --> pdb=" O THR 5 343 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain '5' and resid 265 through 267 Processing sheet with id=AC2, first strand: chain '5' and resid 393 through 394 removed outlier: 7.757A pdb=" N ASN 5 393 " --> pdb=" O VAL 5 564 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain '5' and resid 747 through 750 removed outlier: 7.235A pdb=" N THR 5 633 " --> pdb=" O LYS 5 803 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N GLY 5 805 " --> pdb=" O THR 5 633 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LEU 5 635 " --> pdb=" O GLY 5 805 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain '5' and resid 662 through 663 Processing sheet with id=AC5, first strand: chain '5' and resid 835 through 839 removed outlier: 3.979A pdb=" N ILE 5 901 " --> pdb=" O PHE 5 889 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain '6' and resid 341 through 343 removed outlier: 3.648A pdb=" N GLY 6 341 " --> pdb=" O PRO 6 231 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain '6' and resid 662 through 663 removed outlier: 6.550A pdb=" N VAL 6 706 " --> pdb=" O ILE 6 663 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ILE 6 746 " --> pdb=" O SER 6 705 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE 6 634 " --> pdb=" O ILE 6 747 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET 6 749 " --> pdb=" O PHE 6 634 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N SER 6 751 " --> pdb=" O PHE 6 636 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N THR 6 633 " --> pdb=" O LYS 6 803 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N GLY 6 805 " --> pdb=" O THR 6 633 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N LEU 6 635 " --> pdb=" O GLY 6 805 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain '6' and resid 836 through 839 Processing sheet with id=AC9, first strand: chain 'd' and resid 792 through 793 Processing sheet with id=AD1, first strand: chain 'c' and resid 792 through 793 Processing sheet with id=AD2, first strand: chain 'b' and resid 792 through 793 Processing sheet with id=AD3, first strand: chain 'a' and resid 792 through 793 Processing sheet with id=AD4, first strand: chain 'g' and resid 792 through 793 Processing sheet with id=AD5, first strand: chain 'f' and resid 792 through 793 Processing sheet with id=AD6, first strand: chain 'e' and resid 792 through 793 2296 hydrogen bonds defined for protein. 6636 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: 22.75 Time building geometry restraints manager: 13.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.35: 18486 1.35 - 1.53: 37408 1.53 - 1.71: 2235 1.71 - 1.89: 239 1.89 - 2.08: 12 Bond restraints: 58380 Sorted by residual: bond pdb=" C4 AGS 11003 " pdb=" C5 AGS 11003 " ideal model delta sigma weight residual 1.386 1.471 -0.085 1.00e-02 1.00e+04 7.21e+01 bond pdb=" C5 AGS 11003 " pdb=" C6 AGS 11003 " ideal model delta sigma weight residual 1.409 1.483 -0.074 1.00e-02 1.00e+04 5.45e+01 bond pdb=" C LYS 5 317 " pdb=" N ALA 5 318 " ideal model delta sigma weight residual 1.332 1.243 0.089 1.37e-02 5.33e+03 4.22e+01 bond pdb=" PG AGS 11003 " pdb=" S1G AGS 11003 " ideal model delta sigma weight residual 1.949 2.075 -0.126 2.00e-02 2.50e+03 3.98e+01 bond pdb=" CA TYR B 209 " pdb=" C TYR B 209 " ideal model delta sigma weight residual 1.523 1.608 -0.085 1.35e-02 5.49e+03 3.96e+01 ... (remaining 58375 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 75819 2.54 - 5.08: 2340 5.08 - 7.62: 393 7.62 - 10.16: 133 10.16 - 12.69: 17 Bond angle restraints: 78702 Sorted by residual: angle pdb=" N PHE 6 763 " pdb=" CA PHE 6 763 " pdb=" C PHE 6 763 " ideal model delta sigma weight residual 111.28 123.74 -12.46 1.09e+00 8.42e-01 1.31e+02 angle pdb=" C5 AGS 11003 " pdb=" C4 AGS 11003 " pdb=" N3 AGS 11003 " ideal model delta sigma weight residual 126.80 118.61 8.19 7.41e-01 1.82e+00 1.22e+02 angle pdb=" N LYS 6 486 " pdb=" CA LYS 6 486 " pdb=" C LYS 6 486 " ideal model delta sigma weight residual 111.14 122.94 -11.80 1.08e+00 8.57e-01 1.19e+02 angle pdb=" N SER B 208 " pdb=" CA SER B 208 " pdb=" C SER B 208 " ideal model delta sigma weight residual 112.89 101.27 11.62 1.24e+00 6.50e-01 8.79e+01 angle pdb=" C4 AGS 11003 " pdb=" C5 AGS 11003 " pdb=" N7 AGS 11003 " ideal model delta sigma weight residual 110.73 106.59 4.14 4.52e-01 4.89e+00 8.37e+01 ... (remaining 78697 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.75: 35649 31.75 - 63.51: 318 63.51 - 95.26: 20 95.26 - 127.02: 9 127.02 - 158.77: 5 Dihedral angle restraints: 36001 sinusoidal: 14833 harmonic: 21168 Sorted by residual: dihedral pdb=" CA LYS 5 464 " pdb=" C LYS 5 464 " pdb=" N VAL 5 465 " pdb=" CA VAL 5 465 " ideal model delta harmonic sigma weight residual 180.00 -132.67 -47.33 0 5.00e+00 4.00e-02 8.96e+01 dihedral pdb=" CA LYS 4 464 " pdb=" C LYS 4 464 " pdb=" N VAL 4 465 " pdb=" CA VAL 4 465 " ideal model delta harmonic sigma weight residual 180.00 -137.57 -42.43 0 5.00e+00 4.00e-02 7.20e+01 dihedral pdb=" CA LYS 2 794 " pdb=" C LYS 2 794 " pdb=" N PRO 2 795 " pdb=" CA PRO 2 795 " ideal model delta harmonic sigma weight residual -180.00 -138.14 -41.86 0 5.00e+00 4.00e-02 7.01e+01 ... (remaining 35998 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 8159 0.100 - 0.200: 628 0.200 - 0.300: 58 0.300 - 0.400: 24 0.400 - 0.500: 7 Chirality restraints: 8876 Sorted by residual: chirality pdb=" PB AGS 51001 " pdb=" O2B AGS 51001 " pdb=" O3A AGS 51001 " pdb=" O3B AGS 51001 " both_signs ideal model delta sigma weight residual True 3.18 -2.68 0.50 2.00e-01 2.50e+01 6.26e+00 chirality pdb=" CB ILE E 223 " pdb=" CA ILE E 223 " pdb=" CG1 ILE E 223 " pdb=" CG2 ILE E 223 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.48 2.00e-01 2.50e+01 5.67e+00 chirality pdb=" CA TYR b 707 " pdb=" N TYR b 707 " pdb=" C TYR b 707 " pdb=" CB TYR b 707 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.47e+00 ... (remaining 8873 not shown) Planarity restraints: 9939 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA UNK i 22 " 0.037 2.00e-02 2.50e+03 7.27e-02 5.29e+01 pdb=" C UNK i 22 " -0.126 2.00e-02 2.50e+03 pdb=" O UNK i 22 " 0.047 2.00e-02 2.50e+03 pdb=" N UNK i 23 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS 5 317 " 0.038 2.00e-02 2.50e+03 7.17e-02 5.14e+01 pdb=" C LYS 5 317 " -0.124 2.00e-02 2.50e+03 pdb=" O LYS 5 317 " 0.042 2.00e-02 2.50e+03 pdb=" N ALA 5 318 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA UNK m 25 " -0.026 2.00e-02 2.50e+03 5.22e-02 2.72e+01 pdb=" C UNK m 25 " 0.090 2.00e-02 2.50e+03 pdb=" O UNK m 25 " -0.034 2.00e-02 2.50e+03 pdb=" N UNK m 26 " -0.030 2.00e-02 2.50e+03 ... (remaining 9936 not shown) Histogram of nonbonded interaction distances: 1.08 - 1.84: 11 1.84 - 2.61: 661 2.61 - 3.37: 74059 3.37 - 4.14: 132600 4.14 - 4.90: 242313 Nonbonded interactions: 449644 Sorted by model distance: nonbonded pdb=" O GLY 2 495 " pdb=" CE LYS 2 499 " model vdw 1.079 3.440 nonbonded pdb=" OE2 GLU g 711 " pdb=" OD1 ASP g 769 " model vdw 1.412 3.040 nonbonded pdb=" C GLU 2 496 " pdb=" CD LYS 2 499 " model vdw 1.430 3.670 nonbonded pdb=" CA GLU 2 496 " pdb=" CD LYS 2 499 " model vdw 1.435 3.870 nonbonded pdb=" CE LYS 5 481 " pdb=" CB UNK l 987 " model vdw 1.453 3.840 ... (remaining 449639 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain '1' and (resid 189 through 904 or resid 1001)) selection = (chain '2' and (resid 189 through 904 or resid 1001)) selection = (chain '3' and (resid 189 through 904 or resid 1001)) selection = (chain '4' and (resid 189 through 904 or resid 1001)) selection = (chain '5' and (resid 189 through 904 or resid 1001)) selection = (chain '6' and (resid 189 through 904 or resid 1001)) } ncs_group { reference = chain 'A' selection = (chain 'B' and resid 27 through 217) selection = (chain 'C' and resid 27 through 217) selection = (chain 'D' and resid 27 through 217) selection = (chain 'E' and resid 27 through 217) selection = (chain 'F' and resid 27 through 217) selection = chain 'G' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' } ncs_group { reference = (chain 'h' and resid -1 through 1003) selection = chain 'i' selection = (chain 'j' and resid 10 through 1003) selection = (chain 'l' and resid 6 through 1003) } ncs_group { reference = (chain 'k' and resid 1 through 1004) selection = chain 'm' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.140 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: 0.050 Extract box with map and model: 1.860 Check model and map are aligned: 0.350 Set scattering table: 0.420 Process input model: 107.020 Find NCS groups from input model: 3.290 Set up NCS constraints: 0.440 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 121.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 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 : 0.007 0.126 58380 Z= 0.453 Angle : 1.114 12.694 78702 Z= 0.633 Chirality : 0.062 0.500 8876 Planarity : 0.007 0.083 9939 Dihedral : 10.084 158.771 22290 Min Nonbonded Distance : 1.079 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.88 % Favored : 91.79 % Rotamer: Outliers : 0.49 % Allowed : 0.57 % Favored : 98.95 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.31 % Twisted General : 0.40 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.77 (0.08), residues: 6773 helix: -3.91 (0.05), residues: 3164 sheet: -2.16 (0.21), residues: 477 loop : -2.34 (0.10), residues: 3132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.006 TRP G 171 HIS 0.018 0.002 HIS 3 310 PHE 0.034 0.003 PHE D 144 TYR 0.024 0.003 TYR 3 414 ARG 0.023 0.001 ARG 1 737 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13546 Ramachandran restraints generated. 6773 Oldfield, 0 Emsley, 6773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13546 Ramachandran restraints generated. 6773 Oldfield, 0 Emsley, 6773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2083 residues out of total 6163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 2053 time to evaluate : 5.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 293 LYS cc_start: 0.8714 (mttt) cc_final: 0.8325 (tmtt) REVERT: 1 366 LEU cc_start: 0.9387 (mt) cc_final: 0.9113 (pt) REVERT: 1 378 ILE cc_start: 0.9411 (mt) cc_final: 0.9196 (mt) REVERT: 1 542 GLU cc_start: 0.8845 (mt-10) cc_final: 0.8189 (tm-30) REVERT: 1 555 THR cc_start: 0.8598 (p) cc_final: 0.8390 (t) REVERT: 1 595 LEU cc_start: 0.9287 (mt) cc_final: 0.9071 (mt) REVERT: 1 655 LEU cc_start: 0.8435 (mt) cc_final: 0.8211 (mt) REVERT: 1 662 LEU cc_start: 0.8999 (tp) cc_final: 0.8644 (tt) REVERT: 1 691 ASP cc_start: 0.8663 (m-30) cc_final: 0.8223 (t70) REVERT: 1 716 HIS cc_start: 0.7539 (t70) cc_final: 0.7229 (t-90) REVERT: 1 718 ASP cc_start: 0.8293 (m-30) cc_final: 0.7631 (m-30) REVERT: 1 746 ILE cc_start: 0.8986 (mt) cc_final: 0.8641 (mm) REVERT: 2 206 LEU cc_start: 0.8185 (mt) cc_final: 0.7849 (mt) REVERT: 2 215 GLU cc_start: 0.8552 (tp30) cc_final: 0.8311 (tp30) REVERT: 2 227 ASN cc_start: 0.8682 (m-40) cc_final: 0.8397 (t0) REVERT: 2 266 VAL cc_start: 0.8737 (t) cc_final: 0.8196 (t) REVERT: 2 274 PHE cc_start: 0.7631 (m-80) cc_final: 0.7276 (m-80) REVERT: 2 414 TYR cc_start: 0.8570 (m-80) cc_final: 0.8346 (m-80) REVERT: 2 499 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8557 (mmmm) REVERT: 2 666 ASN cc_start: 0.8815 (m110) cc_final: 0.7858 (p0) REVERT: 2 667 MET cc_start: 0.8890 (mmm) cc_final: 0.8512 (tpp) REVERT: 2 733 ASN cc_start: 0.8378 (m-40) cc_final: 0.7582 (m-40) REVERT: 2 801 ILE cc_start: 0.9487 (mt) cc_final: 0.9248 (mt) REVERT: 2 802 ASP cc_start: 0.8764 (m-30) cc_final: 0.8251 (t0) REVERT: 2 872 LYS cc_start: 0.8213 (ptpp) cc_final: 0.8000 (ptmm) REVERT: 2 880 LYS cc_start: 0.7596 (mttt) cc_final: 0.7137 (tmtt) REVERT: 3 261 LEU cc_start: 0.8566 (mt) cc_final: 0.8284 (tp) REVERT: 3 334 LYS cc_start: 0.8033 (pttp) cc_final: 0.7440 (mptt) REVERT: 3 343 THR cc_start: 0.8329 (p) cc_final: 0.8122 (p) REVERT: 3 412 ASP cc_start: 0.7760 (p0) cc_final: 0.7372 (p0) REVERT: 3 584 LEU cc_start: 0.8197 (mt) cc_final: 0.7994 (mt) REVERT: 3 624 MET cc_start: 0.8375 (mmm) cc_final: 0.8011 (tpp) REVERT: 3 668 SER cc_start: 0.8620 (p) cc_final: 0.7883 (p) REVERT: 3 716 HIS cc_start: 0.8261 (t-90) cc_final: 0.8046 (t-170) REVERT: 3 732 ILE cc_start: 0.9041 (mt) cc_final: 0.8836 (tt) REVERT: 3 736 HIS cc_start: 0.6657 (t70) cc_final: 0.6366 (t70) REVERT: 3 739 ASN cc_start: 0.7862 (m-40) cc_final: 0.7641 (m-40) REVERT: 3 884 ASP cc_start: 0.8016 (m-30) cc_final: 0.7710 (p0) REVERT: 4 221 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8590 (mt-10) REVERT: 4 568 HIS cc_start: 0.8519 (m90) cc_final: 0.7951 (m-70) REVERT: 4 700 ARG cc_start: 0.8736 (mtp85) cc_final: 0.8497 (mtm-85) REVERT: 4 749 MET cc_start: 0.8494 (mmm) cc_final: 0.7711 (mmm) REVERT: 4 818 ILE cc_start: 0.8870 (mt) cc_final: 0.8524 (mm) REVERT: 4 885 ASP cc_start: 0.8049 (m-30) cc_final: 0.7471 (p0) REVERT: 4 899 LEU cc_start: 0.6580 (OUTLIER) cc_final: 0.6355 (pp) REVERT: 5 423 LEU cc_start: 0.9346 (mt) cc_final: 0.9128 (mt) REVERT: 5 571 TYR cc_start: 0.8523 (t80) cc_final: 0.7838 (t80) REVERT: 5 635 LEU cc_start: 0.9268 (tp) cc_final: 0.9026 (tp) REVERT: 5 710 ASP cc_start: 0.8043 (m-30) cc_final: 0.7773 (m-30) REVERT: 5 825 LYS cc_start: 0.9132 (mttt) cc_final: 0.8848 (tptp) REVERT: 5 856 LEU cc_start: 0.9373 (mt) cc_final: 0.7957 (mt) REVERT: C 37 LEU cc_start: 0.8024 (mt) cc_final: 0.7495 (pp) REVERT: C 55 HIS cc_start: 0.7675 (m-70) cc_final: 0.6833 (m-70) REVERT: C 114 THR cc_start: 0.9176 (p) cc_final: 0.8803 (t) REVERT: C 197 LEU cc_start: 0.8651 (mt) cc_final: 0.8293 (mp) REVERT: C 202 THR cc_start: 0.8729 (p) cc_final: 0.8291 (p) REVERT: 6 425 LYS cc_start: 0.8321 (mttt) cc_final: 0.8086 (pttt) REVERT: 6 465 VAL cc_start: 0.7971 (p) cc_final: 0.7454 (p) REVERT: 6 559 MET cc_start: 0.3773 (OUTLIER) cc_final: 0.3230 (ppp) REVERT: 6 709 PHE cc_start: 0.6029 (m-80) cc_final: 0.5423 (m-10) REVERT: 6 716 HIS cc_start: 0.7855 (t70) cc_final: 0.6655 (t70) REVERT: 6 763 PHE cc_start: 0.5776 (m-10) cc_final: 0.4889 (m-80) REVERT: 6 862 LEU cc_start: 0.8494 (mt) cc_final: 0.7812 (mt) REVERT: D 136 ILE cc_start: 0.9090 (mt) cc_final: 0.8735 (mt) REVERT: D 137 LEU cc_start: 0.9076 (mt) cc_final: 0.8740 (mt) REVERT: D 144 PHE cc_start: 0.8181 (m-80) cc_final: 0.7868 (m-80) REVERT: D 150 GLN cc_start: 0.8517 (mt0) cc_final: 0.8015 (mt0) REVERT: D 171 TRP cc_start: 0.8460 (m100) cc_final: 0.7755 (m-10) REVERT: E 88 LEU cc_start: 0.8500 (mt) cc_final: 0.8289 (mt) REVERT: E 142 ASN cc_start: 0.8956 (m-40) cc_final: 0.8117 (m-40) REVERT: E 160 ASP cc_start: 0.7674 (m-30) cc_final: 0.7463 (m-30) REVERT: E 201 CYS cc_start: 0.8673 (m) cc_final: 0.7854 (m) REVERT: d 740 SER cc_start: 0.8178 (p) cc_final: 0.7908 (t) REVERT: d 772 LYS cc_start: 0.8298 (tttt) cc_final: 0.7816 (tppt) REVERT: d 776 ASN cc_start: 0.8112 (m-40) cc_final: 0.7646 (m110) REVERT: c 739 MET cc_start: 0.7932 (ttp) cc_final: 0.7628 (ttp) REVERT: c 767 PHE cc_start: 0.6863 (m-80) cc_final: 0.6606 (m-80) REVERT: b 778 TYR cc_start: 0.8042 (m-80) cc_final: 0.7589 (m-10) REVERT: B 81 SER cc_start: 0.8846 (p) cc_final: 0.8489 (t) REVERT: B 88 LEU cc_start: 0.8404 (mt) cc_final: 0.8082 (mt) REVERT: B 228 TYR cc_start: 0.7926 (m-80) cc_final: 0.7636 (m-80) REVERT: a 731 LEU cc_start: 0.8707 (mp) cc_final: 0.8237 (mt) REVERT: a 792 LEU cc_start: 0.8158 (tt) cc_final: 0.7743 (tp) REVERT: A 148 LEU cc_start: 0.8916 (mt) cc_final: 0.8491 (tt) REVERT: g 719 THR cc_start: 0.8592 (p) cc_final: 0.8315 (t) REVERT: g 731 LEU cc_start: 0.8901 (mp) cc_final: 0.8095 (mp) REVERT: G 120 ASN cc_start: 0.7928 (m-40) cc_final: 0.7531 (m-40) REVERT: G 146 THR cc_start: 0.8578 (p) cc_final: 0.8300 (t) REVERT: G 148 LEU cc_start: 0.9062 (mt) cc_final: 0.8788 (mp) REVERT: G 165 SER cc_start: 0.8707 (p) cc_final: 0.7857 (t) REVERT: f 740 SER cc_start: 0.8254 (p) cc_final: 0.7906 (t) REVERT: f 771 TYR cc_start: 0.6740 (m-80) cc_final: 0.5794 (m-80) REVERT: F 102 THR cc_start: 0.8507 (p) cc_final: 0.7911 (t) REVERT: F 109 ILE cc_start: 0.9157 (mt) cc_final: 0.8816 (mm) REVERT: F 146 THR cc_start: 0.8546 (p) cc_final: 0.8128 (m) REVERT: F 214 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8502 (mm) REVERT: F 229 GLU cc_start: 0.6299 (tt0) cc_final: 0.5925 (tt0) REVERT: F 231 ASP cc_start: 0.6201 (m-30) cc_final: 0.4972 (m-30) REVERT: e 723 THR cc_start: 0.8777 (m) cc_final: 0.7849 (p) REVERT: e 731 LEU cc_start: 0.8723 (mp) cc_final: 0.8309 (mp) REVERT: e 783 ASN cc_start: 0.7327 (m110) cc_final: 0.6980 (m110) REVERT: e 785 PHE cc_start: 0.7763 (t80) cc_final: 0.7167 (t80) REVERT: e 791 GLN cc_start: 0.8197 (tt0) cc_final: 0.7679 (tm-30) outliers start: 30 outliers final: 2 residues processed: 2072 average time/residue: 0.6149 time to fit residues: 2076.0312 Evaluate side-chains 921 residues out of total 6163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 915 time to evaluate : 5.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 702 random chunks: chunk 592 optimal weight: 0.0020 chunk 532 optimal weight: 1.9990 chunk 295 optimal weight: 0.9980 chunk 181 optimal weight: 0.9990 chunk 358 optimal weight: 2.9990 chunk 284 optimal weight: 0.8980 chunk 550 optimal weight: 0.9990 chunk 212 optimal weight: 3.9990 chunk 334 optimal weight: 1.9990 chunk 409 optimal weight: 10.0000 chunk 637 optimal weight: 1.9990 overall best weight: 0.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 290 ASN ** 1 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 716 HIS 1 744 ASN 1 814 ASN 2 198 ASN 2 229 ASN 2 290 ASN 2 560 ASN 2 568 HIS 2 735 ASN ** 2 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 816 HIS ** 3 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 290 ASN 3 326 ASN 3 566 GLN 3 606 ASN 3 666 ASN 3 704 HIS 3 752 ASN 3 816 HIS ** 4 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 530 GLN 4 537 GLN ** 4 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 560 ASN 4 566 GLN ** 4 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 716 HIS ** 4 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 816 HIS ** 4 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 300 ASN ** 5 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 606 ASN 5 657 ASN 5 725 GLN ** 5 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN C 123 ASN C 150 GLN 6 227 ASN 6 229 ASN 6 716 HIS 6 752 ASN D 222 ASN E 55 HIS ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 700 ASN d 734 ASN c 700 ASN b 734 ASN ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 161 GLN a 734 ASN A 55 HIS ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 96 ASN ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS G 150 GLN F 55 HIS F 123 ASN e 734 ASN ** e 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 58380 Z= 0.242 Angle : 0.772 12.388 78702 Z= 0.407 Chirality : 0.048 0.281 8876 Planarity : 0.006 0.141 9939 Dihedral : 10.896 172.976 7975 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.85 % Favored : 93.02 % Rotamer: Outliers : 0.15 % Allowed : 2.60 % Favored : 97.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.40 (0.09), residues: 6773 helix: -2.41 (0.07), residues: 3375 sheet: -1.86 (0.22), residues: 498 loop : -1.93 (0.11), residues: 2900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP A 171 HIS 0.020 0.001 HIS A 55 PHE 0.023 0.002 PHE g 701 TYR 0.036 0.002 TYR 6 846 ARG 0.022 0.001 ARG 5 360 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13546 Ramachandran restraints generated. 6773 Oldfield, 0 Emsley, 6773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13546 Ramachandran restraints generated. 6773 Oldfield, 0 Emsley, 6773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1262 residues out of total 6163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1253 time to evaluate : 5.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 209 ILE cc_start: 0.6656 (tt) cc_final: 0.6072 (mp) REVERT: 1 293 LYS cc_start: 0.8829 (mttt) cc_final: 0.8334 (tmtt) REVERT: 1 366 LEU cc_start: 0.9293 (mt) cc_final: 0.7908 (pt) REVERT: 1 368 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7480 (mp0) REVERT: 1 542 GLU cc_start: 0.8596 (mt-10) cc_final: 0.7931 (tm-30) REVERT: 1 565 TYR cc_start: 0.6869 (m-80) cc_final: 0.6546 (m-80) REVERT: 1 655 LEU cc_start: 0.8437 (mt) cc_final: 0.7980 (mt) REVERT: 1 667 MET cc_start: 0.8302 (mmm) cc_final: 0.8024 (mmm) REVERT: 1 691 ASP cc_start: 0.8720 (m-30) cc_final: 0.8271 (t70) REVERT: 1 701 GLU cc_start: 0.7957 (pt0) cc_final: 0.7494 (pp20) REVERT: 1 716 HIS cc_start: 0.7404 (t-90) cc_final: 0.6711 (t-90) REVERT: 1 718 ASP cc_start: 0.8098 (m-30) cc_final: 0.7471 (m-30) REVERT: 1 756 GLU cc_start: 0.8375 (mp0) cc_final: 0.8118 (tp30) REVERT: 2 266 VAL cc_start: 0.8220 (t) cc_final: 0.7486 (m) REVERT: 2 274 PHE cc_start: 0.7710 (m-80) cc_final: 0.7143 (m-80) REVERT: 2 420 ILE cc_start: 0.9108 (mt) cc_final: 0.8851 (mm) REVERT: 2 534 LYS cc_start: 0.9166 (mttt) cc_final: 0.8777 (tptp) REVERT: 2 568 HIS cc_start: 0.8493 (m90) cc_final: 0.8278 (m-70) REVERT: 2 584 LEU cc_start: 0.8829 (mm) cc_final: 0.8626 (mm) REVERT: 2 666 ASN cc_start: 0.8022 (m110) cc_final: 0.7647 (p0) REVERT: 2 842 LYS cc_start: 0.8911 (mmpt) cc_final: 0.8571 (tptp) REVERT: 2 880 LYS cc_start: 0.7649 (mttt) cc_final: 0.7098 (tmtt) REVERT: 3 334 LYS cc_start: 0.8042 (pttp) cc_final: 0.7488 (mptt) REVERT: 3 374 MET cc_start: 0.8495 (ttm) cc_final: 0.8262 (ttp) REVERT: 3 412 ASP cc_start: 0.7500 (p0) cc_final: 0.7213 (p0) REVERT: 3 534 LYS cc_start: 0.9055 (mttt) cc_final: 0.8708 (ptpp) REVERT: 3 624 MET cc_start: 0.8458 (mmm) cc_final: 0.8219 (tpp) REVERT: 3 716 HIS cc_start: 0.8302 (t-90) cc_final: 0.7644 (t-90) REVERT: 3 725 GLN cc_start: 0.8896 (mt0) cc_final: 0.8557 (mp10) REVERT: 3 731 TYR cc_start: 0.6704 (m-80) cc_final: 0.6187 (m-80) REVERT: 3 736 HIS cc_start: 0.6866 (t70) cc_final: 0.6634 (t70) REVERT: 3 739 ASN cc_start: 0.7750 (m-40) cc_final: 0.7469 (m-40) REVERT: 3 776 ARG cc_start: 0.7632 (tmt170) cc_final: 0.7267 (tmt170) REVERT: 3 867 SER cc_start: 0.8627 (p) cc_final: 0.8421 (t) REVERT: 3 884 ASP cc_start: 0.7840 (m-30) cc_final: 0.7539 (p0) REVERT: 4 414 TYR cc_start: 0.8262 (m-80) cc_final: 0.8041 (m-80) REVERT: 4 568 HIS cc_start: 0.8513 (m90) cc_final: 0.8040 (m90) REVERT: 4 633 THR cc_start: 0.7783 (p) cc_final: 0.7085 (p) REVERT: 4 733 ASN cc_start: 0.8895 (p0) cc_final: 0.8135 (p0) REVERT: 4 734 ASP cc_start: 0.7618 (m-30) cc_final: 0.7270 (t0) REVERT: 4 827 GLU cc_start: 0.8105 (mp0) cc_final: 0.7733 (mp0) REVERT: 5 307 ASP cc_start: 0.8222 (OUTLIER) cc_final: 0.7881 (p0) REVERT: 5 396 ASP cc_start: 0.7885 (m-30) cc_final: 0.7595 (m-30) REVERT: 5 447 ASP cc_start: 0.8689 (m-30) cc_final: 0.8387 (m-30) REVERT: 5 579 MET cc_start: 0.8890 (tpp) cc_final: 0.8613 (tpp) REVERT: 5 827 GLU cc_start: 0.8275 (mt-10) cc_final: 0.7931 (tp30) REVERT: C 55 HIS cc_start: 0.7879 (m-70) cc_final: 0.7248 (m-70) REVERT: C 114 THR cc_start: 0.9140 (p) cc_final: 0.8820 (t) REVERT: C 120 ASN cc_start: 0.9116 (m-40) cc_final: 0.8859 (m-40) REVERT: C 132 PHE cc_start: 0.8584 (m-80) cc_final: 0.8383 (m-10) REVERT: C 136 ILE cc_start: 0.9426 (mt) cc_final: 0.9058 (mt) REVERT: C 139 GLU cc_start: 0.7383 (tt0) cc_final: 0.7132 (tp30) REVERT: C 202 THR cc_start: 0.8970 (p) cc_final: 0.8551 (t) REVERT: 6 425 LYS cc_start: 0.8403 (mttt) cc_final: 0.8115 (ttmm) REVERT: 6 659 LYS cc_start: 0.8934 (mttt) cc_final: 0.8455 (tptt) REVERT: 6 716 HIS cc_start: 0.7961 (t-90) cc_final: 0.7683 (t70) REVERT: 6 757 LEU cc_start: 0.6293 (mt) cc_final: 0.6087 (mt) REVERT: 6 853 ASP cc_start: 0.8685 (p0) cc_final: 0.7633 (p0) REVERT: D 110 TRP cc_start: 0.8898 (t-100) cc_final: 0.8636 (t-100) REVERT: D 114 THR cc_start: 0.9160 (p) cc_final: 0.8797 (p) REVERT: D 136 ILE cc_start: 0.8817 (mt) cc_final: 0.8276 (mt) REVERT: D 150 GLN cc_start: 0.7958 (mt0) cc_final: 0.7698 (mt0) REVERT: E 53 TYR cc_start: 0.7424 (t80) cc_final: 0.6945 (t80) REVERT: E 88 LEU cc_start: 0.9156 (mt) cc_final: 0.8815 (mt) REVERT: E 114 THR cc_start: 0.9160 (p) cc_final: 0.8914 (t) REVERT: E 132 PHE cc_start: 0.8381 (m-80) cc_final: 0.8174 (m-80) REVERT: E 160 ASP cc_start: 0.7717 (m-30) cc_final: 0.7296 (m-30) REVERT: E 168 TYR cc_start: 0.8287 (p90) cc_final: 0.8051 (p90) REVERT: E 194 VAL cc_start: 0.8847 (t) cc_final: 0.8580 (t) REVERT: E 201 CYS cc_start: 0.8773 (m) cc_final: 0.8359 (m) REVERT: d 731 LEU cc_start: 0.9002 (mt) cc_final: 0.8761 (mt) REVERT: c 713 ASP cc_start: 0.7691 (t70) cc_final: 0.6838 (t0) REVERT: c 739 MET cc_start: 0.8319 (ttp) cc_final: 0.7880 (ttp) REVERT: b 810 ILE cc_start: 0.9456 (mm) cc_final: 0.9218 (mm) REVERT: B 51 ASP cc_start: 0.8054 (m-30) cc_final: 0.6932 (m-30) REVERT: B 158 LYS cc_start: 0.9058 (mttt) cc_final: 0.8832 (mttt) REVERT: B 201 CYS cc_start: 0.8753 (m) cc_final: 0.8455 (m) REVERT: a 768 TYR cc_start: 0.7443 (t80) cc_final: 0.7138 (t80) REVERT: A 139 GLU cc_start: 0.7176 (tp30) cc_final: 0.6975 (tp30) REVERT: A 146 THR cc_start: 0.8854 (p) cc_final: 0.8596 (t) REVERT: A 148 LEU cc_start: 0.9054 (mt) cc_final: 0.8785 (tt) REVERT: A 201 CYS cc_start: 0.8575 (m) cc_final: 0.8036 (m) REVERT: g 719 THR cc_start: 0.8800 (p) cc_final: 0.8464 (t) REVERT: g 731 LEU cc_start: 0.9041 (mp) cc_final: 0.8748 (mp) REVERT: G 66 HIS cc_start: 0.7564 (m-70) cc_final: 0.7030 (m-70) REVERT: G 114 THR cc_start: 0.8958 (p) cc_final: 0.8612 (t) REVERT: G 120 ASN cc_start: 0.8514 (m-40) cc_final: 0.7597 (m-40) REVERT: G 139 GLU cc_start: 0.7659 (tm-30) cc_final: 0.6176 (tm-30) REVERT: G 160 ASP cc_start: 0.7050 (m-30) cc_final: 0.6723 (m-30) REVERT: f 731 LEU cc_start: 0.9003 (mp) cc_final: 0.8802 (mt) REVERT: f 739 MET cc_start: 0.8024 (ttm) cc_final: 0.7785 (ttp) REVERT: F 41 ILE cc_start: 0.8216 (mm) cc_final: 0.7905 (tp) REVERT: F 114 THR cc_start: 0.9457 (p) cc_final: 0.9159 (p) REVERT: F 146 THR cc_start: 0.8153 (p) cc_final: 0.7944 (m) REVERT: F 171 TRP cc_start: 0.8380 (m100) cc_final: 0.8102 (m100) REVERT: e 791 GLN cc_start: 0.8065 (tt0) cc_final: 0.7765 (tm-30) REVERT: e 793 ILE cc_start: 0.8767 (mm) cc_final: 0.8283 (mm) outliers start: 9 outliers final: 1 residues processed: 1258 average time/residue: 0.5547 time to fit residues: 1161.8605 Evaluate side-chains 745 residues out of total 6163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 743 time to evaluate : 5.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 702 random chunks: chunk 354 optimal weight: 5.9990 chunk 197 optimal weight: 0.9990 chunk 530 optimal weight: 2.9990 chunk 434 optimal weight: 6.9990 chunk 175 optimal weight: 2.9990 chunk 638 optimal weight: 3.9990 chunk 689 optimal weight: 10.0000 chunk 568 optimal weight: 7.9990 chunk 633 optimal weight: 0.0370 chunk 217 optimal weight: 0.8980 chunk 512 optimal weight: 1.9990 overall best weight: 1.3864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 744 ASN 1 816 HIS ** 2 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 816 HIS ** 3 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 433 GLN ** 3 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 716 HIS ** 4 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 674 HIS C 55 HIS ** 6 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 ASN E 222 ASN ** d 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 796 ASN ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 724 ASN a 733 GLN ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 96 ASN ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 GLN G 96 ASN G 150 GLN G 161 GLN f 787 HIS F 96 ASN ** F 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 161 GLN e 734 ASN ** e 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 787 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 796 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 58380 Z= 0.251 Angle : 0.710 10.540 78702 Z= 0.376 Chirality : 0.047 0.416 8876 Planarity : 0.005 0.069 9939 Dihedral : 10.523 177.192 7975 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.52 % Favored : 92.37 % Rotamer: Outliers : 0.13 % Allowed : 2.47 % Favored : 97.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.10), residues: 6773 helix: -1.60 (0.08), residues: 3371 sheet: -1.59 (0.22), residues: 495 loop : -1.64 (0.12), residues: 2907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP G 171 HIS 0.028 0.002 HIS C 55 PHE 0.034 0.002 PHE G 170 TYR 0.029 0.002 TYR b 803 ARG 0.014 0.001 ARG D 169 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13546 Ramachandran restraints generated. 6773 Oldfield, 0 Emsley, 6773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13546 Ramachandran restraints generated. 6773 Oldfield, 0 Emsley, 6773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1042 residues out of total 6163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1034 time to evaluate : 5.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 209 ILE cc_start: 0.6543 (tt) cc_final: 0.5869 (mp) REVERT: 1 293 LYS cc_start: 0.8830 (mttt) cc_final: 0.8362 (tmtt) REVERT: 1 366 LEU cc_start: 0.9263 (mt) cc_final: 0.8761 (pt) REVERT: 1 542 GLU cc_start: 0.8618 (mt-10) cc_final: 0.7908 (tm-30) REVERT: 1 579 MET cc_start: 0.7510 (tpp) cc_final: 0.7264 (tpp) REVERT: 1 667 MET cc_start: 0.8415 (mmm) cc_final: 0.8013 (mmm) REVERT: 1 691 ASP cc_start: 0.8809 (m-30) cc_final: 0.8254 (t70) REVERT: 1 701 GLU cc_start: 0.7910 (pt0) cc_final: 0.7450 (pp20) REVERT: 1 716 HIS cc_start: 0.7923 (t-90) cc_final: 0.6973 (t-90) REVERT: 1 718 ASP cc_start: 0.8298 (m-30) cc_final: 0.6609 (m-30) REVERT: 1 721 LYS cc_start: 0.9274 (mttt) cc_final: 0.9006 (mttt) REVERT: 1 746 ILE cc_start: 0.8779 (mm) cc_final: 0.8481 (mm) REVERT: 2 197 MET cc_start: 0.8504 (mtt) cc_final: 0.8153 (mtt) REVERT: 2 266 VAL cc_start: 0.8258 (t) cc_final: 0.6611 (t) REVERT: 2 272 ARG cc_start: 0.8617 (ttt180) cc_final: 0.8411 (ttt180) REVERT: 2 274 PHE cc_start: 0.7848 (m-80) cc_final: 0.7136 (m-80) REVERT: 2 420 ILE cc_start: 0.9212 (mt) cc_final: 0.9008 (mm) REVERT: 2 568 HIS cc_start: 0.8530 (m90) cc_final: 0.8283 (m-70) REVERT: 2 724 LEU cc_start: 0.8380 (mt) cc_final: 0.8165 (mt) REVERT: 2 870 MET cc_start: 0.8511 (mmp) cc_final: 0.7919 (mmm) REVERT: 3 334 LYS cc_start: 0.8105 (pttp) cc_final: 0.7518 (mptt) REVERT: 3 534 LYS cc_start: 0.9016 (mttt) cc_final: 0.8649 (ptpp) REVERT: 3 660 ASP cc_start: 0.8467 (m-30) cc_final: 0.8193 (t0) REVERT: 3 714 LYS cc_start: 0.7980 (mmtt) cc_final: 0.7765 (mmtp) REVERT: 3 716 HIS cc_start: 0.8446 (t-90) cc_final: 0.7675 (t-90) REVERT: 3 725 GLN cc_start: 0.8856 (mt0) cc_final: 0.8547 (mp10) REVERT: 3 736 HIS cc_start: 0.7021 (t70) cc_final: 0.6812 (t70) REVERT: 3 776 ARG cc_start: 0.7532 (tmt170) cc_final: 0.7216 (tmt170) REVERT: 4 568 HIS cc_start: 0.8641 (m90) cc_final: 0.8005 (m90) REVERT: 4 827 GLU cc_start: 0.8239 (mp0) cc_final: 0.7939 (mp0) REVERT: 4 876 MET cc_start: 0.8752 (mpp) cc_final: 0.8528 (mpp) REVERT: 4 886 MET cc_start: 0.8384 (mmm) cc_final: 0.8166 (mmm) REVERT: 5 396 ASP cc_start: 0.7862 (m-30) cc_final: 0.7583 (m-30) REVERT: 5 579 MET cc_start: 0.8990 (tpp) cc_final: 0.8729 (tpp) REVERT: 5 701 GLU cc_start: 0.8282 (tm-30) cc_final: 0.7970 (tm-30) REVERT: 5 801 ILE cc_start: 0.8928 (mp) cc_final: 0.8556 (mp) REVERT: 5 845 ASP cc_start: 0.8320 (m-30) cc_final: 0.7994 (p0) REVERT: 5 886 MET cc_start: 0.8717 (mmm) cc_final: 0.8434 (mtp) REVERT: C 111 ASP cc_start: 0.8405 (m-30) cc_final: 0.8123 (m-30) REVERT: C 114 THR cc_start: 0.9081 (p) cc_final: 0.8695 (t) REVERT: C 132 PHE cc_start: 0.8601 (m-80) cc_final: 0.8264 (m-10) REVERT: C 138 ASN cc_start: 0.6662 (t0) cc_final: 0.6303 (t0) REVERT: 6 486 LYS cc_start: 0.8756 (tmtt) cc_final: 0.8304 (mttm) REVERT: 6 659 LYS cc_start: 0.8943 (mttt) cc_final: 0.8435 (mmtt) REVERT: 6 716 HIS cc_start: 0.8176 (t-90) cc_final: 0.7767 (t70) REVERT: 6 886 MET cc_start: 0.4147 (mmp) cc_final: 0.3887 (mmp) REVERT: D 80 TRP cc_start: 0.8521 (m100) cc_final: 0.8286 (m100) REVERT: D 114 THR cc_start: 0.9271 (p) cc_final: 0.8878 (p) REVERT: D 118 TYR cc_start: 0.8375 (t80) cc_final: 0.8153 (t80) REVERT: D 136 ILE cc_start: 0.8988 (mt) cc_final: 0.8583 (mt) REVERT: D 171 TRP cc_start: 0.8313 (m-10) cc_final: 0.7954 (m-10) REVERT: E 53 TYR cc_start: 0.7617 (t80) cc_final: 0.7225 (t80) REVERT: E 93 VAL cc_start: 0.9366 (t) cc_final: 0.9145 (p) REVERT: E 160 ASP cc_start: 0.7594 (m-30) cc_final: 0.7345 (m-30) REVERT: c 713 ASP cc_start: 0.7858 (t70) cc_final: 0.6783 (t0) REVERT: c 739 MET cc_start: 0.8145 (ttp) cc_final: 0.7922 (ttp) REVERT: c 767 PHE cc_start: 0.7169 (m-80) cc_final: 0.6834 (m-80) REVERT: c 769 ASP cc_start: 0.8068 (m-30) cc_final: 0.7563 (m-30) REVERT: b 739 MET cc_start: 0.7913 (ttp) cc_final: 0.7584 (ttp) REVERT: b 773 GLN cc_start: 0.8560 (mp10) cc_final: 0.8138 (mp10) REVERT: B 51 ASP cc_start: 0.7972 (m-30) cc_final: 0.6843 (m-30) REVERT: B 111 ASP cc_start: 0.8405 (m-30) cc_final: 0.8197 (m-30) REVERT: B 120 ASN cc_start: 0.8935 (m110) cc_final: 0.8576 (m110) REVERT: B 136 ILE cc_start: 0.9118 (mt) cc_final: 0.8457 (mt) REVERT: B 171 TRP cc_start: 0.9017 (m100) cc_final: 0.8441 (m100) REVERT: B 210 MET cc_start: 0.8318 (mmm) cc_final: 0.7581 (tpp) REVERT: B 224 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7475 (mp0) REVERT: a 702 TYR cc_start: 0.6369 (m-10) cc_final: 0.6095 (m-10) REVERT: A 148 LEU cc_start: 0.9167 (mt) cc_final: 0.8936 (tt) REVERT: A 160 ASP cc_start: 0.7106 (t70) cc_final: 0.6730 (t0) REVERT: A 171 TRP cc_start: 0.6978 (m100) cc_final: 0.6753 (m100) REVERT: G 114 THR cc_start: 0.9107 (p) cc_final: 0.8773 (t) REVERT: G 120 ASN cc_start: 0.8660 (m-40) cc_final: 0.7803 (m-40) REVERT: G 133 LEU cc_start: 0.8994 (tp) cc_final: 0.8407 (tp) REVERT: G 139 GLU cc_start: 0.7386 (tm-30) cc_final: 0.7116 (tm-30) REVERT: G 161 GLN cc_start: 0.7569 (mm-40) cc_final: 0.7337 (mm110) REVERT: f 670 LYS cc_start: 0.6685 (mmmm) cc_final: 0.5971 (tppp) REVERT: f 731 LEU cc_start: 0.8976 (mp) cc_final: 0.8735 (mt) REVERT: f 739 MET cc_start: 0.8075 (ttm) cc_final: 0.7833 (ttp) REVERT: F 102 THR cc_start: 0.8321 (p) cc_final: 0.8104 (t) REVERT: F 133 LEU cc_start: 0.8918 (mt) cc_final: 0.8572 (tp) outliers start: 8 outliers final: 0 residues processed: 1040 average time/residue: 0.5416 time to fit residues: 954.1717 Evaluate side-chains 641 residues out of total 6163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 641 time to evaluate : 5.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 702 random chunks: chunk 630 optimal weight: 0.1980 chunk 480 optimal weight: 0.0040 chunk 331 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 304 optimal weight: 7.9990 chunk 428 optimal weight: 0.9980 chunk 640 optimal weight: 3.9990 chunk 678 optimal weight: 3.9990 chunk 334 optimal weight: 0.6980 chunk 607 optimal weight: 0.8980 chunk 182 optimal weight: 0.0370 overall best weight: 0.3670 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 290 ASN ** 1 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 744 ASN ** 2 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 816 HIS 3 198 ASN 3 666 ASN ** 4 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 207 GLN ** 4 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 834 ASN 5 560 ASN ** 5 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 834 ASN D 96 ASN ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 734 ASN c 724 ASN b 733 GLN B 120 ASN B 150 GLN ** a 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 96 ASN g 734 ASN G 96 ASN G 142 ASN F 96 ASN F 123 ASN ** F 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 787 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.4868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 58380 Z= 0.187 Angle : 0.657 11.125 78702 Z= 0.345 Chirality : 0.046 0.427 8876 Planarity : 0.004 0.062 9939 Dihedral : 10.287 175.637 7975 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.32 % Favored : 92.59 % Rotamer: Outliers : 0.11 % Allowed : 2.04 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.10), residues: 6773 helix: -1.28 (0.08), residues: 3381 sheet: -1.45 (0.23), residues: 483 loop : -1.58 (0.12), residues: 2909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP G 171 HIS 0.011 0.001 HIS 2 310 PHE 0.027 0.002 PHE G 132 TYR 0.023 0.002 TYR 4 573 ARG 0.011 0.001 ARG A 75 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13546 Ramachandran restraints generated. 6773 Oldfield, 0 Emsley, 6773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13546 Ramachandran restraints generated. 6773 Oldfield, 0 Emsley, 6773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1010 residues out of total 6163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1003 time to evaluate : 5.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 209 ILE cc_start: 0.6408 (tt) cc_final: 0.5765 (mp) REVERT: 1 293 LYS cc_start: 0.8874 (mttt) cc_final: 0.8398 (tmtt) REVERT: 1 366 LEU cc_start: 0.9295 (mt) cc_final: 0.8684 (pt) REVERT: 1 542 GLU cc_start: 0.8587 (mt-10) cc_final: 0.7919 (tm-30) REVERT: 1 667 MET cc_start: 0.8397 (mmm) cc_final: 0.8106 (mmm) REVERT: 1 691 ASP cc_start: 0.8784 (m-30) cc_final: 0.8245 (t70) REVERT: 1 701 GLU cc_start: 0.7910 (pt0) cc_final: 0.7388 (pp20) REVERT: 1 716 HIS cc_start: 0.7898 (t-90) cc_final: 0.6766 (t-90) REVERT: 1 718 ASP cc_start: 0.8230 (m-30) cc_final: 0.7310 (m-30) REVERT: 1 746 ILE cc_start: 0.8725 (mm) cc_final: 0.8470 (mm) REVERT: 1 803 LYS cc_start: 0.8419 (tptp) cc_final: 0.8049 (tppt) REVERT: 2 197 MET cc_start: 0.8591 (mtt) cc_final: 0.8281 (mtp) REVERT: 2 274 PHE cc_start: 0.7803 (m-80) cc_final: 0.7083 (m-80) REVERT: 2 420 ILE cc_start: 0.9206 (mt) cc_final: 0.8969 (mm) REVERT: 2 541 LEU cc_start: 0.8608 (mm) cc_final: 0.8044 (tp) REVERT: 2 568 HIS cc_start: 0.8374 (m90) cc_final: 0.8115 (m-70) REVERT: 2 727 LEU cc_start: 0.9260 (mm) cc_final: 0.9040 (mm) REVERT: 3 334 LYS cc_start: 0.7978 (pttp) cc_final: 0.7435 (mptt) REVERT: 3 534 LYS cc_start: 0.8971 (mttt) cc_final: 0.8629 (ptpp) REVERT: 3 660 ASP cc_start: 0.8394 (m-30) cc_final: 0.8185 (t0) REVERT: 3 716 HIS cc_start: 0.8469 (t-90) cc_final: 0.7693 (t-90) REVERT: 3 725 GLN cc_start: 0.8716 (mt0) cc_final: 0.8429 (mp10) REVERT: 3 739 ASN cc_start: 0.7536 (m-40) cc_final: 0.7226 (m-40) REVERT: 3 876 MET cc_start: 0.8516 (ptp) cc_final: 0.8193 (ptp) REVERT: 4 568 HIS cc_start: 0.8574 (m90) cc_final: 0.7997 (m170) REVERT: 4 731 TYR cc_start: 0.7725 (t80) cc_final: 0.7311 (t80) REVERT: 4 734 ASP cc_start: 0.7714 (m-30) cc_final: 0.7479 (t70) REVERT: 4 886 MET cc_start: 0.8360 (mmm) cc_final: 0.8021 (mmm) REVERT: 5 396 ASP cc_start: 0.7758 (m-30) cc_final: 0.7487 (m-30) REVERT: 5 579 MET cc_start: 0.8914 (tpp) cc_final: 0.8682 (tpp) REVERT: 5 701 GLU cc_start: 0.8281 (tm-30) cc_final: 0.7914 (tm-30) REVERT: 5 801 ILE cc_start: 0.8878 (mp) cc_final: 0.8526 (mp) REVERT: 5 845 ASP cc_start: 0.8224 (m-30) cc_final: 0.7994 (p0) REVERT: 5 886 MET cc_start: 0.8753 (mmm) cc_final: 0.8443 (mtp) REVERT: C 55 HIS cc_start: 0.7861 (m-70) cc_final: 0.7497 (m-70) REVERT: C 76 LYS cc_start: 0.8599 (tttt) cc_final: 0.8312 (tttm) REVERT: C 108 GLU cc_start: 0.6894 (mm-30) cc_final: 0.6595 (mm-30) REVERT: C 114 THR cc_start: 0.9072 (p) cc_final: 0.8796 (t) REVERT: C 132 PHE cc_start: 0.8490 (m-80) cc_final: 0.8163 (m-10) REVERT: C 138 ASN cc_start: 0.6217 (t0) cc_final: 0.5872 (t0) REVERT: 6 425 LYS cc_start: 0.8489 (mttt) cc_final: 0.8132 (ttmm) REVERT: 6 486 LYS cc_start: 0.8822 (tmtt) cc_final: 0.8332 (mttm) REVERT: 6 559 MET cc_start: 0.5337 (ppp) cc_final: 0.4778 (ppp) REVERT: 6 560 ASN cc_start: 0.7539 (m110) cc_final: 0.7098 (t0) REVERT: 6 624 MET cc_start: 0.7935 (mtm) cc_final: 0.7555 (mtt) REVERT: 6 659 LYS cc_start: 0.8882 (mttt) cc_final: 0.8419 (mmtt) REVERT: 6 716 HIS cc_start: 0.8142 (t-90) cc_final: 0.7721 (t70) REVERT: D 114 THR cc_start: 0.9141 (p) cc_final: 0.8797 (p) REVERT: D 136 ILE cc_start: 0.9004 (mt) cc_final: 0.8718 (mt) REVERT: D 201 CYS cc_start: 0.7714 (m) cc_final: 0.7360 (m) REVERT: E 53 TYR cc_start: 0.7577 (t80) cc_final: 0.7075 (t80) REVERT: E 84 TRP cc_start: 0.8462 (m100) cc_final: 0.8078 (m100) REVERT: E 93 VAL cc_start: 0.9330 (t) cc_final: 0.9100 (p) REVERT: E 160 ASP cc_start: 0.7603 (m-30) cc_final: 0.7243 (m-30) REVERT: E 194 VAL cc_start: 0.8844 (t) cc_final: 0.8451 (t) REVERT: d 731 LEU cc_start: 0.8851 (mt) cc_final: 0.8440 (mt) REVERT: d 776 ASN cc_start: 0.8469 (m-40) cc_final: 0.8258 (m-40) REVERT: c 670 LYS cc_start: 0.7853 (mmmt) cc_final: 0.7461 (mmmm) REVERT: b 739 MET cc_start: 0.7830 (ttp) cc_final: 0.7492 (ttp) REVERT: b 773 GLN cc_start: 0.8542 (mp10) cc_final: 0.8264 (mp10) REVERT: b 774 ILE cc_start: 0.9051 (mt) cc_final: 0.8846 (mt) REVERT: b 802 ILE cc_start: 0.8680 (pt) cc_final: 0.8091 (pt) REVERT: B 43 ASP cc_start: 0.8593 (m-30) cc_final: 0.8314 (m-30) REVERT: B 51 ASP cc_start: 0.7785 (m-30) cc_final: 0.6685 (m-30) REVERT: B 111 ASP cc_start: 0.8315 (m-30) cc_final: 0.7990 (m-30) REVERT: B 120 ASN cc_start: 0.9122 (m-40) cc_final: 0.8781 (m110) REVERT: B 138 ASN cc_start: 0.7276 (m-40) cc_final: 0.7009 (m110) REVERT: B 171 TRP cc_start: 0.8953 (m100) cc_final: 0.8311 (m100) REVERT: B 210 MET cc_start: 0.8203 (mmm) cc_final: 0.7604 (tpp) REVERT: a 702 TYR cc_start: 0.6216 (m-10) cc_final: 0.5991 (m-10) REVERT: a 731 LEU cc_start: 0.8607 (mt) cc_final: 0.8058 (mt) REVERT: a 740 SER cc_start: 0.7431 (p) cc_final: 0.7091 (p) REVERT: A 160 ASP cc_start: 0.6852 (t70) cc_final: 0.6287 (t0) REVERT: G 88 LEU cc_start: 0.8671 (mt) cc_final: 0.8453 (mt) REVERT: G 92 ILE cc_start: 0.9243 (pt) cc_final: 0.8806 (mt) REVERT: G 114 THR cc_start: 0.9006 (p) cc_final: 0.8622 (t) REVERT: G 120 ASN cc_start: 0.8400 (m-40) cc_final: 0.7785 (m-40) REVERT: G 133 LEU cc_start: 0.8792 (tp) cc_final: 0.8372 (tp) REVERT: G 134 HIS cc_start: 0.8071 (t70) cc_final: 0.7730 (t70) REVERT: G 168 TYR cc_start: 0.7432 (p90) cc_final: 0.7098 (p90) REVERT: f 670 LYS cc_start: 0.6910 (mmmm) cc_final: 0.6496 (tppp) REVERT: f 727 LEU cc_start: 0.7778 (mp) cc_final: 0.7534 (mp) REVERT: f 731 LEU cc_start: 0.8961 (mp) cc_final: 0.8727 (mt) REVERT: F 70 LYS cc_start: 0.8610 (pttp) cc_final: 0.8307 (ptmt) REVERT: F 118 TYR cc_start: 0.7771 (t80) cc_final: 0.7391 (t80) REVERT: e 785 PHE cc_start: 0.7626 (t80) cc_final: 0.7420 (t80) outliers start: 7 outliers final: 2 residues processed: 1009 average time/residue: 0.5275 time to fit residues: 912.9899 Evaluate side-chains 662 residues out of total 6163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 660 time to evaluate : 4.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 702 random chunks: chunk 565 optimal weight: 0.7980 chunk 385 optimal weight: 2.9990 chunk 9 optimal weight: 8.9990 chunk 505 optimal weight: 4.9990 chunk 279 optimal weight: 0.9990 chunk 579 optimal weight: 0.8980 chunk 469 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 346 optimal weight: 0.7980 chunk 609 optimal weight: 0.5980 chunk 171 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 744 ASN 1 816 HIS ** 2 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 517 ASN 2 606 ASN 2 816 HIS 3 530 GLN 3 736 HIS ** 4 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 606 ASN ** 4 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 55 HIS 6 752 ASN D 96 ASN ** D 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 GLN B 96 ASN ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 GLN a 733 GLN ** a 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 96 ASN g 784 ASN G 96 ASN G 161 GLN F 96 ASN ** F 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 787 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.5180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 58380 Z= 0.193 Angle : 0.640 8.955 78702 Z= 0.335 Chirality : 0.045 0.380 8876 Planarity : 0.004 0.069 9939 Dihedral : 10.127 177.142 7975 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.46 % Favored : 92.47 % Rotamer: Outliers : 0.03 % Allowed : 1.78 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.39 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.10), residues: 6773 helix: -0.96 (0.08), residues: 3368 sheet: -1.34 (0.23), residues: 482 loop : -1.44 (0.12), residues: 2923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP E 80 HIS 0.014 0.001 HIS 2 310 PHE 0.023 0.001 PHE G 170 TYR 0.022 0.001 TYR 6 491 ARG 0.010 0.000 ARG 5 737 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13546 Ramachandran restraints generated. 6773 Oldfield, 0 Emsley, 6773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13546 Ramachandran restraints generated. 6773 Oldfield, 0 Emsley, 6773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 937 residues out of total 6163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 935 time to evaluate : 5.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 209 ILE cc_start: 0.6277 (tt) cc_final: 0.5599 (mp) REVERT: 1 293 LYS cc_start: 0.8870 (mttt) cc_final: 0.8360 (tmtt) REVERT: 1 366 LEU cc_start: 0.9293 (mt) cc_final: 0.8667 (pt) REVERT: 1 542 GLU cc_start: 0.8576 (mt-10) cc_final: 0.7907 (tm-30) REVERT: 1 595 LEU cc_start: 0.9433 (pp) cc_final: 0.8894 (tp) REVERT: 1 667 MET cc_start: 0.8459 (mmm) cc_final: 0.8222 (mmm) REVERT: 1 691 ASP cc_start: 0.8818 (m-30) cc_final: 0.8272 (t70) REVERT: 1 701 GLU cc_start: 0.7956 (pt0) cc_final: 0.7427 (pp20) REVERT: 1 716 HIS cc_start: 0.7887 (t-90) cc_final: 0.6639 (t-90) REVERT: 1 718 ASP cc_start: 0.8251 (m-30) cc_final: 0.7295 (m-30) REVERT: 1 746 ILE cc_start: 0.8785 (mm) cc_final: 0.8532 (mm) REVERT: 2 266 VAL cc_start: 0.8021 (t) cc_final: 0.7532 (t) REVERT: 2 274 PHE cc_start: 0.7853 (m-80) cc_final: 0.7049 (m-80) REVERT: 2 420 ILE cc_start: 0.9265 (mt) cc_final: 0.9034 (mm) REVERT: 2 534 LYS cc_start: 0.9212 (mttt) cc_final: 0.8947 (mtmm) REVERT: 2 568 HIS cc_start: 0.8352 (m90) cc_final: 0.8096 (m-70) REVERT: 2 724 LEU cc_start: 0.8536 (mt) cc_final: 0.8308 (mt) REVERT: 2 727 LEU cc_start: 0.9218 (mm) cc_final: 0.8955 (mm) REVERT: 2 870 MET cc_start: 0.8663 (tpp) cc_final: 0.8365 (mmm) REVERT: 3 334 LYS cc_start: 0.8021 (pttp) cc_final: 0.7491 (mptt) REVERT: 3 660 ASP cc_start: 0.8424 (m-30) cc_final: 0.8186 (t0) REVERT: 3 716 HIS cc_start: 0.8496 (t-90) cc_final: 0.7637 (t-90) REVERT: 3 876 MET cc_start: 0.8580 (ptp) cc_final: 0.8346 (ptp) REVERT: 4 423 LEU cc_start: 0.9435 (mt) cc_final: 0.9149 (mt) REVERT: 4 568 HIS cc_start: 0.8670 (m90) cc_final: 0.7979 (m170) REVERT: 4 615 ASP cc_start: 0.9062 (m-30) cc_final: 0.8835 (m-30) REVERT: 4 667 MET cc_start: 0.7658 (mmp) cc_final: 0.7406 (mmp) REVERT: 4 778 MET cc_start: 0.9119 (tpp) cc_final: 0.8220 (tmm) REVERT: 4 779 GLU cc_start: 0.8671 (tp30) cc_final: 0.8468 (tp30) REVERT: 4 827 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8554 (mm-30) REVERT: 4 886 MET cc_start: 0.8389 (mmm) cc_final: 0.8032 (mmm) REVERT: 5 374 MET cc_start: 0.8433 (mpp) cc_final: 0.8028 (mmm) REVERT: 5 396 ASP cc_start: 0.7724 (m-30) cc_final: 0.7473 (m-30) REVERT: 5 596 TYR cc_start: 0.6552 (m-10) cc_final: 0.6160 (m-10) REVERT: 5 701 GLU cc_start: 0.8239 (tm-30) cc_final: 0.7908 (tm-30) REVERT: 5 750 THR cc_start: 0.8081 (p) cc_final: 0.7835 (t) REVERT: 5 801 ILE cc_start: 0.8859 (mp) cc_final: 0.8496 (mp) REVERT: 5 886 MET cc_start: 0.8758 (mmm) cc_final: 0.8550 (mtp) REVERT: C 76 LYS cc_start: 0.8648 (tttt) cc_final: 0.8433 (tttm) REVERT: C 111 ASP cc_start: 0.8174 (m-30) cc_final: 0.7845 (m-30) REVERT: C 114 THR cc_start: 0.9106 (p) cc_final: 0.8769 (t) REVERT: C 132 PHE cc_start: 0.8524 (m-80) cc_final: 0.8176 (m-10) REVERT: C 138 ASN cc_start: 0.6252 (t0) cc_final: 0.5905 (t0) REVERT: C 150 GLN cc_start: 0.8401 (mt0) cc_final: 0.8189 (mt0) REVERT: 6 486 LYS cc_start: 0.8847 (tmtt) cc_final: 0.8323 (mttm) REVERT: 6 559 MET cc_start: 0.5186 (ppp) cc_final: 0.4957 (ppp) REVERT: 6 624 MET cc_start: 0.7939 (mtm) cc_final: 0.7726 (mtt) REVERT: 6 659 LYS cc_start: 0.8924 (mttt) cc_final: 0.8538 (mmmt) REVERT: 6 716 HIS cc_start: 0.8122 (t-90) cc_final: 0.7750 (t70) REVERT: D 84 TRP cc_start: 0.8409 (m100) cc_final: 0.7298 (m100) REVERT: D 89 VAL cc_start: 0.9312 (t) cc_final: 0.9009 (p) REVERT: D 201 CYS cc_start: 0.7933 (m) cc_final: 0.7470 (m) REVERT: E 53 TYR cc_start: 0.7650 (t80) cc_final: 0.7036 (t80) REVERT: E 84 TRP cc_start: 0.8445 (m100) cc_final: 0.8035 (m100) REVERT: E 160 ASP cc_start: 0.7632 (m-30) cc_final: 0.7322 (m-30) REVERT: d 731 LEU cc_start: 0.8814 (mt) cc_final: 0.8418 (mt) REVERT: b 773 GLN cc_start: 0.8573 (mp10) cc_final: 0.8235 (mp10) REVERT: B 51 ASP cc_start: 0.7754 (m-30) cc_final: 0.6685 (m-30) REVERT: B 111 ASP cc_start: 0.8287 (m-30) cc_final: 0.7999 (m-30) REVERT: B 120 ASN cc_start: 0.9057 (m-40) cc_final: 0.8718 (m110) REVERT: B 148 LEU cc_start: 0.8862 (mt) cc_final: 0.8640 (mt) REVERT: B 151 ASP cc_start: 0.8376 (m-30) cc_final: 0.8003 (p0) REVERT: B 171 TRP cc_start: 0.8895 (m100) cc_final: 0.8566 (m100) REVERT: B 210 MET cc_start: 0.8270 (mmm) cc_final: 0.7710 (tpp) REVERT: B 214 LEU cc_start: 0.7839 (mt) cc_final: 0.7533 (mt) REVERT: A 148 LEU cc_start: 0.9078 (tt) cc_final: 0.8733 (tt) REVERT: G 114 THR cc_start: 0.9033 (p) cc_final: 0.8717 (t) REVERT: G 133 LEU cc_start: 0.8738 (tp) cc_final: 0.8270 (tp) REVERT: G 134 HIS cc_start: 0.8209 (t70) cc_final: 0.7872 (t-90) REVERT: G 139 GLU cc_start: 0.8036 (tm-30) cc_final: 0.7409 (tm-30) REVERT: F 133 LEU cc_start: 0.8521 (tp) cc_final: 0.8265 (tp) REVERT: e 726 GLN cc_start: 0.7351 (pp30) cc_final: 0.7116 (pp30) outliers start: 2 outliers final: 0 residues processed: 937 average time/residue: 0.5281 time to fit residues: 851.8015 Evaluate side-chains 629 residues out of total 6163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 628 time to evaluate : 5.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-dev-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-dev-5461/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-dev-5461/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: 70.9555 > 50: distance: 35 - 40: 28.493 distance: 40 - 41: 30.024 distance: 41 - 42: 18.893 distance: 41 - 44: 43.888 distance: 46 - 47: 11.008 distance: 47 - 48: 32.626 distance: 47 - 50: 11.187 distance: 48 - 49: 13.423 distance: 48 - 54: 45.387 distance: 50 - 51: 22.970 distance: 51 - 52: 15.791 distance: 51 - 53: 30.995 distance: 54 - 55: 45.582 distance: 55 - 56: 58.305 distance: 55 - 58: 40.805 distance: 56 - 57: 43.773 distance: 56 - 62: 46.972 distance: 59 - 60: 39.531 distance: 63 - 64: 39.527 distance: 63 - 66: 41.429 distance: 64 - 65: 26.969 distance: 66 - 67: 50.265 distance: 67 - 68: 41.415 distance: 67 - 69: 12.942 distance: 68 - 70: 33.169 distance: 69 - 71: 13.874 distance: 70 - 72: 23.084 distance: 71 - 72: 34.670 distance: 73 - 74: 42.929 distance: 74 - 75: 19.312 distance: 74 - 77: 17.264 distance: 75 - 76: 6.988 distance: 75 - 84: 41.864 distance: 76 - 104: 5.090 distance: 77 - 78: 39.778 distance: 79 - 80: 9.054 distance: 80 - 81: 20.054 distance: 81 - 82: 44.912 distance: 81 - 83: 51.749 distance: 84 - 85: 31.314 distance: 85 - 86: 31.445 distance: 85 - 88: 41.183 distance: 86 - 87: 25.942 distance: 86 - 93: 43.743 distance: 89 - 90: 13.643 distance: 90 - 91: 44.779 distance: 91 - 92: 16.585 distance: 93 - 94: 31.770 distance: 94 - 95: 7.063 distance: 94 - 97: 50.096 distance: 95 - 96: 13.314 distance: 95 - 104: 4.603 distance: 96 - 117: 56.561 distance: 98 - 99: 57.189 distance: 98 - 100: 21.021 distance: 99 - 101: 34.153 distance: 100 - 102: 9.380 distance: 101 - 103: 11.737 distance: 102 - 103: 48.634 distance: 104 - 105: 48.788 distance: 105 - 106: 48.366 distance: 105 - 108: 39.956 distance: 108 - 109: 36.716 distance: 108 - 110: 32.911 distance: 111 - 112: 38.453 distance: 112 - 113: 38.247 distance: 112 - 115: 27.879 distance: 115 - 116: 10.055 distance: 117 - 118: 55.755 distance: 118 - 119: 41.246 distance: 119 - 121: 35.017