Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 05:56:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e10_8951/04_2023/6e10_8951_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e10_8951/04_2023/6e10_8951.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e10_8951/04_2023/6e10_8951.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e10_8951/04_2023/6e10_8951.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e10_8951/04_2023/6e10_8951_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e10_8951/04_2023/6e10_8951_updated.pdb" } resolution = 4.16 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 150 5.16 5 C 36520 2.51 5 N 9621 2.21 5 O 11025 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1 PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 202": "NH1" <-> "NH2" Residue "1 PHE 764": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 852": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 518": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 361": "NH1" <-> "NH2" Residue "4 ARG 446": "NH1" <-> "NH2" Residue "4 PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 73": "NH1" <-> "NH2" Residue "B PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 737": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 759": "OD1" <-> "OD2" Residue "a PHE 799": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 73": "NH1" <-> "NH2" Residue "A PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 737": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 799": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 73": "NH1" <-> "NH2" Residue "G PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 737": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 799": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 73": "NH1" <-> "NH2" Residue "F PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 737": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 799": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 73": "NH1" <-> "NH2" Residue "E GLU 91": "OE1" <-> "OE2" Residue "E PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 737": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 799": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 73": "NH1" <-> "NH2" Residue "D PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 737": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 799": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 73": "NH1" <-> "NH2" Residue "C PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 737": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 799": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 57352 Number of models: 1 Model: "" Number of chains: 34 Chain: "1" Number of atoms: 5763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5763 Classifications: {'peptide': 719} Link IDs: {'PTRANS': 22, 'TRANS': 696} Chain: "2" Number of atoms: 5759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5759 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 22, 'TRANS': 695} Chain: "3" Number of atoms: 5759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5759 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 22, 'TRANS': 695} Chain: "4" Number of atoms: 5759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5759 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 22, 'TRANS': 695} Chain: "5" Number of atoms: 5701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 711, 5701 Classifications: {'peptide': 711} Link IDs: {'PTRANS': 20, 'TRANS': 690} Chain breaks: 1 Chain: "6" Number of atoms: 5759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5759 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 22, 'TRANS': 695} 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: 1287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1287 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain: "A" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1557 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 8, 'TRANS': 180} Chain: "g" Number of atoms: 1287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1287 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain: "G" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1604 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 8, 'TRANS': 186} Chain: "f" Number of atoms: 1287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1287 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 4, 'TRANS': 151} 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: 1287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1287 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain: "E" 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: "d" Number of atoms: 1287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1287 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 4, 'TRANS': 151} 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: "c" Number of atoms: 1287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1287 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 4, 'TRANS': 151} 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: "b" Number of atoms: 1287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1287 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain: "0" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 75 Classifications: {'peptide': 15} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'TRANS': 14} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'UNK:plan-1': 15} Unresolved non-hydrogen planarities: 15 Chain: "h" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 250 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'TRANS': 49} Chain breaks: 1 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 50 Planarities with less than four sites: {'UNK:plan-1': 50} Unresolved non-hydrogen planarities: 50 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: 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: "k" 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: "l" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 285 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'TRANS': 56} Chain breaks: 1 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 57 Planarities with less than four sites: {'UNK:plan-1': 57} Unresolved non-hydrogen planarities: 57 Chain: "m" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 165 Classifications: {'peptide': 33} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'TRANS': 32} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'UNK:plan-1': 33} Unresolved non-hydrogen planarities: 33 Chain: "n" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 175 Classifications: {'peptide': 35} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'TRANS': 34} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'UNK:plan-1': 35} Unresolved non-hydrogen planarities: 35 Chain: "1" 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: "2" 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: "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: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 93 Unusual residues: {'AGS': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "5" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 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: 23.67, per 1000 atoms: 0.41 Number of scatterers: 57352 At special positions: 0 Unit cell: (189.28, 174.72, 216.32, 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 150 16.00 P 36 15.00 O 11025 8.00 N 9621 7.00 C 36520 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 140 " distance=2.04 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 140 " distance=2.04 Simple disulfide: pdb=" SG CYS G 113 " - pdb=" SG CYS G 140 " distance=2.04 Simple disulfide: pdb=" SG CYS F 113 " - pdb=" SG CYS F 140 " distance=2.03 Simple disulfide: pdb=" SG CYS E 113 " - pdb=" SG CYS E 140 " distance=2.03 Simple disulfide: pdb=" SG CYS D 113 " - pdb=" SG CYS D 140 " distance=2.04 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 140 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 18.65 Conformation dependent library (CDL) restraints added in 6.2 seconds 13562 Ramachandran restraints generated. 6781 Oldfield, 0 Emsley, 6781 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13666 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 327 helices and 31 sheets defined 55.2% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.54 Creating SS restraints... Processing helix chain '1' and resid 187 through 190 No H-bonds generated for 'chain '1' and resid 187 through 190' Processing helix chain '1' and resid 198 through 202 Processing helix chain '1' and resid 213 through 223 removed outlier: 3.519A pdb=" N ARG 1 217 " --> pdb=" O ASP 1 213 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE 1 219 " --> pdb=" O GLU 1 215 " (cutoff:3.500A) Processing helix chain '1' and resid 241 through 254 removed outlier: 3.540A pdb=" N GLU 1 246 " --> pdb=" O THR 1 242 " (cutoff:3.500A) Processing helix chain '1' and resid 259 through 261 No H-bonds generated for 'chain '1' and resid 259 through 261' Processing helix chain '1' and resid 288 through 295 removed outlier: 3.643A pdb=" N ILE 1 292 " --> pdb=" O MET 1 288 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLU 1 294 " --> pdb=" O ASN 1 290 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU 1 295 " --> pdb=" O ILE 1 291 " (cutoff:3.500A) Processing helix chain '1' and resid 309 through 313 Processing helix chain '1' and resid 324 through 329 Processing helix chain '1' and resid 331 through 333 No H-bonds generated for 'chain '1' and resid 331 through 333' Processing helix chain '1' and resid 345 through 350 Processing helix chain '1' and resid 352 through 355 No H-bonds generated for 'chain '1' and resid 352 through 355' Processing helix chain '1' and resid 372 through 389 removed outlier: 3.749A pdb=" N SER 1 381 " --> pdb=" O LYS 1 377 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N SER 1 384 " --> pdb=" O ARG 1 380 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LYS 1 385 " --> pdb=" O SER 1 381 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN 1 388 " --> pdb=" O SER 1 384 " (cutoff:3.500A) Processing helix chain '1' and resid 396 through 409 removed outlier: 3.632A pdb=" N ALA 1 403 " --> pdb=" O LEU 1 399 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N SER 1 406 " --> pdb=" O ALA 1 402 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG 1 408 " --> pdb=" O LYS 1 404 " (cutoff:3.500A) Processing helix chain '1' and resid 415 through 434 removed outlier: 3.549A pdb=" N ILE 1 420 " --> pdb=" O PRO 1 416 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU 1 423 " --> pdb=" O ALA 1 419 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER 1 428 " --> pdb=" O ASN 1 424 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLN 1 431 " --> pdb=" O CYS 1 427 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL 1 432 " --> pdb=" O SER 1 428 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLN 1 433 " --> pdb=" O PHE 1 429 " (cutoff:3.500A) Processing helix chain '1' and resid 439 through 450 removed outlier: 4.192A pdb=" N THR 1 444 " --> pdb=" O ILE 1 441 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU 1 445 " --> pdb=" O ASP 1 442 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG 1 446 " --> pdb=" O VAL 1 443 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASP 1 447 " --> pdb=" O THR 1 444 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE 1 448 " --> pdb=" O GLU 1 445 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU 1 449 " --> pdb=" O ARG 1 446 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG 1 450 " --> pdb=" O ASP 1 447 " (cutoff:3.500A) Processing helix chain '1' and resid 469 through 507 removed outlier: 3.671A pdb=" N ILE 1 474 " --> pdb=" O TYR 1 470 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS 1 475 " --> pdb=" O ASN 1 471 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU 1 476 " --> pdb=" O LYS 1 472 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N PHE 1 477 " --> pdb=" O LEU 1 473 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLU 1 478 " --> pdb=" O ILE 1 474 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLU 1 479 " --> pdb=" O LYS 1 475 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS 1 480 " --> pdb=" O GLU 1 476 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LYS 1 481 " --> pdb=" O PHE 1 477 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLU 1 482 " --> pdb=" O GLU 1 478 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLN 1 483 " --> pdb=" O GLU 1 479 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU 1 484 " --> pdb=" O LYS 1 480 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS 1 485 " --> pdb=" O LYS 1 481 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS 1 486 " --> pdb=" O GLU 1 482 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N TYR 1 487 " --> pdb=" O GLN 1 483 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR 1 488 " --> pdb=" O LEU 1 484 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU 1 489 " --> pdb=" O LYS 1 485 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS 1 499 " --> pdb=" O GLY 1 495 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG 1 500 " --> pdb=" O GLU 1 496 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU 1 503 " --> pdb=" O LYS 1 499 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU 1 505 " --> pdb=" O LYS 1 501 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LYS 1 506 " --> pdb=" O LYS 1 502 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS 1 507 " --> pdb=" O GLU 1 503 " (cutoff:3.500A) Processing helix chain '1' and resid 510 through 515 removed outlier: 3.674A pdb=" N THR 1 515 " --> pdb=" O LEU 1 511 " (cutoff:3.500A) Processing helix chain '1' and resid 530 through 538 Processing helix chain '1' and resid 540 through 554 removed outlier: 3.659A pdb=" N GLU 1 552 " --> pdb=" O VAL 1 548 " (cutoff:3.500A) Processing helix chain '1' and resid 566 through 576 removed outlier: 3.670A pdb=" N ASP 1 576 " --> pdb=" O ILE 1 572 " (cutoff:3.500A) Processing helix chain '1' and resid 591 through 602 removed outlier: 4.047A pdb=" N TYR 1 596 " --> pdb=" O ALA 1 592 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASN 1 597 " --> pdb=" O LEU 1 593 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER 1 602 " --> pdb=" O SER 1 598 " (cutoff:3.500A) Processing helix chain '1' and resid 607 through 621 removed outlier: 3.688A pdb=" N ALA 1 616 " --> pdb=" O SER 1 612 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL 1 617 " --> pdb=" O LEU 1 613 " (cutoff:3.500A) Processing helix chain '1' and resid 646 through 654 Processing helix chain '1' and resid 667 through 670 Processing helix chain '1' and resid 674 through 680 removed outlier: 3.516A pdb=" N SER 1 677 " --> pdb=" O HIS 1 674 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR 1 680 " --> pdb=" O SER 1 677 " (cutoff:3.500A) Processing helix chain '1' and resid 695 through 701 removed outlier: 4.016A pdb=" N ARG 1 700 " --> pdb=" O THR 1 696 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLU 1 701 " --> pdb=" O GLU 1 697 " (cutoff:3.500A) Processing helix chain '1' and resid 717 through 728 removed outlier: 3.672A pdb=" N VAL 1 722 " --> pdb=" O ASP 1 718 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLN 1 725 " --> pdb=" O LYS 1 721 " (cutoff:3.500A) Processing helix chain '1' and resid 774 through 792 removed outlier: 3.626A pdb=" N GLU 1 779 " --> pdb=" O LYS 1 775 " (cutoff:3.500A) Processing helix chain '1' and resid 796 through 800 removed outlier: 3.649A pdb=" N ARG 1 800 " --> pdb=" O GLU 1 796 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 796 through 800' Processing helix chain '1' and resid 812 through 830 removed outlier: 4.010A pdb=" N LYS 1 817 " --> pdb=" O LYS 1 813 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL 1 819 " --> pdb=" O LEU 1 815 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ALA 1 820 " --> pdb=" O HIS 1 816 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU 1 821 " --> pdb=" O LYS 1 817 " (cutoff:3.500A) Processing helix chain '1' and resid 841 through 851 removed outlier: 4.257A pdb=" N ILE 1 847 " --> pdb=" O ALA 1 843 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP 1 849 " --> pdb=" O ASP 1 845 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLN 1 850 " --> pdb=" O TYR 1 846 " (cutoff:3.500A) Processing helix chain '1' and resid 859 through 867 removed outlier: 4.053A pdb=" N PHE 1 864 " --> pdb=" O THR 1 861 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ILE 1 865 " --> pdb=" O LEU 1 862 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N SER 1 867 " --> pdb=" O PHE 1 864 " (cutoff:3.500A) Processing helix chain '1' and resid 869 through 872 No H-bonds generated for 'chain '1' and resid 869 through 872' Processing helix chain '2' and resid 190 through 192 No H-bonds generated for 'chain '2' and resid 190 through 192' Processing helix chain '2' and resid 197 through 203 removed outlier: 3.738A pdb=" N VAL 2 201 " --> pdb=" O ASN 2 198 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG 2 202 " --> pdb=" O GLU 2 199 " (cutoff:3.500A) Processing helix chain '2' and resid 213 through 223 removed outlier: 3.819A pdb=" N ARG 2 217 " --> pdb=" O ASP 2 213 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ALA 2 218 " --> pdb=" O GLU 2 214 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE 2 219 " --> pdb=" O GLU 2 215 " (cutoff:3.500A) Processing helix chain '2' and resid 241 through 254 removed outlier: 3.792A pdb=" N VAL 2 245 " --> pdb=" O LYS 2 241 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS 2 254 " --> pdb=" O TYR 2 250 " (cutoff:3.500A) Processing helix chain '2' and resid 271 through 274 No H-bonds generated for 'chain '2' and resid 271 through 274' Processing helix chain '2' and resid 283 through 296 removed outlier: 3.857A pdb=" N ILE 2 291 " --> pdb=" O ARG 2 287 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU 2 294 " --> pdb=" O ASN 2 290 " (cutoff:3.500A) Processing helix chain '2' and resid 324 through 332 removed outlier: 3.633A pdb=" N LEU 2 328 " --> pdb=" O ALA 2 324 " (cutoff:3.500A) Proline residue: 2 330 - end of helix Processing helix chain '2' and resid 345 through 350 Processing helix chain '2' and resid 352 through 355 No H-bonds generated for 'chain '2' and resid 352 through 355' Processing helix chain '2' and resid 372 through 390 removed outlier: 3.594A pdb=" N VAL 2 376 " --> pdb=" O ASP 2 373 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ARG 2 380 " --> pdb=" O LYS 2 377 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS 2 383 " --> pdb=" O ARG 2 380 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N SER 2 384 " --> pdb=" O SER 2 381 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS 2 385 " --> pdb=" O LEU 2 382 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU 2 387 " --> pdb=" O SER 2 384 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN 2 388 " --> pdb=" O LYS 2 385 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE 2 389 " --> pdb=" O TYR 2 386 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR 2 390 " --> pdb=" O GLU 2 387 " (cutoff:3.500A) Processing helix chain '2' and resid 396 through 408 removed outlier: 3.590A pdb=" N SER 2 406 " --> pdb=" O ALA 2 402 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG 2 408 " --> pdb=" O LYS 2 404 " (cutoff:3.500A) Processing helix chain '2' and resid 415 through 435 removed outlier: 4.198A pdb=" N ALA 2 419 " --> pdb=" O PRO 2 416 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE 2 420 " --> pdb=" O ASP 2 417 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU 2 422 " --> pdb=" O ALA 2 419 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU 2 423 " --> pdb=" O ILE 2 420 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS 2 425 " --> pdb=" O LEU 2 422 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU 2 430 " --> pdb=" O CYS 2 427 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN 2 431 " --> pdb=" O SER 2 428 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL 2 432 " --> pdb=" O PHE 2 429 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU 2 434 " --> pdb=" O GLN 2 431 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER 2 435 " --> pdb=" O VAL 2 432 " (cutoff:3.500A) Processing helix chain '2' and resid 439 through 457 removed outlier: 4.174A pdb=" N GLU 2 449 " --> pdb=" O GLU 2 445 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU 2 454 " --> pdb=" O ARG 2 450 " (cutoff:3.500A) Processing helix chain '2' and resid 464 through 506 removed outlier: 3.630A pdb=" N LYS 2 469 " --> pdb=" O VAL 2 465 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS 2 481 " --> pdb=" O PHE 2 477 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS 2 486 " --> pdb=" O GLU 2 482 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU 2 489 " --> pdb=" O LYS 2 485 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU 2 503 " --> pdb=" O LYS 2 499 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU 2 505 " --> pdb=" O LYS 2 501 " (cutoff:3.500A) Processing helix chain '2' and resid 510 through 518 Processing helix chain '2' and resid 526 through 540 removed outlier: 4.045A pdb=" N GLN 2 530 " --> pdb=" O PRO 2 526 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LEU 2 533 " --> pdb=" O LEU 2 529 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N LYS 2 534 " --> pdb=" O GLN 2 530 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLN 2 537 " --> pdb=" O LEU 2 533 " (cutoff:3.500A) Processing helix chain '2' and resid 543 through 553 removed outlier: 3.745A pdb=" N GLU 2 552 " --> pdb=" O VAL 2 548 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA 2 553 " --> pdb=" O ALA 2 549 " (cutoff:3.500A) Processing helix chain '2' and resid 566 through 576 Processing helix chain '2' and resid 581 through 583 No H-bonds generated for 'chain '2' and resid 581 through 583' Processing helix chain '2' and resid 590 through 593 No H-bonds generated for 'chain '2' and resid 590 through 593' Processing helix chain '2' and resid 595 through 602 removed outlier: 3.582A pdb=" N LYS 2 601 " --> pdb=" O ASN 2 597 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER 2 602 " --> pdb=" O SER 2 598 " (cutoff:3.500A) Processing helix chain '2' and resid 607 through 621 removed outlier: 3.672A pdb=" N ALA 2 616 " --> pdb=" O SER 2 612 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL 2 617 " --> pdb=" O LEU 2 613 " (cutoff:3.500A) Processing helix chain '2' and resid 645 through 655 removed outlier: 3.560A pdb=" N LEU 2 655 " --> pdb=" O LEU 2 651 " (cutoff:3.500A) Processing helix chain '2' and resid 659 through 661 No H-bonds generated for 'chain '2' and resid 659 through 661' Processing helix chain '2' and resid 667 through 670 Processing helix chain '2' and resid 673 through 680 removed outlier: 3.941A pdb=" N VAL 2 676 " --> pdb=" O ALA 2 673 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER 2 677 " --> pdb=" O HIS 2 674 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N THR 2 680 " --> pdb=" O SER 2 677 " (cutoff:3.500A) Processing helix chain '2' and resid 696 through 701 Processing helix chain '2' and resid 717 through 728 removed outlier: 3.593A pdb=" N LYS 2 721 " --> pdb=" O ALA 2 717 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL 2 722 " --> pdb=" O ASP 2 718 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N GLN 2 725 " --> pdb=" O LYS 2 721 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE 2 726 " --> pdb=" O VAL 2 722 " (cutoff:3.500A) Processing helix chain '2' and resid 763 through 766 No H-bonds generated for 'chain '2' and resid 763 through 766' Processing helix chain '2' and resid 772 through 792 removed outlier: 4.436A pdb=" N VAL 2 777 " --> pdb=" O GLU 2 773 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER 2 784 " --> pdb=" O ASP 2 780 " (cutoff:3.500A) Processing helix chain '2' and resid 796 through 800 Processing helix chain '2' and resid 812 through 829 removed outlier: 3.811A pdb=" N LYS 2 817 " --> pdb=" O LYS 2 813 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS 2 824 " --> pdb=" O ALA 2 820 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS 2 828 " --> pdb=" O LYS 2 824 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG 2 829 " --> pdb=" O LYS 2 825 " (cutoff:3.500A) Processing helix chain '2' and resid 841 through 850 Processing helix chain '2' and resid 859 through 878 removed outlier: 3.745A pdb=" N MET 2 870 " --> pdb=" O GLU 2 866 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N THR 2 871 " --> pdb=" O SER 2 867 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU 2 878 " --> pdb=" O ALA 2 874 " (cutoff:3.500A) Processing helix chain '3' and resid 197 through 202 removed outlier: 3.544A pdb=" N VAL 3 201 " --> pdb=" O MET 3 197 " (cutoff:3.500A) Processing helix chain '3' and resid 213 through 223 removed outlier: 3.571A pdb=" N ALA 3 218 " --> pdb=" O GLU 3 214 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE 3 219 " --> pdb=" O GLU 3 215 " (cutoff:3.500A) Processing helix chain '3' and resid 241 through 253 removed outlier: 3.893A pdb=" N VAL 3 245 " --> pdb=" O LYS 3 241 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TYR 3 250 " --> pdb=" O GLU 3 246 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG 3 251 " --> pdb=" O GLY 3 247 " (cutoff:3.500A) Processing helix chain '3' and resid 259 through 261 No H-bonds generated for 'chain '3' and resid 259 through 261' Processing helix chain '3' and resid 271 through 274 No H-bonds generated for 'chain '3' and resid 271 through 274' Processing helix chain '3' and resid 284 through 295 removed outlier: 3.576A pdb=" N ILE 3 291 " --> pdb=" O ARG 3 287 " (cutoff:3.500A) Processing helix chain '3' and resid 309 through 312 No H-bonds generated for 'chain '3' and resid 309 through 312' Processing helix chain '3' and resid 324 through 332 Proline residue: 3 330 - end of helix Processing helix chain '3' and resid 345 through 350 removed outlier: 3.615A pdb=" N LYS 3 350 " --> pdb=" O ALA 3 346 " (cutoff:3.500A) Processing helix chain '3' and resid 356 through 359 No H-bonds generated for 'chain '3' and resid 356 through 359' Processing helix chain '3' and resid 373 through 381 removed outlier: 4.217A pdb=" N LYS 3 377 " --> pdb=" O ASP 3 373 " (cutoff:3.500A) Processing helix chain '3' and resid 383 through 389 Processing helix chain '3' and resid 396 through 409 removed outlier: 3.541A pdb=" N ILE 3 405 " --> pdb=" O ALA 3 401 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N SER 3 406 " --> pdb=" O ALA 3 402 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE 3 409 " --> pdb=" O ILE 3 405 " (cutoff:3.500A) Processing helix chain '3' and resid 415 through 435 removed outlier: 3.803A pdb=" N ALA 3 419 " --> pdb=" O PRO 3 416 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ILE 3 420 " --> pdb=" O ASP 3 417 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU 3 422 " --> pdb=" O ALA 3 419 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N CYS 3 427 " --> pdb=" O ASN 3 424 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU 3 430 " --> pdb=" O CYS 3 427 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLN 3 431 " --> pdb=" O SER 3 428 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL 3 432 " --> pdb=" O PHE 3 429 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER 3 435 " --> pdb=" O VAL 3 432 " (cutoff:3.500A) Processing helix chain '3' and resid 439 through 458 removed outlier: 3.607A pdb=" N ARG 3 446 " --> pdb=" O ASP 3 442 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU 3 449 " --> pdb=" O GLU 3 445 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR 3 453 " --> pdb=" O GLU 3 449 " (cutoff:3.500A) Processing helix chain '3' and resid 465 through 506 removed outlier: 3.690A pdb=" N ASN 3 471 " --> pdb=" O LYS 3 468 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE 3 474 " --> pdb=" O ASN 3 471 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU 3 478 " --> pdb=" O LYS 3 475 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU 3 479 " --> pdb=" O GLU 3 476 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LYS 3 480 " --> pdb=" O PHE 3 477 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N TYR 3 488 " --> pdb=" O LYS 3 485 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE 3 493 " --> pdb=" O GLU 3 490 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N THR 3 494 " --> pdb=" O TYR 3 491 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS 3 499 " --> pdb=" O GLU 3 496 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG 3 500 " --> pdb=" O ARG 3 497 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU 3 503 " --> pdb=" O ARG 3 500 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE 3 504 " --> pdb=" O LYS 3 501 " (cutoff:3.500A) Processing helix chain '3' and resid 508 through 516 removed outlier: 3.574A pdb=" N GLU 3 513 " --> pdb=" O ASN 3 509 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N THR 3 515 " --> pdb=" O LEU 3 511 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N GLN 3 516 " --> pdb=" O LYS 3 512 " (cutoff:3.500A) Processing helix chain '3' and resid 531 through 553 removed outlier: 3.909A pdb=" N GLU 3 535 " --> pdb=" O ASN 3 531 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLN 3 537 " --> pdb=" O LEU 3 533 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N TYR 3 540 " --> pdb=" O ALA 3 536 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU 3 541 " --> pdb=" O GLN 3 537 " (cutoff:3.500A) Processing helix chain '3' and resid 566 through 577 Processing helix chain '3' and resid 595 through 602 removed outlier: 3.640A pdb=" N SER 3 600 " --> pdb=" O TYR 3 596 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LYS 3 601 " --> pdb=" O ASN 3 597 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER 3 602 " --> pdb=" O SER 3 598 " (cutoff:3.500A) Processing helix chain '3' and resid 607 through 621 removed outlier: 3.521A pdb=" N LYS 3 611 " --> pdb=" O GLU 3 607 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER 3 612 " --> pdb=" O ASP 3 608 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL 3 617 " --> pdb=" O LEU 3 613 " (cutoff:3.500A) Processing helix chain '3' and resid 646 through 655 removed outlier: 3.550A pdb=" N LEU 3 651 " --> pdb=" O LEU 3 647 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA 3 652 " --> pdb=" O ALA 3 648 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE 3 653 " --> pdb=" O LYS 3 649 " (cutoff:3.500A) Processing helix chain '3' and resid 659 through 661 No H-bonds generated for 'chain '3' and resid 659 through 661' Processing helix chain '3' and resid 667 through 669 No H-bonds generated for 'chain '3' and resid 667 through 669' Processing helix chain '3' and resid 673 through 680 removed outlier: 3.807A pdb=" N VAL 3 676 " --> pdb=" O ALA 3 673 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N SER 3 677 " --> pdb=" O HIS 3 674 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N THR 3 680 " --> pdb=" O SER 3 677 " (cutoff:3.500A) Processing helix chain '3' and resid 696 through 701 removed outlier: 3.600A pdb=" N GLU 3 701 " --> pdb=" O GLU 3 697 " (cutoff:3.500A) Processing helix chain '3' and resid 717 through 728 removed outlier: 3.640A pdb=" N VAL 3 722 " --> pdb=" O ASP 3 718 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLN 3 725 " --> pdb=" O LYS 3 721 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE 3 726 " --> pdb=" O VAL 3 722 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY 3 728 " --> pdb=" O LEU 3 724 " (cutoff:3.500A) Processing helix chain '3' and resid 772 through 776 removed outlier: 3.664A pdb=" N ARG 3 776 " --> pdb=" O GLU 3 773 " (cutoff:3.500A) Processing helix chain '3' and resid 778 through 791 removed outlier: 3.756A pdb=" N SER 3 784 " --> pdb=" O ASP 3 780 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS 3 791 " --> pdb=" O LYS 3 787 " (cutoff:3.500A) Processing helix chain '3' and resid 795 through 800 removed outlier: 3.657A pdb=" N ARG 3 800 " --> pdb=" O GLU 3 796 " (cutoff:3.500A) Processing helix chain '3' and resid 812 through 829 removed outlier: 3.763A pdb=" N LYS 3 817 " --> pdb=" O LYS 3 813 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA 3 820 " --> pdb=" O HIS 3 816 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS 3 828 " --> pdb=" O LYS 3 824 " (cutoff:3.500A) Processing helix chain '3' and resid 841 through 850 removed outlier: 3.543A pdb=" N ILE 3 847 " --> pdb=" O ALA 3 843 " (cutoff:3.500A) Processing helix chain '3' and resid 860 through 867 Processing helix chain '3' and resid 869 through 878 removed outlier: 3.511A pdb=" N PHE 3 873 " --> pdb=" O ILE 3 869 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N TYR 3 877 " --> pdb=" O PHE 3 873 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU 3 878 " --> pdb=" O ALA 3 874 " (cutoff:3.500A) Processing helix chain '4' and resid 189 through 193 Processing helix chain '4' and resid 199 through 202 No H-bonds generated for 'chain '4' and resid 199 through 202' Processing helix chain '4' and resid 213 through 223 removed outlier: 3.512A pdb=" N SER 4 222 " --> pdb=" O ALA 4 218 " (cutoff:3.500A) Processing helix chain '4' and resid 242 through 254 removed outlier: 3.528A pdb=" N LYS 4 254 " --> pdb=" O TYR 4 250 " (cutoff:3.500A) Processing helix chain '4' and resid 271 through 274 No H-bonds generated for 'chain '4' and resid 271 through 274' Processing helix chain '4' and resid 276 through 278 No H-bonds generated for 'chain '4' and resid 276 through 278' Processing helix chain '4' and resid 283 through 296 removed outlier: 3.583A pdb=" N ILE 4 291 " --> pdb=" O ARG 4 287 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLU 4 294 " --> pdb=" O ASN 4 290 " (cutoff:3.500A) Processing helix chain '4' and resid 309 through 311 No H-bonds generated for 'chain '4' and resid 309 through 311' Processing helix chain '4' and resid 324 through 334 removed outlier: 3.920A pdb=" N LEU 4 328 " --> pdb=" O ALA 4 324 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS 4 329 " --> pdb=" O ALA 4 325 " (cutoff:3.500A) Proline residue: 4 330 - end of helix removed outlier: 3.706A pdb=" N SER 4 333 " --> pdb=" O LYS 4 329 " (cutoff:3.500A) Processing helix chain '4' and resid 345 through 355 removed outlier: 3.931A pdb=" N LYS 4 350 " --> pdb=" O ALA 4 346 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU 4 353 " --> pdb=" O ARG 4 349 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N SER 4 354 " --> pdb=" O LYS 4 350 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N CYS 4 355 " --> pdb=" O PHE 4 351 " (cutoff:3.500A) Processing helix chain '4' and resid 375 through 381 Processing helix chain '4' and resid 383 through 388 Processing helix chain '4' and resid 396 through 408 removed outlier: 3.533A pdb=" N ALA 4 403 " --> pdb=" O LEU 4 399 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER 4 406 " --> pdb=" O ALA 4 402 " (cutoff:3.500A) Processing helix chain '4' and resid 415 through 435 removed outlier: 3.878A pdb=" N ILE 4 420 " --> pdb=" O PRO 4 416 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU 4 430 " --> pdb=" O ALA 4 426 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLN 4 431 " --> pdb=" O CYS 4 427 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL 4 432 " --> pdb=" O SER 4 428 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN 4 433 " --> pdb=" O PHE 4 429 " (cutoff:3.500A) Processing helix chain '4' and resid 439 through 459 removed outlier: 3.856A pdb=" N THR 4 444 " --> pdb=" O ILE 4 440 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE 4 448 " --> pdb=" O THR 4 444 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR 4 453 " --> pdb=" O GLU 4 449 " (cutoff:3.500A) Processing helix chain '4' and resid 465 through 487 removed outlier: 3.877A pdb=" N LYS 4 469 " --> pdb=" O VAL 4 465 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS 4 485 " --> pdb=" O LYS 4 481 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS 4 486 " --> pdb=" O GLU 4 482 " (cutoff:3.500A) Processing helix chain '4' and resid 490 through 516 removed outlier: 3.846A pdb=" N ASN 4 509 " --> pdb=" O GLU 4 505 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ASP 4 510 " --> pdb=" O LYS 4 506 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU 4 514 " --> pdb=" O ASP 4 510 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N THR 4 515 " --> pdb=" O LEU 4 511 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN 4 516 " --> pdb=" O LYS 4 512 " (cutoff:3.500A) Processing helix chain '4' and resid 534 through 538 removed outlier: 3.563A pdb=" N GLN 4 538 " --> pdb=" O GLU 4 535 " (cutoff:3.500A) Processing helix chain '4' and resid 540 through 553 removed outlier: 3.716A pdb=" N GLU 4 546 " --> pdb=" O GLU 4 542 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU 4 552 " --> pdb=" O VAL 4 548 " (cutoff:3.500A) Processing helix chain '4' and resid 566 through 576 removed outlier: 3.505A pdb=" N ILE 4 572 " --> pdb=" O HIS 4 568 " (cutoff:3.500A) Processing helix chain '4' and resid 592 through 602 removed outlier: 3.725A pdb=" N LEU 4 595 " --> pdb=" O ALA 4 592 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TYR 4 596 " --> pdb=" O LEU 4 593 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU 4 599 " --> pdb=" O TYR 4 596 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER 4 600 " --> pdb=" O ASN 4 597 " (cutoff:3.500A) Processing helix chain '4' and resid 607 through 622 removed outlier: 3.672A pdb=" N ASP 4 615 " --> pdb=" O LYS 4 611 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS 4 619 " --> pdb=" O ASP 4 615 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA 4 620 " --> pdb=" O ALA 4 616 " (cutoff:3.500A) Processing helix chain '4' and resid 644 through 654 removed outlier: 4.266A pdb=" N ALA 4 648 " --> pdb=" O LYS 4 644 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA 4 652 " --> pdb=" O ALA 4 648 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE 4 653 " --> pdb=" O LYS 4 649 " (cutoff:3.500A) Processing helix chain '4' and resid 659 through 661 No H-bonds generated for 'chain '4' and resid 659 through 661' Processing helix chain '4' and resid 667 through 670 Processing helix chain '4' and resid 673 through 678 removed outlier: 4.143A pdb=" N VAL 4 676 " --> pdb=" O ALA 4 673 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER 4 677 " --> pdb=" O HIS 4 674 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS 4 678 " --> pdb=" O SER 4 675 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 673 through 678' Processing helix chain '4' and resid 696 through 701 Processing helix chain '4' and resid 717 through 728 removed outlier: 3.560A pdb=" N VAL 4 722 " --> pdb=" O ASP 4 718 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLN 4 725 " --> pdb=" O LYS 4 721 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE 4 726 " --> pdb=" O VAL 4 722 " (cutoff:3.500A) Processing helix chain '4' and resid 772 through 792 removed outlier: 3.535A pdb=" N ARG 4 776 " --> pdb=" O PRO 4 772 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N VAL 4 777 " --> pdb=" O GLU 4 773 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N MET 4 778 " --> pdb=" O TYR 4 774 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU 4 779 " --> pdb=" O LYS 4 775 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP 4 780 " --> pdb=" O ARG 4 776 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER 4 784 " --> pdb=" O ASP 4 780 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS 4 791 " --> pdb=" O LYS 4 787 " (cutoff:3.500A) Processing helix chain '4' and resid 795 through 800 Processing helix chain '4' and resid 812 through 824 removed outlier: 4.127A pdb=" N LYS 4 817 " --> pdb=" O LYS 4 813 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE 4 818 " --> pdb=" O ASN 4 814 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA 4 820 " --> pdb=" O HIS 4 816 " (cutoff:3.500A) Processing helix chain '4' and resid 841 through 850 Processing helix chain '4' and resid 859 through 867 Processing helix chain '4' and resid 869 through 878 removed outlier: 3.540A pdb=" N TYR 4 877 " --> pdb=" O PHE 4 873 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU 4 878 " --> pdb=" O ALA 4 874 " (cutoff:3.500A) Processing helix chain '5' and resid 189 through 192 removed outlier: 3.644A pdb=" N GLN 5 192 " --> pdb=" O TYR 5 189 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 189 through 192' Processing helix chain '5' and resid 198 through 203 Processing helix chain '5' and resid 213 through 223 removed outlier: 3.647A pdb=" N ALA 5 218 " --> pdb=" O GLU 5 214 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER 5 222 " --> pdb=" O ALA 5 218 " (cutoff:3.500A) Processing helix chain '5' and resid 237 through 239 No H-bonds generated for 'chain '5' and resid 237 through 239' Processing helix chain '5' and resid 241 through 253 removed outlier: 4.272A pdb=" N VAL 5 245 " --> pdb=" O LYS 5 241 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR 5 250 " --> pdb=" O GLU 5 246 " (cutoff:3.500A) Processing helix chain '5' and resid 259 through 261 No H-bonds generated for 'chain '5' and resid 259 through 261' Processing helix chain '5' and resid 271 through 274 No H-bonds generated for 'chain '5' and resid 271 through 274' Processing helix chain '5' and resid 286 through 296 removed outlier: 3.730A pdb=" N LYS 5 293 " --> pdb=" O LYS 5 289 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLU 5 294 " --> pdb=" O ASN 5 290 " (cutoff:3.500A) Processing helix chain '5' and resid 309 through 314 Processing helix chain '5' and resid 324 through 333 removed outlier: 3.582A pdb=" N LEU 5 328 " --> pdb=" O ALA 5 324 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS 5 329 " --> pdb=" O ALA 5 325 " (cutoff:3.500A) Proline residue: 5 330 - end of helix Processing helix chain '5' and resid 345 through 352 removed outlier: 3.866A pdb=" N LYS 5 350 " --> pdb=" O ALA 5 346 " (cutoff:3.500A) Processing helix chain '5' and resid 372 through 381 removed outlier: 3.574A pdb=" N LYS 5 377 " --> pdb=" O ASP 5 373 " (cutoff:3.500A) Processing helix chain '5' and resid 383 through 389 Processing helix chain '5' and resid 396 through 409 removed outlier: 3.542A pdb=" N ALA 5 403 " --> pdb=" O LEU 5 399 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER 5 406 " --> pdb=" O ALA 5 402 " (cutoff:3.500A) Processing helix chain '5' and resid 415 through 435 removed outlier: 3.731A pdb=" N ALA 5 419 " --> pdb=" O LEU 5 415 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE 5 420 " --> pdb=" O PRO 5 416 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU 5 423 " --> pdb=" O ALA 5 419 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER 5 428 " --> pdb=" O ASN 5 424 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU 5 430 " --> pdb=" O ALA 5 426 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN 5 433 " --> pdb=" O PHE 5 429 " (cutoff:3.500A) Processing helix chain '5' and resid 439 through 458 removed outlier: 3.765A pdb=" N TYR 5 453 " --> pdb=" O GLU 5 449 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR 5 457 " --> pdb=" O TYR 5 453 " (cutoff:3.500A) Processing helix chain '5' and resid 464 through 508 removed outlier: 3.557A pdb=" N LYS 5 468 " --> pdb=" O LYS 5 464 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS 5 469 " --> pdb=" O VAL 5 465 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE 5 474 " --> pdb=" O TYR 5 470 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU 5 479 " --> pdb=" O LYS 5 475 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS 5 480 " --> pdb=" O GLU 5 476 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS 5 481 " --> pdb=" O PHE 5 477 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU 5 482 " --> pdb=" O GLU 5 478 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS 5 486 " --> pdb=" O GLU 5 482 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLU 5 489 " --> pdb=" O LYS 5 485 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG 5 497 " --> pdb=" O ILE 5 493 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU 5 498 " --> pdb=" O THR 5 494 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS 5 499 " --> pdb=" O GLY 5 495 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLU 5 503 " --> pdb=" O LYS 5 499 " (cutoff:3.500A) Processing helix chain '5' and resid 511 through 516 removed outlier: 4.148A pdb=" N THR 5 515 " --> pdb=" O LEU 5 511 " (cutoff:3.500A) Processing helix chain '5' and resid 531 through 540 removed outlier: 3.574A pdb=" N GLN 5 538 " --> pdb=" O LYS 5 534 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS 5 539 " --> pdb=" O GLU 5 535 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N TYR 5 540 " --> pdb=" O ALA 5 536 " (cutoff:3.500A) Processing helix chain '5' and resid 543 through 553 removed outlier: 3.798A pdb=" N THR 5 547 " --> pdb=" O LEU 5 543 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU 5 552 " --> pdb=" O VAL 5 548 " (cutoff:3.500A) Processing helix chain '5' and resid 566 through 576 Processing helix chain '5' and resid 584 through 586 No H-bonds generated for 'chain '5' and resid 584 through 586' Processing helix chain '5' and resid 593 through 602 removed outlier: 3.618A pdb=" N TYR 5 596 " --> pdb=" O LEU 5 593 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN 5 597 " --> pdb=" O LYS 5 594 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER 5 598 " --> pdb=" O LEU 5 595 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU 5 599 " --> pdb=" O TYR 5 596 " (cutoff:3.500A) Processing helix chain '5' and resid 607 through 622 removed outlier: 3.641A pdb=" N LYS 5 611 " --> pdb=" O GLU 5 607 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER 5 612 " --> pdb=" O ASP 5 608 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS 5 619 " --> pdb=" O ASP 5 615 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA 5 620 " --> pdb=" O ALA 5 616 " (cutoff:3.500A) Processing helix chain '5' and resid 644 through 654 removed outlier: 4.021A pdb=" N ALA 5 648 " --> pdb=" O LYS 5 644 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU 5 651 " --> pdb=" O LEU 5 647 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA 5 652 " --> pdb=" O ALA 5 648 " (cutoff:3.500A) Processing helix chain '5' and resid 667 through 669 No H-bonds generated for 'chain '5' and resid 667 through 669' Processing helix chain '5' and resid 673 through 678 removed outlier: 3.924A pdb=" N VAL 5 676 " --> pdb=" O ALA 5 673 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SER 5 677 " --> pdb=" O HIS 5 674 " (cutoff:3.500A) Processing helix chain '5' and resid 695 through 701 Processing helix chain '5' and resid 717 through 728 removed outlier: 3.657A pdb=" N LYS 5 721 " --> pdb=" O ALA 5 717 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL 5 722 " --> pdb=" O ASP 5 718 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLN 5 725 " --> pdb=" O LYS 5 721 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE 5 726 " --> pdb=" O VAL 5 722 " (cutoff:3.500A) Processing helix chain '5' and resid 761 through 765 Processing helix chain '5' and resid 772 through 792 Processing helix chain '5' and resid 795 through 800 removed outlier: 3.922A pdb=" N ASN 5 799 " --> pdb=" O GLU 5 796 " (cutoff:3.500A) Processing helix chain '5' and resid 812 through 829 removed outlier: 4.446A pdb=" N LYS 5 817 " --> pdb=" O LYS 5 813 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA 5 820 " --> pdb=" O HIS 5 816 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG 5 822 " --> pdb=" O ILE 5 818 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE 5 823 " --> pdb=" O VAL 5 819 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS 5 824 " --> pdb=" O ALA 5 820 " (cutoff:3.500A) Processing helix chain '5' and resid 841 through 851 removed outlier: 3.693A pdb=" N ASP 5 845 " --> pdb=" O GLU 5 841 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER 5 851 " --> pdb=" O ILE 5 847 " (cutoff:3.500A) Processing helix chain '5' and resid 859 through 878 removed outlier: 3.512A pdb=" N ILE 5 865 " --> pdb=" O THR 5 861 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N MET 5 870 " --> pdb=" O GLU 5 866 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N THR 5 871 " --> pdb=" O SER 5 867 " (cutoff:3.500A) Processing helix chain '6' and resid 189 through 193 Processing helix chain '6' and resid 198 through 202 Processing helix chain '6' and resid 216 through 223 removed outlier: 3.612A pdb=" N SER 6 222 " --> pdb=" O ALA 6 218 " (cutoff:3.500A) Processing helix chain '6' and resid 243 through 253 removed outlier: 3.718A pdb=" N LEU 6 248 " --> pdb=" O ILE 6 244 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N VAL 6 249 " --> pdb=" O VAL 6 245 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N TYR 6 250 " --> pdb=" O GLU 6 246 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE 6 252 " --> pdb=" O LEU 6 248 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU 6 253 " --> pdb=" O VAL 6 249 " (cutoff:3.500A) Processing helix chain '6' and resid 259 through 261 No H-bonds generated for 'chain '6' and resid 259 through 261' Processing helix chain '6' and resid 286 through 296 removed outlier: 3.935A pdb=" N ILE 6 291 " --> pdb=" O ARG 6 287 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU 6 295 " --> pdb=" O ILE 6 291 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS 6 296 " --> pdb=" O ILE 6 292 " (cutoff:3.500A) Processing helix chain '6' and resid 309 through 312 No H-bonds generated for 'chain '6' and resid 309 through 312' Processing helix chain '6' and resid 329 through 332 No H-bonds generated for 'chain '6' and resid 329 through 332' Processing helix chain '6' and resid 352 through 354 No H-bonds generated for 'chain '6' and resid 352 through 354' Processing helix chain '6' and resid 358 through 361 No H-bonds generated for 'chain '6' and resid 358 through 361' Processing helix chain '6' and resid 372 through 389 removed outlier: 4.474A pdb=" N LYS 6 377 " --> pdb=" O ASP 6 373 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ILE 6 378 " --> pdb=" O MET 6 374 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N SER 6 384 " --> pdb=" O ARG 6 380 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N LYS 6 385 " --> pdb=" O SER 6 381 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N TYR 6 386 " --> pdb=" O LEU 6 382 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN 6 388 " --> pdb=" O SER 6 384 " (cutoff:3.500A) Processing helix chain '6' and resid 396 through 408 removed outlier: 3.607A pdb=" N VAL 6 400 " --> pdb=" O ASP 6 396 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA 6 401 " --> pdb=" O LYS 6 397 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS 6 404 " --> pdb=" O VAL 6 400 " (cutoff:3.500A) Processing helix chain '6' and resid 415 through 434 removed outlier: 3.870A pdb=" N ALA 6 419 " --> pdb=" O PRO 6 416 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE 6 420 " --> pdb=" O ASP 6 417 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU 6 422 " --> pdb=" O ALA 6 419 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS 6 425 " --> pdb=" O LEU 6 422 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N CYS 6 427 " --> pdb=" O ASN 6 424 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N SER 6 428 " --> pdb=" O LYS 6 425 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU 6 434 " --> pdb=" O GLN 6 431 " (cutoff:3.500A) Processing helix chain '6' and resid 439 through 458 removed outlier: 3.605A pdb=" N ARG 6 446 " --> pdb=" O ASP 6 442 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR 6 453 " --> pdb=" O GLU 6 449 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU 6 454 " --> pdb=" O ARG 6 450 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LEU 6 458 " --> pdb=" O GLU 6 454 " (cutoff:3.500A) Processing helix chain '6' and resid 464 through 487 removed outlier: 3.579A pdb=" N LYS 6 475 " --> pdb=" O ASN 6 471 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS 6 481 " --> pdb=" O PHE 6 477 " (cutoff:3.500A) Processing helix chain '6' and resid 490 through 507 removed outlier: 3.981A pdb=" N GLU 6 503 " --> pdb=" O LYS 6 499 " (cutoff:3.500A) Processing helix chain '6' and resid 511 through 513 No H-bonds generated for 'chain '6' and resid 511 through 513' Processing helix chain '6' and resid 529 through 553 removed outlier: 3.530A pdb=" N LEU 6 533 " --> pdb=" O LEU 6 529 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS 6 534 " --> pdb=" O GLN 6 530 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA 6 536 " --> pdb=" O SER 6 532 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N TYR 6 544 " --> pdb=" O TYR 6 540 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS 6 545 " --> pdb=" O LEU 6 541 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU 6 552 " --> pdb=" O VAL 6 548 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA 6 553 " --> pdb=" O ALA 6 549 " (cutoff:3.500A) Processing helix chain '6' and resid 566 through 576 Processing helix chain '6' and resid 592 through 602 removed outlier: 3.839A pdb=" N TYR 6 596 " --> pdb=" O LEU 6 593 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU 6 599 " --> pdb=" O TYR 6 596 " (cutoff:3.500A) Processing helix chain '6' and resid 607 through 621 removed outlier: 3.781A pdb=" N SER 6 612 " --> pdb=" O ASP 6 608 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL 6 617 " --> pdb=" O LEU 6 613 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA 6 620 " --> pdb=" O ALA 6 616 " (cutoff:3.500A) Processing helix chain '6' and resid 644 through 654 removed outlier: 4.466A pdb=" N ALA 6 648 " --> pdb=" O LYS 6 644 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA 6 652 " --> pdb=" O ALA 6 648 " (cutoff:3.500A) Processing helix chain '6' and resid 673 through 680 Processing helix chain '6' and resid 694 through 701 removed outlier: 3.554A pdb=" N VAL 6 699 " --> pdb=" O LEU 6 695 " (cutoff:3.500A) Processing helix chain '6' and resid 712 through 714 No H-bonds generated for 'chain '6' and resid 712 through 714' Processing helix chain '6' and resid 717 through 728 removed outlier: 4.040A pdb=" N GLN 6 725 " --> pdb=" O LYS 6 721 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE 6 726 " --> pdb=" O VAL 6 722 " (cutoff:3.500A) Processing helix chain '6' and resid 773 through 792 removed outlier: 3.526A pdb=" N GLU 6 779 " --> pdb=" O LYS 6 775 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASP 6 780 " --> pdb=" O ARG 6 776 " (cutoff:3.500A) Processing helix chain '6' and resid 795 through 800 removed outlier: 3.641A pdb=" N ASN 6 799 " --> pdb=" O GLU 6 796 " (cutoff:3.500A) Processing helix chain '6' and resid 812 through 829 removed outlier: 3.843A pdb=" N ALA 6 820 " --> pdb=" O HIS 6 816 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS 6 824 " --> pdb=" O ALA 6 820 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU 6 827 " --> pdb=" O PHE 6 823 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS 6 828 " --> pdb=" O LYS 6 824 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG 6 829 " --> pdb=" O LYS 6 825 " (cutoff:3.500A) Processing helix chain '6' and resid 841 through 849 removed outlier: 3.696A pdb=" N ASP 6 845 " --> pdb=" O GLU 6 841 " (cutoff:3.500A) Processing helix chain '6' and resid 859 through 867 Processing helix chain '6' and resid 869 through 878 removed outlier: 3.824A pdb=" N MET 6 876 " --> pdb=" O LYS 6 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 56 removed outlier: 3.845A pdb=" N ALA B 36 " --> pdb=" O ALA B 32 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) Proline residue: B 44 - end of helix removed outlier: 3.599A pdb=" N LYS B 50 " --> pdb=" O SER B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 72 removed outlier: 4.176A pdb=" N LYS B 70 " --> pdb=" O HIS B 66 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N PHE B 71 " --> pdb=" O LYS B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 92 removed outlier: 3.606A pdb=" N MET B 83 " --> pdb=" O ARG B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 120 removed outlier: 3.580A pdb=" N GLU B 108 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE B 109 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASN B 120 " --> pdb=" O ALA B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 147 removed outlier: 3.652A pdb=" N ASN B 138 " --> pdb=" O HIS B 134 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA B 145 " --> pdb=" O ARG B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 165 removed outlier: 3.530A pdb=" N GLN B 161 " --> pdb=" O ALA B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 171 removed outlier: 3.739A pdb=" N PHE B 170 " --> pdb=" O ILE B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 181 Processing helix chain 'B' and resid 186 through 188 No H-bonds generated for 'chain 'B' and resid 186 through 188' Processing helix chain 'B' and resid 199 through 201 No H-bonds generated for 'chain 'B' and resid 199 through 201' Processing helix chain 'B' and resid 203 through 218 removed outlier: 3.616A pdb=" N LYS B 213 " --> pdb=" O TYR B 209 " (cutoff:3.500A) Processing helix chain 'a' and resid 670 through 676 removed outlier: 4.565A pdb=" N LYS a 674 " --> pdb=" O LYS a 670 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LEU a 675 " --> pdb=" O ASP a 671 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE a 676 " --> pdb=" O ILE a 672 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 670 through 676' Processing helix chain 'a' and resid 688 through 695 Processing helix chain 'a' and resid 727 through 732 Processing helix chain 'a' and resid 745 through 754 removed outlier: 3.650A pdb=" N LYS a 750 " --> pdb=" O ILE a 746 " (cutoff:3.500A) Processing helix chain 'a' and resid 768 through 778 removed outlier: 3.581A pdb=" N GLN a 773 " --> pdb=" O ASP a 769 " (cutoff:3.500A) Processing helix chain 'a' and resid 807 through 815 Processing helix chain 'A' and resid 29 through 56 removed outlier: 3.907A pdb=" N ALA A 36 " --> pdb=" O ALA A 32 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 37 " --> pdb=" O ALA A 33 " (cutoff:3.500A) Proline residue: A 44 - end of helix removed outlier: 3.640A pdb=" N LYS A 50 " --> pdb=" O SER A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 72 removed outlier: 4.168A pdb=" N LYS A 70 " --> pdb=" O HIS A 66 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N PHE A 71 " --> pdb=" O LYS A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 92 removed outlier: 3.780A pdb=" N ARG A 79 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TRP A 80 " --> pdb=" O LYS A 76 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N MET A 83 " --> pdb=" O ARG A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 120 removed outlier: 3.621A pdb=" N GLU A 108 " --> pdb=" O LYS A 104 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASN A 120 " --> pdb=" O ALA A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 147 removed outlier: 3.680A pdb=" N ASN A 138 " --> pdb=" O HIS A 134 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 165 removed outlier: 3.507A pdb=" N GLN A 161 " --> pdb=" O ALA A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 170 removed outlier: 3.760A pdb=" N PHE A 170 " --> pdb=" O ILE A 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 167 through 170' Processing helix chain 'A' and resid 177 through 181 Processing helix chain 'A' and resid 203 through 214 Processing helix chain 'g' and resid 670 through 676 removed outlier: 4.568A pdb=" N LYS g 674 " --> pdb=" O LYS g 670 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU g 675 " --> pdb=" O ASP g 671 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE g 676 " --> pdb=" O ILE g 672 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 670 through 676' Processing helix chain 'g' and resid 688 through 695 Processing helix chain 'g' and resid 727 through 732 Processing helix chain 'g' and resid 745 through 755 removed outlier: 3.651A pdb=" N LYS g 750 " --> pdb=" O ILE g 746 " (cutoff:3.500A) Processing helix chain 'g' and resid 769 through 778 removed outlier: 3.581A pdb=" N GLN g 773 " --> pdb=" O ASP g 769 " (cutoff:3.500A) Processing helix chain 'g' and resid 807 through 815 Processing helix chain 'G' and resid 29 through 56 removed outlier: 3.857A pdb=" N ALA G 36 " --> pdb=" O ALA G 32 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Proline residue: G 44 - end of helix removed outlier: 3.600A pdb=" N LYS G 50 " --> pdb=" O SER G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 72 removed outlier: 4.205A pdb=" N LYS G 70 " --> pdb=" O HIS G 66 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE G 71 " --> pdb=" O LYS G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 92 removed outlier: 3.752A pdb=" N ARG G 79 " --> pdb=" O ARG G 75 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TRP G 80 " --> pdb=" O LYS G 76 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET G 83 " --> pdb=" O ARG G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 120 removed outlier: 3.585A pdb=" N GLU G 108 " --> pdb=" O LYS G 104 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE G 109 " --> pdb=" O ALA G 105 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASN G 120 " --> pdb=" O ALA G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 147 removed outlier: 3.665A pdb=" N ASN G 138 " --> pdb=" O HIS G 134 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA G 145 " --> pdb=" O ARG G 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 165 removed outlier: 3.517A pdb=" N GLN G 161 " --> pdb=" O ALA G 157 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 171 removed outlier: 3.784A pdb=" N PHE G 170 " --> pdb=" O ILE G 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 181 removed outlier: 3.739A pdb=" N GLY G 180 " --> pdb=" O TYR G 176 " (cutoff:3.500A) Processing helix chain 'G' and resid 203 through 220 removed outlier: 4.723A pdb=" N LYS G 220 " --> pdb=" O SER G 216 " (cutoff:3.500A) Processing helix chain 'f' and resid 670 through 676 removed outlier: 4.566A pdb=" N LYS f 674 " --> pdb=" O LYS f 670 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LEU f 675 " --> pdb=" O ASP f 671 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE f 676 " --> pdb=" O ILE f 672 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 670 through 676' Processing helix chain 'f' and resid 688 through 695 Processing helix chain 'f' and resid 727 through 732 Processing helix chain 'f' and resid 745 through 756 removed outlier: 3.649A pdb=" N LYS f 750 " --> pdb=" O ILE f 746 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS f 756 " --> pdb=" O LYS f 752 " (cutoff:3.500A) Processing helix chain 'f' and resid 765 through 778 removed outlier: 3.801A pdb=" N ALA f 770 " --> pdb=" O GLY f 766 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS f 772 " --> pdb=" O TYR f 768 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLN f 773 " --> pdb=" O ASP f 769 " (cutoff:3.500A) Processing helix chain 'f' and resid 807 through 815 Processing helix chain 'F' and resid 29 through 56 removed outlier: 3.916A pdb=" N ALA F 36 " --> pdb=" O ALA F 32 " (cutoff:3.500A) Proline residue: F 44 - end of helix removed outlier: 3.752A pdb=" N LYS F 50 " --> pdb=" O SER F 46 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP F 51 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 72 removed outlier: 4.347A pdb=" N LYS F 70 " --> pdb=" O HIS F 66 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N PHE F 71 " --> pdb=" O LYS F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 92 removed outlier: 3.514A pdb=" N MET F 83 " --> pdb=" O ARG F 79 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU F 87 " --> pdb=" O MET F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 118 removed outlier: 3.647A pdb=" N GLU F 108 " --> pdb=" O LYS F 104 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE F 109 " --> pdb=" O ALA F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 145 removed outlier: 3.599A pdb=" N ASN F 138 " --> pdb=" O HIS F 134 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN F 142 " --> pdb=" O ASN F 138 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA F 145 " --> pdb=" O ARG F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 164 removed outlier: 4.109A pdb=" N GLN F 161 " --> pdb=" O ALA F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 169 No H-bonds generated for 'chain 'F' and resid 167 through 169' Processing helix chain 'F' and resid 174 through 181 removed outlier: 3.888A pdb=" N LYS F 178 " --> pdb=" O GLU F 174 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ILE F 179 " --> pdb=" O PRO F 175 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLY F 180 " --> pdb=" O TYR F 176 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG F 181 " --> pdb=" O LEU F 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 174 through 181' Processing helix chain 'F' and resid 186 through 188 No H-bonds generated for 'chain 'F' and resid 186 through 188' Processing helix chain 'F' and resid 203 through 212 Processing helix chain 'F' and resid 215 through 222 removed outlier: 4.059A pdb=" N SER F 219 " --> pdb=" O LYS F 215 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS F 220 " --> pdb=" O SER F 216 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS F 221 " --> pdb=" O MET F 217 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASN F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 215 through 222' Processing helix chain 'e' and resid 670 through 676 removed outlier: 4.565A pdb=" N LYS e 674 " --> pdb=" O LYS e 670 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU e 675 " --> pdb=" O ASP e 671 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE e 676 " --> pdb=" O ILE e 672 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 670 through 676' Processing helix chain 'e' and resid 688 through 695 Processing helix chain 'e' and resid 727 through 732 Processing helix chain 'e' and resid 745 through 756 removed outlier: 3.650A pdb=" N LYS e 750 " --> pdb=" O ILE e 746 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS e 756 " --> pdb=" O LYS e 752 " (cutoff:3.500A) Processing helix chain 'e' and resid 770 through 778 Processing helix chain 'e' and resid 807 through 815 Processing helix chain 'E' and resid 29 through 56 removed outlier: 3.914A pdb=" N ALA E 36 " --> pdb=" O ALA E 32 " (cutoff:3.500A) Proline residue: E 44 - end of helix removed outlier: 3.752A pdb=" N LYS E 50 " --> pdb=" O SER E 46 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP E 51 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 72 removed outlier: 4.347A pdb=" N LYS E 70 " --> pdb=" O HIS E 66 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE E 71 " --> pdb=" O LYS E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 93 removed outlier: 3.540A pdb=" N MET E 83 " --> pdb=" O ARG E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 118 removed outlier: 3.648A pdb=" N GLU E 108 " --> pdb=" O LYS E 104 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE E 109 " --> pdb=" O ALA E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 145 removed outlier: 3.599A pdb=" N ASN E 138 " --> pdb=" O HIS E 134 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN E 142 " --> pdb=" O ASN E 138 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA E 145 " --> pdb=" O ARG E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 164 removed outlier: 3.734A pdb=" N GLN E 161 " --> pdb=" O ALA E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 169 No H-bonds generated for 'chain 'E' and resid 167 through 169' Processing helix chain 'E' and resid 174 through 181 removed outlier: 3.600A pdb=" N LYS E 178 " --> pdb=" O GLU E 174 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE E 179 " --> pdb=" O PRO E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 188 No H-bonds generated for 'chain 'E' and resid 186 through 188' Processing helix chain 'E' and resid 203 through 214 Processing helix chain 'd' and resid 670 through 676 removed outlier: 4.566A pdb=" N LYS d 674 " --> pdb=" O LYS d 670 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU d 675 " --> pdb=" O ASP d 671 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE d 676 " --> pdb=" O ILE d 672 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 670 through 676' Processing helix chain 'd' and resid 688 through 695 Processing helix chain 'd' and resid 727 through 732 Processing helix chain 'd' and resid 745 through 754 removed outlier: 3.652A pdb=" N LYS d 750 " --> pdb=" O ILE d 746 " (cutoff:3.500A) Processing helix chain 'd' and resid 758 through 760 No H-bonds generated for 'chain 'd' and resid 758 through 760' Processing helix chain 'd' and resid 764 through 767 No H-bonds generated for 'chain 'd' and resid 764 through 767' Processing helix chain 'd' and resid 770 through 778 Processing helix chain 'd' and resid 807 through 815 Processing helix chain 'D' and resid 29 through 56 removed outlier: 3.906A pdb=" N ALA D 36 " --> pdb=" O ALA D 32 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU D 37 " --> pdb=" O ALA D 33 " (cutoff:3.500A) Proline residue: D 44 - end of helix removed outlier: 3.601A pdb=" N LYS D 50 " --> pdb=" O SER D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 72 removed outlier: 4.173A pdb=" N LYS D 70 " --> pdb=" O HIS D 66 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N PHE D 71 " --> pdb=" O LYS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 92 removed outlier: 3.759A pdb=" N ARG D 79 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TRP D 80 " --> pdb=" O LYS D 76 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N MET D 83 " --> pdb=" O ARG D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 118 removed outlier: 3.584A pdb=" N GLU D 108 " --> pdb=" O LYS D 104 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE D 109 " --> pdb=" O ALA D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 147 removed outlier: 3.654A pdb=" N ASN D 138 " --> pdb=" O HIS D 134 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA D 145 " --> pdb=" O ARG D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 165 removed outlier: 3.514A pdb=" N GLN D 161 " --> pdb=" O ALA D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 170 removed outlier: 3.754A pdb=" N PHE D 170 " --> pdb=" O ILE D 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 167 through 170' Processing helix chain 'D' and resid 176 through 181 removed outlier: 3.720A pdb=" N GLY D 180 " --> pdb=" O TYR D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 220 removed outlier: 3.926A pdb=" N SER D 216 " --> pdb=" O GLU D 212 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LYS D 220 " --> pdb=" O SER D 216 " (cutoff:3.500A) Processing helix chain 'c' and resid 670 through 676 removed outlier: 4.567A pdb=" N LYS c 674 " --> pdb=" O LYS c 670 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU c 675 " --> pdb=" O ASP c 671 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE c 676 " --> pdb=" O ILE c 672 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 670 through 676' Processing helix chain 'c' and resid 688 through 695 Processing helix chain 'c' and resid 727 through 732 Processing helix chain 'c' and resid 745 through 754 removed outlier: 3.650A pdb=" N LYS c 750 " --> pdb=" O ILE c 746 " (cutoff:3.500A) Processing helix chain 'c' and resid 762 through 765 No H-bonds generated for 'chain 'c' and resid 762 through 765' Processing helix chain 'c' and resid 768 through 778 removed outlier: 3.784A pdb=" N LYS c 772 " --> pdb=" O TYR c 768 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN c 773 " --> pdb=" O ASP c 769 " (cutoff:3.500A) Processing helix chain 'c' and resid 807 through 815 Processing helix chain 'C' and resid 29 through 56 removed outlier: 3.894A pdb=" N ALA C 36 " --> pdb=" O ALA C 32 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU C 37 " --> pdb=" O ALA C 33 " (cutoff:3.500A) Proline residue: C 44 - end of helix removed outlier: 3.640A pdb=" N LYS C 50 " --> pdb=" O SER C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 72 removed outlier: 4.173A pdb=" N LYS C 70 " --> pdb=" O HIS C 66 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N PHE C 71 " --> pdb=" O LYS C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 92 removed outlier: 3.752A pdb=" N ARG C 79 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TRP C 80 " --> pdb=" O LYS C 76 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET C 83 " --> pdb=" O ARG C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 120 removed outlier: 3.616A pdb=" N GLU C 108 " --> pdb=" O LYS C 104 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE C 109 " --> pdb=" O ALA C 105 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN C 119 " --> pdb=" O ILE C 115 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASN C 120 " --> pdb=" O ALA C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 147 removed outlier: 3.684A pdb=" N ASN C 138 " --> pdb=" O HIS C 134 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA C 145 " --> pdb=" O ARG C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 165 removed outlier: 3.537A pdb=" N GLN C 161 " --> pdb=" O ALA C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 170 removed outlier: 3.776A pdb=" N PHE C 170 " --> pdb=" O ILE C 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 167 through 170' Processing helix chain 'C' and resid 177 through 181 Processing helix chain 'C' and resid 203 through 220 removed outlier: 3.550A pdb=" N MET C 210 " --> pdb=" O LEU C 206 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU C 211 " --> pdb=" O SER C 207 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N SER C 216 " --> pdb=" O GLU C 212 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET C 217 " --> pdb=" O LYS C 213 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N SER C 219 " --> pdb=" O LYS C 215 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS C 220 " --> pdb=" O SER C 216 " (cutoff:3.500A) Processing helix chain 'b' and resid 670 through 676 removed outlier: 4.567A pdb=" N LYS b 674 " --> pdb=" O LYS b 670 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LEU b 675 " --> pdb=" O ASP b 671 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE b 676 " --> pdb=" O ILE b 672 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 670 through 676' Processing helix chain 'b' and resid 688 through 695 Processing helix chain 'b' and resid 727 through 732 Processing helix chain 'b' and resid 745 through 756 removed outlier: 3.650A pdb=" N LYS b 750 " --> pdb=" O ILE b 746 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LYS b 756 " --> pdb=" O LYS b 752 " (cutoff:3.500A) Processing helix chain 'b' and resid 763 through 778 removed outlier: 4.084A pdb=" N PHE b 767 " --> pdb=" O ASP b 763 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ASP b 769 " --> pdb=" O ASP b 765 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N ALA b 770 " --> pdb=" O GLY b 766 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN b 773 " --> pdb=" O ASP b 769 " (cutoff:3.500A) Processing helix chain 'b' and resid 807 through 815 Processing helix chain 'h' and resid 937 through 965 Processing helix chain 'h' and resid 996 through 1003 Processing helix chain 'i' and resid 937 through 963 Processing helix chain 'i' and resid 995 through 1001 Processing helix chain 'j' and resid 939 through 972 Processing helix chain 'j' and resid 996 through 1003 Processing helix chain 'k' and resid 943 through 973 Processing helix chain 'k' and resid 995 through 1003 removed outlier: 3.981A pdb=" N UNK k1002 " --> pdb=" O UNK k 998 " (cutoff:3.500A) Processing helix chain 'l' and resid 937 through 968 Processing helix chain 'l' and resid 996 through 1003 Processing helix chain 'm' and resid 937 through 967 Processing helix chain 'n' and resid -3 through 29 removed outlier: 3.576A pdb=" N UNK n 28 " --> pdb=" O UNK n 24 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain '1' and resid 339 through 343 removed outlier: 3.522A pdb=" N GLY 1 341 " --> pdb=" O PRO 1 231 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR 1 343 " --> pdb=" O LEU 1 233 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLU 1 363 " --> pdb=" O VAL 1 232 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N VAL 1 234 " --> pdb=" O GLU 1 363 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N ILE 1 365 " --> pdb=" O VAL 1 234 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '1' and resid 265 through 268 Processing sheet with id= C, first strand: chain '1' and resid 634 through 636 removed outlier: 6.147A pdb=" N VAL 1 707 " --> pdb=" O ILE 1 748 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N THR 1 750 " --> pdb=" O VAL 1 707 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N PHE 1 709 " --> pdb=" O THR 1 750 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain '2' and resid 230 through 235 removed outlier: 6.365A pdb=" N LEU 2 339 " --> pdb=" O PRO 2 231 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N LEU 2 233 " --> pdb=" O LEU 2 339 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N GLY 2 341 " --> pdb=" O LEU 2 233 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N GLY 2 235 " --> pdb=" O GLY 2 341 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N THR 2 343 " --> pdb=" O GLY 2 235 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain '2' and resid 265 through 268 Processing sheet with id= F, first strand: chain '2' and resid 748 through 750 removed outlier: 6.395A pdb=" N PHE 2 634 " --> pdb=" O MET 2 749 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LYS 2 803 " --> pdb=" O LEU 2 635 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N LEU 2 637 " --> pdb=" O LYS 2 803 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLY 2 805 " --> pdb=" O LEU 2 637 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain '2' and resid 837 through 839 removed outlier: 6.177A pdb=" N VAL 2 888 " --> pdb=" O SER 2 838 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain '3' and resid 339 through 344 removed outlier: 6.166A pdb=" N GLU 3 363 " --> pdb=" O VAL 3 232 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL 3 234 " --> pdb=" O GLU 3 363 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N ILE 3 365 " --> pdb=" O VAL 3 234 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain '3' and resid 265 through 267 removed outlier: 3.738A pdb=" N ILE 3 267 " --> pdb=" O ILE 3 303 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain '3' and resid 803 through 806 removed outlier: 4.159A pdb=" N LYS 3 803 " --> pdb=" O THR 3 633 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N PHE 3 634 " --> pdb=" O THR 3 745 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE 3 747 " --> pdb=" O PHE 3 634 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N PHE 3 636 " --> pdb=" O ILE 3 747 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N MET 3 749 " --> pdb=" O PHE 3 636 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N SER 3 705 " --> pdb=" O ILE 3 746 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ILE 3 748 " --> pdb=" O SER 3 705 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N VAL 3 707 " --> pdb=" O ILE 3 748 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N THR 3 750 " --> pdb=" O VAL 3 707 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N PHE 3 709 " --> pdb=" O THR 3 750 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain '3' and resid 837 through 839 removed outlier: 6.099A pdb=" N VAL 3 888 " --> pdb=" O SER 3 838 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain '4' and resid 339 through 343 removed outlier: 6.469A pdb=" N GLU 4 363 " --> pdb=" O VAL 4 232 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL 4 234 " --> pdb=" O GLU 4 363 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ILE 4 365 " --> pdb=" O VAL 4 234 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain '4' and resid 265 through 268 Processing sheet with id= N, first strand: chain '4' and resid 633 through 636 removed outlier: 6.826A pdb=" N ILE 4 747 " --> pdb=" O PHE 4 634 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N PHE 4 636 " --> pdb=" O ILE 4 747 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N MET 4 749 " --> pdb=" O PHE 4 636 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N VAL 4 707 " --> pdb=" O ILE 4 748 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N THR 4 750 " --> pdb=" O VAL 4 707 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N PHE 4 709 " --> pdb=" O THR 4 750 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE 4 663 " --> pdb=" O LEU 4 708 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ASP 4 710 " --> pdb=" O ILE 4 663 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N VAL 4 665 " --> pdb=" O ASP 4 710 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain '4' and resid 837 through 839 removed outlier: 6.075A pdb=" N VAL 4 888 " --> pdb=" O SER 4 838 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain '5' and resid 194 through 196 removed outlier: 3.714A pdb=" N ALA 5 342 " --> pdb=" O VAL 5 306 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N GLU 5 363 " --> pdb=" O VAL 5 232 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N VAL 5 234 " --> pdb=" O GLU 5 363 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N ILE 5 365 " --> pdb=" O VAL 5 234 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain '5' and resid 748 through 750 removed outlier: 6.580A pdb=" N PHE 5 634 " --> pdb=" O MET 5 749 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY 5 805 " --> pdb=" O LEU 5 635 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain '5' and resid 662 through 665 removed outlier: 7.015A pdb=" N VAL 5 706 " --> pdb=" O ILE 5 663 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N VAL 5 665 " --> pdb=" O VAL 5 706 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU 5 708 " --> pdb=" O VAL 5 665 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain '5' and resid 731 through 733 Processing sheet with id= T, first strand: chain '5' and resid 835 through 839 removed outlier: 6.687A pdb=" N MET 5 886 " --> pdb=" O GLN 5 836 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N SER 5 838 " --> pdb=" O MET 5 886 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL 5 888 " --> pdb=" O SER 5 838 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain '6' and resid 364 through 366 removed outlier: 6.915A pdb=" N VAL 6 232 " --> pdb=" O ILE 6 365 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain '6' and resid 265 through 269 removed outlier: 3.970A pdb=" N ILE 6 267 " --> pdb=" O ILE 6 303 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N PHE 6 305 " --> pdb=" O ILE 6 267 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain '6' and resid 633 through 635 removed outlier: 6.555A pdb=" N ILE 6 747 " --> pdb=" O PHE 6 634 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain '6' and resid 836 through 839 Processing sheet with id= Y, first strand: chain 'a' and resid 789 through 793 removed outlier: 3.507A pdb=" N ASN a 796 " --> pdb=" O ILE a 793 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'g' and resid 789 through 793 removed outlier: 3.506A pdb=" N ASN g 796 " --> pdb=" O ILE g 793 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'f' and resid 789 through 793 removed outlier: 3.507A pdb=" N ASN f 796 " --> pdb=" O ILE f 793 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'e' and resid 789 through 793 removed outlier: 3.508A pdb=" N ASN e 796 " --> pdb=" O ILE e 793 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'd' and resid 789 through 793 removed outlier: 3.506A pdb=" N ASN d 796 " --> pdb=" O ILE d 793 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'c' and resid 789 through 793 removed outlier: 3.506A pdb=" N ASN c 796 " --> pdb=" O ILE c 793 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'b' and resid 789 through 793 removed outlier: 3.505A pdb=" N ASN b 796 " --> pdb=" O ILE b 793 " (cutoff:3.500A) 2037 hydrogen bonds defined for protein. 5733 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: 16.41 Time building geometry restraints manager: 20.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.05 - 1.26: 9728 1.26 - 1.46: 20222 1.46 - 1.67: 28136 1.67 - 1.87: 237 1.87 - 2.07: 12 Bond restraints: 58335 Sorted by residual: bond pdb=" N UNK 0 7 " pdb=" CA UNK 0 7 " ideal model delta sigma weight residual 1.458 1.232 0.226 1.90e-02 2.77e+03 1.42e+02 bond pdb=" C UNK 0 9 " pdb=" N UNK 0 10 " ideal model delta sigma weight residual 1.329 1.485 -0.156 1.40e-02 5.10e+03 1.23e+02 bond pdb=" CA UNK 0 7 " pdb=" CB UNK 0 7 " ideal model delta sigma weight residual 1.530 1.334 0.196 2.00e-02 2.50e+03 9.62e+01 bond pdb=" CA UNK j 989 " pdb=" CB UNK j 989 " ideal model delta sigma weight residual 1.530 1.337 0.193 2.00e-02 2.50e+03 9.32e+01 bond pdb=" C UNK 0 9 " pdb=" O UNK 0 9 " ideal model delta sigma weight residual 1.232 1.051 0.181 2.00e-02 2.50e+03 8.21e+01 ... (remaining 58330 not shown) Histogram of bond angle deviations from ideal: 93.04 - 101.66: 110 101.66 - 110.27: 13124 110.27 - 118.89: 34694 118.89 - 127.50: 30257 127.50 - 136.12: 462 Bond angle restraints: 78647 Sorted by residual: angle pdb=" N GLU a 762 " pdb=" CA GLU a 762 " pdb=" C GLU a 762 " ideal model delta sigma weight residual 112.89 98.46 14.43 1.24e+00 6.50e-01 1.35e+02 angle pdb=" C5 AGS 21001 " pdb=" C4 AGS 21001 " pdb=" N3 AGS 21001 " ideal model delta sigma weight residual 126.80 118.64 8.16 7.41e-01 1.82e+00 1.21e+02 angle pdb=" C5 AGS 11001 " pdb=" C4 AGS 11001 " pdb=" N3 AGS 11001 " ideal model delta sigma weight residual 126.80 118.68 8.12 7.41e-01 1.82e+00 1.20e+02 angle pdb=" N TYR b 768 " pdb=" CA TYR b 768 " pdb=" CB TYR b 768 " ideal model delta sigma weight residual 110.07 125.75 -15.68 1.45e+00 4.76e-01 1.17e+02 angle pdb=" N LYS b 756 " pdb=" CA LYS b 756 " pdb=" C LYS b 756 " ideal model delta sigma weight residual 111.14 122.04 -10.90 1.08e+00 8.57e-01 1.02e+02 ... (remaining 78642 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.55: 35450 34.55 - 69.10: 364 69.10 - 103.64: 18 103.64 - 138.19: 6 138.19 - 172.74: 6 Dihedral angle restraints: 35844 sinusoidal: 14705 harmonic: 21139 Sorted by residual: dihedral pdb=" CA LYS B 221 " pdb=" C LYS B 221 " pdb=" N ASN B 222 " pdb=" CA ASN B 222 " ideal model delta harmonic sigma weight residual -180.00 -121.15 -58.85 0 5.00e+00 4.00e-02 1.39e+02 dihedral pdb=" CA GLN g 760 " pdb=" C GLN g 760 " pdb=" N GLN g 761 " pdb=" CA GLN g 761 " ideal model delta harmonic sigma weight residual -180.00 -121.97 -58.03 0 5.00e+00 4.00e-02 1.35e+02 dihedral pdb=" CA LYS 4 760 " pdb=" C LYS 4 760 " pdb=" N LYS 4 761 " pdb=" CA LYS 4 761 " ideal model delta harmonic sigma weight residual -180.00 -132.36 -47.64 0 5.00e+00 4.00e-02 9.08e+01 ... (remaining 35841 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.181: 8734 0.181 - 0.363: 108 0.363 - 0.544: 19 0.544 - 0.725: 9 0.725 - 0.907: 2 Chirality restraints: 8872 Sorted by residual: chirality pdb=" CA ASP a 763 " pdb=" N ASP a 763 " pdb=" C ASP a 763 " pdb=" CB ASP a 763 " both_signs ideal model delta sigma weight residual False 2.51 1.60 0.91 2.00e-01 2.50e+01 2.06e+01 chirality pdb=" CA UNK 0 7 " pdb=" N UNK 0 7 " pdb=" C UNK 0 7 " pdb=" CB UNK 0 7 " both_signs ideal model delta sigma weight residual False 2.52 1.68 0.84 2.00e-01 2.50e+01 1.78e+01 chirality pdb=" CA PHE b 767 " pdb=" N PHE b 767 " pdb=" C PHE b 767 " pdb=" CB PHE b 767 " both_signs ideal model delta sigma weight residual False 2.51 1.81 0.70 2.00e-01 2.50e+01 1.22e+01 ... (remaining 8869 not shown) Planarity restraints: 9930 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU f 755 " 0.029 2.00e-02 2.50e+03 5.82e-02 3.39e+01 pdb=" C GLU f 755 " -0.101 2.00e-02 2.50e+03 pdb=" O GLU f 755 " 0.038 2.00e-02 2.50e+03 pdb=" N LYS f 756 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN 1 752 " -0.025 2.00e-02 2.50e+03 5.00e-02 2.50e+01 pdb=" C ASN 1 752 " 0.086 2.00e-02 2.50e+03 pdb=" O ASN 1 752 " -0.033 2.00e-02 2.50e+03 pdb=" N LEU 1 753 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN g 761 " 0.025 2.00e-02 2.50e+03 4.97e-02 2.47e+01 pdb=" C GLN g 761 " -0.086 2.00e-02 2.50e+03 pdb=" O GLN g 761 " 0.032 2.00e-02 2.50e+03 pdb=" N GLU g 762 " 0.029 2.00e-02 2.50e+03 ... (remaining 9927 not shown) Histogram of nonbonded interaction distances: 1.06 - 1.83: 31 1.83 - 2.60: 703 2.60 - 3.37: 75204 3.37 - 4.13: 134800 4.13 - 4.90: 248032 Nonbonded interactions: 458770 Sorted by model distance: nonbonded pdb=" OE1 GLU C 211 " pdb=" NZ LYS b 775 " model vdw 1.063 2.520 nonbonded pdb=" NZ LYS f 753 " pdb=" NZ LYS f 757 " model vdw 1.065 3.200 nonbonded pdb=" NH2 ARG 4 776 " pdb=" OH TYR d 803 " model vdw 1.147 2.520 nonbonded pdb=" O LYS c 757 " pdb=" OE1 GLU c 758 " model vdw 1.159 3.040 nonbonded pdb=" OE2 GLU B 211 " pdb=" NZ LYS a 775 " model vdw 1.209 2.520 ... (remaining 458765 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain '1' and (resid 187 through 519 or resid 527 through 904 or resid 1001)) selection = (chain '2' and (resid 187 through 519 or resid 527 through 904 or resid 1001)) selection = (chain '3' and (resid 187 through 519 or resid 527 through 904 or resid 1001)) selection = (chain '4' and (resid 187 through 519 or resid 527 through 904 or resid 1001)) selection = chain '5' selection = (chain '6' and (resid 187 through 519 or resid 527 through 904 or resid 1001)) } ncs_group { reference = chain 'A' selection = (chain 'B' and resid 27 through 215) selection = (chain 'C' and resid 27 through 215) selection = (chain 'D' and resid 27 through 215) selection = (chain 'E' and resid 27 through 215) selection = (chain 'F' and resid 27 through 215) selection = (chain 'G' and resid 27 through 215) } 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 940 through 1004) selection = chain 'i' selection = (chain 'j' and resid 945 through 1004) selection = (chain 'k' and resid 954 through 1004) selection = (chain 'l' and resid 947 through 1004) } ncs_group { reference = chain 'm' selection = (chain 'n' and resid -2 through 30) } 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: 4.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 23.880 Check model and map are aligned: 0.650 Set scattering table: 0.390 Process input model: 108.320 Find NCS groups from input model: 3.560 Set up NCS constraints: 0.370 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 144.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 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 : 0.008 0.226 58335 Z= 0.493 Angle : 1.162 19.007 78647 Z= 0.679 Chirality : 0.067 0.907 8872 Planarity : 0.007 0.080 9930 Dihedral : 10.727 172.738 22157 Min Nonbonded Distance : 1.063 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.80 % Favored : 93.76 % Rotamer Outliers : 1.07 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.47 % 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: -4.45 (0.08), residues: 6781 helix: -3.89 (0.05), residues: 3325 sheet: -2.56 (0.20), residues: 451 loop : -1.63 (0.10), residues: 3005 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13562 Ramachandran restraints generated. 6781 Oldfield, 0 Emsley, 6781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13562 Ramachandran restraints generated. 6781 Oldfield, 0 Emsley, 6781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2173 residues out of total 6172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 2107 time to evaluate : 5.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 16 residues processed: 2158 average time/residue: 0.5983 time to fit residues: 2081.9017 Evaluate side-chains 918 residues out of total 6172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 902 time to evaluate : 5.406 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.4356 time to fit residues: 20.0837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 699 random chunks: chunk 590 optimal weight: 0.8980 chunk 529 optimal weight: 1.9990 chunk 293 optimal weight: 5.9990 chunk 180 optimal weight: 0.6980 chunk 357 optimal weight: 3.9990 chunk 283 optimal weight: 7.9990 chunk 547 optimal weight: 1.9990 chunk 212 optimal weight: 6.9990 chunk 333 optimal weight: 1.9990 chunk 407 optimal weight: 3.9990 chunk 634 optimal weight: 5.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 388 ASN 1 433 GLN 1 509 ASN 1 531 ASN 1 556 HIS 1 557 ASN 1 752 ASN 1 834 ASN 2 207 GLN 2 300 ASN 2 310 HIS 2 431 GLN 2 517 ASN 2 606 ASN 2 661 ASN 2 704 HIS ** 2 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 816 HIS ** 2 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 893 ASN 3 262 GLN ** 3 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 424 ASN 3 560 ASN ** 3 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 568 HIS 3 661 ASN 3 893 ASN 4 196 ASN 4 560 ASN 4 566 GLN 4 657 ASN 4 704 HIS 4 725 GLN 4 768 ASN 4 834 ASN 4 893 ASN 5 560 ASN 5 566 GLN 5 606 ASN 5 704 HIS 5 736 HIS 6 198 ASN ** 6 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 433 GLN ** 6 704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 ASN B 66 HIS ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 HIS B 205 HIS a 717 ASN a 783 ASN A 55 HIS A 112 GLN A 188 HIS ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 717 ASN ** g 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 787 HIS ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 HIS ** G 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 188 HIS f 717 ASN f 724 ASN f 733 GLN F 55 HIS ** F 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 123 ASN ** F 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 717 ASN ** e 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 791 GLN E 123 ASN E 134 HIS E 188 HIS E 196 GLN d 717 ASN ** d 738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 HIS D 134 HIS D 188 HIS c 717 ASN ** c 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 HIS C 188 HIS b 717 ASN b 724 ASN b 783 ASN b 787 HIS Total number of N/Q/H flips: 75 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.076 58335 Z= 0.287 Angle : 0.738 10.315 78647 Z= 0.388 Chirality : 0.046 0.259 8872 Planarity : 0.005 0.064 9930 Dihedral : 8.963 163.289 7838 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.21 % Favored : 94.53 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: -2.70 (0.09), residues: 6781 helix: -1.98 (0.07), residues: 3446 sheet: -2.33 (0.21), residues: 466 loop : -1.19 (0.11), residues: 2869 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13562 Ramachandran restraints generated. 6781 Oldfield, 0 Emsley, 6781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13562 Ramachandran restraints generated. 6781 Oldfield, 0 Emsley, 6781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1204 residues out of total 6172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 1190 time to evaluate : 5.466 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 outliers start: 14 outliers final: 2 residues processed: 1201 average time/residue: 0.5587 time to fit residues: 1124.4903 Evaluate side-chains 704 residues out of total 6172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 702 time to evaluate : 5.507 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4036 time to fit residues: 8.7809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 699 random chunks: chunk 352 optimal weight: 1.9990 chunk 197 optimal weight: 1.9990 chunk 528 optimal weight: 1.9990 chunk 432 optimal weight: 0.7980 chunk 175 optimal weight: 9.9990 chunk 635 optimal weight: 0.9990 chunk 686 optimal weight: 20.0000 chunk 566 optimal weight: 0.9990 chunk 630 optimal weight: 5.9990 chunk 216 optimal weight: 0.9980 chunk 510 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 433 GLN 2 704 HIS ** 2 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 893 ASN 4 834 ASN 5 236 ASN 6 297 ASN 6 310 HIS 6 606 ASN ** 6 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 ASN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 161 GLN a 733 GLN ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 784 ASN ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 119 ASN ** G 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 724 ASN ** F 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 123 ASN ** F 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 222 ASN d 734 ASN ** d 738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 787 HIS D 134 HIS c 734 ASN c 738 HIS C 123 ASN b 724 ASN b 761 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.4392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 58335 Z= 0.212 Angle : 0.643 9.854 78647 Z= 0.335 Chirality : 0.043 0.200 8872 Planarity : 0.004 0.100 9930 Dihedral : 8.626 163.518 7838 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.50 % Favored : 94.28 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.89 (0.10), residues: 6781 helix: -1.16 (0.08), residues: 3436 sheet: -2.10 (0.22), residues: 464 loop : -1.00 (0.12), residues: 2881 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13562 Ramachandran restraints generated. 6781 Oldfield, 0 Emsley, 6781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13562 Ramachandran restraints generated. 6781 Oldfield, 0 Emsley, 6781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1044 residues out of total 6172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1037 time to evaluate : 5.445 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 outliers start: 7 outliers final: 0 residues processed: 1042 average time/residue: 0.5406 time to fit residues: 960.8949 Evaluate side-chains 648 residues out of total 6172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 648 time to evaluate : 5.481 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.3587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 699 random chunks: chunk 628 optimal weight: 2.9990 chunk 478 optimal weight: 6.9990 chunk 330 optimal weight: 3.9990 chunk 70 optimal weight: 10.0000 chunk 303 optimal weight: 6.9990 chunk 427 optimal weight: 6.9990 chunk 638 optimal weight: 0.9980 chunk 675 optimal weight: 10.0000 chunk 333 optimal weight: 5.9990 chunk 604 optimal weight: 0.9990 chunk 182 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 433 GLN ** 1 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 704 HIS ** 2 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 893 ASN 4 198 ASN 4 270 ASN 4 310 HIS 4 393 ASN ** 4 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 736 HIS 5 236 ASN 5 290 ASN 5 297 ASN 5 310 HIS 5 326 ASN 5 560 ASN 5 736 HIS 6 203 ASN 6 388 ASN 6 424 ASN ** 6 704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 816 HIS ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 733 GLN ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 717 ASN g 784 ASN G 55 HIS ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 119 ASN ** G 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 724 ASN ** F 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 196 GLN ** F 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 776 ASN e 783 ASN e 791 GLN E 196 GLN ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 HIS D 161 GLN c 738 HIS b 724 ASN b 734 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.5127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.077 58335 Z= 0.350 Angle : 0.731 9.717 78647 Z= 0.379 Chirality : 0.045 0.414 8872 Planarity : 0.005 0.064 9930 Dihedral : 8.640 161.643 7838 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.36 % Favored : 93.42 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.48 (0.10), residues: 6781 helix: -0.73 (0.08), residues: 3484 sheet: -2.03 (0.21), residues: 484 loop : -0.89 (0.12), residues: 2813 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13562 Ramachandran restraints generated. 6781 Oldfield, 0 Emsley, 6781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13562 Ramachandran restraints generated. 6781 Oldfield, 0 Emsley, 6781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 898 residues out of total 6172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 891 time to evaluate : 6.431 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 outliers start: 7 outliers final: 1 residues processed: 897 average time/residue: 0.5386 time to fit residues: 831.2776 Evaluate side-chains 584 residues out of total 6172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 583 time to evaluate : 5.448 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4067 time to fit residues: 8.1397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 699 random chunks: chunk 562 optimal weight: 4.9990 chunk 383 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 503 optimal weight: 2.9990 chunk 278 optimal weight: 0.9980 chunk 576 optimal weight: 3.9990 chunk 467 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 345 optimal weight: 0.9980 chunk 606 optimal weight: 1.9990 chunk 170 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 310 HIS ** 1 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 560 ASN ** 1 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 207 GLN 2 704 HIS ** 2 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 893 ASN 4 560 ASN 4 736 HIS 4 799 ASN 5 236 ASN ** 5 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 431 GLN 5 560 ASN 5 674 HIS ** 6 704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 134 HIS a 734 ASN ** a 787 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 HIS ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 724 ASN ** F 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 738 HIS b 724 ASN ** b 751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 761 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.5378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.073 58335 Z= 0.209 Angle : 0.627 9.823 78647 Z= 0.324 Chirality : 0.043 0.354 8872 Planarity : 0.004 0.059 9930 Dihedral : 8.475 155.847 7838 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.90 % Favored : 93.88 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.20 (0.10), residues: 6781 helix: -0.49 (0.08), residues: 3512 sheet: -1.82 (0.22), residues: 484 loop : -0.81 (0.12), residues: 2785 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13562 Ramachandran restraints generated. 6781 Oldfield, 0 Emsley, 6781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13562 Ramachandran restraints generated. 6781 Oldfield, 0 Emsley, 6781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 898 residues out of total 6172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 894 time to evaluate : 5.741 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 outliers start: 4 outliers final: 2 residues processed: 896 average time/residue: 0.5361 time to fit residues: 831.1467 Evaluate side-chains 609 residues out of total 6172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 607 time to evaluate : 5.524 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4379 time to fit residues: 8.9791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 699 random chunks: chunk 227 optimal weight: 0.0370 chunk 608 optimal weight: 0.7980 chunk 133 optimal weight: 5.9990 chunk 396 optimal weight: 0.2980 chunk 166 optimal weight: 1.9990 chunk 676 optimal weight: 9.9990 chunk 561 optimal weight: 2.9990 chunk 313 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 223 optimal weight: 3.9990 chunk 355 optimal weight: 7.9990 overall best weight: 1.2262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 229 ASN 1 310 HIS ** 1 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 560 ASN ** 1 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 704 HIS ** 2 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 893 ASN 4 560 ASN 5 236 ASN ** 5 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 560 ASN 5 736 HIS 6 270 ASN 6 816 HIS ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 HIS ** a 787 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 724 ASN f 734 ASN ** F 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 791 GLN E 196 GLN E 222 ASN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 HIS ** D 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 738 HIS C 59 ASN b 724 ASN ** b 751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.5612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.073 58335 Z= 0.214 Angle : 0.619 9.186 78647 Z= 0.320 Chirality : 0.044 0.427 8872 Planarity : 0.004 0.057 9930 Dihedral : 8.389 156.516 7838 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.13 % Favored : 93.63 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.05 (0.10), residues: 6781 helix: -0.30 (0.09), residues: 3526 sheet: -1.73 (0.22), residues: 486 loop : -0.82 (0.12), residues: 2769 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13562 Ramachandran restraints generated. 6781 Oldfield, 0 Emsley, 6781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13562 Ramachandran restraints generated. 6781 Oldfield, 0 Emsley, 6781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 872 residues out of total 6172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 870 time to evaluate : 5.456 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 outliers start: 2 outliers final: 1 residues processed: 872 average time/residue: 0.5269 time to fit residues: 799.6275 Evaluate side-chains 597 residues out of total 6172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 596 time to evaluate : 6.601 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4087 time to fit residues: 8.1389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 699 random chunks: chunk 652 optimal weight: 6.9990 chunk 76 optimal weight: 0.0870 chunk 385 optimal weight: 4.9990 chunk 493 optimal weight: 2.9990 chunk 382 optimal weight: 5.9990 chunk 569 optimal weight: 0.9980 chunk 377 optimal weight: 9.9990 chunk 673 optimal weight: 9.9990 chunk 421 optimal weight: 7.9990 chunk 410 optimal weight: 4.9990 chunk 311 optimal weight: 3.9990 overall best weight: 2.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 310 HIS 1 433 GLN ** 1 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 893 ASN ** 3 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 560 ASN ** 4 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 799 ASN 5 236 ASN ** 5 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 768 ASN 5 834 ASN ** 6 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 816 HIS ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 HIS A 134 HIS ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 724 ASN ** f 787 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 119 ASN ** F 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 773 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 ASN ** D 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 738 HIS C 59 ASN C 205 HIS b 700 ASN b 724 ASN b 751 GLN ** b 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.6080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.089 58335 Z= 0.352 Angle : 0.738 10.629 78647 Z= 0.379 Chirality : 0.046 0.412 8872 Planarity : 0.004 0.066 9930 Dihedral : 8.546 157.527 7838 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 18.94 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.27 % Favored : 92.49 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.09 (0.10), residues: 6781 helix: -0.33 (0.09), residues: 3514 sheet: -1.76 (0.22), residues: 473 loop : -0.87 (0.12), residues: 2794 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13562 Ramachandran restraints generated. 6781 Oldfield, 0 Emsley, 6781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13562 Ramachandran restraints generated. 6781 Oldfield, 0 Emsley, 6781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 793 residues out of total 6172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 792 time to evaluate : 6.564 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 outliers start: 1 outliers final: 0 residues processed: 792 average time/residue: 0.5452 time to fit residues: 746.7157 Evaluate side-chains 546 residues out of total 6172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 546 time to evaluate : 5.446 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.3342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 699 random chunks: chunk 416 optimal weight: 6.9990 chunk 269 optimal weight: 3.9990 chunk 402 optimal weight: 3.9990 chunk 202 optimal weight: 0.9980 chunk 132 optimal weight: 0.6980 chunk 130 optimal weight: 0.7980 chunk 428 optimal weight: 0.7980 chunk 459 optimal weight: 0.9980 chunk 333 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 529 optimal weight: 7.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 310 HIS 1 433 GLN ** 1 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 568 HIS ** 1 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 606 ASN 2 744 ASN 2 836 GLN 2 893 ASN ** 3 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 560 ASN 4 736 HIS 5 236 ASN 5 297 ASN 5 310 HIS 5 560 ASN ** 6 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 787 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 HIS ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 724 ASN ** f 787 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 143 ASN E 112 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 ASN D 161 GLN D 196 GLN c 738 HIS C 55 HIS b 724 ASN b 751 GLN b 761 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.6172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.066 58335 Z= 0.187 Angle : 0.634 11.448 78647 Z= 0.325 Chirality : 0.044 0.369 8872 Planarity : 0.004 0.059 9930 Dihedral : 8.431 162.885 7838 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.88 % Favored : 93.89 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.91 (0.10), residues: 6781 helix: -0.17 (0.09), residues: 3520 sheet: -1.59 (0.23), residues: 470 loop : -0.83 (0.12), residues: 2791 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13562 Ramachandran restraints generated. 6781 Oldfield, 0 Emsley, 6781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13562 Ramachandran restraints generated. 6781 Oldfield, 0 Emsley, 6781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 832 residues out of total 6172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 829 time to evaluate : 5.483 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 outliers start: 3 outliers final: 0 residues processed: 830 average time/residue: 0.5217 time to fit residues: 754.6079 Evaluate side-chains 566 residues out of total 6172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 566 time to evaluate : 5.457 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.3184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 699 random chunks: chunk 612 optimal weight: 0.2980 chunk 645 optimal weight: 3.9990 chunk 588 optimal weight: 0.6980 chunk 627 optimal weight: 2.9990 chunk 377 optimal weight: 7.9990 chunk 273 optimal weight: 0.5980 chunk 492 optimal weight: 5.9990 chunk 192 optimal weight: 0.8980 chunk 567 optimal weight: 2.9990 chunk 593 optimal weight: 4.9990 chunk 625 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 310 HIS ** 2 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 744 ASN ** 2 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 893 ASN ** 3 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 560 ASN 5 310 HIS 5 736 HIS ** 6 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS ** a 787 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 724 ASN ** f 787 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 791 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN b 751 GLN b 761 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.6313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.067 58335 Z= 0.196 Angle : 0.641 16.716 78647 Z= 0.327 Chirality : 0.044 0.410 8872 Planarity : 0.004 0.057 9930 Dihedral : 8.329 163.871 7838 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.41 % Favored : 93.38 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.10), residues: 6781 helix: -0.03 (0.09), residues: 3495 sheet: -1.50 (0.23), residues: 460 loop : -0.78 (0.12), residues: 2826 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13562 Ramachandran restraints generated. 6781 Oldfield, 0 Emsley, 6781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13562 Ramachandran restraints generated. 6781 Oldfield, 0 Emsley, 6781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 814 residues out of total 6172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 812 time to evaluate : 5.619 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 outliers start: 2 outliers final: 0 residues processed: 812 average time/residue: 0.5286 time to fit residues: 750.8356 Evaluate side-chains 578 residues out of total 6172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 578 time to evaluate : 5.427 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.2529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 699 random chunks: chunk 412 optimal weight: 0.7980 chunk 663 optimal weight: 3.9990 chunk 405 optimal weight: 6.9990 chunk 314 optimal weight: 0.9980 chunk 461 optimal weight: 9.9990 chunk 696 optimal weight: 10.0000 chunk 640 optimal weight: 1.9990 chunk 554 optimal weight: 0.9990 chunk 57 optimal weight: 0.0270 chunk 428 optimal weight: 2.9990 chunk 340 optimal weight: 0.8980 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 744 ASN 2 836 GLN 2 893 ASN ** 4 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 560 ASN 5 836 GLN ** 6 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 270 ASN ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 787 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 HIS ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 724 ASN ** f 787 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 HIS b 751 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.6421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.066 58335 Z= 0.183 Angle : 0.631 10.582 78647 Z= 0.322 Chirality : 0.044 0.329 8872 Planarity : 0.004 0.058 9930 Dihedral : 8.268 166.218 7838 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.06 % Favored : 93.73 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.71 (0.10), residues: 6781 helix: 0.04 (0.09), residues: 3485 sheet: -1.45 (0.23), residues: 454 loop : -0.80 (0.12), residues: 2842 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13562 Ramachandran restraints generated. 6781 Oldfield, 0 Emsley, 6781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13562 Ramachandran restraints generated. 6781 Oldfield, 0 Emsley, 6781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 827 residues out of total 6172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 824 time to evaluate : 5.537 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 outliers start: 3 outliers final: 0 residues processed: 825 average time/residue: 0.5294 time to fit residues: 766.7824 Evaluate side-chains 577 residues out of total 6172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 577 time to evaluate : 5.417 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.2539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 699 random chunks: chunk 440 optimal weight: 2.9990 chunk 590 optimal weight: 3.9990 chunk 169 optimal weight: 0.0970 chunk 511 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 154 optimal weight: 4.9990 chunk 555 optimal weight: 3.9990 chunk 232 optimal weight: 2.9990 chunk 570 optimal weight: 5.9990 chunk 70 optimal weight: 0.5980 chunk 102 optimal weight: 5.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 530 GLN 2 744 ASN ** 2 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 893 ASN ** 3 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 560 ASN 5 297 ASN ** 5 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 560 ASN 5 834 ASN 5 836 GLN ** 6 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 787 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 HIS ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 724 ASN ** f 787 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 HIS c 738 HIS b 751 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.077126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.062391 restraints weight = 252823.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.063960 restraints weight = 159620.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.064542 restraints weight = 103272.580| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.6659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.072 58335 Z= 0.305 Angle : 0.704 11.510 78647 Z= 0.360 Chirality : 0.045 0.380 8872 Planarity : 0.004 0.060 9930 Dihedral : 8.340 165.646 7838 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 18.20 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.34 % Favored : 92.43 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.10), residues: 6781 helix: -0.05 (0.09), residues: 3498 sheet: -1.55 (0.23), residues: 474 loop : -0.88 (0.12), residues: 2809 =============================================================================== Job complete usr+sys time: 13697.21 seconds wall clock time: 243 minutes 16.35 seconds (14596.35 seconds total)