Starting phenix.real_space_refine on Mon Mar 11 12:26:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e11_8952/03_2024/6e11_8952_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e11_8952/03_2024/6e11_8952.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e11_8952/03_2024/6e11_8952.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e11_8952/03_2024/6e11_8952.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e11_8952/03_2024/6e11_8952_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e11_8952/03_2024/6e11_8952_updated.pdb" } resolution = 4.23 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 36 5.49 5 S 151 5.16 5 C 36554 2.51 5 N 9632 2.21 5 O 11028 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "2 TYR 774": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 319": "OE1" <-> "OE2" Residue "5 TYR 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 764": "OD1" <-> "OD2" Residue "B PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 211": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 57401 Number of models: 1 Model: "" Number of chains: 34 Chain: "i" Number of atoms: 230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 230 Classifications: {'peptide': 46} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'TRANS': 45} Chain breaks: 1 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'UNK:plan-1': 46} Unresolved non-hydrogen planarities: 46 Chain: "j" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 275 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'TRANS': 54} Chain breaks: 1 Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'UNK:plan-1': 55} Unresolved non-hydrogen planarities: 55 Chain: "k" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 300 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'TRANS': 59} Chain breaks: 1 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 180 Unresolved non-hydrogen dihedrals: 60 Planarities with less than four sites: {'UNK:plan-1': 60} Unresolved non-hydrogen planarities: 60 Chain: "1" Number of atoms: 5752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 717, 5752 Classifications: {'peptide': 717} Link IDs: {'PTRANS': 22, 'TRANS': 694} Chain: "2" Number of atoms: 5752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 717, 5752 Classifications: {'peptide': 717} Link IDs: {'PTRANS': 22, 'TRANS': 694} Chain: "3" Number of atoms: 5752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 717, 5752 Classifications: {'peptide': 717} Link IDs: {'PTRANS': 22, 'TRANS': 694} Chain: "4" Number of atoms: 5752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 717, 5752 Classifications: {'peptide': 717} Link IDs: {'PTRANS': 22, 'TRANS': 694} Chain: "5" Number of atoms: 5744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 716, 5744 Classifications: {'peptide': 716} Link IDs: {'PTRANS': 22, 'TRANS': 693} Chain: "C" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1715 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain: "6" Number of atoms: 5744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 716, 5744 Classifications: {'peptide': 716} Link IDs: {'PTRANS': 22, 'TRANS': 693} Chain: "D" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1715 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain: "0" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 30 Classifications: {'peptide': 6} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'TRANS': 5} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'UNK:plan-1': 6} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1724 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 8, 'TRANS': 201} Chain: "d" Number of atoms: 1286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1286 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain breaks: 1 Chain: "c" Number of atoms: 1286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1286 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain breaks: 1 Chain: "b" Number of atoms: 1286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1286 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain breaks: 1 Chain: "B" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1715 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain: "a" Number of atoms: 1286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1286 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain breaks: 1 Chain: "A" Number of atoms: 1571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1571 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 8, 'TRANS': 182} Chain: "g" Number of atoms: 1286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1286 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain breaks: 1 Chain: "G" Number of atoms: 1571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1571 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 8, 'TRANS': 182} Chain: "f" Number of atoms: 1286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1286 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain breaks: 1 Chain: "F" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1715 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain: "e" Number of atoms: 1286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1286 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain breaks: 1 Chain: "n" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 180 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'TRANS': 35} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'UNK:plan-1': 36} Unresolved non-hydrogen planarities: 36 Chain: "h" Number of atoms: 235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 235 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'TRANS': 46} Chain breaks: 1 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'UNK:plan-1': 47} Unresolved non-hydrogen planarities: 47 Chain: "l" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 265 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'TRANS': 52} Chain breaks: 1 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 159 Unresolved non-hydrogen dihedrals: 53 Planarities with less than four sites: {'UNK:plan-1': 53} Unresolved non-hydrogen planarities: 53 Chain: "m" Number of atoms: 290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 290 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'TRANS': 57} Chain breaks: 1 Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 174 Unresolved non-hydrogen dihedrals: 58 Planarities with less than four sites: {'UNK:plan-1': 58} Unresolved non-hydrogen planarities: 58 Chain: "1" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 93 Unusual residues: {'AGS': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "2" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "5" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "6" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 23.14, per 1000 atoms: 0.40 Number of scatterers: 57401 At special positions: 0 Unit cell: (196.56, 187.2, 192.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 151 16.00 P 36 15.00 O 11028 8.00 N 9632 7.00 C 36554 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 140 " distance=2.03 Simple disulfide: pdb=" SG CYS D 113 " - pdb=" SG CYS D 140 " distance=2.03 Simple disulfide: pdb=" SG CYS E 113 " - pdb=" SG CYS E 140 " distance=2.03 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 140 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 140 " distance=2.03 Simple disulfide: pdb=" SG CYS G 113 " - pdb=" SG CYS G 140 " distance=2.03 Simple disulfide: pdb=" SG CYS F 113 " - pdb=" SG CYS F 140 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM57114 O3A AGS 11003 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=11, symmetry=0 Number of additional bonds: simple=11, symmetry=0 Coordination: Other bonds: Time building additional restraints: 18.40 Conformation dependent library (CDL) restraints added in 7.2 seconds 13546 Ramachandran restraints generated. 6773 Oldfield, 0 Emsley, 6773 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13690 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 325 helices and 19 sheets defined 54.2% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.55 Creating SS restraints... Processing helix chain 'i' and resid 2 through 28 Processing helix chain 'i' and resid 996 through 1003 removed outlier: 3.884A pdb=" N UNK i1003 " --> pdb=" O UNK i 999 " (cutoff:3.500A) Processing helix chain 'j' and resid 2 through 31 Processing helix chain 'j' and resid 995 through 1002 Processing helix chain 'k' and resid 0 through 32 Processing helix chain 'k' and resid 995 through 1003 Processing helix chain '1' and resid 198 through 202 Processing helix chain '1' and resid 213 through 223 removed outlier: 3.537A pdb=" N ARG 1 217 " --> pdb=" O ASP 1 213 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA 1 218 " --> pdb=" O GLU 1 214 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER 1 222 " --> pdb=" O ALA 1 218 " (cutoff:3.500A) Processing helix chain '1' and resid 242 through 253 removed outlier: 3.512A pdb=" N VAL 1 249 " --> pdb=" O VAL 1 245 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TYR 1 250 " --> pdb=" O GLU 1 246 " (cutoff:3.500A) 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 271 through 275 removed outlier: 3.691A pdb=" N PHE 1 274 " --> pdb=" O PHE 1 271 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR 1 275 " --> pdb=" O ARG 1 272 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 271 through 275' Processing helix chain '1' and resid 281 through 283 No H-bonds generated for 'chain '1' and resid 281 through 283' Processing helix chain '1' and resid 285 through 296 removed outlier: 3.959A pdb=" N GLU 1 294 " --> pdb=" O ASN 1 290 " (cutoff:3.500A) Processing helix chain '1' and resid 309 through 311 No H-bonds generated for 'chain '1' and resid 309 through 311' Processing helix chain '1' and resid 345 through 354 removed outlier: 4.327A pdb=" N LYS 1 350 " --> pdb=" O ALA 1 346 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N PHE 1 351 " --> pdb=" O GLU 1 347 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE 1 352 " --> pdb=" O TYR 1 348 " (cutoff:3.500A) Processing helix chain '1' and resid 373 through 389 removed outlier: 3.676A pdb=" N LYS 1 377 " --> pdb=" O ASP 1 373 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N SER 1 384 " --> pdb=" O ARG 1 380 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N LYS 1 385 " --> pdb=" O SER 1 381 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR 1 386 " --> pdb=" O LEU 1 382 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU 1 387 " --> pdb=" O LYS 1 383 " (cutoff:3.500A) Processing helix chain '1' and resid 396 through 409 removed outlier: 3.860A pdb=" N VAL 1 400 " --> pdb=" O ASP 1 396 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA 1 403 " --> pdb=" O LEU 1 399 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE 1 405 " --> pdb=" O ALA 1 401 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N SER 1 406 " --> pdb=" O ALA 1 402 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG 1 408 " --> pdb=" O LYS 1 404 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE 1 409 " --> pdb=" O ILE 1 405 " (cutoff:3.500A) Processing helix chain '1' and resid 415 through 434 removed outlier: 3.728A pdb=" N LEU 1 422 " --> pdb=" O LYS 1 418 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LEU 1 423 " --> pdb=" O ALA 1 419 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N SER 1 428 " --> pdb=" O ASN 1 424 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE 1 429 " --> pdb=" O LYS 1 425 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N VAL 1 432 " --> pdb=" O SER 1 428 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN 1 433 " --> pdb=" O PHE 1 429 " (cutoff:3.500A) Processing helix chain '1' and resid 439 through 454 removed outlier: 3.906A pdb=" N ASP 1 447 " --> pdb=" O VAL 1 443 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ILE 1 448 " --> pdb=" O THR 1 444 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLU 1 449 " --> pdb=" O GLU 1 445 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU 1 451 " --> pdb=" O ASP 1 447 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR 1 453 " --> pdb=" O GLU 1 449 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLU 1 454 " --> pdb=" O ARG 1 450 " (cutoff:3.500A) Processing helix chain '1' and resid 465 through 504 removed outlier: 4.331A pdb=" N LEU 1 473 " --> pdb=" O TYR 1 470 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N ILE 1 474 " --> pdb=" O ASN 1 471 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LYS 1 481 " --> pdb=" O GLU 1 478 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLU 1 482 " --> pdb=" O GLU 1 479 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS 1 485 " --> pdb=" O GLU 1 482 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS 1 486 " --> pdb=" O GLN 1 483 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N TYR 1 488 " --> pdb=" O LYS 1 485 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR 1 491 " --> pdb=" O TYR 1 488 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL 1 492 " --> pdb=" O GLU 1 489 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR 1 494 " --> pdb=" O TYR 1 491 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS 1 501 " --> pdb=" O LEU 1 498 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LYS 1 502 " --> pdb=" O LYS 1 499 " (cutoff:3.500A) Processing helix chain '1' and resid 506 through 513 removed outlier: 3.814A pdb=" N LYS 1 512 " --> pdb=" O ASN 1 509 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLU 1 513 " --> pdb=" O ASP 1 510 " (cutoff:3.500A) Processing helix chain '1' and resid 531 through 540 Processing helix chain '1' and resid 543 through 549 removed outlier: 3.539A pdb=" N THR 1 547 " --> pdb=" O LEU 1 543 " (cutoff:3.500A) Processing helix chain '1' and resid 551 through 553 No H-bonds generated for 'chain '1' and resid 551 through 553' Processing helix chain '1' and resid 566 through 576 removed outlier: 3.679A pdb=" N ILE 1 572 " --> pdb=" O HIS 1 568 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR 1 573 " --> pdb=" O VAL 1 569 " (cutoff:3.500A) Processing helix chain '1' and resid 591 through 601 removed outlier: 4.372A pdb=" N TYR 1 596 " --> pdb=" O ALA 1 592 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ASN 1 597 " --> pdb=" O LEU 1 593 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER 1 598 " --> pdb=" O LYS 1 594 " (cutoff:3.500A) Processing helix chain '1' and resid 607 through 620 removed outlier: 3.643A pdb=" N SER 1 612 " --> pdb=" O ASP 1 608 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL 1 617 " --> pdb=" O LEU 1 613 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL 1 618 " --> pdb=" O SER 1 614 " (cutoff:3.500A) Processing helix chain '1' and resid 646 through 653 removed outlier: 3.826A pdb=" N ALA 1 652 " --> pdb=" O ALA 1 648 " (cutoff:3.500A) Processing helix chain '1' and resid 667 through 669 No H-bonds generated for 'chain '1' and resid 667 through 669' Processing helix chain '1' and resid 674 through 680 removed outlier: 3.856A pdb=" N THR 1 680 " --> pdb=" O SER 1 677 " (cutoff:3.500A) Processing helix chain '1' and resid 694 through 701 removed outlier: 3.681A pdb=" N ALA 1 698 " --> pdb=" O GLN 1 694 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL 1 699 " --> pdb=" O LEU 1 695 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG 1 700 " --> pdb=" O THR 1 696 " (cutoff:3.500A) Processing helix chain '1' and resid 712 through 714 No H-bonds generated for 'chain '1' and resid 712 through 714' Processing helix chain '1' and resid 720 through 726 removed outlier: 3.512A pdb=" N LEU 1 724 " --> pdb=" O PHE 1 720 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N GLN 1 725 " --> pdb=" O LYS 1 721 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE 1 726 " --> pdb=" O VAL 1 722 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 720 through 726' Processing helix chain '1' and resid 766 through 768 No H-bonds generated for 'chain '1' and resid 766 through 768' Processing helix chain '1' and resid 774 through 791 removed outlier: 3.552A pdb=" N SER 1 784 " --> pdb=" O ASP 1 780 " (cutoff:3.500A) Processing helix chain '1' and resid 796 through 800 Processing helix chain '1' and resid 812 through 829 removed outlier: 4.220A pdb=" N LYS 1 817 " --> pdb=" O LYS 1 813 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL 1 819 " --> pdb=" O LEU 1 815 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA 1 820 " --> pdb=" O HIS 1 816 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ARG 1 822 " --> pdb=" O ILE 1 818 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE 1 823 " --> pdb=" O VAL 1 819 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS 1 824 " --> pdb=" O ALA 1 820 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU 1 827 " --> pdb=" O PHE 1 823 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LYS 1 828 " --> pdb=" O LYS 1 824 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG 1 829 " --> pdb=" O LYS 1 825 " (cutoff:3.500A) Processing helix chain '1' and resid 841 through 848 removed outlier: 3.969A pdb=" N ASP 1 845 " --> pdb=" O LYS 1 842 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N TYR 1 846 " --> pdb=" O ALA 1 843 " (cutoff:3.500A) Processing helix chain '1' and resid 859 through 868 removed outlier: 3.941A pdb=" N ILE 1 863 " --> pdb=" O ARG 1 859 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL 1 868 " --> pdb=" O PHE 1 864 " (cutoff:3.500A) Processing helix chain '1' and resid 873 through 878 removed outlier: 3.519A pdb=" N LEU 1 878 " --> pdb=" O ALA 1 874 " (cutoff:3.500A) Processing helix chain '2' and resid 198 through 202 Processing helix chain '2' and resid 213 through 223 Processing helix chain '2' and resid 242 through 253 removed outlier: 3.587A pdb=" N VAL 2 249 " --> pdb=" O VAL 2 245 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR 2 250 " --> pdb=" O GLU 2 246 " (cutoff:3.500A) Processing helix chain '2' and resid 259 through 261 No H-bonds generated for 'chain '2' and resid 259 through 261' Processing helix chain '2' and resid 285 through 295 removed outlier: 3.586A pdb=" N GLU 2 294 " --> pdb=" O ASN 2 290 " (cutoff:3.500A) Processing helix chain '2' and resid 309 through 313 Processing helix chain '2' and resid 329 through 333 removed outlier: 3.914A pdb=" N SER 2 333 " --> pdb=" O LYS 2 329 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 329 through 333' Processing helix chain '2' and resid 345 through 352 removed outlier: 4.102A pdb=" N LYS 2 350 " --> pdb=" O ALA 2 346 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N PHE 2 351 " --> pdb=" O GLU 2 347 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE 2 352 " --> pdb=" O TYR 2 348 " (cutoff:3.500A) Processing helix chain '2' and resid 372 through 390 removed outlier: 3.789A pdb=" N VAL 2 376 " --> pdb=" O ASP 2 373 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG 2 380 " --> pdb=" O LYS 2 377 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS 2 383 " --> pdb=" O ARG 2 380 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N SER 2 384 " --> pdb=" O SER 2 381 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU 2 387 " --> pdb=" O SER 2 384 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N ASN 2 388 " --> pdb=" O LYS 2 385 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N TYR 2 390 " --> pdb=" O GLU 2 387 " (cutoff:3.500A) Processing helix chain '2' and resid 396 through 408 removed outlier: 3.847A pdb=" N VAL 2 400 " --> pdb=" O ASP 2 396 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA 2 401 " --> pdb=" O LYS 2 397 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER 2 406 " --> pdb=" O ALA 2 402 " (cutoff:3.500A) Processing helix chain '2' and resid 415 through 434 removed outlier: 3.536A pdb=" N ALA 2 419 " --> pdb=" O LEU 2 415 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE 2 420 " --> pdb=" O PRO 2 416 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU 2 423 " --> pdb=" O ALA 2 419 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU 2 430 " --> pdb=" O ALA 2 426 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL 2 432 " --> pdb=" O SER 2 428 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN 2 433 " --> pdb=" O PHE 2 429 " (cutoff:3.500A) Processing helix chain '2' and resid 439 through 458 removed outlier: 3.972A pdb=" N ARG 2 446 " --> pdb=" O ASP 2 442 " (cutoff:3.500A) Processing helix chain '2' and resid 466 through 473 Processing helix chain '2' and resid 475 through 513 removed outlier: 3.746A pdb=" N GLU 2 479 " --> pdb=" O LYS 2 475 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS 2 486 " --> pdb=" O GLU 2 482 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU 2 489 " --> pdb=" O LYS 2 485 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU 2 498 " --> pdb=" O THR 2 494 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP 2 510 " --> pdb=" O LYS 2 506 " (cutoff:3.500A) Processing helix chain '2' and resid 527 through 540 removed outlier: 3.680A pdb=" N LYS 2 534 " --> pdb=" O GLN 2 530 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA 2 536 " --> pdb=" O SER 2 532 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS 2 539 " --> pdb=" O GLU 2 535 " (cutoff:3.500A) Processing helix chain '2' and resid 543 through 553 removed outlier: 3.523A pdb=" N VAL 2 551 " --> pdb=" O THR 2 547 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU 2 552 " --> pdb=" O VAL 2 548 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ALA 2 553 " --> pdb=" O ALA 2 549 " (cutoff:3.500A) Processing helix chain '2' and resid 566 through 576 Processing helix chain '2' and resid 592 through 602 removed outlier: 4.022A pdb=" N LEU 2 595 " --> pdb=" O ALA 2 592 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N TYR 2 596 " --> pdb=" O LEU 2 593 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASN 2 597 " --> pdb=" O LYS 2 594 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU 2 599 " --> pdb=" O TYR 2 596 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER 2 600 " --> pdb=" O ASN 2 597 " (cutoff:3.500A) Processing helix chain '2' and resid 607 through 621 removed outlier: 3.771A pdb=" N SER 2 612 " --> pdb=" O ASP 2 608 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA 2 620 " --> pdb=" O ALA 2 616 " (cutoff:3.500A) Processing helix chain '2' and resid 646 through 654 removed outlier: 4.182A pdb=" N ALA 2 652 " --> pdb=" O ALA 2 648 " (cutoff:3.500A) Processing helix chain '2' and resid 669 through 671 No H-bonds generated for 'chain '2' and resid 669 through 671' Processing helix chain '2' and resid 676 through 680 removed outlier: 4.190A pdb=" N THR 2 680 " --> pdb=" O SER 2 677 " (cutoff:3.500A) Processing helix chain '2' and resid 694 through 701 removed outlier: 4.029A pdb=" N ALA 2 698 " --> pdb=" O GLN 2 694 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL 2 699 " --> pdb=" O LEU 2 695 " (cutoff:3.500A) Processing helix chain '2' and resid 712 through 714 No H-bonds generated for 'chain '2' and resid 712 through 714' Processing helix chain '2' and resid 717 through 726 removed outlier: 3.710A pdb=" N VAL 2 722 " --> pdb=" O ASP 2 718 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLN 2 725 " --> pdb=" O LYS 2 721 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE 2 726 " --> pdb=" O VAL 2 722 " (cutoff:3.500A) Processing helix chain '2' and resid 773 through 789 Processing helix chain '2' and resid 795 through 800 removed outlier: 3.527A pdb=" N ARG 2 800 " --> pdb=" O PHE 2 797 " (cutoff:3.500A) Processing helix chain '2' and resid 812 through 827 removed outlier: 4.455A pdb=" N LYS 2 817 " --> pdb=" O LYS 2 813 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA 2 820 " --> pdb=" O HIS 2 816 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE 2 823 " --> pdb=" O VAL 2 819 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS 2 824 " --> pdb=" O ALA 2 820 " (cutoff:3.500A) Processing helix chain '2' and resid 841 through 850 removed outlier: 4.827A pdb=" N TYR 2 846 " --> pdb=" O LYS 2 842 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE 2 847 " --> pdb=" O ALA 2 843 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN 2 850 " --> pdb=" O TYR 2 846 " (cutoff:3.500A) Processing helix chain '2' and resid 859 through 867 Processing helix chain '2' and resid 869 through 878 removed outlier: 3.866A pdb=" N LYS 2 872 " --> pdb=" O ILE 2 869 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE 2 873 " --> pdb=" O MET 2 870 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ILE 2 875 " --> pdb=" O LYS 2 872 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N MET 2 876 " --> pdb=" O PHE 2 873 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR 2 877 " --> pdb=" O ALA 2 874 " (cutoff:3.500A) Processing helix chain '3' and resid 198 through 202 removed outlier: 3.571A pdb=" N ARG 3 202 " --> pdb=" O ASN 3 198 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 198 through 202' Processing helix chain '3' and resid 213 through 223 removed outlier: 3.941A pdb=" N ALA 3 218 " --> pdb=" O GLU 3 214 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER 3 222 " --> pdb=" O ALA 3 218 " (cutoff:3.500A) Processing helix chain '3' and resid 243 through 253 removed outlier: 3.559A pdb=" N VAL 3 249 " --> pdb=" O VAL 3 245 " (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 284 through 296 removed outlier: 4.181A pdb=" N MET 3 288 " --> pdb=" O PHE 3 284 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU 3 294 " --> pdb=" O ASN 3 290 " (cutoff:3.500A) Processing helix chain '3' and resid 299 through 301 No H-bonds generated for 'chain '3' and resid 299 through 301' Processing helix chain '3' and resid 309 through 313 Processing helix chain '3' and resid 323 through 326 No H-bonds generated for 'chain '3' and resid 323 through 326' Processing helix chain '3' and resid 345 through 352 removed outlier: 3.745A pdb=" N ARG 3 349 " --> pdb=" O ILE 3 345 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N LYS 3 350 " --> pdb=" O ALA 3 346 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N PHE 3 351 " --> pdb=" O GLU 3 347 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE 3 352 " --> pdb=" O TYR 3 348 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 345 through 352' Processing helix chain '3' and resid 373 through 387 removed outlier: 3.540A pdb=" N LYS 3 377 " --> pdb=" O ASP 3 373 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER 3 381 " --> pdb=" O LYS 3 377 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N SER 3 384 " --> pdb=" O ARG 3 380 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N LYS 3 385 " --> pdb=" O SER 3 381 " (cutoff:3.500A) Processing helix chain '3' and resid 396 through 404 Processing helix chain '3' and resid 417 through 434 removed outlier: 3.509A pdb=" N LEU 3 422 " --> pdb=" O LYS 3 418 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU 3 423 " --> pdb=" O ALA 3 419 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N CYS 3 427 " --> pdb=" O LEU 3 423 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N SER 3 428 " --> pdb=" O ASN 3 424 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN 3 433 " --> pdb=" O PHE 3 429 " (cutoff:3.500A) Processing helix chain '3' and resid 439 through 457 removed outlier: 3.506A pdb=" N VAL 3 443 " --> pdb=" O ARG 3 439 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE 3 448 " --> pdb=" O THR 3 444 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU 3 449 " --> pdb=" O GLU 3 445 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR 3 453 " --> pdb=" O GLU 3 449 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER 3 456 " --> pdb=" O SER 3 452 " (cutoff:3.500A) Processing helix chain '3' and resid 466 through 515 removed outlier: 4.509A pdb=" N LYS 3 475 " --> pdb=" O ASN 3 471 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N GLU 3 482 " --> pdb=" O GLU 3 478 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLU 3 489 " --> pdb=" O LYS 3 485 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG 3 497 " --> pdb=" O ILE 3 493 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS 3 499 " --> pdb=" O GLY 3 495 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU 3 503 " --> pdb=" O LYS 3 499 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS 3 512 " --> pdb=" O LEU 3 508 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU 3 513 " --> pdb=" O ASN 3 509 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU 3 514 " --> pdb=" O ASP 3 510 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR 3 515 " --> pdb=" O LEU 3 511 " (cutoff:3.500A) Processing helix chain '3' and resid 519 through 522 No H-bonds generated for 'chain '3' and resid 519 through 522' Processing helix chain '3' and resid 527 through 540 removed outlier: 3.527A pdb=" N LEU 3 533 " --> pdb=" O LEU 3 529 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS 3 534 " --> pdb=" O GLN 3 530 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN 3 538 " --> pdb=" O LYS 3 534 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS 3 539 " --> pdb=" O GLU 3 535 " (cutoff:3.500A) Processing helix chain '3' and resid 543 through 553 removed outlier: 3.668A pdb=" N THR 3 547 " --> pdb=" O LEU 3 543 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU 3 552 " --> pdb=" O VAL 3 548 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA 3 553 " --> pdb=" O ALA 3 549 " (cutoff:3.500A) Processing helix chain '3' and resid 566 through 576 removed outlier: 3.727A pdb=" N ILE 3 572 " --> pdb=" O HIS 3 568 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU 3 574 " --> pdb=" O SER 3 570 " (cutoff:3.500A) Processing helix chain '3' and resid 591 through 602 removed outlier: 3.614A pdb=" N LEU 3 595 " --> pdb=" O ALA 3 592 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N TYR 3 596 " --> pdb=" O LEU 3 593 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN 3 597 " --> pdb=" O LYS 3 594 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU 3 599 " --> pdb=" O TYR 3 596 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER 3 600 " --> pdb=" O ASN 3 597 " (cutoff:3.500A) Processing helix chain '3' and resid 607 through 618 removed outlier: 3.711A pdb=" N ALA 3 616 " --> pdb=" O SER 3 612 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL 3 617 " --> pdb=" O LEU 3 613 " (cutoff:3.500A) Processing helix chain '3' and resid 648 through 654 Processing helix chain '3' and resid 667 through 670 Processing helix chain '3' and resid 673 through 678 removed outlier: 3.954A pdb=" N VAL 3 676 " --> pdb=" O ALA 3 673 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N SER 3 677 " --> pdb=" O HIS 3 674 " (cutoff:3.500A) Processing helix chain '3' and resid 698 through 701 No H-bonds generated for 'chain '3' and resid 698 through 701' Processing helix chain '3' and resid 717 through 728 removed outlier: 3.772A pdb=" N LYS 3 721 " --> pdb=" O ALA 3 717 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL 3 722 " --> pdb=" O ASP 3 718 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLN 3 725 " --> pdb=" O LYS 3 721 " (cutoff:3.500A) Processing helix chain '3' and resid 766 through 768 No H-bonds generated for 'chain '3' and resid 766 through 768' Processing helix chain '3' and resid 774 through 792 removed outlier: 4.390A pdb=" N MET 3 778 " --> pdb=" O LYS 3 775 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N GLU 3 779 " --> pdb=" O ARG 3 776 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL 3 781 " --> pdb=" O MET 3 778 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU 3 783 " --> pdb=" O ASP 3 780 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LYS 3 790 " --> pdb=" O LYS 3 787 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL 3 792 " --> pdb=" O CYS 3 789 " (cutoff:3.500A) Processing helix chain '3' and resid 812 through 830 removed outlier: 4.209A pdb=" N LYS 3 817 " --> pdb=" O LYS 3 813 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS 3 824 " --> pdb=" O ALA 3 820 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS 3 828 " --> pdb=" O LYS 3 824 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG 3 829 " --> pdb=" O LYS 3 825 " (cutoff:3.500A) Processing helix chain '3' and resid 841 through 851 removed outlier: 3.771A pdb=" N ASP 3 845 " --> pdb=" O GLU 3 841 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR 3 846 " --> pdb=" O LYS 3 842 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN 3 850 " --> pdb=" O TYR 3 846 " (cutoff:3.500A) Processing helix chain '3' and resid 860 through 867 removed outlier: 3.681A pdb=" N ILE 3 865 " --> pdb=" O THR 3 861 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU 3 866 " --> pdb=" O LEU 3 862 " (cutoff:3.500A) Processing helix chain '3' and resid 871 through 878 Processing helix chain '4' and resid 198 through 202 Processing helix chain '4' and resid 213 through 220 removed outlier: 4.262A pdb=" N ALA 4 218 " --> pdb=" O GLU 4 214 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE 4 219 " --> pdb=" O GLU 4 215 " (cutoff:3.500A) Processing helix chain '4' and resid 242 through 253 removed outlier: 3.561A pdb=" N VAL 4 249 " --> pdb=" O VAL 4 245 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG 4 251 " --> pdb=" O GLY 4 247 " (cutoff:3.500A) Processing helix chain '4' and resid 259 through 261 No H-bonds generated for 'chain '4' and resid 259 through 261' Processing helix chain '4' and resid 281 through 296 removed outlier: 4.145A pdb=" N GLU 4 285 " --> pdb=" O ARG 4 281 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG 4 287 " --> pdb=" O GLU 4 283 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N MET 4 288 " --> pdb=" O PHE 4 284 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU 4 294 " --> pdb=" O ASN 4 290 " (cutoff:3.500A) 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 345 through 354 removed outlier: 3.758A pdb=" N ARG 4 349 " --> pdb=" O ILE 4 345 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N LYS 4 350 " --> pdb=" O ALA 4 346 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N PHE 4 351 " --> pdb=" O GLU 4 347 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE 4 352 " --> pdb=" O TYR 4 348 " (cutoff:3.500A) Processing helix chain '4' and resid 373 through 387 removed outlier: 4.018A pdb=" N LYS 4 377 " --> pdb=" O ASP 4 373 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N SER 4 384 " --> pdb=" O ARG 4 380 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N LYS 4 385 " --> pdb=" O SER 4 381 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TYR 4 386 " --> pdb=" O LEU 4 382 " (cutoff:3.500A) Processing helix chain '4' and resid 396 through 408 removed outlier: 4.129A pdb=" N SER 4 406 " --> pdb=" O ALA 4 402 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG 4 408 " --> pdb=" O LYS 4 404 " (cutoff:3.500A) Processing helix chain '4' and resid 415 through 435 removed outlier: 3.620A pdb=" N LEU 4 422 " --> pdb=" O LYS 4 418 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU 4 423 " --> pdb=" O ALA 4 419 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU 4 430 " --> pdb=" O ALA 4 426 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL 4 432 " --> pdb=" O SER 4 428 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLN 4 433 " --> pdb=" O PHE 4 429 " (cutoff:3.500A) Processing helix chain '4' and resid 439 through 459 removed outlier: 3.507A pdb=" N VAL 4 443 " --> pdb=" O ARG 4 439 " (cutoff:3.500A) Processing helix chain '4' and resid 466 through 501 removed outlier: 3.661A pdb=" N LYS 4 472 " --> pdb=" O LYS 4 469 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ILE 4 474 " --> pdb=" O ASN 4 471 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU 4 478 " --> pdb=" O LYS 4 475 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS 4 480 " --> pdb=" O PHE 4 477 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N LYS 4 481 " --> pdb=" O GLU 4 478 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN 4 483 " --> pdb=" O LYS 4 480 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS 4 485 " --> pdb=" O GLU 4 482 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N TYR 4 488 " --> pdb=" O LYS 4 485 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE 4 493 " --> pdb=" O GLU 4 490 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N THR 4 494 " --> pdb=" O TYR 4 491 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARG 4 500 " --> pdb=" O ARG 4 497 " (cutoff:3.500A) Processing helix chain '4' and resid 504 through 515 removed outlier: 3.828A pdb=" N LYS 4 512 " --> pdb=" O LEU 4 508 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLU 4 513 " --> pdb=" O ASN 4 509 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU 4 514 " --> pdb=" O ASP 4 510 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N THR 4 515 " --> pdb=" O LEU 4 511 " (cutoff:3.500A) Processing helix chain '4' and resid 532 through 540 removed outlier: 3.513A pdb=" N GLN 4 538 " --> pdb=" O LYS 4 534 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LYS 4 539 " --> pdb=" O GLU 4 535 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N TYR 4 540 " --> pdb=" O ALA 4 536 " (cutoff:3.500A) Processing helix chain '4' and resid 543 through 549 Processing helix chain '4' and resid 566 through 576 removed outlier: 3.533A pdb=" N TYR 4 571 " --> pdb=" O GLU 4 567 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ILE 4 572 " --> pdb=" O HIS 4 568 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU 4 574 " --> pdb=" O SER 4 570 " (cutoff:3.500A) Processing helix chain '4' and resid 593 through 602 removed outlier: 3.935A pdb=" N TYR 4 596 " --> pdb=" O LEU 4 593 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASN 4 597 " --> pdb=" O LYS 4 594 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU 4 599 " --> pdb=" O TYR 4 596 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER 4 600 " --> pdb=" O ASN 4 597 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER 4 602 " --> pdb=" O LEU 4 599 " (cutoff:3.500A) Processing helix chain '4' and resid 607 through 621 removed outlier: 3.756A pdb=" N VAL 4 617 " --> pdb=" O LEU 4 613 " (cutoff:3.500A) Processing helix chain '4' and resid 647 through 653 removed outlier: 3.820A pdb=" N ALA 4 652 " --> pdb=" O ALA 4 648 " (cutoff:3.500A) Processing helix chain '4' and resid 667 through 670 removed outlier: 3.641A pdb=" N PHE 4 670 " --> pdb=" O MET 4 667 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 667 through 670' Processing helix chain '4' and resid 674 through 680 removed outlier: 4.261A pdb=" N THR 4 680 " --> pdb=" O SER 4 677 " (cutoff:3.500A) Processing helix chain '4' and resid 694 through 701 removed outlier: 3.614A pdb=" N ARG 4 700 " --> pdb=" O THR 4 696 " (cutoff:3.500A) Processing helix chain '4' and resid 717 through 726 removed outlier: 3.577A pdb=" N LYS 4 721 " --> pdb=" O ALA 4 717 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU 4 723 " --> pdb=" O VAL 4 719 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLN 4 725 " --> pdb=" O LYS 4 721 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE 4 726 " --> pdb=" O VAL 4 722 " (cutoff:3.500A) Processing helix chain '4' and resid 774 through 792 removed outlier: 4.391A pdb=" N LEU 4 783 " --> pdb=" O GLU 4 779 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE 4 786 " --> pdb=" O ARG 4 782 " (cutoff:3.500A) Processing helix chain '4' and resid 796 through 800 Processing helix chain '4' and resid 812 through 818 removed outlier: 3.617A pdb=" N HIS 4 816 " --> pdb=" O LYS 4 812 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N LYS 4 817 " --> pdb=" O LYS 4 813 " (cutoff:3.500A) Processing helix chain '4' and resid 820 through 829 removed outlier: 3.793A pdb=" N LYS 4 824 " --> pdb=" O ALA 4 820 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS 4 825 " --> pdb=" O LEU 4 821 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS 4 828 " --> pdb=" O LYS 4 824 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG 4 829 " --> pdb=" O LYS 4 825 " (cutoff:3.500A) Processing helix chain '4' and resid 841 through 851 removed outlier: 3.679A pdb=" N GLN 4 850 " --> pdb=" O TYR 4 846 " (cutoff:3.500A) Processing helix chain '4' and resid 859 through 878 removed outlier: 3.694A pdb=" N GLU 4 866 " --> pdb=" O LEU 4 862 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N MET 4 870 " --> pdb=" O GLU 4 866 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N THR 4 871 " --> pdb=" O SER 4 867 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LYS 4 872 " --> pdb=" O VAL 4 868 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE 4 873 " --> pdb=" O ILE 4 869 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA 4 874 " --> pdb=" O MET 4 870 " (cutoff:3.500A) Processing helix chain '5' and resid 198 through 203 Processing helix chain '5' and resid 213 through 223 removed outlier: 4.054A pdb=" N ALA 5 218 " --> pdb=" O GLU 5 214 " (cutoff:3.500A) Processing helix chain '5' and resid 242 through 250 removed outlier: 4.303A pdb=" N VAL 5 249 " --> pdb=" O VAL 5 245 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TYR 5 250 " --> pdb=" O GLU 5 246 " (cutoff:3.500A) Processing helix chain '5' and resid 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 283 through 291 removed outlier: 3.627A pdb=" N ARG 5 287 " --> pdb=" O GLU 5 283 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASN 5 290 " --> pdb=" O THR 5 286 " (cutoff:3.500A) Processing helix chain '5' and resid 293 through 295 No H-bonds generated for 'chain '5' and resid 293 through 295' Processing helix chain '5' and resid 309 through 314 Processing helix chain '5' and resid 345 through 352 removed outlier: 3.916A pdb=" N LYS 5 350 " --> pdb=" O ALA 5 346 " (cutoff:3.500A) Processing helix chain '5' and resid 372 through 387 removed outlier: 3.556A pdb=" N VAL 5 376 " --> pdb=" O VAL 5 372 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LYS 5 377 " --> pdb=" O ASP 5 373 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N SER 5 384 " --> pdb=" O ARG 5 380 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N LYS 5 385 " --> pdb=" O SER 5 381 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N TYR 5 386 " --> pdb=" O LEU 5 382 " (cutoff:3.500A) Processing helix chain '5' and resid 396 through 407 removed outlier: 4.155A pdb=" N SER 5 406 " --> pdb=" O ALA 5 402 " (cutoff:3.500A) Processing helix chain '5' and resid 415 through 434 removed outlier: 3.839A pdb=" N LEU 5 430 " --> pdb=" O ALA 5 426 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN 5 431 " --> pdb=" O CYS 5 427 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL 5 432 " --> pdb=" O SER 5 428 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLN 5 433 " --> pdb=" O PHE 5 429 " (cutoff:3.500A) Processing helix chain '5' and resid 439 through 458 removed outlier: 3.535A pdb=" N VAL 5 443 " --> pdb=" O ARG 5 439 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU 5 449 " --> pdb=" O GLU 5 445 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU 5 451 " --> pdb=" O ASP 5 447 " (cutoff:3.500A) Processing helix chain '5' and resid 467 through 514 removed outlier: 3.698A pdb=" N ASN 5 471 " --> pdb=" O LYS 5 467 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N LYS 5 475 " --> pdb=" O ASN 5 471 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLU 5 482 " --> pdb=" O GLU 5 478 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN 5 483 " --> pdb=" O GLU 5 479 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLU 5 489 " --> pdb=" O LYS 5 485 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU 5 498 " --> pdb=" O THR 5 494 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS 5 499 " --> pdb=" O GLY 5 495 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE 5 504 " --> pdb=" O ARG 5 500 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS 5 506 " --> pdb=" O LYS 5 502 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LYS 5 507 " --> pdb=" O GLU 5 503 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN 5 509 " --> pdb=" O GLU 5 505 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU 5 513 " --> pdb=" O ASN 5 509 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU 5 514 " --> pdb=" O ASP 5 510 " (cutoff:3.500A) Processing helix chain '5' and resid 520 through 522 No H-bonds generated for 'chain '5' and resid 520 through 522' Processing helix chain '5' and resid 527 through 540 removed outlier: 3.593A pdb=" N LYS 5 534 " --> pdb=" O GLN 5 530 " (cutoff:3.500A) Processing helix chain '5' and resid 543 through 552 removed outlier: 3.959A pdb=" N GLU 5 552 " --> pdb=" O VAL 5 548 " (cutoff:3.500A) Processing helix chain '5' and resid 566 through 576 removed outlier: 3.616A pdb=" N SER 5 570 " --> pdb=" O GLU 5 567 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N TYR 5 571 " --> pdb=" O HIS 5 568 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR 5 573 " --> pdb=" O SER 5 570 " (cutoff:3.500A) Processing helix chain '5' and resid 595 through 602 removed outlier: 3.734A pdb=" N SER 5 600 " --> pdb=" O TYR 5 596 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS 5 601 " --> pdb=" O ASN 5 597 " (cutoff:3.500A) Processing helix chain '5' and resid 607 through 621 Processing helix chain '5' and resid 647 through 654 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 680 removed outlier: 3.701A pdb=" N VAL 5 676 " --> pdb=" O ALA 5 673 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N SER 5 677 " --> pdb=" O HIS 5 674 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE 5 679 " --> pdb=" O VAL 5 676 " (cutoff:3.500A) Processing helix chain '5' and resid 696 through 701 Processing helix chain '5' and resid 717 through 728 removed outlier: 3.570A pdb=" N LYS 5 721 " --> pdb=" O ALA 5 717 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL 5 722 " --> pdb=" O ASP 5 718 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLN 5 725 " --> pdb=" O LYS 5 721 " (cutoff:3.500A) Processing helix chain '5' and resid 775 through 792 removed outlier: 3.546A pdb=" N ILE 5 786 " --> pdb=" O ARG 5 782 " (cutoff:3.500A) Processing helix chain '5' and resid 796 through 799 No H-bonds generated for 'chain '5' and resid 796 through 799' Processing helix chain '5' and resid 812 through 827 removed outlier: 3.660A pdb=" N HIS 5 816 " --> pdb=" O LYS 5 812 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LYS 5 817 " --> pdb=" O LYS 5 813 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ALA 5 820 " --> pdb=" O HIS 5 816 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS 5 824 " --> pdb=" O ALA 5 820 " (cutoff:3.500A) Processing helix chain '5' and resid 841 through 851 removed outlier: 3.508A pdb=" N ASP 5 845 " --> pdb=" O GLU 5 841 " (cutoff:3.500A) Processing helix chain '5' and resid 859 through 867 Processing helix chain '5' and resid 871 through 878 removed outlier: 3.643A pdb=" N MET 5 876 " --> pdb=" O LYS 5 872 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 56 removed outlier: 3.888A pdb=" N THR C 34 " --> pdb=" O ASP C 30 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR C 39 " --> pdb=" O SER C 35 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP C 43 " --> pdb=" O THR C 39 " (cutoff:3.500A) Proline residue: C 44 - end of helix removed outlier: 3.682A pdb=" N LYS C 50 " --> pdb=" O SER C 46 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP C 51 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLU C 54 " --> pdb=" O LYS C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 72 removed outlier: 3.631A pdb=" N LYS C 67 " --> pdb=" O LYS C 63 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS C 70 " --> pdb=" O HIS C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 93 removed outlier: 4.197A pdb=" N TRP C 80 " --> pdb=" O LYS C 76 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N MET C 83 " --> pdb=" O ARG C 79 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU C 87 " --> pdb=" O MET C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 120 removed outlier: 3.593A pdb=" N LYS C 104 " --> pdb=" O LYS C 100 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA C 105 " --> pdb=" O LYS C 101 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE C 109 " --> pdb=" O ALA C 105 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASN C 120 " --> pdb=" O ALA C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 147 removed outlier: 3.534A pdb=" N HIS C 134 " --> pdb=" O LEU C 130 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASN C 138 " --> pdb=" O HIS C 134 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS C 147 " --> pdb=" O ASN C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 163 removed outlier: 3.774A pdb=" N GLN C 161 " --> pdb=" O ALA C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 169 No H-bonds generated for 'chain 'C' and resid 167 through 169' Processing helix chain 'C' and resid 174 through 181 removed outlier: 3.616A pdb=" N LYS C 178 " --> pdb=" O GLU C 174 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE C 179 " --> pdb=" O PRO C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 188 No H-bonds generated for 'chain 'C' and resid 186 through 188' Processing helix chain 'C' and resid 199 through 201 No H-bonds generated for 'chain 'C' and resid 199 through 201' Processing helix chain 'C' and resid 203 through 219 removed outlier: 3.527A pdb=" N SER C 208 " --> pdb=" O LYS C 204 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU C 211 " --> pdb=" O SER C 207 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS C 215 " --> pdb=" O GLU C 211 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N SER C 216 " --> pdb=" O GLU C 212 " (cutoff:3.500A) Processing helix chain '6' and resid 213 through 223 removed outlier: 3.781A pdb=" N ARG 6 217 " --> pdb=" O ASP 6 213 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ALA 6 218 " --> pdb=" O GLU 6 214 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ILE 6 219 " --> pdb=" O GLU 6 215 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU 6 221 " --> pdb=" O ARG 6 217 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N SER 6 222 " --> pdb=" O ALA 6 218 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU 6 223 " --> pdb=" O ILE 6 219 " (cutoff:3.500A) Processing helix chain '6' and resid 237 through 239 No H-bonds generated for 'chain '6' and resid 237 through 239' Processing helix chain '6' and resid 243 through 254 removed outlier: 3.712A pdb=" N GLY 6 247 " --> pdb=" O THR 6 243 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG 6 251 " --> pdb=" O GLY 6 247 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ILE 6 252 " --> pdb=" O LEU 6 248 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLU 6 253 " --> pdb=" O VAL 6 249 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LYS 6 254 " --> pdb=" O TYR 6 250 " (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 284 through 292 removed outlier: 3.706A pdb=" N LYS 6 289 " --> pdb=" O GLU 6 285 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASN 6 290 " --> pdb=" O THR 6 286 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ILE 6 291 " --> pdb=" O ARG 6 287 " (cutoff:3.500A) Processing helix chain '6' and resid 310 through 314 removed outlier: 3.722A pdb=" N GLY 6 314 " --> pdb=" O HIS 6 310 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 310 through 314' Processing helix chain '6' and resid 328 through 333 removed outlier: 3.730A pdb=" N SER 6 333 " --> pdb=" O LYS 6 329 " (cutoff:3.500A) Processing helix chain '6' and resid 346 through 350 removed outlier: 4.366A pdb=" N LYS 6 350 " --> pdb=" O ALA 6 346 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 346 through 350' Processing helix chain '6' and resid 352 through 355 No H-bonds generated for 'chain '6' and resid 352 through 355' Processing helix chain '6' and resid 376 through 390 removed outlier: 4.062A pdb=" N SER 6 381 " --> pdb=" O LYS 6 377 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N LEU 6 382 " --> pdb=" O ILE 6 378 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS 6 383 " --> pdb=" O LEU 6 379 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER 6 384 " --> pdb=" O ARG 6 380 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LYS 6 385 " --> pdb=" O SER 6 381 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR 6 386 " --> pdb=" O LEU 6 382 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ASN 6 388 " --> pdb=" O SER 6 384 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N PHE 6 389 " --> pdb=" O LYS 6 385 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR 6 390 " --> pdb=" O TYR 6 386 " (cutoff:3.500A) Processing helix chain '6' and resid 396 through 409 removed outlier: 4.151A pdb=" N ALA 6 403 " --> pdb=" O LEU 6 399 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER 6 406 " --> pdb=" O ALA 6 402 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG 6 408 " --> pdb=" O LYS 6 404 " (cutoff:3.500A) Processing helix chain '6' and resid 415 through 434 removed outlier: 4.067A pdb=" N ALA 6 419 " --> pdb=" O LEU 6 415 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE 6 420 " --> pdb=" O PRO 6 416 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASP 6 421 " --> pdb=" O ASP 6 417 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU 6 422 " --> pdb=" O LYS 6 418 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU 6 423 " --> pdb=" O ALA 6 419 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ASN 6 424 " --> pdb=" O ILE 6 420 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LYS 6 425 " --> pdb=" O ASP 6 421 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA 6 426 " --> pdb=" O LEU 6 422 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N CYS 6 427 " --> pdb=" O LEU 6 423 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N SER 6 428 " --> pdb=" O ASN 6 424 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE 6 429 " --> pdb=" O LYS 6 425 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU 6 430 " --> pdb=" O ALA 6 426 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN 6 431 " --> pdb=" O CYS 6 427 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL 6 432 " --> pdb=" O SER 6 428 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLN 6 433 " --> pdb=" O PHE 6 429 " (cutoff:3.500A) Processing helix chain '6' and resid 439 through 457 removed outlier: 3.647A pdb=" N GLU 6 445 " --> pdb=" O ILE 6 441 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ARG 6 446 " --> pdb=" O ASP 6 442 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASP 6 447 " --> pdb=" O VAL 6 443 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LEU 6 451 " --> pdb=" O ASP 6 447 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER 6 452 " --> pdb=" O ILE 6 448 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU 6 454 " --> pdb=" O ARG 6 450 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N THR 6 457 " --> pdb=" O TYR 6 453 " (cutoff:3.500A) Processing helix chain '6' and resid 465 through 507 removed outlier: 5.864A pdb=" N ILE 6 474 " --> pdb=" O ASN 6 471 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU 6 478 " --> pdb=" O LYS 6 475 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS 6 481 " --> pdb=" O GLU 6 478 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLU 6 482 " --> pdb=" O GLU 6 479 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU 6 484 " --> pdb=" O LYS 6 481 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS 6 485 " --> pdb=" O GLU 6 482 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N TYR 6 487 " --> pdb=" O LEU 6 484 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N TYR 6 488 " --> pdb=" O LYS 6 485 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLU 6 496 " --> pdb=" O ILE 6 493 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ARG 6 497 " --> pdb=" O THR 6 494 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS 6 502 " --> pdb=" O LYS 6 499 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N GLU 6 503 " --> pdb=" O ARG 6 500 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ILE 6 504 " --> pdb=" O LYS 6 501 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS 6 506 " --> pdb=" O GLU 6 503 " (cutoff:3.500A) Processing helix chain '6' and resid 510 through 516 removed outlier: 3.722A pdb=" N LEU 6 514 " --> pdb=" O ASP 6 510 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR 6 515 " --> pdb=" O LEU 6 511 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLN 6 516 " --> pdb=" O LYS 6 512 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 510 through 516' Processing helix chain '6' and resid 527 through 537 removed outlier: 4.173A pdb=" N SER 6 532 " --> pdb=" O GLU 6 528 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N LEU 6 533 " --> pdb=" O LEU 6 529 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LYS 6 534 " --> pdb=" O GLN 6 530 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN 6 537 " --> pdb=" O LEU 6 533 " (cutoff:3.500A) Processing helix chain '6' and resid 539 through 541 No H-bonds generated for 'chain '6' and resid 539 through 541' Processing helix chain '6' and resid 544 through 553 removed outlier: 3.806A pdb=" N VAL 6 548 " --> pdb=" O TYR 6 544 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA 6 549 " --> pdb=" O LYS 6 545 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL 6 551 " --> pdb=" O THR 6 547 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLU 6 552 " --> pdb=" O VAL 6 548 " (cutoff:3.500A) Processing helix chain '6' and resid 566 through 576 removed outlier: 3.605A pdb=" N SER 6 570 " --> pdb=" O GLN 6 566 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE 6 572 " --> pdb=" O HIS 6 568 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG 6 575 " --> pdb=" O TYR 6 571 " (cutoff:3.500A) Processing helix chain '6' and resid 591 through 602 removed outlier: 3.849A pdb=" N TYR 6 596 " --> pdb=" O LEU 6 593 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN 6 597 " --> pdb=" O LYS 6 594 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER 6 600 " --> pdb=" O ASN 6 597 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LYS 6 601 " --> pdb=" O SER 6 598 " (cutoff:3.500A) Processing helix chain '6' and resid 607 through 616 removed outlier: 3.818A pdb=" N SER 6 612 " --> pdb=" O ASP 6 608 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP 6 615 " --> pdb=" O LYS 6 611 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA 6 616 " --> pdb=" O SER 6 612 " (cutoff:3.500A) Processing helix chain '6' and resid 618 through 621 No H-bonds generated for 'chain '6' and resid 618 through 621' Processing helix chain '6' and resid 646 through 654 Processing helix chain '6' and resid 667 through 669 No H-bonds generated for 'chain '6' and resid 667 through 669' Processing helix chain '6' and resid 673 through 680 removed outlier: 4.015A pdb=" N VAL 6 676 " --> pdb=" O ALA 6 673 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N THR 6 680 " --> pdb=" O SER 6 677 " (cutoff:3.500A) Processing helix chain '6' and resid 694 through 701 removed outlier: 4.459A pdb=" N VAL 6 699 " --> pdb=" O LEU 6 695 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG 6 700 " --> pdb=" O THR 6 696 " (cutoff:3.500A) Processing helix chain '6' and resid 719 through 727 removed outlier: 3.619A pdb=" N ILE 6 726 " --> pdb=" O LEU 6 723 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU 6 727 " --> pdb=" O LEU 6 724 " (cutoff:3.500A) Processing helix chain '6' and resid 760 through 763 No H-bonds generated for 'chain '6' and resid 760 through 763' Processing helix chain '6' and resid 774 through 791 Processing helix chain '6' and resid 796 through 800 Processing helix chain '6' and resid 814 through 827 removed outlier: 4.166A pdb=" N ILE 6 818 " --> pdb=" O LEU 6 815 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N VAL 6 819 " --> pdb=" O HIS 6 816 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU 6 827 " --> pdb=" O LYS 6 824 " (cutoff:3.500A) Processing helix chain '6' and resid 842 through 851 removed outlier: 3.590A pdb=" N TYR 6 846 " --> pdb=" O LYS 6 842 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE 6 848 " --> pdb=" O ILE 6 844 " (cutoff:3.500A) Processing helix chain '6' and resid 859 through 866 Processing helix chain '6' and resid 871 through 878 removed outlier: 3.704A pdb=" N MET 6 876 " --> pdb=" O LYS 6 872 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 56 removed outlier: 3.887A pdb=" N THR D 34 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR D 39 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE D 41 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP D 43 " --> pdb=" O THR D 39 " (cutoff:3.500A) Proline residue: D 44 - end of helix removed outlier: 3.682A pdb=" N LYS D 50 " --> pdb=" O SER D 46 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP D 51 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLU D 54 " --> pdb=" O LYS D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 72 removed outlier: 3.631A pdb=" N LYS D 67 " --> pdb=" O LYS D 63 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS D 70 " --> pdb=" O HIS D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 93 removed outlier: 4.197A pdb=" N TRP D 80 " --> pdb=" O LYS D 76 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N MET D 83 " --> pdb=" O ARG D 79 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU D 87 " --> pdb=" O MET D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 120 removed outlier: 3.593A pdb=" N LYS D 104 " --> pdb=" O LYS D 100 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA D 105 " --> pdb=" O LYS D 101 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE D 109 " --> pdb=" O ALA D 105 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASN D 120 " --> pdb=" O ALA D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 147 removed outlier: 3.533A pdb=" N HIS D 134 " --> pdb=" O LEU D 130 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASN D 138 " --> pdb=" O HIS D 134 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS D 147 " --> pdb=" O ASN D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 163 removed outlier: 3.603A pdb=" N GLN D 161 " --> pdb=" O ALA D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 169 No H-bonds generated for 'chain 'D' and resid 167 through 169' Processing helix chain 'D' and resid 174 through 181 removed outlier: 3.615A pdb=" N LYS D 178 " --> pdb=" O GLU D 174 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE D 179 " --> pdb=" O PRO D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 188 No H-bonds generated for 'chain 'D' and resid 186 through 188' Processing helix chain 'D' and resid 199 through 201 No H-bonds generated for 'chain 'D' and resid 199 through 201' Processing helix chain 'D' and resid 203 through 219 removed outlier: 3.527A pdb=" N SER D 208 " --> pdb=" O LYS D 204 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU D 211 " --> pdb=" O SER D 207 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS D 215 " --> pdb=" O GLU D 211 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N SER D 216 " --> pdb=" O GLU D 212 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N SER D 219 " --> pdb=" O LYS D 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 56 removed outlier: 3.888A pdb=" N THR E 34 " --> pdb=" O ASP E 30 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR E 39 " --> pdb=" O SER E 35 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE E 41 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP E 43 " --> pdb=" O THR E 39 " (cutoff:3.500A) Proline residue: E 44 - end of helix removed outlier: 3.681A pdb=" N LYS E 50 " --> pdb=" O SER E 46 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP E 51 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLU E 54 " --> pdb=" O LYS E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 72 removed outlier: 3.631A pdb=" N LYS E 67 " --> pdb=" O LYS E 63 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS E 70 " --> pdb=" O HIS E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 93 removed outlier: 4.197A pdb=" N TRP E 80 " --> pdb=" O LYS E 76 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N MET E 83 " --> pdb=" O ARG E 79 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU E 87 " --> pdb=" O MET E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 120 removed outlier: 3.592A pdb=" N LYS E 104 " --> pdb=" O LYS E 100 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA E 105 " --> pdb=" O LYS E 101 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE E 109 " --> pdb=" O ALA E 105 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASN E 120 " --> pdb=" O ALA E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 147 removed outlier: 3.532A pdb=" N HIS E 134 " --> pdb=" O LEU E 130 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASN E 138 " --> pdb=" O HIS E 134 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS E 147 " --> pdb=" O ASN E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 163 removed outlier: 3.775A 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: 3.615A pdb=" N LYS E 178 " --> pdb=" O GLU E 174 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE E 179 " --> pdb=" O PRO E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 188 No H-bonds generated for 'chain 'E' and resid 186 through 188' Processing helix chain 'E' and resid 199 through 201 No H-bonds generated for 'chain 'E' and resid 199 through 201' Processing helix chain 'E' and resid 203 through 219 removed outlier: 3.527A pdb=" N SER E 208 " --> pdb=" O LYS E 204 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU E 211 " --> pdb=" O SER E 207 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS E 215 " --> pdb=" O GLU E 211 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N SER E 216 " --> pdb=" O GLU E 212 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU E 218 " --> pdb=" O LEU E 214 " (cutoff:3.500A) Processing helix chain 'd' and resid 670 through 676 removed outlier: 3.689A pdb=" N LYS d 674 " --> pdb=" O LYS d 670 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU d 675 " --> pdb=" O ASP d 671 " (cutoff:3.500A) Processing helix chain 'd' and resid 688 through 695 removed outlier: 4.074A pdb=" N LYS d 693 " --> pdb=" O ASN d 689 " (cutoff:3.500A) Processing helix chain 'd' and resid 727 through 732 Processing helix chain 'd' and resid 744 through 755 removed outlier: 3.540A pdb=" N LYS d 752 " --> pdb=" O TYR d 748 " (cutoff:3.500A) Processing helix chain 'd' and resid 762 through 778 removed outlier: 3.509A pdb=" N GLY d 766 " --> pdb=" O GLU d 762 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N PHE d 767 " --> pdb=" O ASP d 763 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N ALA d 770 " --> pdb=" O GLY d 766 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N TYR d 771 " --> pdb=" O PHE d 767 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS d 772 " --> pdb=" O TYR d 768 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN d 776 " --> pdb=" O LYS d 772 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR d 778 " --> pdb=" O ILE d 774 " (cutoff:3.500A) Processing helix chain 'd' and resid 807 through 815 Processing helix chain 'c' and resid 670 through 676 removed outlier: 3.688A pdb=" N LYS c 674 " --> pdb=" O LYS c 670 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU c 675 " --> pdb=" O ASP c 671 " (cutoff:3.500A) Processing helix chain 'c' and resid 688 through 695 removed outlier: 4.074A pdb=" N LYS c 693 " --> pdb=" O ASN c 689 " (cutoff:3.500A) Processing helix chain 'c' and resid 727 through 732 Processing helix chain 'c' and resid 745 through 755 removed outlier: 3.598A pdb=" N LYS c 750 " --> pdb=" O ILE c 746 " (cutoff:3.500A) Processing helix chain 'c' and resid 765 through 778 removed outlier: 3.520A pdb=" N TYR c 771 " --> pdb=" O PHE c 767 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TYR c 778 " --> pdb=" O ILE c 774 " (cutoff:3.500A) Processing helix chain 'c' and resid 807 through 815 Processing helix chain 'b' and resid 670 through 676 removed outlier: 3.688A pdb=" N LYS b 674 " --> pdb=" O LYS b 670 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU b 675 " --> pdb=" O ASP b 671 " (cutoff:3.500A) Processing helix chain 'b' and resid 688 through 695 removed outlier: 4.074A pdb=" N LYS b 693 " --> pdb=" O ASN b 689 " (cutoff:3.500A) Processing helix chain 'b' and resid 727 through 732 Processing helix chain 'b' and resid 745 through 755 removed outlier: 3.581A pdb=" N LYS b 750 " --> pdb=" O ILE b 746 " (cutoff:3.500A) Processing helix chain 'b' and resid 762 through 778 removed outlier: 3.508A pdb=" N GLY b 766 " --> pdb=" O GLU b 762 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N PHE b 767 " --> pdb=" O ASP b 763 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N ALA b 770 " --> pdb=" O GLY b 766 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N TYR b 771 " --> pdb=" O PHE b 767 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS b 772 " --> pdb=" O TYR b 768 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN b 776 " --> pdb=" O LYS b 772 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR b 778 " --> pdb=" O ILE b 774 " (cutoff:3.500A) Processing helix chain 'b' and resid 807 through 815 Processing helix chain 'B' and resid 30 through 56 removed outlier: 3.888A pdb=" N THR B 34 " --> pdb=" O ASP B 30 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR B 39 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP B 43 " --> pdb=" O THR B 39 " (cutoff:3.500A) Proline residue: B 44 - end of helix removed outlier: 3.682A pdb=" N LYS B 50 " --> pdb=" O SER B 46 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP B 51 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLU B 54 " --> pdb=" O LYS B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 72 removed outlier: 3.630A pdb=" N LYS B 67 " --> pdb=" O LYS B 63 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS B 70 " --> pdb=" O HIS B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 93 removed outlier: 4.197A pdb=" N TRP B 80 " --> pdb=" O LYS B 76 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N MET B 83 " --> pdb=" O ARG B 79 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU B 87 " --> pdb=" O MET B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 120 removed outlier: 3.593A pdb=" N LYS B 104 " --> pdb=" O LYS B 100 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA B 105 " --> pdb=" O LYS B 101 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE B 109 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASN B 120 " --> pdb=" O ALA B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 147 removed outlier: 3.534A pdb=" N HIS B 134 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASN B 138 " --> pdb=" O HIS B 134 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS B 147 " --> pdb=" O ASN B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 163 removed outlier: 3.773A pdb=" N GLN B 161 " --> pdb=" O ALA B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 169 No H-bonds generated for 'chain 'B' and resid 167 through 169' Processing helix chain 'B' and resid 174 through 181 removed outlier: 3.615A pdb=" N LYS B 178 " --> pdb=" O GLU B 174 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE B 179 " --> pdb=" O PRO B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 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 211 removed outlier: 3.527A pdb=" N SER B 208 " --> pdb=" O LYS B 204 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU B 211 " --> pdb=" O SER B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 218 Processing helix chain 'a' and resid 670 through 676 removed outlier: 3.687A pdb=" N LYS a 674 " --> pdb=" O LYS a 670 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU a 675 " --> pdb=" O ASP a 671 " (cutoff:3.500A) Processing helix chain 'a' and resid 688 through 695 removed outlier: 4.073A pdb=" N LYS a 693 " --> pdb=" O ASN a 689 " (cutoff:3.500A) Processing helix chain 'a' and resid 727 through 732 Processing helix chain 'a' and resid 745 through 755 Processing helix chain 'a' and resid 762 through 778 removed outlier: 3.509A pdb=" N GLY a 766 " --> pdb=" O GLU a 762 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N PHE a 767 " --> pdb=" O ASP a 763 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ALA a 770 " --> pdb=" O GLY a 766 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N TYR a 771 " --> pdb=" O PHE a 767 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LYS a 772 " --> pdb=" O TYR a 768 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN a 776 " --> pdb=" O LYS a 772 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TYR a 778 " --> pdb=" O ILE a 774 " (cutoff:3.500A) Processing helix chain 'a' and resid 807 through 815 Processing helix chain 'A' and resid 30 through 56 removed outlier: 3.888A pdb=" N THR A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR A 39 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP A 43 " --> pdb=" O THR A 39 " (cutoff:3.500A) Proline residue: A 44 - end of helix removed outlier: 3.683A pdb=" N LYS A 50 " --> pdb=" O SER A 46 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLU A 54 " --> pdb=" O LYS A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 72 removed outlier: 3.631A pdb=" N LYS A 67 " --> pdb=" O LYS A 63 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS A 70 " --> pdb=" O HIS A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 93 removed outlier: 4.197A pdb=" N TRP A 80 " --> pdb=" O LYS A 76 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N MET A 83 " --> pdb=" O ARG A 79 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU A 87 " --> pdb=" O MET A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 120 removed outlier: 3.592A pdb=" N LYS A 104 " --> pdb=" O LYS A 100 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA A 105 " --> pdb=" O LYS A 101 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASN A 120 " --> pdb=" O ALA A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 147 removed outlier: 3.534A pdb=" N HIS A 134 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASN A 138 " --> pdb=" O HIS A 134 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS A 147 " --> pdb=" O ASN A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 163 removed outlier: 3.774A pdb=" N GLN A 161 " --> pdb=" O ALA A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 169 No H-bonds generated for 'chain 'A' and resid 167 through 169' Processing helix chain 'A' and resid 174 through 181 removed outlier: 3.615A pdb=" N LYS A 178 " --> pdb=" O GLU A 174 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE A 179 " --> pdb=" O PRO A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 188 No H-bonds generated for 'chain 'A' and resid 186 through 188' Processing helix chain 'A' and resid 199 through 201 No H-bonds generated for 'chain 'A' and resid 199 through 201' Processing helix chain 'A' and resid 203 through 213 removed outlier: 3.528A pdb=" N SER A 208 " --> pdb=" O LYS A 204 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU A 211 " --> pdb=" O SER A 207 " (cutoff:3.500A) Processing helix chain 'g' and resid 670 through 676 removed outlier: 3.688A pdb=" N LYS g 674 " --> pdb=" O LYS g 670 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU g 675 " --> pdb=" O ASP g 671 " (cutoff:3.500A) Processing helix chain 'g' and resid 688 through 695 removed outlier: 4.072A pdb=" N LYS g 693 " --> pdb=" O ASN g 689 " (cutoff:3.500A) Processing helix chain 'g' and resid 727 through 732 Processing helix chain 'g' and resid 744 through 755 removed outlier: 3.502A pdb=" N TYR g 748 " --> pdb=" O LYS g 744 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS g 752 " --> pdb=" O TYR g 748 " (cutoff:3.500A) Processing helix chain 'g' and resid 762 through 765 No H-bonds generated for 'chain 'g' and resid 762 through 765' Processing helix chain 'g' and resid 770 through 778 removed outlier: 3.688A pdb=" N TYR g 778 " --> pdb=" O ILE g 774 " (cutoff:3.500A) Processing helix chain 'g' and resid 807 through 815 Processing helix chain 'G' and resid 30 through 56 removed outlier: 3.888A pdb=" N THR G 34 " --> pdb=" O ASP G 30 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR G 39 " --> pdb=" O SER G 35 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE G 41 " --> pdb=" O LEU G 37 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP G 43 " --> pdb=" O THR G 39 " (cutoff:3.500A) Proline residue: G 44 - end of helix removed outlier: 3.682A pdb=" N LYS G 50 " --> pdb=" O SER G 46 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP G 51 " --> pdb=" O LEU G 47 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU G 54 " --> pdb=" O LYS G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 72 removed outlier: 3.630A pdb=" N LYS G 67 " --> pdb=" O LYS G 63 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS G 70 " --> pdb=" O HIS G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 93 removed outlier: 4.197A pdb=" N TRP G 80 " --> pdb=" O LYS G 76 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N MET G 83 " --> pdb=" O ARG G 79 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU G 87 " --> pdb=" O MET G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 120 removed outlier: 3.592A pdb=" N LYS G 104 " --> pdb=" O LYS G 100 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA G 105 " --> pdb=" O LYS G 101 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE G 109 " --> pdb=" O ALA G 105 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASN G 120 " --> pdb=" O ALA G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 129 through 147 removed outlier: 3.534A pdb=" N HIS G 134 " --> pdb=" O LEU G 130 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASN G 138 " --> pdb=" O HIS G 134 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS G 147 " --> pdb=" O ASN G 143 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 163 removed outlier: 3.774A pdb=" N GLN G 161 " --> pdb=" O ALA G 157 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 169 No H-bonds generated for 'chain 'G' and resid 167 through 169' Processing helix chain 'G' and resid 174 through 181 removed outlier: 3.615A pdb=" N LYS G 178 " --> pdb=" O GLU G 174 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE G 179 " --> pdb=" O PRO G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 186 through 188 No H-bonds generated for 'chain 'G' and resid 186 through 188' Processing helix chain 'G' and resid 199 through 201 No H-bonds generated for 'chain 'G' and resid 199 through 201' Processing helix chain 'G' and resid 203 through 213 removed outlier: 3.527A pdb=" N SER G 208 " --> pdb=" O LYS G 204 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU G 211 " --> pdb=" O SER G 207 " (cutoff:3.500A) Processing helix chain 'f' and resid 670 through 676 removed outlier: 3.689A pdb=" N LYS f 674 " --> pdb=" O LYS f 670 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU f 675 " --> pdb=" O ASP f 671 " (cutoff:3.500A) Processing helix chain 'f' and resid 688 through 695 removed outlier: 4.073A pdb=" N LYS f 693 " --> pdb=" O ASN f 689 " (cutoff:3.500A) Processing helix chain 'f' and resid 727 through 732 Processing helix chain 'f' and resid 745 through 755 Processing helix chain 'f' and resid 762 through 765 No H-bonds generated for 'chain 'f' and resid 762 through 765' Processing helix chain 'f' and resid 769 through 778 removed outlier: 3.693A pdb=" N GLN f 773 " --> pdb=" O ASP f 769 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TYR f 778 " --> pdb=" O ILE f 774 " (cutoff:3.500A) Processing helix chain 'f' and resid 807 through 815 Processing helix chain 'F' and resid 30 through 56 removed outlier: 3.888A pdb=" N THR F 34 " --> pdb=" O ASP F 30 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR F 39 " --> pdb=" O SER F 35 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE F 41 " --> pdb=" O LEU F 37 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP F 43 " --> pdb=" O THR F 39 " (cutoff:3.500A) Proline residue: F 44 - end of helix removed outlier: 3.682A pdb=" N LYS F 50 " --> pdb=" O SER F 46 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP F 51 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLU F 54 " --> pdb=" O LYS F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 72 removed outlier: 3.630A pdb=" N LYS F 67 " --> pdb=" O LYS F 63 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS F 70 " --> pdb=" O HIS F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 93 removed outlier: 4.197A pdb=" N TRP F 80 " --> pdb=" O LYS F 76 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N MET F 83 " --> pdb=" O ARG F 79 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU F 87 " --> pdb=" O MET F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 120 removed outlier: 3.592A pdb=" N LYS F 104 " --> pdb=" O LYS F 100 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA F 105 " --> pdb=" O LYS F 101 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE F 109 " --> pdb=" O ALA F 105 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASN F 120 " --> pdb=" O ALA F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 129 through 147 removed outlier: 3.533A pdb=" N HIS F 134 " --> pdb=" O LEU F 130 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASN F 138 " --> pdb=" O HIS F 134 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS F 147 " --> pdb=" O ASN F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 163 removed outlier: 3.774A 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: 3.615A pdb=" N LYS F 178 " --> pdb=" O GLU F 174 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE F 179 " --> pdb=" O PRO F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 188 No H-bonds generated for 'chain 'F' and resid 186 through 188' Processing helix chain 'F' and resid 199 through 201 No H-bonds generated for 'chain 'F' and resid 199 through 201' Processing helix chain 'F' and resid 203 through 220 removed outlier: 3.528A pdb=" N SER F 208 " --> pdb=" O LYS F 204 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU F 212 " --> pdb=" O SER F 208 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET F 217 " --> pdb=" O LYS F 213 " (cutoff:3.500A) Processing helix chain 'e' and resid 670 through 676 removed outlier: 3.689A pdb=" N LYS e 674 " --> pdb=" O LYS e 670 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU e 675 " --> pdb=" O ASP e 671 " (cutoff:3.500A) Processing helix chain 'e' and resid 688 through 695 removed outlier: 4.074A pdb=" N LYS e 693 " --> pdb=" O ASN e 689 " (cutoff:3.500A) Processing helix chain 'e' and resid 727 through 732 Processing helix chain 'e' and resid 745 through 755 removed outlier: 3.886A pdb=" N LYS e 750 " --> pdb=" O ILE e 746 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS e 752 " --> pdb=" O TYR e 748 " (cutoff:3.500A) Processing helix chain 'e' and resid 762 through 778 removed outlier: 3.509A pdb=" N GLY e 766 " --> pdb=" O GLU e 762 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N PHE e 767 " --> pdb=" O ASP e 763 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ALA e 770 " --> pdb=" O GLY e 766 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N TYR e 771 " --> pdb=" O PHE e 767 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS e 772 " --> pdb=" O TYR e 768 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR e 778 " --> pdb=" O ILE e 774 " (cutoff:3.500A) Processing helix chain 'e' and resid 807 through 815 Processing helix chain 'n' and resid -3 through 30 Processing helix chain 'h' and resid -1 through 27 Processing helix chain 'h' and resid 995 through 1002 Processing helix chain 'l' and resid 0 through 32 removed outlier: 3.515A pdb=" N UNK l 30 " --> pdb=" O UNK l 26 " (cutoff:3.500A) Processing helix chain 'l' and resid 995 through 1002 Processing helix chain 'm' and resid -2 through 30 Processing helix chain 'm' and resid 996 through 1002 Processing sheet with id= A, first strand: chain '1' and resid 340 through 344 removed outlier: 8.278A pdb=" N THR 1 343 " --> pdb=" O PRO 1 231 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N LEU 1 233 " --> pdb=" O THR 1 343 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N GLU 1 363 " --> pdb=" O VAL 1 232 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N VAL 1 234 " --> pdb=" O GLU 1 363 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ILE 1 365 " --> pdb=" O VAL 1 234 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain '1' and resid 748 through 751 removed outlier: 7.227A pdb=" N PHE 1 634 " --> pdb=" O MET 1 749 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N SER 1 751 " --> pdb=" O PHE 1 634 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N PHE 1 636 " --> pdb=" O SER 1 751 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LYS 1 803 " --> pdb=" O LEU 1 635 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N LEU 1 637 " --> pdb=" O LYS 1 803 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLY 1 805 " --> pdb=" O LEU 1 637 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain '2' and resid 363 through 367 removed outlier: 3.524A pdb=" N VAL 2 234 " --> pdb=" O ILE 2 365 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LEU 2 339 " --> pdb=" O PRO 2 231 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N LEU 2 233 " --> pdb=" O LEU 2 339 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLY 2 341 " --> pdb=" O LEU 2 233 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N GLY 2 235 " --> pdb=" O GLY 2 341 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU 2 304 " --> pdb=" O ILE 2 340 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain '2' and resid 803 through 807 removed outlier: 3.515A pdb=" N LYS 2 803 " --> pdb=" O THR 2 633 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N PHE 2 634 " --> pdb=" O THR 2 745 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ILE 2 747 " --> pdb=" O PHE 2 634 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N PHE 2 636 " --> pdb=" O ILE 2 747 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N MET 2 749 " --> pdb=" O PHE 2 636 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N GLY 2 638 " --> pdb=" O MET 2 749 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N SER 2 705 " --> pdb=" O ILE 2 746 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N ILE 2 748 " --> pdb=" O SER 2 705 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL 2 707 " --> pdb=" O ILE 2 748 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N THR 2 750 " --> pdb=" O VAL 2 707 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N PHE 2 709 " --> pdb=" O THR 2 750 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain '2' and resid 836 through 839 Processing sheet with id= F, first strand: chain '3' and resid 340 through 342 removed outlier: 5.382A pdb=" N GLU 3 363 " --> pdb=" O VAL 3 232 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain '3' and resid 265 through 268 Processing sheet with id= H, first strand: chain '3' and resid 634 through 637 Processing sheet with id= I, first strand: chain '3' and resid 836 through 839 removed outlier: 3.695A pdb=" N ASP 3 891 " --> pdb=" O LEU 3 899 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU 3 899 " --> pdb=" O ASP 3 891 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain '4' and resid 339 through 344 removed outlier: 5.832A pdb=" N GLU 4 363 " --> pdb=" O VAL 4 232 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N VAL 4 234 " --> pdb=" O GLU 4 363 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ILE 4 365 " --> pdb=" O VAL 4 234 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain '4' and resid 747 through 751 removed outlier: 6.698A pdb=" N LYS 4 803 " --> pdb=" O LEU 4 635 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N LEU 4 637 " --> pdb=" O LYS 4 803 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLY 4 805 " --> pdb=" O LEU 4 637 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain '4' and resid 835 through 839 removed outlier: 6.038A pdb=" N MET 4 886 " --> pdb=" O GLN 4 836 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N SER 4 838 " --> pdb=" O MET 4 886 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N VAL 4 888 " --> pdb=" O SER 4 838 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP 4 891 " --> pdb=" O LEU 4 899 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU 4 899 " --> pdb=" O ASP 4 891 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain '5' and resid 230 through 235 removed outlier: 6.614A pdb=" N LEU 5 339 " --> pdb=" O PRO 5 231 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N LEU 5 233 " --> pdb=" O LEU 5 339 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N GLY 5 341 " --> pdb=" O LEU 5 233 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N GLY 5 235 " --> pdb=" O GLY 5 341 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N THR 5 343 " --> pdb=" O GLY 5 235 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain '5' and resid 265 through 267 Processing sheet with id= O, first strand: chain '5' and resid 803 through 806 removed outlier: 3.836A pdb=" N LYS 5 803 " --> pdb=" O THR 5 633 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE 5 747 " --> pdb=" O PHE 5 634 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N PHE 5 636 " --> pdb=" O ILE 5 747 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N MET 5 749 " --> pdb=" O PHE 5 636 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL 5 707 " --> pdb=" O ILE 5 748 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N THR 5 750 " --> pdb=" O VAL 5 707 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N PHE 5 709 " --> pdb=" O THR 5 750 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain '5' and resid 835 through 839 removed outlier: 6.843A pdb=" N MET 5 886 " --> pdb=" O GLN 5 836 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N SER 5 838 " --> pdb=" O MET 5 886 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N VAL 5 888 " --> pdb=" O SER 5 838 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE 5 901 " --> pdb=" O PHE 5 889 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain '6' and resid 363 through 366 removed outlier: 7.406A pdb=" N GLY 6 341 " --> pdb=" O LEU 6 233 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain '6' and resid 803 through 806 removed outlier: 3.891A pdb=" N LYS 6 803 " --> pdb=" O THR 6 633 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N PHE 6 634 " --> pdb=" O THR 6 745 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ILE 6 747 " --> pdb=" O PHE 6 634 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N PHE 6 636 " --> pdb=" O ILE 6 747 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N MET 6 749 " --> pdb=" O PHE 6 636 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N SER 6 705 " --> pdb=" O ILE 6 746 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N ILE 6 748 " --> pdb=" O SER 6 705 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL 6 707 " --> pdb=" O ILE 6 748 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain '6' and resid 836 through 839 1845 hydrogen bonds defined for protein. 5070 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: 15.39 Time building geometry restraints manager: 20.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.35: 18486 1.35 - 1.53: 37408 1.53 - 1.71: 2235 1.71 - 1.89: 239 1.89 - 2.08: 12 Bond restraints: 58380 Sorted by residual: bond pdb=" C4 AGS 11003 " pdb=" C5 AGS 11003 " ideal model delta sigma weight residual 1.386 1.471 -0.085 1.00e-02 1.00e+04 7.21e+01 bond pdb=" C5 AGS 11003 " pdb=" C6 AGS 11003 " ideal model delta sigma weight residual 1.409 1.483 -0.074 1.00e-02 1.00e+04 5.45e+01 bond pdb=" C LYS 5 317 " pdb=" N ALA 5 318 " ideal model delta sigma weight residual 1.332 1.243 0.089 1.37e-02 5.33e+03 4.22e+01 bond pdb=" PG AGS 11003 " pdb=" S1G AGS 11003 " ideal model delta sigma weight residual 1.949 2.075 -0.126 2.00e-02 2.50e+03 3.98e+01 bond pdb=" CA TYR B 209 " pdb=" C TYR B 209 " ideal model delta sigma weight residual 1.523 1.608 -0.085 1.35e-02 5.49e+03 3.96e+01 ... (remaining 58375 not shown) Histogram of bond angle deviations from ideal: 97.56 - 105.26: 874 105.26 - 112.96: 31653 112.96 - 120.67: 27049 120.67 - 128.37: 18769 128.37 - 136.07: 357 Bond angle restraints: 78702 Sorted by residual: angle pdb=" N PHE 6 763 " pdb=" CA PHE 6 763 " pdb=" C PHE 6 763 " ideal model delta sigma weight residual 111.28 123.74 -12.46 1.09e+00 8.42e-01 1.31e+02 angle pdb=" C5 AGS 11003 " pdb=" C4 AGS 11003 " pdb=" N3 AGS 11003 " ideal model delta sigma weight residual 126.80 118.61 8.19 7.41e-01 1.82e+00 1.22e+02 angle pdb=" N LYS 6 486 " pdb=" CA LYS 6 486 " pdb=" C LYS 6 486 " ideal model delta sigma weight residual 111.14 122.94 -11.80 1.08e+00 8.57e-01 1.19e+02 angle pdb=" N SER B 208 " pdb=" CA SER B 208 " pdb=" C SER B 208 " ideal model delta sigma weight residual 112.89 101.27 11.62 1.24e+00 6.50e-01 8.79e+01 angle pdb=" C4 AGS 11003 " pdb=" C5 AGS 11003 " pdb=" N7 AGS 11003 " ideal model delta sigma weight residual 110.73 106.59 4.14 4.52e-01 4.89e+00 8.37e+01 ... (remaining 78697 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.75: 35649 31.75 - 63.51: 318 63.51 - 95.26: 20 95.26 - 127.02: 9 127.02 - 158.77: 5 Dihedral angle restraints: 36001 sinusoidal: 14833 harmonic: 21168 Sorted by residual: dihedral pdb=" CA LYS 5 464 " pdb=" C LYS 5 464 " pdb=" N VAL 5 465 " pdb=" CA VAL 5 465 " ideal model delta harmonic sigma weight residual 180.00 -132.67 -47.33 0 5.00e+00 4.00e-02 8.96e+01 dihedral pdb=" CA LYS 4 464 " pdb=" C LYS 4 464 " pdb=" N VAL 4 465 " pdb=" CA VAL 4 465 " ideal model delta harmonic sigma weight residual 180.00 -137.57 -42.43 0 5.00e+00 4.00e-02 7.20e+01 dihedral pdb=" CA LYS 2 794 " pdb=" C LYS 2 794 " pdb=" N PRO 2 795 " pdb=" CA PRO 2 795 " ideal model delta harmonic sigma weight residual -180.00 -138.14 -41.86 0 5.00e+00 4.00e-02 7.01e+01 ... (remaining 35998 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 8159 0.100 - 0.200: 628 0.200 - 0.300: 58 0.300 - 0.400: 24 0.400 - 0.500: 7 Chirality restraints: 8876 Sorted by residual: chirality pdb=" PB AGS 51001 " pdb=" O2B AGS 51001 " pdb=" O3A AGS 51001 " pdb=" O3B AGS 51001 " both_signs ideal model delta sigma weight residual True 3.18 -2.68 0.50 2.00e-01 2.50e+01 6.26e+00 chirality pdb=" CB ILE E 223 " pdb=" CA ILE E 223 " pdb=" CG1 ILE E 223 " pdb=" CG2 ILE E 223 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.48 2.00e-01 2.50e+01 5.67e+00 chirality pdb=" CA TYR b 707 " pdb=" N TYR b 707 " pdb=" C TYR b 707 " pdb=" CB TYR b 707 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.47e+00 ... (remaining 8873 not shown) Planarity restraints: 9939 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA UNK i 22 " 0.037 2.00e-02 2.50e+03 7.27e-02 5.29e+01 pdb=" C UNK i 22 " -0.126 2.00e-02 2.50e+03 pdb=" O UNK i 22 " 0.047 2.00e-02 2.50e+03 pdb=" N UNK i 23 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS 5 317 " 0.038 2.00e-02 2.50e+03 7.17e-02 5.14e+01 pdb=" C LYS 5 317 " -0.124 2.00e-02 2.50e+03 pdb=" O LYS 5 317 " 0.042 2.00e-02 2.50e+03 pdb=" N ALA 5 318 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA UNK m 25 " -0.026 2.00e-02 2.50e+03 5.22e-02 2.72e+01 pdb=" C UNK m 25 " 0.090 2.00e-02 2.50e+03 pdb=" O UNK m 25 " -0.034 2.00e-02 2.50e+03 pdb=" N UNK m 26 " -0.030 2.00e-02 2.50e+03 ... (remaining 9936 not shown) Histogram of nonbonded interaction distances: 1.08 - 1.84: 11 1.84 - 2.61: 705 2.61 - 3.37: 74460 3.37 - 4.14: 133457 4.14 - 4.90: 242815 Nonbonded interactions: 451448 Sorted by model distance: nonbonded pdb=" O GLY 2 495 " pdb=" CE LYS 2 499 " model vdw 1.079 3.440 nonbonded pdb=" OE2 GLU g 711 " pdb=" OD1 ASP g 769 " model vdw 1.412 3.040 nonbonded pdb=" C GLU 2 496 " pdb=" CD LYS 2 499 " model vdw 1.430 3.670 nonbonded pdb=" CA GLU 2 496 " pdb=" CD LYS 2 499 " model vdw 1.435 3.870 nonbonded pdb=" CE LYS 5 481 " pdb=" CB UNK l 987 " model vdw 1.453 3.840 ... (remaining 451443 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 189 through 904 or resid 1001)) selection = (chain '2' and (resid 189 through 904 or resid 1001)) selection = (chain '3' and (resid 189 through 904 or resid 1001)) selection = (chain '4' and (resid 189 through 904 or resid 1001)) selection = (chain '5' and (resid 189 through 904 or resid 1001)) selection = (chain '6' and (resid 189 through 904 or resid 1001)) } ncs_group { reference = chain 'A' selection = (chain 'B' and resid 27 through 217) selection = (chain 'C' and resid 27 through 217) selection = (chain 'D' and resid 27 through 217) selection = (chain 'E' and resid 27 through 217) selection = (chain 'F' and resid 27 through 217) selection = chain 'G' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' } ncs_group { reference = (chain 'h' and resid -1 through 1003) selection = chain 'i' selection = (chain 'j' and resid 10 through 1003) selection = (chain 'l' and resid 6 through 1003) } ncs_group { reference = (chain 'k' and resid 1 through 1004) selection = chain 'm' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 22.100 Check model and map are aligned: 0.610 Set scattering table: 0.410 Process input model: 112.940 Find NCS groups from input model: 3.420 Set up NCS constraints: 0.440 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 146.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.126 58380 Z= 0.448 Angle : 1.114 12.694 78702 Z= 0.633 Chirality : 0.062 0.500 8876 Planarity : 0.007 0.083 9939 Dihedral : 10.084 158.771 22290 Min Nonbonded Distance : 1.079 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.88 % Favored : 91.79 % Rotamer: Outliers : 0.49 % Allowed : 0.57 % Favored : 98.95 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.31 % Twisted General : 0.40 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.77 (0.08), residues: 6773 helix: -3.91 (0.05), residues: 3164 sheet: -2.16 (0.21), residues: 477 loop : -2.34 (0.10), residues: 3132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.006 TRP G 171 HIS 0.018 0.002 HIS 3 310 PHE 0.034 0.003 PHE D 144 TYR 0.024 0.003 TYR 3 414 ARG 0.023 0.001 ARG 1 737 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13546 Ramachandran restraints generated. 6773 Oldfield, 0 Emsley, 6773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13546 Ramachandran restraints generated. 6773 Oldfield, 0 Emsley, 6773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2083 residues out of total 6163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 2053 time to evaluate : 4.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 293 LYS cc_start: 0.8714 (mttt) cc_final: 0.8325 (tmtt) REVERT: 1 366 LEU cc_start: 0.9387 (mt) cc_final: 0.9113 (pt) REVERT: 1 378 ILE cc_start: 0.9411 (mt) cc_final: 0.9196 (mt) REVERT: 1 542 GLU cc_start: 0.8845 (mt-10) cc_final: 0.8189 (tm-30) REVERT: 1 555 THR cc_start: 0.8598 (p) cc_final: 0.8390 (t) REVERT: 1 595 LEU cc_start: 0.9287 (mt) cc_final: 0.9071 (mt) REVERT: 1 655 LEU cc_start: 0.8435 (mt) cc_final: 0.8211 (mt) REVERT: 1 662 LEU cc_start: 0.8999 (tp) cc_final: 0.8644 (tt) REVERT: 1 691 ASP cc_start: 0.8663 (m-30) cc_final: 0.8223 (t70) REVERT: 1 716 HIS cc_start: 0.7539 (t70) cc_final: 0.7229 (t-90) REVERT: 1 718 ASP cc_start: 0.8293 (m-30) cc_final: 0.7631 (m-30) REVERT: 1 746 ILE cc_start: 0.8986 (mt) cc_final: 0.8641 (mm) REVERT: 2 206 LEU cc_start: 0.8185 (mt) cc_final: 0.7849 (mt) REVERT: 2 215 GLU cc_start: 0.8552 (tp30) cc_final: 0.8311 (tp30) REVERT: 2 227 ASN cc_start: 0.8682 (m-40) cc_final: 0.8397 (t0) REVERT: 2 266 VAL cc_start: 0.8737 (t) cc_final: 0.8196 (t) REVERT: 2 274 PHE cc_start: 0.7631 (m-80) cc_final: 0.7276 (m-80) REVERT: 2 414 TYR cc_start: 0.8570 (m-80) cc_final: 0.8346 (m-80) REVERT: 2 499 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8557 (mmmm) REVERT: 2 666 ASN cc_start: 0.8815 (m110) cc_final: 0.7858 (p0) REVERT: 2 667 MET cc_start: 0.8890 (mmm) cc_final: 0.8512 (tpp) REVERT: 2 733 ASN cc_start: 0.8378 (m-40) cc_final: 0.7582 (m-40) REVERT: 2 801 ILE cc_start: 0.9487 (mt) cc_final: 0.9248 (mt) REVERT: 2 802 ASP cc_start: 0.8764 (m-30) cc_final: 0.8251 (t0) REVERT: 2 872 LYS cc_start: 0.8213 (ptpp) cc_final: 0.8000 (ptmm) REVERT: 2 880 LYS cc_start: 0.7596 (mttt) cc_final: 0.7137 (tmtt) REVERT: 3 261 LEU cc_start: 0.8566 (mt) cc_final: 0.8284 (tp) REVERT: 3 334 LYS cc_start: 0.8033 (pttp) cc_final: 0.7440 (mptt) REVERT: 3 343 THR cc_start: 0.8329 (p) cc_final: 0.8122 (p) REVERT: 3 412 ASP cc_start: 0.7760 (p0) cc_final: 0.7372 (p0) REVERT: 3 584 LEU cc_start: 0.8197 (mt) cc_final: 0.7994 (mt) REVERT: 3 624 MET cc_start: 0.8375 (mmm) cc_final: 0.8011 (tpp) REVERT: 3 668 SER cc_start: 0.8620 (p) cc_final: 0.7883 (p) REVERT: 3 716 HIS cc_start: 0.8261 (t-90) cc_final: 0.8046 (t-170) REVERT: 3 732 ILE cc_start: 0.9041 (mt) cc_final: 0.8836 (tt) REVERT: 3 736 HIS cc_start: 0.6657 (t70) cc_final: 0.6366 (t70) REVERT: 3 739 ASN cc_start: 0.7862 (m-40) cc_final: 0.7641 (m-40) REVERT: 3 884 ASP cc_start: 0.8016 (m-30) cc_final: 0.7710 (p0) REVERT: 4 221 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8590 (mt-10) REVERT: 4 568 HIS cc_start: 0.8519 (m90) cc_final: 0.7951 (m-70) REVERT: 4 700 ARG cc_start: 0.8736 (mtp85) cc_final: 0.8497 (mtm-85) REVERT: 4 749 MET cc_start: 0.8494 (mmm) cc_final: 0.7711 (mmm) REVERT: 4 818 ILE cc_start: 0.8870 (mt) cc_final: 0.8524 (mm) REVERT: 4 885 ASP cc_start: 0.8049 (m-30) cc_final: 0.7471 (p0) REVERT: 4 899 LEU cc_start: 0.6580 (OUTLIER) cc_final: 0.6355 (pp) REVERT: 5 423 LEU cc_start: 0.9346 (mt) cc_final: 0.9128 (mt) REVERT: 5 571 TYR cc_start: 0.8523 (t80) cc_final: 0.7838 (t80) REVERT: 5 635 LEU cc_start: 0.9268 (tp) cc_final: 0.9026 (tp) REVERT: 5 710 ASP cc_start: 0.8043 (m-30) cc_final: 0.7773 (m-30) REVERT: 5 825 LYS cc_start: 0.9132 (mttt) cc_final: 0.8848 (tptp) REVERT: 5 856 LEU cc_start: 0.9373 (mt) cc_final: 0.7957 (mt) REVERT: C 37 LEU cc_start: 0.8024 (mt) cc_final: 0.7495 (pp) REVERT: C 55 HIS cc_start: 0.7675 (m-70) cc_final: 0.6833 (m-70) REVERT: C 114 THR cc_start: 0.9176 (p) cc_final: 0.8803 (t) REVERT: C 197 LEU cc_start: 0.8651 (mt) cc_final: 0.8293 (mp) REVERT: C 202 THR cc_start: 0.8729 (p) cc_final: 0.8291 (p) REVERT: 6 425 LYS cc_start: 0.8321 (mttt) cc_final: 0.8086 (pttt) REVERT: 6 465 VAL cc_start: 0.7971 (p) cc_final: 0.7454 (p) REVERT: 6 559 MET cc_start: 0.3773 (OUTLIER) cc_final: 0.3230 (ppp) REVERT: 6 709 PHE cc_start: 0.6029 (m-80) cc_final: 0.5423 (m-10) REVERT: 6 716 HIS cc_start: 0.7855 (t70) cc_final: 0.6655 (t70) REVERT: 6 763 PHE cc_start: 0.5776 (m-10) cc_final: 0.4889 (m-80) REVERT: 6 862 LEU cc_start: 0.8494 (mt) cc_final: 0.7812 (mt) REVERT: D 136 ILE cc_start: 0.9090 (mt) cc_final: 0.8735 (mt) REVERT: D 137 LEU cc_start: 0.9076 (mt) cc_final: 0.8740 (mt) REVERT: D 144 PHE cc_start: 0.8181 (m-80) cc_final: 0.7868 (m-80) REVERT: D 150 GLN cc_start: 0.8517 (mt0) cc_final: 0.8015 (mt0) REVERT: D 171 TRP cc_start: 0.8460 (m100) cc_final: 0.7755 (m-10) REVERT: E 88 LEU cc_start: 0.8500 (mt) cc_final: 0.8289 (mt) REVERT: E 142 ASN cc_start: 0.8956 (m-40) cc_final: 0.8117 (m-40) REVERT: E 160 ASP cc_start: 0.7674 (m-30) cc_final: 0.7463 (m-30) REVERT: E 201 CYS cc_start: 0.8673 (m) cc_final: 0.7854 (m) REVERT: d 740 SER cc_start: 0.8178 (p) cc_final: 0.7908 (t) REVERT: d 772 LYS cc_start: 0.8298 (tttt) cc_final: 0.7816 (tppt) REVERT: d 776 ASN cc_start: 0.8112 (m-40) cc_final: 0.7646 (m110) REVERT: c 739 MET cc_start: 0.7932 (ttp) cc_final: 0.7628 (ttp) REVERT: c 767 PHE cc_start: 0.6863 (m-80) cc_final: 0.6606 (m-80) REVERT: b 778 TYR cc_start: 0.8042 (m-80) cc_final: 0.7589 (m-10) REVERT: B 81 SER cc_start: 0.8846 (p) cc_final: 0.8489 (t) REVERT: B 88 LEU cc_start: 0.8404 (mt) cc_final: 0.8082 (mt) REVERT: B 228 TYR cc_start: 0.7926 (m-80) cc_final: 0.7636 (m-80) REVERT: a 731 LEU cc_start: 0.8707 (mp) cc_final: 0.8237 (mt) REVERT: a 792 LEU cc_start: 0.8158 (tt) cc_final: 0.7743 (tp) REVERT: A 148 LEU cc_start: 0.8916 (mt) cc_final: 0.8491 (tt) REVERT: g 719 THR cc_start: 0.8592 (p) cc_final: 0.8315 (t) REVERT: g 731 LEU cc_start: 0.8901 (mp) cc_final: 0.8095 (mp) REVERT: G 120 ASN cc_start: 0.7928 (m-40) cc_final: 0.7531 (m-40) REVERT: G 146 THR cc_start: 0.8578 (p) cc_final: 0.8300 (t) REVERT: G 148 LEU cc_start: 0.9062 (mt) cc_final: 0.8788 (mp) REVERT: G 165 SER cc_start: 0.8707 (p) cc_final: 0.7857 (t) REVERT: f 740 SER cc_start: 0.8254 (p) cc_final: 0.7906 (t) REVERT: f 771 TYR cc_start: 0.6740 (m-80) cc_final: 0.5794 (m-80) REVERT: F 102 THR cc_start: 0.8507 (p) cc_final: 0.7911 (t) REVERT: F 109 ILE cc_start: 0.9157 (mt) cc_final: 0.8816 (mm) REVERT: F 146 THR cc_start: 0.8546 (p) cc_final: 0.8128 (m) REVERT: F 214 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8502 (mm) REVERT: F 229 GLU cc_start: 0.6299 (tt0) cc_final: 0.5925 (tt0) REVERT: F 231 ASP cc_start: 0.6201 (m-30) cc_final: 0.4972 (m-30) REVERT: e 723 THR cc_start: 0.8777 (m) cc_final: 0.7849 (p) REVERT: e 731 LEU cc_start: 0.8723 (mp) cc_final: 0.8309 (mp) REVERT: e 783 ASN cc_start: 0.7327 (m110) cc_final: 0.6980 (m110) REVERT: e 785 PHE cc_start: 0.7763 (t80) cc_final: 0.7167 (t80) REVERT: e 791 GLN cc_start: 0.8197 (tt0) cc_final: 0.7679 (tm-30) outliers start: 30 outliers final: 2 residues processed: 2072 average time/residue: 0.6121 time to fit residues: 2058.4004 Evaluate side-chains 921 residues out of total 6163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 915 time to evaluate : 4.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 702 random chunks: chunk 592 optimal weight: 0.4980 chunk 532 optimal weight: 0.7980 chunk 295 optimal weight: 0.7980 chunk 181 optimal weight: 3.9990 chunk 358 optimal weight: 2.9990 chunk 284 optimal weight: 1.9990 chunk 550 optimal weight: 0.9990 chunk 212 optimal weight: 2.9990 chunk 334 optimal weight: 7.9990 chunk 409 optimal weight: 10.0000 chunk 637 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 290 ASN 1 300 ASN ** 1 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 606 ASN 1 716 HIS 1 744 ASN 1 814 ASN 2 198 ASN 2 229 ASN 2 290 ASN 2 424 ASN 2 560 ASN 2 566 GLN 2 568 HIS ** 2 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 735 ASN ** 2 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 814 ASN 2 816 HIS 3 198 ASN 3 290 ASN 3 326 ASN 3 566 GLN 3 704 HIS ** 3 768 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 816 HIS ** 4 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 530 GLN 4 537 GLN ** 4 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 560 ASN 4 566 GLN 4 606 ASN 4 716 HIS ** 4 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 816 HIS ** 4 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 290 ASN 5 300 ASN ** 5 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 509 ASN ** 5 556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 566 GLN ** 5 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 606 ASN 5 657 ASN ** 5 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN C 123 ASN C 150 GLN 6 227 ASN ** 6 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 716 HIS 6 752 ASN E 55 HIS ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 700 ASN d 734 ASN c 700 ASN c 724 ASN b 734 ASN ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 733 GLN a 734 ASN a 776 ASN A 55 HIS ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 96 ASN g 734 ASN G 66 HIS ** G 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 734 ASN F 55 HIS F 123 ASN e 733 GLN e 734 ASN ** e 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 59 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 58380 Z= 0.227 Angle : 0.720 12.444 78702 Z= 0.379 Chirality : 0.046 0.284 8876 Planarity : 0.005 0.089 9939 Dihedral : 10.919 170.057 7975 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.00 % Favored : 92.82 % Rotamer: Outliers : 0.15 % Allowed : 2.35 % Favored : 97.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.31 % 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: -3.47 (0.09), residues: 6773 helix: -2.49 (0.07), residues: 3309 sheet: -1.81 (0.22), residues: 492 loop : -1.99 (0.11), residues: 2972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP A 171 HIS 0.017 0.001 HIS A 55 PHE 0.034 0.002 PHE g 701 TYR 0.034 0.002 TYR 6 846 ARG 0.014 0.001 ARG 5 360 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13546 Ramachandran restraints generated. 6773 Oldfield, 0 Emsley, 6773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13546 Ramachandran restraints generated. 6773 Oldfield, 0 Emsley, 6773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1252 residues out of total 6163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1243 time to evaluate : 5.117 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: 1 293 LYS cc_start: 0.8821 (mttt) cc_final: 0.8335 (tmtt) REVERT: 1 366 LEU cc_start: 0.9289 (mt) cc_final: 0.8765 (pt) REVERT: 1 655 LEU cc_start: 0.8458 (mt) cc_final: 0.8225 (mp) REVERT: 1 667 MET cc_start: 0.8319 (mmm) cc_final: 0.7916 (mmm) REVERT: 1 691 ASP cc_start: 0.8737 (m-30) cc_final: 0.8288 (t70) REVERT: 1 716 HIS cc_start: 0.7420 (t-90) cc_final: 0.6604 (t70) REVERT: 1 718 ASP cc_start: 0.8103 (m-30) cc_final: 0.6562 (m-30) REVERT: 1 721 LYS cc_start: 0.9189 (mttt) cc_final: 0.8941 (mttt) REVERT: 1 747 ILE cc_start: 0.9252 (mp) cc_final: 0.9005 (mp) REVERT: 2 274 PHE cc_start: 0.7653 (m-80) cc_final: 0.7170 (m-80) REVERT: 2 414 TYR cc_start: 0.8514 (m-80) cc_final: 0.8249 (m-80) REVERT: 2 534 LYS cc_start: 0.9171 (mttt) cc_final: 0.8786 (tptp) REVERT: 2 666 ASN cc_start: 0.7970 (m110) cc_final: 0.7617 (p0) REVERT: 2 667 MET cc_start: 0.8588 (mmm) cc_final: 0.8376 (tpp) REVERT: 2 802 ASP cc_start: 0.8742 (m-30) cc_final: 0.8244 (t0) REVERT: 2 870 MET cc_start: 0.8540 (mmp) cc_final: 0.8215 (mmm) REVERT: 2 880 LYS cc_start: 0.7642 (mttt) cc_final: 0.7112 (tmtt) REVERT: 3 334 LYS cc_start: 0.8013 (pttp) cc_final: 0.7458 (mptt) REVERT: 3 412 ASP cc_start: 0.7518 (p0) cc_final: 0.7234 (p0) REVERT: 3 534 LYS cc_start: 0.9050 (mttt) cc_final: 0.8697 (ptpp) REVERT: 3 716 HIS cc_start: 0.8377 (t-90) cc_final: 0.7697 (t-90) REVERT: 3 725 GLN cc_start: 0.8940 (mt0) cc_final: 0.8650 (mp10) REVERT: 3 731 TYR cc_start: 0.6682 (m-80) cc_final: 0.6194 (m-80) REVERT: 3 739 ASN cc_start: 0.7761 (m-40) cc_final: 0.7533 (m-40) REVERT: 3 778 MET cc_start: 0.8152 (mmp) cc_final: 0.7882 (tpp) REVERT: 3 884 ASP cc_start: 0.7813 (m-30) cc_final: 0.7565 (p0) REVERT: 4 568 HIS cc_start: 0.8533 (m90) cc_final: 0.8189 (m-70) REVERT: 4 818 ILE cc_start: 0.8669 (mt) cc_final: 0.8444 (mm) REVERT: 4 827 GLU cc_start: 0.8309 (mp0) cc_final: 0.8082 (mp0) REVERT: 4 885 ASP cc_start: 0.7864 (m-30) cc_final: 0.7546 (p0) REVERT: 5 307 ASP cc_start: 0.8238 (OUTLIER) cc_final: 0.7840 (p0) REVERT: 5 396 ASP cc_start: 0.8119 (m-30) cc_final: 0.7873 (m-30) REVERT: 5 447 ASP cc_start: 0.8682 (m-30) cc_final: 0.8362 (m-30) REVERT: 5 571 TYR cc_start: 0.8425 (t80) cc_final: 0.8011 (t80) REVERT: 5 579 MET cc_start: 0.8948 (tpp) cc_final: 0.8650 (tpp) REVERT: 5 799 ASN cc_start: 0.8351 (m-40) cc_final: 0.7975 (t0) REVERT: C 37 LEU cc_start: 0.8070 (mt) cc_final: 0.7853 (pp) REVERT: C 55 HIS cc_start: 0.7770 (m-70) cc_final: 0.7076 (m-70) REVERT: C 91 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7588 (mm-30) REVERT: C 120 ASN cc_start: 0.9128 (m-40) cc_final: 0.8907 (m-40) REVERT: C 132 PHE cc_start: 0.8736 (m-80) cc_final: 0.8528 (m-10) REVERT: C 139 GLU cc_start: 0.7396 (tt0) cc_final: 0.7108 (tp30) REVERT: 6 425 LYS cc_start: 0.8437 (mttt) cc_final: 0.8182 (ttmm) REVERT: 6 716 HIS cc_start: 0.7640 (t-90) cc_final: 0.7347 (t70) REVERT: 6 757 LEU cc_start: 0.6465 (mt) cc_final: 0.6239 (mt) REVERT: 6 829 ARG cc_start: 0.7852 (mtt180) cc_final: 0.6827 (mtt90) REVERT: 6 853 ASP cc_start: 0.8607 (p0) cc_final: 0.7497 (p0) REVERT: D 150 GLN cc_start: 0.8035 (mt0) cc_final: 0.7769 (mt0) REVERT: E 53 TYR cc_start: 0.7459 (t80) cc_final: 0.6894 (t80) REVERT: E 88 LEU cc_start: 0.9149 (mt) cc_final: 0.8858 (mt) REVERT: E 160 ASP cc_start: 0.7713 (m-30) cc_final: 0.7226 (m-30) REVERT: E 194 VAL cc_start: 0.8829 (t) cc_final: 0.8540 (t) REVERT: E 201 CYS cc_start: 0.8616 (m) cc_final: 0.7743 (m) REVERT: d 740 SER cc_start: 0.8355 (p) cc_final: 0.8027 (t) REVERT: c 703 GLU cc_start: 0.7891 (tm-30) cc_final: 0.7621 (tm-30) REVERT: c 714 LEU cc_start: 0.8876 (mt) cc_final: 0.8335 (mt) REVERT: c 739 MET cc_start: 0.8294 (ttp) cc_final: 0.7872 (ttp) REVERT: c 767 PHE cc_start: 0.6942 (m-80) cc_final: 0.6667 (m-80) REVERT: b 791 GLN cc_start: 0.8267 (tt0) cc_final: 0.7875 (tm-30) REVERT: b 810 ILE cc_start: 0.9469 (mm) cc_final: 0.9156 (mm) REVERT: B 51 ASP cc_start: 0.8065 (m-30) cc_final: 0.7769 (m-30) REVERT: B 77 VAL cc_start: 0.8898 (m) cc_final: 0.8614 (t) REVERT: B 126 GLU cc_start: 0.7261 (pm20) cc_final: 0.7023 (pm20) REVERT: B 150 GLN cc_start: 0.8231 (pm20) cc_final: 0.7923 (pm20) REVERT: B 201 CYS cc_start: 0.8618 (m) cc_final: 0.8332 (m) REVERT: a 768 TYR cc_start: 0.7500 (t80) cc_final: 0.7199 (t80) REVERT: A 146 THR cc_start: 0.8833 (p) cc_final: 0.8600 (t) REVERT: A 171 TRP cc_start: 0.7112 (m100) cc_final: 0.6902 (m100) REVERT: A 203 LEU cc_start: 0.8487 (mt) cc_final: 0.8273 (tp) REVERT: g 731 LEU cc_start: 0.8994 (mp) cc_final: 0.8685 (mt) REVERT: G 66 HIS cc_start: 0.7599 (m-70) cc_final: 0.6992 (m-70) REVERT: G 111 ASP cc_start: 0.7125 (m-30) cc_final: 0.6915 (m-30) REVERT: G 114 THR cc_start: 0.9019 (p) cc_final: 0.8705 (t) REVERT: G 120 ASN cc_start: 0.8396 (m-40) cc_final: 0.7633 (m-40) REVERT: G 139 GLU cc_start: 0.7548 (tm-30) cc_final: 0.6216 (tm-30) REVERT: f 739 MET cc_start: 0.8066 (ttm) cc_final: 0.7861 (ttp) REVERT: F 41 ILE cc_start: 0.8206 (mm) cc_final: 0.7875 (tp) REVERT: F 133 LEU cc_start: 0.8809 (mt) cc_final: 0.8381 (tp) REVERT: F 171 TRP cc_start: 0.8381 (m100) cc_final: 0.8083 (m100) REVERT: e 791 GLN cc_start: 0.8091 (tt0) cc_final: 0.7694 (tm-30) REVERT: e 793 ILE cc_start: 0.8749 (mm) cc_final: 0.8201 (mm) outliers start: 9 outliers final: 1 residues processed: 1249 average time/residue: 0.5962 time to fit residues: 1250.6623 Evaluate side-chains 741 residues out of total 6163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 739 time to evaluate : 5.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 702 random chunks: chunk 354 optimal weight: 5.9990 chunk 197 optimal weight: 3.9990 chunk 530 optimal weight: 0.7980 chunk 434 optimal weight: 5.9990 chunk 175 optimal weight: 3.9990 chunk 638 optimal weight: 0.7980 chunk 689 optimal weight: 10.0000 chunk 568 optimal weight: 0.3980 chunk 633 optimal weight: 3.9990 chunk 217 optimal weight: 0.9990 chunk 512 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 300 ASN ** 1 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 816 HIS 2 198 ASN 2 227 ASN 2 568 HIS 2 744 ASN 2 816 HIS ** 3 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 752 ASN ** 3 768 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 198 ASN ** 4 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 530 GLN ** 4 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 716 HIS ** 4 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 556 HIS 5 568 HIS 5 674 HIS 5 834 ASN C 55 HIS ** 6 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 ASN D 120 ASN d 726 GLN ** d 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 816 ASN ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 724 ASN ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 96 ASN G 96 ASN ** G 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 161 GLN f 734 ASN ** f 787 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 HIS F 96 ASN ** F 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.4227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 58380 Z= 0.194 Angle : 0.650 8.145 78702 Z= 0.342 Chirality : 0.045 0.356 8876 Planarity : 0.004 0.120 9939 Dihedral : 10.446 170.953 7975 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.56 % Favored : 92.31 % Rotamer: Outliers : 0.13 % Allowed : 1.98 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % 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: -2.80 (0.09), residues: 6773 helix: -1.87 (0.08), residues: 3314 sheet: -1.55 (0.22), residues: 503 loop : -1.72 (0.11), residues: 2956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP G 171 HIS 0.016 0.001 HIS C 55 PHE 0.031 0.002 PHE G 170 TYR 0.028 0.002 TYR b 803 ARG 0.009 0.001 ARG 2 281 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13546 Ramachandran restraints generated. 6773 Oldfield, 0 Emsley, 6773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13546 Ramachandran restraints generated. 6773 Oldfield, 0 Emsley, 6773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1092 residues out of total 6163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1084 time to evaluate : 5.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 293 LYS cc_start: 0.8836 (mttt) cc_final: 0.8350 (tmtt) REVERT: 1 358 PHE cc_start: 0.7170 (m-80) cc_final: 0.6953 (m-80) REVERT: 1 366 LEU cc_start: 0.9263 (mt) cc_final: 0.8754 (pt) REVERT: 1 667 MET cc_start: 0.8385 (mmm) cc_final: 0.8039 (mmm) REVERT: 1 691 ASP cc_start: 0.8764 (m-30) cc_final: 0.8239 (t70) REVERT: 1 701 GLU cc_start: 0.8047 (pt0) cc_final: 0.7598 (pp20) REVERT: 1 716 HIS cc_start: 0.7795 (t-90) cc_final: 0.7045 (t-90) REVERT: 1 718 ASP cc_start: 0.8153 (m-30) cc_final: 0.6835 (m-30) REVERT: 1 721 LYS cc_start: 0.9245 (mttt) cc_final: 0.8856 (mttm) REVERT: 1 746 ILE cc_start: 0.8912 (mm) cc_final: 0.8564 (mm) REVERT: 2 272 ARG cc_start: 0.8526 (ttt180) cc_final: 0.8321 (ttt180) REVERT: 2 274 PHE cc_start: 0.7721 (m-80) cc_final: 0.7076 (m-80) REVERT: 2 367 VAL cc_start: 0.9270 (t) cc_final: 0.9031 (t) REVERT: 2 731 TYR cc_start: 0.7461 (m-80) cc_final: 0.7229 (m-80) REVERT: 2 739 ASN cc_start: 0.8374 (m-40) cc_final: 0.8089 (m110) REVERT: 2 761 LYS cc_start: 0.8990 (mttt) cc_final: 0.8747 (mttm) REVERT: 2 802 ASP cc_start: 0.8726 (m-30) cc_final: 0.8171 (t0) REVERT: 2 880 LYS cc_start: 0.7727 (mttt) cc_final: 0.7114 (tmtt) REVERT: 3 334 LYS cc_start: 0.7983 (pttp) cc_final: 0.7403 (mptt) REVERT: 3 534 LYS cc_start: 0.9003 (mttt) cc_final: 0.8626 (ptpp) REVERT: 3 579 MET cc_start: 0.8402 (tpp) cc_final: 0.7999 (tpp) REVERT: 3 716 HIS cc_start: 0.8508 (t-90) cc_final: 0.7714 (t-90) REVERT: 3 725 GLN cc_start: 0.8913 (mt0) cc_final: 0.8518 (mp10) REVERT: 4 288 MET cc_start: 0.8197 (ptp) cc_final: 0.7977 (ptm) REVERT: 4 374 MET cc_start: 0.8436 (mmp) cc_final: 0.8182 (mmm) REVERT: 4 568 HIS cc_start: 0.8558 (m90) cc_final: 0.8079 (m90) REVERT: 4 749 MET cc_start: 0.8290 (mmm) cc_final: 0.8090 (mmm) REVERT: 4 818 ILE cc_start: 0.8755 (mt) cc_final: 0.8534 (mm) REVERT: 4 827 GLU cc_start: 0.8224 (mp0) cc_final: 0.7756 (mp0) REVERT: 4 876 MET cc_start: 0.8881 (mpp) cc_final: 0.8569 (mpp) REVERT: 4 885 ASP cc_start: 0.7772 (m-30) cc_final: 0.7508 (p0) REVERT: 5 396 ASP cc_start: 0.8120 (m-30) cc_final: 0.7798 (m-30) REVERT: 5 579 MET cc_start: 0.8969 (tpp) cc_final: 0.8676 (tpp) REVERT: 5 635 LEU cc_start: 0.9083 (tp) cc_final: 0.8835 (tp) REVERT: 5 701 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7917 (tm-30) REVERT: 5 845 ASP cc_start: 0.8399 (m-30) cc_final: 0.7977 (p0) REVERT: C 37 LEU cc_start: 0.8173 (mt) cc_final: 0.7972 (pp) REVERT: C 109 ILE cc_start: 0.9468 (mm) cc_final: 0.9230 (mm) REVERT: C 111 ASP cc_start: 0.8181 (m-30) cc_final: 0.7863 (m-30) REVERT: C 114 THR cc_start: 0.9014 (p) cc_final: 0.8620 (t) REVERT: C 132 PHE cc_start: 0.8700 (m-80) cc_final: 0.8343 (m-10) REVERT: C 138 ASN cc_start: 0.6394 (t0) cc_final: 0.6004 (t0) REVERT: 6 425 LYS cc_start: 0.8475 (mttt) cc_final: 0.8134 (ttmm) REVERT: 6 624 MET cc_start: 0.7823 (mtm) cc_final: 0.7466 (mtt) REVERT: 6 716 HIS cc_start: 0.7621 (t-90) cc_final: 0.7128 (t-170) REVERT: D 80 TRP cc_start: 0.8363 (m100) cc_final: 0.8113 (m100) REVERT: D 126 GLU cc_start: 0.7911 (pm20) cc_final: 0.7566 (pm20) REVERT: D 136 ILE cc_start: 0.8876 (mt) cc_final: 0.8492 (mt) REVERT: D 171 TRP cc_start: 0.8165 (m-10) cc_final: 0.7825 (m-10) REVERT: E 53 TYR cc_start: 0.7481 (t80) cc_final: 0.6940 (t80) REVERT: E 80 TRP cc_start: 0.8612 (m100) cc_final: 0.8382 (m100) REVERT: E 160 ASP cc_start: 0.7737 (m-30) cc_final: 0.7327 (m-30) REVERT: d 731 LEU cc_start: 0.9035 (mt) cc_final: 0.8697 (mt) REVERT: c 714 LEU cc_start: 0.8751 (mt) cc_final: 0.8455 (mt) REVERT: c 739 MET cc_start: 0.8194 (ttp) cc_final: 0.7989 (ttp) REVERT: b 773 GLN cc_start: 0.8502 (mp10) cc_final: 0.8246 (mp10) REVERT: B 51 ASP cc_start: 0.7956 (m-30) cc_final: 0.6714 (m-30) REVERT: B 77 VAL cc_start: 0.8864 (m) cc_final: 0.8554 (t) REVERT: B 84 TRP cc_start: 0.7949 (m100) cc_final: 0.7093 (m100) REVERT: B 111 ASP cc_start: 0.8391 (m-30) cc_final: 0.8092 (m-30) REVERT: B 120 ASN cc_start: 0.8974 (m110) cc_final: 0.8558 (m110) REVERT: B 224 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7423 (mp0) REVERT: a 672 ILE cc_start: 0.8115 (mt) cc_final: 0.7837 (tp) REVERT: a 702 TYR cc_start: 0.6254 (m-10) cc_final: 0.6013 (m-10) REVERT: a 768 TYR cc_start: 0.7299 (t80) cc_final: 0.7000 (t80) REVERT: A 139 GLU cc_start: 0.7509 (tp30) cc_final: 0.7067 (tp30) REVERT: A 148 LEU cc_start: 0.9098 (tt) cc_final: 0.8530 (tt) REVERT: g 739 MET cc_start: 0.8648 (ttp) cc_final: 0.8444 (ttp) REVERT: g 800 THR cc_start: 0.8131 (p) cc_final: 0.7342 (p) REVERT: G 133 LEU cc_start: 0.8957 (tp) cc_final: 0.8441 (tp) REVERT: f 670 LYS cc_start: 0.6623 (mmmm) cc_final: 0.5800 (tppp) REVERT: f 731 LEU cc_start: 0.8861 (mt) cc_final: 0.8474 (mt) REVERT: F 70 LYS cc_start: 0.8550 (pttp) cc_final: 0.8290 (ptpt) REVERT: F 91 GLU cc_start: 0.7222 (tp30) cc_final: 0.6730 (tp30) REVERT: F 102 THR cc_start: 0.8330 (p) cc_final: 0.8122 (t) REVERT: F 133 LEU cc_start: 0.8815 (mt) cc_final: 0.8382 (tp) REVERT: e 731 LEU cc_start: 0.8909 (mt) cc_final: 0.8552 (mt) outliers start: 8 outliers final: 1 residues processed: 1090 average time/residue: 0.5339 time to fit residues: 984.3194 Evaluate side-chains 670 residues out of total 6163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 669 time to evaluate : 5.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 702 random chunks: chunk 630 optimal weight: 4.9990 chunk 480 optimal weight: 3.9990 chunk 331 optimal weight: 9.9990 chunk 70 optimal weight: 9.9990 chunk 304 optimal weight: 6.9990 chunk 428 optimal weight: 10.0000 chunk 640 optimal weight: 0.0870 chunk 678 optimal weight: 1.9990 chunk 334 optimal weight: 10.0000 chunk 607 optimal weight: 2.9990 chunk 182 optimal weight: 2.9990 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 229 ASN ** 1 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 300 ASN ** 1 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 531 ASN 1 568 HIS 2 203 ASN 2 517 ASN 2 568 HIS ** 2 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 752 ASN 2 816 HIS 3 203 ASN ** 3 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 557 ASN ** 3 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 704 HIS ** 3 768 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 850 GLN 4 198 ASN ** 4 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 424 ASN 4 530 GLN ** 4 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 388 ASN ** 5 556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 799 ASN C 55 HIS ** 6 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 814 ASN D 96 ASN ** D 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 796 ASN B 120 ASN ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 ASN ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 96 ASN G 96 ASN ** G 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 ASN G 161 GLN ** f 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 787 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 ASN F 123 ASN F 134 HIS ** F 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 787 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 796 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.4927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 58380 Z= 0.339 Angle : 0.737 11.815 78702 Z= 0.383 Chirality : 0.047 0.392 8876 Planarity : 0.005 0.061 9939 Dihedral : 10.293 176.486 7975 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.11 % Favored : 91.75 % Rotamer: Outliers : 0.11 % Allowed : 2.82 % Favored : 97.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.39 % Twisted General : 0.06 % 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: -2.25 (0.10), residues: 6773 helix: -1.33 (0.08), residues: 3285 sheet: -1.33 (0.23), residues: 480 loop : -1.57 (0.12), residues: 3008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP C 85 HIS 0.010 0.002 HIS A 55 PHE 0.031 0.002 PHE G 170 TYR 0.029 0.002 TYR 2 573 ARG 0.008 0.001 ARG 3 776 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13546 Ramachandran restraints generated. 6773 Oldfield, 0 Emsley, 6773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13546 Ramachandran restraints generated. 6773 Oldfield, 0 Emsley, 6773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 882 residues out of total 6163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 875 time to evaluate : 5.404 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: 1 196 ASN cc_start: 0.7693 (t0) cc_final: 0.7435 (t0) REVERT: 1 250 TYR cc_start: 0.8318 (t80) cc_final: 0.8016 (t80) REVERT: 1 293 LYS cc_start: 0.8831 (mttt) cc_final: 0.8432 (tmtt) REVERT: 1 358 PHE cc_start: 0.7167 (m-80) cc_final: 0.6964 (m-80) REVERT: 1 366 LEU cc_start: 0.9371 (mt) cc_final: 0.8807 (pt) REVERT: 1 667 MET cc_start: 0.8484 (mmm) cc_final: 0.8086 (mmm) REVERT: 1 691 ASP cc_start: 0.8857 (m-30) cc_final: 0.8297 (t0) REVERT: 1 716 HIS cc_start: 0.8164 (t-90) cc_final: 0.7094 (t-90) REVERT: 1 718 ASP cc_start: 0.8078 (m-30) cc_final: 0.6374 (m-30) REVERT: 1 721 LYS cc_start: 0.9390 (mttt) cc_final: 0.9144 (mttt) REVERT: 1 746 ILE cc_start: 0.8994 (mm) cc_final: 0.8684 (mm) REVERT: 2 274 PHE cc_start: 0.7873 (m-80) cc_final: 0.7206 (m-80) REVERT: 2 534 LYS cc_start: 0.9236 (mttt) cc_final: 0.8977 (mtmm) REVERT: 2 802 ASP cc_start: 0.8877 (m-30) cc_final: 0.8358 (t0) REVERT: 2 870 MET cc_start: 0.8765 (mmp) cc_final: 0.8379 (tpp) REVERT: 2 880 LYS cc_start: 0.7796 (mttt) cc_final: 0.7213 (tmtt) REVERT: 3 334 LYS cc_start: 0.8081 (pttp) cc_final: 0.7494 (mptt) REVERT: 3 579 MET cc_start: 0.8558 (tpp) cc_final: 0.8326 (tpp) REVERT: 3 660 ASP cc_start: 0.8590 (m-30) cc_final: 0.8240 (t70) REVERT: 3 716 HIS cc_start: 0.8600 (t-90) cc_final: 0.7846 (t-90) REVERT: 3 725 GLN cc_start: 0.8840 (mt0) cc_final: 0.8435 (mp10) REVERT: 3 778 MET cc_start: 0.8567 (mmp) cc_final: 0.8272 (tpp) REVERT: 4 374 MET cc_start: 0.8514 (mmp) cc_final: 0.8292 (mmm) REVERT: 4 568 HIS cc_start: 0.8763 (m90) cc_final: 0.8192 (m90) REVERT: 4 778 MET cc_start: 0.8612 (tmm) cc_final: 0.8408 (tmm) REVERT: 4 818 ILE cc_start: 0.8920 (mt) cc_final: 0.8697 (mm) REVERT: 5 396 ASP cc_start: 0.8233 (m-30) cc_final: 0.7888 (m-30) REVERT: 5 542 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8018 (pm20) REVERT: 5 571 TYR cc_start: 0.8569 (t80) cc_final: 0.8261 (t80) REVERT: 5 579 MET cc_start: 0.9146 (tpp) cc_final: 0.8886 (tpp) REVERT: 5 596 TYR cc_start: 0.6657 (m-80) cc_final: 0.6251 (m-80) REVERT: 5 629 LYS cc_start: 0.8434 (mtmt) cc_final: 0.7848 (mmmm) REVERT: 5 701 GLU cc_start: 0.8331 (tm-30) cc_final: 0.7967 (tm-30) REVERT: 5 845 ASP cc_start: 0.8358 (m-30) cc_final: 0.8064 (p0) REVERT: C 132 PHE cc_start: 0.8812 (m-80) cc_final: 0.8564 (m-10) REVERT: C 138 ASN cc_start: 0.6571 (t0) cc_final: 0.6071 (t0) REVERT: 6 624 MET cc_start: 0.7889 (mtm) cc_final: 0.7563 (mtt) REVERT: 6 853 ASP cc_start: 0.8408 (p0) cc_final: 0.8144 (p0) REVERT: E 160 ASP cc_start: 0.7616 (m-30) cc_final: 0.7328 (m-30) REVERT: d 751 GLN cc_start: 0.7566 (pt0) cc_final: 0.7224 (pt0) REVERT: b 765 ASP cc_start: 0.7697 (m-30) cc_final: 0.7414 (m-30) REVERT: B 43 ASP cc_start: 0.8750 (m-30) cc_final: 0.8498 (m-30) REVERT: B 51 ASP cc_start: 0.7855 (m-30) cc_final: 0.6780 (m-30) REVERT: B 77 VAL cc_start: 0.9052 (m) cc_final: 0.8826 (t) REVERT: B 111 ASP cc_start: 0.8494 (m-30) cc_final: 0.8105 (m-30) REVERT: B 120 ASN cc_start: 0.9189 (m-40) cc_final: 0.8681 (m110) REVERT: B 136 ILE cc_start: 0.9214 (mt) cc_final: 0.8768 (mt) REVERT: B 139 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7514 (tp30) REVERT: B 160 ASP cc_start: 0.8200 (t70) cc_final: 0.7856 (t70) REVERT: B 161 GLN cc_start: 0.8529 (mp10) cc_final: 0.7906 (mp10) REVERT: a 672 ILE cc_start: 0.8231 (mt) cc_final: 0.7853 (tp) REVERT: a 768 TYR cc_start: 0.7308 (t80) cc_final: 0.7038 (t80) REVERT: g 739 MET cc_start: 0.8691 (ttp) cc_final: 0.8484 (ttp) REVERT: G 54 GLU cc_start: 0.7341 (mp0) cc_final: 0.6993 (mp0) REVERT: G 111 ASP cc_start: 0.7795 (m-30) cc_final: 0.7463 (m-30) REVERT: G 133 LEU cc_start: 0.9055 (tp) cc_final: 0.8522 (tp) REVERT: f 731 LEU cc_start: 0.8952 (mt) cc_final: 0.8611 (mt) REVERT: F 133 LEU cc_start: 0.8995 (mt) cc_final: 0.8756 (tp) REVERT: F 137 LEU cc_start: 0.8712 (mm) cc_final: 0.8488 (mm) REVERT: F 210 MET cc_start: 0.8499 (mmp) cc_final: 0.8224 (tpp) outliers start: 7 outliers final: 0 residues processed: 882 average time/residue: 0.5282 time to fit residues: 797.5856 Evaluate side-chains 585 residues out of total 6163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 585 time to evaluate : 5.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 702 random chunks: chunk 565 optimal weight: 0.7980 chunk 385 optimal weight: 0.9980 chunk 9 optimal weight: 8.9990 chunk 505 optimal weight: 4.9990 chunk 279 optimal weight: 4.9990 chunk 579 optimal weight: 2.9990 chunk 469 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 346 optimal weight: 0.6980 chunk 609 optimal weight: 3.9990 chunk 171 optimal weight: 0.0970 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 744 ASN ** 1 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 816 HIS 2 568 HIS 2 733 ASN 2 744 ASN 2 816 HIS 3 704 HIS 3 744 ASN 3 768 ASN 3 850 GLN 4 198 ASN ** 4 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 834 ASN 5 509 ASN ** 5 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 ASN ** 6 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 ASN ** D 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 734 ASN d 783 ASN d 816 ASN ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 ASN a 733 GLN ** a 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 112 GLN g 724 ASN ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 96 ASN ** G 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 787 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 796 ASN F 96 ASN ** F 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 787 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.5196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 58380 Z= 0.184 Angle : 0.611 8.719 78702 Z= 0.320 Chirality : 0.044 0.443 8876 Planarity : 0.004 0.054 9939 Dihedral : 10.036 176.380 7975 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.04 % Favored : 92.85 % Rotamer: Outliers : 0.02 % Allowed : 1.41 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % 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: -1.89 (0.10), residues: 6773 helix: -0.97 (0.09), residues: 3246 sheet: -1.27 (0.23), residues: 482 loop : -1.44 (0.12), residues: 3045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 110 HIS 0.010 0.001 HIS G 66 PHE 0.022 0.002 PHE G 170 TYR 0.024 0.001 TYR 4 573 ARG 0.014 0.001 ARG 5 737 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13546 Ramachandran restraints generated. 6773 Oldfield, 0 Emsley, 6773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13546 Ramachandran restraints generated. 6773 Oldfield, 0 Emsley, 6773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 889 residues out of total 6163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 888 time to evaluate : 5.099 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: 1 250 TYR cc_start: 0.8274 (t80) cc_final: 0.7991 (t80) REVERT: 1 293 LYS cc_start: 0.8826 (mttt) cc_final: 0.8376 (tmtt) REVERT: 1 366 LEU cc_start: 0.9341 (mt) cc_final: 0.8747 (pt) REVERT: 1 667 MET cc_start: 0.8481 (mmm) cc_final: 0.8170 (mmm) REVERT: 1 691 ASP cc_start: 0.8847 (m-30) cc_final: 0.8256 (t70) REVERT: 1 716 HIS cc_start: 0.7928 (t-90) cc_final: 0.7074 (t-90) REVERT: 1 718 ASP cc_start: 0.8007 (m-30) cc_final: 0.6893 (p0) REVERT: 1 721 LYS cc_start: 0.9325 (mttt) cc_final: 0.9084 (mttt) REVERT: 1 746 ILE cc_start: 0.9017 (mm) cc_final: 0.8725 (mm) REVERT: 2 272 ARG cc_start: 0.8479 (ttt180) cc_final: 0.8169 (ttt180) REVERT: 2 274 PHE cc_start: 0.7878 (m-80) cc_final: 0.7168 (m-80) REVERT: 2 534 LYS cc_start: 0.9219 (mttt) cc_final: 0.8960 (mtmm) REVERT: 2 761 LYS cc_start: 0.8990 (mttt) cc_final: 0.8776 (mttm) REVERT: 2 828 LYS cc_start: 0.9056 (mmtt) cc_final: 0.8710 (tptt) REVERT: 2 880 LYS cc_start: 0.7754 (mttt) cc_final: 0.7162 (tmtt) REVERT: 3 334 LYS cc_start: 0.8069 (pttp) cc_final: 0.7499 (mptt) REVERT: 3 660 ASP cc_start: 0.8484 (m-30) cc_final: 0.8110 (t0) REVERT: 3 716 HIS cc_start: 0.8621 (t-90) cc_final: 0.7758 (t-90) REVERT: 3 725 GLN cc_start: 0.8748 (mt0) cc_final: 0.8355 (mp10) REVERT: 3 778 MET cc_start: 0.8555 (mmp) cc_final: 0.8311 (tpp) REVERT: 4 374 MET cc_start: 0.8502 (mmp) cc_final: 0.8228 (mmm) REVERT: 4 568 HIS cc_start: 0.8699 (m90) cc_final: 0.8116 (m90) REVERT: 4 734 ASP cc_start: 0.8038 (m-30) cc_final: 0.7669 (t0) REVERT: 5 396 ASP cc_start: 0.8095 (m-30) cc_final: 0.7788 (m-30) REVERT: 5 542 GLU cc_start: 0.8432 (mt-10) cc_final: 0.7999 (pm20) REVERT: 5 571 TYR cc_start: 0.8526 (t80) cc_final: 0.8120 (t80) REVERT: 5 579 MET cc_start: 0.9093 (tpp) cc_final: 0.8886 (tpp) REVERT: 5 629 LYS cc_start: 0.8346 (mtmt) cc_final: 0.7771 (mmmm) REVERT: 5 701 GLU cc_start: 0.8319 (tm-30) cc_final: 0.7921 (tm-30) REVERT: C 132 PHE cc_start: 0.8560 (m-80) cc_final: 0.8338 (m-10) REVERT: C 138 ASN cc_start: 0.6300 (t0) cc_final: 0.5696 (t0) REVERT: C 200 GLU cc_start: 0.7922 (mp0) cc_final: 0.7716 (mt-10) REVERT: 6 624 MET cc_start: 0.7925 (mtm) cc_final: 0.7687 (mtt) REVERT: 6 815 LEU cc_start: 0.8310 (mt) cc_final: 0.7898 (tt) REVERT: D 84 TRP cc_start: 0.8530 (m100) cc_final: 0.7580 (m100) REVERT: E 53 TYR cc_start: 0.7556 (t80) cc_final: 0.7316 (t80) REVERT: E 84 TRP cc_start: 0.8533 (m100) cc_final: 0.8076 (m100) REVERT: E 88 LEU cc_start: 0.9295 (mt) cc_final: 0.8979 (mt) REVERT: E 160 ASP cc_start: 0.7680 (m-30) cc_final: 0.7300 (m-30) REVERT: d 751 GLN cc_start: 0.7470 (pt0) cc_final: 0.6968 (pt0) REVERT: b 765 ASP cc_start: 0.7578 (m-30) cc_final: 0.7340 (m-30) REVERT: B 43 ASP cc_start: 0.8677 (m-30) cc_final: 0.8400 (m-30) REVERT: B 51 ASP cc_start: 0.7812 (m-30) cc_final: 0.6616 (m-30) REVERT: B 77 VAL cc_start: 0.9174 (m) cc_final: 0.8680 (t) REVERT: B 111 ASP cc_start: 0.8425 (m-30) cc_final: 0.8159 (m-30) REVERT: B 160 ASP cc_start: 0.8077 (t70) cc_final: 0.7560 (t70) REVERT: B 161 GLN cc_start: 0.8423 (mp10) cc_final: 0.7792 (mp10) REVERT: a 672 ILE cc_start: 0.8140 (mt) cc_final: 0.7831 (tp) REVERT: a 748 TYR cc_start: 0.7614 (t80) cc_final: 0.7377 (t80) REVERT: a 768 TYR cc_start: 0.6964 (t80) cc_final: 0.6708 (t80) REVERT: A 137 LEU cc_start: 0.8650 (mt) cc_final: 0.8400 (mt) REVERT: A 139 GLU cc_start: 0.7552 (tp30) cc_final: 0.7072 (tp30) REVERT: A 142 ASN cc_start: 0.8664 (m-40) cc_final: 0.8246 (m-40) REVERT: g 773 GLN cc_start: 0.8583 (mp10) cc_final: 0.8327 (mp10) REVERT: G 111 ASP cc_start: 0.7628 (m-30) cc_final: 0.6985 (m-30) REVERT: G 114 THR cc_start: 0.9277 (p) cc_final: 0.9024 (t) REVERT: G 133 LEU cc_start: 0.8744 (tp) cc_final: 0.8286 (tp) REVERT: f 731 LEU cc_start: 0.8938 (mt) cc_final: 0.8478 (mt) REVERT: F 91 GLU cc_start: 0.7161 (tp30) cc_final: 0.6891 (tp30) REVERT: F 133 LEU cc_start: 0.9027 (mt) cc_final: 0.8716 (tp) REVERT: F 163 ILE cc_start: 0.9068 (mt) cc_final: 0.8851 (mt) outliers start: 1 outliers final: 0 residues processed: 889 average time/residue: 0.5248 time to fit residues: 798.0333 Evaluate side-chains 602 residues out of total 6163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 602 time to evaluate : 5.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 702 random chunks: chunk 228 optimal weight: 6.9990 chunk 611 optimal weight: 1.9990 chunk 134 optimal weight: 0.5980 chunk 398 optimal weight: 20.0000 chunk 167 optimal weight: 0.6980 chunk 679 optimal weight: 0.9990 chunk 563 optimal weight: 1.9990 chunk 314 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 224 optimal weight: 0.6980 chunk 356 optimal weight: 6.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 290 ASN ** 1 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 744 ASN 2 431 GLN 2 568 HIS 2 744 ASN 2 814 ASN 2 816 HIS ** 3 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 290 ASN ** 5 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 166 GLN ** 6 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 ASN ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 724 ASN ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 112 GLN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 96 ASN ** G 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 726 GLN f 787 HIS F 96 ASN ** e 787 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.5405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 58380 Z= 0.203 Angle : 0.610 11.646 78702 Z= 0.319 Chirality : 0.045 0.460 8876 Planarity : 0.004 0.053 9939 Dihedral : 9.883 178.845 7975 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.57 % Favored : 92.29 % Rotamer: Outliers : 0.02 % Allowed : 1.48 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % 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: -1.66 (0.10), residues: 6773 helix: -0.77 (0.09), residues: 3278 sheet: -1.13 (0.23), residues: 471 loop : -1.36 (0.12), residues: 3024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 110 HIS 0.007 0.001 HIS 2 310 PHE 0.023 0.002 PHE G 132 TYR 0.027 0.001 TYR 5 264 ARG 0.012 0.000 ARG 3 408 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13546 Ramachandran restraints generated. 6773 Oldfield, 0 Emsley, 6773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13546 Ramachandran restraints generated. 6773 Oldfield, 0 Emsley, 6773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 859 residues out of total 6163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 858 time to evaluate : 5.056 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: 1 250 TYR cc_start: 0.8308 (t80) cc_final: 0.7976 (t80) REVERT: 1 293 LYS cc_start: 0.8795 (mttt) cc_final: 0.8351 (tmtt) REVERT: 1 366 LEU cc_start: 0.9356 (mt) cc_final: 0.8757 (pt) REVERT: 1 595 LEU cc_start: 0.9415 (pp) cc_final: 0.8935 (tp) REVERT: 1 667 MET cc_start: 0.8462 (mmm) cc_final: 0.8154 (mmm) REVERT: 1 691 ASP cc_start: 0.8869 (m-30) cc_final: 0.8276 (t70) REVERT: 1 716 HIS cc_start: 0.8031 (t-90) cc_final: 0.7069 (t-90) REVERT: 1 718 ASP cc_start: 0.7953 (m-30) cc_final: 0.7403 (p0) REVERT: 1 746 ILE cc_start: 0.9033 (mm) cc_final: 0.8727 (mm) REVERT: 2 274 PHE cc_start: 0.7859 (m-80) cc_final: 0.7159 (m-80) REVERT: 2 559 MET cc_start: 0.8512 (ppp) cc_final: 0.8136 (ppp) REVERT: 2 733 ASN cc_start: 0.8629 (m-40) cc_final: 0.8305 (m-40) REVERT: 2 761 LYS cc_start: 0.8942 (mttt) cc_final: 0.8685 (mttm) REVERT: 2 787 LYS cc_start: 0.9190 (tmmt) cc_final: 0.8984 (tmmt) REVERT: 2 802 ASP cc_start: 0.8846 (m-30) cc_final: 0.8266 (t70) REVERT: 2 810 LEU cc_start: 0.8813 (mm) cc_final: 0.8441 (tp) REVERT: 2 828 LYS cc_start: 0.9112 (mmtt) cc_final: 0.8809 (tptt) REVERT: 3 334 LYS cc_start: 0.8106 (pttp) cc_final: 0.7524 (mptt) REVERT: 3 411 LYS cc_start: 0.7759 (ptpt) cc_final: 0.7024 (pptt) REVERT: 3 534 LYS cc_start: 0.9029 (mttt) cc_final: 0.8657 (ptpp) REVERT: 3 660 ASP cc_start: 0.8567 (m-30) cc_final: 0.8224 (t0) REVERT: 3 725 GLN cc_start: 0.8794 (mt0) cc_final: 0.8473 (mp10) REVERT: 3 739 ASN cc_start: 0.7748 (m-40) cc_final: 0.6862 (m-40) REVERT: 3 778 MET cc_start: 0.8602 (mmp) cc_final: 0.8324 (tpp) REVERT: 4 310 HIS cc_start: 0.7733 (m-70) cc_final: 0.7258 (m170) REVERT: 4 374 MET cc_start: 0.8478 (mmp) cc_final: 0.8212 (mmm) REVERT: 4 568 HIS cc_start: 0.8667 (m90) cc_final: 0.8061 (m90) REVERT: 4 734 ASP cc_start: 0.8115 (m-30) cc_final: 0.7728 (t0) REVERT: 4 779 GLU cc_start: 0.8535 (tp30) cc_final: 0.8328 (tm-30) REVERT: 5 396 ASP cc_start: 0.8095 (m-30) cc_final: 0.7796 (m-30) REVERT: 5 571 TYR cc_start: 0.8545 (t80) cc_final: 0.8142 (t80) REVERT: 5 596 TYR cc_start: 0.6587 (m-10) cc_final: 0.6230 (m-10) REVERT: 5 629 LYS cc_start: 0.8302 (mtmt) cc_final: 0.7777 (mmmm) REVERT: 5 701 GLU cc_start: 0.8285 (tm-30) cc_final: 0.7908 (tm-30) REVERT: C 114 THR cc_start: 0.8992 (p) cc_final: 0.8601 (t) REVERT: C 138 ASN cc_start: 0.6068 (t0) cc_final: 0.5557 (t0) REVERT: C 200 GLU cc_start: 0.7873 (mp0) cc_final: 0.7657 (mt-10) REVERT: 6 624 MET cc_start: 0.7851 (mtm) cc_final: 0.7621 (mtt) REVERT: 6 815 LEU cc_start: 0.8388 (mt) cc_final: 0.8005 (tp) REVERT: 6 830 LEU cc_start: 0.8873 (mt) cc_final: 0.8602 (pp) REVERT: D 148 LEU cc_start: 0.9170 (mt) cc_final: 0.8811 (mp) REVERT: E 53 TYR cc_start: 0.7679 (t80) cc_final: 0.7399 (t80) REVERT: E 84 TRP cc_start: 0.8566 (m100) cc_final: 0.8071 (m100) REVERT: E 160 ASP cc_start: 0.7680 (m-30) cc_final: 0.7325 (m-30) REVERT: B 43 ASP cc_start: 0.8667 (m-30) cc_final: 0.8402 (m-30) REVERT: B 51 ASP cc_start: 0.7803 (m-30) cc_final: 0.6775 (m-30) REVERT: B 77 VAL cc_start: 0.9071 (m) cc_final: 0.8682 (t) REVERT: B 111 ASP cc_start: 0.8311 (m-30) cc_final: 0.8099 (m-30) REVERT: B 126 GLU cc_start: 0.7690 (pm20) cc_final: 0.7244 (pm20) REVERT: B 160 ASP cc_start: 0.8121 (t70) cc_final: 0.7680 (t70) REVERT: B 161 GLN cc_start: 0.8435 (mp10) cc_final: 0.7922 (mp10) REVERT: B 201 CYS cc_start: 0.8894 (m) cc_final: 0.8368 (m) REVERT: a 672 ILE cc_start: 0.8149 (mt) cc_final: 0.7876 (tp) REVERT: a 689 ASN cc_start: 0.7651 (t0) cc_final: 0.6532 (t0) REVERT: a 748 TYR cc_start: 0.7624 (t80) cc_final: 0.7389 (t80) REVERT: a 785 PHE cc_start: 0.7687 (t80) cc_final: 0.7470 (t80) REVERT: a 810 ILE cc_start: 0.9291 (mt) cc_final: 0.9063 (mm) REVERT: A 139 GLU cc_start: 0.7403 (tp30) cc_final: 0.7019 (tp30) REVERT: A 212 GLU cc_start: 0.7382 (tt0) cc_final: 0.7063 (tp30) REVERT: G 111 ASP cc_start: 0.7654 (m-30) cc_final: 0.7338 (m-30) REVERT: G 114 THR cc_start: 0.9196 (p) cc_final: 0.8906 (t) REVERT: G 133 LEU cc_start: 0.8797 (tp) cc_final: 0.8370 (tp) REVERT: f 731 LEU cc_start: 0.8935 (mt) cc_final: 0.8489 (mt) REVERT: F 171 TRP cc_start: 0.8366 (m100) cc_final: 0.7600 (m100) REVERT: e 755 GLU cc_start: 0.8534 (mm-30) cc_final: 0.8317 (mm-30) outliers start: 1 outliers final: 0 residues processed: 859 average time/residue: 0.5278 time to fit residues: 777.6631 Evaluate side-chains 588 residues out of total 6163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 588 time to evaluate : 4.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 702 random chunks: chunk 654 optimal weight: 0.9980 chunk 76 optimal weight: 7.9990 chunk 386 optimal weight: 0.7980 chunk 496 optimal weight: 0.7980 chunk 384 optimal weight: 0.9990 chunk 571 optimal weight: 7.9990 chunk 379 optimal weight: 0.7980 chunk 676 optimal weight: 0.7980 chunk 423 optimal weight: 20.0000 chunk 412 optimal weight: 0.4980 chunk 312 optimal weight: 9.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 597 ASN 1 744 ASN 2 568 HIS 2 744 ASN 2 814 ASN 2 816 HIS ** 3 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 768 ASN ** 4 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 834 ASN 5 290 ASN ** 5 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 834 ASN ** 6 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 310 HIS ** 6 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 119 ASN E 150 GLN ** d 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 751 GLN ** d 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 776 ASN A 59 ASN A 112 GLN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 96 ASN ** G 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 ASN ** e 787 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.5632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 58380 Z= 0.176 Angle : 0.596 9.003 78702 Z= 0.311 Chirality : 0.044 0.359 8876 Planarity : 0.003 0.050 9939 Dihedral : 9.719 178.712 7975 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.41 % Favored : 92.47 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % 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: -1.49 (0.10), residues: 6773 helix: -0.60 (0.09), residues: 3263 sheet: -0.99 (0.23), residues: 485 loop : -1.32 (0.12), residues: 3025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 80 HIS 0.012 0.001 HIS A 55 PHE 0.025 0.001 PHE 3 763 TYR 0.023 0.001 TYR D 186 ARG 0.009 0.000 ARG G 79 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13546 Ramachandran restraints generated. 6773 Oldfield, 0 Emsley, 6773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13546 Ramachandran restraints generated. 6773 Oldfield, 0 Emsley, 6773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 871 residues out of total 6163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 871 time to evaluate : 5.038 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: 1 293 LYS cc_start: 0.8772 (mttt) cc_final: 0.8331 (tmtt) REVERT: 1 366 LEU cc_start: 0.9365 (mt) cc_final: 0.8778 (pt) REVERT: 1 408 ARG cc_start: 0.7436 (mtt180) cc_final: 0.7047 (ttt180) REVERT: 1 667 MET cc_start: 0.8493 (mmm) cc_final: 0.8148 (mmm) REVERT: 1 691 ASP cc_start: 0.8903 (m-30) cc_final: 0.8301 (t70) REVERT: 1 716 HIS cc_start: 0.7964 (t-90) cc_final: 0.7048 (t-90) REVERT: 1 718 ASP cc_start: 0.7929 (m-30) cc_final: 0.7319 (p0) REVERT: 1 746 ILE cc_start: 0.9059 (mm) cc_final: 0.8758 (mm) REVERT: 2 274 PHE cc_start: 0.7861 (m-80) cc_final: 0.7213 (m-80) REVERT: 2 414 TYR cc_start: 0.8406 (m-80) cc_final: 0.8157 (m-80) REVERT: 2 559 MET cc_start: 0.8484 (ppp) cc_final: 0.8162 (ppp) REVERT: 2 587 GLU cc_start: 0.7044 (pt0) cc_final: 0.6404 (tt0) REVERT: 2 733 ASN cc_start: 0.8580 (m-40) cc_final: 0.8248 (m-40) REVERT: 2 787 LYS cc_start: 0.9158 (tmmt) cc_final: 0.8938 (tmmt) REVERT: 2 802 ASP cc_start: 0.8777 (m-30) cc_final: 0.8260 (t70) REVERT: 2 810 LEU cc_start: 0.8801 (mm) cc_final: 0.8480 (tp) REVERT: 2 828 LYS cc_start: 0.9140 (mmtt) cc_final: 0.8801 (tptt) REVERT: 3 334 LYS cc_start: 0.8147 (pttp) cc_final: 0.7522 (mptt) REVERT: 3 411 LYS cc_start: 0.7843 (ptpt) cc_final: 0.7039 (pptt) REVERT: 3 660 ASP cc_start: 0.8501 (m-30) cc_final: 0.8192 (t0) REVERT: 3 725 GLN cc_start: 0.8727 (mt0) cc_final: 0.8431 (mp10) REVERT: 3 739 ASN cc_start: 0.7758 (m-40) cc_final: 0.6794 (m-40) REVERT: 3 778 MET cc_start: 0.8597 (mmp) cc_final: 0.8289 (tpp) REVERT: 4 310 HIS cc_start: 0.7768 (m-70) cc_final: 0.7304 (m170) REVERT: 4 568 HIS cc_start: 0.8528 (m90) cc_final: 0.8025 (m170) REVERT: 4 734 ASP cc_start: 0.8108 (m-30) cc_final: 0.7834 (t0) REVERT: 4 765 ASP cc_start: 0.6815 (t70) cc_final: 0.6255 (p0) REVERT: 4 779 GLU cc_start: 0.8479 (tp30) cc_final: 0.8120 (tm-30) REVERT: 5 396 ASP cc_start: 0.8075 (m-30) cc_final: 0.7735 (m-30) REVERT: 5 571 TYR cc_start: 0.8486 (t80) cc_final: 0.8266 (t80) REVERT: 5 596 TYR cc_start: 0.6482 (m-10) cc_final: 0.6157 (m-10) REVERT: 5 635 LEU cc_start: 0.9017 (tp) cc_final: 0.8512 (mt) REVERT: 5 701 GLU cc_start: 0.8259 (tm-30) cc_final: 0.7909 (tm-30) REVERT: 5 801 ILE cc_start: 0.9027 (mt) cc_final: 0.8621 (mp) REVERT: C 84 TRP cc_start: 0.8853 (m100) cc_final: 0.8043 (m100) REVERT: 6 624 MET cc_start: 0.7851 (mtm) cc_final: 0.7645 (mtt) REVERT: 6 667 MET cc_start: 0.7283 (ttt) cc_final: 0.7069 (ttm) REVERT: 6 815 LEU cc_start: 0.8480 (mt) cc_final: 0.8049 (tt) REVERT: 6 830 LEU cc_start: 0.8927 (mt) cc_final: 0.8620 (pp) REVERT: D 84 TRP cc_start: 0.8414 (m100) cc_final: 0.7707 (m100) REVERT: D 148 LEU cc_start: 0.8973 (mt) cc_final: 0.8635 (mp) REVERT: D 201 CYS cc_start: 0.8239 (m) cc_final: 0.8030 (m) REVERT: D 210 MET cc_start: 0.8626 (mmm) cc_final: 0.7992 (mmm) REVERT: E 53 TYR cc_start: 0.7700 (t80) cc_final: 0.7453 (t80) REVERT: E 80 TRP cc_start: 0.8595 (m100) cc_final: 0.8254 (m100) REVERT: E 84 TRP cc_start: 0.8553 (m100) cc_final: 0.8007 (m100) REVERT: E 150 GLN cc_start: 0.7848 (mt0) cc_final: 0.7553 (mt0) REVERT: E 160 ASP cc_start: 0.7667 (m-30) cc_final: 0.7275 (m-30) REVERT: b 765 ASP cc_start: 0.7745 (m-30) cc_final: 0.7377 (m-30) REVERT: B 43 ASP cc_start: 0.8693 (m-30) cc_final: 0.8441 (m-30) REVERT: B 51 ASP cc_start: 0.7856 (m-30) cc_final: 0.6783 (m-30) REVERT: B 77 VAL cc_start: 0.8995 (m) cc_final: 0.8571 (t) REVERT: B 111 ASP cc_start: 0.8185 (m-30) cc_final: 0.7949 (m-30) REVERT: B 126 GLU cc_start: 0.7653 (pm20) cc_final: 0.7287 (pm20) REVERT: B 160 ASP cc_start: 0.8108 (t70) cc_final: 0.7651 (t70) REVERT: B 171 TRP cc_start: 0.8961 (m100) cc_final: 0.8651 (m100) REVERT: B 201 CYS cc_start: 0.8824 (m) cc_final: 0.8268 (m) REVERT: a 672 ILE cc_start: 0.8136 (mt) cc_final: 0.7865 (tp) REVERT: a 768 TYR cc_start: 0.7031 (t80) cc_final: 0.6766 (t80) REVERT: A 139 GLU cc_start: 0.7119 (tp30) cc_final: 0.6917 (tp30) REVERT: A 142 ASN cc_start: 0.8612 (m-40) cc_final: 0.8251 (m-40) REVERT: A 212 GLU cc_start: 0.7388 (tt0) cc_final: 0.7137 (tp30) REVERT: G 111 ASP cc_start: 0.7658 (m-30) cc_final: 0.7171 (m-30) REVERT: G 114 THR cc_start: 0.9230 (p) cc_final: 0.8900 (t) REVERT: G 133 LEU cc_start: 0.8887 (tp) cc_final: 0.8448 (tp) REVERT: f 731 LEU cc_start: 0.8904 (mt) cc_final: 0.8445 (mt) REVERT: F 84 TRP cc_start: 0.8181 (m100) cc_final: 0.7941 (m100) REVERT: F 171 TRP cc_start: 0.8260 (m100) cc_final: 0.7875 (m100) REVERT: e 755 GLU cc_start: 0.8394 (mm-30) cc_final: 0.7824 (tm-30) outliers start: 0 outliers final: 0 residues processed: 871 average time/residue: 0.5142 time to fit residues: 768.9711 Evaluate side-chains 598 residues out of total 6163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 598 time to evaluate : 5.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 702 random chunks: chunk 418 optimal weight: 0.9990 chunk 270 optimal weight: 1.9990 chunk 404 optimal weight: 6.9990 chunk 203 optimal weight: 0.8980 chunk 132 optimal weight: 0.9990 chunk 131 optimal weight: 0.8980 chunk 430 optimal weight: 0.9980 chunk 460 optimal weight: 3.9990 chunk 334 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 531 optimal weight: 0.7980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 744 ASN ** 1 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 568 HIS 2 744 ASN 2 814 ASN 2 816 HIS ** 3 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 483 GLN ** 4 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 666 ASN ** 4 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 290 ASN ** 5 556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 566 GLN ** 5 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 736 HIS 5 834 ASN ** C 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 816 HIS D 59 ASN ** d 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 733 GLN A 59 ASN g 734 ASN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 ASN F 161 GLN ** e 751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 787 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.5795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 58380 Z= 0.189 Angle : 0.600 10.365 78702 Z= 0.311 Chirality : 0.044 0.337 8876 Planarity : 0.004 0.082 9939 Dihedral : 9.598 179.114 7975 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.47 % Favored : 92.40 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % 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: -1.34 (0.10), residues: 6773 helix: -0.46 (0.09), residues: 3273 sheet: -0.94 (0.23), residues: 483 loop : -1.26 (0.12), residues: 3017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 110 HIS 0.005 0.001 HIS 2 816 PHE 0.024 0.002 PHE 3 763 TYR 0.023 0.001 TYR D 186 ARG 0.009 0.000 ARG G 79 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13546 Ramachandran restraints generated. 6773 Oldfield, 0 Emsley, 6773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13546 Ramachandran restraints generated. 6773 Oldfield, 0 Emsley, 6773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 838 residues out of total 6163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 838 time to evaluate : 5.131 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: 1 293 LYS cc_start: 0.8756 (mttt) cc_final: 0.8303 (tmtt) REVERT: 1 317 LYS cc_start: 0.8535 (tppt) cc_final: 0.7589 (ttpt) REVERT: 1 366 LEU cc_start: 0.9360 (mt) cc_final: 0.8744 (pt) REVERT: 1 408 ARG cc_start: 0.7432 (mtt180) cc_final: 0.7056 (ttt180) REVERT: 1 667 MET cc_start: 0.8439 (mmm) cc_final: 0.8133 (mmm) REVERT: 1 691 ASP cc_start: 0.8908 (m-30) cc_final: 0.8313 (t70) REVERT: 1 716 HIS cc_start: 0.7927 (t-90) cc_final: 0.7163 (t-90) REVERT: 1 718 ASP cc_start: 0.7984 (m-30) cc_final: 0.7359 (p0) REVERT: 1 746 ILE cc_start: 0.9051 (mm) cc_final: 0.8754 (mm) REVERT: 2 274 PHE cc_start: 0.7806 (m-80) cc_final: 0.7198 (m-80) REVERT: 2 534 LYS cc_start: 0.9243 (mttt) cc_final: 0.8949 (mtmm) REVERT: 2 559 MET cc_start: 0.8484 (ppp) cc_final: 0.8180 (ppp) REVERT: 2 587 GLU cc_start: 0.7080 (pt0) cc_final: 0.6487 (tt0) REVERT: 2 802 ASP cc_start: 0.8718 (m-30) cc_final: 0.8309 (t70) REVERT: 2 810 LEU cc_start: 0.8789 (mm) cc_final: 0.8516 (tp) REVERT: 3 334 LYS cc_start: 0.8187 (pttp) cc_final: 0.7567 (mptt) REVERT: 3 411 LYS cc_start: 0.7898 (ptpt) cc_final: 0.7181 (pptt) REVERT: 3 660 ASP cc_start: 0.8488 (m-30) cc_final: 0.8194 (t0) REVERT: 3 725 GLN cc_start: 0.8707 (mt0) cc_final: 0.8399 (mp10) REVERT: 3 778 MET cc_start: 0.8621 (mmp) cc_final: 0.8316 (tpp) REVERT: 4 307 ASP cc_start: 0.5976 (t0) cc_final: 0.5462 (t0) REVERT: 4 308 GLU cc_start: 0.6871 (mp0) cc_final: 0.5869 (mp0) REVERT: 4 568 HIS cc_start: 0.8630 (m90) cc_final: 0.8054 (m170) REVERT: 4 734 ASP cc_start: 0.8145 (m-30) cc_final: 0.7878 (t0) REVERT: 4 779 GLU cc_start: 0.8490 (tp30) cc_final: 0.8076 (tm-30) REVERT: 5 396 ASP cc_start: 0.8104 (m-30) cc_final: 0.7828 (m-30) REVERT: 5 635 LEU cc_start: 0.9133 (tp) cc_final: 0.8611 (mt) REVERT: 5 701 GLU cc_start: 0.8302 (tm-30) cc_final: 0.7916 (tm-30) REVERT: 5 801 ILE cc_start: 0.9050 (mt) cc_final: 0.8584 (mp) REVERT: C 84 TRP cc_start: 0.8886 (m100) cc_final: 0.8158 (m100) REVERT: C 138 ASN cc_start: 0.6365 (t0) cc_final: 0.6092 (t0) REVERT: 6 624 MET cc_start: 0.7834 (mtm) cc_final: 0.7622 (mtt) REVERT: 6 659 LYS cc_start: 0.8892 (mttt) cc_final: 0.8509 (mmmt) REVERT: 6 815 LEU cc_start: 0.8433 (mt) cc_final: 0.7979 (tt) REVERT: 6 830 LEU cc_start: 0.8873 (mt) cc_final: 0.8589 (pp) REVERT: D 84 TRP cc_start: 0.8423 (m100) cc_final: 0.7714 (m100) REVERT: D 146 THR cc_start: 0.9183 (p) cc_final: 0.8975 (p) REVERT: D 148 LEU cc_start: 0.8966 (mt) cc_final: 0.8623 (mp) REVERT: D 150 GLN cc_start: 0.7148 (mt0) cc_final: 0.6892 (mt0) REVERT: D 210 MET cc_start: 0.8699 (mmm) cc_final: 0.8060 (mmm) REVERT: E 80 TRP cc_start: 0.8577 (m100) cc_final: 0.8309 (m100) REVERT: E 84 TRP cc_start: 0.8597 (m100) cc_final: 0.8063 (m100) REVERT: E 150 GLN cc_start: 0.7808 (mt0) cc_final: 0.7549 (mt0) REVERT: E 160 ASP cc_start: 0.7652 (m-30) cc_final: 0.7290 (m-30) REVERT: E 210 MET cc_start: 0.8827 (mmp) cc_final: 0.8573 (mmp) REVERT: b 765 ASP cc_start: 0.7647 (m-30) cc_final: 0.7166 (m-30) REVERT: B 43 ASP cc_start: 0.8686 (m-30) cc_final: 0.8473 (m-30) REVERT: B 51 ASP cc_start: 0.7858 (m-30) cc_final: 0.6888 (m-30) REVERT: B 111 ASP cc_start: 0.8298 (m-30) cc_final: 0.8017 (m-30) REVERT: B 126 GLU cc_start: 0.7640 (pm20) cc_final: 0.7295 (pm20) REVERT: B 201 CYS cc_start: 0.8826 (m) cc_final: 0.8297 (m) REVERT: a 672 ILE cc_start: 0.8148 (mt) cc_final: 0.7858 (tp) REVERT: a 689 ASN cc_start: 0.7763 (t0) cc_final: 0.7466 (t0) REVERT: A 139 GLU cc_start: 0.7075 (tp30) cc_final: 0.6853 (tp30) REVERT: A 142 ASN cc_start: 0.8587 (m-40) cc_final: 0.8210 (m-40) REVERT: A 212 GLU cc_start: 0.7397 (tt0) cc_final: 0.7116 (tp30) REVERT: g 773 GLN cc_start: 0.8615 (mp10) cc_final: 0.8406 (mp10) REVERT: G 54 GLU cc_start: 0.7467 (mp0) cc_final: 0.7250 (mp0) REVERT: G 111 ASP cc_start: 0.7726 (m-30) cc_final: 0.7245 (m-30) REVERT: G 114 THR cc_start: 0.9229 (p) cc_final: 0.8964 (t) REVERT: G 133 LEU cc_start: 0.8827 (tp) cc_final: 0.8418 (tp) REVERT: G 134 HIS cc_start: 0.8277 (t70) cc_final: 0.7985 (t-90) REVERT: f 731 LEU cc_start: 0.8928 (mt) cc_final: 0.8478 (mt) REVERT: F 171 TRP cc_start: 0.8320 (m100) cc_final: 0.7959 (m100) REVERT: e 755 GLU cc_start: 0.8361 (mm-30) cc_final: 0.7867 (tm-30) outliers start: 0 outliers final: 0 residues processed: 838 average time/residue: 0.5184 time to fit residues: 748.6574 Evaluate side-chains 580 residues out of total 6163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 580 time to evaluate : 5.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 702 random chunks: chunk 615 optimal weight: 0.9990 chunk 648 optimal weight: 7.9990 chunk 591 optimal weight: 2.9990 chunk 630 optimal weight: 0.0870 chunk 379 optimal weight: 0.8980 chunk 274 optimal weight: 0.6980 chunk 495 optimal weight: 0.9990 chunk 193 optimal weight: 2.9990 chunk 569 optimal weight: 0.5980 chunk 596 optimal weight: 1.9990 chunk 628 optimal weight: 0.0370 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 744 ASN ** 1 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 229 ASN 2 657 ASN 2 744 ASN 2 816 HIS ** 3 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 568 HIS 3 816 HIS ** 4 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 509 ASN ** 5 556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 834 ASN C 66 HIS ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 HIS ** d 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 751 GLN ** d 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 724 ASN ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 776 ASN A 59 ASN g 734 ASN g 791 GLN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 ASN ** e 751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 787 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.5949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 58380 Z= 0.159 Angle : 0.594 9.838 78702 Z= 0.306 Chirality : 0.043 0.302 8876 Planarity : 0.003 0.064 9939 Dihedral : 9.465 179.328 7975 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.44 % Favored : 92.46 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.05 % 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: -1.27 (0.10), residues: 6773 helix: -0.40 (0.09), residues: 3305 sheet: -0.89 (0.23), residues: 482 loop : -1.24 (0.12), residues: 2986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 171 HIS 0.008 0.001 HIS A 55 PHE 0.025 0.001 PHE 3 763 TYR 0.038 0.001 TYR 2 414 ARG 0.008 0.000 ARG G 79 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13546 Ramachandran restraints generated. 6773 Oldfield, 0 Emsley, 6773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13546 Ramachandran restraints generated. 6773 Oldfield, 0 Emsley, 6773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 846 residues out of total 6163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 846 time to evaluate : 5.216 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: 1 293 LYS cc_start: 0.8762 (mttt) cc_final: 0.8299 (tmtt) REVERT: 1 317 LYS cc_start: 0.8482 (tppt) cc_final: 0.7581 (ttpt) REVERT: 1 366 LEU cc_start: 0.9361 (mt) cc_final: 0.8753 (pt) REVERT: 1 590 LYS cc_start: 0.7970 (ttmt) cc_final: 0.7649 (tptp) REVERT: 1 667 MET cc_start: 0.8407 (mmm) cc_final: 0.8131 (mmm) REVERT: 1 691 ASP cc_start: 0.8887 (m-30) cc_final: 0.8288 (t70) REVERT: 1 716 HIS cc_start: 0.7969 (t-90) cc_final: 0.7105 (t70) REVERT: 1 718 ASP cc_start: 0.7943 (m-30) cc_final: 0.7142 (m-30) REVERT: 1 746 ILE cc_start: 0.9038 (mm) cc_final: 0.8760 (mm) REVERT: 2 274 PHE cc_start: 0.7813 (m-80) cc_final: 0.7155 (m-80) REVERT: 2 534 LYS cc_start: 0.9218 (mttt) cc_final: 0.8931 (mtmm) REVERT: 2 587 GLU cc_start: 0.7039 (pt0) cc_final: 0.6625 (tt0) REVERT: 2 802 ASP cc_start: 0.8713 (m-30) cc_final: 0.8322 (t70) REVERT: 2 810 LEU cc_start: 0.8776 (mm) cc_final: 0.8557 (tp) REVERT: 2 828 LYS cc_start: 0.9128 (mmtt) cc_final: 0.8919 (mptt) REVERT: 2 870 MET cc_start: 0.8629 (mmm) cc_final: 0.8086 (mmp) REVERT: 3 334 LYS cc_start: 0.8161 (pttp) cc_final: 0.7542 (mptt) REVERT: 3 411 LYS cc_start: 0.7863 (ptpt) cc_final: 0.7160 (pptt) REVERT: 3 624 MET cc_start: 0.8097 (tpp) cc_final: 0.7850 (tpp) REVERT: 3 637 LEU cc_start: 0.9324 (mt) cc_final: 0.9100 (mt) REVERT: 3 660 ASP cc_start: 0.8510 (m-30) cc_final: 0.8158 (t0) REVERT: 3 725 GLN cc_start: 0.8644 (mt0) cc_final: 0.8283 (mp10) REVERT: 3 778 MET cc_start: 0.8570 (mmp) cc_final: 0.8301 (tpp) REVERT: 4 373 ASP cc_start: 0.7657 (t0) cc_final: 0.7285 (t0) REVERT: 4 374 MET cc_start: 0.8366 (mmp) cc_final: 0.8101 (mmm) REVERT: 4 421 ASP cc_start: 0.8758 (t70) cc_final: 0.8546 (t0) REVERT: 4 568 HIS cc_start: 0.8526 (m90) cc_final: 0.8045 (m170) REVERT: 4 633 THR cc_start: 0.7771 (p) cc_final: 0.6946 (p) REVERT: 4 667 MET cc_start: 0.7459 (mmp) cc_final: 0.7204 (mmp) REVERT: 4 734 ASP cc_start: 0.8188 (m-30) cc_final: 0.7933 (t0) REVERT: 4 779 GLU cc_start: 0.8387 (tp30) cc_final: 0.8025 (tm-30) REVERT: 5 268 SER cc_start: 0.8586 (m) cc_final: 0.8336 (p) REVERT: 5 374 MET cc_start: 0.8301 (mpp) cc_final: 0.8040 (mmm) REVERT: 5 396 ASP cc_start: 0.8071 (m-30) cc_final: 0.7797 (m-30) REVERT: 5 596 TYR cc_start: 0.6767 (m-10) cc_final: 0.6415 (m-10) REVERT: 5 629 LYS cc_start: 0.8367 (ptpt) cc_final: 0.8121 (tppt) REVERT: 5 635 LEU cc_start: 0.9095 (tp) cc_final: 0.8624 (mt) REVERT: 5 701 GLU cc_start: 0.8168 (tm-30) cc_final: 0.7865 (tm-30) REVERT: 5 749 MET cc_start: 0.8254 (tpp) cc_final: 0.8046 (mmm) REVERT: 5 801 ILE cc_start: 0.9039 (mt) cc_final: 0.8543 (mp) REVERT: C 84 TRP cc_start: 0.8865 (m100) cc_final: 0.8126 (m100) REVERT: 6 624 MET cc_start: 0.7863 (mtm) cc_final: 0.7660 (mtt) REVERT: 6 659 LYS cc_start: 0.8877 (mttt) cc_final: 0.8526 (mmmt) REVERT: 6 716 HIS cc_start: 0.8015 (t-90) cc_final: 0.7535 (t70) REVERT: 6 815 LEU cc_start: 0.8443 (mt) cc_final: 0.7976 (tt) REVERT: 6 830 LEU cc_start: 0.8867 (mt) cc_final: 0.8586 (pp) REVERT: D 84 TRP cc_start: 0.8375 (m100) cc_final: 0.7779 (m100) REVERT: D 88 LEU cc_start: 0.9007 (tp) cc_final: 0.8794 (tp) REVERT: D 125 VAL cc_start: 0.9267 (t) cc_final: 0.9052 (t) REVERT: D 146 THR cc_start: 0.9188 (p) cc_final: 0.8977 (p) REVERT: D 148 LEU cc_start: 0.8910 (mt) cc_final: 0.8588 (mp) REVERT: D 159 ILE cc_start: 0.9513 (mt) cc_final: 0.9112 (mm) REVERT: D 201 CYS cc_start: 0.8167 (m) cc_final: 0.7855 (m) REVERT: E 84 TRP cc_start: 0.8566 (m100) cc_final: 0.8083 (m100) REVERT: E 93 VAL cc_start: 0.9278 (m) cc_final: 0.9050 (p) REVERT: E 150 GLN cc_start: 0.7823 (mt0) cc_final: 0.7518 (mt0) REVERT: E 160 ASP cc_start: 0.7726 (m-30) cc_final: 0.7265 (m-30) REVERT: E 210 MET cc_start: 0.8796 (mmp) cc_final: 0.8580 (mmp) REVERT: b 765 ASP cc_start: 0.7503 (m-30) cc_final: 0.7077 (m-30) REVERT: B 43 ASP cc_start: 0.8705 (m-30) cc_final: 0.8482 (m-30) REVERT: B 51 ASP cc_start: 0.7809 (m-30) cc_final: 0.6782 (m-30) REVERT: B 111 ASP cc_start: 0.8209 (m-30) cc_final: 0.7906 (m-30) REVERT: B 125 VAL cc_start: 0.7930 (p) cc_final: 0.7642 (p) REVERT: B 126 GLU cc_start: 0.7687 (pm20) cc_final: 0.7294 (pm20) REVERT: B 201 CYS cc_start: 0.8848 (m) cc_final: 0.8291 (m) REVERT: a 672 ILE cc_start: 0.8101 (mt) cc_final: 0.7857 (tp) REVERT: a 689 ASN cc_start: 0.7810 (t0) cc_final: 0.7558 (t0) REVERT: A 103 GLU cc_start: 0.7202 (tm-30) cc_final: 0.6838 (tm-30) REVERT: A 139 GLU cc_start: 0.6990 (tp30) cc_final: 0.6746 (tp30) REVERT: A 142 ASN cc_start: 0.8552 (m-40) cc_final: 0.8350 (m-40) REVERT: A 212 GLU cc_start: 0.7384 (tt0) cc_final: 0.7117 (tp30) REVERT: g 773 GLN cc_start: 0.8609 (mp10) cc_final: 0.8292 (mp10) REVERT: G 54 GLU cc_start: 0.7432 (mp0) cc_final: 0.7199 (mp0) REVERT: G 114 THR cc_start: 0.9220 (p) cc_final: 0.8959 (t) REVERT: G 133 LEU cc_start: 0.8746 (tp) cc_final: 0.8311 (tp) REVERT: f 731 LEU cc_start: 0.8884 (mt) cc_final: 0.8514 (mt) REVERT: F 171 TRP cc_start: 0.8269 (m100) cc_final: 0.8032 (m100) REVERT: e 785 PHE cc_start: 0.7483 (t80) cc_final: 0.7178 (t80) outliers start: 0 outliers final: 0 residues processed: 846 average time/residue: 0.5121 time to fit residues: 744.1953 Evaluate side-chains 583 residues out of total 6163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 583 time to evaluate : 5.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 702 random chunks: chunk 414 optimal weight: 2.9990 chunk 666 optimal weight: 0.7980 chunk 406 optimal weight: 0.4980 chunk 316 optimal weight: 0.2980 chunk 463 optimal weight: 2.9990 chunk 699 optimal weight: 20.0000 chunk 643 optimal weight: 0.9990 chunk 556 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 430 optimal weight: 0.7980 chunk 341 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 300 ASN ** 1 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 744 ASN ** 1 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 568 HIS ** 3 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 816 HIS ** 4 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 834 ASN ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 751 GLN c 784 ASN ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 ASN a 733 GLN ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 734 ASN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 HIS ** e 751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 787 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.6089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 58380 Z= 0.169 Angle : 0.592 11.090 78702 Z= 0.305 Chirality : 0.044 0.311 8876 Planarity : 0.003 0.061 9939 Dihedral : 9.368 179.094 7975 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.49 % Favored : 92.41 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.39 % Twisted General : 0.06 % 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: -1.17 (0.10), residues: 6773 helix: -0.30 (0.09), residues: 3308 sheet: -0.87 (0.23), residues: 481 loop : -1.21 (0.12), residues: 2984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP E 80 HIS 0.007 0.001 HIS E 134 PHE 0.026 0.001 PHE 3 763 TYR 0.026 0.001 TYR 5 348 ARG 0.007 0.000 ARG G 79 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13546 Ramachandran restraints generated. 6773 Oldfield, 0 Emsley, 6773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13546 Ramachandran restraints generated. 6773 Oldfield, 0 Emsley, 6773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 819 residues out of total 6163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 819 time to evaluate : 5.144 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: 1 293 LYS cc_start: 0.8755 (mttt) cc_final: 0.8308 (tmtt) REVERT: 1 317 LYS cc_start: 0.8499 (tppt) cc_final: 0.7564 (ttpt) REVERT: 1 366 LEU cc_start: 0.9370 (mt) cc_final: 0.8740 (pt) REVERT: 1 408 ARG cc_start: 0.7365 (mtt180) cc_final: 0.7043 (ttt180) REVERT: 1 555 THR cc_start: 0.8758 (p) cc_final: 0.8061 (t) REVERT: 1 590 LYS cc_start: 0.7970 (ttmt) cc_final: 0.7657 (tptp) REVERT: 1 667 MET cc_start: 0.8440 (mmm) cc_final: 0.8201 (mmm) REVERT: 1 691 ASP cc_start: 0.8938 (m-30) cc_final: 0.8293 (t70) REVERT: 1 716 HIS cc_start: 0.7939 (t-90) cc_final: 0.7078 (t70) REVERT: 1 718 ASP cc_start: 0.7967 (m-30) cc_final: 0.7390 (m-30) REVERT: 1 721 LYS cc_start: 0.9321 (mttt) cc_final: 0.9066 (mtpt) REVERT: 1 746 ILE cc_start: 0.9041 (mm) cc_final: 0.8718 (mm) REVERT: 2 274 PHE cc_start: 0.7820 (m-80) cc_final: 0.7145 (m-80) REVERT: 2 364 LYS cc_start: 0.8649 (ptmt) cc_final: 0.8430 (ttpt) REVERT: 2 534 LYS cc_start: 0.9212 (mttt) cc_final: 0.8872 (mtmm) REVERT: 2 559 MET cc_start: 0.8432 (ppp) cc_final: 0.8215 (ppp) REVERT: 2 573 TYR cc_start: 0.8588 (t80) cc_final: 0.8341 (t80) REVERT: 2 587 GLU cc_start: 0.7232 (pt0) cc_final: 0.6899 (tt0) REVERT: 2 802 ASP cc_start: 0.8738 (m-30) cc_final: 0.8349 (t70) REVERT: 2 810 LEU cc_start: 0.8786 (mm) cc_final: 0.8537 (tp) REVERT: 2 870 MET cc_start: 0.8626 (mmm) cc_final: 0.8106 (mmp) REVERT: 3 334 LYS cc_start: 0.8207 (pttp) cc_final: 0.7589 (mptt) REVERT: 3 411 LYS cc_start: 0.7935 (ptpt) cc_final: 0.7230 (pptt) REVERT: 3 660 ASP cc_start: 0.8482 (m-30) cc_final: 0.8181 (t0) REVERT: 3 667 MET cc_start: 0.7802 (mmm) cc_final: 0.7298 (mmm) REVERT: 3 725 GLN cc_start: 0.8622 (mt0) cc_final: 0.8270 (mp10) REVERT: 3 778 MET cc_start: 0.8568 (mmp) cc_final: 0.8313 (tpp) REVERT: 4 374 MET cc_start: 0.8294 (mmp) cc_final: 0.8011 (mmm) REVERT: 4 421 ASP cc_start: 0.8740 (t70) cc_final: 0.8518 (t0) REVERT: 4 568 HIS cc_start: 0.8531 (m90) cc_final: 0.8033 (m170) REVERT: 4 734 ASP cc_start: 0.8045 (m-30) cc_final: 0.7757 (t0) REVERT: 4 779 GLU cc_start: 0.8325 (tp30) cc_final: 0.8006 (tm-30) REVERT: 5 374 MET cc_start: 0.8303 (mpp) cc_final: 0.8046 (mmm) REVERT: 5 396 ASP cc_start: 0.8080 (m-30) cc_final: 0.7819 (m-30) REVERT: 5 596 TYR cc_start: 0.6819 (m-10) cc_final: 0.6395 (m-10) REVERT: 5 635 LEU cc_start: 0.9084 (tp) cc_final: 0.8640 (mt) REVERT: 5 701 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7863 (tm-30) REVERT: 5 736 HIS cc_start: 0.7758 (m90) cc_final: 0.7451 (m90) REVERT: 5 749 MET cc_start: 0.8329 (tpp) cc_final: 0.8106 (mmm) REVERT: 5 801 ILE cc_start: 0.9030 (mt) cc_final: 0.8556 (mp) REVERT: C 84 TRP cc_start: 0.8875 (m100) cc_final: 0.8116 (m100) REVERT: 6 659 LYS cc_start: 0.8877 (mttt) cc_final: 0.8516 (mmmt) REVERT: 6 716 HIS cc_start: 0.8087 (t-90) cc_final: 0.7555 (t70) REVERT: 6 815 LEU cc_start: 0.8536 (mt) cc_final: 0.8004 (tt) REVERT: 6 830 LEU cc_start: 0.8878 (mt) cc_final: 0.8587 (pp) REVERT: D 84 TRP cc_start: 0.8383 (m100) cc_final: 0.7786 (m100) REVERT: D 88 LEU cc_start: 0.9051 (tp) cc_final: 0.8811 (tp) REVERT: D 148 LEU cc_start: 0.8881 (mt) cc_final: 0.8571 (mp) REVERT: D 159 ILE cc_start: 0.9523 (mt) cc_final: 0.9258 (mm) REVERT: E 84 TRP cc_start: 0.8511 (m100) cc_final: 0.8090 (m100) REVERT: E 93 VAL cc_start: 0.9237 (m) cc_final: 0.9030 (p) REVERT: E 150 GLN cc_start: 0.8004 (mt0) cc_final: 0.7639 (mt0) REVERT: E 160 ASP cc_start: 0.7772 (m-30) cc_final: 0.7292 (m-30) REVERT: b 765 ASP cc_start: 0.7513 (m-30) cc_final: 0.7057 (m-30) REVERT: B 43 ASP cc_start: 0.8688 (m-30) cc_final: 0.8471 (m-30) REVERT: B 51 ASP cc_start: 0.7772 (m-30) cc_final: 0.6644 (m-30) REVERT: B 77 VAL cc_start: 0.9074 (m) cc_final: 0.8568 (t) REVERT: B 125 VAL cc_start: 0.7864 (p) cc_final: 0.7575 (p) REVERT: B 126 GLU cc_start: 0.7741 (pm20) cc_final: 0.7350 (pm20) REVERT: B 138 ASN cc_start: 0.7570 (m-40) cc_final: 0.7323 (m110) REVERT: B 201 CYS cc_start: 0.8849 (m) cc_final: 0.8345 (m) REVERT: a 672 ILE cc_start: 0.8126 (mt) cc_final: 0.7837 (tp) REVERT: a 689 ASN cc_start: 0.7845 (t0) cc_final: 0.7580 (t0) REVERT: A 103 GLU cc_start: 0.7200 (tm-30) cc_final: 0.6745 (tm-30) REVERT: A 139 GLU cc_start: 0.7080 (tp30) cc_final: 0.6769 (tp30) REVERT: A 142 ASN cc_start: 0.8584 (m-40) cc_final: 0.8283 (m-40) REVERT: A 212 GLU cc_start: 0.7386 (tt0) cc_final: 0.7004 (tp30) REVERT: G 78 LEU cc_start: 0.8952 (mt) cc_final: 0.8187 (mm) REVERT: G 114 THR cc_start: 0.9216 (p) cc_final: 0.8969 (t) REVERT: G 133 LEU cc_start: 0.8756 (tp) cc_final: 0.8302 (tp) REVERT: G 134 HIS cc_start: 0.8225 (t70) cc_final: 0.8004 (t-90) REVERT: f 670 LYS cc_start: 0.6132 (tppt) cc_final: 0.5121 (tppt) REVERT: f 731 LEU cc_start: 0.8820 (mt) cc_final: 0.8461 (mt) REVERT: F 171 TRP cc_start: 0.8284 (m100) cc_final: 0.8003 (m100) REVERT: F 210 MET cc_start: 0.7773 (tpp) cc_final: 0.7529 (tpt) REVERT: e 755 GLU cc_start: 0.8360 (mm-30) cc_final: 0.7841 (tm-30) REVERT: e 785 PHE cc_start: 0.7467 (t80) cc_final: 0.7084 (t80) outliers start: 0 outliers final: 0 residues processed: 819 average time/residue: 0.5122 time to fit residues: 722.5612 Evaluate side-chains 580 residues out of total 6163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 580 time to evaluate : 5.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 702 random chunks: chunk 442 optimal weight: 0.0170 chunk 593 optimal weight: 0.9990 chunk 170 optimal weight: 0.0270 chunk 513 optimal weight: 0.2980 chunk 82 optimal weight: 0.9990 chunk 154 optimal weight: 0.6980 chunk 557 optimal weight: 0.6980 chunk 233 optimal weight: 5.9990 chunk 572 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 overall best weight: 0.3476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 597 ASN 1 744 ASN ** 1 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 568 HIS ** 3 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 816 HIS ** 4 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 530 GLN ** 4 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 834 ASN ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 787 HIS ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 776 ASN ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 734 ASN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 66 HIS ** e 751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.088469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.071178 restraints weight = 242947.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.072822 restraints weight = 155000.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.073639 restraints weight = 105389.663| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.6220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 58380 Z= 0.151 Angle : 0.584 13.914 78702 Z= 0.299 Chirality : 0.043 0.297 8876 Planarity : 0.003 0.053 9939 Dihedral : 9.215 175.669 7975 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.22 % Favored : 92.71 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.06 % 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: 6773 helix: -0.23 (0.09), residues: 3312 sheet: -0.80 (0.24), residues: 470 loop : -1.17 (0.12), residues: 2991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP E 80 HIS 0.004 0.001 HIS 2 674 PHE 0.026 0.001 PHE 3 763 TYR 0.023 0.001 TYR 5 348 ARG 0.007 0.000 ARG G 79 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14162.01 seconds wall clock time: 250 minutes 42.31 seconds (15042.31 seconds total)