Starting phenix.real_space_refine on Thu Jan 18 06:08:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ba8_15940/01_2024/8ba8_15940_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ba8_15940/01_2024/8ba8_15940.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ba8_15940/01_2024/8ba8_15940.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ba8_15940/01_2024/8ba8_15940.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ba8_15940/01_2024/8ba8_15940_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ba8_15940/01_2024/8ba8_15940_trim_updated.pdb" } resolution = 3.4 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: 10 Type Number sf(0) Gaussians K 14 8.98 5 P 28 5.49 5 Mg 14 5.21 5 S 280 5.16 5 Be 7 3.05 5 C 33705 2.51 5 N 9387 2.21 5 O 10969 1.98 5 F 21 1.80 5 H 55734 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 460": "OE1" <-> "OE2" Residue "B PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 5": "OD1" <-> "OD2" Residue "I PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ASP 121": "OD1" <-> "OD2" Residue "L TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L GLU 308": "OE1" <-> "OE2" Residue "M ASP 121": "OD1" <-> "OD2" Residue "N ASP 473": "OD1" <-> "OD2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 110159 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 7854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 7854 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 14, 'TRANS': 510} Chain: "B" Number of atoms: 7854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 7854 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 14, 'TRANS': 510} Chain: "C" Number of atoms: 7854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 7854 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 14, 'TRANS': 510} Chain: "D" Number of atoms: 7854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 7854 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 14, 'TRANS': 510} Chain: "E" Number of atoms: 7854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 7854 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 14, 'TRANS': 510} Chain: "F" Number of atoms: 7854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 7854 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 14, 'TRANS': 510} Chain: "G" Number of atoms: 7854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 7854 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 14, 'TRANS': 510} Chain: "H" Number of atoms: 7818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 7818 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 13, 'TRANS': 509} Chain: "I" Number of atoms: 7818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 7818 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 13, 'TRANS': 509} Chain: "J" Number of atoms: 7818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 7818 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 13, 'TRANS': 509} Chain: "K" Number of atoms: 7818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 7818 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 13, 'TRANS': 509} Chain: "L" Number of atoms: 7818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 7818 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 13, 'TRANS': 509} Chain: "M" Number of atoms: 7818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 7818 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 13, 'TRANS': 509} Chain: "N" Number of atoms: 7818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 7818 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 13, 'TRANS': 509} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 33 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 33 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 33 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 33 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 33 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 33 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 33 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "H" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Time building chain proxies: 33.61, per 1000 atoms: 0.31 Number of scatterers: 110159 At special positions: 0 Unit cell: (171.935, 174.374, 185.349, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 10 Type Number sf(0) K 14 19.00 S 280 16.00 P 28 15.00 Mg 14 11.99 F 21 9.00 O 10969 8.00 N 9387 7.00 C 33705 6.00 Be 7 4.00 H 55734 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 65.14 Conformation dependent library (CDL) restraints added in 8.3 seconds 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13272 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 280 helices and 70 sheets defined 62.2% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 28.31 Creating SS restraints... Processing helix chain 'A' and resid 9 through 28 removed outlier: 3.954A pdb=" N ALA A 26 " --> pdb=" O VAL A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 61 removed outlier: 3.709A pdb=" N GLU A 59 " --> pdb=" O SER A 55 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N GLU A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 85 removed outlier: 4.053A pdb=" N VAL A 77 " --> pdb=" O MET A 73 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 110 removed outlier: 3.748A pdb=" N GLY A 110 " --> pdb=" O ALA A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 135 Processing helix chain 'A' and resid 140 through 153 Processing helix chain 'A' and resid 155 through 170 Processing helix chain 'A' and resid 201 through 206 removed outlier: 4.440A pdb=" N ILE A 205 " --> pdb=" O SER A 201 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ASN A 206 " --> pdb=" O PRO A 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 201 through 206' Processing helix chain 'A' and resid 229 through 234 removed outlier: 4.474A pdb=" N MET A 233 " --> pdb=" O ASN A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 244 Processing helix chain 'A' and resid 255 through 266 Processing helix chain 'A' and resid 282 through 297 Processing helix chain 'A' and resid 313 through 318 removed outlier: 5.580A pdb=" N GLY A 318 " --> pdb=" O LEU A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 356 Processing helix chain 'A' and resid 358 through 375 removed outlier: 3.618A pdb=" N GLY A 375 " --> pdb=" O LYS A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 410 Processing helix chain 'A' and resid 416 through 427 Processing helix chain 'A' and resid 433 through 459 removed outlier: 3.753A pdb=" N GLU A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA A 449 " --> pdb=" O ARG A 445 " (cutoff:3.500A) Proline residue: A 450 - end of helix removed outlier: 3.551A pdb=" N CYS A 458 " --> pdb=" O ILE A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 473 removed outlier: 4.555A pdb=" N ASP A 473 " --> pdb=" O VAL A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 492 Processing helix chain 'A' and resid 496 through 517 removed outlier: 3.633A pdb=" N LEU A 513 " --> pdb=" O SER A 509 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N THR A 516 " --> pdb=" O GLY A 512 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N THR A 517 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 28 removed outlier: 3.667A pdb=" N LYS C 15 " --> pdb=" O ASP C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 61 removed outlier: 3.760A pdb=" N GLU C 59 " --> pdb=" O SER C 55 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N GLU C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 85 removed outlier: 3.784A pdb=" N GLU C 76 " --> pdb=" O GLN C 72 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL C 77 " --> pdb=" O MET C 73 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA C 78 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 110 removed outlier: 3.582A pdb=" N GLY C 110 " --> pdb=" O ALA C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 135 Processing helix chain 'C' and resid 140 through 153 Processing helix chain 'C' and resid 155 through 170 Processing helix chain 'C' and resid 201 through 206 removed outlier: 4.521A pdb=" N ILE C 205 " --> pdb=" O SER C 201 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ASN C 206 " --> pdb=" O PRO C 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 201 through 206' Processing helix chain 'C' and resid 229 through 234 removed outlier: 4.311A pdb=" N MET C 233 " --> pdb=" O ASN C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 244 Processing helix chain 'C' and resid 255 through 266 removed outlier: 3.939A pdb=" N THR C 261 " --> pdb=" O GLU C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 297 removed outlier: 3.596A pdb=" N LYS C 286 " --> pdb=" O GLY C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 318 removed outlier: 5.342A pdb=" N GLY C 318 " --> pdb=" O LEU C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 356 removed outlier: 4.131A pdb=" N GLU C 354 " --> pdb=" O ARG C 350 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU C 355 " --> pdb=" O GLN C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 375 removed outlier: 5.657A pdb=" N GLY C 375 " --> pdb=" O LYS C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 410 removed outlier: 3.771A pdb=" N GLU C 408 " --> pdb=" O ARG C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 427 Processing helix chain 'C' and resid 433 through 459 removed outlier: 3.973A pdb=" N GLU C 448 " --> pdb=" O LEU C 444 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ALA C 449 " --> pdb=" O ARG C 445 " (cutoff:3.500A) Proline residue: C 450 - end of helix Processing helix chain 'C' and resid 461 through 473 removed outlier: 4.619A pdb=" N ASP C 473 " --> pdb=" O VAL C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 492 Processing helix chain 'C' and resid 496 through 517 removed outlier: 3.696A pdb=" N LEU C 513 " --> pdb=" O SER C 509 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N THR C 516 " --> pdb=" O GLY C 512 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N THR C 517 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 28 Processing helix chain 'F' and resid 52 through 61 removed outlier: 3.501A pdb=" N VAL F 56 " --> pdb=" O ASP F 52 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU F 59 " --> pdb=" O SER F 55 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N GLU F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 85 removed outlier: 3.747A pdb=" N VAL F 77 " --> pdb=" O MET F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 110 removed outlier: 3.662A pdb=" N GLY F 110 " --> pdb=" O ALA F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 135 Processing helix chain 'F' and resid 140 through 153 Processing helix chain 'F' and resid 155 through 170 Processing helix chain 'F' and resid 201 through 206 removed outlier: 4.108A pdb=" N ILE F 205 " --> pdb=" O SER F 201 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N ASN F 206 " --> pdb=" O PRO F 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 201 through 206' Processing helix chain 'F' and resid 229 through 234 removed outlier: 4.446A pdb=" N MET F 233 " --> pdb=" O ASN F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 235 through 244 Processing helix chain 'F' and resid 255 through 266 removed outlier: 4.105A pdb=" N THR F 261 " --> pdb=" O GLU F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 297 removed outlier: 3.743A pdb=" N LYS F 286 " --> pdb=" O GLY F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 318 removed outlier: 3.546A pdb=" N LEU F 317 " --> pdb=" O THR F 313 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N GLY F 318 " --> pdb=" O LEU F 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 313 through 318' Processing helix chain 'F' and resid 338 through 356 removed outlier: 3.625A pdb=" N ILE F 353 " --> pdb=" O ILE F 349 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLU F 354 " --> pdb=" O ARG F 350 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU F 355 " --> pdb=" O GLN F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 358 through 375 removed outlier: 3.517A pdb=" N ARG F 368 " --> pdb=" O LYS F 364 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLY F 375 " --> pdb=" O LYS F 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 410 Processing helix chain 'F' and resid 416 through 427 Processing helix chain 'F' and resid 433 through 459 removed outlier: 3.868A pdb=" N GLU F 448 " --> pdb=" O LEU F 444 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA F 449 " --> pdb=" O ARG F 445 " (cutoff:3.500A) Proline residue: F 450 - end of helix removed outlier: 3.544A pdb=" N CYS F 458 " --> pdb=" O ILE F 454 " (cutoff:3.500A) Processing helix chain 'F' and resid 461 through 473 removed outlier: 4.625A pdb=" N ASP F 473 " --> pdb=" O VAL F 469 " (cutoff:3.500A) Processing helix chain 'F' and resid 487 through 492 Processing helix chain 'F' and resid 496 through 517 removed outlier: 3.512A pdb=" N LEU F 513 " --> pdb=" O SER F 509 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR F 516 " --> pdb=" O GLY F 512 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR F 517 " --> pdb=" O LEU F 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 28 removed outlier: 3.698A pdb=" N LYS B 15 " --> pdb=" O ASP B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 61 removed outlier: 3.850A pdb=" N GLU B 59 " --> pdb=" O SER B 55 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N GLU B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 85 removed outlier: 3.546A pdb=" N VAL B 77 " --> pdb=" O MET B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 110 removed outlier: 3.504A pdb=" N GLY B 110 " --> pdb=" O ALA B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 135 Processing helix chain 'B' and resid 140 through 153 Processing helix chain 'B' and resid 155 through 170 Processing helix chain 'B' and resid 229 through 234 removed outlier: 4.269A pdb=" N MET B 233 " --> pdb=" O ASN B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 244 Processing helix chain 'B' and resid 256 through 269 removed outlier: 3.510A pdb=" N ALA B 260 " --> pdb=" O GLY B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 297 Processing helix chain 'B' and resid 313 through 318 removed outlier: 5.865A pdb=" N GLY B 318 " --> pdb=" O LEU B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 357 removed outlier: 5.441A pdb=" N THR B 357 " --> pdb=" O ILE B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 374 removed outlier: 4.500A pdb=" N LYS B 364 " --> pdb=" O TYR B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 409 Processing helix chain 'B' and resid 416 through 428 removed outlier: 3.553A pdb=" N ALA B 427 " --> pdb=" O ALA B 423 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ASP B 428 " --> pdb=" O SER B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 459 removed outlier: 4.157A pdb=" N GLU B 448 " --> pdb=" O LEU B 444 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA B 449 " --> pdb=" O ARG B 445 " (cutoff:3.500A) Proline residue: B 450 - end of helix removed outlier: 3.546A pdb=" N CYS B 458 " --> pdb=" O ILE B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 473 removed outlier: 4.800A pdb=" N ASP B 473 " --> pdb=" O VAL B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 492 Processing helix chain 'B' and resid 496 through 517 removed outlier: 4.096A pdb=" N THR B 516 " --> pdb=" O GLY B 512 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N THR B 517 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 28 removed outlier: 3.737A pdb=" N LYS D 15 " --> pdb=" O ASP D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 61 removed outlier: 3.767A pdb=" N GLU D 59 " --> pdb=" O SER D 55 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N GLU D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 85 removed outlier: 4.030A pdb=" N GLU D 76 " --> pdb=" O GLN D 72 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N VAL D 77 " --> pdb=" O MET D 73 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA D 78 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ALA D 84 " --> pdb=" O LYS D 80 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N ALA D 85 " --> pdb=" O ALA D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 110 removed outlier: 3.530A pdb=" N GLY D 110 " --> pdb=" O ALA D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 135 Processing helix chain 'D' and resid 140 through 153 Processing helix chain 'D' and resid 155 through 170 removed outlier: 3.522A pdb=" N GLY D 159 " --> pdb=" O ASP D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 244 removed outlier: 4.006A pdb=" N MET D 233 " --> pdb=" O ASN D 229 " (cutoff:3.500A) Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 255 through 266 Processing helix chain 'D' and resid 282 through 297 Processing helix chain 'D' and resid 313 through 318 removed outlier: 5.723A pdb=" N GLY D 318 " --> pdb=" O LEU D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 356 removed outlier: 3.828A pdb=" N GLU D 354 " --> pdb=" O ARG D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 375 removed outlier: 4.767A pdb=" N GLY D 375 " --> pdb=" O LYS D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 409 Processing helix chain 'D' and resid 416 through 428 removed outlier: 3.587A pdb=" N ALA D 427 " --> pdb=" O ALA D 423 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N ASP D 428 " --> pdb=" O SER D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 459 removed outlier: 4.103A pdb=" N GLU D 448 " --> pdb=" O LEU D 444 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ALA D 449 " --> pdb=" O ARG D 445 " (cutoff:3.500A) Proline residue: D 450 - end of helix Processing helix chain 'D' and resid 461 through 473 removed outlier: 4.785A pdb=" N ASP D 473 " --> pdb=" O VAL D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 492 Processing helix chain 'D' and resid 496 through 517 removed outlier: 3.797A pdb=" N THR D 516 " --> pdb=" O GLY D 512 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR D 517 " --> pdb=" O LEU D 513 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 28 removed outlier: 3.640A pdb=" N LYS E 15 " --> pdb=" O ASP E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 61 removed outlier: 4.073A pdb=" N GLU E 59 " --> pdb=" O SER E 55 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N GLU E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 85 removed outlier: 3.689A pdb=" N GLU E 76 " --> pdb=" O GLN E 72 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL E 77 " --> pdb=" O MET E 73 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA E 78 " --> pdb=" O VAL E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 110 Processing helix chain 'E' and resid 112 through 135 Processing helix chain 'E' and resid 140 through 153 Processing helix chain 'E' and resid 155 through 170 Processing helix chain 'E' and resid 231 through 241 Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 256 through 269 removed outlier: 5.753A pdb=" N GLY E 269 " --> pdb=" O ASN E 265 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 297 Processing helix chain 'E' and resid 313 through 318 removed outlier: 5.467A pdb=" N GLY E 318 " --> pdb=" O LEU E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 357 removed outlier: 5.234A pdb=" N THR E 357 " --> pdb=" O ILE E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 373 removed outlier: 3.680A pdb=" N ARG E 368 " --> pdb=" O LYS E 364 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL E 369 " --> pdb=" O LEU E 365 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ALA E 370 " --> pdb=" O GLN E 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 385 through 410 Processing helix chain 'E' and resid 416 through 427 Processing helix chain 'E' and resid 433 through 459 removed outlier: 3.639A pdb=" N GLU E 448 " --> pdb=" O LEU E 444 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA E 449 " --> pdb=" O ARG E 445 " (cutoff:3.500A) Proline residue: E 450 - end of helix removed outlier: 3.603A pdb=" N CYS E 458 " --> pdb=" O ILE E 454 " (cutoff:3.500A) Processing helix chain 'E' and resid 461 through 473 removed outlier: 4.690A pdb=" N ASP E 473 " --> pdb=" O VAL E 469 " (cutoff:3.500A) Processing helix chain 'E' and resid 487 through 492 Processing helix chain 'E' and resid 496 through 517 removed outlier: 4.110A pdb=" N THR E 516 " --> pdb=" O GLY E 512 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N THR E 517 " --> pdb=" O LEU E 513 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 28 Processing helix chain 'G' and resid 52 through 61 removed outlier: 3.928A pdb=" N GLU G 59 " --> pdb=" O SER G 55 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N GLU G 61 " --> pdb=" O ALA G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 85 removed outlier: 3.863A pdb=" N GLU G 76 " --> pdb=" O GLN G 72 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL G 77 " --> pdb=" O MET G 73 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA G 78 " --> pdb=" O VAL G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 110 Processing helix chain 'G' and resid 112 through 135 Processing helix chain 'G' and resid 140 through 153 Processing helix chain 'G' and resid 155 through 170 Processing helix chain 'G' and resid 231 through 241 Proline residue: G 235 - end of helix Processing helix chain 'G' and resid 256 through 269 Processing helix chain 'G' and resid 282 through 297 removed outlier: 3.815A pdb=" N ALA G 287 " --> pdb=" O ASP G 283 " (cutoff:3.500A) Processing helix chain 'G' and resid 313 through 318 removed outlier: 5.170A pdb=" N GLY G 318 " --> pdb=" O LEU G 314 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 357 removed outlier: 5.145A pdb=" N THR G 357 " --> pdb=" O ILE G 353 " (cutoff:3.500A) Processing helix chain 'G' and resid 358 through 373 Processing helix chain 'G' and resid 385 through 410 Processing helix chain 'G' and resid 416 through 427 removed outlier: 3.652A pdb=" N ALA G 427 " --> pdb=" O ALA G 423 " (cutoff:3.500A) Processing helix chain 'G' and resid 433 through 459 removed outlier: 3.785A pdb=" N GLU G 448 " --> pdb=" O LEU G 444 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA G 449 " --> pdb=" O ARG G 445 " (cutoff:3.500A) Proline residue: G 450 - end of helix removed outlier: 3.537A pdb=" N CYS G 458 " --> pdb=" O ILE G 454 " (cutoff:3.500A) Processing helix chain 'G' and resid 461 through 473 removed outlier: 4.516A pdb=" N ASP G 473 " --> pdb=" O VAL G 469 " (cutoff:3.500A) Processing helix chain 'G' and resid 487 through 492 Processing helix chain 'G' and resid 496 through 517 removed outlier: 3.757A pdb=" N LEU G 513 " --> pdb=" O SER G 509 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N THR G 516 " --> pdb=" O GLY G 512 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR G 517 " --> pdb=" O LEU G 513 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 28 removed outlier: 3.723A pdb=" N LYS H 15 " --> pdb=" O ASP H 11 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 61 removed outlier: 5.448A pdb=" N GLU H 61 " --> pdb=" O ALA H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 86 removed outlier: 3.626A pdb=" N VAL H 74 " --> pdb=" O GLY H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 110 removed outlier: 3.565A pdb=" N GLU H 102 " --> pdb=" O ALA H 98 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 135 Processing helix chain 'H' and resid 140 through 153 Processing helix chain 'H' and resid 155 through 170 Processing helix chain 'H' and resid 201 through 206 removed outlier: 4.903A pdb=" N ILE H 205 " --> pdb=" O SER H 201 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ASN H 206 " --> pdb=" O PRO H 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 201 through 206' Processing helix chain 'H' and resid 229 through 244 removed outlier: 4.027A pdb=" N MET H 233 " --> pdb=" O ASN H 229 " (cutoff:3.500A) Proline residue: H 235 - end of helix Processing helix chain 'H' and resid 255 through 267 removed outlier: 4.504A pdb=" N THR H 261 " --> pdb=" O GLU H 257 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU H 262 " --> pdb=" O ALA H 258 " (cutoff:3.500A) Processing helix chain 'H' and resid 282 through 297 removed outlier: 4.016A pdb=" N MET H 288 " --> pdb=" O ARG H 284 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N LEU H 289 " --> pdb=" O ARG H 285 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN H 290 " --> pdb=" O LYS H 286 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASP H 291 " --> pdb=" O ALA H 287 " (cutoff:3.500A) Processing helix chain 'H' and resid 313 through 318 removed outlier: 5.661A pdb=" N GLY H 318 " --> pdb=" O LEU H 314 " (cutoff:3.500A) Processing helix chain 'H' and resid 339 through 357 removed outlier: 3.528A pdb=" N GLN H 351 " --> pdb=" O ALA H 347 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU H 354 " --> pdb=" O ARG H 350 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N THR H 357 " --> pdb=" O ILE H 353 " (cutoff:3.500A) Processing helix chain 'H' and resid 358 through 375 removed outlier: 5.832A pdb=" N GLY H 374 " --> pdb=" O ALA H 370 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLY H 375 " --> pdb=" O LYS H 371 " (cutoff:3.500A) Processing helix chain 'H' and resid 385 through 410 Processing helix chain 'H' and resid 416 through 427 Processing helix chain 'H' and resid 433 through 459 removed outlier: 3.759A pdb=" N GLU H 448 " --> pdb=" O LEU H 444 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA H 449 " --> pdb=" O ARG H 445 " (cutoff:3.500A) Proline residue: H 450 - end of helix Processing helix chain 'H' and resid 461 through 473 removed outlier: 4.514A pdb=" N ASP H 473 " --> pdb=" O VAL H 469 " (cutoff:3.500A) Processing helix chain 'H' and resid 487 through 492 Processing helix chain 'H' and resid 496 through 517 removed outlier: 3.554A pdb=" N THR H 500 " --> pdb=" O PRO H 496 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 28 removed outlier: 3.712A pdb=" N LYS I 15 " --> pdb=" O ASP I 11 " (cutoff:3.500A) Processing helix chain 'I' and resid 52 through 61 removed outlier: 5.490A pdb=" N GLU I 61 " --> pdb=" O ALA I 57 " (cutoff:3.500A) Processing helix chain 'I' and resid 65 through 86 removed outlier: 3.565A pdb=" N VAL I 74 " --> pdb=" O GLY I 70 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 110 removed outlier: 3.538A pdb=" N GLU I 102 " --> pdb=" O ALA I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 112 through 135 Processing helix chain 'I' and resid 140 through 153 Processing helix chain 'I' and resid 155 through 170 Processing helix chain 'I' and resid 201 through 206 removed outlier: 5.057A pdb=" N ILE I 205 " --> pdb=" O SER I 201 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ASN I 206 " --> pdb=" O PRO I 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 201 through 206' Processing helix chain 'I' and resid 229 through 244 removed outlier: 5.050A pdb=" N MET I 233 " --> pdb=" O ASN I 229 " (cutoff:3.500A) Proline residue: I 235 - end of helix Processing helix chain 'I' and resid 255 through 267 removed outlier: 4.462A pdb=" N THR I 261 " --> pdb=" O GLU I 257 " (cutoff:3.500A) Processing helix chain 'I' and resid 282 through 297 Processing helix chain 'I' and resid 313 through 318 removed outlier: 5.334A pdb=" N GLY I 318 " --> pdb=" O LEU I 314 " (cutoff:3.500A) Processing helix chain 'I' and resid 339 through 357 removed outlier: 5.201A pdb=" N THR I 357 " --> pdb=" O ILE I 353 " (cutoff:3.500A) Processing helix chain 'I' and resid 358 through 375 removed outlier: 5.912A pdb=" N GLY I 375 " --> pdb=" O LYS I 371 " (cutoff:3.500A) Processing helix chain 'I' and resid 385 through 410 Processing helix chain 'I' and resid 416 through 427 Processing helix chain 'I' and resid 433 through 459 removed outlier: 3.798A pdb=" N GLU I 448 " --> pdb=" O LEU I 444 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA I 449 " --> pdb=" O ARG I 445 " (cutoff:3.500A) Proline residue: I 450 - end of helix Processing helix chain 'I' and resid 461 through 473 removed outlier: 4.513A pdb=" N ASP I 473 " --> pdb=" O VAL I 469 " (cutoff:3.500A) Processing helix chain 'I' and resid 487 through 492 Processing helix chain 'I' and resid 496 through 517 Processing helix chain 'J' and resid 9 through 28 removed outlier: 3.794A pdb=" N LYS J 15 " --> pdb=" O ASP J 11 " (cutoff:3.500A) Processing helix chain 'J' and resid 52 through 61 removed outlier: 5.395A pdb=" N GLU J 61 " --> pdb=" O ALA J 57 " (cutoff:3.500A) Processing helix chain 'J' and resid 65 through 86 Processing helix chain 'J' and resid 88 through 110 removed outlier: 3.834A pdb=" N GLU J 102 " --> pdb=" O ALA J 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 135 Processing helix chain 'J' and resid 140 through 153 Processing helix chain 'J' and resid 155 through 170 Processing helix chain 'J' and resid 201 through 206 removed outlier: 6.166A pdb=" N ILE J 205 " --> pdb=" O SER J 201 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ASN J 206 " --> pdb=" O PRO J 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 201 through 206' Processing helix chain 'J' and resid 229 through 244 removed outlier: 4.574A pdb=" N MET J 233 " --> pdb=" O ASN J 229 " (cutoff:3.500A) Proline residue: J 235 - end of helix Processing helix chain 'J' and resid 255 through 267 removed outlier: 6.536A pdb=" N LEU J 259 " --> pdb=" O GLU J 255 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LEU J 262 " --> pdb=" O ALA J 258 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ASN J 265 " --> pdb=" O THR J 261 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N THR J 266 " --> pdb=" O LEU J 262 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N MET J 267 " --> pdb=" O VAL J 263 " (cutoff:3.500A) Processing helix chain 'J' and resid 282 through 297 removed outlier: 4.014A pdb=" N LYS J 286 " --> pdb=" O GLY J 282 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN J 290 " --> pdb=" O LYS J 286 " (cutoff:3.500A) Processing helix chain 'J' and resid 313 through 318 removed outlier: 5.752A pdb=" N GLY J 318 " --> pdb=" O LEU J 314 " (cutoff:3.500A) Processing helix chain 'J' and resid 339 through 357 removed outlier: 3.796A pdb=" N GLU J 354 " --> pdb=" O ARG J 350 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU J 355 " --> pdb=" O GLN J 351 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N THR J 357 " --> pdb=" O ILE J 353 " (cutoff:3.500A) Processing helix chain 'J' and resid 358 through 375 removed outlier: 5.532A pdb=" N GLY J 374 " --> pdb=" O ALA J 370 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N GLY J 375 " --> pdb=" O LYS J 371 " (cutoff:3.500A) Processing helix chain 'J' and resid 385 through 410 Processing helix chain 'J' and resid 416 through 427 Processing helix chain 'J' and resid 433 through 459 removed outlier: 3.781A pdb=" N GLU J 448 " --> pdb=" O LEU J 444 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA J 449 " --> pdb=" O ARG J 445 " (cutoff:3.500A) Proline residue: J 450 - end of helix Processing helix chain 'J' and resid 461 through 473 removed outlier: 4.334A pdb=" N ASP J 473 " --> pdb=" O VAL J 469 " (cutoff:3.500A) Processing helix chain 'J' and resid 487 through 492 Processing helix chain 'J' and resid 496 through 517 removed outlier: 3.558A pdb=" N THR J 500 " --> pdb=" O PRO J 496 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 28 removed outlier: 3.657A pdb=" N LYS K 15 " --> pdb=" O ASP K 11 " (cutoff:3.500A) Processing helix chain 'K' and resid 52 through 61 removed outlier: 5.458A pdb=" N GLU K 61 " --> pdb=" O ALA K 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 65 through 86 removed outlier: 3.574A pdb=" N VAL K 74 " --> pdb=" O GLY K 70 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLY K 86 " --> pdb=" O ASN K 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 110 removed outlier: 3.717A pdb=" N GLU K 102 " --> pdb=" O ALA K 98 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 135 Processing helix chain 'K' and resid 140 through 153 Processing helix chain 'K' and resid 155 through 170 Processing helix chain 'K' and resid 201 through 206 removed outlier: 5.883A pdb=" N ILE K 205 " --> pdb=" O SER K 201 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASN K 206 " --> pdb=" O PRO K 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 201 through 206' Processing helix chain 'K' and resid 229 through 244 removed outlier: 7.013A pdb=" N MET K 233 " --> pdb=" O ASN K 229 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N LEU K 234 " --> pdb=" O ILE K 230 " (cutoff:3.500A) Proline residue: K 235 - end of helix Processing helix chain 'K' and resid 255 through 267 removed outlier: 4.981A pdb=" N THR K 261 " --> pdb=" O GLU K 257 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N MET K 267 " --> pdb=" O VAL K 263 " (cutoff:3.500A) Processing helix chain 'K' and resid 282 through 297 Processing helix chain 'K' and resid 313 through 318 removed outlier: 5.643A pdb=" N GLY K 318 " --> pdb=" O LEU K 314 " (cutoff:3.500A) Processing helix chain 'K' and resid 339 through 357 removed outlier: 3.808A pdb=" N GLU K 354 " --> pdb=" O ARG K 350 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N THR K 357 " --> pdb=" O ILE K 353 " (cutoff:3.500A) Processing helix chain 'K' and resid 358 through 375 removed outlier: 3.755A pdb=" N ALA K 370 " --> pdb=" O GLN K 366 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N GLY K 374 " --> pdb=" O ALA K 370 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY K 375 " --> pdb=" O LYS K 371 " (cutoff:3.500A) Processing helix chain 'K' and resid 385 through 410 Processing helix chain 'K' and resid 416 through 427 Processing helix chain 'K' and resid 433 through 459 removed outlier: 3.894A pdb=" N GLU K 448 " --> pdb=" O LEU K 444 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA K 449 " --> pdb=" O ARG K 445 " (cutoff:3.500A) Proline residue: K 450 - end of helix Processing helix chain 'K' and resid 461 through 473 removed outlier: 4.476A pdb=" N ASP K 473 " --> pdb=" O VAL K 469 " (cutoff:3.500A) Processing helix chain 'K' and resid 487 through 492 Processing helix chain 'K' and resid 496 through 517 Processing helix chain 'L' and resid 9 through 28 removed outlier: 3.603A pdb=" N LYS L 15 " --> pdb=" O ASP L 11 " (cutoff:3.500A) Processing helix chain 'L' and resid 52 through 61 removed outlier: 3.827A pdb=" N GLU L 59 " --> pdb=" O SER L 55 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE L 60 " --> pdb=" O VAL L 56 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N GLU L 61 " --> pdb=" O ALA L 57 " (cutoff:3.500A) Processing helix chain 'L' and resid 65 through 86 Processing helix chain 'L' and resid 88 through 110 removed outlier: 3.585A pdb=" N GLU L 102 " --> pdb=" O ALA L 98 " (cutoff:3.500A) Processing helix chain 'L' and resid 112 through 135 Processing helix chain 'L' and resid 140 through 153 Processing helix chain 'L' and resid 155 through 170 Processing helix chain 'L' and resid 201 through 206 removed outlier: 4.961A pdb=" N ILE L 205 " --> pdb=" O SER L 201 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ASN L 206 " --> pdb=" O PRO L 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 201 through 206' Processing helix chain 'L' and resid 229 through 244 removed outlier: 4.513A pdb=" N MET L 233 " --> pdb=" O ASN L 229 " (cutoff:3.500A) Proline residue: L 235 - end of helix Processing helix chain 'L' and resid 255 through 267 removed outlier: 3.803A pdb=" N LEU L 259 " --> pdb=" O GLU L 255 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL L 264 " --> pdb=" O ALA L 260 " (cutoff:3.500A) Processing helix chain 'L' and resid 282 through 297 removed outlier: 3.516A pdb=" N LYS L 286 " --> pdb=" O GLY L 282 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLN L 290 " --> pdb=" O LYS L 286 " (cutoff:3.500A) Processing helix chain 'L' and resid 313 through 318 removed outlier: 5.147A pdb=" N GLY L 318 " --> pdb=" O LEU L 314 " (cutoff:3.500A) Processing helix chain 'L' and resid 339 through 357 removed outlier: 3.989A pdb=" N THR L 357 " --> pdb=" O ILE L 353 " (cutoff:3.500A) Processing helix chain 'L' and resid 358 through 375 removed outlier: 5.613A pdb=" N GLY L 374 " --> pdb=" O ALA L 370 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N GLY L 375 " --> pdb=" O LYS L 371 " (cutoff:3.500A) Processing helix chain 'L' and resid 385 through 410 Processing helix chain 'L' and resid 416 through 427 Processing helix chain 'L' and resid 433 through 459 removed outlier: 3.857A pdb=" N GLU L 448 " --> pdb=" O LEU L 444 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA L 449 " --> pdb=" O ARG L 445 " (cutoff:3.500A) Proline residue: L 450 - end of helix Processing helix chain 'L' and resid 461 through 473 removed outlier: 4.907A pdb=" N ASP L 473 " --> pdb=" O VAL L 469 " (cutoff:3.500A) Processing helix chain 'L' and resid 487 through 492 Processing helix chain 'L' and resid 496 through 517 Processing helix chain 'M' and resid 9 through 28 removed outlier: 3.973A pdb=" N LYS M 15 " --> pdb=" O ASP M 11 " (cutoff:3.500A) Processing helix chain 'M' and resid 52 through 61 removed outlier: 3.718A pdb=" N GLU M 59 " --> pdb=" O SER M 55 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N GLU M 61 " --> pdb=" O ALA M 57 " (cutoff:3.500A) Processing helix chain 'M' and resid 65 through 86 removed outlier: 3.604A pdb=" N VAL M 74 " --> pdb=" O GLY M 70 " (cutoff:3.500A) Processing helix chain 'M' and resid 88 through 110 Processing helix chain 'M' and resid 112 through 135 Processing helix chain 'M' and resid 140 through 153 Processing helix chain 'M' and resid 155 through 170 Processing helix chain 'M' and resid 201 through 206 removed outlier: 5.588A pdb=" N ILE M 205 " --> pdb=" O SER M 201 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ASN M 206 " --> pdb=" O PRO M 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 201 through 206' Processing helix chain 'M' and resid 229 through 244 removed outlier: 4.311A pdb=" N MET M 233 " --> pdb=" O ASN M 229 " (cutoff:3.500A) Proline residue: M 235 - end of helix removed outlier: 3.829A pdb=" N ALA M 239 " --> pdb=" O PRO M 235 " (cutoff:3.500A) Processing helix chain 'M' and resid 255 through 267 removed outlier: 5.069A pdb=" N LEU M 259 " --> pdb=" O GLU M 255 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ALA M 260 " --> pdb=" O GLY M 256 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N THR M 261 " --> pdb=" O GLU M 257 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU M 262 " --> pdb=" O ALA M 258 " (cutoff:3.500A) Processing helix chain 'M' and resid 282 through 297 Processing helix chain 'M' and resid 313 through 318 removed outlier: 5.492A pdb=" N GLY M 318 " --> pdb=" O LEU M 314 " (cutoff:3.500A) Processing helix chain 'M' and resid 339 through 357 removed outlier: 3.804A pdb=" N GLN M 343 " --> pdb=" O GLU M 339 " (cutoff:3.500A) Processing helix chain 'M' and resid 358 through 375 removed outlier: 3.951A pdb=" N ARG M 362 " --> pdb=" O SER M 358 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LEU M 365 " --> pdb=" O ASP M 361 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N ARG M 368 " --> pdb=" O LYS M 364 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N GLY M 374 " --> pdb=" O ALA M 370 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY M 375 " --> pdb=" O LYS M 371 " (cutoff:3.500A) Processing helix chain 'M' and resid 385 through 410 removed outlier: 3.685A pdb=" N GLU M 391 " --> pdb=" O VAL M 387 " (cutoff:3.500A) Processing helix chain 'M' and resid 416 through 427 Processing helix chain 'M' and resid 433 through 459 removed outlier: 3.791A pdb=" N GLU M 448 " --> pdb=" O LEU M 444 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA M 449 " --> pdb=" O ARG M 445 " (cutoff:3.500A) Proline residue: M 450 - end of helix removed outlier: 3.521A pdb=" N CYS M 458 " --> pdb=" O ILE M 454 " (cutoff:3.500A) Processing helix chain 'M' and resid 461 through 473 removed outlier: 4.501A pdb=" N ASP M 473 " --> pdb=" O VAL M 469 " (cutoff:3.500A) Processing helix chain 'M' and resid 487 through 492 Processing helix chain 'M' and resid 496 through 517 Processing helix chain 'N' and resid 9 through 28 Processing helix chain 'N' and resid 52 through 61 removed outlier: 3.733A pdb=" N GLU N 59 " --> pdb=" O SER N 55 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N GLU N 61 " --> pdb=" O ALA N 57 " (cutoff:3.500A) Processing helix chain 'N' and resid 65 through 86 removed outlier: 3.586A pdb=" N VAL N 74 " --> pdb=" O GLY N 70 " (cutoff:3.500A) Processing helix chain 'N' and resid 88 through 110 Processing helix chain 'N' and resid 112 through 135 Processing helix chain 'N' and resid 140 through 153 removed outlier: 4.553A pdb=" N SER N 151 " --> pdb=" O VAL N 147 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA N 152 " --> pdb=" O GLY N 148 " (cutoff:3.500A) Processing helix chain 'N' and resid 155 through 170 removed outlier: 3.735A pdb=" N GLY N 159 " --> pdb=" O ASP N 155 " (cutoff:3.500A) Processing helix chain 'N' and resid 201 through 206 removed outlier: 4.619A pdb=" N ILE N 205 " --> pdb=" O SER N 201 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N ASN N 206 " --> pdb=" O PRO N 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 201 through 206' Processing helix chain 'N' and resid 229 through 244 removed outlier: 3.870A pdb=" N MET N 233 " --> pdb=" O ASN N 229 " (cutoff:3.500A) Proline residue: N 235 - end of helix Processing helix chain 'N' and resid 255 through 267 removed outlier: 3.578A pdb=" N ALA N 260 " --> pdb=" O GLY N 256 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N LEU N 262 " --> pdb=" O ALA N 258 " (cutoff:3.500A) Processing helix chain 'N' and resid 282 through 297 removed outlier: 3.751A pdb=" N THR N 294 " --> pdb=" O GLN N 290 " (cutoff:3.500A) Processing helix chain 'N' and resid 313 through 318 removed outlier: 3.601A pdb=" N LEU N 317 " --> pdb=" O THR N 313 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N GLY N 318 " --> pdb=" O LEU N 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 313 through 318' Processing helix chain 'N' and resid 339 through 357 removed outlier: 3.873A pdb=" N GLU N 354 " --> pdb=" O ARG N 350 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU N 355 " --> pdb=" O GLN N 351 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR N 357 " --> pdb=" O ILE N 353 " (cutoff:3.500A) Processing helix chain 'N' and resid 358 through 375 removed outlier: 5.398A pdb=" N GLY N 374 " --> pdb=" O ALA N 370 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N GLY N 375 " --> pdb=" O LYS N 371 " (cutoff:3.500A) Processing helix chain 'N' and resid 385 through 410 Processing helix chain 'N' and resid 416 through 427 Processing helix chain 'N' and resid 433 through 459 removed outlier: 3.925A pdb=" N GLU N 448 " --> pdb=" O LEU N 444 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA N 449 " --> pdb=" O ARG N 445 " (cutoff:3.500A) Proline residue: N 450 - end of helix Processing helix chain 'N' and resid 461 through 473 removed outlier: 4.464A pdb=" N ASP N 473 " --> pdb=" O VAL N 469 " (cutoff:3.500A) Processing helix chain 'N' and resid 487 through 492 Processing helix chain 'N' and resid 496 through 517 removed outlier: 3.564A pdb=" N THR N 500 " --> pdb=" O PRO N 496 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'A' and resid 4 through 8 Processing sheet with id= 2, first strand: chain 'A' and resid 37 through 41 Processing sheet with id= 3, first strand: chain 'A' and resid 212 through 215 removed outlier: 3.970A pdb=" N THR A 329 " --> pdb=" O ASN A 326 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N ASP A 328 " --> pdb=" O ARG A 197 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N GLN A 184 " --> pdb=" O GLY A 382 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLY A 382 " --> pdb=" O GLN A 184 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'A' and resid 218 through 223 removed outlier: 3.598A pdb=" N ALA A 223 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A 247 " --> pdb=" O LYS A 272 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'A' and resid 477 through 480 removed outlier: 3.523A pdb=" N GLU A 484 " --> pdb=" O ASN A 479 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'C' and resid 4 through 8 Processing sheet with id= 7, first strand: chain 'C' and resid 37 through 41 Processing sheet with id= 8, first strand: chain 'C' and resid 212 through 215 removed outlier: 3.641A pdb=" N THR C 329 " --> pdb=" O ASN C 326 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ASP C 328 " --> pdb=" O ARG C 197 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N GLN C 184 " --> pdb=" O GLY C 382 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLY C 382 " --> pdb=" O GLN C 184 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'C' and resid 218 through 223 removed outlier: 3.740A pdb=" N ILE C 250 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'C' and resid 477 through 480 removed outlier: 3.563A pdb=" N GLU C 484 " --> pdb=" O ASN C 479 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'F' and resid 4 through 8 Processing sheet with id= 12, first strand: chain 'F' and resid 37 through 41 Processing sheet with id= 13, first strand: chain 'F' and resid 212 through 215 removed outlier: 3.660A pdb=" N THR F 329 " --> pdb=" O ASN F 326 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ASP F 328 " --> pdb=" O ARG F 197 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N GLN F 184 " --> pdb=" O GLY F 382 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLY F 382 " --> pdb=" O GLN F 184 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'F' and resid 218 through 223 Processing sheet with id= 15, first strand: chain 'F' and resid 477 through 480 Processing sheet with id= 16, first strand: chain 'B' and resid 4 through 8 Processing sheet with id= 17, first strand: chain 'B' and resid 37 through 41 Processing sheet with id= 18, first strand: chain 'B' and resid 193 through 196 removed outlier: 3.533A pdb=" N ARG B 322 " --> pdb=" O ILE B 333 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'B' and resid 218 through 222 Processing sheet with id= 20, first strand: chain 'D' and resid 4 through 8 Processing sheet with id= 21, first strand: chain 'D' and resid 37 through 41 Processing sheet with id= 22, first strand: chain 'D' and resid 174 through 179 removed outlier: 3.629A pdb=" N ALA D 377 " --> pdb=" O VAL D 174 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'D' and resid 212 through 216 removed outlier: 6.699A pdb=" N ARG D 322 " --> pdb=" O ILE D 333 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'D' and resid 218 through 223 removed outlier: 3.534A pdb=" N ILE D 250 " --> pdb=" O LEU D 221 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLU D 252 " --> pdb=" O ALA D 223 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'D' and resid 477 through 480 removed outlier: 3.608A pdb=" N GLU D 484 " --> pdb=" O ASN D 479 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'E' and resid 4 through 8 Processing sheet with id= 27, first strand: chain 'E' and resid 37 through 41 Processing sheet with id= 28, first strand: chain 'E' and resid 184 through 191 removed outlier: 4.785A pdb=" N GLN E 184 " --> pdb=" O GLY E 382 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY E 382 " --> pdb=" O GLN E 184 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL E 376 " --> pdb=" O VAL E 190 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'E' and resid 193 through 196 removed outlier: 3.894A pdb=" N THR E 329 " --> pdb=" O ASN E 326 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG E 322 " --> pdb=" O ILE E 333 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL E 213 " --> pdb=" O ILE E 325 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'E' and resid 218 through 224 removed outlier: 3.582A pdb=" N GLU E 252 " --> pdb=" O ALA E 223 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'G' and resid 4 through 8 Processing sheet with id= 32, first strand: chain 'G' and resid 37 through 41 Processing sheet with id= 33, first strand: chain 'G' and resid 184 through 191 removed outlier: 4.996A pdb=" N GLN G 184 " --> pdb=" O GLY G 382 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLY G 382 " --> pdb=" O GLN G 184 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU G 186 " --> pdb=" O LYS G 380 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL G 376 " --> pdb=" O VAL G 190 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'G' and resid 193 through 196 removed outlier: 3.683A pdb=" N THR G 329 " --> pdb=" O ASN G 326 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL G 323 " --> pdb=" O LEU G 215 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU G 215 " --> pdb=" O VAL G 323 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL G 213 " --> pdb=" O ILE G 325 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'G' and resid 218 through 224 removed outlier: 3.956A pdb=" N GLU G 252 " --> pdb=" O ALA G 223 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA G 274 " --> pdb=" O LEU G 247 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'H' and resid 4 through 8 Processing sheet with id= 37, first strand: chain 'H' and resid 37 through 41 Processing sheet with id= 38, first strand: chain 'H' and resid 192 through 196 removed outlier: 3.673A pdb=" N THR H 329 " --> pdb=" O ASN H 326 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ARG H 322 " --> pdb=" O ILE H 333 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'H' and resid 218 through 223 removed outlier: 3.922A pdb=" N LEU H 247 " --> pdb=" O LYS H 272 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'H' and resid 477 through 480 removed outlier: 3.972A pdb=" N GLU H 484 " --> pdb=" O ASN H 479 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'I' and resid 4 through 8 Processing sheet with id= 42, first strand: chain 'I' and resid 37 through 41 Processing sheet with id= 43, first strand: chain 'I' and resid 192 through 196 removed outlier: 3.678A pdb=" N THR I 329 " --> pdb=" O ASN I 326 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ARG I 322 " --> pdb=" O ILE I 333 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL I 323 " --> pdb=" O LEU I 215 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'I' and resid 218 through 223 Processing sheet with id= 45, first strand: chain 'I' and resid 477 through 480 removed outlier: 6.205A pdb=" N GLU I 484 " --> pdb=" O ASN I 479 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'J' and resid 4 through 8 Processing sheet with id= 47, first strand: chain 'J' and resid 37 through 41 Processing sheet with id= 48, first strand: chain 'J' and resid 192 through 196 removed outlier: 4.012A pdb=" N THR J 329 " --> pdb=" O ASN J 326 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ARG J 322 " --> pdb=" O ILE J 333 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'J' and resid 218 through 223 removed outlier: 3.826A pdb=" N ALA J 251 " --> pdb=" O VAL J 276 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'J' and resid 477 through 480 Processing sheet with id= 51, first strand: chain 'K' and resid 4 through 8 Processing sheet with id= 52, first strand: chain 'K' and resid 37 through 41 Processing sheet with id= 53, first strand: chain 'K' and resid 192 through 196 removed outlier: 6.571A pdb=" N ARG K 322 " --> pdb=" O ILE K 333 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'K' and resid 218 through 223 Processing sheet with id= 55, first strand: chain 'K' and resid 477 through 480 removed outlier: 3.700A pdb=" N GLU K 484 " --> pdb=" O ASN K 479 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'L' and resid 4 through 8 Processing sheet with id= 57, first strand: chain 'L' and resid 37 through 41 Processing sheet with id= 58, first strand: chain 'L' and resid 192 through 196 removed outlier: 3.542A pdb=" N THR L 329 " --> pdb=" O ASN L 326 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ARG L 322 " --> pdb=" O ILE L 333 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'L' and resid 218 through 223 removed outlier: 4.116A pdb=" N LEU L 247 " --> pdb=" O LYS L 272 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'L' and resid 477 through 480 removed outlier: 3.549A pdb=" N GLU L 484 " --> pdb=" O ASN L 479 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'M' and resid 4 through 8 Processing sheet with id= 62, first strand: chain 'M' and resid 37 through 41 Processing sheet with id= 63, first strand: chain 'M' and resid 192 through 196 removed outlier: 3.846A pdb=" N THR M 329 " --> pdb=" O ASN M 326 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ARG M 322 " --> pdb=" O ILE M 333 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'M' and resid 218 through 223 removed outlier: 3.902A pdb=" N LEU M 247 " --> pdb=" O LYS M 272 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'M' and resid 477 through 480 removed outlier: 3.845A pdb=" N GLU M 484 " --> pdb=" O ASN M 479 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'N' and resid 4 through 8 Processing sheet with id= 67, first strand: chain 'N' and resid 37 through 41 Processing sheet with id= 68, first strand: chain 'N' and resid 192 through 196 removed outlier: 3.864A pdb=" N THR N 329 " --> pdb=" O ASN N 326 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ARG N 322 " --> pdb=" O ILE N 333 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'N' and resid 218 through 223 Processing sheet with id= 70, first strand: chain 'N' and resid 477 through 480 removed outlier: 3.598A pdb=" N GLU N 484 " --> pdb=" O ASN N 479 " (cutoff:3.500A) 3525 hydrogen bonds defined for protein. 10506 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: 39.80 Time building geometry restraints manager: 68.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 55692 1.03 - 1.22: 51 1.22 - 1.42: 20458 1.42 - 1.62: 33811 1.62 - 1.82: 518 Bond restraints: 110530 Sorted by residual: bond pdb=" C4 ADP H 603 " pdb=" C5 ADP H 603 " ideal model delta sigma weight residual 1.490 1.459 0.031 2.00e-02 2.50e+03 2.40e+00 bond pdb=" CB ARG I 268 " pdb=" CG ARG I 268 " ideal model delta sigma weight residual 1.520 1.565 -0.045 3.00e-02 1.11e+03 2.30e+00 bond pdb=" C4 ADP N 601 " pdb=" C5 ADP N 601 " ideal model delta sigma weight residual 1.490 1.460 0.030 2.00e-02 2.50e+03 2.28e+00 bond pdb=" C4 ADP K2002 " pdb=" C5 ADP K2002 " ideal model delta sigma weight residual 1.490 1.460 0.030 2.00e-02 2.50e+03 2.21e+00 bond pdb=" CB GLU K 483 " pdb=" CG GLU K 483 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.17e+00 ... (remaining 110525 not shown) Histogram of bond angle deviations from ideal: 60.27 - 75.53: 3 75.53 - 90.79: 34 90.79 - 106.06: 1095 106.06 - 121.32: 179606 121.32 - 136.59: 20582 Bond angle restraints: 201320 Sorted by residual: angle pdb=" C GLU C 367 " pdb=" N ARG C 368 " pdb=" H ARG C 368 " ideal model delta sigma weight residual 124.93 70.43 54.50 3.00e+00 1.11e-01 3.30e+02 angle pdb=" CA ARG C 368 " pdb=" N ARG C 368 " pdb=" H ARG C 368 " ideal model delta sigma weight residual 114.63 60.27 54.36 3.00e+00 1.11e-01 3.28e+02 angle pdb=" C LYS M 4 " pdb=" CA LYS M 4 " pdb=" HA LYS M 4 " ideal model delta sigma weight residual 109.00 73.57 35.43 3.00e+00 1.11e-01 1.39e+02 angle pdb=" HE2 LYS N 390 " pdb=" CE LYS N 390 " pdb=" HE3 LYS N 390 " ideal model delta sigma weight residual 110.00 75.69 34.31 3.00e+00 1.11e-01 1.31e+02 angle pdb=" N LYS M 4 " pdb=" CA LYS M 4 " pdb=" HA LYS M 4 " ideal model delta sigma weight residual 110.00 76.03 33.97 3.00e+00 1.11e-01 1.28e+02 ... (remaining 201315 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.51: 47633 35.51 - 71.02: 1626 71.02 - 106.53: 108 106.53 - 142.03: 17 142.03 - 177.54: 8 Dihedral angle restraints: 49392 sinusoidal: 27776 harmonic: 21616 Sorted by residual: dihedral pdb=" O1B ADP F 602 " pdb=" O3A ADP F 602 " pdb=" PB ADP F 602 " pdb=" PA ADP F 602 " ideal model delta sinusoidal sigma weight residual 300.00 122.45 177.54 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2A ADP K2002 " pdb=" O3A ADP K2002 " pdb=" PA ADP K2002 " pdb=" PB ADP K2002 " ideal model delta sinusoidal sigma weight residual 300.00 125.71 174.30 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O2A ADP M 603 " pdb=" O3A ADP M 603 " pdb=" PA ADP M 603 " pdb=" PB ADP M 603 " ideal model delta sinusoidal sigma weight residual 300.00 135.89 164.11 1 2.00e+01 2.50e-03 4.71e+01 ... (remaining 49389 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 8210 0.078 - 0.156: 760 0.156 - 0.234: 16 0.234 - 0.312: 1 0.312 - 0.390: 1 Chirality restraints: 8988 Sorted by residual: chirality pdb=" CA LYS M 4 " pdb=" N LYS M 4 " pdb=" C LYS M 4 " pdb=" CB LYS M 4 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.80e+00 chirality pdb=" CB ILE H 493 " pdb=" CA ILE H 493 " pdb=" CG1 ILE H 493 " pdb=" CG2 ILE H 493 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.25 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CG LEU A 365 " pdb=" CB LEU A 365 " pdb=" CD1 LEU A 365 " pdb=" CD2 LEU A 365 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.78e-01 ... (remaining 8985 not shown) Planarity restraints: 16758 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN K 457 " -0.030 2.00e-02 2.50e+03 3.60e-02 1.95e+01 pdb=" CG ASN K 457 " 0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN K 457 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN K 457 " 0.055 2.00e-02 2.50e+03 pdb="HD21 ASN K 457 " 0.001 2.00e-02 2.50e+03 pdb="HD22 ASN K 457 " -0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 290 " -0.022 2.00e-02 2.50e+03 2.90e-02 1.26e+01 pdb=" CD GLN A 290 " 0.016 2.00e-02 2.50e+03 pdb=" OE1 GLN A 290 " 0.002 2.00e-02 2.50e+03 pdb=" NE2 GLN A 290 " 0.048 2.00e-02 2.50e+03 pdb="HE21 GLN A 290 " 0.000 2.00e-02 2.50e+03 pdb="HE22 GLN A 290 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 421 " 0.271 9.50e-02 1.11e+02 9.13e-02 1.20e+01 pdb=" NE ARG G 421 " -0.009 2.00e-02 2.50e+03 pdb=" CZ ARG G 421 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG G 421 " -0.020 2.00e-02 2.50e+03 pdb=" NH2 ARG G 421 " -0.022 2.00e-02 2.50e+03 pdb="HH11 ARG G 421 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG G 421 " 0.008 2.00e-02 2.50e+03 pdb="HH21 ARG G 421 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG G 421 " 0.021 2.00e-02 2.50e+03 ... (remaining 16755 not shown) Histogram of nonbonded interaction distances: 0.94 - 1.78: 303 1.78 - 2.62: 142135 2.62 - 3.46: 458288 3.46 - 4.30: 662166 4.30 - 5.14: 1146891 Warning: very small nonbonded interaction distances. Nonbonded interactions: 2409783 Sorted by model distance: nonbonded pdb=" F3 BEF A 601 " pdb=" O2B ADP A 602 " model vdw 0.942 2.270 nonbonded pdb=" F2 BEF D 601 " pdb=" O2B ADP D 604 " model vdw 1.307 2.270 nonbonded pdb=" BE BEF D 601 " pdb=" O2B ADP D 604 " model vdw 1.400 2.300 nonbonded pdb=" BE BEF A 601 " pdb=" O2B ADP A 602 " model vdw 1.401 2.300 nonbonded pdb=" OE1 GLU D 172 " pdb=" H GLU D 172 " model vdw 1.454 1.850 ... (remaining 2409778 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 2 through 524) selection = (chain 'B' and resid 2 through 524) selection = (chain 'C' and resid 2 through 524) selection = (chain 'D' and resid 2 through 524) selection = (chain 'E' and resid 2 through 524) selection = (chain 'F' and resid 2 through 524) selection = (chain 'G' and resid 2 through 524) selection = (chain 'H' and resid 2 through 524) selection = (chain 'I' and resid 2 through 524) selection = (chain 'J' and resid 2 through 524) selection = (chain 'K' and resid 2 through 524) selection = (chain 'L' and resid 2 through 524) selection = (chain 'M' and resid 2 through 524) selection = (chain 'N' and resid 2 through 524) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.980 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: 1.180 Extract box with map and model: 20.310 Check model and map are aligned: 1.170 Set scattering table: 0.740 Process input model: 286.000 Find NCS groups from input model: 5.120 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 319.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 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 : 0.004 0.068 54796 Z= 0.250 Angle : 0.772 22.298 74046 Z= 0.391 Chirality : 0.045 0.390 8988 Planarity : 0.007 0.108 9625 Dihedral : 16.390 177.543 20657 Min Nonbonded Distance : 0.942 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.07 % Allowed : 16.58 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.09), residues: 7308 helix: -1.77 (0.07), residues: 4042 sheet: -0.58 (0.17), residues: 768 loop : -0.88 (0.12), residues: 2498 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 401 PHE 0.027 0.002 PHE K 195 TYR 0.023 0.002 TYR N 478 ARG 0.023 0.003 ARG C 345 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 273 time to evaluate : 6.105 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: D 488 MET cc_start: 0.8575 (mmm) cc_final: 0.8338 (mmt) REVERT: H 488 MET cc_start: 0.9024 (mmm) cc_final: 0.8382 (mmt) REVERT: K 288 MET cc_start: 0.6132 (mtt) cc_final: 0.5921 (mtt) outliers start: 4 outliers final: 2 residues processed: 277 average time/residue: 1.3526 time to fit residues: 620.4772 Evaluate side-chains 264 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 262 time to evaluate : 6.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 333 ILE Chi-restraints excluded: chain H residue 482 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 614 optimal weight: 3.9990 chunk 551 optimal weight: 10.0000 chunk 306 optimal weight: 0.5980 chunk 188 optimal weight: 6.9990 chunk 372 optimal weight: 5.9990 chunk 294 optimal weight: 9.9990 chunk 570 optimal weight: 2.9990 chunk 220 optimal weight: 2.9990 chunk 346 optimal weight: 6.9990 chunk 424 optimal weight: 4.9990 chunk 661 optimal weight: 4.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 ASN N 37 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 54796 Z= 0.400 Angle : 0.687 26.328 74046 Z= 0.360 Chirality : 0.044 0.386 8988 Planarity : 0.004 0.051 9625 Dihedral : 9.135 167.604 7885 Min Nonbonded Distance : 1.656 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.88 % Allowed : 14.53 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.09), residues: 7308 helix: 0.34 (0.08), residues: 4138 sheet: -0.63 (0.16), residues: 847 loop : -0.55 (0.12), residues: 2323 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 401 PHE 0.014 0.001 PHE M 44 TYR 0.014 0.001 TYR E 199 ARG 0.011 0.001 ARG G 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 262 time to evaluate : 6.231 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: D 488 MET cc_start: 0.8698 (mmm) cc_final: 0.8445 (mmt) REVERT: G 518 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.7596 (tm-30) REVERT: H 488 MET cc_start: 0.9004 (mmm) cc_final: 0.8274 (mmt) REVERT: J 73 MET cc_start: 0.7845 (mtm) cc_final: 0.7643 (mtm) REVERT: M 193 MET cc_start: 0.8176 (tpt) cc_final: 0.7950 (tpt) outliers start: 50 outliers final: 24 residues processed: 304 average time/residue: 1.3080 time to fit residues: 661.8099 Evaluate side-chains 284 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 259 time to evaluate : 5.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 436 GLN Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 351 GLN Chi-restraints excluded: chain D residue 521 VAL Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 307 MET Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 73 MET Chi-restraints excluded: chain G residue 348 GLN Chi-restraints excluded: chain G residue 518 GLU Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 288 MET Chi-restraints excluded: chain H residue 333 ILE Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 288 MET Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain K residue 8 PHE Chi-restraints excluded: chain K residue 440 ILE Chi-restraints excluded: chain L residue 281 PHE Chi-restraints excluded: chain L residue 365 LEU Chi-restraints excluded: chain L residue 484 GLU Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain M residue 317 LEU Chi-restraints excluded: chain N residue 483 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 367 optimal weight: 1.9990 chunk 205 optimal weight: 0.5980 chunk 550 optimal weight: 0.8980 chunk 450 optimal weight: 4.9990 chunk 182 optimal weight: 6.9990 chunk 662 optimal weight: 0.9990 chunk 715 optimal weight: 4.9990 chunk 589 optimal weight: 0.6980 chunk 656 optimal weight: 5.9990 chunk 225 optimal weight: 1.9990 chunk 531 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 54796 Z= 0.181 Angle : 0.591 25.750 74046 Z= 0.298 Chirality : 0.041 0.376 8988 Planarity : 0.003 0.044 9625 Dihedral : 8.121 163.053 7884 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.88 % Allowed : 13.79 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.10), residues: 7308 helix: 1.59 (0.08), residues: 4142 sheet: -0.63 (0.17), residues: 820 loop : -0.31 (0.13), residues: 2346 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS G 401 PHE 0.013 0.001 PHE B 195 TYR 0.012 0.001 TYR E 199 ARG 0.004 0.000 ARG A 268 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 262 time to evaluate : 6.214 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: D 488 MET cc_start: 0.8641 (mmm) cc_final: 0.8424 (mmt) REVERT: G 518 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7535 (tm-30) REVERT: H 288 MET cc_start: 0.8014 (OUTLIER) cc_final: 0.7493 (mpt) REVERT: H 488 MET cc_start: 0.8895 (mmm) cc_final: 0.8100 (mmp) REVERT: K 351 GLN cc_start: 0.9076 (tp40) cc_final: 0.8762 (tp-100) REVERT: K 389 MET cc_start: 0.8708 (tpt) cc_final: 0.8440 (tpt) outliers start: 50 outliers final: 25 residues processed: 305 average time/residue: 1.2868 time to fit residues: 658.1716 Evaluate side-chains 286 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 259 time to evaluate : 6.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain B residue 436 GLN Chi-restraints excluded: chain D residue 521 VAL Chi-restraints excluded: chain F residue 36 ARG Chi-restraints excluded: chain G residue 73 MET Chi-restraints excluded: chain G residue 237 LEU Chi-restraints excluded: chain G residue 348 GLN Chi-restraints excluded: chain G residue 518 GLU Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 288 MET Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 288 MET Chi-restraints excluded: chain J residue 16 MET Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 265 ASN Chi-restraints excluded: chain J residue 389 MET Chi-restraints excluded: chain K residue 8 PHE Chi-restraints excluded: chain K residue 169 VAL Chi-restraints excluded: chain L residue 365 LEU Chi-restraints excluded: chain L residue 378 VAL Chi-restraints excluded: chain L residue 484 GLU Chi-restraints excluded: chain M residue 302 SER Chi-restraints excluded: chain M residue 317 LEU Chi-restraints excluded: chain N residue 308 GLU Chi-restraints excluded: chain N residue 343 GLN Chi-restraints excluded: chain N residue 483 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 654 optimal weight: 10.0000 chunk 497 optimal weight: 3.9990 chunk 343 optimal weight: 7.9990 chunk 73 optimal weight: 20.0000 chunk 316 optimal weight: 0.0570 chunk 444 optimal weight: 7.9990 chunk 664 optimal weight: 3.9990 chunk 703 optimal weight: 10.0000 chunk 347 optimal weight: 20.0000 chunk 629 optimal weight: 2.9990 chunk 189 optimal weight: 20.0000 overall best weight: 3.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 54796 Z= 0.465 Angle : 0.663 26.191 74046 Z= 0.346 Chirality : 0.044 0.398 8988 Planarity : 0.004 0.038 9625 Dihedral : 8.155 172.364 7882 Min Nonbonded Distance : 1.637 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.04 % Allowed : 13.91 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.10), residues: 7308 helix: 1.65 (0.08), residues: 4150 sheet: -0.54 (0.17), residues: 798 loop : -0.51 (0.12), residues: 2360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS M 401 PHE 0.018 0.001 PHE M 44 TYR 0.012 0.001 TYR A 485 ARG 0.004 0.001 ARG K 36 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 262 time to evaluate : 6.306 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: B 73 MET cc_start: 0.8631 (mtm) cc_final: 0.8429 (mtm) REVERT: D 488 MET cc_start: 0.8747 (mmm) cc_final: 0.8407 (mmt) REVERT: G 267 MET cc_start: 0.8092 (mmm) cc_final: 0.7602 (mtt) REVERT: G 518 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.7662 (tm-30) REVERT: H 102 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8156 (mp0) REVERT: H 288 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7588 (mpt) REVERT: J 288 MET cc_start: 0.9165 (mpt) cc_final: 0.8952 (mpt) REVERT: K 351 GLN cc_start: 0.9059 (tp40) cc_final: 0.8734 (tp-100) REVERT: K 389 MET cc_start: 0.8742 (tpt) cc_final: 0.8466 (tpt) outliers start: 59 outliers final: 43 residues processed: 312 average time/residue: 1.3264 time to fit residues: 695.8865 Evaluate side-chains 306 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 260 time to evaluate : 6.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain B residue 436 GLN Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain D residue 352 GLN Chi-restraints excluded: chain D residue 521 VAL Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 363 GLU Chi-restraints excluded: chain F residue 447 MET Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 73 MET Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 348 GLN Chi-restraints excluded: chain G residue 499 VAL Chi-restraints excluded: chain G residue 518 GLU Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain H residue 288 MET Chi-restraints excluded: chain H residue 328 ASP Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 288 MET Chi-restraints excluded: chain I residue 424 SER Chi-restraints excluded: chain J residue 16 MET Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 397 GLU Chi-restraints excluded: chain K residue 8 PHE Chi-restraints excluded: chain K residue 44 PHE Chi-restraints excluded: chain K residue 169 VAL Chi-restraints excluded: chain K residue 345 ARG Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 82 ASN Chi-restraints excluded: chain L residue 281 PHE Chi-restraints excluded: chain L residue 351 GLN Chi-restraints excluded: chain L residue 365 LEU Chi-restraints excluded: chain L residue 378 VAL Chi-restraints excluded: chain L residue 484 GLU Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain L residue 522 THR Chi-restraints excluded: chain M residue 302 SER Chi-restraints excluded: chain N residue 206 ASN Chi-restraints excluded: chain N residue 308 GLU Chi-restraints excluded: chain N residue 483 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 586 optimal weight: 1.9990 chunk 399 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 523 optimal weight: 1.9990 chunk 290 optimal weight: 9.9990 chunk 600 optimal weight: 20.0000 chunk 486 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 359 optimal weight: 0.7980 chunk 631 optimal weight: 1.9990 chunk 177 optimal weight: 10.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 54796 Z= 0.177 Angle : 0.567 25.838 74046 Z= 0.284 Chirality : 0.041 0.378 8988 Planarity : 0.003 0.040 9625 Dihedral : 7.726 156.857 7882 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.74 % Favored : 97.25 % Rotamer: Outliers : 0.92 % Allowed : 13.76 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.10), residues: 7308 helix: 2.08 (0.08), residues: 4147 sheet: -0.60 (0.16), residues: 914 loop : -0.25 (0.13), residues: 2247 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 401 PHE 0.012 0.001 PHE B 195 TYR 0.009 0.001 TYR E 199 ARG 0.004 0.000 ARG L 368 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 261 time to evaluate : 6.224 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: B 73 MET cc_start: 0.8578 (mtm) cc_final: 0.8356 (mtm) REVERT: G 267 MET cc_start: 0.7945 (mmm) cc_final: 0.7553 (mtt) REVERT: G 518 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.7526 (tm-30) REVERT: H 288 MET cc_start: 0.8067 (OUTLIER) cc_final: 0.7467 (mpt) REVERT: H 488 MET cc_start: 0.8973 (mmm) cc_final: 0.8163 (mmp) REVERT: K 351 GLN cc_start: 0.9079 (tp40) cc_final: 0.8733 (tp-100) REVERT: K 389 MET cc_start: 0.8668 (tpt) cc_final: 0.8391 (tpt) REVERT: L 114 MET cc_start: 0.8573 (mmm) cc_final: 0.8341 (mmm) REVERT: M 155 ASP cc_start: 0.7920 (OUTLIER) cc_final: 0.7654 (m-30) outliers start: 52 outliers final: 34 residues processed: 303 average time/residue: 1.3385 time to fit residues: 677.9463 Evaluate side-chains 297 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 260 time to evaluate : 5.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain B residue 436 GLN Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain D residue 352 GLN Chi-restraints excluded: chain D residue 521 VAL Chi-restraints excluded: chain F residue 36 ARG Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain G residue 73 MET Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 237 LEU Chi-restraints excluded: chain G residue 348 GLN Chi-restraints excluded: chain G residue 518 GLU Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 288 MET Chi-restraints excluded: chain H residue 328 ASP Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 288 MET Chi-restraints excluded: chain J residue 16 MET Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 265 ASN Chi-restraints excluded: chain J residue 389 MET Chi-restraints excluded: chain J residue 397 GLU Chi-restraints excluded: chain K residue 8 PHE Chi-restraints excluded: chain K residue 169 VAL Chi-restraints excluded: chain K residue 177 VAL Chi-restraints excluded: chain K residue 345 ARG Chi-restraints excluded: chain L residue 281 PHE Chi-restraints excluded: chain L residue 365 LEU Chi-restraints excluded: chain L residue 378 VAL Chi-restraints excluded: chain L residue 484 GLU Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain M residue 155 ASP Chi-restraints excluded: chain M residue 302 SER Chi-restraints excluded: chain N residue 308 GLU Chi-restraints excluded: chain N residue 366 GLN Chi-restraints excluded: chain N residue 483 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 236 optimal weight: 9.9990 chunk 633 optimal weight: 1.9990 chunk 139 optimal weight: 9.9990 chunk 413 optimal weight: 1.9990 chunk 173 optimal weight: 5.9990 chunk 704 optimal weight: 8.9990 chunk 584 optimal weight: 1.9990 chunk 326 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 232 optimal weight: 20.0000 chunk 369 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 54796 Z= 0.297 Angle : 0.584 26.157 74046 Z= 0.297 Chirality : 0.041 0.389 8988 Planarity : 0.003 0.040 9625 Dihedral : 7.617 148.332 7882 Min Nonbonded Distance : 1.650 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.31 % Favored : 96.67 % Rotamer: Outliers : 1.03 % Allowed : 13.83 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.10), residues: 7308 helix: 2.14 (0.08), residues: 4149 sheet: -0.61 (0.16), residues: 939 loop : -0.26 (0.13), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS M 401 PHE 0.019 0.001 PHE M 44 TYR 0.010 0.001 TYR A 485 ARG 0.005 0.000 ARG K 345 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 261 time to evaluate : 6.218 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: A 13 ARG cc_start: 0.9224 (OUTLIER) cc_final: 0.7904 (mpp80) REVERT: B 73 MET cc_start: 0.8597 (mtm) cc_final: 0.8357 (mtm) REVERT: D 488 MET cc_start: 0.8718 (mmm) cc_final: 0.8495 (mmt) REVERT: G 267 MET cc_start: 0.7997 (mmm) cc_final: 0.7643 (mtt) REVERT: G 518 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.7619 (tm-30) REVERT: H 102 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8086 (mp0) REVERT: H 288 MET cc_start: 0.8153 (OUTLIER) cc_final: 0.7540 (mpt) REVERT: H 488 MET cc_start: 0.8993 (mmm) cc_final: 0.8208 (mmp) REVERT: I 389 MET cc_start: 0.9009 (tpp) cc_final: 0.8757 (mmm) REVERT: K 351 GLN cc_start: 0.9099 (tp40) cc_final: 0.8752 (tp-100) REVERT: K 389 MET cc_start: 0.8698 (tpt) cc_final: 0.8427 (tpt) REVERT: M 155 ASP cc_start: 0.8016 (OUTLIER) cc_final: 0.7768 (m-30) outliers start: 58 outliers final: 45 residues processed: 310 average time/residue: 1.2993 time to fit residues: 668.1907 Evaluate side-chains 310 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 260 time to evaluate : 6.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ARG Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain B residue 436 GLN Chi-restraints excluded: chain D residue 36 ARG Chi-restraints excluded: chain D residue 352 GLN Chi-restraints excluded: chain D residue 521 VAL Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain F residue 36 ARG Chi-restraints excluded: chain F residue 72 GLN Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 363 GLU Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 73 MET Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 237 LEU Chi-restraints excluded: chain G residue 348 GLN Chi-restraints excluded: chain G residue 499 VAL Chi-restraints excluded: chain G residue 518 GLU Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 288 MET Chi-restraints excluded: chain H residue 328 ASP Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 288 MET Chi-restraints excluded: chain J residue 16 MET Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 153 ASN Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 265 ASN Chi-restraints excluded: chain J residue 389 MET Chi-restraints excluded: chain J residue 397 GLU Chi-restraints excluded: chain K residue 8 PHE Chi-restraints excluded: chain K residue 169 VAL Chi-restraints excluded: chain K residue 177 VAL Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 281 PHE Chi-restraints excluded: chain L residue 365 LEU Chi-restraints excluded: chain L residue 378 VAL Chi-restraints excluded: chain L residue 484 GLU Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain L residue 522 THR Chi-restraints excluded: chain M residue 155 ASP Chi-restraints excluded: chain M residue 302 SER Chi-restraints excluded: chain M residue 334 ASP Chi-restraints excluded: chain N residue 206 ASN Chi-restraints excluded: chain N residue 308 GLU Chi-restraints excluded: chain N residue 343 GLN Chi-restraints excluded: chain N residue 366 GLN Chi-restraints excluded: chain N residue 483 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 679 optimal weight: 0.9980 chunk 79 optimal weight: 9.9990 chunk 401 optimal weight: 5.9990 chunk 514 optimal weight: 0.8980 chunk 398 optimal weight: 2.9990 chunk 592 optimal weight: 0.9980 chunk 393 optimal weight: 2.9990 chunk 701 optimal weight: 9.9990 chunk 439 optimal weight: 2.9990 chunk 427 optimal weight: 1.9990 chunk 323 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 54796 Z= 0.201 Angle : 0.556 26.000 74046 Z= 0.278 Chirality : 0.040 0.382 8988 Planarity : 0.003 0.041 9625 Dihedral : 7.293 136.787 7882 Min Nonbonded Distance : 1.646 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.82 % Favored : 97.17 % Rotamer: Outliers : 0.97 % Allowed : 13.91 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.10), residues: 7308 helix: 2.29 (0.08), residues: 4152 sheet: -0.33 (0.18), residues: 777 loop : -0.32 (0.13), residues: 2379 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 401 PHE 0.011 0.001 PHE M 66 TYR 0.009 0.001 TYR H 360 ARG 0.010 0.000 ARG K 345 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 262 time to evaluate : 6.201 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: B 73 MET cc_start: 0.8512 (mtm) cc_final: 0.8256 (mtm) REVERT: G 267 MET cc_start: 0.8046 (mmm) cc_final: 0.7652 (mtt) REVERT: G 518 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.7527 (tm-30) REVERT: H 288 MET cc_start: 0.8081 (OUTLIER) cc_final: 0.7489 (mpt) REVERT: H 488 MET cc_start: 0.8964 (mmm) cc_final: 0.8127 (mmp) REVERT: K 351 GLN cc_start: 0.9142 (tp40) cc_final: 0.8794 (tp-100) REVERT: K 389 MET cc_start: 0.8665 (tpt) cc_final: 0.8387 (tpt) REVERT: L 114 MET cc_start: 0.8569 (mmm) cc_final: 0.8349 (mmm) REVERT: M 155 ASP cc_start: 0.7862 (OUTLIER) cc_final: 0.7656 (m-30) outliers start: 55 outliers final: 44 residues processed: 309 average time/residue: 1.3335 time to fit residues: 691.0598 Evaluate side-chains 308 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 261 time to evaluate : 6.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain B residue 436 GLN Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain D residue 36 ARG Chi-restraints excluded: chain D residue 352 GLN Chi-restraints excluded: chain D residue 521 VAL Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain F residue 36 ARG Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 363 GLU Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 73 MET Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 237 LEU Chi-restraints excluded: chain G residue 499 VAL Chi-restraints excluded: chain G residue 518 GLU Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 288 MET Chi-restraints excluded: chain H residue 328 ASP Chi-restraints excluded: chain H residue 424 SER Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 288 MET Chi-restraints excluded: chain J residue 16 MET Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 265 ASN Chi-restraints excluded: chain J residue 389 MET Chi-restraints excluded: chain J residue 397 GLU Chi-restraints excluded: chain K residue 8 PHE Chi-restraints excluded: chain K residue 169 VAL Chi-restraints excluded: chain K residue 177 VAL Chi-restraints excluded: chain L residue 281 PHE Chi-restraints excluded: chain L residue 365 LEU Chi-restraints excluded: chain L residue 378 VAL Chi-restraints excluded: chain L residue 484 GLU Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain L residue 522 THR Chi-restraints excluded: chain M residue 155 ASP Chi-restraints excluded: chain M residue 302 SER Chi-restraints excluded: chain M residue 334 ASP Chi-restraints excluded: chain N residue 308 GLU Chi-restraints excluded: chain N residue 343 GLN Chi-restraints excluded: chain N residue 366 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 434 optimal weight: 7.9990 chunk 280 optimal weight: 10.0000 chunk 419 optimal weight: 3.9990 chunk 211 optimal weight: 1.9990 chunk 137 optimal weight: 10.0000 chunk 135 optimal weight: 10.0000 chunk 446 optimal weight: 0.9980 chunk 478 optimal weight: 1.9990 chunk 346 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 chunk 551 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 54796 Z= 0.308 Angle : 0.582 26.250 74046 Z= 0.296 Chirality : 0.041 0.391 8988 Planarity : 0.003 0.040 9625 Dihedral : 7.243 146.064 7882 Min Nonbonded Distance : 1.696 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.37 % Favored : 96.62 % Rotamer: Outliers : 1.06 % Allowed : 13.99 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.10), residues: 7308 helix: 2.26 (0.08), residues: 4151 sheet: -0.34 (0.17), residues: 845 loop : -0.44 (0.13), residues: 2312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS M 401 PHE 0.023 0.001 PHE M 44 TYR 0.010 0.001 TYR A 485 ARG 0.007 0.000 ARG K 345 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 261 time to evaluate : 6.152 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: A 13 ARG cc_start: 0.9228 (OUTLIER) cc_final: 0.7883 (mpp80) REVERT: B 73 MET cc_start: 0.8592 (mtm) cc_final: 0.8339 (mtm) REVERT: G 518 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.7616 (tm-30) REVERT: H 102 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8077 (mp0) REVERT: H 288 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7546 (mpt) REVERT: H 488 MET cc_start: 0.8989 (mmm) cc_final: 0.8175 (mmp) REVERT: I 389 MET cc_start: 0.8921 (mmm) cc_final: 0.8592 (mmm) REVERT: K 307 MET cc_start: 0.7832 (tmm) cc_final: 0.7305 (tmm) REVERT: K 351 GLN cc_start: 0.9149 (tp40) cc_final: 0.8916 (tp40) REVERT: K 389 MET cc_start: 0.8704 (tpt) cc_final: 0.8445 (tpt) REVERT: M 155 ASP cc_start: 0.7987 (OUTLIER) cc_final: 0.7751 (m-30) outliers start: 60 outliers final: 48 residues processed: 313 average time/residue: 1.3561 time to fit residues: 711.0422 Evaluate side-chains 314 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 261 time to evaluate : 6.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ARG Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain B residue 436 GLN Chi-restraints excluded: chain D residue 36 ARG Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 352 GLN Chi-restraints excluded: chain D residue 521 VAL Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain E residue 514 MET Chi-restraints excluded: chain F residue 36 ARG Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 363 GLU Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 73 MET Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 499 VAL Chi-restraints excluded: chain G residue 518 GLU Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 288 MET Chi-restraints excluded: chain H residue 328 ASP Chi-restraints excluded: chain H residue 381 VAL Chi-restraints excluded: chain H residue 424 SER Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 288 MET Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 265 ASN Chi-restraints excluded: chain J residue 389 MET Chi-restraints excluded: chain J residue 397 GLU Chi-restraints excluded: chain K residue 8 PHE Chi-restraints excluded: chain K residue 169 VAL Chi-restraints excluded: chain K residue 177 VAL Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 281 PHE Chi-restraints excluded: chain L residue 351 GLN Chi-restraints excluded: chain L residue 365 LEU Chi-restraints excluded: chain L residue 484 GLU Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain L residue 522 THR Chi-restraints excluded: chain M residue 155 ASP Chi-restraints excluded: chain M residue 302 SER Chi-restraints excluded: chain M residue 334 ASP Chi-restraints excluded: chain M residue 372 LEU Chi-restraints excluded: chain N residue 308 GLU Chi-restraints excluded: chain N residue 343 GLN Chi-restraints excluded: chain N residue 366 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 638 optimal weight: 1.9990 chunk 672 optimal weight: 2.9990 chunk 613 optimal weight: 1.9990 chunk 653 optimal weight: 8.9990 chunk 393 optimal weight: 3.9990 chunk 284 optimal weight: 0.6980 chunk 513 optimal weight: 0.1980 chunk 200 optimal weight: 0.9980 chunk 590 optimal weight: 0.0570 chunk 618 optimal weight: 0.6980 chunk 651 optimal weight: 5.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 54796 Z= 0.146 Angle : 0.546 25.909 74046 Z= 0.270 Chirality : 0.040 0.376 8988 Planarity : 0.003 0.041 9625 Dihedral : 6.804 132.699 7882 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.70 % Favored : 97.29 % Rotamer: Outliers : 0.74 % Allowed : 14.36 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.10), residues: 7308 helix: 2.42 (0.08), residues: 4155 sheet: -0.28 (0.18), residues: 767 loop : -0.31 (0.13), residues: 2386 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS I 401 PHE 0.011 0.001 PHE G 195 TYR 0.009 0.001 TYR H 360 ARG 0.007 0.000 ARG K 345 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 262 time to evaluate : 6.277 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: A 111 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.8368 (mtp) REVERT: B 73 MET cc_start: 0.8471 (mtm) cc_final: 0.8193 (mtm) REVERT: G 267 MET cc_start: 0.8004 (mmm) cc_final: 0.7600 (mtt) REVERT: G 518 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.7576 (tm-30) REVERT: H 288 MET cc_start: 0.8003 (OUTLIER) cc_final: 0.7373 (mpt) REVERT: H 488 MET cc_start: 0.8916 (mmm) cc_final: 0.8113 (mmp) REVERT: K 307 MET cc_start: 0.7652 (tmm) cc_final: 0.7136 (tmm) REVERT: K 351 GLN cc_start: 0.9126 (tp40) cc_final: 0.8881 (tp40) REVERT: K 389 MET cc_start: 0.8642 (tpt) cc_final: 0.8408 (tpt) REVERT: L 114 MET cc_start: 0.8487 (mmm) cc_final: 0.8263 (mmm) outliers start: 42 outliers final: 37 residues processed: 296 average time/residue: 1.2993 time to fit residues: 639.0307 Evaluate side-chains 301 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 261 time to evaluate : 6.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain B residue 436 GLN Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain D residue 36 ARG Chi-restraints excluded: chain D residue 352 GLN Chi-restraints excluded: chain D residue 521 VAL Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain E residue 514 MET Chi-restraints excluded: chain F residue 36 ARG Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 73 MET Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 499 VAL Chi-restraints excluded: chain G residue 518 GLU Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 288 MET Chi-restraints excluded: chain H residue 381 VAL Chi-restraints excluded: chain H residue 424 SER Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 288 MET Chi-restraints excluded: chain I residue 424 SER Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 265 ASN Chi-restraints excluded: chain J residue 389 MET Chi-restraints excluded: chain J residue 397 GLU Chi-restraints excluded: chain K residue 8 PHE Chi-restraints excluded: chain K residue 169 VAL Chi-restraints excluded: chain K residue 177 VAL Chi-restraints excluded: chain L residue 281 PHE Chi-restraints excluded: chain L residue 365 LEU Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain M residue 302 SER Chi-restraints excluded: chain M residue 334 ASP Chi-restraints excluded: chain N residue 343 GLN Chi-restraints excluded: chain N residue 366 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 429 optimal weight: 3.9990 chunk 691 optimal weight: 2.9990 chunk 422 optimal weight: 3.9990 chunk 328 optimal weight: 3.9990 chunk 480 optimal weight: 2.9990 chunk 725 optimal weight: 0.9980 chunk 667 optimal weight: 2.9990 chunk 577 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 446 optimal weight: 10.0000 chunk 354 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 475 ASN ** F 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 54796 Z= 0.266 Angle : 0.567 26.259 74046 Z= 0.285 Chirality : 0.041 0.390 8988 Planarity : 0.003 0.040 9625 Dihedral : 6.812 139.029 7882 Min Nonbonded Distance : 1.631 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.27 % Favored : 96.72 % Rotamer: Outliers : 0.80 % Allowed : 14.27 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.10), residues: 7308 helix: 2.40 (0.08), residues: 4162 sheet: -0.33 (0.17), residues: 880 loop : -0.40 (0.13), residues: 2266 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS H 401 PHE 0.026 0.001 PHE M 44 TYR 0.009 0.001 TYR H 360 ARG 0.006 0.000 ARG K 345 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 261 time to evaluate : 6.162 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: A 13 ARG cc_start: 0.9227 (OUTLIER) cc_final: 0.7892 (mpp80) REVERT: A 111 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8406 (mtp) REVERT: B 73 MET cc_start: 0.8557 (mtm) cc_final: 0.8287 (mtm) REVERT: G 267 MET cc_start: 0.8005 (mmm) cc_final: 0.7613 (mtt) REVERT: G 518 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.7496 (tm-30) REVERT: H 288 MET cc_start: 0.8080 (OUTLIER) cc_final: 0.7425 (mpt) REVERT: H 488 MET cc_start: 0.8957 (mmm) cc_final: 0.8134 (mmp) REVERT: K 307 MET cc_start: 0.7977 (tmm) cc_final: 0.7463 (tmm) REVERT: K 351 GLN cc_start: 0.9137 (tp40) cc_final: 0.8894 (tp40) REVERT: K 389 MET cc_start: 0.8684 (tpt) cc_final: 0.8454 (tpt) outliers start: 45 outliers final: 40 residues processed: 296 average time/residue: 1.2926 time to fit residues: 636.5363 Evaluate side-chains 305 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 261 time to evaluate : 6.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ARG Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain B residue 436 GLN Chi-restraints excluded: chain D residue 36 ARG Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 352 GLN Chi-restraints excluded: chain D residue 521 VAL Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain E residue 514 MET Chi-restraints excluded: chain F residue 36 ARG Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 73 MET Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 499 VAL Chi-restraints excluded: chain G residue 518 GLU Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 288 MET Chi-restraints excluded: chain H residue 381 VAL Chi-restraints excluded: chain H residue 424 SER Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 288 MET Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 265 ASN Chi-restraints excluded: chain J residue 389 MET Chi-restraints excluded: chain J residue 397 GLU Chi-restraints excluded: chain K residue 8 PHE Chi-restraints excluded: chain K residue 169 VAL Chi-restraints excluded: chain K residue 177 VAL Chi-restraints excluded: chain L residue 281 PHE Chi-restraints excluded: chain L residue 351 GLN Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain L residue 522 THR Chi-restraints excluded: chain M residue 302 SER Chi-restraints excluded: chain M residue 334 ASP Chi-restraints excluded: chain N residue 308 GLU Chi-restraints excluded: chain N residue 343 GLN Chi-restraints excluded: chain N residue 366 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 458 optimal weight: 2.9990 chunk 615 optimal weight: 1.9990 chunk 176 optimal weight: 10.0000 chunk 532 optimal weight: 2.9990 chunk 85 optimal weight: 20.0000 chunk 160 optimal weight: 0.0050 chunk 578 optimal weight: 2.9990 chunk 242 optimal weight: 8.9990 chunk 593 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.068144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.040872 restraints weight = 725996.600| |-----------------------------------------------------------------------------| r_work (start): 0.2723 rms_B_bonded: 3.04 r_work: 0.2575 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 54796 Z= 0.216 Angle : 0.557 25.987 74046 Z= 0.277 Chirality : 0.040 0.384 8988 Planarity : 0.003 0.040 9625 Dihedral : 6.674 132.280 7882 Min Nonbonded Distance : 1.682 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.13 % Favored : 96.85 % Rotamer: Outliers : 0.88 % Allowed : 14.18 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.10), residues: 7308 helix: 2.43 (0.08), residues: 4155 sheet: -0.20 (0.18), residues: 751 loop : -0.44 (0.12), residues: 2402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS I 401 PHE 0.011 0.001 PHE B 195 TYR 0.009 0.001 TYR H 360 ARG 0.006 0.000 ARG K 345 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15388.24 seconds wall clock time: 268 minutes 36.11 seconds (16116.11 seconds total)