Starting phenix.real_space_refine on Wed Sep 25 11:17:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bnp_7116/09_2024/6bnp_7116.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bnp_7116/09_2024/6bnp_7116.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bnp_7116/09_2024/6bnp_7116.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bnp_7116/09_2024/6bnp_7116.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bnp_7116/09_2024/6bnp_7116.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bnp_7116/09_2024/6bnp_7116.cif" } resolution = 4.6 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 ------------------------------------------------------------------------------- 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= 1.000 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: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 8 5.21 5 S 310 5.16 5 C 35822 2.51 5 N 9738 2.21 5 O 10898 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 544 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 56792 Number of models: 1 Model: "" Number of chains: 22 Chain: "I" Number of atoms: 5612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 704, 5612 Classifications: {'peptide': 704} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 20, 'TRANS': 681} Chain: "J" Number of atoms: 5612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 704, 5612 Classifications: {'peptide': 704} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 20, 'TRANS': 681} Chain: "K" Number of atoms: 5612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 704, 5612 Classifications: {'peptide': 704} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 20, 'TRANS': 681} Chain: "L" Number of atoms: 5612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 704, 5612 Classifications: {'peptide': 704} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 20, 'TRANS': 681} Chain: "M" Number of atoms: 5612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 704, 5612 Classifications: {'peptide': 704} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 20, 'TRANS': 681} Chain: "N" Number of atoms: 5612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 704, 5612 Classifications: {'peptide': 704} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 20, 'TRANS': 681} Chain: "A" Number of atoms: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2862 Classifications: {'peptide': 367} Modifications used: {'COO': 1} Link IDs: {'CIS': 10, 'PTRANS': 19, 'TRANS': 337} Chain: "B" Number of atoms: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2862 Classifications: {'peptide': 367} Modifications used: {'COO': 1} Link IDs: {'CIS': 10, 'PTRANS': 19, 'TRANS': 337} Chain: "C" Number of atoms: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2862 Classifications: {'peptide': 367} Modifications used: {'COO': 1} Link IDs: {'CIS': 10, 'PTRANS': 19, 'TRANS': 337} Chain: "D" Number of atoms: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2862 Classifications: {'peptide': 367} Modifications used: {'COO': 1} Link IDs: {'CIS': 10, 'PTRANS': 19, 'TRANS': 337} Chain: "E" Number of atoms: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2862 Classifications: {'peptide': 367} Modifications used: {'COO': 1} Link IDs: {'CIS': 10, 'PTRANS': 19, 'TRANS': 337} Chain: "F" Number of atoms: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2862 Classifications: {'peptide': 367} Modifications used: {'COO': 1} Link IDs: {'CIS': 10, 'PTRANS': 19, 'TRANS': 337} Chain: "G" Number of atoms: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2862 Classifications: {'peptide': 367} Modifications used: {'COO': 1} Link IDs: {'CIS': 10, 'PTRANS': 19, 'TRANS': 337} Chain: "H" Number of atoms: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2862 Classifications: {'peptide': 367} Modifications used: {'COO': 1} Link IDs: {'CIS': 10, 'PTRANS': 19, 'TRANS': 337} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 23.80, per 1000 atoms: 0.42 Number of scatterers: 56792 At special positions: 0 Unit cell: (194.31, 213.36, 280.67, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 310 16.00 P 16 15.00 Mg 8 11.99 O 10898 8.00 N 9738 7.00 C 35822 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.66 Conformation dependent library (CDL) restraints added in 5.3 seconds 14264 Ramachandran restraints generated. 7132 Oldfield, 0 Emsley, 7132 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13332 Finding SS restraints... Secondary structure from input PDB file: 371 helices and 92 sheets defined 48.4% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.10 Creating SS restraints... Processing helix chain 'I' and resid 46 through 48 No H-bonds generated for 'chain 'I' and resid 46 through 48' Processing helix chain 'I' and resid 61 through 65 removed outlier: 3.533A pdb=" N LEU I 65 " --> pdb=" O ASN I 62 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 80 Processing helix chain 'I' and resid 81 through 84 removed outlier: 3.588A pdb=" N ASP I 84 " --> pdb=" O TYR I 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 81 through 84' Processing helix chain 'I' and resid 108 through 116 Processing helix chain 'I' and resid 127 through 137 removed outlier: 3.713A pdb=" N LYS I 133 " --> pdb=" O ALA I 129 " (cutoff:3.500A) Processing helix chain 'I' and resid 156 through 171 removed outlier: 3.623A pdb=" N THR I 161 " --> pdb=" O LYS I 157 " (cutoff:3.500A) Processing helix chain 'I' and resid 178 through 185 removed outlier: 3.730A pdb=" N ILE I 182 " --> pdb=" O ILE I 178 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL I 183 " --> pdb=" O ASP I 179 " (cutoff:3.500A) Processing helix chain 'I' and resid 185 through 193 removed outlier: 4.030A pdb=" N LEU I 189 " --> pdb=" O ALA I 185 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU I 190 " --> pdb=" O ASN I 186 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA I 191 " --> pdb=" O PRO I 187 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE I 192 " --> pdb=" O LEU I 188 " (cutoff:3.500A) Processing helix chain 'I' and resid 231 through 237 removed outlier: 3.834A pdb=" N ILE I 235 " --> pdb=" O GLU I 231 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N CYS I 236 " --> pdb=" O LYS I 232 " (cutoff:3.500A) Processing helix chain 'I' and resid 246 through 255 removed outlier: 4.661A pdb=" N CYS I 252 " --> pdb=" O PHE I 248 " (cutoff:3.500A) Processing helix chain 'I' and resid 256 through 264 removed outlier: 3.924A pdb=" N GLU I 261 " --> pdb=" O GLU I 257 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ARG I 262 " --> pdb=" O ASP I 258 " (cutoff:3.500A) Processing helix chain 'I' and resid 267 through 270 Processing helix chain 'I' and resid 271 through 276 removed outlier: 3.968A pdb=" N ARG I 276 " --> pdb=" O ARG I 272 " (cutoff:3.500A) Processing helix chain 'I' and resid 284 through 289 removed outlier: 3.760A pdb=" N LYS I 289 " --> pdb=" O LYS I 285 " (cutoff:3.500A) Processing helix chain 'I' and resid 290 through 291 No H-bonds generated for 'chain 'I' and resid 290 through 291' Processing helix chain 'I' and resid 292 through 296 Processing helix chain 'I' and resid 297 through 304 Processing helix chain 'I' and resid 312 through 328 removed outlier: 3.672A pdb=" N PHE I 317 " --> pdb=" O ASP I 313 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE I 318 " --> pdb=" O HIS I 314 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS I 325 " --> pdb=" O CYS I 321 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS I 326 " --> pdb=" O THR I 322 " (cutoff:3.500A) Processing helix chain 'I' and resid 330 through 346 removed outlier: 4.320A pdb=" N VAL I 341 " --> pdb=" O LEU I 337 " (cutoff:3.500A) Processing helix chain 'I' and resid 366 through 368 No H-bonds generated for 'chain 'I' and resid 366 through 368' Processing helix chain 'I' and resid 369 through 380 removed outlier: 3.984A pdb=" N CYS I 375 " --> pdb=" O ALA I 371 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLU I 377 " --> pdb=" O GLU I 373 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LEU I 378 " --> pdb=" O TYR I 374 " (cutoff:3.500A) Processing helix chain 'I' and resid 382 through 390 removed outlier: 3.550A pdb=" N ARG I 387 " --> pdb=" O GLN I 383 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL I 388 " --> pdb=" O ASP I 384 " (cutoff:3.500A) Processing helix chain 'I' and resid 412 through 441 removed outlier: 3.532A pdb=" N ALA I 424 " --> pdb=" O ARG I 420 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N SER I 429 " --> pdb=" O LYS I 425 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP I 433 " --> pdb=" O SER I 429 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N HIS I 434 " --> pdb=" O HIS I 430 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN I 441 " --> pdb=" O ASN I 437 " (cutoff:3.500A) Processing helix chain 'I' and resid 467 through 494 removed outlier: 3.608A pdb=" N LYS I 479 " --> pdb=" O TYR I 475 " (cutoff:3.500A) Processing helix chain 'I' and resid 511 through 519 removed outlier: 3.601A pdb=" N LEU I 517 " --> pdb=" O ASP I 513 " (cutoff:3.500A) Processing helix chain 'I' and resid 524 through 535 removed outlier: 3.559A pdb=" N GLU I 531 " --> pdb=" O ASP I 527 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN I 533 " --> pdb=" O LEU I 529 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ARG I 534 " --> pdb=" O ASP I 530 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU I 535 " --> pdb=" O GLU I 531 " (cutoff:3.500A) Processing helix chain 'I' and resid 540 through 551 removed outlier: 3.523A pdb=" N THR I 544 " --> pdb=" O ASP I 540 " (cutoff:3.500A) Processing helix chain 'I' and resid 559 through 563 Processing helix chain 'I' and resid 565 through 571 removed outlier: 3.858A pdb=" N ASN I 570 " --> pdb=" O ILE I 567 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE I 571 " --> pdb=" O HIS I 568 " (cutoff:3.500A) Processing helix chain 'I' and resid 572 through 574 No H-bonds generated for 'chain 'I' and resid 572 through 574' Processing helix chain 'I' and resid 592 through 598 Processing helix chain 'I' and resid 602 through 610 removed outlier: 4.978A pdb=" N LEU I 608 " --> pdb=" O SER I 604 " (cutoff:3.500A) Processing helix chain 'I' and resid 614 through 621 removed outlier: 3.709A pdb=" N ARG I 618 " --> pdb=" O ASP I 614 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU I 619 " --> pdb=" O LYS I 615 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU I 620 " --> pdb=" O PHE I 616 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N PHE I 621 " --> pdb=" O ILE I 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 614 through 621' Processing helix chain 'I' and resid 632 through 636 removed outlier: 3.527A pdb=" N ALA I 635 " --> pdb=" O LYS I 632 " (cutoff:3.500A) Processing helix chain 'I' and resid 645 through 660 removed outlier: 4.033A pdb=" N LEU I 651 " --> pdb=" O PHE I 647 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU I 654 " --> pdb=" O GLN I 650 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LYS I 657 " --> pdb=" O LEU I 653 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER I 660 " --> pdb=" O ASP I 656 " (cutoff:3.500A) Processing helix chain 'I' and resid 681 through 690 removed outlier: 3.594A pdb=" N LEU I 686 " --> pdb=" O GLY I 682 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N SER I 687 " --> pdb=" O ALA I 683 " (cutoff:3.500A) Processing helix chain 'I' and resid 693 through 699 Processing helix chain 'J' and resid 36 through 40 removed outlier: 3.874A pdb=" N THR J 40 " --> pdb=" O LYS J 37 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 48 No H-bonds generated for 'chain 'J' and resid 46 through 48' Processing helix chain 'J' and resid 61 through 65 Processing helix chain 'J' and resid 69 through 80 removed outlier: 3.563A pdb=" N LYS J 78 " --> pdb=" O LEU J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 81 through 84 removed outlier: 3.731A pdb=" N ASP J 84 " --> pdb=" O TYR J 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 81 through 84' Processing helix chain 'J' and resid 108 through 116 removed outlier: 3.523A pdb=" N TYR J 115 " --> pdb=" O THR J 111 " (cutoff:3.500A) Processing helix chain 'J' and resid 127 through 140 removed outlier: 3.516A pdb=" N LYS J 133 " --> pdb=" O ALA J 129 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET J 138 " --> pdb=" O ALA J 134 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS J 139 " --> pdb=" O PHE J 135 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL J 140 " --> pdb=" O ARG J 136 " (cutoff:3.500A) Processing helix chain 'J' and resid 156 through 171 removed outlier: 3.767A pdb=" N THR J 161 " --> pdb=" O LYS J 157 " (cutoff:3.500A) Processing helix chain 'J' and resid 178 through 185 removed outlier: 4.007A pdb=" N ILE J 182 " --> pdb=" O ILE J 178 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL J 183 " --> pdb=" O ASP J 179 " (cutoff:3.500A) Processing helix chain 'J' and resid 185 through 193 removed outlier: 4.154A pdb=" N PHE J 192 " --> pdb=" O LEU J 188 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY J 193 " --> pdb=" O LEU J 189 " (cutoff:3.500A) Processing helix chain 'J' and resid 232 through 236 removed outlier: 3.563A pdb=" N ILE J 235 " --> pdb=" O LYS J 232 " (cutoff:3.500A) Processing helix chain 'J' and resid 246 through 255 removed outlier: 4.648A pdb=" N CYS J 252 " --> pdb=" O PHE J 248 " (cutoff:3.500A) Processing helix chain 'J' and resid 256 through 264 removed outlier: 3.713A pdb=" N GLU J 261 " --> pdb=" O GLU J 257 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ARG J 262 " --> pdb=" O ASP J 258 " (cutoff:3.500A) Processing helix chain 'J' and resid 267 through 271 Processing helix chain 'J' and resid 286 through 290 Processing helix chain 'J' and resid 297 through 304 Processing helix chain 'J' and resid 312 through 328 removed outlier: 4.057A pdb=" N PHE J 317 " --> pdb=" O ASP J 313 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ILE J 318 " --> pdb=" O HIS J 314 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS J 325 " --> pdb=" O CYS J 321 " (cutoff:3.500A) Processing helix chain 'J' and resid 330 through 346 removed outlier: 3.960A pdb=" N LEU J 335 " --> pdb=" O ASP J 331 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP J 336 " --> pdb=" O GLU J 332 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL J 340 " --> pdb=" O ASP J 336 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL J 341 " --> pdb=" O LEU J 337 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU J 345 " --> pdb=" O VAL J 341 " (cutoff:3.500A) Processing helix chain 'J' and resid 366 through 368 No H-bonds generated for 'chain 'J' and resid 366 through 368' Processing helix chain 'J' and resid 369 through 380 removed outlier: 4.007A pdb=" N CYS J 375 " --> pdb=" O ALA J 371 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU J 377 " --> pdb=" O GLU J 373 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N LEU J 378 " --> pdb=" O TYR J 374 " (cutoff:3.500A) Processing helix chain 'J' and resid 384 through 390 removed outlier: 4.214A pdb=" N VAL J 388 " --> pdb=" O ASP J 384 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER J 389 " --> pdb=" O ASP J 385 " (cutoff:3.500A) Processing helix chain 'J' and resid 412 through 441 removed outlier: 3.511A pdb=" N ALA J 424 " --> pdb=" O ARG J 420 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N SER J 429 " --> pdb=" O LYS J 425 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP J 433 " --> pdb=" O SER J 429 " (cutoff:3.500A) Processing helix chain 'J' and resid 467 through 494 Processing helix chain 'J' and resid 511 through 519 Processing helix chain 'J' and resid 524 through 535 removed outlier: 3.848A pdb=" N ARG J 534 " --> pdb=" O ASP J 530 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU J 535 " --> pdb=" O GLU J 531 " (cutoff:3.500A) Processing helix chain 'J' and resid 540 through 551 removed outlier: 3.639A pdb=" N THR J 544 " --> pdb=" O ASP J 540 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL J 547 " --> pdb=" O PHE J 543 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N HIS J 548 " --> pdb=" O THR J 544 " (cutoff:3.500A) Processing helix chain 'J' and resid 559 through 563 Processing helix chain 'J' and resid 565 through 570 removed outlier: 3.912A pdb=" N ASN J 570 " --> pdb=" O ILE J 567 " (cutoff:3.500A) Processing helix chain 'J' and resid 572 through 574 No H-bonds generated for 'chain 'J' and resid 572 through 574' Processing helix chain 'J' and resid 592 through 598 Processing helix chain 'J' and resid 602 through 610 removed outlier: 4.472A pdb=" N LEU J 608 " --> pdb=" O SER J 604 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS J 610 " --> pdb=" O GLU J 606 " (cutoff:3.500A) Processing helix chain 'J' and resid 614 through 619 removed outlier: 3.714A pdb=" N ARG J 618 " --> pdb=" O ASP J 614 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU J 619 " --> pdb=" O LYS J 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 614 through 619' Processing helix chain 'J' and resid 620 through 622 No H-bonds generated for 'chain 'J' and resid 620 through 622' Processing helix chain 'J' and resid 645 through 661 removed outlier: 3.603A pdb=" N LEU J 651 " --> pdb=" O PHE J 647 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU J 654 " --> pdb=" O GLN J 650 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS J 657 " --> pdb=" O LEU J 653 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER J 660 " --> pdb=" O ASP J 656 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR J 661 " --> pdb=" O LYS J 657 " (cutoff:3.500A) Processing helix chain 'J' and resid 684 through 690 Processing helix chain 'J' and resid 693 through 699 Processing helix chain 'K' and resid 44 through 48 removed outlier: 3.668A pdb=" N VAL K 48 " --> pdb=" O ILE K 45 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 65 removed outlier: 3.574A pdb=" N SER K 64 " --> pdb=" O ASP K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 83 removed outlier: 3.569A pdb=" N TYR K 81 " --> pdb=" O ILE K 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 116 removed outlier: 3.506A pdb=" N GLN K 116 " --> pdb=" O ILE K 112 " (cutoff:3.500A) Processing helix chain 'K' and resid 127 through 140 removed outlier: 3.664A pdb=" N ALA K 131 " --> pdb=" O VAL K 127 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS K 133 " --> pdb=" O ALA K 129 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE K 135 " --> pdb=" O ALA K 131 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N MET K 138 " --> pdb=" O ALA K 134 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LYS K 139 " --> pdb=" O PHE K 135 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N VAL K 140 " --> pdb=" O ARG K 136 " (cutoff:3.500A) Processing helix chain 'K' and resid 156 through 169 removed outlier: 3.809A pdb=" N THR K 161 " --> pdb=" O LYS K 157 " (cutoff:3.500A) Processing helix chain 'K' and resid 178 through 185 removed outlier: 3.635A pdb=" N ILE K 182 " --> pdb=" O ILE K 178 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL K 183 " --> pdb=" O ASP K 179 " (cutoff:3.500A) Processing helix chain 'K' and resid 185 through 193 removed outlier: 3.806A pdb=" N LEU K 189 " --> pdb=" O ALA K 185 " (cutoff:3.500A) Processing helix chain 'K' and resid 231 through 237 removed outlier: 4.017A pdb=" N CYS K 236 " --> pdb=" O LYS K 232 " (cutoff:3.500A) Processing helix chain 'K' and resid 246 through 255 removed outlier: 4.755A pdb=" N CYS K 252 " --> pdb=" O PHE K 248 " (cutoff:3.500A) Processing helix chain 'K' and resid 256 through 264 removed outlier: 4.925A pdb=" N ARG K 262 " --> pdb=" O ASP K 258 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU K 263 " --> pdb=" O ILE K 259 " (cutoff:3.500A) Processing helix chain 'K' and resid 271 through 276 removed outlier: 3.924A pdb=" N ARG K 276 " --> pdb=" O ARG K 272 " (cutoff:3.500A) Processing helix chain 'K' and resid 284 through 289 removed outlier: 3.810A pdb=" N LYS K 289 " --> pdb=" O LYS K 285 " (cutoff:3.500A) Processing helix chain 'K' and resid 292 through 296 removed outlier: 3.542A pdb=" N LYS K 296 " --> pdb=" O GLN K 293 " (cutoff:3.500A) Processing helix chain 'K' and resid 297 through 304 Processing helix chain 'K' and resid 315 through 328 removed outlier: 3.526A pdb=" N CYS K 321 " --> pdb=" O PHE K 317 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLY K 328 " --> pdb=" O MET K 324 " (cutoff:3.500A) Processing helix chain 'K' and resid 330 through 346 removed outlier: 3.682A pdb=" N VAL K 340 " --> pdb=" O ASP K 336 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL K 341 " --> pdb=" O LEU K 337 " (cutoff:3.500A) Processing helix chain 'K' and resid 366 through 368 No H-bonds generated for 'chain 'K' and resid 366 through 368' Processing helix chain 'K' and resid 369 through 377 removed outlier: 3.864A pdb=" N CYS K 375 " --> pdb=" O ALA K 371 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLU K 377 " --> pdb=" O GLU K 373 " (cutoff:3.500A) Processing helix chain 'K' and resid 382 through 390 removed outlier: 3.625A pdb=" N ARG K 387 " --> pdb=" O GLN K 383 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL K 388 " --> pdb=" O ASP K 384 " (cutoff:3.500A) Processing helix chain 'K' and resid 412 through 441 removed outlier: 3.515A pdb=" N ASP K 421 " --> pdb=" O ASN K 417 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU K 423 " --> pdb=" O ALA K 419 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA K 424 " --> pdb=" O ARG K 420 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR K 426 " --> pdb=" O ALA K 422 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR K 428 " --> pdb=" O ALA K 424 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N SER K 429 " --> pdb=" O LYS K 425 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP K 433 " --> pdb=" O SER K 429 " (cutoff:3.500A) Processing helix chain 'K' and resid 467 through 494 removed outlier: 3.533A pdb=" N CYS K 472 " --> pdb=" O PHE K 468 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE K 473 " --> pdb=" O GLU K 469 " (cutoff:3.500A) Processing helix chain 'K' and resid 511 through 520 Processing helix chain 'K' and resid 524 through 533 removed outlier: 3.583A pdb=" N GLU K 531 " --> pdb=" O ASP K 527 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN K 533 " --> pdb=" O LEU K 529 " (cutoff:3.500A) Processing helix chain 'K' and resid 540 through 551 removed outlier: 3.589A pdb=" N ALA K 546 " --> pdb=" O HIS K 542 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N HIS K 548 " --> pdb=" O THR K 544 " (cutoff:3.500A) Processing helix chain 'K' and resid 559 through 563 Processing helix chain 'K' and resid 565 through 571 removed outlier: 3.668A pdb=" N HIS K 568 " --> pdb=" O LEU K 565 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ASN K 570 " --> pdb=" O ILE K 567 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE K 571 " --> pdb=" O HIS K 568 " (cutoff:3.500A) Processing helix chain 'K' and resid 572 through 574 No H-bonds generated for 'chain 'K' and resid 572 through 574' Processing helix chain 'K' and resid 592 through 598 removed outlier: 3.580A pdb=" N ASN K 597 " --> pdb=" O PHE K 593 " (cutoff:3.500A) Processing helix chain 'K' and resid 602 through 610 removed outlier: 4.689A pdb=" N LEU K 608 " --> pdb=" O SER K 604 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N CYS K 610 " --> pdb=" O GLU K 606 " (cutoff:3.500A) Processing helix chain 'K' and resid 614 through 619 removed outlier: 3.666A pdb=" N ARG K 618 " --> pdb=" O ASP K 614 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU K 619 " --> pdb=" O LYS K 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 614 through 619' Processing helix chain 'K' and resid 645 through 660 removed outlier: 3.756A pdb=" N LEU K 651 " --> pdb=" O PHE K 647 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU K 654 " --> pdb=" O GLN K 650 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LYS K 657 " --> pdb=" O LEU K 653 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER K 660 " --> pdb=" O ASP K 656 " (cutoff:3.500A) Processing helix chain 'K' and resid 684 through 690 removed outlier: 3.859A pdb=" N GLN K 688 " --> pdb=" O GLN K 684 " (cutoff:3.500A) Processing helix chain 'K' and resid 693 through 701 removed outlier: 3.650A pdb=" N VAL K 697 " --> pdb=" O GLY K 693 " (cutoff:3.500A) Processing helix chain 'L' and resid 46 through 48 No H-bonds generated for 'chain 'L' and resid 46 through 48' Processing helix chain 'L' and resid 61 through 65 Processing helix chain 'L' and resid 69 through 83 removed outlier: 3.533A pdb=" N TYR L 81 " --> pdb=" O ILE L 77 " (cutoff:3.500A) Processing helix chain 'L' and resid 108 through 116 Processing helix chain 'L' and resid 127 through 140 removed outlier: 3.791A pdb=" N LYS L 133 " --> pdb=" O ALA L 129 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET L 138 " --> pdb=" O ALA L 134 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LYS L 139 " --> pdb=" O PHE L 135 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL L 140 " --> pdb=" O ARG L 136 " (cutoff:3.500A) Processing helix chain 'L' and resid 156 through 171 removed outlier: 3.755A pdb=" N THR L 161 " --> pdb=" O LYS L 157 " (cutoff:3.500A) Processing helix chain 'L' and resid 178 through 185 removed outlier: 4.264A pdb=" N ILE L 182 " --> pdb=" O ILE L 178 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N VAL L 183 " --> pdb=" O ASP L 179 " (cutoff:3.500A) Processing helix chain 'L' and resid 185 through 193 removed outlier: 3.675A pdb=" N ALA L 191 " --> pdb=" O PRO L 187 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N PHE L 192 " --> pdb=" O LEU L 188 " (cutoff:3.500A) Processing helix chain 'L' and resid 232 through 237 removed outlier: 4.223A pdb=" N CYS L 236 " --> pdb=" O LYS L 232 " (cutoff:3.500A) Processing helix chain 'L' and resid 246 through 255 removed outlier: 4.684A pdb=" N CYS L 252 " --> pdb=" O PHE L 248 " (cutoff:3.500A) Processing helix chain 'L' and resid 256 through 264 removed outlier: 4.811A pdb=" N ARG L 262 " --> pdb=" O ASP L 258 " (cutoff:3.500A) Processing helix chain 'L' and resid 267 through 271 Processing helix chain 'L' and resid 284 through 289 removed outlier: 3.769A pdb=" N LYS L 289 " --> pdb=" O LYS L 285 " (cutoff:3.500A) Processing helix chain 'L' and resid 290 through 291 No H-bonds generated for 'chain 'L' and resid 290 through 291' Processing helix chain 'L' and resid 292 through 296 Processing helix chain 'L' and resid 297 through 304 Processing helix chain 'L' and resid 314 through 328 removed outlier: 4.034A pdb=" N ILE L 318 " --> pdb=" O HIS L 314 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS L 325 " --> pdb=" O CYS L 321 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY L 328 " --> pdb=" O MET L 324 " (cutoff:3.500A) Processing helix chain 'L' and resid 330 through 346 removed outlier: 4.113A pdb=" N VAL L 341 " --> pdb=" O LEU L 337 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL L 344 " --> pdb=" O VAL L 340 " (cutoff:3.500A) Processing helix chain 'L' and resid 366 through 368 No H-bonds generated for 'chain 'L' and resid 366 through 368' Processing helix chain 'L' and resid 369 through 380 removed outlier: 3.716A pdb=" N CYS L 375 " --> pdb=" O ALA L 371 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLU L 377 " --> pdb=" O GLU L 373 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N LEU L 378 " --> pdb=" O TYR L 374 " (cutoff:3.500A) Processing helix chain 'L' and resid 382 through 390 removed outlier: 3.709A pdb=" N ARG L 387 " --> pdb=" O GLN L 383 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL L 388 " --> pdb=" O ASP L 384 " (cutoff:3.500A) Processing helix chain 'L' and resid 412 through 441 removed outlier: 3.633A pdb=" N ALA L 424 " --> pdb=" O ARG L 420 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR L 428 " --> pdb=" O ALA L 424 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N SER L 429 " --> pdb=" O LYS L 425 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP L 433 " --> pdb=" O SER L 429 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS L 434 " --> pdb=" O HIS L 430 " (cutoff:3.500A) Processing helix chain 'L' and resid 467 through 497 removed outlier: 4.007A pdb=" N GLN L 497 " --> pdb=" O GLN L 493 " (cutoff:3.500A) Processing helix chain 'L' and resid 511 through 519 Processing helix chain 'L' and resid 524 through 535 removed outlier: 4.025A pdb=" N ARG L 534 " --> pdb=" O ASP L 530 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU L 535 " --> pdb=" O GLU L 531 " (cutoff:3.500A) Processing helix chain 'L' and resid 540 through 551 removed outlier: 3.530A pdb=" N VAL L 547 " --> pdb=" O PHE L 543 " (cutoff:3.500A) Processing helix chain 'L' and resid 559 through 563 Processing helix chain 'L' and resid 565 through 571 removed outlier: 4.127A pdb=" N ASN L 570 " --> pdb=" O ILE L 567 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE L 571 " --> pdb=" O HIS L 568 " (cutoff:3.500A) Processing helix chain 'L' and resid 572 through 574 No H-bonds generated for 'chain 'L' and resid 572 through 574' Processing helix chain 'L' and resid 592 through 598 Processing helix chain 'L' and resid 602 through 610 removed outlier: 4.888A pdb=" N LEU L 608 " --> pdb=" O SER L 604 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N CYS L 610 " --> pdb=" O GLU L 606 " (cutoff:3.500A) Processing helix chain 'L' and resid 614 through 619 removed outlier: 3.967A pdb=" N ARG L 618 " --> pdb=" O ASP L 614 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU L 619 " --> pdb=" O LYS L 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 614 through 619' Processing helix chain 'L' and resid 632 through 636 removed outlier: 3.636A pdb=" N ALA L 635 " --> pdb=" O LYS L 632 " (cutoff:3.500A) Processing helix chain 'L' and resid 645 through 661 removed outlier: 3.503A pdb=" N LEU L 651 " --> pdb=" O PHE L 647 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU L 654 " --> pdb=" O GLN L 650 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LYS L 657 " --> pdb=" O LEU L 653 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER L 660 " --> pdb=" O ASP L 656 " (cutoff:3.500A) Processing helix chain 'L' and resid 681 through 690 removed outlier: 3.678A pdb=" N LEU L 686 " --> pdb=" O GLY L 682 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N SER L 687 " --> pdb=" O ALA L 683 " (cutoff:3.500A) Processing helix chain 'L' and resid 693 through 699 removed outlier: 3.792A pdb=" N VAL L 697 " --> pdb=" O GLY L 693 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 48 removed outlier: 3.622A pdb=" N VAL M 48 " --> pdb=" O ILE M 45 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 65 removed outlier: 3.536A pdb=" N LEU M 65 " --> pdb=" O ASN M 62 " (cutoff:3.500A) Processing helix chain 'M' and resid 69 through 83 Processing helix chain 'M' and resid 108 through 116 Processing helix chain 'M' and resid 127 through 140 removed outlier: 3.632A pdb=" N LYS M 133 " --> pdb=" O ALA M 129 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE M 135 " --> pdb=" O ALA M 131 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N MET M 138 " --> pdb=" O ALA M 134 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS M 139 " --> pdb=" O PHE M 135 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL M 140 " --> pdb=" O ARG M 136 " (cutoff:3.500A) Processing helix chain 'M' and resid 156 through 171 removed outlier: 3.837A pdb=" N THR M 161 " --> pdb=" O LYS M 157 " (cutoff:3.500A) Processing helix chain 'M' and resid 178 through 185 removed outlier: 3.709A pdb=" N ILE M 182 " --> pdb=" O ILE M 178 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL M 183 " --> pdb=" O ASP M 179 " (cutoff:3.500A) Processing helix chain 'M' and resid 185 through 193 removed outlier: 4.067A pdb=" N LEU M 189 " --> pdb=" O ALA M 185 " (cutoff:3.500A) Processing helix chain 'M' and resid 246 through 255 removed outlier: 4.832A pdb=" N CYS M 252 " --> pdb=" O PHE M 248 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA M 255 " --> pdb=" O LEU M 251 " (cutoff:3.500A) Processing helix chain 'M' and resid 256 through 264 removed outlier: 3.771A pdb=" N GLU M 261 " --> pdb=" O GLU M 257 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ARG M 262 " --> pdb=" O ASP M 258 " (cutoff:3.500A) Processing helix chain 'M' and resid 267 through 270 Processing helix chain 'M' and resid 271 through 276 removed outlier: 3.955A pdb=" N ARG M 276 " --> pdb=" O ARG M 272 " (cutoff:3.500A) Processing helix chain 'M' and resid 284 through 289 removed outlier: 3.701A pdb=" N LYS M 289 " --> pdb=" O LYS M 285 " (cutoff:3.500A) Processing helix chain 'M' and resid 292 through 296 Processing helix chain 'M' and resid 297 through 304 Processing helix chain 'M' and resid 315 through 328 removed outlier: 3.890A pdb=" N LYS M 325 " --> pdb=" O CYS M 321 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS M 326 " --> pdb=" O THR M 322 " (cutoff:3.500A) Processing helix chain 'M' and resid 330 through 346 removed outlier: 3.547A pdb=" N ASP M 336 " --> pdb=" O GLU M 332 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N VAL M 341 " --> pdb=" O LEU M 337 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU M 345 " --> pdb=" O VAL M 341 " (cutoff:3.500A) Processing helix chain 'M' and resid 366 through 368 No H-bonds generated for 'chain 'M' and resid 366 through 368' Processing helix chain 'M' and resid 369 through 377 removed outlier: 3.938A pdb=" N CYS M 375 " --> pdb=" O ALA M 371 " (cutoff:3.500A) Processing helix chain 'M' and resid 382 through 390 removed outlier: 3.784A pdb=" N ARG M 387 " --> pdb=" O GLN M 383 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL M 388 " --> pdb=" O ASP M 384 " (cutoff:3.500A) Processing helix chain 'M' and resid 412 through 441 removed outlier: 3.677A pdb=" N ALA M 424 " --> pdb=" O ARG M 420 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N SER M 429 " --> pdb=" O LYS M 425 " (cutoff:3.500A) Processing helix chain 'M' and resid 467 through 494 removed outlier: 3.575A pdb=" N ILE M 473 " --> pdb=" O GLU M 469 " (cutoff:3.500A) Processing helix chain 'M' and resid 511 through 519 Processing helix chain 'M' and resid 524 through 535 removed outlier: 3.775A pdb=" N ARG M 534 " --> pdb=" O ASP M 530 " (cutoff:3.500A) Processing helix chain 'M' and resid 540 through 551 Processing helix chain 'M' and resid 559 through 563 Processing helix chain 'M' and resid 565 through 569 Processing helix chain 'M' and resid 572 through 574 No H-bonds generated for 'chain 'M' and resid 572 through 574' Processing helix chain 'M' and resid 592 through 598 removed outlier: 3.655A pdb=" N LYS M 596 " --> pdb=" O GLN M 592 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASN M 597 " --> pdb=" O PHE M 593 " (cutoff:3.500A) Processing helix chain 'M' and resid 602 through 610 removed outlier: 4.656A pdb=" N LEU M 608 " --> pdb=" O SER M 604 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N CYS M 610 " --> pdb=" O GLU M 606 " (cutoff:3.500A) Processing helix chain 'M' and resid 614 through 619 removed outlier: 3.901A pdb=" N ARG M 618 " --> pdb=" O ASP M 614 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU M 619 " --> pdb=" O LYS M 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 614 through 619' Processing helix chain 'M' and resid 620 through 622 No H-bonds generated for 'chain 'M' and resid 620 through 622' Processing helix chain 'M' and resid 642 through 661 removed outlier: 4.212A pdb=" N LYS M 648 " --> pdb=" O GLY M 644 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU M 651 " --> pdb=" O PHE M 647 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU M 654 " --> pdb=" O GLN M 650 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYS M 657 " --> pdb=" O LEU M 653 " (cutoff:3.500A) Processing helix chain 'M' and resid 684 through 690 Processing helix chain 'M' and resid 693 through 702 removed outlier: 4.096A pdb=" N VAL M 697 " --> pdb=" O GLY M 693 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLN M 702 " --> pdb=" O LEU M 698 " (cutoff:3.500A) Processing helix chain 'N' and resid 69 through 80 removed outlier: 3.505A pdb=" N LEU N 73 " --> pdb=" O ASN N 69 " (cutoff:3.500A) Processing helix chain 'N' and resid 81 through 84 removed outlier: 3.611A pdb=" N ASP N 84 " --> pdb=" O TYR N 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 81 through 84' Processing helix chain 'N' and resid 108 through 116 removed outlier: 3.510A pdb=" N TYR N 115 " --> pdb=" O THR N 111 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN N 116 " --> pdb=" O ILE N 112 " (cutoff:3.500A) Processing helix chain 'N' and resid 126 through 140 removed outlier: 3.580A pdb=" N ILE N 130 " --> pdb=" O HIS N 126 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS N 133 " --> pdb=" O ALA N 129 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N MET N 138 " --> pdb=" O ALA N 134 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS N 139 " --> pdb=" O PHE N 135 " (cutoff:3.500A) Processing helix chain 'N' and resid 156 through 171 removed outlier: 3.826A pdb=" N THR N 161 " --> pdb=" O LYS N 157 " (cutoff:3.500A) Processing helix chain 'N' and resid 177 through 185 removed outlier: 3.679A pdb=" N ARG N 181 " --> pdb=" O ASP N 177 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N VAL N 183 " --> pdb=" O ASP N 179 " (cutoff:3.500A) Processing helix chain 'N' and resid 185 through 193 removed outlier: 3.919A pdb=" N PHE N 192 " --> pdb=" O LEU N 188 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY N 193 " --> pdb=" O LEU N 189 " (cutoff:3.500A) Processing helix chain 'N' and resid 231 through 237 removed outlier: 3.919A pdb=" N ILE N 235 " --> pdb=" O GLU N 231 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N CYS N 236 " --> pdb=" O LYS N 232 " (cutoff:3.500A) Processing helix chain 'N' and resid 246 through 255 removed outlier: 4.548A pdb=" N CYS N 252 " --> pdb=" O PHE N 248 " (cutoff:3.500A) Processing helix chain 'N' and resid 256 through 264 removed outlier: 3.680A pdb=" N GLU N 261 " --> pdb=" O GLU N 257 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ARG N 262 " --> pdb=" O ASP N 258 " (cutoff:3.500A) Processing helix chain 'N' and resid 267 through 271 Processing helix chain 'N' and resid 284 through 291 removed outlier: 4.030A pdb=" N GLN N 290 " --> pdb=" O GLU N 286 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE N 291 " --> pdb=" O THR N 287 " (cutoff:3.500A) Processing helix chain 'N' and resid 292 through 296 Processing helix chain 'N' and resid 297 through 304 Processing helix chain 'N' and resid 312 through 328 removed outlier: 3.541A pdb=" N PHE N 317 " --> pdb=" O ASP N 313 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ILE N 318 " --> pdb=" O HIS N 314 " (cutoff:3.500A) Processing helix chain 'N' and resid 330 through 346 removed outlier: 4.142A pdb=" N VAL N 341 " --> pdb=" O LEU N 337 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU N 345 " --> pdb=" O VAL N 341 " (cutoff:3.500A) Processing helix chain 'N' and resid 366 through 368 No H-bonds generated for 'chain 'N' and resid 366 through 368' Processing helix chain 'N' and resid 369 through 380 removed outlier: 3.797A pdb=" N CYS N 375 " --> pdb=" O ALA N 371 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLU N 377 " --> pdb=" O GLU N 373 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N LEU N 378 " --> pdb=" O TYR N 374 " (cutoff:3.500A) Processing helix chain 'N' and resid 382 through 390 removed outlier: 4.136A pdb=" N ARG N 387 " --> pdb=" O GLN N 383 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N VAL N 388 " --> pdb=" O ASP N 384 " (cutoff:3.500A) Processing helix chain 'N' and resid 412 through 441 removed outlier: 3.685A pdb=" N ALA N 424 " --> pdb=" O ARG N 420 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR N 428 " --> pdb=" O ALA N 424 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N SER N 429 " --> pdb=" O LYS N 425 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP N 433 " --> pdb=" O SER N 429 " (cutoff:3.500A) Processing helix chain 'N' and resid 467 through 494 Processing helix chain 'N' and resid 511 through 519 removed outlier: 3.556A pdb=" N LEU N 517 " --> pdb=" O ASP N 513 " (cutoff:3.500A) Processing helix chain 'N' and resid 524 through 535 removed outlier: 3.505A pdb=" N GLU N 531 " --> pdb=" O ASP N 527 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN N 533 " --> pdb=" O LEU N 529 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG N 534 " --> pdb=" O ASP N 530 " (cutoff:3.500A) Processing helix chain 'N' and resid 540 through 551 removed outlier: 3.641A pdb=" N HIS N 548 " --> pdb=" O THR N 544 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LYS N 550 " --> pdb=" O ALA N 546 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N HIS N 551 " --> pdb=" O VAL N 547 " (cutoff:3.500A) Processing helix chain 'N' and resid 565 through 571 removed outlier: 3.732A pdb=" N ASN N 570 " --> pdb=" O ILE N 567 " (cutoff:3.500A) Processing helix chain 'N' and resid 572 through 574 No H-bonds generated for 'chain 'N' and resid 572 through 574' Processing helix chain 'N' and resid 602 through 610 removed outlier: 4.870A pdb=" N LEU N 608 " --> pdb=" O SER N 604 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS N 610 " --> pdb=" O GLU N 606 " (cutoff:3.500A) Processing helix chain 'N' and resid 614 through 621 removed outlier: 3.644A pdb=" N ARG N 618 " --> pdb=" O ASP N 614 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU N 619 " --> pdb=" O LYS N 615 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU N 620 " --> pdb=" O PHE N 616 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N PHE N 621 " --> pdb=" O ILE N 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 614 through 621' Processing helix chain 'N' and resid 645 through 660 removed outlier: 3.604A pdb=" N LEU N 651 " --> pdb=" O PHE N 647 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU N 654 " --> pdb=" O GLN N 650 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LYS N 657 " --> pdb=" O LEU N 653 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER N 660 " --> pdb=" O ASP N 656 " (cutoff:3.500A) Processing helix chain 'N' and resid 684 through 690 removed outlier: 3.504A pdb=" N GLN N 690 " --> pdb=" O LEU N 686 " (cutoff:3.500A) Processing helix chain 'N' and resid 693 through 699 removed outlier: 3.991A pdb=" N VAL N 697 " --> pdb=" O GLY N 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 78 through 93 removed outlier: 3.609A pdb=" N MET A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LYS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU A 93 " --> pdb=" O THR A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 128 Processing helix chain 'A' and resid 137 through 146 removed outlier: 3.967A pdb=" N SER A 141 " --> pdb=" O GLN A 137 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N TYR A 143 " --> pdb=" O VAL A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 175 removed outlier: 3.990A pdb=" N ILE A 175 " --> pdb=" O PRO A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 175' Processing helix chain 'A' and resid 182 through 195 Processing helix chain 'A' and resid 202 through 216 removed outlier: 3.628A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL A 209 " --> pdb=" O GLU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 232 removed outlier: 3.663A pdb=" N THR A 229 " --> pdb=" O ASN A 225 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 removed outlier: 4.126A pdb=" N PHE A 255 " --> pdb=" O GLY A 251 " (cutoff:3.500A) Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 261 through 262 No H-bonds generated for 'chain 'A' and resid 261 through 262' Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 273 through 283 removed outlier: 3.594A pdb=" N TYR A 279 " --> pdb=" O HIS A 275 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE A 282 " --> pdb=" O THR A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 294 removed outlier: 3.588A pdb=" N ARG A 290 " --> pdb=" O ASP A 286 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS A 291 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ASP A 292 " --> pdb=" O ASP A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 305 Processing helix chain 'A' and resid 310 through 321 removed outlier: 3.741A pdb=" N ALA A 319 " --> pdb=" O LYS A 315 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A 320 " --> pdb=" O GLU A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 349 Processing helix chain 'A' and resid 351 through 356 removed outlier: 4.173A pdb=" N TRP A 356 " --> pdb=" O GLN A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 367 through 370 removed outlier: 4.094A pdb=" N VAL A 370 " --> pdb=" O PRO A 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 367 through 370' Processing helix chain 'B' and resid 78 through 93 removed outlier: 4.287A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU B 93 " --> pdb=" O THR B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.681A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 128 Processing helix chain 'B' and resid 137 through 146 removed outlier: 3.946A pdb=" N SER B 141 " --> pdb=" O GLN B 137 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N TYR B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 removed outlier: 4.187A pdb=" N ILE B 175 " --> pdb=" O PRO B 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 172 through 175' Processing helix chain 'B' and resid 182 through 194 Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 202 through 216 removed outlier: 3.642A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL B 209 " --> pdb=" O GLU B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 232 removed outlier: 3.635A pdb=" N THR B 229 " --> pdb=" O ASN B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 260 removed outlier: 4.150A pdb=" N PHE B 255 " --> pdb=" O GLY B 251 " (cutoff:3.500A) Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 261 through 262 No H-bonds generated for 'chain 'B' and resid 261 through 262' Processing helix chain 'B' and resid 263 through 267 Processing helix chain 'B' and resid 273 through 283 Processing helix chain 'B' and resid 289 through 294 Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 310 through 321 Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 349 removed outlier: 3.737A pdb=" N ILE B 345 " --> pdb=" O ILE B 341 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER B 348 " --> pdb=" O SER B 344 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU B 349 " --> pdb=" O ILE B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 355 Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 367 through 370 removed outlier: 3.872A pdb=" N VAL B 370 " --> pdb=" O PRO B 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 367 through 370' Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 78 through 93 removed outlier: 4.184A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU C 93 " --> pdb=" O THR C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.852A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.528A pdb=" N MET C 119 " --> pdb=" O ASN C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 removed outlier: 3.984A pdb=" N SER C 141 " --> pdb=" O GLN C 137 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA C 144 " --> pdb=" O LEU C 140 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER C 145 " --> pdb=" O SER C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 194 Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 202 through 216 removed outlier: 4.110A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL C 209 " --> pdb=" O GLU C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 232 removed outlier: 3.962A pdb=" N SER C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 260 removed outlier: 4.174A pdb=" N PHE C 255 " --> pdb=" O GLY C 251 " (cutoff:3.500A) Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 261 through 262 No H-bonds generated for 'chain 'C' and resid 261 through 262' Processing helix chain 'C' and resid 263 through 267 Processing helix chain 'C' and resid 273 through 283 Processing helix chain 'C' and resid 289 through 294 removed outlier: 3.503A pdb=" N LEU C 293 " --> pdb=" O ILE C 289 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR C 294 " --> pdb=" O ARG C 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 289 through 294' Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 310 through 321 removed outlier: 3.692A pdb=" N ALA C 319 " --> pdb=" O LYS C 315 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU C 320 " --> pdb=" O GLU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 349 removed outlier: 4.092A pdb=" N SER C 348 " --> pdb=" O SER C 344 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LEU C 349 " --> pdb=" O ILE C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 356 removed outlier: 4.134A pdb=" N TRP C 356 " --> pdb=" O GLN C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'D' and resid 56 through 61 Processing helix chain 'D' and resid 78 through 93 removed outlier: 3.578A pdb=" N MET D 82 " --> pdb=" O ASN D 78 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LYS D 84 " --> pdb=" O ASP D 80 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU D 93 " --> pdb=" O THR D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 128 Processing helix chain 'D' and resid 137 through 145 removed outlier: 3.639A pdb=" N SER D 141 " --> pdb=" O GLN D 137 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N TYR D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA D 144 " --> pdb=" O LEU D 140 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N SER D 145 " --> pdb=" O SER D 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 137 through 145' Processing helix chain 'D' and resid 182 through 194 Processing helix chain 'D' and resid 195 through 197 No H-bonds generated for 'chain 'D' and resid 195 through 197' Processing helix chain 'D' and resid 202 through 216 removed outlier: 3.831A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL D 209 " --> pdb=" O GLU D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 232 removed outlier: 3.595A pdb=" N THR D 229 " --> pdb=" O ASN D 225 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 260 removed outlier: 4.168A pdb=" N PHE D 255 " --> pdb=" O GLY D 251 " (cutoff:3.500A) Proline residue: D 258 - end of helix Processing helix chain 'D' and resid 261 through 262 No H-bonds generated for 'chain 'D' and resid 261 through 262' Processing helix chain 'D' and resid 263 through 267 Processing helix chain 'D' and resid 273 through 283 Processing helix chain 'D' and resid 286 through 294 removed outlier: 4.371A pdb=" N LYS D 291 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N ASP D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 305 Processing helix chain 'D' and resid 310 through 321 removed outlier: 3.629A pdb=" N ALA D 319 " --> pdb=" O LYS D 315 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU D 320 " --> pdb=" O GLU D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 349 removed outlier: 3.617A pdb=" N ILE D 345 " --> pdb=" O ILE D 341 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU D 349 " --> pdb=" O ILE D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 355 removed outlier: 3.603A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'E' and resid 56 through 61 Processing helix chain 'E' and resid 78 through 93 removed outlier: 4.017A pdb=" N LYS E 84 " --> pdb=" O ASP E 80 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU E 93 " --> pdb=" O THR E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 100 Processing helix chain 'E' and resid 116 through 128 Processing helix chain 'E' and resid 137 through 145 removed outlier: 4.048A pdb=" N SER E 141 " --> pdb=" O GLN E 137 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU E 142 " --> pdb=" O ALA E 138 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N TYR E 143 " --> pdb=" O VAL E 139 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N SER E 145 " --> pdb=" O SER E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 194 removed outlier: 3.571A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 202 through 217 removed outlier: 4.256A pdb=" N GLU E 207 " --> pdb=" O THR E 203 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ILE E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL E 209 " --> pdb=" O GLU E 205 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N CYS E 217 " --> pdb=" O LYS E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 232 removed outlier: 3.510A pdb=" N ALA E 231 " --> pdb=" O MET E 227 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N SER E 232 " --> pdb=" O ALA E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 260 Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 261 through 262 No H-bonds generated for 'chain 'E' and resid 261 through 262' Processing helix chain 'E' and resid 263 through 267 Processing helix chain 'E' and resid 273 through 283 removed outlier: 3.595A pdb=" N TYR E 279 " --> pdb=" O HIS E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 285 No H-bonds generated for 'chain 'E' and resid 284 through 285' Processing helix chain 'E' and resid 286 through 288 No H-bonds generated for 'chain 'E' and resid 286 through 288' Processing helix chain 'E' and resid 289 through 294 Processing helix chain 'E' and resid 310 through 321 removed outlier: 3.507A pdb=" N ALA E 319 " --> pdb=" O LYS E 315 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU E 320 " --> pdb=" O GLU E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 334 through 336 No H-bonds generated for 'chain 'E' and resid 334 through 336' Processing helix chain 'E' and resid 337 through 349 removed outlier: 3.544A pdb=" N ILE E 345 " --> pdb=" O ILE E 341 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER E 348 " --> pdb=" O SER E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 355 Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 367 through 371 removed outlier: 3.653A pdb=" N HIS E 371 " --> pdb=" O SER E 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 60 Processing helix chain 'F' and resid 78 through 93 removed outlier: 3.815A pdb=" N LYS F 84 " --> pdb=" O ASP F 80 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU F 93 " --> pdb=" O THR F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 128 Processing helix chain 'F' and resid 137 through 145 removed outlier: 3.926A pdb=" N SER F 141 " --> pdb=" O GLN F 137 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU F 142 " --> pdb=" O ALA F 138 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N TYR F 143 " --> pdb=" O VAL F 139 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA F 144 " --> pdb=" O LEU F 140 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N SER F 145 " --> pdb=" O SER F 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 137 through 145' Processing helix chain 'F' and resid 182 through 194 removed outlier: 3.506A pdb=" N THR F 194 " --> pdb=" O MET F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 197 No H-bonds generated for 'chain 'F' and resid 195 through 197' Processing helix chain 'F' and resid 202 through 216 removed outlier: 3.943A pdb=" N GLU F 207 " --> pdb=" O THR F 203 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ILE F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL F 209 " --> pdb=" O GLU F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 232 removed outlier: 3.589A pdb=" N SER F 232 " --> pdb=" O ALA F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 260 removed outlier: 3.917A pdb=" N PHE F 255 " --> pdb=" O GLY F 251 " (cutoff:3.500A) Proline residue: F 258 - end of helix Processing helix chain 'F' and resid 273 through 283 Processing helix chain 'F' and resid 286 through 294 removed outlier: 3.530A pdb=" N ARG F 290 " --> pdb=" O ASP F 286 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LYS F 291 " --> pdb=" O ILE F 287 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ASP F 292 " --> pdb=" O ASP F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 305 Processing helix chain 'F' and resid 310 through 321 removed outlier: 3.657A pdb=" N ALA F 319 " --> pdb=" O LYS F 315 " (cutoff:3.500A) Processing helix chain 'F' and resid 334 through 336 No H-bonds generated for 'chain 'F' and resid 334 through 336' Processing helix chain 'F' and resid 337 through 349 removed outlier: 3.539A pdb=" N ILE F 345 " --> pdb=" O ILE F 341 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER F 348 " --> pdb=" O SER F 344 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU F 349 " --> pdb=" O ILE F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 351 through 355 Processing helix chain 'F' and resid 359 through 366 Processing helix chain 'G' and resid 56 through 60 Processing helix chain 'G' and resid 78 through 93 removed outlier: 3.935A pdb=" N LYS G 84 " --> pdb=" O ASP G 80 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU G 93 " --> pdb=" O THR G 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 101 removed outlier: 3.761A pdb=" N HIS G 101 " --> pdb=" O PRO G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 128 Processing helix chain 'G' and resid 137 through 146 removed outlier: 4.023A pdb=" N SER G 141 " --> pdb=" O GLN G 137 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LEU G 142 " --> pdb=" O ALA G 138 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N TYR G 143 " --> pdb=" O VAL G 139 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 175 removed outlier: 3.795A pdb=" N ILE G 175 " --> pdb=" O PRO G 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 172 through 175' Processing helix chain 'G' and resid 182 through 194 removed outlier: 3.572A pdb=" N THR G 194 " --> pdb=" O MET G 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 197 No H-bonds generated for 'chain 'G' and resid 195 through 197' Processing helix chain 'G' and resid 202 through 216 removed outlier: 3.684A pdb=" N GLU G 207 " --> pdb=" O THR G 203 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ILE G 208 " --> pdb=" O ALA G 204 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL G 209 " --> pdb=" O GLU G 205 " (cutoff:3.500A) Processing helix chain 'G' and resid 222 through 232 removed outlier: 3.536A pdb=" N SER G 232 " --> pdb=" O ALA G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 251 through 257 removed outlier: 4.239A pdb=" N PHE G 255 " --> pdb=" O GLY G 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 258 through 261 removed outlier: 3.621A pdb=" N LEU G 261 " --> pdb=" O PRO G 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 258 through 261' Processing helix chain 'G' and resid 263 through 268 removed outlier: 3.605A pdb=" N PHE G 266 " --> pdb=" O GLN G 263 " (cutoff:3.500A) Processing helix chain 'G' and resid 273 through 283 removed outlier: 3.670A pdb=" N TYR G 279 " --> pdb=" O HIS G 275 " (cutoff:3.500A) Processing helix chain 'G' and resid 286 through 294 removed outlier: 3.525A pdb=" N ARG G 290 " --> pdb=" O ASP G 286 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LYS G 291 " --> pdb=" O ILE G 287 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ASP G 292 " --> pdb=" O ASP G 288 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU G 293 " --> pdb=" O ILE G 289 " (cutoff:3.500A) Processing helix chain 'G' and resid 301 through 305 Processing helix chain 'G' and resid 310 through 321 removed outlier: 3.721A pdb=" N ALA G 319 " --> pdb=" O LYS G 315 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU G 320 " --> pdb=" O GLU G 316 " (cutoff:3.500A) Processing helix chain 'G' and resid 334 through 336 No H-bonds generated for 'chain 'G' and resid 334 through 336' Processing helix chain 'G' and resid 337 through 349 removed outlier: 3.603A pdb=" N SER G 348 " --> pdb=" O SER G 344 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU G 349 " --> pdb=" O ILE G 345 " (cutoff:3.500A) Processing helix chain 'G' and resid 351 through 355 Processing helix chain 'G' and resid 359 through 366 Processing helix chain 'H' and resid 56 through 61 Processing helix chain 'H' and resid 78 through 93 removed outlier: 3.891A pdb=" N LYS H 84 " --> pdb=" O ASP H 80 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU H 93 " --> pdb=" O THR H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 101 removed outlier: 3.812A pdb=" N HIS H 101 " --> pdb=" O PRO H 98 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 128 removed outlier: 3.515A pdb=" N MET H 119 " --> pdb=" O ASN H 115 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 145 removed outlier: 3.885A pdb=" N SER H 141 " --> pdb=" O GLN H 137 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU H 142 " --> pdb=" O ALA H 138 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR H 143 " --> pdb=" O VAL H 139 " (cutoff:3.500A) Processing helix chain 'H' and resid 172 through 175 removed outlier: 3.926A pdb=" N ILE H 175 " --> pdb=" O PRO H 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 172 through 175' Processing helix chain 'H' and resid 182 through 194 removed outlier: 3.806A pdb=" N THR H 194 " --> pdb=" O MET H 190 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 197 No H-bonds generated for 'chain 'H' and resid 195 through 197' Processing helix chain 'H' and resid 202 through 216 removed outlier: 3.605A pdb=" N GLU H 207 " --> pdb=" O THR H 203 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE H 208 " --> pdb=" O ALA H 204 " (cutoff:3.500A) Processing helix chain 'H' and resid 222 through 232 removed outlier: 3.817A pdb=" N THR H 229 " --> pdb=" O ASN H 225 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER H 232 " --> pdb=" O ALA H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 251 through 260 removed outlier: 3.935A pdb=" N PHE H 255 " --> pdb=" O GLY H 251 " (cutoff:3.500A) Proline residue: H 258 - end of helix Processing helix chain 'H' and resid 261 through 262 No H-bonds generated for 'chain 'H' and resid 261 through 262' Processing helix chain 'H' and resid 263 through 268 removed outlier: 3.549A pdb=" N PHE H 266 " --> pdb=" O GLN H 263 " (cutoff:3.500A) Processing helix chain 'H' and resid 273 through 283 removed outlier: 3.692A pdb=" N TYR H 279 " --> pdb=" O HIS H 275 " (cutoff:3.500A) Processing helix chain 'H' and resid 286 through 294 removed outlier: 3.603A pdb=" N ARG H 290 " --> pdb=" O ASP H 286 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LYS H 291 " --> pdb=" O ILE H 287 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ASP H 292 " --> pdb=" O ASP H 288 " (cutoff:3.500A) Processing helix chain 'H' and resid 310 through 321 removed outlier: 3.654A pdb=" N ALA H 319 " --> pdb=" O LYS H 315 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU H 320 " --> pdb=" O GLU H 316 " (cutoff:3.500A) Processing helix chain 'H' and resid 334 through 336 No H-bonds generated for 'chain 'H' and resid 334 through 336' Processing helix chain 'H' and resid 337 through 349 removed outlier: 3.502A pdb=" N LEU H 349 " --> pdb=" O ILE H 345 " (cutoff:3.500A) Processing helix chain 'H' and resid 351 through 355 removed outlier: 3.575A pdb=" N GLN H 354 " --> pdb=" O THR H 351 " (cutoff:3.500A) Processing helix chain 'H' and resid 359 through 366 Processing helix chain 'H' and resid 367 through 370 removed outlier: 3.867A pdb=" N VAL H 370 " --> pdb=" O PRO H 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 367 through 370' Processing sheet with id=AA1, first strand: chain 'I' and resid 41 through 44 removed outlier: 6.985A pdb=" N SER I 28 " --> pdb=" O ILE I 24 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ILE I 24 " --> pdb=" O SER I 28 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N THR I 30 " --> pdb=" O VAL I 22 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE I 49 " --> pdb=" O TRP I 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 87 through 90 removed outlier: 6.098A pdb=" N LEU I 94 " --> pdb=" O ARG I 667 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ILE I 669 " --> pdb=" O LEU I 94 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ALA I 96 " --> pdb=" O ILE I 669 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N SER I 146 " --> pdb=" O SER I 664 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ILE I 666 " --> pdb=" O SER I 146 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE I 148 " --> pdb=" O ILE I 666 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N CYS I 668 " --> pdb=" O ILE I 148 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N SER I 150 " --> pdb=" O CYS I 668 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N GLN I 145 " --> pdb=" O GLY I 453 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N LEU I 455 " --> pdb=" O GLN I 145 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE I 147 " --> pdb=" O LEU I 455 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL I 210 " --> pdb=" O VAL I 454 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY I 222 " --> pdb=" O HIS I 213 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 194 through 195 Processing sheet with id=AA4, first strand: chain 'I' and resid 282 through 283 removed outlier: 3.746A pdb=" N ALA I 283 " --> pdb=" O LEU I 306 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'I' and resid 352 through 354 removed outlier: 3.508A pdb=" N ASN I 363 " --> pdb=" O GLU I 353 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 392 through 396 Processing sheet with id=AA7, first strand: chain 'I' and resid 557 through 558 Processing sheet with id=AA8, first strand: chain 'J' and resid 41 through 44 removed outlier: 7.068A pdb=" N SER J 28 " --> pdb=" O ILE J 24 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ILE J 24 " --> pdb=" O SER J 28 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N THR J 30 " --> pdb=" O VAL J 22 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE J 49 " --> pdb=" O TRP J 8 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 87 through 90 removed outlier: 6.186A pdb=" N LEU J 94 " --> pdb=" O ARG J 667 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ILE J 669 " --> pdb=" O LEU J 94 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ALA J 96 " --> pdb=" O ILE J 669 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N SER J 146 " --> pdb=" O SER J 664 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ILE J 666 " --> pdb=" O SER J 146 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ILE J 148 " --> pdb=" O ILE J 666 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N CYS J 668 " --> pdb=" O ILE J 148 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLN J 145 " --> pdb=" O GLY J 453 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N LEU J 455 " --> pdb=" O GLN J 145 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ILE J 147 " --> pdb=" O LEU J 455 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL J 210 " --> pdb=" O VAL J 454 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY J 222 " --> pdb=" O HIS J 213 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 194 through 195 Processing sheet with id=AB2, first strand: chain 'J' and resid 352 through 353 Processing sheet with id=AB3, first strand: chain 'J' and resid 392 through 396 Processing sheet with id=AB4, first strand: chain 'J' and resid 557 through 558 removed outlier: 3.594A pdb=" N SER J 558 " --> pdb=" O ILE J 578 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE J 578 " --> pdb=" O SER J 558 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 41 through 43 removed outlier: 7.247A pdb=" N THR K 30 " --> pdb=" O VAL K 22 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE K 49 " --> pdb=" O TRP K 8 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 87 through 90 removed outlier: 6.009A pdb=" N LEU K 94 " --> pdb=" O ARG K 667 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ILE K 669 " --> pdb=" O LEU K 94 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ALA K 96 " --> pdb=" O ILE K 669 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N SER K 146 " --> pdb=" O SER K 664 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ILE K 666 " --> pdb=" O SER K 146 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE K 148 " --> pdb=" O ILE K 666 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N CYS K 668 " --> pdb=" O ILE K 148 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N GLN K 145 " --> pdb=" O GLY K 453 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N LEU K 455 " --> pdb=" O GLN K 145 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE K 147 " --> pdb=" O LEU K 455 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL K 210 " --> pdb=" O VAL K 454 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY K 222 " --> pdb=" O HIS K 213 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 194 through 197 removed outlier: 6.582A pdb=" N ALA K 195 " --> pdb=" O ASN K 202 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ASN K 202 " --> pdb=" O ALA K 195 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 282 through 283 Processing sheet with id=AB9, first strand: chain 'K' and resid 352 through 354 Processing sheet with id=AC1, first strand: chain 'K' and resid 392 through 396 Processing sheet with id=AC2, first strand: chain 'K' and resid 557 through 558 Processing sheet with id=AC3, first strand: chain 'L' and resid 41 through 44 removed outlier: 7.218A pdb=" N SER L 28 " --> pdb=" O ILE L 24 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ILE L 24 " --> pdb=" O SER L 28 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N THR L 30 " --> pdb=" O VAL L 22 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE L 49 " --> pdb=" O TRP L 8 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 87 through 90 removed outlier: 5.880A pdb=" N LEU L 94 " --> pdb=" O ARG L 667 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ILE L 669 " --> pdb=" O LEU L 94 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ALA L 96 " --> pdb=" O ILE L 669 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N SER L 146 " --> pdb=" O SER L 664 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N ILE L 666 " --> pdb=" O SER L 146 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE L 148 " --> pdb=" O ILE L 666 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N CYS L 668 " --> pdb=" O ILE L 148 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N GLN L 145 " --> pdb=" O GLY L 453 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N LEU L 455 " --> pdb=" O GLN L 145 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ILE L 147 " --> pdb=" O LEU L 455 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY L 222 " --> pdb=" O HIS L 213 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 194 through 195 Processing sheet with id=AC6, first strand: chain 'L' and resid 352 through 353 removed outlier: 3.769A pdb=" N ASN L 363 " --> pdb=" O GLU L 353 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 392 through 396 Processing sheet with id=AC8, first strand: chain 'L' and resid 557 through 558 removed outlier: 3.682A pdb=" N SER L 558 " --> pdb=" O ILE L 578 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE L 578 " --> pdb=" O SER L 558 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 41 through 43 removed outlier: 7.360A pdb=" N THR M 30 " --> pdb=" O VAL M 22 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE M 49 " --> pdb=" O TRP M 8 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 87 through 90 removed outlier: 6.056A pdb=" N LEU M 94 " --> pdb=" O ARG M 667 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ILE M 669 " --> pdb=" O LEU M 94 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ALA M 96 " --> pdb=" O ILE M 669 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N SER M 146 " --> pdb=" O SER M 664 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ILE M 666 " --> pdb=" O SER M 146 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE M 148 " --> pdb=" O ILE M 666 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N CYS M 668 " --> pdb=" O ILE M 148 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLN M 145 " --> pdb=" O GLY M 453 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N LEU M 455 " --> pdb=" O GLN M 145 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ILE M 147 " --> pdb=" O LEU M 455 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY M 222 " --> pdb=" O HIS M 213 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 282 through 283 Processing sheet with id=AD3, first strand: chain 'M' and resid 352 through 353 Processing sheet with id=AD4, first strand: chain 'M' and resid 392 through 396 Processing sheet with id=AD5, first strand: chain 'M' and resid 557 through 558 removed outlier: 3.636A pdb=" N ILE M 578 " --> pdb=" O SER M 558 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 41 through 43 removed outlier: 7.071A pdb=" N THR N 30 " --> pdb=" O VAL N 22 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N PHE N 49 " --> pdb=" O TRP N 8 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 87 through 90 removed outlier: 6.079A pdb=" N LEU N 94 " --> pdb=" O ARG N 667 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE N 669 " --> pdb=" O LEU N 94 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ALA N 96 " --> pdb=" O ILE N 669 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N SER N 146 " --> pdb=" O SER N 664 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ILE N 666 " --> pdb=" O SER N 146 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ILE N 148 " --> pdb=" O ILE N 666 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N CYS N 668 " --> pdb=" O ILE N 148 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N GLN N 145 " --> pdb=" O GLY N 453 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N LEU N 455 " --> pdb=" O GLN N 145 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ILE N 147 " --> pdb=" O LEU N 455 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL N 210 " --> pdb=" O VAL N 454 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLY N 222 " --> pdb=" O HIS N 213 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 194 through 195 Processing sheet with id=AD9, first strand: chain 'N' and resid 352 through 354 Processing sheet with id=AE1, first strand: chain 'N' and resid 392 through 396 Processing sheet with id=AE2, first strand: chain 'N' and resid 557 through 558 Processing sheet with id=AE3, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.644A pdb=" N PHE A 31 " --> pdb=" O VAL A 17 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL A 17 " --> pdb=" O PHE A 31 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.697A pdb=" N ARG A 37 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 41 through 42 removed outlier: 3.937A pdb=" N GLN A 41 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 155 through 156 removed outlier: 6.181A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 71 through 72 removed outlier: 3.551A pdb=" N ILE A 75 " --> pdb=" O GLU A 72 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'A' and resid 131 through 132 Processing sheet with id=AE9, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AF1, first strand: chain 'A' and resid 169 through 170 removed outlier: 4.213A pdb=" N GLY A 156 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER A 155 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'A' and resid 238 through 241 removed outlier: 3.588A pdb=" N ILE A 250 " --> pdb=" O LYS A 238 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.578A pdb=" N PHE B 31 " --> pdb=" O VAL B 17 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.921A pdb=" N ARG B 37 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AF6, first strand: chain 'B' and resid 131 through 132 Processing sheet with id=AF7, first strand: chain 'B' and resid 155 through 156 removed outlier: 3.538A pdb=" N GLY B 156 " --> pdb=" O VAL B 159 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'B' and resid 169 through 170 removed outlier: 7.015A pdb=" N VAL B 298 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'B' and resid 238 through 241 removed outlier: 3.521A pdb=" N ILE B 250 " --> pdb=" O LYS B 238 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 29 through 31 removed outlier: 3.680A pdb=" N PHE C 31 " --> pdb=" O VAL C 17 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL C 17 " --> pdb=" O PHE C 31 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.507A pdb=" N VAL C 35 " --> pdb=" O LYS C 68 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG C 37 " --> pdb=" O THR C 66 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AG4, first strand: chain 'C' and resid 131 through 132 Processing sheet with id=AG5, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AG6, first strand: chain 'D' and resid 29 through 32 removed outlier: 3.634A pdb=" N PHE D 31 " --> pdb=" O VAL D 17 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR D 133 " --> pdb=" O THR D 103 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.737A pdb=" N ARG D 37 " --> pdb=" O THR D 66 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AG9, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AH1, first strand: chain 'D' and resid 169 through 170 removed outlier: 3.719A pdb=" N GLY D 156 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'D' and resid 238 through 241 removed outlier: 3.557A pdb=" N ILE D 250 " --> pdb=" O LYS D 238 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'E' and resid 29 through 31 removed outlier: 3.533A pdb=" N PHE E 31 " --> pdb=" O VAL E 17 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR E 133 " --> pdb=" O THR E 103 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'E' and resid 53 through 54 removed outlier: 3.514A pdb=" N TYR E 53 " --> pdb=" O GLY E 36 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ARG E 37 " --> pdb=" O THR E 66 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AH6, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AH7, first strand: chain 'E' and resid 169 through 170 removed outlier: 6.839A pdb=" N VAL E 298 " --> pdb=" O THR E 149 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'E' and resid 238 through 241 Processing sheet with id=AH9, first strand: chain 'F' and resid 29 through 32 removed outlier: 3.523A pdb=" N VAL F 17 " --> pdb=" O PHE F 31 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU F 8 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N THR F 106 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N CYS F 10 " --> pdb=" O THR F 106 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ALA F 135 " --> pdb=" O THR F 103 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU F 105 " --> pdb=" O ALA F 135 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'F' and resid 53 through 54 removed outlier: 3.527A pdb=" N VAL F 35 " --> pdb=" O LYS F 68 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ARG F 37 " --> pdb=" O THR F 66 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'F' and resid 71 through 72 Processing sheet with id=AI3, first strand: chain 'F' and resid 131 through 132 Processing sheet with id=AI4, first strand: chain 'F' and resid 155 through 156 Processing sheet with id=AI5, first strand: chain 'F' and resid 169 through 170 removed outlier: 6.763A pdb=" N VAL F 298 " --> pdb=" O THR F 149 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ILE F 151 " --> pdb=" O VAL F 298 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ASN F 297 " --> pdb=" O ILE F 330 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'F' and resid 238 through 241 Processing sheet with id=AI7, first strand: chain 'G' and resid 29 through 31 removed outlier: 6.275A pdb=" N LEU G 8 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N THR G 106 " --> pdb=" O LEU G 8 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N CYS G 10 " --> pdb=" O THR G 106 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N ALA G 135 " --> pdb=" O THR G 103 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU G 105 " --> pdb=" O ALA G 135 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'G' and resid 53 through 54 removed outlier: 3.577A pdb=" N VAL G 35 " --> pdb=" O LYS G 68 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG G 37 " --> pdb=" O THR G 66 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'G' and resid 71 through 72 Processing sheet with id=AJ1, first strand: chain 'G' and resid 131 through 132 Processing sheet with id=AJ2, first strand: chain 'G' and resid 169 through 170 Processing sheet with id=AJ3, first strand: chain 'G' and resid 169 through 170 removed outlier: 3.562A pdb=" N ASP G 154 " --> pdb=" O HIS G 161 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ILE G 151 " --> pdb=" O VAL G 298 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ASN G 297 " --> pdb=" O ILE G 330 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'G' and resid 238 through 241 removed outlier: 3.757A pdb=" N ILE G 250 " --> pdb=" O LYS G 238 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'H' and resid 29 through 31 removed outlier: 3.636A pdb=" N PHE H 31 " --> pdb=" O VAL H 17 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LEU H 8 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N THR H 106 " --> pdb=" O LEU H 8 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N CYS H 10 " --> pdb=" O THR H 106 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N ALA H 135 " --> pdb=" O THR H 103 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU H 105 " --> pdb=" O ALA H 135 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'H' and resid 53 through 54 removed outlier: 4.038A pdb=" N ARG H 37 " --> pdb=" O THR H 66 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'H' and resid 71 through 72 Processing sheet with id=AJ8, first strand: chain 'H' and resid 131 through 132 Processing sheet with id=AJ9, first strand: chain 'H' and resid 155 through 156 Processing sheet with id=AK1, first strand: chain 'H' and resid 169 through 170 removed outlier: 6.048A pdb=" N ILE H 151 " --> pdb=" O VAL H 298 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ASN H 297 " --> pdb=" O ILE H 330 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'H' and resid 238 through 241 removed outlier: 3.794A pdb=" N ILE H 250 " --> pdb=" O LYS H 238 " (cutoff:3.500A) 2172 hydrogen bonds defined for protein. 5796 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: 23.70 Time building geometry restraints manager: 11.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.28: 9663 1.28 - 1.43: 14836 1.43 - 1.59: 32895 1.59 - 1.74: 39 1.74 - 1.89: 499 Bond restraints: 57932 Sorted by residual: bond pdb=" CA THR C 260 " pdb=" C THR C 260 " ideal model delta sigma weight residual 1.523 1.819 -0.296 1.34e-02 5.57e+03 4.88e+02 bond pdb=" C PRO G 258 " pdb=" O PRO G 258 " ideal model delta sigma weight residual 1.237 1.459 -0.222 1.16e-02 7.43e+03 3.67e+02 bond pdb=" C GLU C 259 " pdb=" N THR C 260 " ideal model delta sigma weight residual 1.332 1.591 -0.259 1.40e-02 5.10e+03 3.41e+02 bond pdb=" CA CYS C 257 " pdb=" C CYS C 257 " ideal model delta sigma weight residual 1.521 1.685 -0.164 1.17e-02 7.31e+03 1.96e+02 bond pdb=" C THR C 260 " pdb=" N LEU C 261 " ideal model delta sigma weight residual 1.332 1.488 -0.156 1.40e-02 5.10e+03 1.24e+02 ... (remaining 57927 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.01: 77866 7.01 - 14.02: 437 14.02 - 21.02: 13 21.02 - 28.03: 2 28.03 - 35.04: 4 Bond angle restraints: 78322 Sorted by residual: angle pdb=" O GLU C 259 " pdb=" C GLU C 259 " pdb=" N THR C 260 " ideal model delta sigma weight residual 122.12 141.80 -19.68 1.06e+00 8.90e-01 3.45e+02 angle pdb=" C THR C 260 " pdb=" N LEU C 261 " pdb=" CA LEU C 261 " ideal model delta sigma weight residual 121.54 156.58 -35.04 1.91e+00 2.74e-01 3.37e+02 angle pdb=" C THR C 260 " pdb=" CA THR C 260 " pdb=" CB THR C 260 " ideal model delta sigma weight residual 110.42 75.73 34.69 1.99e+00 2.53e-01 3.04e+02 angle pdb=" C GLU C 259 " pdb=" N THR C 260 " pdb=" CA THR C 260 " ideal model delta sigma weight residual 121.54 89.54 32.00 1.91e+00 2.74e-01 2.81e+02 angle pdb=" N THR C 260 " pdb=" CA THR C 260 " pdb=" CB THR C 260 " ideal model delta sigma weight residual 110.49 136.71 -26.22 1.69e+00 3.50e-01 2.41e+02 ... (remaining 78317 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.54: 32575 20.54 - 41.08: 1624 41.08 - 61.62: 443 61.62 - 82.16: 272 82.16 - 102.70: 78 Dihedral angle restraints: 34992 sinusoidal: 14248 harmonic: 20744 Sorted by residual: dihedral pdb=" CA GLY I 636 " pdb=" C GLY I 636 " pdb=" N LYS I 637 " pdb=" CA LYS I 637 " ideal model delta harmonic sigma weight residual -180.00 -77.30 -102.70 0 5.00e+00 4.00e-02 4.22e+02 dihedral pdb=" CA GLY M 636 " pdb=" C GLY M 636 " pdb=" N LYS M 637 " pdb=" CA LYS M 637 " ideal model delta harmonic sigma weight residual -180.00 -78.76 -101.24 0 5.00e+00 4.00e-02 4.10e+02 dihedral pdb=" CA GLY L 636 " pdb=" C GLY L 636 " pdb=" N LYS L 637 " pdb=" CA LYS L 637 " ideal model delta harmonic sigma weight residual -180.00 -81.84 -98.16 0 5.00e+00 4.00e-02 3.85e+02 ... (remaining 34989 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.218: 8296 0.218 - 0.436: 347 0.436 - 0.653: 13 0.653 - 0.871: 1 0.871 - 1.089: 1 Chirality restraints: 8658 Sorted by residual: chirality pdb=" CA THR C 260 " pdb=" N THR C 260 " pdb=" C THR C 260 " pdb=" CB THR C 260 " both_signs ideal model delta sigma weight residual False 2.53 1.44 1.09 2.00e-01 2.50e+01 2.96e+01 chirality pdb=" CA PRO C 258 " pdb=" N PRO C 258 " pdb=" C PRO C 258 " pdb=" CB PRO C 258 " both_signs ideal model delta sigma weight residual False 2.72 3.44 -0.72 2.00e-01 2.50e+01 1.30e+01 chirality pdb=" CA CYS C 257 " pdb=" N CYS C 257 " pdb=" C CYS C 257 " pdb=" CB CYS C 257 " both_signs ideal model delta sigma weight residual False 2.51 3.15 -0.64 2.00e-01 2.50e+01 1.03e+01 ... (remaining 8655 not shown) Planarity restraints: 10170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 362 " -0.190 2.00e-02 2.50e+03 1.07e-01 2.29e+02 pdb=" CG TYR E 362 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR E 362 " 0.079 2.00e-02 2.50e+03 pdb=" CD2 TYR E 362 " 0.088 2.00e-02 2.50e+03 pdb=" CE1 TYR E 362 " 0.069 2.00e-02 2.50e+03 pdb=" CE2 TYR E 362 " 0.063 2.00e-02 2.50e+03 pdb=" CZ TYR E 362 " 0.019 2.00e-02 2.50e+03 pdb=" OH TYR E 362 " -0.175 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 362 " 0.187 2.00e-02 2.50e+03 1.07e-01 2.28e+02 pdb=" CG TYR A 362 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR A 362 " -0.078 2.00e-02 2.50e+03 pdb=" CD2 TYR A 362 " -0.078 2.00e-02 2.50e+03 pdb=" CE1 TYR A 362 " -0.069 2.00e-02 2.50e+03 pdb=" CE2 TYR A 362 " -0.068 2.00e-02 2.50e+03 pdb=" CZ TYR A 362 " -0.025 2.00e-02 2.50e+03 pdb=" OH TYR A 362 " 0.178 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 362 " 0.183 2.00e-02 2.50e+03 1.03e-01 2.13e+02 pdb=" CG TYR G 362 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TYR G 362 " -0.072 2.00e-02 2.50e+03 pdb=" CD2 TYR G 362 " -0.079 2.00e-02 2.50e+03 pdb=" CE1 TYR G 362 " -0.069 2.00e-02 2.50e+03 pdb=" CE2 TYR G 362 " -0.061 2.00e-02 2.50e+03 pdb=" CZ TYR G 362 " -0.021 2.00e-02 2.50e+03 pdb=" OH TYR G 362 " 0.169 2.00e-02 2.50e+03 ... (remaining 10167 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 37 2.43 - 3.05: 29464 3.05 - 3.67: 82310 3.67 - 4.28: 123815 4.28 - 4.90: 202043 Nonbonded interactions: 437669 Sorted by model distance: nonbonded pdb=" OE1 GLN G 137 " pdb="MG MG G 401 " model vdw 1.814 2.170 nonbonded pdb=" OE1 GLN H 137 " pdb="MG MG H 401 " model vdw 1.817 2.170 nonbonded pdb=" OE1 GLN A 137 " pdb="MG MG A 401 " model vdw 1.817 2.170 nonbonded pdb=" OE1 GLN B 137 " pdb="MG MG B 401 " model vdw 1.819 2.170 nonbonded pdb=" OE1 GLN E 137 " pdb="MG MG E 401 " model vdw 1.819 2.170 ... (remaining 437664 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } pdb_interpretation.ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 1.600 Check model and map are aligned: 0.320 Set scattering table: 0.390 Process input model: 98.800 Find NCS groups from input model: 1.820 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.030 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4758 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 : 0.015 0.296 57932 Z= 0.999 Angle : 2.104 35.040 78322 Z= 1.431 Chirality : 0.107 1.089 8658 Planarity : 0.024 0.328 10170 Dihedral : 16.183 102.705 21660 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 0.55 Ramachandran Plot: Outliers : 1.33 % Allowed : 8.33 % Favored : 90.34 % Rotamer: Outliers : 1.80 % Allowed : 6.03 % Favored : 92.17 % Cbeta Deviations : 0.36 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.34 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.94 (0.08), residues: 7132 helix: -3.58 (0.06), residues: 2726 sheet: -1.80 (0.16), residues: 942 loop : -1.89 (0.09), residues: 3464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.113 0.022 TRP A 340 HIS 0.015 0.003 HIS N 246 PHE 0.082 0.013 PHE H 127 TYR 0.190 0.026 TYR E 362 ARG 0.023 0.003 ARG L 556 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14264 Ramachandran restraints generated. 7132 Oldfield, 0 Emsley, 7132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14264 Ramachandran restraints generated. 7132 Oldfield, 0 Emsley, 7132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 50 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 GLU cc_start: 0.5638 (OUTLIER) cc_final: 0.5212 (mp0) REVERT: A 283 MET cc_start: 0.6701 (mmm) cc_final: 0.6206 (mmm) outliers start: 11 outliers final: 0 residues processed: 59 average time/residue: 0.1344 time to fit residues: 9.4489 Evaluate side-chains 26 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 25 time to evaluate : 0.243 Evaluate side-chains 98 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 91 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 34 LEU cc_start: 0.4403 (OUTLIER) cc_final: 0.4076 (tm) REVERT: I 182 ILE cc_start: 0.6197 (mt) cc_final: 0.5648 (tp) REVERT: I 216 GLU cc_start: 0.6518 (OUTLIER) cc_final: 0.4740 (tp30) outliers start: 7 outliers final: 0 residues processed: 96 average time/residue: 0.2000 time to fit residues: 23.5051 Evaluate side-chains 41 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 39 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 597 optimal weight: 9.9990 chunk 536 optimal weight: 8.9990 chunk 297 optimal weight: 0.6980 chunk 183 optimal weight: 0.8980 chunk 361 optimal weight: 0.5980 chunk 286 optimal weight: 6.9990 chunk 554 optimal weight: 2.9990 chunk 214 optimal weight: 10.0000 chunk 337 optimal weight: 9.9990 chunk 413 optimal weight: 0.0870 chunk 642 optimal weight: 7.9990 overall best weight: 1.0560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 92 ASN ** K 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 477 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5049 moved from start: 0.8416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 57932 Z= 0.221 Angle : 0.829 11.790 78322 Z= 0.462 Chirality : 0.048 0.194 8658 Planarity : 0.007 0.089 10170 Dihedral : 8.034 94.262 7854 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 1.23 % Allowed : 4.60 % Favored : 94.17 % Rotamer: Outliers : 0.19 % Allowed : 3.19 % Favored : 96.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.34 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -2.52 (0.09), residues: 7132 helix: -1.53 (0.08), residues: 2938 sheet: -1.18 (0.15), residues: 1070 loop : -1.86 (0.10), residues: 3124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP F 340 HIS 0.007 0.001 HIS B 87 PHE 0.030 0.002 PHE M 209 TYR 0.018 0.001 TYR I 115 ARG 0.009 0.001 ARG F 28 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12856 Ramachandran restraints generated. 6428 Oldfield, 0 Emsley, 6428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12856 Ramachandran restraints generated. 6428 Oldfield, 0 Emsley, 6428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.249 Fit side-chains revert: symmetry clash REVERT: A 189 LEU cc_start: 0.8733 (tp) cc_final: 0.8511 (tp) REVERT: A 283 MET cc_start: 0.6847 (mmm) cc_final: 0.6499 (mmm) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.0930 time to fit residues: 4.1163 Evaluate side-chains 22 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.248 Evaluate side-chains 63 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 61 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 324 MET cc_start: 0.5811 (mtp) cc_final: 0.5524 (mtp) outliers start: 2 outliers final: 1 residues processed: 62 average time/residue: 0.1899 time to fit residues: 14.9855 Evaluate side-chains 22 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 21 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 357 optimal weight: 20.0000 chunk 199 optimal weight: 3.9990 chunk 535 optimal weight: 0.5980 chunk 437 optimal weight: 30.0000 chunk 177 optimal weight: 4.9990 chunk 644 optimal weight: 0.9980 chunk 695 optimal weight: 10.0000 chunk 573 optimal weight: 2.9990 chunk 638 optimal weight: 4.9990 chunk 219 optimal weight: 10.0000 chunk 516 optimal weight: 0.0470 overall best weight: 1.7282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 92 ASN C 115 ASN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 314 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5167 moved from start: 0.8905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 57932 Z= 0.192 Angle : 0.748 9.420 78322 Z= 0.408 Chirality : 0.045 0.203 8658 Planarity : 0.006 0.065 10170 Dihedral : 7.225 85.399 7854 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.99 % Favored : 94.64 % Rotamer: Outliers : 0.10 % Allowed : 3.42 % Favored : 96.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.34 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.09), residues: 7132 helix: -0.68 (0.09), residues: 2858 sheet: -0.94 (0.16), residues: 966 loop : -1.56 (0.10), residues: 3308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP N 8 HIS 0.020 0.002 HIS N 227 PHE 0.038 0.002 PHE L 163 TYR 0.040 0.002 TYR L 107 ARG 0.022 0.001 ARG N 243 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12126 Ramachandran restraints generated. 6063 Oldfield, 0 Emsley, 6063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12126 Ramachandran restraints generated. 6063 Oldfield, 0 Emsley, 6063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.249 Fit side-chains revert: symmetry clash REVERT: C 189 LEU cc_start: 0.8906 (tp) cc_final: 0.8441 (tp) REVERT: C 233 SER cc_start: 0.6409 (m) cc_final: 0.6181 (t) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0856 time to fit residues: 3.0332 Evaluate side-chains 20 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.246 Evaluate side-chains 35 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 34 time to evaluate : 0.491 Fit side-chains REVERT: K 138 MET cc_start: 0.5809 (tpp) cc_final: 0.5454 (tpp) outliers start: 1 outliers final: 0 residues processed: 35 average time/residue: 0.1719 time to fit residues: 8.1595 Evaluate side-chains 19 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 636 optimal weight: 0.0980 chunk 484 optimal weight: 9.9990 chunk 334 optimal weight: 8.9990 chunk 71 optimal weight: 5.9990 chunk 307 optimal weight: 0.1980 chunk 432 optimal weight: 0.0170 chunk 646 optimal weight: 2.9990 chunk 684 optimal weight: 2.9990 chunk 337 optimal weight: 9.9990 chunk 612 optimal weight: 3.9990 chunk 184 optimal weight: 0.0970 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5159 moved from start: 0.9104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 57932 Z= 0.212 Angle : 0.758 10.752 78322 Z= 0.407 Chirality : 0.045 0.228 8658 Planarity : 0.006 0.069 10170 Dihedral : 7.115 85.491 7854 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.80 % Favored : 94.84 % Rotamer: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.34 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.09), residues: 7132 helix: -0.36 (0.10), residues: 2852 sheet: -0.82 (0.16), residues: 906 loop : -1.62 (0.10), residues: 3374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP J 8 HIS 0.020 0.001 HIS L 227 PHE 0.032 0.002 PHE L 163 TYR 0.041 0.002 TYR L 107 ARG 0.017 0.001 ARG N 243 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12126 Ramachandran restraints generated. 6063 Oldfield, 0 Emsley, 6063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12126 Ramachandran restraints generated. 6063 Oldfield, 0 Emsley, 6063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.247 Fit side-chains REVERT: C 123 MET cc_start: 0.6380 (ppp) cc_final: 0.5155 (ppp) REVERT: C 189 LEU cc_start: 0.8918 (tp) cc_final: 0.8422 (tp) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.1177 time to fit residues: 3.4686 Evaluate side-chains 19 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.247 Evaluate side-chains 32 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.490 Fit side-chains REVERT: K 103 ILE cc_start: 0.4228 (mm) cc_final: 0.3996 (mm) REVERT: K 138 MET cc_start: 0.5945 (tpp) cc_final: 0.5601 (tpp) REVERT: K 659 ARG cc_start: 0.7482 (mpt90) cc_final: 0.6676 (mtp85) REVERT: K 694 MET cc_start: 0.5923 (mmt) cc_final: 0.5712 (mmm) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.1839 time to fit residues: 7.8649 Evaluate side-chains 19 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 569 optimal weight: 9.9990 chunk 388 optimal weight: 9.9990 chunk 9 optimal weight: 30.0000 chunk 509 optimal weight: 1.9990 chunk 282 optimal weight: 8.9990 chunk 583 optimal weight: 9.9990 chunk 473 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 349 optimal weight: 10.0000 chunk 614 optimal weight: 5.9990 chunk 172 optimal weight: 0.0040 overall best weight: 5.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 HIS Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 116 GLN K 481 GLN K 652 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5599 moved from start: 0.9864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 57932 Z= 0.265 Angle : 0.798 9.710 78322 Z= 0.430 Chirality : 0.046 0.211 8658 Planarity : 0.006 0.053 10170 Dihedral : 6.806 75.233 7854 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.30 % Favored : 94.34 % Rotamer: Outliers : 0.10 % Allowed : 2.67 % Favored : 97.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.34 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.10), residues: 7132 helix: -0.30 (0.09), residues: 2926 sheet: -1.03 (0.15), residues: 1016 loop : -1.32 (0.11), residues: 3190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP K 8 HIS 0.021 0.002 HIS K 227 PHE 0.038 0.003 PHE M 163 TYR 0.037 0.003 TYR L 107 ARG 0.016 0.001 ARG J 243 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12126 Ramachandran restraints generated. 6063 Oldfield, 0 Emsley, 6063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12126 Ramachandran restraints generated. 6063 Oldfield, 0 Emsley, 6063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.248 Fit side-chains REVERT: C 82 MET cc_start: 0.8014 (tpp) cc_final: 0.7607 (tpp) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0881 time to fit residues: 2.7631 Evaluate side-chains 18 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.246 Evaluate side-chains 26 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 25 time to evaluate : 0.490 Fit side-chains revert: symmetry clash REVERT: K 103 ILE cc_start: 0.4672 (mm) cc_final: 0.4434 (mm) REVERT: K 138 MET cc_start: 0.5924 (tpp) cc_final: 0.5660 (tpp) outliers start: 1 outliers final: 0 residues processed: 26 average time/residue: 0.1596 time to fit residues: 5.9171 Evaluate side-chains 16 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 230 optimal weight: 6.9990 chunk 616 optimal weight: 7.9990 chunk 135 optimal weight: 9.9990 chunk 401 optimal weight: 9.9990 chunk 168 optimal weight: 50.0000 chunk 685 optimal weight: 0.6980 chunk 568 optimal weight: 20.0000 chunk 317 optimal weight: 20.0000 chunk 56 optimal weight: 9.9990 chunk 226 optimal weight: 0.8980 chunk 359 optimal weight: 0.0870 overall best weight: 3.3362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5585 moved from start: 1.0146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 57932 Z= 0.191 Angle : 0.685 7.129 78322 Z= 0.372 Chirality : 0.044 0.206 8658 Planarity : 0.005 0.049 10170 Dihedral : 6.405 69.337 7854 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.82 % Favored : 94.90 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.34 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.10), residues: 7132 helix: 0.14 (0.10), residues: 2968 sheet: -0.78 (0.17), residues: 862 loop : -1.29 (0.11), residues: 3302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP J 8 HIS 0.019 0.002 HIS N 227 PHE 0.030 0.002 PHE J 163 TYR 0.044 0.002 TYR L 67 ARG 0.013 0.001 ARG L 243 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12126 Ramachandran restraints generated. 6063 Oldfield, 0 Emsley, 6063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12126 Ramachandran restraints generated. 6063 Oldfield, 0 Emsley, 6063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.250 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0889 time to fit residues: 2.7941 Evaluate side-chains 17 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.251 Evaluate side-chains 23 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.494 Fit side-chains revert: symmetry clash REVERT: K 66 MET cc_start: 0.3886 (ttt) cc_final: 0.3643 (ttt) REVERT: K 138 MET cc_start: 0.5818 (tpp) cc_final: 0.5537 (tpp) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1758 time to fit residues: 5.7237 Evaluate side-chains 17 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 660 optimal weight: 0.0970 chunk 77 optimal weight: 20.0000 chunk 390 optimal weight: 4.9990 chunk 500 optimal weight: 0.0040 chunk 387 optimal weight: 10.0000 chunk 576 optimal weight: 0.2980 chunk 382 optimal weight: 9.9990 chunk 682 optimal weight: 8.9990 chunk 427 optimal weight: 5.9990 chunk 416 optimal weight: 0.0670 chunk 315 optimal weight: 0.9990 overall best weight: 0.2930 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN A 297 ASN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 482 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5479 moved from start: 1.0218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 57932 Z= 0.153 Angle : 0.666 11.371 78322 Z= 0.357 Chirality : 0.044 0.200 8658 Planarity : 0.005 0.055 10170 Dihedral : 5.873 61.299 7854 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.74 % Favored : 94.98 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.34 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.10), residues: 7132 helix: 0.38 (0.10), residues: 2952 sheet: -0.88 (0.16), residues: 898 loop : -1.22 (0.11), residues: 3282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP K 8 HIS 0.019 0.001 HIS N 227 PHE 0.027 0.002 PHE J 163 TYR 0.039 0.002 TYR J 107 ARG 0.013 0.001 ARG M 243 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12126 Ramachandran restraints generated. 6063 Oldfield, 0 Emsley, 6063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12126 Ramachandran restraints generated. 6063 Oldfield, 0 Emsley, 6063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.252 Fit side-chains REVERT: A 119 MET cc_start: 0.7363 (ppp) cc_final: 0.6783 (ppp) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0907 time to fit residues: 2.8468 Evaluate side-chains 17 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.255 Evaluate side-chains 21 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.495 Fit side-chains REVERT: K 138 MET cc_start: 0.5856 (tpp) cc_final: 0.5601 (tpp) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.0985 time to fit residues: 3.6718 Evaluate side-chains 16 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 422 optimal weight: 30.0000 chunk 272 optimal weight: 0.7980 chunk 407 optimal weight: 8.9990 chunk 205 optimal weight: 10.0000 chunk 134 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 chunk 433 optimal weight: 0.9980 chunk 464 optimal weight: 2.9990 chunk 337 optimal weight: 7.9990 chunk 63 optimal weight: 9.9990 chunk 536 optimal weight: 0.6980 overall best weight: 2.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 HIS Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 270 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5602 moved from start: 1.0536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 57932 Z= 0.177 Angle : 0.662 8.446 78322 Z= 0.360 Chirality : 0.043 0.197 8658 Planarity : 0.005 0.048 10170 Dihedral : 5.806 55.738 7854 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.85 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.34 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.10), residues: 7132 helix: 0.46 (0.10), residues: 2990 sheet: -0.77 (0.17), residues: 848 loop : -1.25 (0.11), residues: 3294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP L 8 HIS 0.019 0.001 HIS M 227 PHE 0.028 0.002 PHE M 163 TYR 0.036 0.002 TYR J 107 ARG 0.011 0.001 ARG M 243 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12126 Ramachandran restraints generated. 6063 Oldfield, 0 Emsley, 6063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12126 Ramachandran restraints generated. 6063 Oldfield, 0 Emsley, 6063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.251 Fit side-chains REVERT: A 132 MET cc_start: 0.6729 (tmm) cc_final: 0.6260 (tmm) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.0964 time to fit residues: 2.6108 Evaluate side-chains 18 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.247 Evaluate side-chains 17 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.535 Fit side-chains REVERT: K 138 MET cc_start: 0.5822 (tpp) cc_final: 0.5524 (tpp) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.1202 time to fit residues: 3.7036 Evaluate side-chains 14 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 620 optimal weight: 0.9980 chunk 653 optimal weight: 3.9990 chunk 596 optimal weight: 0.0980 chunk 635 optimal weight: 6.9990 chunk 382 optimal weight: 0.9980 chunk 277 optimal weight: 0.4980 chunk 499 optimal weight: 0.0030 chunk 195 optimal weight: 2.9990 chunk 574 optimal weight: 0.0270 chunk 601 optimal weight: 10.0000 chunk 633 optimal weight: 0.0870 overall best weight: 0.1426 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5475 moved from start: 1.0602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 57932 Z= 0.146 Angle : 0.647 6.899 78322 Z= 0.348 Chirality : 0.043 0.188 8658 Planarity : 0.005 0.064 10170 Dihedral : 5.391 41.967 7854 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.51 % Favored : 95.20 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.34 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.10), residues: 7132 helix: 0.56 (0.10), residues: 2990 sheet: -0.72 (0.17), residues: 808 loop : -1.22 (0.10), residues: 3334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP M 8 HIS 0.019 0.001 HIS I 227 PHE 0.026 0.001 PHE J 163 TYR 0.037 0.002 TYR J 107 ARG 0.013 0.001 ARG M 243 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12126 Ramachandran restraints generated. 6063 Oldfield, 0 Emsley, 6063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12126 Ramachandran restraints generated. 6063 Oldfield, 0 Emsley, 6063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.247 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.0900 time to fit residues: 2.7077 Evaluate side-chains 18 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.251 Evaluate side-chains 22 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.497 Fit side-chains REVERT: K 138 MET cc_start: 0.5809 (tpp) cc_final: 0.5557 (tpp) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0984 time to fit residues: 3.7854 Evaluate side-chains 15 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 417 optimal weight: 9.9990 chunk 672 optimal weight: 0.0000 chunk 410 optimal weight: 5.9990 chunk 318 optimal weight: 7.9990 chunk 467 optimal weight: 0.9980 chunk 705 optimal weight: 3.9990 chunk 649 optimal weight: 8.9990 chunk 561 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 433 optimal weight: 0.6980 chunk 344 optimal weight: 1.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5493 moved from start: 1.0666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 57932 Z= 0.141 Angle : 0.643 9.142 78322 Z= 0.345 Chirality : 0.043 0.290 8658 Planarity : 0.005 0.064 10170 Dihedral : 5.243 52.368 7854 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.66 % Favored : 95.18 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.34 % 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: -0.59 (0.10), residues: 7132 helix: 0.63 (0.10), residues: 2990 sheet: -0.66 (0.17), residues: 808 loop : -1.25 (0.10), residues: 3334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP M 8 HIS 0.019 0.001 HIS N 227 PHE 0.027 0.001 PHE M 163 TYR 0.036 0.002 TYR J 107 ARG 0.012 0.001 ARG J 243 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12126 Ramachandran restraints generated. 6063 Oldfield, 0 Emsley, 6063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12126 Ramachandran restraints generated. 6063 Oldfield, 0 Emsley, 6063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.250 Fit side-chains REVERT: A 132 MET cc_start: 0.6727 (tmm) cc_final: 0.6322 (tmm) REVERT: A 283 MET cc_start: 0.7862 (mmm) cc_final: 0.6995 (mtp) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.0912 time to fit residues: 2.7431 Evaluate side-chains 18 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.250 Evaluate side-chains 19 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.493 Fit side-chains REVERT: K 138 MET cc_start: 0.5851 (tpp) cc_final: 0.5629 (tpp) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.1197 time to fit residues: 3.7928 Evaluate side-chains 14 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 446 optimal weight: 9.9990 chunk 598 optimal weight: 7.9990 chunk 172 optimal weight: 5.9990 chunk 517 optimal weight: 0.4980 chunk 82 optimal weight: 7.9990 chunk 156 optimal weight: 10.0000 chunk 562 optimal weight: 9.9990 chunk 235 optimal weight: 30.0000 chunk 577 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 103 optimal weight: 0.6980 overall best weight: 3.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 186 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.033154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.029707 restraints weight = 31406.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.030394 restraints weight = 19053.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.030902 restraints weight = 13244.126| |-----------------------------------------------------------------------------| r_work (final): 0.2735 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.046146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.039718 restraints weight = 52133.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.040625 restraints weight = 32846.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.041307 restraints weight = 23003.310| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 1.0926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 57932 Z= 0.189 Angle : 0.691 20.178 78322 Z= 0.364 Chirality : 0.043 0.232 8658 Planarity : 0.005 0.079 10170 Dihedral : 5.404 55.740 7854 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.99 % Favored : 94.84 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.34 % 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: -0.48 (0.10), residues: 7132 helix: 0.73 (0.10), residues: 2942 sheet: -0.78 (0.16), residues: 872 loop : -1.12 (0.11), residues: 3318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP L 8 HIS 0.020 0.001 HIS N 227 PHE 0.028 0.002 PHE M 163 TYR 0.034 0.002 TYR M 107 ARG 0.011 0.001 ARG N 243 =============================================================================== Job complete usr+sys time: 4954.04 seconds wall clock time: 90 minutes 37.80 seconds (5437.80 seconds total)