Starting phenix.real_space_refine on Fri Jan 17 02:50:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6bnp_7116/01_2025/6bnp_7116.cif Found real_map, /net/cci-nas-00/data/ceres_data/6bnp_7116/01_2025/6bnp_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/cci-nas-00/data/ceres_data/6bnp_7116/01_2025/6bnp_7116.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6bnp_7116/01_2025/6bnp_7116.map" model { file = "/net/cci-nas-00/data/ceres_data/6bnp_7116/01_2025/6bnp_7116.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6bnp_7116/01_2025/6bnp_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): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 24.01, 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: 10.04 Conformation dependent library (CDL) restraints added in 5.6 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: 6.20 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: 28.94 Time building geometry restraints manager: 12.14 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: 0.02 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: 6.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 1.620 Check model and map are aligned: 0.340 Set scattering table: 0.390 Process input model: 106.650 Find NCS groups from input model: 1.790 Set up NCS constraints: 0.290 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.850 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.256 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: 0.1610 time to fit residues: 11.3094 Evaluate side-chains 26 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 25 time to evaluate : 0.255 Evaluate side-chains 98 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.501 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: 0.2082 time to fit residues: 24.5533 Evaluate side-chains 41 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 39 time to evaluate : 0.576 ------------------------------------------------------------------------------- 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: 6.9990 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 ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.037599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.033370 restraints weight = 30805.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.034254 restraints weight = 18662.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.034897 restraints weight = 12587.839| |-----------------------------------------------------------------------------| r_work (final): 0.2887 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.049510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.043132 restraints weight = 47025.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.044159 restraints weight = 29634.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.044874 restraints weight = 20457.232| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6422 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 L 209 TYR 0.018 0.001 TYR N 115 ARG 0.009 0.001 ARG E 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 to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: A 269 MET cc_start: 0.8304 (mpp) cc_final: 0.7465 (mpp) REVERT: A 282 ILE cc_start: 0.8709 (mt) cc_final: 0.8455 (mm) REVERT: A 283 MET cc_start: 0.7686 (mmm) cc_final: 0.7472 (mmm) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.0936 time to fit residues: 4.1520 Evaluate side-chains 22 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.253 Evaluate side-chains 63 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 61 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 138 MET cc_start: 0.7900 (ttm) cc_final: 0.6741 (tpp) REVERT: K 694 MET cc_start: 0.8393 (mmm) cc_final: 0.8134 (mmt) outliers start: 2 outliers final: 1 residues processed: 62 average time/residue: 0.1834 time to fit residues: 14.5171 Evaluate side-chains 22 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 21 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 685 optimal weight: 0.3980 chunk 344 optimal weight: 0.8980 chunk 667 optimal weight: 0.6980 chunk 253 optimal weight: 0.7980 chunk 321 optimal weight: 0.7980 chunk 178 optimal weight: 10.0000 chunk 531 optimal weight: 9.9990 chunk 702 optimal weight: 9.9990 chunk 232 optimal weight: 0.0670 chunk 627 optimal weight: 2.9990 chunk 172 optimal weight: 0.0770 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 115 ASN A 354 GLN Total number of N/Q/H flips: 3 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.037687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.033755 restraints weight = 29980.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.034566 restraints weight = 19133.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.035159 restraints weight = 13259.871| |-----------------------------------------------------------------------------| r_work (final): 0.2908 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.044791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.039058 restraints weight = 63490.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.039765 restraints weight = 42376.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.040343 restraints weight = 31093.476| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6582 moved from start: 0.8889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 57932 Z= 0.185 Angle : 0.748 10.104 78322 Z= 0.406 Chirality : 0.045 0.219 8658 Planarity : 0.006 0.064 10170 Dihedral : 7.156 82.182 7854 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.68 % Favored : 94.95 % Rotamer: Outliers : 0.23 % Allowed : 2.84 % Favored : 96.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.34 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -1.76 (0.09), residues: 7132 helix: -0.73 (0.09), residues: 2858 sheet: -0.92 (0.16), residues: 990 loop : -1.56 (0.10), residues: 3284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP J 8 HIS 0.019 0.001 HIS N 227 PHE 0.037 0.002 PHE L 163 TYR 0.042 0.002 TYR N 107 ARG 0.022 0.001 ARG J 243 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11452 Ramachandran restraints generated. 5726 Oldfield, 0 Emsley, 5726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11452 Ramachandran restraints generated. 5726 Oldfield, 0 Emsley, 5726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 27 time to evaluate : 0.255 Fit side-chains revert: symmetry clash REVERT: A 269 MET cc_start: 0.8174 (mpp) cc_final: 0.7880 (mpp) REVERT: A 282 ILE cc_start: 0.8938 (mt) cc_final: 0.8736 (mm) outliers start: 1 outliers final: 0 residues processed: 28 average time/residue: 0.0890 time to fit residues: 3.4556 Evaluate side-chains 21 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.258 Evaluate side-chains 35 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 34 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 77 ILE cc_start: 0.8787 (pt) cc_final: 0.8566 (tp) REVERT: M 138 MET cc_start: 0.6791 (ttm) cc_final: 0.5599 (tpp) REVERT: M 386 LEU cc_start: 0.9484 (tp) cc_final: 0.9282 (tp) REVERT: M 522 LEU cc_start: 0.5714 (mp) cc_final: 0.5489 (tp) REVERT: M 645 ASN cc_start: 0.7733 (t0) cc_final: 0.7489 (t0) outliers start: 1 outliers final: 0 residues processed: 35 average time/residue: 0.1681 time to fit residues: 8.0596 Evaluate side-chains 21 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 433 optimal weight: 10.0000 chunk 468 optimal weight: 4.9990 chunk 435 optimal weight: 8.9990 chunk 551 optimal weight: 7.9990 chunk 532 optimal weight: 0.0060 chunk 507 optimal weight: 9.9990 chunk 678 optimal weight: 5.9990 chunk 186 optimal weight: 10.0000 chunk 294 optimal weight: 8.9990 chunk 93 optimal weight: 0.0020 chunk 226 optimal weight: 8.9990 overall best weight: 3.8010 ------------------------------------------------------------------------------- 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: ** M 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 581 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.037139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.033372 restraints weight = 31849.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.034131 restraints weight = 20067.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.034692 restraints weight = 13912.857| |-----------------------------------------------------------------------------| r_work (final): 0.2889 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.044965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.039228 restraints weight = 63182.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.039955 restraints weight = 42018.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.040518 restraints weight = 30879.568| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6666 moved from start: 0.9077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 57932 Z= 0.233 Angle : 0.785 13.576 78322 Z= 0.418 Chirality : 0.046 0.375 8658 Planarity : 0.006 0.084 10170 Dihedral : 7.080 83.868 7854 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.80 % Favored : 94.84 % Rotamer: Outliers : 0.10 % Allowed : 2.26 % Favored : 97.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.34 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -1.47 (0.09), residues: 7132 helix: -0.34 (0.10), residues: 2852 sheet: -0.73 (0.17), residues: 930 loop : -1.57 (0.10), residues: 3350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP L 8 HIS 0.021 0.002 HIS N 227 PHE 0.040 0.002 PHE L 163 TYR 0.041 0.002 TYR N 107 ARG 0.040 0.001 ARG K 572 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11452 Ramachandran restraints generated. 5726 Oldfield, 0 Emsley, 5726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11452 Ramachandran restraints generated. 5726 Oldfield, 0 Emsley, 5726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: A 233 SER cc_start: 0.8083 (m) cc_final: 0.7815 (t) REVERT: A 269 MET cc_start: 0.8126 (mpp) cc_final: 0.7769 (mpp) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.1144 time to fit residues: 4.1793 Evaluate side-chains 21 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.256 Evaluate side-chains 31 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 30 time to evaluate : 0.506 Fit side-chains revert: symmetry clash REVERT: M 138 MET cc_start: 0.6978 (ttm) cc_final: 0.5772 (tpp) REVERT: M 386 LEU cc_start: 0.9488 (tp) cc_final: 0.9287 (tp) REVERT: M 645 ASN cc_start: 0.7788 (t0) cc_final: 0.7558 (t0) outliers start: 1 outliers final: 1 residues processed: 30 average time/residue: 0.1124 time to fit residues: 5.3253 Evaluate side-chains 16 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 15 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 529 optimal weight: 7.9990 chunk 585 optimal weight: 9.9990 chunk 498 optimal weight: 9.9990 chunk 591 optimal weight: 0.8980 chunk 628 optimal weight: 4.9990 chunk 84 optimal weight: 0.0070 chunk 295 optimal weight: 9.9990 chunk 608 optimal weight: 0.8980 chunk 158 optimal weight: 4.9990 chunk 650 optimal weight: 0.6980 chunk 319 optimal weight: 0.9990 overall best weight: 0.7000 ------------------------------------------------------------------------------- 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: M 581 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.037057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.032967 restraints weight = 31300.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.033813 restraints weight = 19448.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.034443 restraints weight = 13317.210| |-----------------------------------------------------------------------------| r_work (final): 0.2876 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.045009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.039312 restraints weight = 62720.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.040071 restraints weight = 41223.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.040645 restraints weight = 29839.854| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6651 moved from start: 0.9317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 57932 Z= 0.161 Angle : 0.672 7.162 78322 Z= 0.367 Chirality : 0.044 0.197 8658 Planarity : 0.005 0.058 10170 Dihedral : 6.478 83.447 7854 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.68 % Favored : 94.95 % Rotamer: Outliers : 0.10 % Allowed : 1.51 % Favored : 98.39 % 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: -1.18 (0.10), residues: 7132 helix: -0.05 (0.10), residues: 2870 sheet: -0.79 (0.16), residues: 946 loop : -1.39 (0.10), residues: 3316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP K 8 HIS 0.020 0.001 HIS I 227 PHE 0.037 0.002 PHE I 163 TYR 0.040 0.002 TYR L 107 ARG 0.017 0.001 ARG L 243 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11452 Ramachandran restraints generated. 5726 Oldfield, 0 Emsley, 5726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11452 Ramachandran restraints generated. 5726 Oldfield, 0 Emsley, 5726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.260 Fit side-chains revert: symmetry clash REVERT: A 233 SER cc_start: 0.7825 (m) cc_final: 0.7451 (t) REVERT: A 269 MET cc_start: 0.8179 (mpp) cc_final: 0.7873 (mpp) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.0897 time to fit residues: 3.3609 Evaluate side-chains 21 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.254 Evaluate side-chains 27 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 26 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 138 MET cc_start: 0.6551 (ttm) cc_final: 0.5419 (tpp) REVERT: M 395 MET cc_start: 0.7440 (mpp) cc_final: 0.5997 (pmm) REVERT: M 645 ASN cc_start: 0.7695 (t0) cc_final: 0.7350 (t0) outliers start: 1 outliers final: 1 residues processed: 27 average time/residue: 0.1050 time to fit residues: 4.7197 Evaluate side-chains 18 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 376 optimal weight: 0.0670 chunk 657 optimal weight: 0.0770 chunk 569 optimal weight: 6.9990 chunk 427 optimal weight: 10.0000 chunk 577 optimal weight: 3.9990 chunk 225 optimal weight: 0.0670 chunk 352 optimal weight: 7.9990 chunk 28 optimal weight: 7.9990 chunk 205 optimal weight: 9.9990 chunk 245 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 overall best weight: 1.2418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN 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: M 116 GLN M 482 GLN M 581 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.037087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.033245 restraints weight = 31292.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.034003 restraints weight = 20113.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.034572 restraints weight = 14098.449| |-----------------------------------------------------------------------------| r_work (final): 0.2874 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.044462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.038700 restraints weight = 62163.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.039430 restraints weight = 40539.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.039929 restraints weight = 29455.973| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6673 moved from start: 0.9398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 57932 Z= 0.161 Angle : 0.668 7.193 78322 Z= 0.366 Chirality : 0.044 0.187 8658 Planarity : 0.005 0.050 10170 Dihedral : 6.310 83.740 7854 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.74 % Favored : 94.90 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % 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: -1.15 (0.10), residues: 7132 helix: 0.00 (0.10), residues: 2924 sheet: -0.84 (0.16), residues: 946 loop : -1.40 (0.11), residues: 3262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP K 8 HIS 0.020 0.001 HIS I 227 PHE 0.031 0.002 PHE J 163 TYR 0.044 0.002 TYR L 67 ARG 0.014 0.001 ARG M 243 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11452 Ramachandran restraints generated. 5726 Oldfield, 0 Emsley, 5726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11452 Ramachandran restraints generated. 5726 Oldfield, 0 Emsley, 5726 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 to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.260 Fit side-chains REVERT: A 47 MET cc_start: 0.6179 (ttm) cc_final: 0.5155 (tpp) REVERT: A 233 SER cc_start: 0.7968 (m) cc_final: 0.7635 (t) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0881 time to fit residues: 3.1237 Evaluate side-chains 21 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.256 Evaluate side-chains 23 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.508 Fit side-chains REVERT: M 138 MET cc_start: 0.6468 (ttm) cc_final: 0.5164 (tpp) REVERT: M 395 MET cc_start: 0.7770 (mpp) cc_final: 0.6122 (pmm) REVERT: M 645 ASN cc_start: 0.7582 (t0) cc_final: 0.7198 (t0) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1021 time to fit residues: 4.0355 Evaluate side-chains 14 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 704, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 801, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.7962 > 50: distance: 10 - 11: 3.151 distance: 10 - 13: 4.682 distance: 11 - 12: 3.270 distance: 11 - 18: 3.819 distance: 18 - 19: 4.303 distance: 19 - 20: 7.867 distance: 19 - 22: 10.972 distance: 20 - 21: 19.798 distance: 20 - 29: 26.827 distance: 22 - 23: 4.199 distance: 23 - 24: 4.261 distance: 24 - 25: 11.432 distance: 25 - 26: 15.507 distance: 29 - 30: 16.243 distance: 30 - 31: 8.341 distance: 30 - 33: 14.970 distance: 31 - 32: 4.525 distance: 31 - 37: 5.791 distance: 33 - 34: 9.532 distance: 34 - 35: 11.258 distance: 34 - 36: 3.832 distance: 37 - 38: 3.513 distance: 38 - 39: 6.600 distance: 38 - 41: 4.126 distance: 39 - 49: 6.558 distance: 42 - 43: 4.351 distance: 42 - 44: 5.869 distance: 43 - 45: 8.843 distance: 44 - 46: 4.072 distance: 45 - 47: 20.019 distance: 46 - 47: 15.975 distance: 47 - 48: 22.579 distance: 49 - 50: 5.409 distance: 50 - 51: 3.374 distance: 51 - 52: 8.425 distance: 51 - 59: 10.183 distance: 52 - 90: 19.889 distance: 54 - 55: 5.522 distance: 54 - 56: 3.956 distance: 55 - 57: 8.305 distance: 56 - 58: 7.584 distance: 57 - 58: 5.193 distance: 59 - 60: 17.304 distance: 60 - 61: 10.282 distance: 60 - 63: 13.864 distance: 61 - 62: 19.393 distance: 61 - 67: 24.170 distance: 63 - 64: 9.278 distance: 63 - 65: 9.971 distance: 64 - 66: 4.347 distance: 67 - 68: 9.545 distance: 68 - 69: 19.862 distance: 68 - 71: 19.587 distance: 69 - 70: 14.666 distance: 69 - 78: 15.166 distance: 72 - 73: 7.305 distance: 72 - 74: 4.822 distance: 73 - 75: 4.013 distance: 75 - 77: 14.683 distance: 76 - 77: 14.427 distance: 78 - 79: 11.560 distance: 79 - 80: 48.044 distance: 79 - 82: 31.794 distance: 80 - 81: 23.109 distance: 80 - 90: 25.815 distance: 82 - 83: 13.608 distance: 83 - 84: 8.687 distance: 83 - 85: 8.219 distance: 84 - 86: 14.854 distance: 85 - 87: 13.774 distance: 86 - 88: 42.202 distance: 87 - 88: 39.921 distance: 88 - 89: 69.796 distance: 90 - 91: 17.883 distance: 91 - 94: 6.516 distance: 92 - 93: 3.026 distance: 94 - 95: 4.143