Starting phenix.real_space_refine on Wed Sep 25 19:50:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ras_19023/09_2024/8ras_19023.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ras_19023/09_2024/8ras_19023.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ras_19023/09_2024/8ras_19023.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ras_19023/09_2024/8ras_19023.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ras_19023/09_2024/8ras_19023.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ras_19023/09_2024/8ras_19023.cif" } resolution = 2.62 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.140 sd= 0.155 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: 8 Type Number sf(0) Gaussians Fe 2 7.16 5 Zn 1 6.06 5 P 80 5.49 5 Mg 1 5.21 5 S 268 5.16 5 C 36108 2.51 5 N 9924 2.21 5 O 10931 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 89 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 57315 Number of models: 1 Model: "" Number of chains: 45 Chain: "A" Number of atoms: 2449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2449 Classifications: {'peptide': 301} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 286} Chain breaks: 2 Chain: "B" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1722 Classifications: {'peptide': 216} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 205} Chain breaks: 1 Chain: "C" Number of atoms: 5772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 5772 Classifications: {'peptide': 726} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 34, 'TRANS': 691} Chain breaks: 7 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 4787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4787 Classifications: {'peptide': 585} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 553} Chain breaks: 6 Chain: "E" Number of atoms: 7308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 912, 7308 Classifications: {'peptide': 912} Link IDs: {'PTRANS': 33, 'TRANS': 878} Chain breaks: 18 Chain: "F" Number of atoms: 4593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4593 Classifications: {'peptide': 568} Link IDs: {'PTRANS': 22, 'TRANS': 545} Chain breaks: 4 Chain: "G" Number of atoms: 3040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3040 Classifications: {'peptide': 385} Link IDs: {'PTRANS': 8, 'TRANS': 376} Chain breaks: 2 Chain: "H" Number of atoms: 3701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3701 Classifications: {'peptide': 440} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 405} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 1771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1771 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Chain: "J" Number of atoms: 1970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1970 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 14, 'TRANS': 219} Chain breaks: 1 Chain: "K" Number of atoms: 3022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 3022 Classifications: {'peptide': 374} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 350} Chain: "L" Number of atoms: 3348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3348 Classifications: {'peptide': 408} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 381} Chain breaks: 2 Chain: "M" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1714 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 15, 'TRANS': 188} Chain: "N" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1759 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 201} Chain breaks: 1 Chain: "O" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 923 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 107} Chain: "P" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 865 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 101} Chain: "Q" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1740 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 209} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 944 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain breaks: 2 Chain: "S" Number of atoms: 3056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3056 Classifications: {'peptide': 386} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 364} Chain breaks: 1 Chain: "T" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 881 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 1 Chain: "X" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 638 Classifications: {'DNA': 31} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 30} Chain breaks: 1 Chain: "Y" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 813 Classifications: {'DNA': 40} Link IDs: {'rna3p': 39} Chain: "Z" Number of atoms: 215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 215 Classifications: {'RNA': 10} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 5, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 8} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "D" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "E" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "I" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "K" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "L" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "M" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "N" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "O" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "S" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16437 SG CYS E 220 97.283 113.428 109.446 1.00 66.65 S ATOM 16906 SG CYS E 293 94.634 112.057 111.778 1.00 55.31 S ATOM 16964 SG CYS E 300 95.151 110.521 108.259 1.00 54.48 S ATOM 16989 SG CYS E 303 97.725 109.883 110.759 1.00 70.32 S Time building chain proxies: 23.01, per 1000 atoms: 0.40 Number of scatterers: 57315 At special positions: 0 Unit cell: (149, 210, 267, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 Fe 2 26.01 S 268 16.00 P 80 15.00 Mg 1 11.99 O 10931 8.00 N 9924 7.00 C 36108 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: 10.37 Conformation dependent library (CDL) restraints added in 5.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E8001 " pdb="ZN ZN E8001 " - pdb=" SG CYS E 300 " pdb="ZN ZN E8001 " - pdb=" SG CYS E 220 " pdb="ZN ZN E8001 " - pdb=" SG CYS E 303 " pdb="ZN ZN E8001 " - pdb=" SG CYS E 293 " Number of angles added : 6 13370 Ramachandran restraints generated. 6685 Oldfield, 0 Emsley, 6685 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12804 Finding SS restraints... Secondary structure from input PDB file: 295 helices and 60 sheets defined 47.0% alpha, 12.8% beta 37 base pairs and 56 stacking pairs defined. Time for finding SS restraints: 15.11 Creating SS restraints... Processing helix chain 'A' and resid 40 through 56 removed outlier: 3.526A pdb=" N THR A 44 " --> pdb=" O GLY A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 93 removed outlier: 3.513A pdb=" N GLU A 93 " --> pdb=" O MET A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 227 Processing helix chain 'A' and resid 228 through 231 Processing helix chain 'A' and resid 249 through 262 removed outlier: 4.201A pdb=" N PHE A 253 " --> pdb=" O PRO A 249 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN A 262 " --> pdb=" O VAL A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 290 Processing helix chain 'A' and resid 294 through 301 Processing helix chain 'A' and resid 302 through 309 Processing helix chain 'A' and resid 313 through 327 Processing helix chain 'B' and resid 40 through 56 removed outlier: 3.614A pdb=" N THR B 44 " --> pdb=" O GLY B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 93 removed outlier: 3.568A pdb=" N GLU B 93 " --> pdb=" O MET B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 227 Processing helix chain 'B' and resid 228 through 231 Processing helix chain 'C' and resid 16 through 29 Processing helix chain 'C' and resid 29 through 36 Processing helix chain 'C' and resid 65 through 72 removed outlier: 3.623A pdb=" N VAL C 70 " --> pdb=" O GLU C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 310 No H-bonds generated for 'chain 'C' and resid 308 through 310' Processing helix chain 'C' and resid 316 through 330 removed outlier: 3.640A pdb=" N ALA C 330 " --> pdb=" O GLY C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 372 Processing helix chain 'C' and resid 382 through 389 removed outlier: 3.785A pdb=" N ILE C 387 " --> pdb=" O PRO C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 418 Processing helix chain 'C' and resid 472 through 477 removed outlier: 4.102A pdb=" N GLU C 477 " --> pdb=" O PRO C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 496 removed outlier: 3.597A pdb=" N GLU C 496 " --> pdb=" O ILE C 493 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 493 through 496' Processing helix chain 'C' and resid 513 through 515 No H-bonds generated for 'chain 'C' and resid 513 through 515' Processing helix chain 'C' and resid 529 through 533 removed outlier: 3.802A pdb=" N ILE C 533 " --> pdb=" O ALA C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 539 Processing helix chain 'C' and resid 540 through 552 removed outlier: 3.752A pdb=" N MET C 546 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG C 552 " --> pdb=" O SER C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 578 removed outlier: 4.001A pdb=" N GLY C 578 " --> pdb=" O ALA C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 677 through 682 Processing helix chain 'C' and resid 857 through 863 removed outlier: 4.158A pdb=" N SER C 861 " --> pdb=" O LEU C 857 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG C 862 " --> pdb=" O GLY C 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 865 through 881 Processing helix chain 'C' and resid 889 through 893 Processing helix chain 'C' and resid 896 through 914 Processing helix chain 'C' and resid 988 through 999 Processing helix chain 'C' and resid 1000 through 1007 Processing helix chain 'C' and resid 1014 through 1028 removed outlier: 3.552A pdb=" N GLN C1019 " --> pdb=" O ILE C1015 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE C1026 " --> pdb=" O LEU C1022 " (cutoff:3.500A) Processing helix chain 'C' and resid 1038 through 1050 Processing helix chain 'D' and resid 16 through 25 Processing helix chain 'D' and resid 57 through 62 Processing helix chain 'D' and resid 98 through 102 Processing helix chain 'D' and resid 115 through 120 Processing helix chain 'D' and resid 124 through 131 Processing helix chain 'D' and resid 133 through 143 Processing helix chain 'D' and resid 168 through 173 removed outlier: 3.821A pdb=" N TYR D 173 " --> pdb=" O GLN D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 179 Processing helix chain 'D' and resid 181 through 189 removed outlier: 4.407A pdb=" N ASN D 189 " --> pdb=" O GLU D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 205 removed outlier: 3.538A pdb=" N ILE D 199 " --> pdb=" O GLY D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 225 removed outlier: 3.674A pdb=" N GLU D 225 " --> pdb=" O GLN D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 257 removed outlier: 3.968A pdb=" N LYS D 241 " --> pdb=" O ILE D 237 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE D 254 " --> pdb=" O LEU D 250 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE D 255 " --> pdb=" O ALA D 251 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG D 256 " --> pdb=" O LYS D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 263 Processing helix chain 'D' and resid 273 through 277 Processing helix chain 'D' and resid 292 through 310 removed outlier: 3.561A pdb=" N THR D 305 " --> pdb=" O TYR D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 337 Processing helix chain 'D' and resid 355 through 361 Processing helix chain 'D' and resid 365 through 370 Processing helix chain 'D' and resid 399 through 406 Processing helix chain 'D' and resid 406 through 417 removed outlier: 3.575A pdb=" N GLN D 417 " --> pdb=" O GLY D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 432 Processing helix chain 'D' and resid 434 through 446 removed outlier: 4.018A pdb=" N TRP D 438 " --> pdb=" O LYS D 434 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLU D 439 " --> pdb=" O PRO D 435 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN D 446 " --> pdb=" O GLN D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 461 No H-bonds generated for 'chain 'D' and resid 459 through 461' Processing helix chain 'D' and resid 479 through 481 No H-bonds generated for 'chain 'D' and resid 479 through 481' Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 502 through 513 Processing helix chain 'D' and resid 514 through 518 Processing helix chain 'D' and resid 533 through 544 Processing helix chain 'D' and resid 548 through 552 Processing helix chain 'D' and resid 583 through 593 Processing helix chain 'D' and resid 655 through 676 Processing helix chain 'E' and resid 15 through 31 Processing helix chain 'E' and resid 31 through 54 removed outlier: 3.507A pdb=" N HIS E 37 " --> pdb=" O ALA E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 88 Processing helix chain 'E' and resid 92 through 123 removed outlier: 4.338A pdb=" N ASN E 116 " --> pdb=" O ARG E 112 " (cutoff:3.500A) Proline residue: E 117 - end of helix Processing helix chain 'E' and resid 126 through 134 Processing helix chain 'E' and resid 139 through 148 removed outlier: 3.512A pdb=" N LEU E 146 " --> pdb=" O GLN E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 210 removed outlier: 3.894A pdb=" N TYR E 183 " --> pdb=" O ILE E 179 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLY E 184 " --> pdb=" O ILE E 180 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA E 185 " --> pdb=" O SER E 181 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N SER E 197 " --> pdb=" O ALA E 193 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR E 201 " --> pdb=" O SER E 197 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL E 210 " --> pdb=" O LEU E 206 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 247 Processing helix chain 'E' and resid 270 through 280 Processing helix chain 'E' and resid 289 through 293 removed outlier: 3.706A pdb=" N CYS E 293 " --> pdb=" O PRO E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 305 Processing helix chain 'E' and resid 319 through 330 Processing helix chain 'E' and resid 365 through 369 removed outlier: 3.747A pdb=" N LEU E 368 " --> pdb=" O ASN E 365 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL E 369 " --> pdb=" O GLU E 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 365 through 369' Processing helix chain 'E' and resid 566 through 570 Processing helix chain 'E' and resid 986 through 990 Processing helix chain 'E' and resid 1001 through 1006 Processing helix chain 'E' and resid 1008 through 1013 removed outlier: 4.742A pdb=" N LYS E1013 " --> pdb=" O ASP E1010 " (cutoff:3.500A) Processing helix chain 'E' and resid 1146 through 1154 Processing helix chain 'E' and resid 1163 through 1180 removed outlier: 3.671A pdb=" N ARG E1174 " --> pdb=" O LYS E1170 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N CYS E1175 " --> pdb=" O GLY E1171 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR E1177 " --> pdb=" O ASN E1173 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ARG E1178 " --> pdb=" O ARG E1174 " (cutoff:3.500A) Processing helix chain 'E' and resid 1183 through 1211 Processing helix chain 'E' and resid 1217 through 1229 removed outlier: 3.843A pdb=" N ILE E1221 " --> pdb=" O HIS E1217 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLN E1227 " --> pdb=" O ILE E1223 " (cutoff:3.500A) Processing helix chain 'E' and resid 1251 through 1261 Processing helix chain 'E' and resid 1273 through 1279 removed outlier: 3.553A pdb=" N SER E1278 " --> pdb=" O ILE E1274 " (cutoff:3.500A) Processing helix chain 'E' and resid 1283 through 1289 removed outlier: 3.553A pdb=" N GLU E1287 " --> pdb=" O SER E1283 " (cutoff:3.500A) Processing helix chain 'E' and resid 1292 through 1303 removed outlier: 3.944A pdb=" N ARG E1303 " --> pdb=" O LYS E1299 " (cutoff:3.500A) Processing helix chain 'E' and resid 1311 through 1319 removed outlier: 3.884A pdb=" N ASN E1315 " --> pdb=" O GLY E1311 " (cutoff:3.500A) Processing helix chain 'E' and resid 1324 through 1328 Processing helix chain 'F' and resid 64 through 84 Processing helix chain 'F' and resid 86 through 101 Processing helix chain 'F' and resid 105 through 119 removed outlier: 3.967A pdb=" N ASN F 119 " --> pdb=" O ALA F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 136 Processing helix chain 'F' and resid 140 through 155 Processing helix chain 'F' and resid 156 through 170 Processing helix chain 'F' and resid 174 through 188 Processing helix chain 'F' and resid 190 through 204 Processing helix chain 'F' and resid 209 through 223 Processing helix chain 'F' and resid 225 through 239 Processing helix chain 'F' and resid 244 through 256 removed outlier: 4.054A pdb=" N VAL F 254 " --> pdb=" O CYS F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 273 removed outlier: 4.190A pdb=" N ALA F 264 " --> pdb=" O ILE F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 279 Processing helix chain 'F' and resid 281 through 294 Processing helix chain 'F' and resid 300 through 314 Processing helix chain 'F' and resid 321 through 335 Processing helix chain 'F' and resid 337 through 350 removed outlier: 4.091A pdb=" N ASN F 350 " --> pdb=" O ARG F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 360 removed outlier: 3.550A pdb=" N ASN F 360 " --> pdb=" O LYS F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 361 through 363 No H-bonds generated for 'chain 'F' and resid 361 through 363' Processing helix chain 'F' and resid 366 through 378 removed outlier: 3.505A pdb=" N GLU F 378 " --> pdb=" O ALA F 374 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 394 Processing helix chain 'F' and resid 411 through 415 removed outlier: 4.286A pdb=" N SER F 415 " --> pdb=" O LEU F 412 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 439 Processing helix chain 'F' and resid 459 through 463 Processing helix chain 'F' and resid 474 through 496 removed outlier: 3.609A pdb=" N GLN F 495 " --> pdb=" O LEU F 491 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER F 496 " --> pdb=" O ARG F 492 " (cutoff:3.500A) Processing helix chain 'F' and resid 541 through 549 Processing helix chain 'F' and resid 558 through 567 Processing helix chain 'F' and resid 607 through 616 removed outlier: 3.557A pdb=" N LEU F 616 " --> pdb=" O LYS F 612 " (cutoff:3.500A) Processing helix chain 'F' and resid 744 through 755 Processing helix chain 'F' and resid 759 through 763 Processing helix chain 'F' and resid 765 through 770 removed outlier: 3.515A pdb=" N VAL F 769 " --> pdb=" O THR F 765 " (cutoff:3.500A) Processing helix chain 'F' and resid 772 through 779 removed outlier: 3.504A pdb=" N GLU F 775 " --> pdb=" O TRP F 772 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS F 776 " --> pdb=" O THR F 773 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS F 779 " --> pdb=" O LYS F 776 " (cutoff:3.500A) Processing helix chain 'F' and resid 787 through 805 Processing helix chain 'F' and resid 810 through 817 removed outlier: 3.736A pdb=" N ILE F 817 " --> pdb=" O ASP F 813 " (cutoff:3.500A) Processing helix chain 'F' and resid 836 through 840 removed outlier: 3.750A pdb=" N LEU F 840 " --> pdb=" O THR F 836 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 836 through 840' Processing helix chain 'G' and resid 421 through 433 Processing helix chain 'G' and resid 435 through 448 Processing helix chain 'G' and resid 454 through 468 removed outlier: 3.908A pdb=" N ALA G 468 " --> pdb=" O ALA G 464 " (cutoff:3.500A) Processing helix chain 'G' and resid 470 through 484 removed outlier: 3.881A pdb=" N HIS G 482 " --> pdb=" O PHE G 478 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU G 483 " --> pdb=" O ASN G 479 " (cutoff:3.500A) Processing helix chain 'G' and resid 489 through 503 removed outlier: 3.590A pdb=" N GLY G 503 " --> pdb=" O SER G 499 " (cutoff:3.500A) Processing helix chain 'G' and resid 505 through 520 Processing helix chain 'G' and resid 524 through 538 Processing helix chain 'G' and resid 540 through 555 removed outlier: 3.871A pdb=" N ARG G 555 " --> pdb=" O MET G 551 " (cutoff:3.500A) Processing helix chain 'G' and resid 559 through 573 removed outlier: 3.638A pdb=" N LEU G 563 " --> pdb=" O ASP G 559 " (cutoff:3.500A) Processing helix chain 'G' and resid 575 through 587 Processing helix chain 'G' and resid 588 through 590 No H-bonds generated for 'chain 'G' and resid 588 through 590' Processing helix chain 'G' and resid 594 through 608 removed outlier: 3.821A pdb=" N TYR G 598 " --> pdb=" O SER G 594 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR G 608 " --> pdb=" O VAL G 604 " (cutoff:3.500A) Processing helix chain 'G' and resid 610 through 624 removed outlier: 3.896A pdb=" N GLU G 620 " --> pdb=" O GLU G 616 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N SER G 623 " --> pdb=" O GLU G 619 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASN G 624 " --> pdb=" O GLU G 620 " (cutoff:3.500A) Processing helix chain 'G' and resid 628 through 638 removed outlier: 3.827A pdb=" N LYS G 638 " --> pdb=" O GLY G 634 " (cutoff:3.500A) Processing helix chain 'G' and resid 646 through 658 removed outlier: 4.402A pdb=" N VAL G 650 " --> pdb=" O ASN G 646 " (cutoff:3.500A) Processing helix chain 'G' and resid 661 through 679 removed outlier: 3.939A pdb=" N ARG G 667 " --> pdb=" O GLY G 663 " (cutoff:3.500A) Processing helix chain 'G' and resid 681 through 696 removed outlier: 3.623A pdb=" N LYS G 694 " --> pdb=" O ASN G 690 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG G 695 " --> pdb=" O GLU G 691 " (cutoff:3.500A) Processing helix chain 'G' and resid 717 through 735 removed outlier: 3.947A pdb=" N ILE G 735 " --> pdb=" O ASP G 731 " (cutoff:3.500A) Processing helix chain 'G' and resid 753 through 758 Processing helix chain 'G' and resid 759 through 764 removed outlier: 3.863A pdb=" N GLU G 763 " --> pdb=" O SER G 759 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER G 764 " --> pdb=" O ALA G 760 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 759 through 764' Processing helix chain 'G' and resid 764 through 779 Processing helix chain 'G' and resid 795 through 802 removed outlier: 3.510A pdb=" N GLN G 801 " --> pdb=" O SER G 797 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 80 removed outlier: 3.550A pdb=" N ARG H 73 " --> pdb=" O ASP H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 89 through 99 Processing helix chain 'H' and resid 109 through 118 Processing helix chain 'H' and resid 120 through 131 Processing helix chain 'H' and resid 134 through 143 removed outlier: 3.526A pdb=" N TRP H 138 " --> pdb=" O THR H 134 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N PHE H 143 " --> pdb=" O TYR H 139 " (cutoff:3.500A) Processing helix chain 'H' and resid 179 through 188 Processing helix chain 'H' and resid 189 through 195 removed outlier: 3.518A pdb=" N MET H 193 " --> pdb=" O HIS H 190 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 217 removed outlier: 3.697A pdb=" N THR H 213 " --> pdb=" O GLU H 210 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL H 214 " --> pdb=" O ASP H 211 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ASP H 215 " --> pdb=" O ALA H 212 " (cutoff:3.500A) Processing helix chain 'H' and resid 219 through 248 removed outlier: 5.647A pdb=" N ASP H 238 " --> pdb=" O GLU H 234 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N ARG H 239 " --> pdb=" O ALA H 235 " (cutoff:3.500A) Processing helix chain 'H' and resid 258 through 262 Processing helix chain 'H' and resid 268 through 272 Processing helix chain 'H' and resid 308 through 314 removed outlier: 4.194A pdb=" N TRP H 312 " --> pdb=" O ASN H 308 " (cutoff:3.500A) Processing helix chain 'H' and resid 349 through 353 Processing helix chain 'H' and resid 370 through 378 Processing helix chain 'H' and resid 403 through 424 Processing helix chain 'H' and resid 473 through 484 Processing helix chain 'H' and resid 503 through 538 Processing helix chain 'I' and resid 67 through 75 Processing helix chain 'I' and resid 77 through 91 Processing helix chain 'I' and resid 100 through 110 removed outlier: 3.549A pdb=" N ASN I 110 " --> pdb=" O LYS I 106 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 133 Processing helix chain 'I' and resid 144 through 154 removed outlier: 3.545A pdb=" N GLU I 148 " --> pdb=" O LYS I 144 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN I 149 " --> pdb=" O GLY I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 156 through 170 Processing helix chain 'I' and resid 198 through 203 Processing helix chain 'I' and resid 213 through 218 removed outlier: 3.903A pdb=" N TYR I 217 " --> pdb=" O TRP I 213 " (cutoff:3.500A) Processing helix chain 'I' and resid 224 through 236 removed outlier: 3.560A pdb=" N TYR I 228 " --> pdb=" O GLU I 224 " (cutoff:3.500A) Processing helix chain 'I' and resid 238 through 250 removed outlier: 3.642A pdb=" N ALA I 242 " --> pdb=" O SER I 238 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER I 244 " --> pdb=" O ASN I 240 " (cutoff:3.500A) Processing helix chain 'J' and resid 205 through 210 Processing helix chain 'J' and resid 234 through 238 Processing helix chain 'J' and resid 254 through 266 removed outlier: 3.748A pdb=" N VAL J 258 " --> pdb=" O ASP J 254 " (cutoff:3.500A) Processing helix chain 'J' and resid 277 through 307 removed outlier: 6.066A pdb=" N HIS J 289 " --> pdb=" O ARG J 285 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LEU J 290 " --> pdb=" O ALA J 286 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N PHE J 291 " --> pdb=" O ARG J 287 " (cutoff:3.500A) Processing helix chain 'J' and resid 307 through 313 Processing helix chain 'J' and resid 314 through 316 No H-bonds generated for 'chain 'J' and resid 314 through 316' Processing helix chain 'J' and resid 324 through 336 Processing helix chain 'J' and resid 338 through 348 Processing helix chain 'J' and resid 351 through 359 Processing helix chain 'J' and resid 360 through 362 No H-bonds generated for 'chain 'J' and resid 360 through 362' Processing helix chain 'J' and resid 368 through 373 Processing helix chain 'J' and resid 375 through 380 Processing helix chain 'J' and resid 381 through 383 No H-bonds generated for 'chain 'J' and resid 381 through 383' Processing helix chain 'J' and resid 390 through 393 Processing helix chain 'J' and resid 415 through 423 Processing helix chain 'K' and resid 118 through 122 Processing helix chain 'K' and resid 123 through 128 Processing helix chain 'K' and resid 130 through 134 Processing helix chain 'K' and resid 139 through 150 removed outlier: 3.666A pdb=" N VAL K 143 " --> pdb=" O PRO K 139 " (cutoff:3.500A) Processing helix chain 'K' and resid 163 through 176 Processing helix chain 'K' and resid 200 through 204 Processing helix chain 'K' and resid 213 through 217 Processing helix chain 'K' and resid 219 through 223 removed outlier: 3.568A pdb=" N LEU K 223 " --> pdb=" O ALA K 220 " (cutoff:3.500A) Processing helix chain 'K' and resid 224 through 231 Processing helix chain 'K' and resid 239 through 242 Processing helix chain 'K' and resid 243 through 261 Processing helix chain 'K' and resid 271 through 276 Processing helix chain 'K' and resid 277 through 291 removed outlier: 3.528A pdb=" N THR K 281 " --> pdb=" O SER K 277 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N LYS K 287 " --> pdb=" O LYS K 283 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N SER K 288 " --> pdb=" O LEU K 284 " (cutoff:3.500A) Processing helix chain 'K' and resid 299 through 307 Processing helix chain 'K' and resid 307 through 317 removed outlier: 3.690A pdb=" N TYR K 311 " --> pdb=" O ASP K 307 " (cutoff:3.500A) Processing helix chain 'K' and resid 325 through 330 removed outlier: 3.618A pdb=" N LYS K 330 " --> pdb=" O GLU K 327 " (cutoff:3.500A) Processing helix chain 'K' and resid 339 through 344 Processing helix chain 'K' and resid 345 through 347 No H-bonds generated for 'chain 'K' and resid 345 through 347' Processing helix chain 'K' and resid 391 through 407 removed outlier: 3.660A pdb=" N THR K 406 " --> pdb=" O ARG K 402 " (cutoff:3.500A) Processing helix chain 'K' and resid 408 through 412 removed outlier: 3.549A pdb=" N PHE K 411 " --> pdb=" O PRO K 408 " (cutoff:3.500A) Processing helix chain 'K' and resid 413 through 432 removed outlier: 3.875A pdb=" N PHE K 423 " --> pdb=" O ARG K 419 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA K 424 " --> pdb=" O GLN K 420 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN K 432 " --> pdb=" O GLY K 428 " (cutoff:3.500A) Processing helix chain 'K' and resid 443 through 455 Processing helix chain 'K' and resid 456 through 460 Processing helix chain 'L' and resid 76 through 85 removed outlier: 3.989A pdb=" N TYR L 80 " --> pdb=" O ASP L 76 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY L 83 " --> pdb=" O PHE L 79 " (cutoff:3.500A) Processing helix chain 'L' and resid 125 through 127 No H-bonds generated for 'chain 'L' and resid 125 through 127' Processing helix chain 'L' and resid 147 through 155 removed outlier: 3.812A pdb=" N ASP L 151 " --> pdb=" O HIS L 147 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER L 155 " --> pdb=" O ASP L 151 " (cutoff:3.500A) Processing helix chain 'L' and resid 161 through 176 removed outlier: 3.679A pdb=" N ARG L 165 " --> pdb=" O ASP L 161 " (cutoff:3.500A) Processing helix chain 'L' and resid 180 through 185 Processing helix chain 'L' and resid 186 through 188 No H-bonds generated for 'chain 'L' and resid 186 through 188' Processing helix chain 'L' and resid 196 through 200 Processing helix chain 'L' and resid 201 through 207 removed outlier: 3.705A pdb=" N GLU L 207 " --> pdb=" O GLU L 203 " (cutoff:3.500A) Processing helix chain 'L' and resid 210 through 232 Processing helix chain 'L' and resid 237 through 242 Processing helix chain 'L' and resid 246 through 261 removed outlier: 3.850A pdb=" N PHE L 250 " --> pdb=" O ASP L 246 " (cutoff:3.500A) Processing helix chain 'L' and resid 329 through 337 Processing helix chain 'L' and resid 359 through 367 Processing helix chain 'L' and resid 389 through 399 Processing helix chain 'L' and resid 410 through 432 removed outlier: 3.687A pdb=" N GLU L 414 " --> pdb=" O ILE L 410 " (cutoff:3.500A) Processing helix chain 'L' and resid 435 through 445 Processing helix chain 'L' and resid 450 through 480 Processing helix chain 'M' and resid 137 through 139 No H-bonds generated for 'chain 'M' and resid 137 through 139' Processing helix chain 'M' and resid 234 through 236 No H-bonds generated for 'chain 'M' and resid 234 through 236' Processing helix chain 'M' and resid 276 through 278 No H-bonds generated for 'chain 'M' and resid 276 through 278' Processing helix chain 'M' and resid 297 through 299 No H-bonds generated for 'chain 'M' and resid 297 through 299' Processing helix chain 'M' and resid 301 through 323 Processing helix chain 'M' and resid 327 through 330 Processing helix chain 'N' and resid 65 through 76 Processing helix chain 'N' and resid 76 through 88 Processing helix chain 'N' and resid 99 through 107 removed outlier: 3.611A pdb=" N ASN N 107 " --> pdb=" O LEU N 103 " (cutoff:3.500A) Processing helix chain 'N' and resid 108 through 110 No H-bonds generated for 'chain 'N' and resid 108 through 110' Processing helix chain 'N' and resid 114 through 130 Processing helix chain 'N' and resid 141 through 152 Processing helix chain 'N' and resid 153 through 168 Processing helix chain 'N' and resid 210 through 215 Processing helix chain 'N' and resid 225 through 229 Processing helix chain 'N' and resid 236 through 248 Processing helix chain 'N' and resid 250 through 270 removed outlier: 3.559A pdb=" N GLN N 270 " --> pdb=" O ALA N 266 " (cutoff:3.500A) Processing helix chain 'O' and resid 83 through 93 Processing helix chain 'O' and resid 109 through 125 removed outlier: 4.384A pdb=" N LEU O 113 " --> pdb=" O GLY O 109 " (cutoff:3.500A) Processing helix chain 'O' and resid 139 through 146 Processing helix chain 'O' and resid 173 through 185 removed outlier: 3.543A pdb=" N MET O 185 " --> pdb=" O ILE O 181 " (cutoff:3.500A) Processing helix chain 'P' and resid 83 through 93 Processing helix chain 'P' and resid 108 through 125 Processing helix chain 'P' and resid 139 through 146 Processing helix chain 'P' and resid 173 through 184 removed outlier: 3.511A pdb=" N MET P 177 " --> pdb=" O PRO P 173 " (cutoff:3.500A) Processing helix chain 'Q' and resid 351 through 361 Processing helix chain 'Q' and resid 540 through 548 removed outlier: 3.948A pdb=" N TYR Q 544 " --> pdb=" O ARG Q 540 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASN Q 545 " --> pdb=" O HIS Q 541 " (cutoff:3.500A) Processing helix chain 'Q' and resid 595 through 608 removed outlier: 3.614A pdb=" N ARG Q 607 " --> pdb=" O LEU Q 603 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU Q 608 " --> pdb=" O ASP Q 604 " (cutoff:3.500A) Processing helix chain 'Q' and resid 625 through 628 removed outlier: 3.787A pdb=" N LYS Q 628 " --> pdb=" O GLU Q 625 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 625 through 628' Processing helix chain 'Q' and resid 629 through 640 removed outlier: 4.513A pdb=" N THR Q 633 " --> pdb=" O ARG Q 629 " (cutoff:3.500A) Processing helix chain 'Q' and resid 654 through 664 removed outlier: 3.714A pdb=" N ILE Q 658 " --> pdb=" O ASP Q 654 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU Q 663 " --> pdb=" O LEU Q 659 " (cutoff:3.500A) Processing helix chain 'Q' and resid 669 through 679 Processing helix chain 'Q' and resid 696 through 707 removed outlier: 3.627A pdb=" N ALA Q 700 " --> pdb=" O VAL Q 696 " (cutoff:3.500A) Processing helix chain 'Q' and resid 735 through 746 Processing helix chain 'Q' and resid 746 through 753 removed outlier: 4.465A pdb=" N LEU Q 750 " --> pdb=" O TYR Q 746 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N HIS Q 751 " --> pdb=" O VAL Q 747 " (cutoff:3.500A) Processing helix chain 'R' and resid 68 through 79 Processing helix chain 'R' and resid 80 through 91 Processing helix chain 'R' and resid 95 through 114 Processing helix chain 'R' and resid 115 through 118 removed outlier: 3.509A pdb=" N TYR R 118 " --> pdb=" O ARG R 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 115 through 118' Processing helix chain 'R' and resid 123 through 136 removed outlier: 3.702A pdb=" N LEU R 136 " --> pdb=" O ARG R 132 " (cutoff:3.500A) Processing helix chain 'R' and resid 141 through 145 Processing helix chain 'S' and resid 193 through 197 Processing helix chain 'S' and resid 225 through 232 Processing helix chain 'S' and resid 249 through 260 Processing helix chain 'S' and resid 273 through 286 Processing helix chain 'S' and resid 322 through 326 Processing helix chain 'S' and resid 328 through 332 removed outlier: 3.505A pdb=" N ILE S 332 " --> pdb=" O LYS S 329 " (cutoff:3.500A) Processing helix chain 'S' and resid 333 through 340 removed outlier: 3.684A pdb=" N LEU S 337 " --> pdb=" O ASN S 333 " (cutoff:3.500A) Processing helix chain 'S' and resid 348 through 351 removed outlier: 3.625A pdb=" N LEU S 351 " --> pdb=" O HIS S 348 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 348 through 351' Processing helix chain 'S' and resid 352 through 369 Processing helix chain 'S' and resid 380 through 385 removed outlier: 4.127A pdb=" N GLN S 385 " --> pdb=" O PRO S 382 " (cutoff:3.500A) Processing helix chain 'S' and resid 386 through 399 removed outlier: 5.154A pdb=" N GLU S 396 " --> pdb=" O SER S 392 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N VAL S 397 " --> pdb=" O LEU S 393 " (cutoff:3.500A) Processing helix chain 'S' and resid 408 through 415 Processing helix chain 'S' and resid 429 through 433 Processing helix chain 'S' and resid 487 through 505 removed outlier: 3.575A pdb=" N GLY S 491 " --> pdb=" O MET S 487 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN S 505 " --> pdb=" O MET S 501 " (cutoff:3.500A) Processing helix chain 'S' and resid 506 through 509 removed outlier: 3.935A pdb=" N MET S 509 " --> pdb=" O PRO S 506 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 506 through 509' Processing helix chain 'S' and resid 511 through 538 Processing helix chain 'S' and resid 568 through 573 Processing helix chain 'T' and resid 40 through 46 Processing helix chain 'T' and resid 54 through 61 Processing helix chain 'T' and resid 62 through 66 removed outlier: 3.688A pdb=" N ARG T 65 " --> pdb=" O GLY T 62 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 24 removed outlier: 5.398A pdb=" N TRP A 15 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N SER A 35 " --> pdb=" O TRP A 15 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N CYS A 17 " --> pdb=" O ILE A 33 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE A 33 " --> pdb=" O CYS A 17 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU A 27 " --> pdb=" O ASP A 23 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N GLU A 197 " --> pdb=" O PRO A 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 66 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 59 through 66 current: chain 'A' and resid 121 through 122 No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 96 through 97 Processing sheet with id=AA4, first strand: chain 'A' and resid 114 through 117 removed outlier: 3.534A pdb=" N ALA A 137 " --> pdb=" O ILE A 116 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 14 through 24 removed outlier: 6.352A pdb=" N ARG B 31 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N SER B 20 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N TYR B 29 " --> pdb=" O SER B 20 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ARG B 22 " --> pdb=" O LEU B 27 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N LEU B 27 " --> pdb=" O ARG B 22 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLU B 197 " --> pdb=" O PRO B 36 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N SER B 188 " --> pdb=" O GLU R 159 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 121 through 122 removed outlier: 3.688A pdb=" N VAL B 110 " --> pdb=" O LEU B 145 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG B 64 " --> pdb=" O LYS B 150 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLU B 152 " --> pdb=" O ILE B 62 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N ILE B 62 " --> pdb=" O GLU B 152 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ASN B 154 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N THR B 60 " --> pdb=" O ASN B 154 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 96 through 97 removed outlier: 3.542A pdb=" N LYS B 97 " --> pdb=" O GLU B 128 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 114 through 117 Processing sheet with id=AA9, first strand: chain 'C' and resid 102 through 105 removed outlier: 3.791A pdb=" N GLY C 102 " --> pdb=" O LEU C 80 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU C 79 " --> pdb=" O VAL C 60 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU C 59 " --> pdb=" O ILE J 427 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 113 through 115 Processing sheet with id=AB2, first strand: chain 'C' and resid 312 through 315 removed outlier: 3.503A pdb=" N LEU C 127 " --> pdb=" O ARG C 313 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 443 through 444 removed outlier: 3.530A pdb=" N SER C 452 " --> pdb=" O LEU C 471 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 468 through 471 current: chain 'C' and resid 498 through 503 Processing sheet with id=AB4, first strand: chain 'C' and resid 565 through 566 Processing sheet with id=AB5, first strand: chain 'C' and resid 581 through 582 removed outlier: 6.327A pdb=" N ALA C 581 " --> pdb=" O LEU C 640 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 604 through 609 removed outlier: 7.014A pdb=" N LYS C 596 " --> pdb=" O THR C 592 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N THR C 592 " --> pdb=" O LYS C 596 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ILE C 598 " --> pdb=" O LEU C 590 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 612 through 615 Processing sheet with id=AB8, first strand: chain 'C' and resid 646 through 647 Processing sheet with id=AB9, first strand: chain 'C' and resid 655 through 656 removed outlier: 7.552A pdb=" N ILE C 675 " --> pdb=" O SER C 833 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ILE C 835 " --> pdb=" O ILE C 675 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ALA C 660 " --> pdb=" O PHE C 854 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ILE C 943 " --> pdb=" O TYR C 661 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 687 through 693 removed outlier: 6.884A pdb=" N TYR C 809 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY C 785 " --> pdb=" O VAL C 734 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 961 through 963 removed outlier: 7.504A pdb=" N ILE D 476 " --> pdb=" O ARG D 381 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL D 383 " --> pdb=" O ILE D 476 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N LEU D 478 " --> pdb=" O VAL D 383 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL D 385 " --> pdb=" O LEU D 478 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 985 through 987 removed outlier: 3.722A pdb=" N GLN C 985 " --> pdb=" O VAL D 376 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 1067 through 1070 removed outlier: 4.828A pdb=" N HIS C1057 " --> pdb=" O LYS C1070 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N HIS D 7 " --> pdb=" O VAL C1060 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 105 through 114 removed outlier: 10.278A pdb=" N LEU D 109 " --> pdb=" O PRO D 270 " (cutoff:3.500A) removed outlier: 10.275A pdb=" N CYS D 111 " --> pdb=" O LEU D 268 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LEU D 268 " --> pdb=" O CYS D 111 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 146 through 148 Processing sheet with id=AC7, first strand: chain 'D' and resid 580 through 581 removed outlier: 4.078A pdb=" N ILE D 650 " --> pdb=" O TRP D 606 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LEU M 266 " --> pdb=" O ILE M 293 " (cutoff:3.500A) removed outlier: 8.844A pdb=" N HIS M 295 " --> pdb=" O LEU M 266 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL J 188 " --> pdb=" O VAL M 267 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 215 through 217 Processing sheet with id=AC9, first strand: chain 'E' and resid 226 through 228 removed outlier: 4.283A pdb=" N VAL E 250 " --> pdb=" O ARG E 288 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 255 through 257 removed outlier: 6.432A pdb=" N ILE E 257 " --> pdb=" O CYS E 261 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N CYS E 261 " --> pdb=" O ILE E 257 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 353 through 355 Processing sheet with id=AD3, first strand: chain 'E' and resid 397 through 402 removed outlier: 3.734A pdb=" N LEU E 387 " --> pdb=" O ILE E 402 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 438 through 443 removed outlier: 3.769A pdb=" N VAL E1130 " --> pdb=" O ILE E 442 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N LEU E1129 " --> pdb=" O HIS E1116 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 448 through 451 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 474 through 480 current: chain 'E' and resid 1030 through 1031 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 1030 through 1031 current: chain 'E' and resid 1089 through 1094 removed outlier: 6.459A pdb=" N VAL E1100 " --> pdb=" O LEU E1092 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 1099 through 1109 current: chain 'H' and resid 290 through 294 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 301 through 304 current: chain 'H' and resid 340 through 346 Processing sheet with id=AD6, first strand: chain 'E' and resid 499 through 500 removed outlier: 7.277A pdb=" N GLN E 499 " --> pdb=" O HIS H 364 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'E' and resid 572 through 573 removed outlier: 3.915A pdb=" N GLY E 875 " --> pdb=" O ARG E 856 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG E 856 " --> pdb=" O GLY E 875 " (cutoff:3.500A) removed outlier: 8.855A pdb=" N VAL H 463 " --> pdb=" O ALA E 857 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N PHE E 859 " --> pdb=" O VAL H 463 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N LEU H 465 " --> pdb=" O PHE E 859 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLU E 861 " --> pdb=" O LEU H 465 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 600 through 601 removed outlier: 3.947A pdb=" N SER E 600 " --> pdb=" O PHE E 617 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE E 617 " --> pdb=" O SER E 600 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'E' and resid 613 through 614 Processing sheet with id=AE1, first strand: chain 'E' and resid 924 through 926 Processing sheet with id=AE2, first strand: chain 'E' and resid 1015 through 1016 Processing sheet with id=AE3, first strand: chain 'E' and resid 1039 through 1042 removed outlier: 3.718A pdb=" N ASN E1047 " --> pdb=" O ASN E1042 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 1248 through 1250 removed outlier: 4.768A pdb=" N LYS E1231 " --> pdb=" O VAL E1270 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 702 through 704 removed outlier: 6.131A pdb=" N TRP G 709 " --> pdb=" O VAL G 747 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL G 749 " --> pdb=" O TRP G 709 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL G 711 " --> pdb=" O VAL G 749 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 187 through 194 removed outlier: 3.717A pdb=" N ARG I 187 " --> pdb=" O LYS I 182 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N GLY I 175 " --> pdb=" O ASP I 211 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ASP I 211 " --> pdb=" O GLY I 175 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N VAL I 177 " --> pdb=" O ASN I 209 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ASN I 209 " --> pdb=" O VAL I 177 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU I 179 " --> pdb=" O ILE I 207 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 213 through 214 Processing sheet with id=AE8, first strand: chain 'K' and resid 183 through 186 removed outlier: 6.640A pdb=" N LYS K 184 " --> pdb=" O PHE K 156 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLY K 158 " --> pdb=" O LYS K 184 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N ASP K 186 " --> pdb=" O GLY K 158 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL K 160 " --> pdb=" O ASP K 186 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N VAL K 93 " --> pdb=" O ALA K 155 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N MET K 157 " --> pdb=" O VAL K 93 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N CYS K 95 " --> pdb=" O MET K 157 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N LYS K 159 " --> pdb=" O CYS K 95 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE K 233 " --> pdb=" O LEU K 92 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ASN K 237 " --> pdb=" O PHE K 96 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N PHE K 234 " --> pdb=" O PHE K 265 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ASP K 267 " --> pdb=" O PHE K 234 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N PHE K 236 " --> pdb=" O ASP K 267 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE K 295 " --> pdb=" O VAL K 355 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N THR K 357 " --> pdb=" O ILE K 295 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL K 297 " --> pdb=" O THR K 357 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 206 through 211 removed outlier: 6.585A pdb=" N ARG K 195 " --> pdb=" O VAL K 210 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR O 153 " --> pdb=" O PHE O 103 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ILE O 100 " --> pdb=" O VAL O 132 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N VAL O 134 " --> pdb=" O ILE O 100 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ASP O 102 " --> pdb=" O VAL O 134 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ARG O 80 " --> pdb=" O LYS O 133 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ASP O 135 " --> pdb=" O ARG O 80 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 73 through 74 Processing sheet with id=AF2, first strand: chain 'L' and resid 89 through 90 removed outlier: 3.501A pdb=" N ARG L 117 " --> pdb=" O SER L 308 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL L 306 " --> pdb=" O ILE L 119 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLU L 121 " --> pdb=" O LEU L 304 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU L 304 " --> pdb=" O GLU L 121 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 138 through 139 removed outlier: 3.590A pdb=" N THR L 129 " --> pdb=" O PHE L 139 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 286 through 287 removed outlier: 5.840A pdb=" N ASN L 286 " --> pdb=" O ILE L 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'L' and resid 357 through 358 removed outlier: 6.306A pdb=" N ILE L 357 " --> pdb=" O TRP L 402 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'L' and resid 368 through 369 Processing sheet with id=AF7, first strand: chain 'M' and resid 141 through 145 removed outlier: 6.709A pdb=" N GLU M 168 " --> pdb=" O ARG M 154 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ARG M 194 " --> pdb=" O LYS M 231 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LYS M 231 " --> pdb=" O ARG M 194 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ALA M 196 " --> pdb=" O LEU M 229 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LEU M 229 " --> pdb=" O ALA M 196 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N SER M 198 " --> pdb=" O VAL M 227 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N VAL M 227 " --> pdb=" O SER M 198 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N TYR M 200 " --> pdb=" O SER M 225 " (cutoff:3.500A) removed outlier: 14.036A pdb=" N GLU M 223 " --> pdb=" O ASP M 254 " (cutoff:3.500A) removed outlier: 11.675A pdb=" N ASP M 254 " --> pdb=" O GLU M 223 " (cutoff:3.500A) removed outlier: 11.187A pdb=" N SER M 225 " --> pdb=" O VAL M 252 " (cutoff:3.500A) removed outlier: 9.690A pdb=" N VAL M 252 " --> pdb=" O SER M 225 " (cutoff:3.500A) removed outlier: 10.352A pdb=" N VAL M 227 " --> pdb=" O ILE M 250 " (cutoff:3.500A) removed outlier: 9.300A pdb=" N ILE M 250 " --> pdb=" O VAL M 227 " (cutoff:3.500A) removed outlier: 10.628A pdb=" N LEU M 229 " --> pdb=" O GLU M 248 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N GLU M 248 " --> pdb=" O LEU M 229 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS M 231 " --> pdb=" O ASP M 246 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ARG M 183 " --> pdb=" O ILE M 260 " (cutoff:3.500A) removed outlier: 8.773A pdb=" N ARG M 262 " --> pdb=" O ARG M 183 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'N' and resid 200 through 206 removed outlier: 7.246A pdb=" N GLY N 172 " --> pdb=" O ASP N 223 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ASP N 223 " --> pdb=" O GLY N 172 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N THR N 174 " --> pdb=" O THR N 221 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N THR N 221 " --> pdb=" O THR N 174 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU N 176 " --> pdb=" O LEU N 219 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'P' and resid 80 through 81 removed outlier: 5.905A pdb=" N ARG P 80 " --> pdb=" O LYS P 133 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ASP P 135 " --> pdb=" O ARG P 80 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ILE P 100 " --> pdb=" O VAL P 132 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N VAL P 134 " --> pdb=" O ILE P 100 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ASP P 102 " --> pdb=" O VAL P 134 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N THR S 305 " --> pdb=" O VAL S 319 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'Q' and resid 586 through 591 removed outlier: 6.569A pdb=" N GLY Q 587 " --> pdb=" O VAL Q 714 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N VAL Q 716 " --> pdb=" O GLY Q 587 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ILE Q 589 " --> pdb=" O VAL Q 716 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ILE Q 615 " --> pdb=" O VAL Q 715 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N ALA Q 717 " --> pdb=" O ILE Q 615 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL Q 617 " --> pdb=" O ALA Q 717 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ILE Q 614 " --> pdb=" O VAL Q 642 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N MET Q 644 " --> pdb=" O ILE Q 614 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N THR Q 616 " --> pdb=" O MET Q 644 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'Q' and resid 724 through 727 Processing sheet with id=AG3, first strand: chain 'S' and resid 293 through 296 removed outlier: 6.387A pdb=" N LYS S 294 " --> pdb=" O PHE S 266 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N GLY S 268 " --> pdb=" O LYS S 294 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N ASP S 296 " --> pdb=" O GLY S 268 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU S 270 " --> pdb=" O ASP S 296 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N MET S 342 " --> pdb=" O LEU S 202 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N THR S 346 " --> pdb=" O PHE S 206 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N PHE S 343 " --> pdb=" O PHE S 374 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ASP S 376 " --> pdb=" O PHE S 343 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N PHE S 345 " --> pdb=" O ASP S 376 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE S 404 " --> pdb=" O PHE S 453 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N THR S 455 " --> pdb=" O ILE S 404 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL S 406 " --> pdb=" O THR S 455 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'S' and resid 218 through 219 Processing sheet with id=AG5, first strand: chain 'T' and resid 48 through 49 removed outlier: 3.813A pdb=" N LYS T 48 " --> pdb=" O ARG T 113 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP T 83 " --> pdb=" O LYS T 135 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU T 89 " --> pdb=" O SER T 129 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N SER T 129 " --> pdb=" O GLU T 89 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'T' and resid 75 through 80 removed outlier: 3.727A pdb=" N TRP T 78 " --> pdb=" O ALA T 120 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA T 120 " --> pdb=" O TRP T 78 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL T 93 " --> pdb=" O PHE T 106 " (cutoff:3.500A) 2425 hydrogen bonds defined for protein. 6747 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 97 hydrogen bonds 194 hydrogen bond angles 0 basepair planarities 37 basepair parallelities 56 stacking parallelities Total time for adding SS restraints: 28.98 Time building geometry restraints manager: 12.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 18400 1.34 - 1.46: 10543 1.46 - 1.58: 28952 1.58 - 1.70: 157 1.70 - 1.82: 444 Bond restraints: 58496 Sorted by residual: bond pdb=" C2 SAH L8001 " pdb=" N3 SAH L8001 " ideal model delta sigma weight residual 1.322 1.380 -0.058 2.00e-02 2.50e+03 8.37e+00 bond pdb=" C8 SAH L8001 " pdb=" N7 SAH L8001 " ideal model delta sigma weight residual 1.299 1.351 -0.052 2.00e-02 2.50e+03 6.88e+00 bond pdb=" C2 SAH L8001 " pdb=" N1 SAH L8001 " ideal model delta sigma weight residual 1.330 1.379 -0.049 2.00e-02 2.50e+03 6.09e+00 bond pdb=" C6 SAH L8001 " pdb=" N1 SAH L8001 " ideal model delta sigma weight residual 1.338 1.377 -0.039 2.00e-02 2.50e+03 3.75e+00 bond pdb=" CG ARG H 519 " pdb=" CD ARG H 519 " ideal model delta sigma weight residual 1.520 1.467 0.053 3.00e-02 1.11e+03 3.10e+00 ... (remaining 58491 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 78656 2.21 - 4.42: 655 4.42 - 6.63: 86 6.63 - 8.84: 18 8.84 - 11.05: 4 Bond angle restraints: 79419 Sorted by residual: angle pdb=" CA GLU F 365 " pdb=" CB GLU F 365 " pdb=" CG GLU F 365 " ideal model delta sigma weight residual 114.10 123.74 -9.64 2.00e+00 2.50e-01 2.32e+01 angle pdb=" C CYS G 599 " pdb=" N MET G 600 " pdb=" CA MET G 600 " ideal model delta sigma weight residual 121.58 113.10 8.48 1.95e+00 2.63e-01 1.89e+01 angle pdb=" CG SAH L8001 " pdb=" SD SAH L8001 " pdb=" C5' SAH L8001 " ideal model delta sigma weight residual 101.77 90.72 11.05 3.00e+00 1.11e-01 1.36e+01 angle pdb=" N GLU F 365 " pdb=" CA GLU F 365 " pdb=" CB GLU F 365 " ideal model delta sigma weight residual 114.27 108.63 5.64 1.64e+00 3.72e-01 1.18e+01 angle pdb=" CB LYS Q 675 " pdb=" CG LYS Q 675 " pdb=" CD LYS Q 675 " ideal model delta sigma weight residual 111.30 119.01 -7.71 2.30e+00 1.89e-01 1.12e+01 ... (remaining 79414 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.48: 32453 27.48 - 54.96: 2332 54.96 - 82.45: 267 82.45 - 109.93: 30 109.93 - 137.41: 1 Dihedral angle restraints: 35083 sinusoidal: 15256 harmonic: 19827 Sorted by residual: dihedral pdb=" CA ILE E1182 " pdb=" C ILE E1182 " pdb=" N PRO E1183 " pdb=" CA PRO E1183 " ideal model delta harmonic sigma weight residual 180.00 -141.18 -38.82 0 5.00e+00 4.00e-02 6.03e+01 dihedral pdb=" CA LEU S 314 " pdb=" C LEU S 314 " pdb=" N LYS S 315 " pdb=" CA LYS S 315 " ideal model delta harmonic sigma weight residual 180.00 157.12 22.88 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA ASP L 246 " pdb=" C ASP L 246 " pdb=" N ALA L 247 " pdb=" CA ALA L 247 " ideal model delta harmonic sigma weight residual -180.00 -157.85 -22.15 0 5.00e+00 4.00e-02 1.96e+01 ... (remaining 35080 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 6402 0.041 - 0.082: 1561 0.082 - 0.123: 611 0.123 - 0.164: 34 0.164 - 0.205: 4 Chirality restraints: 8612 Sorted by residual: chirality pdb=" CA PRO E1183 " pdb=" N PRO E1183 " pdb=" C PRO E1183 " pdb=" CB PRO E1183 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CG LEU G 497 " pdb=" CB LEU G 497 " pdb=" CD1 LEU G 497 " pdb=" CD2 LEU G 497 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.30e-01 chirality pdb=" CA MET G 600 " pdb=" N MET G 600 " pdb=" C MET G 600 " pdb=" CB MET G 600 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.88e-01 ... (remaining 8609 not shown) Planarity restraints: 9969 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 625 " 0.074 5.00e-02 4.00e+02 1.11e-01 1.96e+01 pdb=" N PRO C 626 " -0.191 5.00e-02 4.00e+02 pdb=" CA PRO C 626 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO C 626 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU F 365 " 0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C GLU F 365 " -0.056 2.00e-02 2.50e+03 pdb=" O GLU F 365 " 0.021 2.00e-02 2.50e+03 pdb=" N ASP F 366 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 652 " -0.017 2.00e-02 2.50e+03 1.50e-02 4.49e+00 pdb=" CG TYR G 652 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR G 652 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR G 652 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR G 652 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR G 652 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR G 652 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR G 652 " -0.002 2.00e-02 2.50e+03 ... (remaining 9966 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 584 2.56 - 3.15: 43944 3.15 - 3.73: 93695 3.73 - 4.32: 134915 4.32 - 4.90: 218156 Nonbonded interactions: 491294 Sorted by model distance: nonbonded pdb=" OD1 ASP D 491 " pdb="MG MG D 701 " model vdw 1.980 2.170 nonbonded pdb=" OD1 ASP D 489 " pdb="MG MG D 701 " model vdw 1.996 2.170 nonbonded pdb=" OD1 ASP D 493 " pdb="MG MG D 701 " model vdw 2.049 2.170 nonbonded pdb=" OD2 ASP I 211 " pdb="FE FE I8001 " model vdw 2.070 2.260 nonbonded pdb=" OD2 ASP N 223 " pdb="FE FE N8001 " model vdw 2.097 2.260 ... (remaining 491289 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'O' and resid 78 through 185) selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 16.440 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: 0.040 Extract box with map and model: 2.980 Check model and map are aligned: 0.330 Set scattering table: 0.400 Process input model: 124.990 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:10.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 156.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 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 : 0.003 0.073 58496 Z= 0.171 Angle : 0.514 11.046 79419 Z= 0.265 Chirality : 0.041 0.205 8612 Planarity : 0.004 0.111 9969 Dihedral : 17.476 137.411 22279 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.05 % Favored : 96.89 % Rotamer: Outliers : 0.93 % Allowed : 19.19 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.29 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.10), residues: 6685 helix: 1.08 (0.10), residues: 2752 sheet: 0.24 (0.17), residues: 868 loop : -0.05 (0.11), residues: 3065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP H 517 HIS 0.005 0.001 HIS F 344 PHE 0.017 0.001 PHE I 172 TYR 0.037 0.001 TYR G 652 ARG 0.015 0.000 ARG C 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13370 Ramachandran restraints generated. 6685 Oldfield, 0 Emsley, 6685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13370 Ramachandran restraints generated. 6685 Oldfield, 0 Emsley, 6685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 997 residues out of total 6021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 941 time to evaluate : 4.861 Fit side-chains revert: symmetry clash REVERT: A 74 TYR cc_start: 0.7691 (m-80) cc_final: 0.7428 (m-80) REVERT: A 141 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8296 (pt0) REVERT: A 143 ILE cc_start: 0.7894 (mp) cc_final: 0.7471 (tp) REVERT: A 289 LYS cc_start: 0.7724 (ptpp) cc_final: 0.7518 (ptpp) REVERT: B 86 GLU cc_start: 0.8498 (mm-30) cc_final: 0.7815 (tm-30) REVERT: B 150 LYS cc_start: 0.8315 (ttpt) cc_final: 0.7831 (tppp) REVERT: C 506 GLU cc_start: 0.7292 (pm20) cc_final: 0.7073 (pm20) REVERT: C 612 MET cc_start: 0.7316 (mtm) cc_final: 0.6999 (mtm) REVERT: C 614 GLN cc_start: 0.7756 (mm-40) cc_final: 0.7535 (mm110) REVERT: C 729 MET cc_start: 0.6612 (mtm) cc_final: 0.6188 (mtp) REVERT: C 940 GLN cc_start: 0.8777 (mm110) cc_final: 0.8473 (mm110) REVERT: C 977 ARG cc_start: 0.8193 (ttt180) cc_final: 0.7859 (ttt90) REVERT: C 1020 GLU cc_start: 0.7578 (mm-30) cc_final: 0.7297 (mp0) REVERT: C 1035 GLU cc_start: 0.7809 (tt0) cc_final: 0.7592 (mt-10) REVERT: D 349 HIS cc_start: 0.7612 (m170) cc_final: 0.7381 (m170) REVERT: E 405 LYS cc_start: 0.8056 (mmmt) cc_final: 0.7698 (mmtm) REVERT: E 572 ARG cc_start: 0.7071 (ttm170) cc_final: 0.6705 (ttm170) REVERT: E 804 GLU cc_start: 0.7235 (mt-10) cc_final: 0.6734 (pt0) REVERT: E 841 LEU cc_start: 0.7258 (tt) cc_final: 0.6950 (pt) REVERT: E 1151 GLN cc_start: 0.8477 (tt0) cc_final: 0.8248 (pt0) REVERT: E 1182 ILE cc_start: 0.7555 (pp) cc_final: 0.7113 (pt) REVERT: F 407 ARG cc_start: 0.7544 (tpt170) cc_final: 0.7289 (tpm-80) REVERT: G 643 ASP cc_start: 0.7504 (m-30) cc_final: 0.7223 (m-30) REVERT: G 658 ASN cc_start: 0.6974 (t0) cc_final: 0.6745 (t0) REVERT: G 694 LYS cc_start: 0.6366 (pttt) cc_final: 0.5594 (tppt) REVERT: H 525 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8037 (tp30) REVERT: H 535 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7749 (mp10) REVERT: I 141 MET cc_start: 0.6708 (mmm) cc_final: 0.6476 (tpp) REVERT: I 143 ILE cc_start: 0.7701 (OUTLIER) cc_final: 0.7421 (tp) REVERT: I 146 VAL cc_start: 0.8152 (t) cc_final: 0.7939 (m) REVERT: J 274 LYS cc_start: 0.8570 (mmmm) cc_final: 0.8369 (tptp) REVERT: J 416 MET cc_start: 0.9062 (tpt) cc_final: 0.8822 (tpt) REVERT: K 314 ARG cc_start: 0.7828 (ttp80) cc_final: 0.7605 (ttp80) REVERT: K 410 MET cc_start: 0.7997 (mtp) cc_final: 0.7786 (mtp) REVERT: L 192 ASP cc_start: 0.8235 (OUTLIER) cc_final: 0.7960 (p0) REVERT: L 463 ARG cc_start: 0.8399 (ttt180) cc_final: 0.8159 (ttt-90) REVERT: M 169 MET cc_start: 0.8262 (mtp) cc_final: 0.7890 (mtm) REVERT: M 176 THR cc_start: 0.8750 (m) cc_final: 0.8462 (p) REVERT: N 64 MET cc_start: 0.6449 (ttt) cc_final: 0.6232 (mtp) REVERT: O 94 GLU cc_start: 0.7952 (tp30) cc_final: 0.7573 (tp30) REVERT: Q 632 MET cc_start: 0.4842 (mpt) cc_final: 0.4339 (mtm) REVERT: R 113 LYS cc_start: 0.8259 (mttp) cc_final: 0.8059 (ttmm) outliers start: 56 outliers final: 29 residues processed: 987 average time/residue: 1.5277 time to fit residues: 1879.6634 Evaluate side-chains 795 residues out of total 6021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 762 time to evaluate : 4.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain B residue 109 CYS Chi-restraints excluded: chain C residue 659 VAL Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 1021 VAL Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 515 SER Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain F residue 412 LEU Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain G residue 480 THR Chi-restraints excluded: chain G residue 579 CYS Chi-restraints excluded: chain G residue 708 VAL Chi-restraints excluded: chain G residue 711 VAL Chi-restraints excluded: chain H residue 516 HIS Chi-restraints excluded: chain H residue 525 GLU Chi-restraints excluded: chain H residue 535 GLN Chi-restraints excluded: chain I residue 143 ILE Chi-restraints excluded: chain J residue 335 THR Chi-restraints excluded: chain L residue 192 ASP Chi-restraints excluded: chain L residue 303 ILE Chi-restraints excluded: chain N residue 63 HIS Chi-restraints excluded: chain N residue 158 VAL Chi-restraints excluded: chain Q residue 579 LEU Chi-restraints excluded: chain Q residue 595 THR Chi-restraints excluded: chain Q residue 633 THR Chi-restraints excluded: chain Q residue 669 THR Chi-restraints excluded: chain S residue 273 ASP Chi-restraints excluded: chain S residue 334 VAL Chi-restraints excluded: chain T residue 133 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 682 random chunks: chunk 575 optimal weight: 0.9990 chunk 516 optimal weight: 0.9990 chunk 286 optimal weight: 9.9990 chunk 176 optimal weight: 9.9990 chunk 348 optimal weight: 7.9990 chunk 276 optimal weight: 0.0050 chunk 534 optimal weight: 10.0000 chunk 206 optimal weight: 3.9990 chunk 325 optimal weight: 3.9990 chunk 397 optimal weight: 50.0000 chunk 619 optimal weight: 4.9990 overall best weight: 2.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 ASN A 193 ASN A 276 GLN A 303 GLN B 14 GLN B 76 ASN B 196 GLN C 58 GLN C 414 HIS C 516 HIS C 542 ASN C 551 GLN C 623 HIS C 624 GLN C 812 GLN C 867 GLN C 974 GLN C 982 GLN C1014 HIS C1057 HIS C1068 ASN D 128 ASN D 464 GLN D 670 GLN E 90 ASN E 378 HIS E 922 HIS E1011 ASN E1020 HIS E1038 ASN E1053 GLN E1291 GLN F 84 ASN F 270 ASN F 363 ASN F 788 GLN ** G 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 628 ASN G 630 HIS G 640 ASN ** H 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 149 GLN I 171 GLN J 329 GLN J 415 ASN K 110 HIS K 112 ASN K 328 GLN K 414 GLN L 220 GLN L 233 HIS M 142 HIS M 190 GLN ** O 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 183 ASN P 88 GLN P 147 GLN Q 725 GLN Q 745 GLN R 71 GLN S 195 HIS S 284 ASN S 371 ASN S 395 GLN S 510 ASN S 562 ASN T 81 GLN T 84 GLN Total number of N/Q/H flips: 65 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 58496 Z= 0.237 Angle : 0.571 10.576 79419 Z= 0.302 Chirality : 0.044 0.231 8612 Planarity : 0.005 0.070 9969 Dihedral : 11.476 139.543 8481 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.46 % Favored : 96.50 % Rotamer: Outliers : 3.50 % Allowed : 17.49 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.29 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.10), residues: 6685 helix: 1.12 (0.10), residues: 2831 sheet: 0.22 (0.17), residues: 826 loop : -0.06 (0.11), residues: 3028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP G 678 HIS 0.008 0.001 HIS F 487 PHE 0.021 0.001 PHE D 187 TYR 0.033 0.001 TYR G 652 ARG 0.009 0.000 ARG S 231 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13370 Ramachandran restraints generated. 6685 Oldfield, 0 Emsley, 6685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13370 Ramachandran restraints generated. 6685 Oldfield, 0 Emsley, 6685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1040 residues out of total 6021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 829 time to evaluate : 4.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 MET cc_start: 0.8273 (OUTLIER) cc_final: 0.7746 (mtm) REVERT: A 111 GLN cc_start: 0.7711 (OUTLIER) cc_final: 0.7458 (tt0) REVERT: A 141 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8310 (pt0) REVERT: B 38 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8224 (mtt) REVERT: B 119 ARG cc_start: 0.7774 (ttm110) cc_final: 0.7559 (ttp80) REVERT: B 150 LYS cc_start: 0.8679 (ttpt) cc_final: 0.8096 (tppp) REVERT: C 313 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7202 (ptp90) REVERT: C 495 GLU cc_start: 0.8341 (mp0) cc_final: 0.7941 (mp0) REVERT: C 506 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7197 (pm20) REVERT: C 596 LYS cc_start: 0.7795 (OUTLIER) cc_final: 0.7396 (pttt) REVERT: C 612 MET cc_start: 0.7475 (mtm) cc_final: 0.7195 (mtm) REVERT: C 729 MET cc_start: 0.6934 (OUTLIER) cc_final: 0.6481 (mtp) REVERT: C 970 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8538 (tt) REVERT: C 977 ARG cc_start: 0.8248 (ttt180) cc_final: 0.7847 (ttt90) REVERT: C 1035 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7536 (mt-10) REVERT: C 1063 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8082 (mmpt) REVERT: D 147 PHE cc_start: 0.7422 (t80) cc_final: 0.7157 (t80) REVERT: D 397 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.8921 (mp) REVERT: D 595 ARG cc_start: 0.8450 (mtt-85) cc_final: 0.8181 (mtt-85) REVERT: E 572 ARG cc_start: 0.7080 (OUTLIER) cc_final: 0.6737 (ttm170) REVERT: E 841 LEU cc_start: 0.6728 (OUTLIER) cc_final: 0.6429 (pt) REVERT: E 1131 THR cc_start: 0.8679 (OUTLIER) cc_final: 0.8273 (t) REVERT: F 407 ARG cc_start: 0.7711 (tpt170) cc_final: 0.7452 (tpm-80) REVERT: F 488 ARG cc_start: 0.6325 (OUTLIER) cc_final: 0.4580 (mmp-170) REVERT: G 472 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.7145 (pp20) REVERT: G 596 MET cc_start: 0.5461 (mpm) cc_final: 0.5143 (mtm) REVERT: G 643 ASP cc_start: 0.7508 (m-30) cc_final: 0.7236 (m-30) REVERT: G 658 ASN cc_start: 0.7031 (t0) cc_final: 0.6805 (t0) REVERT: H 525 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8003 (tp30) REVERT: I 143 ILE cc_start: 0.7791 (OUTLIER) cc_final: 0.7388 (tp) REVERT: J 317 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8491 (ptpp) REVERT: M 169 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.8175 (mtm) REVERT: M 176 THR cc_start: 0.8746 (m) cc_final: 0.8317 (p) REVERT: M 221 GLU cc_start: 0.7717 (pp20) cc_final: 0.7509 (pp20) REVERT: N 64 MET cc_start: 0.6557 (ttt) cc_final: 0.6331 (mtp) REVERT: O 94 GLU cc_start: 0.7949 (tp30) cc_final: 0.7516 (tp30) REVERT: O 131 ILE cc_start: 0.9155 (OUTLIER) cc_final: 0.8795 (mm) REVERT: O 160 ASP cc_start: 0.7640 (t0) cc_final: 0.7301 (t0) REVERT: P 86 GLU cc_start: 0.7239 (tm-30) cc_final: 0.7018 (tm-30) REVERT: P 90 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7610 (mm) REVERT: R 113 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7989 (ttmm) REVERT: R 122 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.7933 (ttmt) REVERT: S 229 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.8448 (tt0) outliers start: 211 outliers final: 58 residues processed: 963 average time/residue: 1.4840 time to fit residues: 1792.2956 Evaluate side-chains 822 residues out of total 6021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 739 time to evaluate : 4.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 38 MET Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 367 SER Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 505 GLN Chi-restraints excluded: chain C residue 506 GLU Chi-restraints excluded: chain C residue 596 LYS Chi-restraints excluded: chain C residue 729 MET Chi-restraints excluded: chain C residue 939 GLU Chi-restraints excluded: chain C residue 956 VAL Chi-restraints excluded: chain C residue 970 LEU Chi-restraints excluded: chain C residue 1021 VAL Chi-restraints excluded: chain C residue 1035 GLU Chi-restraints excluded: chain C residue 1063 LYS Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 517 MET Chi-restraints excluded: chain D residue 638 LEU Chi-restraints excluded: chain D residue 645 LYS Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 572 ARG Chi-restraints excluded: chain E residue 841 LEU Chi-restraints excluded: chain E residue 928 PHE Chi-restraints excluded: chain E residue 945 ASN Chi-restraints excluded: chain E residue 1131 THR Chi-restraints excluded: chain E residue 1177 THR Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 488 ARG Chi-restraints excluded: chain F residue 804 GLU Chi-restraints excluded: chain F residue 836 THR Chi-restraints excluded: chain G residue 463 GLU Chi-restraints excluded: chain G residue 472 GLU Chi-restraints excluded: chain G residue 517 VAL Chi-restraints excluded: chain G residue 527 THR Chi-restraints excluded: chain G residue 533 GLU Chi-restraints excluded: chain G residue 549 VAL Chi-restraints excluded: chain G residue 551 MET Chi-restraints excluded: chain G residue 579 CYS Chi-restraints excluded: chain G residue 732 LEU Chi-restraints excluded: chain H residue 516 HIS Chi-restraints excluded: chain H residue 525 GLU Chi-restraints excluded: chain H residue 527 LEU Chi-restraints excluded: chain I residue 143 ILE Chi-restraints excluded: chain I residue 197 ILE Chi-restraints excluded: chain J residue 317 LYS Chi-restraints excluded: chain J residue 335 THR Chi-restraints excluded: chain K residue 180 THR Chi-restraints excluded: chain K residue 284 LEU Chi-restraints excluded: chain K residue 390 THR Chi-restraints excluded: chain L residue 303 ILE Chi-restraints excluded: chain M residue 136 ILE Chi-restraints excluded: chain M residue 169 MET Chi-restraints excluded: chain M residue 261 THR Chi-restraints excluded: chain M residue 301 ASP Chi-restraints excluded: chain N residue 144 LEU Chi-restraints excluded: chain N residue 158 VAL Chi-restraints excluded: chain N residue 203 VAL Chi-restraints excluded: chain O residue 124 GLU Chi-restraints excluded: chain O residue 131 ILE Chi-restraints excluded: chain P residue 89 ASP Chi-restraints excluded: chain P residue 90 LEU Chi-restraints excluded: chain P residue 120 MET Chi-restraints excluded: chain Q residue 595 THR Chi-restraints excluded: chain Q residue 633 THR Chi-restraints excluded: chain Q residue 643 THR Chi-restraints excluded: chain Q residue 713 MET Chi-restraints excluded: chain R residue 113 LYS Chi-restraints excluded: chain R residue 122 LYS Chi-restraints excluded: chain S residue 229 GLN Chi-restraints excluded: chain S residue 297 SER Chi-restraints excluded: chain T residue 122 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 682 random chunks: chunk 344 optimal weight: 20.0000 chunk 192 optimal weight: 0.8980 chunk 515 optimal weight: 9.9990 chunk 421 optimal weight: 9.9990 chunk 170 optimal weight: 6.9990 chunk 620 optimal weight: 3.9990 chunk 670 optimal weight: 9.9990 chunk 552 optimal weight: 4.9990 chunk 615 optimal weight: 9.9990 chunk 211 optimal weight: 4.9990 chunk 497 optimal weight: 7.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 58 GLN C 116 ASN C 542 ASN C 883 HIS C 982 GLN C1068 ASN D 583 ASN D 670 GLN D 674 GLN E 87 HIS E1020 HIS ** E1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 116 HIS ** G 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 628 ASN ** H 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 126 ASN I 149 GLN I 171 GLN ** I 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 58496 Z= 0.408 Angle : 0.644 12.701 79419 Z= 0.337 Chirality : 0.047 0.200 8612 Planarity : 0.005 0.060 9969 Dihedral : 11.652 137.172 8451 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.90 % Favored : 96.04 % Rotamer: Outliers : 4.17 % Allowed : 17.86 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.29 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.10), residues: 6685 helix: 0.88 (0.10), residues: 2841 sheet: 0.08 (0.17), residues: 846 loop : -0.27 (0.11), residues: 2998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP K 127 HIS 0.014 0.001 HIS F 487 PHE 0.030 0.002 PHE B 226 TYR 0.023 0.002 TYR G 652 ARG 0.010 0.001 ARG S 231 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13370 Ramachandran restraints generated. 6685 Oldfield, 0 Emsley, 6685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13370 Ramachandran restraints generated. 6685 Oldfield, 0 Emsley, 6685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1038 residues out of total 6021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 251 poor density : 787 time to evaluate : 5.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 119 ARG cc_start: 0.7962 (ttm110) cc_final: 0.7740 (ttp80) REVERT: C 108 ASN cc_start: 0.7565 (t0) cc_final: 0.7353 (t0) REVERT: C 313 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.7353 (ptp90) REVERT: C 471 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8725 (mp) REVERT: C 495 GLU cc_start: 0.8554 (mp0) cc_final: 0.7947 (mp0) REVERT: C 1020 GLU cc_start: 0.7917 (mp0) cc_final: 0.7486 (mp0) REVERT: C 1063 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8284 (mmpt) REVERT: D 14 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8481 (tt) REVERT: D 147 PHE cc_start: 0.7664 (t80) cc_final: 0.7325 (t80) REVERT: D 442 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.8386 (pp30) REVERT: D 595 ARG cc_start: 0.8446 (mtt-85) cc_final: 0.8008 (mtt-85) REVERT: D 663 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.8229 (mmm-85) REVERT: D 666 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.7977 (tm-30) REVERT: E 576 ARG cc_start: 0.7348 (OUTLIER) cc_final: 0.7139 (ttp-170) REVERT: F 203 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.7983 (mpt-90) REVERT: F 407 ARG cc_start: 0.7809 (tpt170) cc_final: 0.7506 (tpm-80) REVERT: F 418 GLU cc_start: 0.5768 (OUTLIER) cc_final: 0.5490 (pt0) REVERT: F 452 ARG cc_start: 0.8178 (tpp80) cc_final: 0.7944 (tpp80) REVERT: F 488 ARG cc_start: 0.6518 (OUTLIER) cc_final: 0.4782 (mmp-170) REVERT: G 596 MET cc_start: 0.5712 (mpm) cc_final: 0.5357 (mtm) REVERT: G 621 MET cc_start: 0.5975 (tpt) cc_final: 0.5627 (tmt) REVERT: H 318 ARG cc_start: 0.8033 (ptp90) cc_final: 0.7588 (mtm-85) REVERT: H 542 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7108 (mt-10) REVERT: I 95 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.7516 (ttm-80) REVERT: I 143 ILE cc_start: 0.7810 (OUTLIER) cc_final: 0.7537 (tp) REVERT: I 243 MET cc_start: 0.8063 (tpp) cc_final: 0.7691 (mmt) REVERT: L 160 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7971 (ptt180) REVERT: L 440 GLN cc_start: 0.8603 (tp40) cc_final: 0.8263 (tp-100) REVERT: L 444 ASP cc_start: 0.8224 (m-30) cc_final: 0.7651 (m-30) REVERT: N 63 HIS cc_start: 0.5556 (OUTLIER) cc_final: 0.5254 (m90) REVERT: N 252 GLU cc_start: 0.6823 (OUTLIER) cc_final: 0.6621 (tt0) REVERT: N 268 ARG cc_start: 0.7091 (OUTLIER) cc_final: 0.6722 (mtp180) REVERT: O 94 GLU cc_start: 0.7920 (tp30) cc_final: 0.7594 (tp30) REVERT: O 141 GLU cc_start: 0.8167 (mp0) cc_final: 0.7880 (pm20) REVERT: R 38 ARG cc_start: 0.6134 (mtm180) cc_final: 0.5888 (mtm-85) REVERT: R 122 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.7907 (tttt) REVERT: S 229 GLN cc_start: 0.8889 (OUTLIER) cc_final: 0.8383 (tt0) REVERT: S 386 SER cc_start: 0.7781 (t) cc_final: 0.7580 (t) outliers start: 251 outliers final: 80 residues processed: 949 average time/residue: 1.4942 time to fit residues: 1783.6510 Evaluate side-chains 822 residues out of total 6021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 722 time to evaluate : 4.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 109 CYS Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 367 SER Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 505 GLN Chi-restraints excluded: chain C residue 506 GLU Chi-restraints excluded: chain C residue 729 MET Chi-restraints excluded: chain C residue 923 TYR Chi-restraints excluded: chain C residue 939 GLU Chi-restraints excluded: chain C residue 956 VAL Chi-restraints excluded: chain C residue 1021 VAL Chi-restraints excluded: chain C residue 1024 THR Chi-restraints excluded: chain C residue 1063 LYS Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 442 GLN Chi-restraints excluded: chain D residue 517 MET Chi-restraints excluded: chain D residue 645 LYS Chi-restraints excluded: chain D residue 663 ARG Chi-restraints excluded: chain D residue 666 GLU Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 388 SER Chi-restraints excluded: chain E residue 469 LEU Chi-restraints excluded: chain E residue 576 ARG Chi-restraints excluded: chain E residue 808 ILE Chi-restraints excluded: chain E residue 901 MET Chi-restraints excluded: chain E residue 928 PHE Chi-restraints excluded: chain E residue 995 LEU Chi-restraints excluded: chain E residue 997 THR Chi-restraints excluded: chain E residue 1003 VAL Chi-restraints excluded: chain E residue 1056 ASN Chi-restraints excluded: chain E residue 1177 THR Chi-restraints excluded: chain E residue 1194 ILE Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 203 ARG Chi-restraints excluded: chain F residue 337 VAL Chi-restraints excluded: chain F residue 385 ILE Chi-restraints excluded: chain F residue 412 LEU Chi-restraints excluded: chain F residue 416 TRP Chi-restraints excluded: chain F residue 418 GLU Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain F residue 488 ARG Chi-restraints excluded: chain F residue 836 THR Chi-restraints excluded: chain G residue 517 VAL Chi-restraints excluded: chain G residue 527 THR Chi-restraints excluded: chain G residue 533 GLU Chi-restraints excluded: chain G residue 549 VAL Chi-restraints excluded: chain G residue 579 CYS Chi-restraints excluded: chain G residue 732 LEU Chi-restraints excluded: chain G residue 822 THR Chi-restraints excluded: chain H residue 516 HIS Chi-restraints excluded: chain H residue 542 GLU Chi-restraints excluded: chain I residue 95 ARG Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 143 ILE Chi-restraints excluded: chain I residue 208 ILE Chi-restraints excluded: chain J residue 335 THR Chi-restraints excluded: chain K residue 88 ASP Chi-restraints excluded: chain K residue 180 THR Chi-restraints excluded: chain K residue 257 SER Chi-restraints excluded: chain K residue 259 LYS Chi-restraints excluded: chain K residue 390 THR Chi-restraints excluded: chain L residue 160 ARG Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain L residue 303 ILE Chi-restraints excluded: chain M residue 136 ILE Chi-restraints excluded: chain M residue 183 ARG Chi-restraints excluded: chain M residue 330 VAL Chi-restraints excluded: chain N residue 63 HIS Chi-restraints excluded: chain N residue 144 LEU Chi-restraints excluded: chain N residue 158 VAL Chi-restraints excluded: chain N residue 203 VAL Chi-restraints excluded: chain N residue 252 GLU Chi-restraints excluded: chain N residue 268 ARG Chi-restraints excluded: chain O residue 124 GLU Chi-restraints excluded: chain Q residue 595 THR Chi-restraints excluded: chain Q residue 633 THR Chi-restraints excluded: chain Q residue 713 MET Chi-restraints excluded: chain Q residue 715 VAL Chi-restraints excluded: chain Q residue 757 THR Chi-restraints excluded: chain R residue 113 LYS Chi-restraints excluded: chain R residue 114 ASN Chi-restraints excluded: chain R residue 121 THR Chi-restraints excluded: chain R residue 122 LYS Chi-restraints excluded: chain R residue 139 ASP Chi-restraints excluded: chain S residue 229 GLN Chi-restraints excluded: chain S residue 272 ASP Chi-restraints excluded: chain S residue 334 VAL Chi-restraints excluded: chain T residue 85 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 682 random chunks: chunk 613 optimal weight: 0.5980 chunk 466 optimal weight: 9.9990 chunk 322 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 chunk 296 optimal weight: 3.9990 chunk 416 optimal weight: 5.9990 chunk 622 optimal weight: 0.6980 chunk 659 optimal weight: 0.7980 chunk 325 optimal weight: 7.9990 chunk 590 optimal weight: 0.7980 chunk 177 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 ASN C 58 GLN C 124 ASN C 542 ASN C1068 ASN D 583 ASN E 310 HIS E1038 ASN E1151 GLN E1206 GLN ** G 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 166 ASN I 171 GLN ** I 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 223 ASN M 161 ASN ** O 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 88 GLN ** T 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 58496 Z= 0.157 Angle : 0.524 14.477 79419 Z= 0.275 Chirality : 0.042 0.230 8612 Planarity : 0.004 0.048 9969 Dihedral : 11.494 146.839 8448 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.01 % Favored : 96.95 % Rotamer: Outliers : 2.81 % Allowed : 19.30 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.29 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.10), residues: 6685 helix: 1.22 (0.10), residues: 2850 sheet: 0.23 (0.18), residues: 804 loop : -0.13 (0.11), residues: 3031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP T 69 HIS 0.006 0.001 HIS F 487 PHE 0.020 0.001 PHE D 157 TYR 0.030 0.001 TYR Q 673 ARG 0.008 0.000 ARG D 239 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13370 Ramachandran restraints generated. 6685 Oldfield, 0 Emsley, 6685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13370 Ramachandran restraints generated. 6685 Oldfield, 0 Emsley, 6685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 955 residues out of total 6021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 786 time to evaluate : 4.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8369 (tm) REVERT: B 66 LYS cc_start: 0.8559 (tttm) cc_final: 0.8307 (tptt) REVERT: B 97 LYS cc_start: 0.9086 (OUTLIER) cc_final: 0.8838 (ptmm) REVERT: B 119 ARG cc_start: 0.7950 (ttm110) cc_final: 0.7745 (ttp80) REVERT: C 108 ASN cc_start: 0.7542 (t0) cc_final: 0.7301 (t0) REVERT: C 313 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7300 (ptp90) REVERT: C 495 GLU cc_start: 0.8440 (mp0) cc_final: 0.7824 (mp0) REVERT: C 1020 GLU cc_start: 0.7822 (mp0) cc_final: 0.7385 (mp0) REVERT: C 1063 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8222 (mmpt) REVERT: D 188 ARG cc_start: 0.7172 (tpt-90) cc_final: 0.6735 (ttt90) REVERT: D 397 LEU cc_start: 0.9460 (OUTLIER) cc_final: 0.9031 (mp) REVERT: D 442 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.8345 (pp30) REVERT: D 595 ARG cc_start: 0.8456 (mtt-85) cc_final: 0.8005 (mtt-85) REVERT: E 84 LYS cc_start: 0.8523 (mmmt) cc_final: 0.8237 (tptm) REVERT: E 405 LYS cc_start: 0.8302 (mppt) cc_final: 0.8037 (mmmt) REVERT: F 167 MET cc_start: 0.8594 (OUTLIER) cc_final: 0.8345 (ttt) REVERT: F 407 ARG cc_start: 0.7726 (tpt170) cc_final: 0.7496 (tpm-80) REVERT: G 596 MET cc_start: 0.5496 (OUTLIER) cc_final: 0.5211 (mtm) REVERT: G 621 MET cc_start: 0.5923 (tpt) cc_final: 0.5723 (tmt) REVERT: G 693 THR cc_start: 0.7049 (OUTLIER) cc_final: 0.6765 (m) REVERT: H 222 PHE cc_start: 0.7864 (t80) cc_final: 0.7479 (t80) REVERT: H 318 ARG cc_start: 0.7970 (ptp90) cc_final: 0.7542 (mtt90) REVERT: H 473 ASP cc_start: 0.7748 (t0) cc_final: 0.6896 (p0) REVERT: H 542 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.6984 (mt-10) REVERT: I 143 ILE cc_start: 0.7796 (OUTLIER) cc_final: 0.7482 (tp) REVERT: I 243 MET cc_start: 0.8019 (tpp) cc_final: 0.7685 (mmt) REVERT: J 274 LYS cc_start: 0.8595 (tptp) cc_final: 0.8318 (mmpt) REVERT: L 218 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.8410 (mpp80) REVERT: L 374 GLU cc_start: 0.8302 (pt0) cc_final: 0.8041 (pp20) REVERT: M 286 ASP cc_start: 0.8469 (m-30) cc_final: 0.8214 (m-30) REVERT: N 63 HIS cc_start: 0.5417 (OUTLIER) cc_final: 0.5104 (m90) REVERT: N 129 GLU cc_start: 0.7373 (mm-30) cc_final: 0.7026 (mm-30) REVERT: N 268 ARG cc_start: 0.7029 (OUTLIER) cc_final: 0.6599 (mtp-110) REVERT: O 141 GLU cc_start: 0.8179 (mp0) cc_final: 0.7858 (pm20) REVERT: P 86 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.7154 (tm-30) REVERT: S 229 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.8365 (tt0) REVERT: S 486 ASP cc_start: 0.8734 (OUTLIER) cc_final: 0.8527 (p0) REVERT: T 89 GLU cc_start: 0.7073 (pm20) cc_final: 0.6788 (pm20) outliers start: 169 outliers final: 45 residues processed: 891 average time/residue: 1.5512 time to fit residues: 1723.2666 Evaluate side-chains 787 residues out of total 6021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 725 time to evaluate : 4.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 367 SER Chi-restraints excluded: chain C residue 505 GLN Chi-restraints excluded: chain C residue 506 GLU Chi-restraints excluded: chain C residue 923 TYR Chi-restraints excluded: chain C residue 943 ILE Chi-restraints excluded: chain C residue 1021 VAL Chi-restraints excluded: chain C residue 1063 LYS Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 442 GLN Chi-restraints excluded: chain D residue 517 MET Chi-restraints excluded: chain D residue 645 LYS Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 358 TYR Chi-restraints excluded: chain E residue 995 LEU Chi-restraints excluded: chain E residue 1056 ASN Chi-restraints excluded: chain E residue 1361 ILE Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 167 MET Chi-restraints excluded: chain G residue 517 VAL Chi-restraints excluded: chain G residue 533 GLU Chi-restraints excluded: chain G residue 549 VAL Chi-restraints excluded: chain G residue 579 CYS Chi-restraints excluded: chain G residue 596 MET Chi-restraints excluded: chain G residue 693 THR Chi-restraints excluded: chain H residue 516 HIS Chi-restraints excluded: chain H residue 525 GLU Chi-restraints excluded: chain H residue 542 GLU Chi-restraints excluded: chain I residue 93 ASP Chi-restraints excluded: chain I residue 143 ILE Chi-restraints excluded: chain I residue 208 ILE Chi-restraints excluded: chain J residue 335 THR Chi-restraints excluded: chain K residue 88 ASP Chi-restraints excluded: chain L residue 192 ASP Chi-restraints excluded: chain L residue 218 ARG Chi-restraints excluded: chain L residue 303 ILE Chi-restraints excluded: chain N residue 63 HIS Chi-restraints excluded: chain N residue 144 LEU Chi-restraints excluded: chain N residue 158 VAL Chi-restraints excluded: chain N residue 203 VAL Chi-restraints excluded: chain N residue 268 ARG Chi-restraints excluded: chain O residue 124 GLU Chi-restraints excluded: chain O residue 168 THR Chi-restraints excluded: chain P residue 86 GLU Chi-restraints excluded: chain P residue 120 MET Chi-restraints excluded: chain Q residue 595 THR Chi-restraints excluded: chain Q residue 618 ILE Chi-restraints excluded: chain R residue 121 THR Chi-restraints excluded: chain R residue 139 ASP Chi-restraints excluded: chain S residue 229 GLN Chi-restraints excluded: chain S residue 272 ASP Chi-restraints excluded: chain S residue 353 LYS Chi-restraints excluded: chain S residue 486 ASP Chi-restraints excluded: chain T residue 68 VAL Chi-restraints excluded: chain T residue 122 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.5227 > 50: distance: 5 - 9: 7.201 distance: 9 - 10: 8.749 distance: 9 - 171: 9.406 distance: 10 - 11: 16.925 distance: 10 - 13: 10.175 distance: 11 - 12: 14.723 distance: 11 - 20: 20.354 distance: 13 - 14: 6.111 distance: 14 - 16: 10.450 distance: 15 - 17: 3.532 distance: 16 - 18: 5.401 distance: 17 - 19: 6.901 distance: 18 - 19: 4.180 distance: 20 - 21: 22.658 distance: 21 - 22: 3.748 distance: 22 - 23: 14.099 distance: 22 - 24: 21.027 distance: 24 - 25: 18.357 distance: 25 - 26: 10.592 distance: 25 - 28: 32.818 distance: 26 - 27: 34.866 distance: 26 - 29: 13.880 distance: 29 - 30: 15.910 distance: 30 - 31: 17.784 distance: 30 - 33: 23.874 distance: 31 - 32: 21.593 distance: 33 - 34: 26.978 distance: 33 - 35: 7.780 distance: 36 - 37: 17.668 distance: 37 - 38: 16.042 distance: 37 - 40: 27.409 distance: 38 - 39: 14.704 distance: 38 - 45: 25.227 distance: 40 - 41: 22.045 distance: 41 - 42: 10.698 distance: 42 - 43: 10.428 distance: 42 - 44: 8.629 distance: 45 - 46: 21.728 distance: 46 - 47: 9.713 distance: 46 - 49: 17.804 distance: 47 - 48: 14.460 distance: 47 - 54: 9.129 distance: 49 - 50: 14.328 distance: 50 - 51: 18.305 distance: 51 - 52: 19.092 distance: 52 - 53: 7.693 distance: 54 - 55: 14.957 distance: 55 - 56: 9.333 distance: 55 - 58: 9.020 distance: 56 - 57: 3.924 distance: 56 - 63: 37.286 distance: 58 - 59: 16.684 distance: 59 - 60: 3.862 distance: 60 - 61: 12.995 distance: 60 - 62: 15.506 distance: 63 - 64: 11.226 distance: 64 - 65: 20.006 distance: 64 - 67: 4.559 distance: 65 - 66: 23.930 distance: 65 - 74: 22.441 distance: 67 - 68: 12.913 distance: 68 - 69: 6.426 distance: 68 - 70: 13.635 distance: 69 - 71: 18.145 distance: 70 - 72: 16.055 distance: 71 - 73: 12.744 distance: 72 - 73: 5.458 distance: 74 - 75: 6.139 distance: 75 - 78: 7.963 distance: 76 - 77: 13.519 distance: 78 - 79: 10.278 distance: 78 - 80: 16.563 distance: 81 - 82: 7.280 distance: 81 - 87: 3.033 distance: 82 - 83: 9.844 distance: 82 - 85: 12.359 distance: 83 - 84: 5.121 distance: 83 - 88: 6.515 distance: 85 - 86: 7.577 distance: 86 - 87: 5.880