Starting phenix.real_space_refine on Fri Apr 5 23:52:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r5o_18935/04_2024/8r5o_18935_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r5o_18935/04_2024/8r5o_18935.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r5o_18935/04_2024/8r5o_18935.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r5o_18935/04_2024/8r5o_18935.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r5o_18935/04_2024/8r5o_18935_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r5o_18935/04_2024/8r5o_18935_updated.pdb" } resolution = 2.49 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= 0.006 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 2 7.16 5 Zn 1 6.06 5 S 267 5.16 5 C 34604 2.51 5 N 9380 2.21 5 O 10219 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 651": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1031": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 773": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 54473 Number of models: 1 Model: "" Number of chains: 41 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: 5170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5170 Classifications: {'peptide': 647} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 30, 'TRANS': 616} Chain breaks: 10 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: 4468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 4468 Classifications: {'peptide': 545} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 514} Chain breaks: 9 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: 4338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4338 Classifications: {'peptide': 537} Link IDs: {'PTRANS': 21, 'TRANS': 515} Chain breaks: 3 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: "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: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 57 Classifications: {'water': 57} Link IDs: {None: 56} Chain: "D" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "E" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} 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: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "J" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "K" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "N" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} 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 15516 SG CYS E 220 98.315 113.275 109.345 1.00 24.20 S ATOM 15985 SG CYS E 293 95.611 111.886 111.531 1.00 32.65 S ATOM 16043 SG CYS E 300 96.172 110.402 108.008 1.00 19.43 S ATOM 16068 SG CYS E 303 98.702 109.720 110.602 1.00 22.53 S Time building chain proxies: 20.48, per 1000 atoms: 0.38 Number of scatterers: 54473 At special positions: 0 Unit cell: (151, 210.5, 268, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 Fe 2 26.01 S 267 16.00 O 10219 8.00 N 9380 7.00 C 34604 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 15.24 Conformation dependent library (CDL) restraints added in 7.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E8001 " pdb="ZN ZN E8001 " - pdb=" SG CYS E 220 " pdb="ZN ZN E8001 " - pdb=" SG CYS E 300 " pdb="ZN ZN E8001 " - pdb=" SG CYS E 303 " pdb="ZN ZN E8001 " - pdb=" SG CYS E 293 " Number of angles added : 6 13050 Ramachandran restraints generated. 6525 Oldfield, 0 Emsley, 6525 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12546 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 285 helices and 56 sheets defined 41.2% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.08 Creating SS restraints... Processing helix chain 'A' and resid 41 through 55 Processing helix chain 'A' and resid 84 through 92 Processing helix chain 'A' and resid 118 through 120 No H-bonds generated for 'chain 'A' and resid 118 through 120' Processing helix chain 'A' and resid 211 through 230 Proline residue: A 228 - end of helix Processing helix chain 'A' and resid 251 through 261 Processing helix chain 'A' and resid 269 through 271 No H-bonds generated for 'chain 'A' and resid 269 through 271' Processing helix chain 'A' and resid 274 through 276 No H-bonds generated for 'chain 'A' and resid 274 through 276' Processing helix chain 'A' and resid 281 through 289 Processing helix chain 'A' and resid 295 through 300 Processing helix chain 'A' and resid 303 through 308 removed outlier: 3.753A pdb=" N ILE A 307 " --> pdb=" O GLN A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 326 removed outlier: 4.347A pdb=" N LYS A 318 " --> pdb=" O GLU A 315 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS A 319 " --> pdb=" O ASP A 316 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP A 322 " --> pdb=" O LYS A 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 55 Processing helix chain 'B' and resid 84 through 93 Processing helix chain 'B' and resid 118 through 120 No H-bonds generated for 'chain 'B' and resid 118 through 120' Processing helix chain 'B' and resid 211 through 230 Proline residue: B 228 - end of helix Processing helix chain 'C' and resid 17 through 28 Processing helix chain 'C' and resid 30 through 35 Processing helix chain 'C' and resid 66 through 71 Processing helix chain 'C' and resid 309 through 311 No H-bonds generated for 'chain 'C' and resid 309 through 311' Processing helix chain 'C' and resid 317 through 328 Processing helix chain 'C' and resid 363 through 371 Processing helix chain 'C' and resid 383 through 391 removed outlier: 4.427A pdb=" N GLY C 390 " --> pdb=" O GLN C 386 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ARG C 391 " --> pdb=" O ILE C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 417 No H-bonds generated for 'chain 'C' and resid 415 through 417' Processing helix chain 'C' and resid 473 through 478 removed outlier: 4.099A pdb=" N GLU C 477 " --> pdb=" O PRO C 473 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N TYR C 478 " --> pdb=" O SER C 474 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 473 through 478' Processing helix chain 'C' and resid 494 through 496 No H-bonds generated for 'chain 'C' and resid 494 through 496' Processing helix chain 'C' and resid 512 through 514 No H-bonds generated for 'chain 'C' and resid 512 through 514' Processing helix chain 'C' and resid 530 through 532 No H-bonds generated for 'chain 'C' and resid 530 through 532' Processing helix chain 'C' and resid 536 through 538 No H-bonds generated for 'chain 'C' and resid 536 through 538' Processing helix chain 'C' and resid 541 through 553 removed outlier: 3.508A pdb=" N LEU C 545 " --> pdb=" O ALA C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 577 Processing helix chain 'C' and resid 677 through 681 removed outlier: 3.956A pdb=" N TYR C 681 " --> pdb=" O CYS C 678 " (cutoff:3.500A) Processing helix chain 'C' and resid 856 through 862 Proline residue: C 860 - end of helix Processing helix chain 'C' and resid 865 through 880 removed outlier: 3.666A pdb=" N CYS C 871 " --> pdb=" O ILE C 868 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER C 872 " --> pdb=" O PHE C 869 " (cutoff:3.500A) Processing helix chain 'C' and resid 890 through 892 No H-bonds generated for 'chain 'C' and resid 890 through 892' Processing helix chain 'C' and resid 897 through 913 Processing helix chain 'C' and resid 916 through 918 No H-bonds generated for 'chain 'C' and resid 916 through 918' Processing helix chain 'C' and resid 991 through 998 Processing helix chain 'C' and resid 1001 through 1008 Processing helix chain 'C' and resid 1039 through 1051 removed outlier: 3.837A pdb=" N LEU C1051 " --> pdb=" O GLU C1047 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 24 removed outlier: 3.548A pdb=" N ALA D 24 " --> pdb=" O ILE D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 61 No H-bonds generated for 'chain 'D' and resid 58 through 61' Processing helix chain 'D' and resid 99 through 101 No H-bonds generated for 'chain 'D' and resid 99 through 101' Processing helix chain 'D' and resid 116 through 119 No H-bonds generated for 'chain 'D' and resid 116 through 119' Processing helix chain 'D' and resid 125 through 130 Processing helix chain 'D' and resid 134 through 142 removed outlier: 4.186A pdb=" N LEU D 140 " --> pdb=" O GLU D 136 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL D 141 " --> pdb=" O LEU D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 178 removed outlier: 5.222A pdb=" N ILE D 175 " --> pdb=" O TRP D 171 " (cutoff:3.500A) Proline residue: D 176 - end of helix Processing helix chain 'D' and resid 181 through 191 removed outlier: 4.091A pdb=" N ILE D 186 " --> pdb=" O GLN D 182 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N PHE D 187 " --> pdb=" O GLY D 183 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ASN D 189 " --> pdb=" O GLU D 185 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ARG D 190 " --> pdb=" O ILE D 186 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLU D 191 " --> pdb=" O PHE D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 204 Processing helix chain 'D' and resid 208 through 224 Processing helix chain 'D' and resid 235 through 256 removed outlier: 3.582A pdb=" N ARG D 239 " --> pdb=" O ARG D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 264 Processing helix chain 'D' and resid 274 through 276 No H-bonds generated for 'chain 'D' and resid 274 through 276' Processing helix chain 'D' and resid 292 through 309 Processing helix chain 'D' and resid 322 through 336 Processing helix chain 'D' and resid 356 through 360 Processing helix chain 'D' and resid 399 through 405 removed outlier: 3.838A pdb=" N GLU D 404 " --> pdb=" O GLU D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 416 Processing helix chain 'D' and resid 423 through 431 Processing helix chain 'D' and resid 435 through 445 removed outlier: 3.759A pdb=" N GLU D 439 " --> pdb=" O PRO D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 512 Processing helix chain 'D' and resid 533 through 543 removed outlier: 3.660A pdb=" N ILE D 537 " --> pdb=" O ASP D 534 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY D 538 " --> pdb=" O MET D 535 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL D 541 " --> pdb=" O GLY D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 551 No H-bonds generated for 'chain 'D' and resid 549 through 551' Processing helix chain 'D' and resid 584 through 592 Processing helix chain 'D' and resid 656 through 675 Processing helix chain 'E' and resid 16 through 30 Processing helix chain 'E' and resid 32 through 53 Processing helix chain 'E' and resid 66 through 87 removed outlier: 4.362A pdb=" N GLY E 69 " --> pdb=" O PRO E 66 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL E 72 " --> pdb=" O GLY E 69 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN E 73 " --> pdb=" O TRP E 70 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU E 76 " --> pdb=" O GLN E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 122 removed outlier: 3.611A pdb=" N TRP E 104 " --> pdb=" O SER E 100 " (cutoff:3.500A) removed outlier: 4.333A 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 127 through 133 removed outlier: 3.675A pdb=" N SER E 132 " --> pdb=" O VAL E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 147 Processing helix chain 'E' and resid 175 through 210 removed outlier: 3.840A pdb=" N TYR E 183 " --> pdb=" O ILE E 179 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLY E 184 " --> pdb=" O ILE E 180 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL E 210 " --> pdb=" O LEU E 206 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 279 Processing helix chain 'E' and resid 301 through 304 No H-bonds generated for 'chain 'E' and resid 301 through 304' Processing helix chain 'E' and resid 320 through 329 Processing helix chain 'E' and resid 366 through 368 No H-bonds generated for 'chain 'E' and resid 366 through 368' Processing helix chain 'E' and resid 567 through 569 No H-bonds generated for 'chain 'E' and resid 567 through 569' Processing helix chain 'E' and resid 886 through 888 No H-bonds generated for 'chain 'E' and resid 886 through 888' Processing helix chain 'E' and resid 987 through 989 No H-bonds generated for 'chain 'E' and resid 987 through 989' Processing helix chain 'E' and resid 1000 through 1006 removed outlier: 3.926A pdb=" N ILE E1004 " --> pdb=" O GLN E1000 " (cutoff:3.500A) Processing helix chain 'E' and resid 1009 through 1014 removed outlier: 4.539A 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 1179 removed outlier: 3.556A pdb=" N CYS E1175 " --> pdb=" O GLY E1171 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N THR E1177 " --> pdb=" O ASN E1173 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ARG E1178 " --> pdb=" O ARG E1174 " (cutoff:3.500A) Processing helix chain 'E' and resid 1185 through 1211 Processing helix chain 'E' and resid 1218 through 1228 removed outlier: 3.634A pdb=" N GLN E1227 " --> pdb=" O ILE E1223 " (cutoff:3.500A) Processing helix chain 'E' and resid 1251 through 1260 Processing helix chain 'E' and resid 1274 through 1278 Processing helix chain 'E' and resid 1284 through 1288 Processing helix chain 'E' and resid 1293 through 1303 removed outlier: 3.592A pdb=" N ARG E1303 " --> pdb=" O LYS E1299 " (cutoff:3.500A) Processing helix chain 'E' and resid 1312 through 1318 Processing helix chain 'E' and resid 1325 through 1327 No H-bonds generated for 'chain 'E' and resid 1325 through 1327' Processing helix chain 'F' and resid 65 through 82 Processing helix chain 'F' and resid 87 through 100 Processing helix chain 'F' and resid 106 through 118 Processing helix chain 'F' and resid 122 through 134 Processing helix chain 'F' and resid 141 through 153 Processing helix chain 'F' and resid 157 through 169 Processing helix chain 'F' and resid 174 through 187 Processing helix chain 'F' and resid 191 through 204 Processing helix chain 'F' and resid 210 through 222 Processing helix chain 'F' and resid 226 through 239 Processing helix chain 'F' and resid 245 through 257 removed outlier: 3.852A pdb=" N VAL F 254 " --> pdb=" O CYS F 250 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N THR F 257 " --> pdb=" O SER F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 272 removed outlier: 3.545A pdb=" N THR F 267 " --> pdb=" O VAL F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 276 through 278 No H-bonds generated for 'chain 'F' and resid 276 through 278' Processing helix chain 'F' and resid 282 through 293 Processing helix chain 'F' and resid 301 through 313 Processing helix chain 'F' and resid 322 through 334 Processing helix chain 'F' and resid 338 through 349 Processing helix chain 'F' and resid 354 through 362 removed outlier: 5.940A pdb=" N ALA F 361 " --> pdb=" O LEU F 358 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 377 Processing helix chain 'F' and resid 381 through 393 Processing helix chain 'F' and resid 412 through 414 No H-bonds generated for 'chain 'F' and resid 412 through 414' Processing helix chain 'F' and resid 432 through 438 Processing helix chain 'F' and resid 460 through 462 No H-bonds generated for 'chain 'F' and resid 460 through 462' Processing helix chain 'F' and resid 475 through 494 removed outlier: 3.555A pdb=" N HIS F 487 " --> pdb=" O TRP F 483 " (cutoff:3.500A) Processing helix chain 'F' and resid 608 through 615 Processing helix chain 'F' and resid 745 through 754 Processing helix chain 'F' and resid 760 through 762 No H-bonds generated for 'chain 'F' and resid 760 through 762' Processing helix chain 'F' and resid 766 through 769 No H-bonds generated for 'chain 'F' and resid 766 through 769' Processing helix chain 'F' and resid 775 through 777 No H-bonds generated for 'chain 'F' and resid 775 through 777' Processing helix chain 'F' and resid 788 through 805 Processing helix chain 'F' and resid 811 through 816 Processing helix chain 'F' and resid 836 through 839 No H-bonds generated for 'chain 'F' and resid 836 through 839' Processing helix chain 'G' and resid 421 through 433 Processing helix chain 'G' and resid 436 through 448 Processing helix chain 'G' and resid 455 through 467 Processing helix chain 'G' and resid 471 through 483 removed outlier: 3.985A pdb=" N HIS G 482 " --> pdb=" O PHE G 478 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU G 483 " --> pdb=" O ASN G 479 " (cutoff:3.500A) Processing helix chain 'G' and resid 490 through 503 removed outlier: 3.563A pdb=" N LEU G 497 " --> pdb=" O PHE G 493 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY G 503 " --> pdb=" O SER G 499 " (cutoff:3.500A) Processing helix chain 'G' and resid 506 through 518 removed outlier: 3.797A pdb=" N ASN G 518 " --> pdb=" O SER G 514 " (cutoff:3.500A) Processing helix chain 'G' and resid 525 through 537 Processing helix chain 'G' and resid 541 through 553 removed outlier: 3.590A pdb=" N GLU G 552 " --> pdb=" O TYR G 548 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS G 553 " --> pdb=" O VAL G 549 " (cutoff:3.500A) Processing helix chain 'G' and resid 560 through 572 removed outlier: 3.596A pdb=" N VAL G 569 " --> pdb=" O ALA G 565 " (cutoff:3.500A) Processing helix chain 'G' and resid 576 through 589 removed outlier: 3.593A pdb=" N LYS G 587 " --> pdb=" O PHE G 583 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER G 589 " --> pdb=" O GLU G 585 " (cutoff:3.500A) Processing helix chain 'G' and resid 595 through 607 Processing helix chain 'G' and resid 611 through 623 removed outlier: 3.725A pdb=" N GLU G 620 " --> pdb=" O GLU G 616 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER G 623 " --> pdb=" O GLU G 619 " (cutoff:3.500A) Processing helix chain 'G' and resid 628 through 638 removed outlier: 3.677A pdb=" N LYS G 638 " --> pdb=" O GLY G 634 " (cutoff:3.500A) Processing helix chain 'G' and resid 648 through 657 Processing helix chain 'G' and resid 661 through 678 removed outlier: 3.927A pdb=" N ARG G 667 " --> pdb=" O GLY G 663 " (cutoff:3.500A) Processing helix chain 'G' and resid 682 through 695 removed outlier: 3.775A pdb=" N LYS G 694 " --> pdb=" O ASN G 690 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG G 695 " --> pdb=" O GLU G 691 " (cutoff:3.500A) Processing helix chain 'G' and resid 718 through 734 removed outlier: 3.501A pdb=" N ASP G 734 " --> pdb=" O ASN G 730 " (cutoff:3.500A) Processing helix chain 'G' and resid 754 through 756 No H-bonds generated for 'chain 'G' and resid 754 through 756' Processing helix chain 'G' and resid 761 through 763 No H-bonds generated for 'chain 'G' and resid 761 through 763' Processing helix chain 'G' and resid 765 through 778 removed outlier: 3.546A pdb=" N ASP G 776 " --> pdb=" O SER G 772 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N HIS G 777 " --> pdb=" O PHE G 773 " (cutoff:3.500A) Processing helix chain 'G' and resid 796 through 800 Processing helix chain 'H' and resid 70 through 79 Processing helix chain 'H' and resid 90 through 98 Processing helix chain 'H' and resid 110 through 119 Processing helix chain 'H' and resid 121 through 131 Processing helix chain 'H' and resid 135 through 141 Processing helix chain 'H' and resid 180 through 194 removed outlier: 4.531A pdb=" N ALA H 189 " --> pdb=" O PHE H 185 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N HIS H 190 " --> pdb=" O ILE H 186 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LYS H 191 " --> pdb=" O ARG H 187 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU H 192 " --> pdb=" O GLU H 188 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N MET H 193 " --> pdb=" O ALA H 189 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ALA H 194 " --> pdb=" O HIS H 190 " (cutoff:3.500A) Processing helix chain 'H' and resid 199 through 201 No H-bonds generated for 'chain 'H' and resid 199 through 201' Processing helix chain 'H' and resid 209 through 212 Processing helix chain 'H' and resid 214 through 216 No H-bonds generated for 'chain 'H' and resid 214 through 216' Processing helix chain 'H' and resid 220 through 247 removed outlier: 5.807A pdb=" N ASP H 238 " --> pdb=" O GLU H 234 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N ARG H 239 " --> pdb=" O ALA H 235 " (cutoff:3.500A) Processing helix chain 'H' and resid 259 through 261 No H-bonds generated for 'chain 'H' and resid 259 through 261' Processing helix chain 'H' and resid 269 through 271 No H-bonds generated for 'chain 'H' and resid 269 through 271' Processing helix chain 'H' and resid 307 through 315 removed outlier: 3.627A pdb=" N ILE H 313 " --> pdb=" O TRP H 310 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ARG H 314 " --> pdb=" O PHE H 311 " (cutoff:3.500A) Processing helix chain 'H' and resid 350 through 352 No H-bonds generated for 'chain 'H' and resid 350 through 352' Processing helix chain 'H' and resid 371 through 377 Processing helix chain 'H' and resid 392 through 394 No H-bonds generated for 'chain 'H' and resid 392 through 394' Processing helix chain 'H' and resid 402 through 423 removed outlier: 3.770A pdb=" N ASP H 405 " --> pdb=" O PRO H 402 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TRP H 408 " --> pdb=" O ASP H 405 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET H 416 " --> pdb=" O ALA H 413 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP H 419 " --> pdb=" O MET H 416 " (cutoff:3.500A) Processing helix chain 'H' and resid 469 through 471 No H-bonds generated for 'chain 'H' and resid 469 through 471' Processing helix chain 'H' and resid 474 through 483 Processing helix chain 'H' and resid 504 through 537 Processing helix chain 'I' and resid 68 through 76 Processing helix chain 'I' and resid 78 through 90 Processing helix chain 'I' and resid 101 through 112 removed outlier: 3.568A pdb=" N ASN I 110 " --> pdb=" O LYS I 106 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N ASN I 111 " --> pdb=" O ALA I 107 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLY I 112 " --> pdb=" O THR I 108 " (cutoff:3.500A) Processing helix chain 'I' and resid 118 through 132 removed outlier: 3.508A pdb=" N TYR I 125 " --> pdb=" O ALA I 121 " (cutoff:3.500A) Processing helix chain 'I' and resid 144 through 154 Processing helix chain 'I' and resid 157 through 170 Processing helix chain 'I' and resid 199 through 202 Processing helix chain 'I' and resid 214 through 216 No H-bonds generated for 'chain 'I' and resid 214 through 216' Processing helix chain 'I' and resid 218 through 221 No H-bonds generated for 'chain 'I' and resid 218 through 221' Processing helix chain 'I' and resid 225 through 235 Processing helix chain 'I' and resid 239 through 251 removed outlier: 3.869A pdb=" N ALA I 251 " --> pdb=" O ALA I 247 " (cutoff:3.500A) Processing helix chain 'J' and resid 206 through 209 No H-bonds generated for 'chain 'J' and resid 206 through 209' Processing helix chain 'J' and resid 235 through 237 No H-bonds generated for 'chain 'J' and resid 235 through 237' Processing helix chain 'J' and resid 255 through 266 Processing helix chain 'J' and resid 278 through 306 removed outlier: 5.754A pdb=" N HIS J 289 " --> pdb=" O ARG J 285 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU J 290 " --> pdb=" O ALA J 286 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE J 291 " --> pdb=" O ARG J 287 " (cutoff:3.500A) Processing helix chain 'J' and resid 308 through 315 removed outlier: 4.236A pdb=" N GLU J 314 " --> pdb=" O ALA J 310 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N TRP J 315 " --> pdb=" O PHE J 311 " (cutoff:3.500A) Processing helix chain 'J' and resid 325 through 335 Processing helix chain 'J' and resid 339 through 349 removed outlier: 3.837A pdb=" N HIS J 349 " --> pdb=" O GLU J 345 " (cutoff:3.500A) Processing helix chain 'J' and resid 352 through 361 removed outlier: 4.535A pdb=" N GLY J 360 " --> pdb=" O ARG J 356 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N THR J 361 " --> pdb=" O ILE J 357 " (cutoff:3.500A) Processing helix chain 'J' and resid 369 through 373 Processing helix chain 'J' and resid 376 through 381 removed outlier: 3.998A pdb=" N GLN J 381 " --> pdb=" O ASP J 377 " (cutoff:3.500A) Processing helix chain 'J' and resid 391 through 393 No H-bonds generated for 'chain 'J' and resid 391 through 393' Processing helix chain 'J' and resid 416 through 422 Processing helix chain 'K' and resid 119 through 127 removed outlier: 4.197A pdb=" N LYS K 123 " --> pdb=" O SER K 120 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TRP K 127 " --> pdb=" O MET K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 131 through 133 No H-bonds generated for 'chain 'K' and resid 131 through 133' Processing helix chain 'K' and resid 140 through 149 Processing helix chain 'K' and resid 164 through 175 Processing helix chain 'K' and resid 201 through 203 No H-bonds generated for 'chain 'K' and resid 201 through 203' Processing helix chain 'K' and resid 214 through 216 No H-bonds generated for 'chain 'K' and resid 214 through 216' Processing helix chain 'K' and resid 220 through 222 No H-bonds generated for 'chain 'K' and resid 220 through 222' Processing helix chain 'K' and resid 225 through 230 Processing helix chain 'K' and resid 238 through 242 Processing helix chain 'K' and resid 244 through 259 removed outlier: 3.528A pdb=" N LYS K 252 " --> pdb=" O SER K 248 " (cutoff:3.500A) Processing helix chain 'K' and resid 272 through 275 Processing helix chain 'K' and resid 278 through 290 removed outlier: 4.767A pdb=" N LYS K 287 " --> pdb=" O LYS K 283 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N SER K 288 " --> pdb=" O LEU K 284 " (cutoff:3.500A) Processing helix chain 'K' and resid 299 through 306 Processing helix chain 'K' and resid 308 through 315 Processing helix chain 'K' and resid 326 through 330 removed outlier: 3.962A pdb=" N LYS K 330 " --> pdb=" O PHE K 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 326 through 330' Processing helix chain 'K' and resid 343 through 346 Processing helix chain 'K' and resid 381 through 383 No H-bonds generated for 'chain 'K' and resid 381 through 383' Processing helix chain 'K' and resid 392 through 406 removed outlier: 3.716A pdb=" N THR K 406 " --> pdb=" O ARG K 402 " (cutoff:3.500A) Processing helix chain 'K' and resid 408 through 411 removed outlier: 3.557A pdb=" N PHE K 411 " --> pdb=" O PRO K 408 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 408 through 411' Processing helix chain 'K' and resid 414 through 433 removed outlier: 3.797A pdb=" N PHE K 423 " --> pdb=" O ARG K 419 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA K 424 " --> pdb=" O GLN K 420 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N TRP K 433 " --> pdb=" O ILE K 429 " (cutoff:3.500A) Processing helix chain 'K' and resid 444 through 454 Processing helix chain 'K' and resid 457 through 459 No H-bonds generated for 'chain 'K' and resid 457 through 459' Processing helix chain 'L' and resid 77 through 86 removed outlier: 4.005A pdb=" N GLY L 83 " --> pdb=" O PHE L 79 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG L 86 " --> pdb=" O ILE L 82 " (cutoff:3.500A) Processing helix chain 'L' and resid 124 through 126 No H-bonds generated for 'chain 'L' and resid 124 through 126' Processing helix chain 'L' and resid 148 through 155 Processing helix chain 'L' and resid 162 through 175 Processing helix chain 'L' and resid 180 through 187 removed outlier: 4.548A pdb=" N ASP L 186 " --> pdb=" O ARG L 182 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N PHE L 187 " --> pdb=" O LEU L 183 " (cutoff:3.500A) Processing helix chain 'L' and resid 197 through 199 No H-bonds generated for 'chain 'L' and resid 197 through 199' Processing helix chain 'L' and resid 202 through 207 removed outlier: 3.639A pdb=" N GLU L 207 " --> pdb=" O GLU L 203 " (cutoff:3.500A) Processing helix chain 'L' and resid 211 through 231 Processing helix chain 'L' and resid 238 through 241 No H-bonds generated for 'chain 'L' and resid 238 through 241' Processing helix chain 'L' and resid 247 through 260 Processing helix chain 'L' and resid 330 through 337 Processing helix chain 'L' and resid 359 through 365 Processing helix chain 'L' and resid 372 through 374 No H-bonds generated for 'chain 'L' and resid 372 through 374' Processing helix chain 'L' and resid 390 through 398 Processing helix chain 'L' and resid 411 through 431 removed outlier: 3.544A pdb=" N LYS L 416 " --> pdb=" O SER L 412 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU L 431 " --> pdb=" O LYS L 427 " (cutoff:3.500A) Processing helix chain 'L' and resid 436 through 445 Processing helix chain 'L' and resid 451 through 479 Processing helix chain 'M' and resid 138 through 140 No H-bonds generated for 'chain 'M' and resid 138 through 140' Processing helix chain 'M' and resid 233 through 235 No H-bonds generated for 'chain 'M' and resid 233 through 235' Processing helix chain 'M' and resid 277 through 279 No H-bonds generated for 'chain 'M' and resid 277 through 279' Processing helix chain 'M' and resid 296 through 298 No H-bonds generated for 'chain 'M' and resid 296 through 298' Processing helix chain 'M' and resid 302 through 324 removed outlier: 4.526A pdb=" N LYS M 324 " --> pdb=" O LYS M 320 " (cutoff:3.500A) Processing helix chain 'M' and resid 328 through 330 No H-bonds generated for 'chain 'M' and resid 328 through 330' Processing helix chain 'N' and resid 66 through 72 Processing helix chain 'N' and resid 76 through 87 Processing helix chain 'N' and resid 99 through 109 removed outlier: 3.546A pdb=" N ASN N 107 " --> pdb=" O LEU N 103 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ARG N 108 " --> pdb=" O LEU N 104 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N GLY N 109 " --> pdb=" O SER N 105 " (cutoff:3.500A) Processing helix chain 'N' and resid 115 through 130 Processing helix chain 'N' and resid 141 through 151 Processing helix chain 'N' and resid 154 through 167 Processing helix chain 'N' and resid 211 through 214 Processing helix chain 'N' and resid 226 through 228 No H-bonds generated for 'chain 'N' and resid 226 through 228' Processing helix chain 'N' and resid 230 through 233 No H-bonds generated for 'chain 'N' and resid 230 through 233' Processing helix chain 'N' and resid 237 through 247 Processing helix chain 'N' and resid 251 through 269 Processing helix chain 'O' and resid 84 through 92 Processing helix chain 'O' and resid 109 through 124 removed outlier: 4.068A pdb=" N LEU O 113 " --> pdb=" O GLY O 109 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN O 116 " --> pdb=" O ILE O 112 " (cutoff:3.500A) Processing helix chain 'O' and resid 140 through 145 Processing helix chain 'O' and resid 174 through 184 Processing helix chain 'P' and resid 84 through 92 Processing helix chain 'P' and resid 109 through 124 Processing helix chain 'P' and resid 140 through 145 Processing helix chain 'P' and resid 174 through 184 Processing helix chain 'Q' and resid 352 through 360 Processing helix chain 'Q' and resid 541 through 547 removed outlier: 3.666A pdb=" N ASN Q 545 " --> pdb=" O HIS Q 541 " (cutoff:3.500A) Processing helix chain 'Q' and resid 596 through 609 removed outlier: 3.845A pdb=" N LEU Q 609 " --> pdb=" O SER Q 605 " (cutoff:3.500A) Processing helix chain 'Q' and resid 629 through 639 removed outlier: 3.662A pdb=" N THR Q 633 " --> pdb=" O ARG Q 629 " (cutoff:3.500A) Processing helix chain 'Q' and resid 655 through 665 removed outlier: 3.971A pdb=" N GLY Q 665 " --> pdb=" O ASP Q 661 " (cutoff:3.500A) Processing helix chain 'Q' and resid 670 through 678 Processing helix chain 'Q' and resid 697 through 706 Processing helix chain 'Q' and resid 736 through 752 removed outlier: 3.531A pdb=" N GLN Q 745 " --> pdb=" O ARG Q 741 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ASP Q 748 " --> pdb=" O LEU Q 744 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N GLU Q 749 " --> pdb=" O GLN Q 745 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU Q 750 " --> pdb=" O TYR Q 746 " (cutoff:3.500A) Processing helix chain 'R' and resid 69 through 78 Processing helix chain 'R' and resid 80 through 92 removed outlier: 3.953A pdb=" N SER R 92 " --> pdb=" O ARG R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 96 through 113 Processing helix chain 'R' and resid 124 through 135 Processing helix chain 'R' and resid 142 through 144 No H-bonds generated for 'chain 'R' and resid 142 through 144' Processing helix chain 'S' and resid 194 through 196 No H-bonds generated for 'chain 'S' and resid 194 through 196' Processing helix chain 'S' and resid 226 through 231 Processing helix chain 'S' and resid 250 through 260 Processing helix chain 'S' and resid 274 through 285 Processing helix chain 'S' and resid 323 through 325 No H-bonds generated for 'chain 'S' and resid 323 through 325' Processing helix chain 'S' and resid 329 through 331 No H-bonds generated for 'chain 'S' and resid 329 through 331' Processing helix chain 'S' and resid 334 through 339 Processing helix chain 'S' and resid 347 through 350 Processing helix chain 'S' and resid 353 through 368 removed outlier: 3.535A pdb=" N THR S 358 " --> pdb=" O LYS S 354 " (cutoff:3.500A) Processing helix chain 'S' and resid 381 through 384 Processing helix chain 'S' and resid 387 through 399 removed outlier: 4.994A pdb=" N GLU S 396 " --> pdb=" O SER S 392 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N VAL S 397 " --> pdb=" O LEU S 393 " (cutoff:3.500A) Processing helix chain 'S' and resid 408 through 414 Processing helix chain 'S' and resid 430 through 432 No H-bonds generated for 'chain 'S' and resid 430 through 432' Processing helix chain 'S' and resid 438 through 444 Proline residue: S 443 - end of helix Processing helix chain 'S' and resid 482 through 484 No H-bonds generated for 'chain 'S' and resid 482 through 484' Processing helix chain 'S' and resid 488 through 504 removed outlier: 3.531A pdb=" N VAL S 504 " --> pdb=" O ARG S 500 " (cutoff:3.500A) Processing helix chain 'S' and resid 506 through 508 No H-bonds generated for 'chain 'S' and resid 506 through 508' Processing helix chain 'S' and resid 512 through 537 removed outlier: 3.547A pdb=" N GLN S 535 " --> pdb=" O TRP S 531 " (cutoff:3.500A) Processing helix chain 'S' and resid 569 through 572 No H-bonds generated for 'chain 'S' and resid 569 through 572' Processing helix chain 'T' and resid 41 through 45 Processing helix chain 'T' and resid 55 through 61 Processing helix chain 'T' and resid 63 through 65 No H-bonds generated for 'chain 'T' and resid 63 through 65' Processing sheet with id= A, first strand: chain 'A' and resid 14 through 22 removed outlier: 6.562A pdb=" N ARG A 31 " --> pdb=" O VAL A 18 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N SER A 20 " --> pdb=" O TYR A 29 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N TYR A 29 " --> pdb=" O SER A 20 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN A 181 " --> pdb=" O TRP A 204 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 104 through 111 removed outlier: 3.706A pdb=" N ARG A 64 " --> pdb=" O LYS A 150 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLU A 152 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ILE A 62 " --> pdb=" O GLU A 152 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ASN A 154 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N THR A 60 " --> pdb=" O ASN A 154 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 114 through 117 Processing sheet with id= D, first strand: chain 'B' and resid 14 through 22 removed outlier: 6.570A pdb=" N ARG B 31 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N SER B 20 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N TYR B 29 " --> pdb=" O SER B 20 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU B 194 " --> pdb=" O ASN B 191 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 169 through 171 removed outlier: 6.504A pdb=" N LYS B 150 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA B 65 " --> pdb=" O GLY B 148 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLY B 148 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N PHE B 67 " --> pdb=" O CYS B 146 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N CYS B 146 " --> pdb=" O PHE B 67 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 114 through 117 Processing sheet with id= G, first strand: chain 'C' and resid 58 through 60 removed outlier: 3.672A pdb=" N GLY C 102 " --> pdb=" O LEU C 80 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 113 through 115 Processing sheet with id= I, first strand: chain 'C' and resid 125 through 128 Processing sheet with id= J, first strand: chain 'C' and resid 392 through 394 Processing sheet with id= K, first strand: chain 'C' and resid 451 through 455 Processing sheet with id= L, first strand: chain 'C' and resid 498 through 503 Processing sheet with id= M, first strand: chain 'C' and resid 605 through 609 removed outlier: 3.589A pdb=" N TYR C 591 " --> pdb=" O ILE C 598 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N SER C 600 " --> pdb=" O ILE C 589 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N ILE C 589 " --> pdb=" O SER C 600 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 944 through 950 removed outlier: 6.528A pdb=" N MET C 852 " --> pdb=" O ALA C 660 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 687 through 693 removed outlier: 3.635A pdb=" N ASP C 789 " --> pdb=" O TYR C 809 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N SER C 811 " --> pdb=" O VAL C 787 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N VAL C 787 " --> pdb=" O SER C 811 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 821 through 823 removed outlier: 7.587A pdb=" N ILE C 675 " --> pdb=" O SER C 833 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ILE C 835 " --> pdb=" O ILE C 675 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 1058 through 1060 Processing sheet with id= R, first strand: chain 'D' and resid 105 through 108 Processing sheet with id= S, first strand: chain 'D' and resid 146 through 148 removed outlier: 3.721A pdb=" N GLY D 162 " --> pdb=" O ALA D 148 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 384 through 386 removed outlier: 6.040A pdb=" N ILE D 476 " --> pdb=" O VAL D 385 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'D' and resid 394 through 397 removed outlier: 7.525A pdb=" N CYS D 395 " --> pdb=" O SER D 465 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N GLN D 467 " --> pdb=" O CYS D 395 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N LEU D 397 " --> pdb=" O GLN D 467 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ILE D 469 " --> pdb=" O LEU D 397 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 602 through 606 removed outlier: 4.183A pdb=" N ILE D 650 " --> pdb=" O TRP D 606 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 226 through 228 Processing sheet with id= X, first strand: chain 'E' and resid 361 through 363 Processing sheet with id= Y, first strand: chain 'E' and resid 370 through 373 removed outlier: 6.764A pdb=" N VAL E 354 " --> pdb=" O ILE E 422 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLU E 424 " --> pdb=" O GLU E 352 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLU E 352 " --> pdb=" O GLU E 424 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 448 through 451 Processing sheet with id= AA, first strand: chain 'E' and resid 467 through 469 Processing sheet with id= AB, first strand: chain 'E' and resid 571 through 573 Processing sheet with id= AC, first strand: chain 'E' and resid 809 through 811 Processing sheet with id= AD, first strand: chain 'E' and resid 924 through 926 Processing sheet with id= AE, first strand: chain 'E' and resid 946 through 949 removed outlier: 6.244A pdb=" N ARG E1102 " --> pdb=" O VAL E1091 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N VAL E1091 " --> pdb=" O ARG E1102 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'E' and resid 1039 through 1042 removed outlier: 3.696A pdb=" N ASN E1047 " --> pdb=" O ASN E1042 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'E' and resid 1248 through 1250 removed outlier: 4.747A pdb=" N LYS E1231 " --> pdb=" O VAL E1270 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'E' and resid 255 through 257 removed outlier: 3.523A pdb=" N ALA E 263 " --> pdb=" O ILE E 255 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE E 257 " --> pdb=" O CYS E 261 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N CYS E 261 " --> pdb=" O ILE E 257 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'E' and resid 438 through 443 removed outlier: 3.579A pdb=" N VAL E1130 " --> pdb=" O ILE E 442 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'G' and resid 702 through 704 removed outlier: 6.582A pdb=" N LEU G 745 " --> pdb=" O TRP G 709 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N VAL G 711 " --> pdb=" O LEU G 745 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL G 747 " --> pdb=" O VAL G 711 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'H' and resid 301 through 304 removed outlier: 6.344A pdb=" N ASP H 294 " --> pdb=" O VAL H 282 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N VAL H 282 " --> pdb=" O ASP H 294 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N GLU H 326 " --> pdb=" O PHE H 344 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N PHE H 344 " --> pdb=" O GLU H 326 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'I' and resid 187 through 194 removed outlier: 3.683A pdb=" N ARG I 187 " --> pdb=" O LYS I 182 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N LEU I 181 " --> pdb=" O PRO I 206 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'K' and resid 153 through 157 removed outlier: 6.240A pdb=" N ILE K 233 " --> pdb=" O CYS K 94 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N PHE K 96 " --> pdb=" O ILE K 233 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N HIS K 235 " --> pdb=" O PHE K 96 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU K 263 " --> pdb=" O PHE K 234 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N PHE K 236 " --> pdb=" O LEU K 263 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N PHE K 265 " --> pdb=" O PHE K 236 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE K 294 " --> pdb=" O PHE K 266 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU K 353 " --> pdb=" O ILE K 295 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N VAL K 297 " --> pdb=" O LEU K 353 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N VAL K 355 " --> pdb=" O VAL K 297 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'K' and resid 158 through 161 Processing sheet with id= AO, first strand: chain 'K' and resid 195 through 199 removed outlier: 6.102A pdb=" N LYS K 197 " --> pdb=" O THR K 209 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N THR K 209 " --> pdb=" O LYS K 197 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LYS K 199 " --> pdb=" O ALA K 207 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ALA K 207 " --> pdb=" O LYS K 199 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'L' and resid 93 through 98 Processing sheet with id= AQ, first strand: chain 'L' and resid 128 through 131 Processing sheet with id= AR, first strand: chain 'L' and resid 293 through 298 removed outlier: 6.309A pdb=" N SER L 308 " --> pdb=" O VAL L 118 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL L 118 " --> pdb=" O SER L 308 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'M' and resid 141 through 145 removed outlier: 6.921A pdb=" N GLU M 168 " --> pdb=" O ARG M 154 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'M' and resid 259 through 262 removed outlier: 4.093A pdb=" N LYS M 231 " --> pdb=" O ASP M 246 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N GLU M 248 " --> pdb=" O LEU M 229 " (cutoff:3.500A) removed outlier: 10.900A pdb=" N LEU M 229 " --> pdb=" O GLU M 248 " (cutoff:3.500A) removed outlier: 9.445A pdb=" N ILE M 250 " --> pdb=" O VAL M 227 " (cutoff:3.500A) removed outlier: 10.396A pdb=" N VAL M 227 " --> pdb=" O ILE M 250 " (cutoff:3.500A) removed outlier: 9.727A pdb=" N VAL M 252 " --> pdb=" O SER M 225 " (cutoff:3.500A) removed outlier: 11.196A pdb=" N SER M 225 " --> pdb=" O VAL M 252 " (cutoff:3.500A) removed outlier: 11.889A pdb=" N ASP M 254 " --> pdb=" O GLU M 223 " (cutoff:3.500A) removed outlier: 14.002A pdb=" N GLU M 223 " --> pdb=" O ASP M 254 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N TYR M 200 " --> pdb=" O SER M 225 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N VAL M 227 " --> pdb=" O SER M 198 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N SER M 198 " --> pdb=" O VAL M 227 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU M 229 " --> pdb=" O ALA M 196 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ALA M 196 " --> pdb=" O LEU M 229 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'M' and resid 265 through 267 removed outlier: 6.775A pdb=" N PHE M 291 " --> pdb=" O LEU M 266 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'N' and resid 199 through 206 removed outlier: 3.566A pdb=" N LYS N 199 " --> pdb=" O LYS N 179 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N TYR N 178 " --> pdb=" O PRO N 218 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'O' and resid 129 through 135 removed outlier: 7.676A pdb=" N VAL O 132 " --> pdb=" O PRO O 98 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE O 100 " --> pdb=" O VAL O 132 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N VAL O 134 " --> pdb=" O ILE O 100 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ASP O 102 " --> pdb=" O VAL O 134 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR O 153 " --> pdb=" O PHE O 103 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'P' and resid 80 through 82 removed outlier: 3.580A pdb=" N ARG P 80 " --> pdb=" O ILE P 131 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ASP P 135 " --> pdb=" O LEU P 82 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N VAL P 132 " --> pdb=" O PRO P 98 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ILE P 100 " --> pdb=" O VAL P 132 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N VAL P 134 " --> pdb=" O ILE P 100 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ASP P 102 " --> pdb=" O VAL P 134 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR P 153 " --> pdb=" O PHE P 103 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'Q' and resid 587 through 590 removed outlier: 6.834A pdb=" N VAL Q 642 " --> pdb=" O THR Q 616 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N ILE Q 618 " --> pdb=" O VAL Q 642 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N MET Q 644 " --> pdb=" O ILE Q 618 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N CYS Q 620 " --> pdb=" O MET Q 644 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N THR Q 646 " --> pdb=" O CYS Q 620 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ARG Q 690 " --> pdb=" O THR Q 643 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N LEU Q 645 " --> pdb=" O ARG Q 690 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N PHE Q 692 " --> pdb=" O LEU Q 645 " (cutoff:3.500A) removed outlier: 9.288A pdb=" N SER Q 647 " --> pdb=" O PHE Q 692 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'Q' and resid 724 through 727 Processing sheet with id= BA, first strand: chain 'S' and resid 263 through 267 removed outlier: 6.634A pdb=" N MET S 342 " --> pdb=" O CYS S 204 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N PHE S 206 " --> pdb=" O MET S 342 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TYR S 344 " --> pdb=" O PHE S 206 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL S 372 " --> pdb=" O PHE S 343 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N PHE S 345 " --> pdb=" O VAL S 372 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N PHE S 374 " --> pdb=" O PHE S 345 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL S 403 " --> pdb=" O TYR S 375 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE S 451 " --> pdb=" O ILE S 404 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N VAL S 406 " --> pdb=" O ILE S 451 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N PHE S 453 " --> pdb=" O VAL S 406 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'S' and resid 268 through 271 Processing sheet with id= BC, first strand: chain 'T' and resid 67 through 71 removed outlier: 3.646A pdb=" N SER T 67 " --> pdb=" O TYR T 132 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ARG T 131 " --> pdb=" O ILE T 88 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ILE T 88 " --> pdb=" O ARG T 131 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N CYS T 133 " --> pdb=" O VAL T 86 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N VAL T 86 " --> pdb=" O CYS T 133 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LYS T 135 " --> pdb=" O GLN T 84 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N GLN T 84 " --> pdb=" O LYS T 135 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'T' and resid 74 through 79 1972 hydrogen bonds defined for protein. 5505 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 18.33 Time building geometry restraints manager: 16.92 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: 17821 1.34 - 1.46: 11233 1.46 - 1.58: 25934 1.58 - 1.70: 1 1.70 - 1.81: 443 Bond restraints: 55432 Sorted by residual: bond pdb=" C2 SAH L8001 " pdb=" N3 SAH L8001 " ideal model delta sigma weight residual 1.322 1.378 -0.056 2.00e-02 2.50e+03 7.75e+00 bond pdb=" C8 SAH L8001 " pdb=" N7 SAH L8001 " ideal model delta sigma weight residual 1.299 1.348 -0.049 2.00e-02 2.50e+03 5.96e+00 bond pdb=" C2 SAH L8001 " pdb=" N1 SAH L8001 " ideal model delta sigma weight residual 1.330 1.377 -0.047 2.00e-02 2.50e+03 5.53e+00 bond pdb=" C6 SAH L8001 " pdb=" N1 SAH L8001 " ideal model delta sigma weight residual 1.338 1.376 -0.038 2.00e-02 2.50e+03 3.62e+00 bond pdb=" CB PRO E1183 " pdb=" CG PRO E1183 " ideal model delta sigma weight residual 1.492 1.586 -0.094 5.00e-02 4.00e+02 3.54e+00 ... (remaining 55427 not shown) Histogram of bond angle deviations from ideal: 91.82 - 100.28: 10 100.28 - 108.74: 3129 108.74 - 117.19: 35773 117.19 - 125.65: 35033 125.65 - 134.11: 984 Bond angle restraints: 74929 Sorted by residual: angle pdb=" C PHE B 226 " pdb=" N ILE B 227 " pdb=" CA ILE B 227 " ideal model delta sigma weight residual 120.24 122.95 -2.71 6.30e-01 2.52e+00 1.84e+01 angle pdb=" N PRO E1183 " pdb=" CA PRO E1183 " pdb=" C PRO E1183 " ideal model delta sigma weight residual 112.47 119.60 -7.13 2.06e+00 2.36e-01 1.20e+01 angle pdb=" CA PRO E1183 " pdb=" N PRO E1183 " pdb=" CD PRO E1183 " ideal model delta sigma weight residual 112.00 107.23 4.77 1.40e+00 5.10e-01 1.16e+01 angle pdb=" CG SAH L8001 " pdb=" SD SAH L8001 " pdb=" C5' SAH L8001 " ideal model delta sigma weight residual 101.77 91.82 9.95 3.00e+00 1.11e-01 1.10e+01 angle pdb=" C LEU A 250 " pdb=" N PHE A 251 " pdb=" CA PHE A 251 " ideal model delta sigma weight residual 120.09 124.03 -3.94 1.25e+00 6.40e-01 9.96e+00 ... (remaining 74924 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 31423 17.97 - 35.93: 1555 35.93 - 53.90: 324 53.90 - 71.86: 86 71.86 - 89.83: 31 Dihedral angle restraints: 33419 sinusoidal: 14009 harmonic: 19410 Sorted by residual: dihedral pdb=" CA GLU F 418 " pdb=" C GLU F 418 " pdb=" N PRO F 419 " pdb=" CA PRO F 419 " ideal model delta harmonic sigma weight residual 180.00 129.23 50.77 0 5.00e+00 4.00e-02 1.03e+02 dihedral pdb=" CA ILE F 417 " pdb=" C ILE F 417 " pdb=" N GLU F 418 " pdb=" CA GLU F 418 " ideal model delta harmonic sigma weight residual -180.00 -155.00 -25.00 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA TRP I 178 " pdb=" C TRP I 178 " pdb=" N LEU I 179 " pdb=" CA LEU I 179 " ideal model delta harmonic sigma weight residual 180.00 158.23 21.77 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 33416 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 6716 0.053 - 0.106: 1201 0.106 - 0.158: 194 0.158 - 0.211: 2 0.211 - 0.264: 1 Chirality restraints: 8114 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 2.45 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA PRO B 125 " pdb=" N PRO B 125 " pdb=" C PRO B 125 " pdb=" CB PRO B 125 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 6.87e-01 chirality pdb=" CA ILE H 305 " pdb=" N ILE H 305 " pdb=" C ILE H 305 " pdb=" CB ILE H 305 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.42e-01 ... (remaining 8111 not shown) Planarity restraints: 9663 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE E1182 " -0.076 5.00e-02 4.00e+02 1.14e-01 2.09e+01 pdb=" N PRO E1183 " 0.197 5.00e-02 4.00e+02 pdb=" CA PRO E1183 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO E1183 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU F 418 " 0.040 5.00e-02 4.00e+02 6.00e-02 5.76e+00 pdb=" N PRO F 419 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO F 419 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO F 419 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY O 109 " -0.030 5.00e-02 4.00e+02 4.49e-02 3.22e+00 pdb=" N PRO O 110 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO O 110 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO O 110 " -0.025 5.00e-02 4.00e+02 ... (remaining 9660 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 498 2.61 - 3.19: 46479 3.19 - 3.76: 86744 3.76 - 4.33: 128693 4.33 - 4.90: 202354 Nonbonded interactions: 464768 Sorted by model distance: nonbonded pdb=" NE2 HIS N 227 " pdb="FE FE N8001 " model vdw 2.042 2.340 nonbonded pdb=" OD2 ASP N 223 " pdb="FE FE N8001 " model vdw 2.058 2.260 nonbonded pdb=" NE2 HIS I 127 " pdb="FE FE I8001 " model vdw 2.080 2.340 nonbonded pdb="FE FE I8001 " pdb=" O HOH I8104 " model vdw 2.116 2.260 nonbonded pdb=" OD2 ASP C 851 " pdb=" O HOH C1101 " model vdw 2.182 2.440 ... (remaining 464763 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain '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: 9.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 43.320 Check model and map are aligned: 0.590 Set scattering table: 0.430 Process input model: 117.180 Find NCS groups from input model: 1.560 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 183.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 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 : 0.002 0.094 55432 Z= 0.153 Angle : 0.455 9.946 74929 Z= 0.240 Chirality : 0.041 0.264 8114 Planarity : 0.004 0.114 9663 Dihedral : 11.765 89.831 20873 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.73 % Favored : 97.24 % Rotamer: Outliers : 0.44 % Allowed : 4.49 % Favored : 95.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.50 % Cis-general : 0.00 % Twisted Proline : 0.30 % 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: 0.35 (0.10), residues: 6525 helix: 0.47 (0.10), residues: 2769 sheet: 0.40 (0.17), residues: 877 loop : 0.13 (0.12), residues: 2879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP K 127 HIS 0.005 0.001 HIS M 142 PHE 0.012 0.001 PHE E1284 TYR 0.013 0.001 TYR C 681 ARG 0.003 0.000 ARG S 244 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13050 Ramachandran restraints generated. 6525 Oldfield, 0 Emsley, 6525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13050 Ramachandran restraints generated. 6525 Oldfield, 0 Emsley, 6525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 823 residues out of total 5900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 797 time to evaluate : 4.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 21 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7324 (tp30) REVERT: C 366 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7805 (mp0) REVERT: C 595 GLU cc_start: 0.7380 (mt-10) cc_final: 0.7141 (mt-10) REVERT: D 298 ARG cc_start: 0.7520 (ttm-80) cc_final: 0.7267 (mtt-85) REVERT: D 345 MET cc_start: 0.4521 (mtp) cc_final: 0.4309 (mtt) REVERT: E 330 GLU cc_start: 0.7588 (tt0) cc_final: 0.7265 (tm-30) REVERT: E 579 ILE cc_start: 0.8430 (mt) cc_final: 0.8145 (mp) REVERT: E 610 ARG cc_start: 0.6653 (ptt-90) cc_final: 0.6392 (ptt-90) REVERT: E 861 GLU cc_start: 0.7486 (tt0) cc_final: 0.7186 (tm-30) REVERT: G 445 TYR cc_start: 0.7231 (t80) cc_final: 0.6960 (t80) REVERT: G 541 PHE cc_start: 0.7491 (m-80) cc_final: 0.7059 (t80) REVERT: G 586 MET cc_start: 0.6851 (mtt) cc_final: 0.6537 (mtp) REVERT: G 596 MET cc_start: 0.7565 (mtm) cc_final: 0.6809 (mtm) REVERT: G 620 GLU cc_start: 0.6729 (tt0) cc_final: 0.6356 (tp30) REVERT: G 624 ASN cc_start: 0.1998 (OUTLIER) cc_final: 0.1479 (m-40) REVERT: H 416 MET cc_start: 0.7881 (ptp) cc_final: 0.7648 (ptm) REVERT: J 287 ARG cc_start: 0.9214 (OUTLIER) cc_final: 0.7996 (mtm110) REVERT: K 280 GLU cc_start: 0.7244 (pp20) cc_final: 0.7034 (pp20) REVERT: L 87 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7759 (tmt-80) REVERT: N 70 ASP cc_start: 0.8101 (m-30) cc_final: 0.7682 (m-30) REVERT: P 174 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8359 (tp) REVERT: P 184 ASP cc_start: 0.7671 (p0) cc_final: 0.7432 (p0) REVERT: R 37 GLN cc_start: 0.7476 (tm-30) cc_final: 0.7101 (tm-30) REVERT: S 355 MET cc_start: 0.8392 (tpt) cc_final: 0.7968 (tpt) REVERT: T 48 LYS cc_start: 0.8375 (tttt) cc_final: 0.8127 (tmmt) outliers start: 26 outliers final: 10 residues processed: 817 average time/residue: 1.6654 time to fit residues: 1649.7788 Evaluate side-chains 662 residues out of total 5900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 648 time to evaluate : 4.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain D residue 514 PHE Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain G residue 624 ASN Chi-restraints excluded: chain G residue 649 ILE Chi-restraints excluded: chain G residue 747 VAL Chi-restraints excluded: chain J residue 287 ARG Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain O residue 128 ASN Chi-restraints excluded: chain P residue 174 LEU Chi-restraints excluded: chain R residue 50 THR Chi-restraints excluded: chain S residue 562 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 556 optimal weight: 0.9990 chunk 499 optimal weight: 0.9980 chunk 277 optimal weight: 3.9990 chunk 170 optimal weight: 5.9990 chunk 336 optimal weight: 20.0000 chunk 266 optimal weight: 10.0000 chunk 516 optimal weight: 1.9990 chunk 199 optimal weight: 6.9990 chunk 314 optimal weight: 20.0000 chunk 384 optimal weight: 9.9990 chunk 598 optimal weight: 9.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 76 ASN A 105 ASN A 196 GLN A 301 ASN B 132 ASN B 196 GLN B 216 HIS C 19 GLN C 322 GLN C 623 HIS D 324 GLN D 417 GLN D 518 ASN D 583 ASN E 370 HIS E 398 HIS E 863 ASN E1027 ASN E1032 ASN E1212 GLN E1282 GLN E1291 GLN F 123 GLN F 495 GLN F 838 HIS G 624 ASN G 754 GLN G 777 HIS H 142 GLN H 308 ASN ** H 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 111 ASN J 329 GLN K 255 GLN L 438 GLN N 242 ASN O 85 GLN O 183 ASN P 88 GLN Q 751 HIS R 114 ASN S 361 GLN T 81 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 55432 Z= 0.249 Angle : 0.554 13.438 74929 Z= 0.293 Chirality : 0.045 0.301 8114 Planarity : 0.005 0.146 9663 Dihedral : 5.064 58.331 7355 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.99 % Favored : 96.97 % Rotamer: Outliers : 1.51 % Allowed : 8.68 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.50 % Cis-general : 0.00 % Twisted Proline : 0.30 % 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: 0.69 (0.10), residues: 6525 helix: 0.99 (0.10), residues: 2789 sheet: 0.45 (0.17), residues: 854 loop : 0.07 (0.12), residues: 2882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP K 127 HIS 0.007 0.001 HIS M 142 PHE 0.021 0.002 PHE L 150 TYR 0.022 0.002 TYR G 458 ARG 0.006 0.001 ARG D 297 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13050 Ramachandran restraints generated. 6525 Oldfield, 0 Emsley, 6525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13050 Ramachandran restraints generated. 6525 Oldfield, 0 Emsley, 6525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 787 residues out of total 5900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 698 time to evaluate : 4.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ASN cc_start: 0.7786 (OUTLIER) cc_final: 0.7551 (m-40) REVERT: C 79 GLU cc_start: 0.6843 (mp0) cc_final: 0.6468 (mp0) REVERT: C 108 ASN cc_start: 0.7071 (t0) cc_final: 0.6838 (t0) REVERT: C 323 ASP cc_start: 0.7764 (t0) cc_final: 0.7448 (t0) REVERT: C 366 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7718 (mp0) REVERT: C 923 TYR cc_start: 0.9125 (OUTLIER) cc_final: 0.8839 (p90) REVERT: D 221 GLN cc_start: 0.8101 (tm-30) cc_final: 0.7557 (tm-30) REVERT: D 236 LYS cc_start: 0.7847 (tptp) cc_final: 0.7624 (tppt) REVERT: E 244 GLN cc_start: 0.7940 (tp40) cc_final: 0.7739 (tp-100) REVERT: E 579 ILE cc_start: 0.8412 (mt) cc_final: 0.8133 (mp) REVERT: E 610 ARG cc_start: 0.6752 (ptt-90) cc_final: 0.6501 (ptt-90) REVERT: E 861 GLU cc_start: 0.7589 (tt0) cc_final: 0.7189 (tm-30) REVERT: E 868 ILE cc_start: 0.8277 (mm) cc_final: 0.8004 (mm) REVERT: K 280 GLU cc_start: 0.7235 (pp20) cc_final: 0.7029 (pp20) REVERT: L 212 GLN cc_start: 0.7910 (mp10) cc_final: 0.7573 (mt0) REVERT: N 66 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7539 (ttt90) REVERT: N 267 GLN cc_start: 0.7873 (tm-30) cc_final: 0.7623 (tm-30) REVERT: P 184 ASP cc_start: 0.7594 (p0) cc_final: 0.7323 (p0) REVERT: R 37 GLN cc_start: 0.7444 (tm-30) cc_final: 0.6914 (tm-30) REVERT: T 48 LYS cc_start: 0.8434 (tttt) cc_final: 0.8170 (tmmt) outliers start: 89 outliers final: 35 residues processed: 750 average time/residue: 1.6730 time to fit residues: 1521.8019 Evaluate side-chains 686 residues out of total 5900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 648 time to evaluate : 4.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 319 LYS Chi-restraints excluded: chain B residue 109 CYS Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 923 TYR Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 514 PHE Chi-restraints excluded: chain D residue 517 MET Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 84 LYS Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 808 ILE Chi-restraints excluded: chain E residue 1182 ILE Chi-restraints excluded: chain F residue 385 ILE Chi-restraints excluded: chain F residue 443 THR Chi-restraints excluded: chain G residue 481 MET Chi-restraints excluded: chain G residue 649 ILE Chi-restraints excluded: chain G residue 747 VAL Chi-restraints excluded: chain J residue 270 LYS Chi-restraints excluded: chain J residue 427 ILE Chi-restraints excluded: chain K residue 277 SER Chi-restraints excluded: chain K residue 284 LEU Chi-restraints excluded: chain L residue 365 VAL Chi-restraints excluded: chain M residue 244 VAL Chi-restraints excluded: chain M residue 256 LYS Chi-restraints excluded: chain N residue 66 ARG Chi-restraints excluded: chain N residue 264 ARG Chi-restraints excluded: chain O residue 126 GLU Chi-restraints excluded: chain O residue 128 ASN Chi-restraints excluded: chain P residue 153 THR Chi-restraints excluded: chain Q residue 638 GLU Chi-restraints excluded: chain Q residue 647 SER Chi-restraints excluded: chain R residue 50 THR Chi-restraints excluded: chain S residue 194 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 332 optimal weight: 5.9990 chunk 185 optimal weight: 9.9990 chunk 498 optimal weight: 3.9990 chunk 407 optimal weight: 10.0000 chunk 165 optimal weight: 1.9990 chunk 599 optimal weight: 10.0000 chunk 647 optimal weight: 10.0000 chunk 533 optimal weight: 0.9990 chunk 594 optimal weight: 8.9990 chunk 204 optimal weight: 9.9990 chunk 480 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A 301 ASN B 132 ASN D 324 GLN E 398 HIS E1212 GLN E1282 GLN F 123 GLN F 495 GLN G 777 HIS H 308 ASN ** H 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 111 ASN J 329 GLN ** K 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 255 GLN ** L 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 85 GLN O 88 GLN O 183 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 55432 Z= 0.345 Angle : 0.599 11.397 74929 Z= 0.317 Chirality : 0.047 0.278 8114 Planarity : 0.005 0.123 9663 Dihedral : 5.105 62.753 7341 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.25 % Favored : 96.70 % Rotamer: Outliers : 1.93 % Allowed : 9.36 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.50 % Cis-general : 0.00 % Twisted Proline : 0.30 % 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: 0.70 (0.10), residues: 6525 helix: 1.08 (0.10), residues: 2777 sheet: 0.48 (0.17), residues: 817 loop : -0.03 (0.11), residues: 2931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP K 127 HIS 0.008 0.001 HIS I 127 PHE 0.026 0.002 PHE K 103 TYR 0.019 0.002 TYR A 74 ARG 0.010 0.001 ARG F 393 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13050 Ramachandran restraints generated. 6525 Oldfield, 0 Emsley, 6525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13050 Ramachandran restraints generated. 6525 Oldfield, 0 Emsley, 6525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 787 residues out of total 5900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 673 time to evaluate : 4.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASP cc_start: 0.8367 (OUTLIER) cc_final: 0.8130 (m-30) REVERT: C 79 GLU cc_start: 0.6809 (mp0) cc_final: 0.6456 (mp0) REVERT: C 323 ASP cc_start: 0.7796 (t0) cc_final: 0.7535 (t0) REVERT: C 366 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7676 (mp0) REVERT: C 599 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7878 (tp) REVERT: C 923 TYR cc_start: 0.9120 (OUTLIER) cc_final: 0.8895 (p90) REVERT: D 221 GLN cc_start: 0.8134 (tm-30) cc_final: 0.7559 (tm-30) REVERT: D 236 LYS cc_start: 0.7873 (tptp) cc_final: 0.7642 (tppt) REVERT: D 423 ILE cc_start: 0.8471 (mm) cc_final: 0.8264 (mm) REVERT: E 579 ILE cc_start: 0.8403 (mt) cc_final: 0.8132 (mp) REVERT: E 610 ARG cc_start: 0.6800 (ptt-90) cc_final: 0.6539 (ptt-90) REVERT: E 861 GLU cc_start: 0.7604 (tt0) cc_final: 0.7163 (tm-30) REVERT: E 1135 GLU cc_start: 0.5707 (tm-30) cc_final: 0.4839 (tt0) REVERT: F 392 ARG cc_start: 0.7810 (OUTLIER) cc_final: 0.7599 (tpp-160) REVERT: G 721 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.8237 (ttp) REVERT: G 793 MET cc_start: 0.7596 (tmm) cc_final: 0.7302 (tmm) REVERT: K 280 GLU cc_start: 0.7252 (pp20) cc_final: 0.7012 (pp20) REVERT: L 87 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.7974 (tmt-80) REVERT: L 159 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7233 (tp30) REVERT: L 415 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.7389 (mtt-85) REVERT: L 440 GLN cc_start: 0.7927 (tp40) cc_final: 0.7716 (tp-100) REVERT: N 66 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7584 (ttt90) REVERT: N 267 GLN cc_start: 0.7849 (tm-30) cc_final: 0.7566 (tm-30) REVERT: O 169 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7598 (mt-10) REVERT: P 184 ASP cc_start: 0.7517 (p0) cc_final: 0.7286 (p0) REVERT: R 37 GLN cc_start: 0.7410 (tm-30) cc_final: 0.6847 (tm-30) REVERT: R 112 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7239 (mp0) REVERT: S 355 MET cc_start: 0.8574 (tpt) cc_final: 0.8227 (tpt) REVERT: S 437 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7740 (mm-30) REVERT: S 439 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7608 (pm20) REVERT: T 48 LYS cc_start: 0.8497 (tttt) cc_final: 0.8231 (tmmt) outliers start: 114 outliers final: 45 residues processed: 737 average time/residue: 1.7005 time to fit residues: 1518.7749 Evaluate side-chains 715 residues out of total 5900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 658 time to evaluate : 4.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 105 ASN Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 319 LYS Chi-restraints excluded: chain B residue 109 CYS Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 599 LEU Chi-restraints excluded: chain C residue 923 TYR Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 205 ASP Chi-restraints excluded: chain D residue 514 PHE Chi-restraints excluded: chain D residue 517 MET Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 401 THR Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 808 ILE Chi-restraints excluded: chain E residue 1182 ILE Chi-restraints excluded: chain E residue 1266 CYS Chi-restraints excluded: chain F residue 392 ARG Chi-restraints excluded: chain F residue 443 THR Chi-restraints excluded: chain G residue 481 MET Chi-restraints excluded: chain G residue 542 GLU Chi-restraints excluded: chain G residue 549 VAL Chi-restraints excluded: chain G residue 649 ILE Chi-restraints excluded: chain G residue 721 MET Chi-restraints excluded: chain G residue 747 VAL Chi-restraints excluded: chain J residue 270 LYS Chi-restraints excluded: chain J residue 427 ILE Chi-restraints excluded: chain K residue 277 SER Chi-restraints excluded: chain K residue 284 LEU Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain L residue 109 ASP Chi-restraints excluded: chain L residue 159 GLU Chi-restraints excluded: chain L residue 365 VAL Chi-restraints excluded: chain L residue 415 ARG Chi-restraints excluded: chain M residue 244 VAL Chi-restraints excluded: chain M residue 256 LYS Chi-restraints excluded: chain N residue 66 ARG Chi-restraints excluded: chain N residue 264 ARG Chi-restraints excluded: chain O residue 128 ASN Chi-restraints excluded: chain O residue 158 SER Chi-restraints excluded: chain O residue 169 GLU Chi-restraints excluded: chain P residue 112 ILE Chi-restraints excluded: chain P residue 153 THR Chi-restraints excluded: chain Q residue 638 GLU Chi-restraints excluded: chain Q residue 647 SER Chi-restraints excluded: chain R residue 36 ILE Chi-restraints excluded: chain R residue 50 THR Chi-restraints excluded: chain R residue 112 GLU Chi-restraints excluded: chain S residue 194 SER Chi-restraints excluded: chain S residue 439 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 592 optimal weight: 7.9990 chunk 450 optimal weight: 1.9990 chunk 311 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 286 optimal weight: 7.9990 chunk 402 optimal weight: 10.0000 chunk 601 optimal weight: 9.9990 chunk 636 optimal weight: 2.9990 chunk 314 optimal weight: 20.0000 chunk 570 optimal weight: 0.6980 chunk 171 optimal weight: 10.0000 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN B 132 ASN E 398 HIS E1212 GLN E1282 GLN F 495 GLN G 777 HIS H 308 ASN ** H 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 68 GLN I 111 ASN J 329 GLN ** K 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 255 GLN M 190 GLN ** O 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 183 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 55432 Z= 0.265 Angle : 0.547 11.100 74929 Z= 0.290 Chirality : 0.045 0.275 8114 Planarity : 0.005 0.116 9663 Dihedral : 4.989 61.810 7341 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.03 % Favored : 96.92 % Rotamer: Outliers : 1.73 % Allowed : 10.39 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.50 % Cis-general : 0.00 % Twisted Proline : 0.30 % 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: 0.77 (0.10), residues: 6525 helix: 1.18 (0.10), residues: 2790 sheet: 0.40 (0.17), residues: 846 loop : -0.00 (0.11), residues: 2889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP K 127 HIS 0.007 0.001 HIS F 344 PHE 0.023 0.002 PHE L 150 TYR 0.017 0.002 TYR M 251 ARG 0.009 0.000 ARG F 393 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13050 Ramachandran restraints generated. 6525 Oldfield, 0 Emsley, 6525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13050 Ramachandran restraints generated. 6525 Oldfield, 0 Emsley, 6525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 771 residues out of total 5900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 669 time to evaluate : 4.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASP cc_start: 0.8371 (OUTLIER) cc_final: 0.8129 (m-30) REVERT: C 79 GLU cc_start: 0.6791 (mp0) cc_final: 0.6423 (mp0) REVERT: C 323 ASP cc_start: 0.7784 (t0) cc_final: 0.7531 (t0) REVERT: C 366 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7629 (mp0) REVERT: C 599 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7897 (tp) REVERT: C 923 TYR cc_start: 0.9107 (OUTLIER) cc_final: 0.8870 (p90) REVERT: D 221 GLN cc_start: 0.8111 (tm-30) cc_final: 0.7568 (tm-30) REVERT: D 236 LYS cc_start: 0.7862 (tptp) cc_final: 0.7641 (tppt) REVERT: E 579 ILE cc_start: 0.8389 (mt) cc_final: 0.8128 (mp) REVERT: E 610 ARG cc_start: 0.6792 (ptt-90) cc_final: 0.6545 (ptt-90) REVERT: E 861 GLU cc_start: 0.7602 (tt0) cc_final: 0.7165 (tm-30) REVERT: G 473 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.6981 (mp0) REVERT: G 721 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.8265 (ttp) REVERT: G 793 MET cc_start: 0.7585 (tmm) cc_final: 0.7316 (tmm) REVERT: K 243 SER cc_start: 0.7785 (t) cc_final: 0.7549 (t) REVERT: K 280 GLU cc_start: 0.7225 (pp20) cc_final: 0.6994 (pp20) REVERT: L 87 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7933 (tmt-80) REVERT: L 159 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.7208 (tp30) REVERT: L 415 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.7486 (mtt-85) REVERT: M 190 GLN cc_start: 0.8741 (mm-40) cc_final: 0.8539 (mm110) REVERT: N 66 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7560 (ttt90) REVERT: N 267 GLN cc_start: 0.7843 (tm-30) cc_final: 0.7568 (tm-30) REVERT: N 269 GLU cc_start: 0.7217 (mt-10) cc_final: 0.6965 (mt-10) REVERT: O 169 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7597 (mt-10) REVERT: P 120 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.7952 (ttp) REVERT: P 184 ASP cc_start: 0.7514 (p0) cc_final: 0.7259 (p0) REVERT: R 37 GLN cc_start: 0.7385 (tm-30) cc_final: 0.6838 (tm-30) REVERT: R 112 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7202 (mp0) REVERT: S 355 MET cc_start: 0.8587 (tpt) cc_final: 0.8141 (tpt) REVERT: S 437 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7756 (mm-30) REVERT: S 439 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7620 (pm20) REVERT: S 587 MET cc_start: 0.6266 (OUTLIER) cc_final: 0.5995 (mtm) REVERT: T 48 LYS cc_start: 0.8493 (tttt) cc_final: 0.8237 (tmmt) outliers start: 102 outliers final: 46 residues processed: 723 average time/residue: 1.7135 time to fit residues: 1497.0655 Evaluate side-chains 713 residues out of total 5900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 653 time to evaluate : 4.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 105 ASN Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 319 LYS Chi-restraints excluded: chain B residue 109 CYS Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 599 LEU Chi-restraints excluded: chain C residue 923 TYR Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 205 ASP Chi-restraints excluded: chain D residue 514 PHE Chi-restraints excluded: chain D residue 517 MET Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 401 THR Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 808 ILE Chi-restraints excluded: chain E residue 1182 ILE Chi-restraints excluded: chain E residue 1266 CYS Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain F residue 443 THR Chi-restraints excluded: chain F residue 836 THR Chi-restraints excluded: chain G residue 473 GLU Chi-restraints excluded: chain G residue 481 MET Chi-restraints excluded: chain G residue 649 ILE Chi-restraints excluded: chain G residue 721 MET Chi-restraints excluded: chain G residue 747 VAL Chi-restraints excluded: chain H residue 215 ASP Chi-restraints excluded: chain H residue 378 CYS Chi-restraints excluded: chain J residue 270 LYS Chi-restraints excluded: chain J residue 427 ILE Chi-restraints excluded: chain K residue 277 SER Chi-restraints excluded: chain K residue 284 LEU Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain L residue 109 ASP Chi-restraints excluded: chain L residue 159 GLU Chi-restraints excluded: chain L residue 365 VAL Chi-restraints excluded: chain L residue 415 ARG Chi-restraints excluded: chain M residue 256 LYS Chi-restraints excluded: chain M residue 296 VAL Chi-restraints excluded: chain N residue 66 ARG Chi-restraints excluded: chain N residue 264 ARG Chi-restraints excluded: chain O residue 128 ASN Chi-restraints excluded: chain O residue 158 SER Chi-restraints excluded: chain O residue 169 GLU Chi-restraints excluded: chain P residue 112 ILE Chi-restraints excluded: chain P residue 120 MET Chi-restraints excluded: chain P residue 153 THR Chi-restraints excluded: chain Q residue 647 SER Chi-restraints excluded: chain R residue 50 THR Chi-restraints excluded: chain R residue 94 ASP Chi-restraints excluded: chain R residue 112 GLU Chi-restraints excluded: chain S residue 194 SER Chi-restraints excluded: chain S residue 439 GLU Chi-restraints excluded: chain S residue 562 ASN Chi-restraints excluded: chain S residue 587 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 530 optimal weight: 5.9990 chunk 361 optimal weight: 0.6980 chunk 9 optimal weight: 10.0000 chunk 474 optimal weight: 10.0000 chunk 262 optimal weight: 8.9990 chunk 543 optimal weight: 6.9990 chunk 440 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 325 optimal weight: 20.0000 chunk 571 optimal weight: 0.8980 chunk 160 optimal weight: 8.9990 overall best weight: 4.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 ASN A 303 GLN B 132 ASN D 583 ASN E1038 ASN E1212 GLN E1282 GLN G 754 GLN G 777 HIS H 308 ASN I 111 ASN J 329 GLN ** K 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 255 GLN ** L 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 440 GLN O 183 ASN R 114 ASN S 277 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 55432 Z= 0.368 Angle : 0.613 12.337 74929 Z= 0.324 Chirality : 0.048 0.282 8114 Planarity : 0.005 0.114 9663 Dihedral : 5.192 64.329 7341 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.33 % Favored : 96.63 % Rotamer: Outliers : 2.07 % Allowed : 10.80 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.50 % Cis-general : 0.00 % Twisted Proline : 0.30 % 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: 0.66 (0.10), residues: 6525 helix: 1.11 (0.10), residues: 2773 sheet: 0.42 (0.17), residues: 823 loop : -0.09 (0.11), residues: 2929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP K 127 HIS 0.007 0.001 HIS I 127 PHE 0.027 0.002 PHE B 226 TYR 0.020 0.002 TYR M 251 ARG 0.009 0.001 ARG T 56 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13050 Ramachandran restraints generated. 6525 Oldfield, 0 Emsley, 6525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13050 Ramachandran restraints generated. 6525 Oldfield, 0 Emsley, 6525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 792 residues out of total 5900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 670 time to evaluate : 4.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASP cc_start: 0.8368 (OUTLIER) cc_final: 0.8131 (m-30) REVERT: C 79 GLU cc_start: 0.6787 (mp0) cc_final: 0.6440 (mp0) REVERT: C 323 ASP cc_start: 0.7806 (t0) cc_final: 0.7456 (t0) REVERT: C 366 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7629 (mp0) REVERT: C 599 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7912 (tp) REVERT: C 923 TYR cc_start: 0.9117 (OUTLIER) cc_final: 0.8875 (p90) REVERT: D 221 GLN cc_start: 0.8104 (tm-30) cc_final: 0.7542 (tm-30) REVERT: E 436 GLU cc_start: 0.3218 (pm20) cc_final: 0.2868 (pm20) REVERT: E 579 ILE cc_start: 0.8406 (mt) cc_final: 0.8151 (mp) REVERT: E 610 ARG cc_start: 0.6823 (ptt-90) cc_final: 0.6563 (ptt-90) REVERT: E 861 GLU cc_start: 0.7596 (tt0) cc_final: 0.7168 (tm-30) REVERT: E 1029 ARG cc_start: 0.6895 (OUTLIER) cc_final: 0.6241 (mtm-85) REVERT: E 1135 GLU cc_start: 0.5639 (tm-30) cc_final: 0.4527 (tt0) REVERT: G 473 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.6966 (mp0) REVERT: G 721 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.8301 (ttp) REVERT: G 793 MET cc_start: 0.7603 (tmm) cc_final: 0.7240 (tmm) REVERT: K 243 SER cc_start: 0.7799 (t) cc_final: 0.7566 (t) REVERT: K 280 GLU cc_start: 0.7255 (pp20) cc_final: 0.6921 (pp20) REVERT: L 87 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7996 (tmt-80) REVERT: L 159 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.7236 (tp30) REVERT: L 415 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.7491 (mtt-85) REVERT: N 66 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7582 (ttt90) REVERT: N 267 GLN cc_start: 0.7848 (tm-30) cc_final: 0.7605 (tm-30) REVERT: O 169 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7584 (mt-10) REVERT: P 120 MET cc_start: 0.8240 (OUTLIER) cc_final: 0.7947 (ttp) REVERT: P 184 ASP cc_start: 0.7471 (p0) cc_final: 0.7250 (p0) REVERT: Q 698 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.7278 (ttm170) REVERT: R 37 GLN cc_start: 0.7369 (tm-30) cc_final: 0.6833 (tm-30) REVERT: R 112 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7205 (mp0) REVERT: S 355 MET cc_start: 0.8585 (tpt) cc_final: 0.8113 (tpt) REVERT: S 437 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7774 (mm-30) REVERT: S 439 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7618 (pm20) REVERT: T 48 LYS cc_start: 0.8510 (tttt) cc_final: 0.8256 (tmmt) REVERT: T 121 ASP cc_start: 0.8038 (OUTLIER) cc_final: 0.7772 (m-30) outliers start: 122 outliers final: 57 residues processed: 741 average time/residue: 1.7062 time to fit residues: 1532.0753 Evaluate side-chains 734 residues out of total 5900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 661 time to evaluate : 4.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 105 ASN Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 319 LYS Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 109 CYS Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 599 LEU Chi-restraints excluded: chain C residue 923 TYR Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 205 ASP Chi-restraints excluded: chain D residue 514 PHE Chi-restraints excluded: chain D residue 517 MET Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 318 GLU Chi-restraints excluded: chain E residue 401 THR Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 808 ILE Chi-restraints excluded: chain E residue 1029 ARG Chi-restraints excluded: chain E residue 1038 ASN Chi-restraints excluded: chain E residue 1099 VAL Chi-restraints excluded: chain E residue 1182 ILE Chi-restraints excluded: chain F residue 356 LYS Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain F residue 443 THR Chi-restraints excluded: chain F residue 836 THR Chi-restraints excluded: chain G residue 473 GLU Chi-restraints excluded: chain G residue 481 MET Chi-restraints excluded: chain G residue 542 GLU Chi-restraints excluded: chain G residue 549 VAL Chi-restraints excluded: chain G residue 649 ILE Chi-restraints excluded: chain G residue 721 MET Chi-restraints excluded: chain G residue 747 VAL Chi-restraints excluded: chain H residue 215 ASP Chi-restraints excluded: chain H residue 378 CYS Chi-restraints excluded: chain J residue 270 LYS Chi-restraints excluded: chain J residue 427 ILE Chi-restraints excluded: chain K residue 277 SER Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain L residue 109 ASP Chi-restraints excluded: chain L residue 159 GLU Chi-restraints excluded: chain L residue 365 VAL Chi-restraints excluded: chain L residue 415 ARG Chi-restraints excluded: chain M residue 244 VAL Chi-restraints excluded: chain M residue 256 LYS Chi-restraints excluded: chain M residue 296 VAL Chi-restraints excluded: chain N residue 66 ARG Chi-restraints excluded: chain N residue 252 GLU Chi-restraints excluded: chain N residue 264 ARG Chi-restraints excluded: chain O residue 128 ASN Chi-restraints excluded: chain O residue 158 SER Chi-restraints excluded: chain O residue 169 GLU Chi-restraints excluded: chain P residue 112 ILE Chi-restraints excluded: chain P residue 120 MET Chi-restraints excluded: chain P residue 153 THR Chi-restraints excluded: chain Q residue 647 SER Chi-restraints excluded: chain Q residue 698 ARG Chi-restraints excluded: chain R residue 36 ILE Chi-restraints excluded: chain R residue 50 THR Chi-restraints excluded: chain R residue 94 ASP Chi-restraints excluded: chain R residue 112 GLU Chi-restraints excluded: chain R residue 121 THR Chi-restraints excluded: chain S residue 194 SER Chi-restraints excluded: chain S residue 240 GLU Chi-restraints excluded: chain S residue 439 GLU Chi-restraints excluded: chain S residue 562 ASN Chi-restraints excluded: chain T residue 121 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 214 optimal weight: 10.0000 chunk 573 optimal weight: 6.9990 chunk 125 optimal weight: 10.0000 chunk 373 optimal weight: 6.9990 chunk 157 optimal weight: 5.9990 chunk 637 optimal weight: 7.9990 chunk 529 optimal weight: 9.9990 chunk 295 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 210 optimal weight: 7.9990 chunk 334 optimal weight: 7.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 GLN B 132 ASN ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 324 GLN ** E 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1038 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1212 GLN E1282 GLN F 495 GLN G 754 GLN G 777 HIS H 308 ASN ** H 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 111 ASN J 184 ASN J 329 GLN K 110 HIS K 255 GLN ** L 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 190 GLN O 183 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.088 55432 Z= 0.504 Angle : 0.694 13.015 74929 Z= 0.367 Chirality : 0.052 0.285 8114 Planarity : 0.006 0.116 9663 Dihedral : 5.405 64.217 7341 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.46 % Favored : 96.49 % Rotamer: Outliers : 2.07 % Allowed : 11.15 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.50 % Cis-general : 0.00 % Twisted Proline : 0.30 % 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: 0.46 (0.10), residues: 6525 helix: 0.92 (0.10), residues: 2775 sheet: 0.27 (0.17), residues: 843 loop : -0.16 (0.11), residues: 2907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP K 127 HIS 0.008 0.002 HIS E 92 PHE 0.032 0.003 PHE K 103 TYR 0.022 0.003 TYR M 251 ARG 0.007 0.001 ARG F 393 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13050 Ramachandran restraints generated. 6525 Oldfield, 0 Emsley, 6525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13050 Ramachandran restraints generated. 6525 Oldfield, 0 Emsley, 6525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 787 residues out of total 5900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 665 time to evaluate : 4.819 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 ASP cc_start: 0.8365 (OUTLIER) cc_final: 0.8133 (m-30) REVERT: B 110 VAL cc_start: 0.8345 (t) cc_final: 0.8021 (m) REVERT: C 79 GLU cc_start: 0.6794 (mp0) cc_final: 0.6445 (mp0) REVERT: C 323 ASP cc_start: 0.7827 (t0) cc_final: 0.7473 (t0) REVERT: C 366 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7623 (mp0) REVERT: C 599 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7946 (tp) REVERT: D 221 GLN cc_start: 0.8103 (tm-30) cc_final: 0.7605 (tm-30) REVERT: D 236 LYS cc_start: 0.7886 (OUTLIER) cc_final: 0.7666 (tptp) REVERT: E 579 ILE cc_start: 0.8432 (mt) cc_final: 0.8177 (mp) REVERT: E 861 GLU cc_start: 0.7619 (tt0) cc_final: 0.7179 (tm-30) REVERT: E 1029 ARG cc_start: 0.6915 (OUTLIER) cc_final: 0.6263 (mtm-85) REVERT: E 1135 GLU cc_start: 0.5660 (tm-30) cc_final: 0.4684 (tt0) REVERT: F 206 MET cc_start: 0.8954 (OUTLIER) cc_final: 0.8256 (mtm) REVERT: G 473 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.6983 (mp0) REVERT: G 721 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.8278 (ttp) REVERT: G 793 MET cc_start: 0.7615 (tmm) cc_final: 0.7307 (tmm) REVERT: L 87 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.8015 (tmt-80) REVERT: L 415 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.7529 (mtt-85) REVERT: L 440 GLN cc_start: 0.7702 (tp40) cc_final: 0.7119 (tm130) REVERT: M 256 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.7989 (mmmt) REVERT: N 66 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7619 (ttt90) REVERT: N 267 GLN cc_start: 0.7842 (tm-30) cc_final: 0.7601 (tm-30) REVERT: N 269 GLU cc_start: 0.7272 (mt-10) cc_final: 0.7036 (mt-10) REVERT: P 184 ASP cc_start: 0.7460 (p0) cc_final: 0.7232 (p0) REVERT: Q 698 ARG cc_start: 0.7900 (OUTLIER) cc_final: 0.7309 (ttm170) REVERT: R 37 GLN cc_start: 0.7365 (tm-30) cc_final: 0.6867 (tm-30) REVERT: R 112 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7230 (mp0) REVERT: S 355 MET cc_start: 0.8552 (tpt) cc_final: 0.8136 (tpt) REVERT: S 439 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7628 (pm20) REVERT: T 48 LYS cc_start: 0.8532 (tttt) cc_final: 0.8283 (tmmt) REVERT: T 121 ASP cc_start: 0.7980 (OUTLIER) cc_final: 0.7753 (m-30) outliers start: 122 outliers final: 60 residues processed: 733 average time/residue: 1.7021 time to fit residues: 1509.4776 Evaluate side-chains 724 residues out of total 5900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 649 time to evaluate : 4.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 105 ASN Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 319 LYS Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 599 LEU Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 205 ASP Chi-restraints excluded: chain D residue 236 LYS Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 514 PHE Chi-restraints excluded: chain D residue 517 MET Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 401 THR Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 1029 ARG Chi-restraints excluded: chain E residue 1099 VAL Chi-restraints excluded: chain E residue 1182 ILE Chi-restraints excluded: chain F residue 206 MET Chi-restraints excluded: chain F residue 356 LYS Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain F residue 443 THR Chi-restraints excluded: chain F residue 836 THR Chi-restraints excluded: chain G residue 473 GLU Chi-restraints excluded: chain G residue 481 MET Chi-restraints excluded: chain G residue 542 GLU Chi-restraints excluded: chain G residue 549 VAL Chi-restraints excluded: chain G residue 649 ILE Chi-restraints excluded: chain G residue 721 MET Chi-restraints excluded: chain G residue 747 VAL Chi-restraints excluded: chain H residue 215 ASP Chi-restraints excluded: chain H residue 378 CYS Chi-restraints excluded: chain J residue 270 LYS Chi-restraints excluded: chain J residue 427 ILE Chi-restraints excluded: chain K residue 277 SER Chi-restraints excluded: chain K residue 284 LEU Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain L residue 109 ASP Chi-restraints excluded: chain L residue 365 VAL Chi-restraints excluded: chain L residue 415 ARG Chi-restraints excluded: chain M residue 244 VAL Chi-restraints excluded: chain M residue 256 LYS Chi-restraints excluded: chain M residue 296 VAL Chi-restraints excluded: chain N residue 66 ARG Chi-restraints excluded: chain N residue 252 GLU Chi-restraints excluded: chain N residue 264 ARG Chi-restraints excluded: chain O residue 127 SER Chi-restraints excluded: chain O residue 128 ASN Chi-restraints excluded: chain O residue 158 SER Chi-restraints excluded: chain P residue 112 ILE Chi-restraints excluded: chain P residue 120 MET Chi-restraints excluded: chain P residue 153 THR Chi-restraints excluded: chain Q residue 361 SER Chi-restraints excluded: chain Q residue 647 SER Chi-restraints excluded: chain Q residue 698 ARG Chi-restraints excluded: chain R residue 36 ILE Chi-restraints excluded: chain R residue 50 THR Chi-restraints excluded: chain R residue 94 ASP Chi-restraints excluded: chain R residue 112 GLU Chi-restraints excluded: chain R residue 116 ASP Chi-restraints excluded: chain R residue 121 THR Chi-restraints excluded: chain S residue 194 SER Chi-restraints excluded: chain S residue 240 GLU Chi-restraints excluded: chain S residue 439 GLU Chi-restraints excluded: chain S residue 490 SER Chi-restraints excluded: chain S residue 562 ASN Chi-restraints excluded: chain T residue 121 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 614 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 363 optimal weight: 6.9990 chunk 465 optimal weight: 10.0000 chunk 360 optimal weight: 2.9990 chunk 536 optimal weight: 0.9980 chunk 356 optimal weight: 0.7980 chunk 635 optimal weight: 3.9990 chunk 397 optimal weight: 1.9990 chunk 387 optimal weight: 8.9990 chunk 293 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN A 303 GLN B 132 ASN D 583 ASN E 398 HIS E1151 GLN E1212 GLN E1282 GLN F 123 GLN F 495 GLN G 777 HIS H 308 ASN H 409 GLN I 111 ASN J 329 GLN K 255 GLN ** L 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 190 GLN O 183 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 55432 Z= 0.206 Angle : 0.518 10.781 74929 Z= 0.275 Chirality : 0.043 0.266 8114 Planarity : 0.004 0.115 9663 Dihedral : 4.939 61.710 7341 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.80 % Favored : 97.15 % Rotamer: Outliers : 1.47 % Allowed : 12.04 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.50 % Cis-general : 0.00 % Twisted Proline : 0.30 % 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: 0.82 (0.10), residues: 6525 helix: 1.29 (0.10), residues: 2778 sheet: 0.33 (0.17), residues: 881 loop : -0.02 (0.12), residues: 2866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP K 127 HIS 0.007 0.001 HIS E 398 PHE 0.020 0.001 PHE L 150 TYR 0.015 0.001 TYR M 251 ARG 0.008 0.000 ARG F 393 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13050 Ramachandran restraints generated. 6525 Oldfield, 0 Emsley, 6525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13050 Ramachandran restraints generated. 6525 Oldfield, 0 Emsley, 6525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 754 residues out of total 5900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 667 time to evaluate : 5.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASP cc_start: 0.8370 (OUTLIER) cc_final: 0.8121 (m-30) REVERT: C 79 GLU cc_start: 0.6753 (mp0) cc_final: 0.6375 (mp0) REVERT: C 323 ASP cc_start: 0.7813 (t0) cc_final: 0.7554 (t0) REVERT: C 366 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7627 (mp0) REVERT: C 599 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7905 (tp) REVERT: C 622 MET cc_start: 0.7661 (mtt) cc_final: 0.7226 (mtp) REVERT: C 923 TYR cc_start: 0.9079 (OUTLIER) cc_final: 0.8841 (p90) REVERT: D 221 GLN cc_start: 0.8147 (tm-30) cc_final: 0.7599 (tm-30) REVERT: E 244 GLN cc_start: 0.7934 (tp40) cc_final: 0.7710 (tp-100) REVERT: E 579 ILE cc_start: 0.8397 (mt) cc_final: 0.8149 (mp) REVERT: E 610 ARG cc_start: 0.6846 (ptt-90) cc_final: 0.6461 (ptt-90) REVERT: E 861 GLU cc_start: 0.7587 (tt0) cc_final: 0.7137 (tm-30) REVERT: E 1029 ARG cc_start: 0.6897 (OUTLIER) cc_final: 0.6245 (mtm-85) REVERT: F 206 MET cc_start: 0.8920 (OUTLIER) cc_final: 0.8619 (mtp) REVERT: G 473 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.6965 (mp0) REVERT: G 586 MET cc_start: 0.6904 (mtt) cc_final: 0.6527 (ttt) REVERT: G 721 MET cc_start: 0.8561 (OUTLIER) cc_final: 0.8306 (ttp) REVERT: L 87 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.8027 (tmt-80) REVERT: M 256 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.7958 (mmmt) REVERT: N 66 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7539 (ttt90) REVERT: N 103 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8598 (tp) REVERT: N 264 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.8000 (tmt170) REVERT: N 267 GLN cc_start: 0.7862 (tm-30) cc_final: 0.7633 (tm-30) REVERT: N 269 GLU cc_start: 0.7287 (mt-10) cc_final: 0.7018 (mt-10) REVERT: P 184 ASP cc_start: 0.7420 (p0) cc_final: 0.7184 (p0) REVERT: Q 698 ARG cc_start: 0.7819 (OUTLIER) cc_final: 0.6956 (ttm-80) REVERT: R 37 GLN cc_start: 0.7269 (tm-30) cc_final: 0.6832 (tm-30) REVERT: R 112 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7171 (mp0) REVERT: S 355 MET cc_start: 0.8603 (tpt) cc_final: 0.8397 (tpt) REVERT: T 48 LYS cc_start: 0.8491 (tttt) cc_final: 0.8243 (tmmt) REVERT: T 121 ASP cc_start: 0.7909 (OUTLIER) cc_final: 0.7666 (m-30) outliers start: 87 outliers final: 39 residues processed: 712 average time/residue: 1.7445 time to fit residues: 1505.0667 Evaluate side-chains 705 residues out of total 5900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 651 time to evaluate : 4.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 105 ASN Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 319 LYS Chi-restraints excluded: chain B residue 109 CYS Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 599 LEU Chi-restraints excluded: chain C residue 923 TYR Chi-restraints excluded: chain D residue 205 ASP Chi-restraints excluded: chain D residue 514 PHE Chi-restraints excluded: chain D residue 517 MET Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 401 THR Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 1029 ARG Chi-restraints excluded: chain E residue 1182 ILE Chi-restraints excluded: chain F residue 206 MET Chi-restraints excluded: chain F residue 443 THR Chi-restraints excluded: chain F residue 836 THR Chi-restraints excluded: chain G residue 473 GLU Chi-restraints excluded: chain G residue 481 MET Chi-restraints excluded: chain G residue 649 ILE Chi-restraints excluded: chain G residue 721 MET Chi-restraints excluded: chain G residue 747 VAL Chi-restraints excluded: chain H residue 378 CYS Chi-restraints excluded: chain J residue 270 LYS Chi-restraints excluded: chain K residue 277 SER Chi-restraints excluded: chain K residue 284 LEU Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain L residue 109 ASP Chi-restraints excluded: chain L residue 365 VAL Chi-restraints excluded: chain M residue 244 VAL Chi-restraints excluded: chain M residue 256 LYS Chi-restraints excluded: chain N residue 66 ARG Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 264 ARG Chi-restraints excluded: chain O residue 127 SER Chi-restraints excluded: chain O residue 128 ASN Chi-restraints excluded: chain O residue 158 SER Chi-restraints excluded: chain P residue 112 ILE Chi-restraints excluded: chain Q residue 647 SER Chi-restraints excluded: chain Q residue 698 ARG Chi-restraints excluded: chain R residue 36 ILE Chi-restraints excluded: chain R residue 50 THR Chi-restraints excluded: chain R residue 94 ASP Chi-restraints excluded: chain R residue 112 GLU Chi-restraints excluded: chain S residue 194 SER Chi-restraints excluded: chain S residue 562 ASN Chi-restraints excluded: chain T residue 121 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 392 optimal weight: 5.9990 chunk 253 optimal weight: 1.9990 chunk 379 optimal weight: 7.9990 chunk 191 optimal weight: 9.9990 chunk 124 optimal weight: 8.9990 chunk 123 optimal weight: 0.8980 chunk 403 optimal weight: 7.9990 chunk 432 optimal weight: 6.9990 chunk 314 optimal weight: 7.9990 chunk 59 optimal weight: 0.9990 chunk 499 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 GLN B 132 ASN C 505 GLN E1212 GLN G 777 HIS H 308 ASN I 111 ASN J 329 GLN K 255 GLN ** L 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 440 GLN M 190 GLN O 88 GLN O 183 ASN T 105 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 55432 Z= 0.260 Angle : 0.553 11.271 74929 Z= 0.292 Chirality : 0.045 0.271 8114 Planarity : 0.005 0.115 9663 Dihedral : 4.990 61.743 7341 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.10 % Favored : 96.86 % Rotamer: Outliers : 1.56 % Allowed : 12.27 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.50 % Cis-general : 0.00 % Twisted Proline : 0.30 % 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: 0.81 (0.10), residues: 6525 helix: 1.26 (0.10), residues: 2790 sheet: 0.32 (0.17), residues: 867 loop : -0.00 (0.12), residues: 2868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP K 127 HIS 0.007 0.001 HIS F 344 PHE 0.023 0.002 PHE B 226 TYR 0.017 0.002 TYR M 251 ARG 0.011 0.000 ARG T 56 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13050 Ramachandran restraints generated. 6525 Oldfield, 0 Emsley, 6525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13050 Ramachandran restraints generated. 6525 Oldfield, 0 Emsley, 6525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 757 residues out of total 5900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 665 time to evaluate : 4.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASP cc_start: 0.8372 (OUTLIER) cc_final: 0.8126 (m-30) REVERT: C 79 GLU cc_start: 0.6768 (mp0) cc_final: 0.6394 (mp0) REVERT: C 323 ASP cc_start: 0.7806 (t0) cc_final: 0.7455 (t0) REVERT: C 366 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7627 (mp0) REVERT: C 599 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7919 (tp) REVERT: C 923 TYR cc_start: 0.9105 (OUTLIER) cc_final: 0.8870 (p90) REVERT: D 221 GLN cc_start: 0.8149 (tm-30) cc_final: 0.7593 (tm-30) REVERT: D 354 LYS cc_start: 0.6770 (mttt) cc_final: 0.6108 (ptmm) REVERT: E 579 ILE cc_start: 0.8405 (mt) cc_final: 0.8158 (mp) REVERT: E 610 ARG cc_start: 0.6819 (ptt-90) cc_final: 0.6435 (ptt-90) REVERT: E 861 GLU cc_start: 0.7592 (tt0) cc_final: 0.7131 (tm-30) REVERT: E 1029 ARG cc_start: 0.6902 (OUTLIER) cc_final: 0.6250 (mtm-85) REVERT: F 206 MET cc_start: 0.8920 (OUTLIER) cc_final: 0.8621 (mtp) REVERT: G 473 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.6958 (mp0) REVERT: G 586 MET cc_start: 0.6892 (mtt) cc_final: 0.6543 (ttt) REVERT: G 721 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.8313 (ttp) REVERT: L 87 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7934 (tmt-80) REVERT: L 415 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.7500 (mtt-85) REVERT: M 256 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.7946 (mmmt) REVERT: N 66 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7553 (ttt90) REVERT: N 267 GLN cc_start: 0.7862 (tm-30) cc_final: 0.7633 (tm-30) REVERT: N 269 GLU cc_start: 0.7287 (mt-10) cc_final: 0.7001 (mt-10) REVERT: O 169 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7590 (mt-10) REVERT: P 184 ASP cc_start: 0.7432 (p0) cc_final: 0.7180 (p0) REVERT: Q 698 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.7239 (ttm170) REVERT: R 37 GLN cc_start: 0.7264 (tm-30) cc_final: 0.6845 (tm-30) REVERT: R 112 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7194 (mp0) REVERT: T 48 LYS cc_start: 0.8499 (tttt) cc_final: 0.8252 (tmmt) REVERT: T 121 ASP cc_start: 0.7891 (OUTLIER) cc_final: 0.7664 (m-30) outliers start: 92 outliers final: 51 residues processed: 721 average time/residue: 1.7094 time to fit residues: 1496.2711 Evaluate side-chains 719 residues out of total 5900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 653 time to evaluate : 4.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 105 ASN Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 319 LYS Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 109 CYS Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 599 LEU Chi-restraints excluded: chain C residue 923 TYR Chi-restraints excluded: chain D residue 205 ASP Chi-restraints excluded: chain D residue 514 PHE Chi-restraints excluded: chain D residue 517 MET Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 401 THR Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 808 ILE Chi-restraints excluded: chain E residue 1029 ARG Chi-restraints excluded: chain E residue 1099 VAL Chi-restraints excluded: chain E residue 1182 ILE Chi-restraints excluded: chain F residue 206 MET Chi-restraints excluded: chain F residue 443 THR Chi-restraints excluded: chain F residue 836 THR Chi-restraints excluded: chain G residue 473 GLU Chi-restraints excluded: chain G residue 481 MET Chi-restraints excluded: chain G residue 542 GLU Chi-restraints excluded: chain G residue 649 ILE Chi-restraints excluded: chain G residue 721 MET Chi-restraints excluded: chain G residue 747 VAL Chi-restraints excluded: chain H residue 131 MET Chi-restraints excluded: chain H residue 378 CYS Chi-restraints excluded: chain J residue 270 LYS Chi-restraints excluded: chain K residue 277 SER Chi-restraints excluded: chain K residue 284 LEU Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain L residue 109 ASP Chi-restraints excluded: chain L residue 365 VAL Chi-restraints excluded: chain L residue 415 ARG Chi-restraints excluded: chain M residue 244 VAL Chi-restraints excluded: chain M residue 256 LYS Chi-restraints excluded: chain M residue 296 VAL Chi-restraints excluded: chain N residue 66 ARG Chi-restraints excluded: chain N residue 252 GLU Chi-restraints excluded: chain N residue 264 ARG Chi-restraints excluded: chain O residue 127 SER Chi-restraints excluded: chain O residue 128 ASN Chi-restraints excluded: chain O residue 158 SER Chi-restraints excluded: chain O residue 169 GLU Chi-restraints excluded: chain P residue 112 ILE Chi-restraints excluded: chain P residue 153 THR Chi-restraints excluded: chain P residue 160 ASP Chi-restraints excluded: chain Q residue 647 SER Chi-restraints excluded: chain Q residue 698 ARG Chi-restraints excluded: chain R residue 36 ILE Chi-restraints excluded: chain R residue 50 THR Chi-restraints excluded: chain R residue 94 ASP Chi-restraints excluded: chain R residue 112 GLU Chi-restraints excluded: chain S residue 194 SER Chi-restraints excluded: chain S residue 562 ASN Chi-restraints excluded: chain T residue 121 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 577 optimal weight: 6.9990 chunk 608 optimal weight: 7.9990 chunk 555 optimal weight: 10.0000 chunk 591 optimal weight: 0.9980 chunk 356 optimal weight: 6.9990 chunk 257 optimal weight: 0.9990 chunk 464 optimal weight: 0.6980 chunk 181 optimal weight: 0.6980 chunk 534 optimal weight: 5.9990 chunk 559 optimal weight: 9.9990 chunk 589 optimal weight: 7.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN A 303 GLN B 132 ASN D 583 ASN E 398 HIS E1212 GLN G 777 HIS H 308 ASN ** H 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 111 ASN J 329 GLN K 255 GLN ** L 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 190 GLN O 88 GLN O 183 ASN T 105 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 55432 Z= 0.193 Angle : 0.511 10.453 74929 Z= 0.270 Chirality : 0.043 0.266 8114 Planarity : 0.004 0.115 9663 Dihedral : 4.819 60.344 7341 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.73 % Favored : 97.23 % Rotamer: Outliers : 1.42 % Allowed : 12.51 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.50 % Cis-general : 0.00 % Twisted Proline : 0.30 % 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: 0.92 (0.10), residues: 6525 helix: 1.37 (0.10), residues: 2789 sheet: 0.33 (0.17), residues: 874 loop : 0.06 (0.12), residues: 2862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP K 127 HIS 0.007 0.001 HIS E 398 PHE 0.020 0.001 PHE L 150 TYR 0.016 0.001 TYR D 649 ARG 0.009 0.000 ARG G 523 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13050 Ramachandran restraints generated. 6525 Oldfield, 0 Emsley, 6525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13050 Ramachandran restraints generated. 6525 Oldfield, 0 Emsley, 6525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 740 residues out of total 5900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 656 time to evaluate : 4.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASP cc_start: 0.8363 (OUTLIER) cc_final: 0.8110 (m-30) REVERT: A 93 GLU cc_start: 0.7571 (pp20) cc_final: 0.7365 (pm20) REVERT: C 79 GLU cc_start: 0.6765 (mp0) cc_final: 0.6380 (mp0) REVERT: C 323 ASP cc_start: 0.7794 (t0) cc_final: 0.7452 (t0) REVERT: C 366 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7607 (mp0) REVERT: C 599 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7918 (tp) REVERT: C 923 TYR cc_start: 0.9077 (OUTLIER) cc_final: 0.8844 (p90) REVERT: D 221 GLN cc_start: 0.8168 (tm-30) cc_final: 0.7624 (tm-30) REVERT: D 354 LYS cc_start: 0.6795 (mttt) cc_final: 0.6105 (ptmm) REVERT: E 244 GLN cc_start: 0.7939 (tp40) cc_final: 0.7674 (tp40) REVERT: E 579 ILE cc_start: 0.8374 (mt) cc_final: 0.8136 (mp) REVERT: E 861 GLU cc_start: 0.7572 (tt0) cc_final: 0.7091 (tm-30) REVERT: E 1029 ARG cc_start: 0.6894 (OUTLIER) cc_final: 0.6252 (mtm-85) REVERT: F 206 MET cc_start: 0.8896 (OUTLIER) cc_final: 0.8598 (mtp) REVERT: G 586 MET cc_start: 0.6881 (mtt) cc_final: 0.6519 (ttt) REVERT: G 721 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.8309 (ttp) REVERT: L 212 GLN cc_start: 0.7919 (mp10) cc_final: 0.7589 (mt0) REVERT: M 256 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.7952 (mmmt) REVERT: N 66 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7547 (ttt90) REVERT: N 264 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7912 (tmt170) REVERT: N 267 GLN cc_start: 0.7869 (tm-30) cc_final: 0.7642 (tm-30) REVERT: N 269 GLU cc_start: 0.7281 (mt-10) cc_final: 0.6988 (mt-10) REVERT: O 169 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7589 (mt-10) REVERT: P 184 ASP cc_start: 0.7416 (p0) cc_final: 0.7165 (p0) REVERT: Q 698 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.7202 (ttm170) REVERT: R 37 GLN cc_start: 0.7228 (tm-30) cc_final: 0.6824 (tm-30) REVERT: R 112 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7150 (mp0) REVERT: T 48 LYS cc_start: 0.8480 (tttt) cc_final: 0.8236 (tmmt) REVERT: T 121 ASP cc_start: 0.7858 (OUTLIER) cc_final: 0.7642 (m-30) outliers start: 84 outliers final: 45 residues processed: 701 average time/residue: 1.7882 time to fit residues: 1519.2675 Evaluate side-chains 706 residues out of total 5900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 648 time to evaluate : 4.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 105 ASN Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 319 LYS Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 109 CYS Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 599 LEU Chi-restraints excluded: chain C residue 923 TYR Chi-restraints excluded: chain D residue 205 ASP Chi-restraints excluded: chain D residue 514 PHE Chi-restraints excluded: chain D residue 517 MET Chi-restraints excluded: chain D residue 537 ILE Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 401 THR Chi-restraints excluded: chain E residue 808 ILE Chi-restraints excluded: chain E residue 1029 ARG Chi-restraints excluded: chain E residue 1182 ILE Chi-restraints excluded: chain F residue 79 MET Chi-restraints excluded: chain F residue 206 MET Chi-restraints excluded: chain F residue 443 THR Chi-restraints excluded: chain F residue 836 THR Chi-restraints excluded: chain G residue 481 MET Chi-restraints excluded: chain G residue 649 ILE Chi-restraints excluded: chain G residue 721 MET Chi-restraints excluded: chain G residue 747 VAL Chi-restraints excluded: chain H residue 378 CYS Chi-restraints excluded: chain J residue 270 LYS Chi-restraints excluded: chain K residue 277 SER Chi-restraints excluded: chain K residue 284 LEU Chi-restraints excluded: chain L residue 109 ASP Chi-restraints excluded: chain L residue 365 VAL Chi-restraints excluded: chain M residue 256 LYS Chi-restraints excluded: chain M residue 296 VAL Chi-restraints excluded: chain N residue 66 ARG Chi-restraints excluded: chain N residue 252 GLU Chi-restraints excluded: chain N residue 264 ARG Chi-restraints excluded: chain O residue 127 SER Chi-restraints excluded: chain O residue 128 ASN Chi-restraints excluded: chain O residue 158 SER Chi-restraints excluded: chain O residue 169 GLU Chi-restraints excluded: chain P residue 112 ILE Chi-restraints excluded: chain P residue 153 THR Chi-restraints excluded: chain Q residue 361 SER Chi-restraints excluded: chain Q residue 647 SER Chi-restraints excluded: chain Q residue 698 ARG Chi-restraints excluded: chain R residue 36 ILE Chi-restraints excluded: chain R residue 50 THR Chi-restraints excluded: chain R residue 94 ASP Chi-restraints excluded: chain R residue 112 GLU Chi-restraints excluded: chain S residue 194 SER Chi-restraints excluded: chain T residue 121 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 388 optimal weight: 9.9990 chunk 625 optimal weight: 7.9990 chunk 382 optimal weight: 5.9990 chunk 296 optimal weight: 10.0000 chunk 435 optimal weight: 0.3980 chunk 656 optimal weight: 8.9990 chunk 604 optimal weight: 0.9990 chunk 522 optimal weight: 9.9990 chunk 54 optimal weight: 0.0370 chunk 403 optimal weight: 7.9990 chunk 320 optimal weight: 5.9990 overall best weight: 2.6864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 GLN B 132 ASN E 398 HIS E1151 GLN E1212 GLN F 123 GLN G 777 HIS H 308 ASN I 111 ASN J 329 GLN K 255 GLN ** L 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 440 GLN M 190 GLN O 88 GLN O 183 ASN T 105 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 55432 Z= 0.238 Angle : 0.538 10.873 74929 Z= 0.284 Chirality : 0.044 0.267 8114 Planarity : 0.005 0.116 9663 Dihedral : 4.885 60.684 7340 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.02 % Favored : 96.93 % Rotamer: Outliers : 1.19 % Allowed : 12.82 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.50 % Cis-general : 0.00 % Twisted Proline : 0.30 % 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: 0.89 (0.10), residues: 6525 helix: 1.35 (0.10), residues: 2787 sheet: 0.32 (0.17), residues: 875 loop : 0.04 (0.12), residues: 2863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP K 127 HIS 0.009 0.001 HIS E 398 PHE 0.022 0.002 PHE L 150 TYR 0.018 0.002 TYR D 649 ARG 0.008 0.000 ARG F 393 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13050 Ramachandran restraints generated. 6525 Oldfield, 0 Emsley, 6525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13050 Ramachandran restraints generated. 6525 Oldfield, 0 Emsley, 6525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 717 residues out of total 5900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 647 time to evaluate : 4.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASP cc_start: 0.8370 (OUTLIER) cc_final: 0.8120 (m-30) REVERT: C 79 GLU cc_start: 0.6760 (mp0) cc_final: 0.6380 (mp0) REVERT: C 323 ASP cc_start: 0.7800 (t0) cc_final: 0.7458 (t0) REVERT: C 366 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7610 (mp0) REVERT: C 599 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7929 (tp) REVERT: C 923 TYR cc_start: 0.9101 (OUTLIER) cc_final: 0.8868 (p90) REVERT: D 221 GLN cc_start: 0.8160 (tm-30) cc_final: 0.7608 (tm-30) REVERT: D 354 LYS cc_start: 0.6791 (mttt) cc_final: 0.6113 (ptmm) REVERT: E 244 GLN cc_start: 0.7953 (tp40) cc_final: 0.7691 (tp40) REVERT: E 579 ILE cc_start: 0.8383 (mt) cc_final: 0.8143 (mp) REVERT: E 861 GLU cc_start: 0.7569 (tt0) cc_final: 0.7100 (tm-30) REVERT: E 1029 ARG cc_start: 0.6900 (OUTLIER) cc_final: 0.6261 (mtm-85) REVERT: F 206 MET cc_start: 0.8905 (OUTLIER) cc_final: 0.8608 (mtp) REVERT: G 584 GLU cc_start: 0.6451 (pp20) cc_final: 0.6182 (mp0) REVERT: G 586 MET cc_start: 0.6877 (mtt) cc_final: 0.6545 (ttt) REVERT: G 721 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.8315 (ttp) REVERT: L 212 GLN cc_start: 0.7927 (mp10) cc_final: 0.7598 (mt0) REVERT: M 256 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.7949 (mmmt) REVERT: N 66 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7545 (ttt90) REVERT: N 103 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8600 (tp) REVERT: N 267 GLN cc_start: 0.7870 (tm-30) cc_final: 0.7641 (tm-30) REVERT: N 269 GLU cc_start: 0.7290 (mt-10) cc_final: 0.6988 (mt-10) REVERT: P 184 ASP cc_start: 0.7425 (p0) cc_final: 0.7177 (p0) REVERT: Q 698 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7211 (ttm170) REVERT: R 37 GLN cc_start: 0.7246 (tm-30) cc_final: 0.6831 (tm-30) REVERT: R 112 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7151 (mp0) REVERT: S 355 MET cc_start: 0.8458 (tpt) cc_final: 0.8131 (tpt) REVERT: T 48 LYS cc_start: 0.8484 (tttt) cc_final: 0.8244 (tmmt) REVERT: T 121 ASP cc_start: 0.7852 (OUTLIER) cc_final: 0.7651 (m-30) outliers start: 70 outliers final: 48 residues processed: 687 average time/residue: 1.7512 time to fit residues: 1459.0799 Evaluate side-chains 703 residues out of total 5900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 643 time to evaluate : 4.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 105 ASN Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 319 LYS Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 109 CYS Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 599 LEU Chi-restraints excluded: chain C residue 881 ASP Chi-restraints excluded: chain C residue 923 TYR Chi-restraints excluded: chain D residue 205 ASP Chi-restraints excluded: chain D residue 514 PHE Chi-restraints excluded: chain D residue 517 MET Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 401 THR Chi-restraints excluded: chain E residue 1029 ARG Chi-restraints excluded: chain E residue 1099 VAL Chi-restraints excluded: chain E residue 1182 ILE Chi-restraints excluded: chain F residue 79 MET Chi-restraints excluded: chain F residue 206 MET Chi-restraints excluded: chain F residue 443 THR Chi-restraints excluded: chain F residue 836 THR Chi-restraints excluded: chain G residue 481 MET Chi-restraints excluded: chain G residue 649 ILE Chi-restraints excluded: chain G residue 721 MET Chi-restraints excluded: chain G residue 747 VAL Chi-restraints excluded: chain H residue 378 CYS Chi-restraints excluded: chain J residue 270 LYS Chi-restraints excluded: chain K residue 277 SER Chi-restraints excluded: chain K residue 284 LEU Chi-restraints excluded: chain L residue 109 ASP Chi-restraints excluded: chain L residue 365 VAL Chi-restraints excluded: chain M residue 256 LYS Chi-restraints excluded: chain M residue 296 VAL Chi-restraints excluded: chain N residue 66 ARG Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 252 GLU Chi-restraints excluded: chain N residue 264 ARG Chi-restraints excluded: chain O residue 127 SER Chi-restraints excluded: chain O residue 128 ASN Chi-restraints excluded: chain O residue 158 SER Chi-restraints excluded: chain P residue 112 ILE Chi-restraints excluded: chain P residue 120 MET Chi-restraints excluded: chain P residue 153 THR Chi-restraints excluded: chain P residue 160 ASP Chi-restraints excluded: chain Q residue 361 SER Chi-restraints excluded: chain Q residue 647 SER Chi-restraints excluded: chain Q residue 698 ARG Chi-restraints excluded: chain R residue 36 ILE Chi-restraints excluded: chain R residue 50 THR Chi-restraints excluded: chain R residue 94 ASP Chi-restraints excluded: chain R residue 112 GLU Chi-restraints excluded: chain S residue 194 SER Chi-restraints excluded: chain T residue 121 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 415 optimal weight: 10.0000 chunk 556 optimal weight: 9.9990 chunk 160 optimal weight: 4.9990 chunk 482 optimal weight: 3.9990 chunk 77 optimal weight: 8.9990 chunk 145 optimal weight: 6.9990 chunk 523 optimal weight: 1.9990 chunk 219 optimal weight: 20.0000 chunk 537 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 GLN B 132 ASN C 128 GLN ** E 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1151 GLN E1212 GLN F 123 GLN G 754 GLN G 777 HIS H 308 ASN H 409 GLN I 111 ASN J 329 GLN K 255 GLN ** L 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 440 GLN M 190 GLN O 88 GLN O 183 ASN T 105 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.075254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.057820 restraints weight = 128307.754| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 1.71 r_work: 0.2769 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 55432 Z= 0.320 Angle : 0.586 11.455 74929 Z= 0.309 Chirality : 0.046 0.273 8114 Planarity : 0.005 0.117 9663 Dihedral : 5.030 62.113 7340 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.16 % Favored : 96.80 % Rotamer: Outliers : 1.32 % Allowed : 12.65 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.50 % Cis-general : 0.00 % Twisted Proline : 0.30 % 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: 0.79 (0.10), residues: 6525 helix: 1.25 (0.10), residues: 2784 sheet: 0.29 (0.17), residues: 859 loop : -0.01 (0.11), residues: 2882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP K 127 HIS 0.010 0.001 HIS E 398 PHE 0.025 0.002 PHE B 226 TYR 0.021 0.002 TYR D 649 ARG 0.010 0.001 ARG G 523 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26465.56 seconds wall clock time: 455 minutes 10.61 seconds (27310.61 seconds total)