Starting phenix.real_space_refine on Sat Dec 16 03:35:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tmm_25996/12_2023/7tmm_25996_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tmm_25996/12_2023/7tmm_25996.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tmm_25996/12_2023/7tmm_25996.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tmm_25996/12_2023/7tmm_25996.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tmm_25996/12_2023/7tmm_25996_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tmm_25996/12_2023/7tmm_25996_updated.pdb" } resolution = 3.5 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= 0.005 sd= 0.114 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 85 5.16 5 C 21530 2.51 5 N 6108 2.21 5 O 5988 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 355": "OE1" <-> "OE2" Residue "C GLU 95": "OE1" <-> "OE2" Residue "C TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 341": "OE1" <-> "OE2" Residue "D PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 264": "OE1" <-> "OE2" Residue "D TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 289": "OE1" <-> "OE2" Residue "E TYR 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 251": "OE1" <-> "OE2" Residue "F TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 101": "OE1" <-> "OE2" Residue "K TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 33713 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 4150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4150 Classifications: {'peptide': 593} Incomplete info: {'truncation_to_alanine': 141} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 562} Unresolved non-hydrogen bonds: 429 Unresolved non-hydrogen angles: 527 Unresolved non-hydrogen dihedrals: 336 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 5, 'ASP:plan': 30, 'GLU:plan': 33, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 289 Chain: "B" Number of atoms: 3375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3375 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 437} Chain breaks: 1 Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 331 Unresolved non-hydrogen dihedrals: 209 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 23, 'ASN:plan1': 6, 'ARG:plan': 2, 'ASP:plan': 21} Unresolved non-hydrogen planarities: 191 Chain: "C" Number of atoms: 3985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 3985 Classifications: {'peptide': 592} Incomplete info: {'truncation_to_alanine': 190} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 561} Unresolved non-hydrogen bonds: 596 Unresolved non-hydrogen angles: 742 Unresolved non-hydrogen dihedrals: 480 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 31, 'PHE:plan': 6, 'GLU:plan': 34, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 390 Chain: "D" Number of atoms: 3266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3266 Classifications: {'peptide': 459} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 433} Chain breaks: 1 Unresolved non-hydrogen bonds: 335 Unresolved non-hydrogen angles: 413 Unresolved non-hydrogen dihedrals: 257 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 30, 'ASN:plan1': 11, 'ARG:plan': 1, 'ASP:plan': 23} Unresolved non-hydrogen planarities: 243 Chain: "E" Number of atoms: 4006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4006 Classifications: {'peptide': 576} Incomplete info: {'truncation_to_alanine': 156} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 546} Chain breaks: 2 Unresolved non-hydrogen bonds: 465 Unresolved non-hydrogen angles: 572 Unresolved non-hydrogen dihedrals: 368 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 2, 'ASN:plan1': 7, 'ASP:plan': 26, 'PHE:plan': 2, 'GLU:plan': 32, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 296 Chain: "F" Number of atoms: 3276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3276 Classifications: {'peptide': 459} Incomplete info: {'truncation_to_alanine': 103} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 433} Chain breaks: 1 Unresolved non-hydrogen bonds: 326 Unresolved non-hydrogen angles: 401 Unresolved non-hydrogen dihedrals: 254 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 21, 'GLU:plan': 28, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 227 Chain: "G" Number of atoms: 1322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1322 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 123} Link IDs: {'PTRANS': 5, 'TRANS': 214} Unresolved non-hydrogen bonds: 443 Unresolved non-hydrogen angles: 538 Unresolved non-hydrogen dihedrals: 357 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 9, 'TYR:plan': 1, 'ASN:plan1': 13, 'ASP:plan': 12, 'PHE:plan': 3, 'GLU:plan': 27, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 279 Chain: "H" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 578 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 1, 'TRANS': 107} Unresolved non-hydrogen bonds: 278 Unresolved non-hydrogen angles: 338 Unresolved non-hydrogen dihedrals: 228 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 14, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 142 Chain: "I" Number of atoms: 1313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1313 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 130} Link IDs: {'PTRANS': 5, 'TRANS': 214} Unresolved non-hydrogen bonds: 452 Unresolved non-hydrogen angles: 549 Unresolved non-hydrogen dihedrals: 364 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 1, 'ASN:plan1': 13, 'ASP:plan': 12, 'PHE:plan': 3, 'GLU:plan': 26, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 266 Chain: "J" Number of atoms: 570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 570 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 1, 'TRANS': 106} Unresolved non-hydrogen bonds: 281 Unresolved non-hydrogen angles: 340 Unresolved non-hydrogen dihedrals: 232 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 146 Chain: "K" Number of atoms: 1288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1288 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 121} Link IDs: {'PTRANS': 5, 'TRANS': 206} Unresolved non-hydrogen bonds: 413 Unresolved non-hydrogen angles: 503 Unresolved non-hydrogen dihedrals: 330 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 1, 'ASN:plan1': 12, 'ASP:plan': 11, 'PHE:plan': 2, 'GLU:plan': 26, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 249 Chain: "L" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 522 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 1, 'TRANS': 97} Unresolved non-hydrogen bonds: 267 Unresolved non-hydrogen angles: 320 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 139 Chain: "M" Number of atoms: 1341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1341 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'PTRANS': 3, 'TRANS': 210} Unresolved non-hydrogen bonds: 392 Unresolved non-hydrogen angles: 487 Unresolved non-hydrogen dihedrals: 310 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 12, 'TYR:plan': 3, 'ASN:plan1': 6, 'ASP:plan': 8, 'PHE:plan': 2, 'GLU:plan': 19, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 254 Chain: "N" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 610 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 105} Unresolved non-hydrogen bonds: 287 Unresolved non-hydrogen angles: 366 Unresolved non-hydrogen dihedrals: 225 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 5, 'ASP:plan': 9, 'PHE:plan': 4, 'GLU:plan': 12, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 172 Chain: "O" Number of atoms: 1873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 1873 Classifications: {'peptide': 359} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 294} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 342} Chain breaks: 1 Unresolved non-hydrogen bonds: 1033 Unresolved non-hydrogen angles: 1316 Unresolved non-hydrogen dihedrals: 839 Unresolved non-hydrogen chiralities: 108 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 5, 'TYR:plan': 9, 'ASN:plan1': 22, 'TRP:plan': 2, 'ASP:plan': 18, 'PHE:plan': 19, 'GLU:plan': 27, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 552 Chain: "P" Number of atoms: 2211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 2211 Classifications: {'peptide': 441} Incomplete info: {'truncation_to_alanine': 401} Link IDs: {'PTRANS': 9, 'TRANS': 431} Chain breaks: 2 Unresolved non-hydrogen bonds: 1399 Unresolved non-hydrogen angles: 1785 Unresolved non-hydrogen dihedrals: 1131 Unresolved non-hydrogen chiralities: 154 Planarities with less than four sites: {'GLN:plan1': 24, 'ASP:plan': 30, 'TYR:plan': 11, 'ASN:plan1': 24, 'TRP:plan': 5, 'HIS:plan': 10, 'PHE:plan': 15, 'GLU:plan': 32, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 718 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 18.65, per 1000 atoms: 0.55 Number of scatterers: 33713 At special positions: 0 Unit cell: (131.84, 169.95, 207.03, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 85 16.00 P 2 15.00 O 5988 8.00 N 6108 7.00 C 21530 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=0, symmetry=0 Time building additional restraints: 15.02 Conformation dependent library (CDL) restraints added in 7.0 seconds 10376 Ramachandran restraints generated. 5188 Oldfield, 0 Emsley, 5188 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9820 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 186 helices and 39 sheets defined 50.5% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.98 Creating SS restraints... Processing helix chain 'A' and resid 112 through 119 Processing helix chain 'A' and resid 238 through 243 Processing helix chain 'A' and resid 262 through 272 removed outlier: 3.715A pdb=" N TYR A 272 " --> pdb=" O SER A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 299 Proline residue: A 298 - end of helix Processing helix chain 'A' and resid 304 through 306 No H-bonds generated for 'chain 'A' and resid 304 through 306' Processing helix chain 'A' and resid 311 through 313 No H-bonds generated for 'chain 'A' and resid 311 through 313' Processing helix chain 'A' and resid 327 through 345 Processing helix chain 'A' and resid 357 through 371 removed outlier: 3.546A pdb=" N ALA A 361 " --> pdb=" O SER A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 379 No H-bonds generated for 'chain 'A' and resid 377 through 379' Processing helix chain 'A' and resid 384 through 394 removed outlier: 3.824A pdb=" N ARG A 394 " --> pdb=" O SER A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 421 No H-bonds generated for 'chain 'A' and resid 419 through 421' Processing helix chain 'A' and resid 426 through 432 Processing helix chain 'A' and resid 443 through 447 Processing helix chain 'A' and resid 466 through 471 removed outlier: 3.580A pdb=" N LYS A 469 " --> pdb=" O VAL A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 502 removed outlier: 3.980A pdb=" N LEU A 501 " --> pdb=" O GLN A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 506 No H-bonds generated for 'chain 'A' and resid 504 through 506' Processing helix chain 'A' and resid 509 through 524 Processing helix chain 'A' and resid 540 through 562 Processing helix chain 'A' and resid 567 through 586 removed outlier: 3.782A pdb=" N ASP A 572 " --> pdb=" O SER A 568 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N ASP A 576 " --> pdb=" O ASP A 572 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N VAL A 577 " --> pdb=" O SER A 573 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LYS A 585 " --> pdb=" O VAL A 581 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N PHE A 586 " --> pdb=" O SER A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 591 No H-bonds generated for 'chain 'A' and resid 589 through 591' Processing helix chain 'A' and resid 593 through 615 Processing helix chain 'B' and resid 15 through 19 removed outlier: 3.805A pdb=" N GLY B 19 " --> pdb=" O ALA B 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 15 through 19' Processing helix chain 'B' and resid 156 through 159 No H-bonds generated for 'chain 'B' and resid 156 through 159' Processing helix chain 'B' and resid 180 through 190 Processing helix chain 'B' and resid 219 through 232 removed outlier: 3.830A pdb=" N GLU B 230 " --> pdb=" O LYS B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 237 Processing helix chain 'B' and resid 250 through 270 removed outlier: 3.927A pdb=" N THR B 255 " --> pdb=" O ARG B 252 " (cutoff:3.500A) Proline residue: B 256 - end of helix removed outlier: 3.611A pdb=" N ALA B 267 " --> pdb=" O GLU B 264 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR B 268 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN B 269 " --> pdb=" O LEU B 266 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR B 270 " --> pdb=" O ALA B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 295 removed outlier: 3.841A pdb=" N ALA B 294 " --> pdb=" O GLU B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 316 removed outlier: 4.031A pdb=" N TYR B 309 " --> pdb=" O GLY B 306 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR B 314 " --> pdb=" O ASP B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 340 No H-bonds generated for 'chain 'B' and resid 338 through 340' Processing helix chain 'B' and resid 345 through 353 Processing helix chain 'B' and resid 362 through 367 Processing helix chain 'B' and resid 396 through 420 removed outlier: 3.598A pdb=" N ASN B 401 " --> pdb=" O GLY B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 424 No H-bonds generated for 'chain 'B' and resid 422 through 424' Processing helix chain 'B' and resid 427 through 440 Processing helix chain 'B' and resid 454 through 467 removed outlier: 4.233A pdb=" N ILE B 467 " --> pdb=" O SER B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 484 Processing helix chain 'C' and resid 112 through 119 Processing helix chain 'C' and resid 238 through 242 Processing helix chain 'C' and resid 262 through 272 Processing helix chain 'C' and resid 287 through 296 Processing helix chain 'C' and resid 311 through 314 Processing helix chain 'C' and resid 326 through 345 removed outlier: 4.751A pdb=" N ILE C 333 " --> pdb=" O ARG C 329 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N TYR C 334 " --> pdb=" O GLU C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 371 Processing helix chain 'C' and resid 377 through 379 No H-bonds generated for 'chain 'C' and resid 377 through 379' Processing helix chain 'C' and resid 384 through 394 removed outlier: 4.010A pdb=" N ARG C 394 " --> pdb=" O SER C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 421 No H-bonds generated for 'chain 'C' and resid 419 through 421' Processing helix chain 'C' and resid 426 through 434 Processing helix chain 'C' and resid 443 through 447 Processing helix chain 'C' and resid 466 through 474 removed outlier: 4.906A pdb=" N ASP C 472 " --> pdb=" O LYS C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 501 Proline residue: C 479 - end of helix Processing helix chain 'C' and resid 504 through 506 No H-bonds generated for 'chain 'C' and resid 504 through 506' Processing helix chain 'C' and resid 509 through 524 Processing helix chain 'C' and resid 540 through 562 Processing helix chain 'C' and resid 567 through 586 removed outlier: 5.379A pdb=" N ASP C 576 " --> pdb=" O ASP C 572 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N VAL C 577 " --> pdb=" O SER C 573 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LYS C 585 " --> pdb=" O VAL C 581 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N PHE C 586 " --> pdb=" O SER C 582 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 591 No H-bonds generated for 'chain 'C' and resid 589 through 591' Processing helix chain 'C' and resid 593 through 613 Processing helix chain 'D' and resid 17 through 20 removed outlier: 3.627A pdb=" N PHE D 20 " --> pdb=" O GLU D 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 17 through 20' Processing helix chain 'D' and resid 106 through 108 No H-bonds generated for 'chain 'D' and resid 106 through 108' Processing helix chain 'D' and resid 141 through 143 No H-bonds generated for 'chain 'D' and resid 141 through 143' Processing helix chain 'D' and resid 156 through 159 No H-bonds generated for 'chain 'D' and resid 156 through 159' Processing helix chain 'D' and resid 180 through 190 Processing helix chain 'D' and resid 219 through 232 removed outlier: 3.808A pdb=" N GLU D 230 " --> pdb=" O LYS D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 237 removed outlier: 3.730A pdb=" N ARG D 237 " --> pdb=" O SER D 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 234 through 237' Processing helix chain 'D' and resid 249 through 268 Proline residue: D 256 - end of helix Processing helix chain 'D' and resid 281 through 294 Processing helix chain 'D' and resid 308 through 316 removed outlier: 4.039A pdb=" N ILE D 315 " --> pdb=" O ASP D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 340 No H-bonds generated for 'chain 'D' and resid 338 through 340' Processing helix chain 'D' and resid 345 through 353 Processing helix chain 'D' and resid 362 through 367 Processing helix chain 'D' and resid 381 through 386 removed outlier: 4.367A pdb=" N LYS D 384 " --> pdb=" O ARG D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 420 removed outlier: 3.527A pdb=" N ASN D 401 " --> pdb=" O GLY D 397 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA D 418 " --> pdb=" O ALA D 414 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N VAL D 419 " --> pdb=" O ALA D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 440 removed outlier: 3.669A pdb=" N GLU D 434 " --> pdb=" O LYS D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 467 removed outlier: 4.389A pdb=" N ILE D 467 " --> pdb=" O SER D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 478 through 483 Processing helix chain 'E' and resid 112 through 119 Processing helix chain 'E' and resid 238 through 243 Processing helix chain 'E' and resid 265 through 271 Processing helix chain 'E' and resid 287 through 296 Processing helix chain 'E' and resid 326 through 345 removed outlier: 4.344A pdb=" N ILE E 333 " --> pdb=" O ARG E 329 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N TYR E 334 " --> pdb=" O GLU E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 371 Processing helix chain 'E' and resid 382 through 394 removed outlier: 4.471A pdb=" N GLY E 385 " --> pdb=" O ALA E 382 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N GLU E 393 " --> pdb=" O SER E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 426 through 431 Processing helix chain 'E' and resid 443 through 447 Processing helix chain 'E' and resid 466 through 474 removed outlier: 3.522A pdb=" N LYS E 469 " --> pdb=" O VAL E 466 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ASP E 472 " --> pdb=" O LYS E 469 " (cutoff:3.500A) Processing helix chain 'E' and resid 478 through 502 removed outlier: 3.773A pdb=" N GLN E 497 " --> pdb=" O GLU E 493 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VAL E 498 " --> pdb=" O GLU E 494 " (cutoff:3.500A) Processing helix chain 'E' and resid 509 through 524 Processing helix chain 'E' and resid 540 through 562 Processing helix chain 'E' and resid 567 through 573 removed outlier: 4.234A pdb=" N ASP E 572 " --> pdb=" O SER E 568 " (cutoff:3.500A) Processing helix chain 'E' and resid 575 through 586 removed outlier: 4.253A pdb=" N LYS E 585 " --> pdb=" O VAL E 581 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N PHE E 586 " --> pdb=" O SER E 582 " (cutoff:3.500A) Processing helix chain 'E' and resid 589 through 591 No H-bonds generated for 'chain 'E' and resid 589 through 591' Processing helix chain 'E' and resid 593 through 612 removed outlier: 4.293A pdb=" N ALA E 612 " --> pdb=" O GLN E 608 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 108 No H-bonds generated for 'chain 'F' and resid 106 through 108' Processing helix chain 'F' and resid 141 through 143 No H-bonds generated for 'chain 'F' and resid 141 through 143' Processing helix chain 'F' and resid 156 through 159 No H-bonds generated for 'chain 'F' and resid 156 through 159' Processing helix chain 'F' and resid 180 through 189 Processing helix chain 'F' and resid 219 through 231 Processing helix chain 'F' and resid 234 through 237 Processing helix chain 'F' and resid 251 through 269 removed outlier: 4.005A pdb=" N THR F 255 " --> pdb=" O ARG F 252 " (cutoff:3.500A) Proline residue: F 256 - end of helix removed outlier: 3.508A pdb=" N TYR F 268 " --> pdb=" O TYR F 265 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLN F 269 " --> pdb=" O LEU F 266 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 294 Processing helix chain 'F' and resid 301 through 303 No H-bonds generated for 'chain 'F' and resid 301 through 303' Processing helix chain 'F' and resid 306 through 316 removed outlier: 4.172A pdb=" N TYR F 309 " --> pdb=" O GLY F 306 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU F 312 " --> pdb=" O TYR F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 340 No H-bonds generated for 'chain 'F' and resid 338 through 340' Processing helix chain 'F' and resid 345 through 353 Processing helix chain 'F' and resid 362 through 367 Processing helix chain 'F' and resid 383 through 386 No H-bonds generated for 'chain 'F' and resid 383 through 386' Processing helix chain 'F' and resid 396 through 420 Processing helix chain 'F' and resid 427 through 440 Processing helix chain 'F' and resid 454 through 467 removed outlier: 4.357A pdb=" N ILE F 467 " --> pdb=" O SER F 463 " (cutoff:3.500A) Processing helix chain 'F' and resid 470 through 472 No H-bonds generated for 'chain 'F' and resid 470 through 472' Processing helix chain 'F' and resid 478 through 484 removed outlier: 3.976A pdb=" N GLU F 483 " --> pdb=" O LYS F 479 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 48 removed outlier: 3.602A pdb=" N THR G 48 " --> pdb=" O GLU G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 112 removed outlier: 3.745A pdb=" N ALA G 111 " --> pdb=" O LEU G 107 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASN G 112 " --> pdb=" O SER G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 132 Proline residue: G 119 - end of helix removed outlier: 3.519A pdb=" N GLN G 122 " --> pdb=" O LYS G 118 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS G 131 " --> pdb=" O GLU G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 163 removed outlier: 3.541A pdb=" N SER G 151 " --> pdb=" O ASP G 147 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N ASP G 154 " --> pdb=" O GLU G 150 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N ASP G 155 " --> pdb=" O SER G 151 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG G 158 " --> pdb=" O ASP G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 203 through 222 removed outlier: 3.931A pdb=" N LEU G 215 " --> pdb=" O SER G 211 " (cutoff:3.500A) Proline residue: G 216 - end of helix Processing helix chain 'H' and resid 6 through 102 removed outlier: 3.506A pdb=" N VAL H 65 " --> pdb=" O ASN H 61 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLY H 66 " --> pdb=" O ALA H 62 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLU H 67 " --> pdb=" O GLY H 63 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLY H 78 " --> pdb=" O ALA H 74 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLU H 79 " --> pdb=" O GLY H 75 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N ASP H 92 " --> pdb=" O GLU H 88 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N ASP H 93 " --> pdb=" O LYS H 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 14 through 110 removed outlier: 3.534A pdb=" N GLU I 30 " --> pdb=" O LYS I 26 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU I 44 " --> pdb=" O ASP I 40 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE I 45 " --> pdb=" O GLN I 41 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER I 108 " --> pdb=" O LYS I 104 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY I 109 " --> pdb=" O GLU I 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 114 through 130 Proline residue: I 119 - end of helix Processing helix chain 'I' and resid 143 through 163 removed outlier: 3.774A pdb=" N VAL I 146 " --> pdb=" O GLU I 143 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ASP I 147 " --> pdb=" O ARG I 144 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS I 153 " --> pdb=" O GLU I 150 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ASP I 154 " --> pdb=" O SER I 151 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS I 163 " --> pdb=" O TYR I 160 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 213 Processing helix chain 'I' and resid 215 through 223 Processing helix chain 'J' and resid 6 through 62 Processing helix chain 'J' and resid 65 through 103 removed outlier: 3.537A pdb=" N GLY J 75 " --> pdb=" O LYS J 71 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY J 78 " --> pdb=" O ALA J 74 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU J 79 " --> pdb=" O GLY J 75 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N ASP J 92 " --> pdb=" O GLU J 88 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ASP J 93 " --> pdb=" O LYS J 89 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 112 removed outlier: 3.849A pdb=" N LYS K 83 " --> pdb=" O THR K 79 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU K 86 " --> pdb=" O ASN K 82 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS K 87 " --> pdb=" O LYS K 83 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL K 88 " --> pdb=" O MET K 84 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER K 108 " --> pdb=" O LYS K 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 114 through 132 Proline residue: K 119 - end of helix removed outlier: 4.406A pdb=" N VAL K 126 " --> pdb=" O GLN K 122 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N LYS K 131 " --> pdb=" O GLU K 127 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU K 132 " --> pdb=" O ALA K 128 " (cutoff:3.500A) Processing helix chain 'K' and resid 143 through 151 removed outlier: 3.862A pdb=" N VAL K 146 " --> pdb=" O GLU K 143 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ASP K 147 " --> pdb=" O ARG K 144 " (cutoff:3.500A) Processing helix chain 'K' and resid 153 through 163 removed outlier: 3.656A pdb=" N GLY K 161 " --> pdb=" O MET K 157 " (cutoff:3.500A) Processing helix chain 'K' and resid 203 through 213 removed outlier: 3.834A pdb=" N GLU K 212 " --> pdb=" O LYS K 208 " (cutoff:3.500A) Processing helix chain 'K' and resid 215 through 223 Processing helix chain 'L' and resid 15 through 61 removed outlier: 3.731A pdb=" N ALA L 35 " --> pdb=" O LYS L 31 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LYS L 36 " --> pdb=" O LEU L 32 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N THR L 37 " --> pdb=" O LYS L 33 " (cutoff:3.500A) Processing helix chain 'L' and resid 65 through 102 removed outlier: 5.448A pdb=" N ASP L 92 " --> pdb=" O GLU L 88 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ASP L 93 " --> pdb=" O LYS L 89 " (cutoff:3.500A) Processing helix chain 'M' and resid 12 through 75 removed outlier: 3.601A pdb=" N GLN M 62 " --> pdb=" O GLY M 58 " (cutoff:3.500A) Processing helix chain 'M' and resid 80 through 85 Processing helix chain 'M' and resid 115 through 117 No H-bonds generated for 'chain 'M' and resid 115 through 117' Processing helix chain 'M' and resid 129 through 175 Processing helix chain 'M' and resid 177 through 216 Processing helix chain 'N' and resid 3 through 5 No H-bonds generated for 'chain 'N' and resid 3 through 5' Processing helix chain 'N' and resid 14 through 23 Processing helix chain 'N' and resid 47 through 58 Processing helix chain 'N' and resid 71 through 76 removed outlier: 3.767A pdb=" N ASN N 76 " --> pdb=" O HIS N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 78 through 83 Processing helix chain 'N' and resid 103 through 105 No H-bonds generated for 'chain 'N' and resid 103 through 105' Processing helix chain 'N' and resid 109 through 111 No H-bonds generated for 'chain 'N' and resid 109 through 111' Processing helix chain 'O' and resid 30 through 34 Processing helix chain 'O' and resid 58 through 87 Processing helix chain 'O' and resid 90 through 93 removed outlier: 3.633A pdb=" N SER O 93 " --> pdb=" O ASN O 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 90 through 93' Processing helix chain 'O' and resid 96 through 98 No H-bonds generated for 'chain 'O' and resid 96 through 98' Processing helix chain 'O' and resid 102 through 104 No H-bonds generated for 'chain 'O' and resid 102 through 104' Processing helix chain 'O' and resid 107 through 111 Processing helix chain 'O' and resid 127 through 166 Processing helix chain 'O' and resid 175 through 178 No H-bonds generated for 'chain 'O' and resid 175 through 178' Processing helix chain 'O' and resid 200 through 212 Processing helix chain 'O' and resid 219 through 221 No H-bonds generated for 'chain 'O' and resid 219 through 221' Processing helix chain 'O' and resid 243 through 252 Processing helix chain 'O' and resid 266 through 319 removed outlier: 3.939A pdb=" N VAL O 297 " --> pdb=" O LYS O 293 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE O 300 " --> pdb=" O TYR O 296 " (cutoff:3.500A) Processing helix chain 'O' and resid 334 through 351 removed outlier: 3.784A pdb=" N LEU O 337 " --> pdb=" O PRO O 334 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N SER O 338 " --> pdb=" O LYS O 335 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS O 339 " --> pdb=" O ASN O 336 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE O 350 " --> pdb=" O ALA O 347 " (cutoff:3.500A) Processing helix chain 'P' and resid 6 through 9 Processing helix chain 'P' and resid 11 through 22 Processing helix chain 'P' and resid 27 through 32 Processing helix chain 'P' and resid 38 through 51 Processing helix chain 'P' and resid 74 through 86 removed outlier: 3.757A pdb=" N ILE P 78 " --> pdb=" O LYS P 75 " (cutoff:3.500A) Proline residue: P 79 - end of helix Processing helix chain 'P' and resid 90 through 105 Processing helix chain 'P' and resid 111 through 119 Processing helix chain 'P' and resid 121 through 130 Processing helix chain 'P' and resid 136 through 151 Processing helix chain 'P' and resid 158 through 165 Processing helix chain 'P' and resid 168 through 175 Processing helix chain 'P' and resid 180 through 195 removed outlier: 4.093A pdb=" N VAL P 195 " --> pdb=" O GLN P 191 " (cutoff:3.500A) Processing helix chain 'P' and resid 197 through 222 removed outlier: 5.017A pdb=" N LYS P 208 " --> pdb=" O TRP P 204 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N LYS P 209 " --> pdb=" O LEU P 205 " (cutoff:3.500A) Proline residue: P 212 - end of helix Processing helix chain 'P' and resid 238 through 255 Processing helix chain 'P' and resid 257 through 266 Processing helix chain 'P' and resid 268 through 280 removed outlier: 3.718A pdb=" N LYS P 279 " --> pdb=" O LEU P 275 " (cutoff:3.500A) Processing helix chain 'P' and resid 284 through 298 Processing helix chain 'P' and resid 305 through 315 Processing helix chain 'P' and resid 318 through 327 Processing helix chain 'P' and resid 333 through 351 Processing helix chain 'P' and resid 355 through 365 Processing helix chain 'P' and resid 372 through 375 No H-bonds generated for 'chain 'P' and resid 372 through 375' Processing helix chain 'P' and resid 377 through 382 Processing helix chain 'P' and resid 384 through 387 No H-bonds generated for 'chain 'P' and resid 384 through 387' Processing helix chain 'P' and resid 389 through 408 removed outlier: 5.653A pdb=" N ILE P 394 " --> pdb=" O ASP P 390 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N PHE P 395 " --> pdb=" O ASN P 391 " (cutoff:3.500A) Processing helix chain 'P' and resid 414 through 432 Processing helix chain 'P' and resid 435 through 444 removed outlier: 3.960A pdb=" N ASP P 439 " --> pdb=" O GLU P 436 " (cutoff:3.500A) Processing helix chain 'P' and resid 446 through 455 removed outlier: 3.653A pdb=" N LEU P 454 " --> pdb=" O ILE P 450 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ASN P 455 " --> pdb=" O MET P 451 " (cutoff:3.500A) Processing helix chain 'P' and resid 459 through 472 Processing sheet with id= A, first strand: chain 'A' and resid 26 through 30 removed outlier: 6.534A pdb=" N ILE A 36 " --> pdb=" O TYR A 28 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG A 62 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N GLN A 71 " --> pdb=" O VAL A 60 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N VAL A 60 " --> pdb=" O GLN A 71 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 93 through 96 Processing sheet with id= C, first strand: chain 'A' and resid 189 through 191 Processing sheet with id= D, first strand: chain 'A' and resid 409 through 412 removed outlier: 7.354A pdb=" N ALA A 277 " --> pdb=" O SER A 351 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ILE A 353 " --> pdb=" O ALA A 277 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE A 279 " --> pdb=" O ILE A 353 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 181 through 185 removed outlier: 6.701A pdb=" N GLU A 199 " --> pdb=" O THR A 183 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ILE A 185 " --> pdb=" O ILE A 197 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N ILE A 197 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N PHE A 209 " --> pdb=" O ILE A 197 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLU A 199 " --> pdb=" O SER A 207 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N SER A 207 " --> pdb=" O GLU A 199 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N GLU A 201 " --> pdb=" O LYS A 205 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LYS A 205 " --> pdb=" O GLU A 201 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 26 through 28 removed outlier: 3.999A pdb=" N LEU B 26 " --> pdb=" O PHE B 95 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 101 through 104 removed outlier: 3.513A pdb=" N LEU B 132 " --> pdb=" O ILE B 102 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 357 through 359 Processing sheet with id= I, first strand: chain 'B' and resid 328 through 331 removed outlier: 7.217A pdb=" N SER B 209 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N ILE B 277 " --> pdb=" O SER B 209 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL B 211 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N THR B 279 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA B 213 " --> pdb=" O THR B 279 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 26 through 31 removed outlier: 6.510A pdb=" N ILE C 36 " --> pdb=" O TYR C 28 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N VAL C 30 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N VAL C 34 " --> pdb=" O VAL C 30 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG C 62 " --> pdb=" O THR C 69 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLN C 71 " --> pdb=" O VAL C 60 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N VAL C 60 " --> pdb=" O GLN C 71 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 93 through 97 Processing sheet with id= L, first strand: chain 'C' and resid 189 through 192 removed outlier: 4.799A pdb=" N GLN C 140 " --> pdb=" O PHE C 162 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE C 162 " --> pdb=" O GLN C 140 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 437 through 439 removed outlier: 3.525A pdb=" N ALA C 414 " --> pdb=" O THR C 252 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ALA C 277 " --> pdb=" O SER C 351 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ILE C 353 " --> pdb=" O ALA C 277 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE C 279 " --> pdb=" O ILE C 353 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 301 through 303 Processing sheet with id= O, first strand: chain 'C' and resid 181 through 185 removed outlier: 6.807A pdb=" N GLU C 199 " --> pdb=" O THR C 183 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 223 through 226 removed outlier: 6.938A pdb=" N VAL C 399 " --> pdb=" O THR C 224 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 26 through 28 removed outlier: 4.258A pdb=" N LEU D 26 " --> pdb=" O PHE D 95 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 101 through 104 removed outlier: 3.551A pdb=" N ASP D 130 " --> pdb=" O VAL D 104 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 172 through 174 Processing sheet with id= T, first strand: chain 'D' and resid 328 through 333 removed outlier: 3.646A pdb=" N SER D 328 " --> pdb=" O ARG D 272 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU D 278 " --> pdb=" O ILE D 332 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ASN D 207 " --> pdb=" O HIS D 273 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N LEU D 275 " --> pdb=" O ASN D 207 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N SER D 209 " --> pdb=" O LEU D 275 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N ILE D 277 " --> pdb=" O SER D 209 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL D 211 " --> pdb=" O ILE D 277 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N PHE D 241 " --> pdb=" O ALA D 214 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N GLY D 216 " --> pdb=" O PHE D 241 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N ASN D 243 " --> pdb=" O GLY D 216 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 85 through 87 removed outlier: 6.502A pdb=" N THR E 69 " --> pdb=" O ILE E 61 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ILE E 63 " --> pdb=" O LYS E 67 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LYS E 67 " --> pdb=" O ILE E 63 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 93 through 96 Processing sheet with id= W, first strand: chain 'E' and resid 189 through 191 Processing sheet with id= X, first strand: chain 'E' and resid 207 through 209 removed outlier: 3.531A pdb=" N TRP E 184 " --> pdb=" O GLU E 199 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 278 through 281 Processing sheet with id= Z, first strand: chain 'E' and resid 349 through 354 removed outlier: 7.762A pdb=" N VAL E 350 " --> pdb=" O THR E 407 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N SER E 409 " --> pdb=" O VAL E 350 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N MET E 352 " --> pdb=" O SER E 409 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N SER E 411 " --> pdb=" O MET E 352 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ALA E 354 " --> pdb=" O SER E 411 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL E 413 " --> pdb=" O ALA E 354 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL E 410 " --> pdb=" O GLY E 396 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 26 through 31 removed outlier: 6.519A pdb=" N ILE E 36 " --> pdb=" O TYR E 28 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N VAL E 30 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N VAL E 34 " --> pdb=" O VAL E 30 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 26 through 28 removed outlier: 3.983A pdb=" N LEU F 26 " --> pdb=" O PHE F 95 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 31 through 35 removed outlier: 6.742A pdb=" N ILE F 40 " --> pdb=" O SER F 32 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N VAL F 34 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LEU F 38 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA F 75 " --> pdb=" O LEU F 41 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU F 69 " --> pdb=" O ILE F 76 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N GLN F 78 " --> pdb=" O VAL F 67 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N VAL F 67 " --> pdb=" O GLN F 78 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 101 through 104 Processing sheet with id= AE, first strand: chain 'F' and resid 357 through 360 removed outlier: 7.558A pdb=" N VAL F 360 " --> pdb=" O PRO F 171 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N PHE F 173 " --> pdb=" O VAL F 360 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'F' and resid 238 through 243 removed outlier: 6.693A pdb=" N ILE F 210 " --> pdb=" O SER F 239 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N PHE F 241 " --> pdb=" O ILE F 210 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N PHE F 212 " --> pdb=" O PHE F 241 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ASN F 243 " --> pdb=" O PHE F 212 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N ALA F 214 " --> pdb=" O ASN F 243 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N SER F 328 " --> pdb=" O VAL F 274 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N THR F 276 " --> pdb=" O SER F 328 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N THR F 330 " --> pdb=" O THR F 276 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'G' and resid 171 through 174 removed outlier: 3.685A pdb=" N VAL G 188 " --> pdb=" O ASN G 201 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'I' and resid 171 through 174 removed outlier: 3.849A pdb=" N VAL I 188 " --> pdb=" O ASN I 201 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'K' and resid 171 through 174 removed outlier: 3.681A pdb=" N VAL K 188 " --> pdb=" O ASN K 201 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'M' and resid 92 through 97 Processing sheet with id= AK, first strand: chain 'N' and resid 8 through 10 removed outlier: 6.112A pdb=" N ILE N 66 " --> pdb=" O ALA N 9 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ALA N 90 " --> pdb=" O LEU N 67 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ILE N 69 " --> pdb=" O ALA N 90 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N LEU N 92 " --> pdb=" O ILE N 69 " (cutoff:3.500A) No H-bonds generated for sheet with id= AK Processing sheet with id= AL, first strand: chain 'O' and resid 387 through 390 Processing sheet with id= AM, first strand: chain 'O' and resid 191 through 193 2030 hydrogen bonds defined for protein. 5598 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: 12.76 Time building geometry restraints manager: 16.04 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: 11478 1.34 - 1.46: 4424 1.46 - 1.57: 18216 1.57 - 1.69: 3 1.69 - 1.81: 153 Bond restraints: 34274 Sorted by residual: bond pdb=" CB MET C 485 " pdb=" CG MET C 485 " ideal model delta sigma weight residual 1.520 1.473 0.047 3.00e-02 1.11e+03 2.48e+00 bond pdb=" CB VAL B 53 " pdb=" CG1 VAL B 53 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.94e+00 bond pdb=" SD MET F 215 " pdb=" CE MET F 215 " ideal model delta sigma weight residual 1.791 1.757 0.034 2.50e-02 1.60e+03 1.87e+00 bond pdb=" CG PRO A 452 " pdb=" CD PRO A 452 " ideal model delta sigma weight residual 1.512 1.475 0.037 2.70e-02 1.37e+03 1.85e+00 bond pdb=" CB VAL E 410 " pdb=" CG2 VAL E 410 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.74e+00 ... (remaining 34269 not shown) Histogram of bond angle deviations from ideal: 97.60 - 105.19: 698 105.19 - 112.79: 19067 112.79 - 120.38: 12618 120.38 - 127.97: 14559 127.97 - 135.57: 188 Bond angle restraints: 47130 Sorted by residual: angle pdb=" C ASP E 377 " pdb=" CA ASP E 377 " pdb=" CB ASP E 377 " ideal model delta sigma weight residual 116.34 110.56 5.78 1.40e+00 5.10e-01 1.70e+01 angle pdb=" CB MET A 547 " pdb=" CG MET A 547 " pdb=" SD MET A 547 " ideal model delta sigma weight residual 112.70 102.63 10.07 3.00e+00 1.11e-01 1.13e+01 angle pdb=" CB MET C 45 " pdb=" CG MET C 45 " pdb=" SD MET C 45 " ideal model delta sigma weight residual 112.70 103.04 9.66 3.00e+00 1.11e-01 1.04e+01 angle pdb=" N TYR A 28 " pdb=" CA TYR A 28 " pdb=" C TYR A 28 " ideal model delta sigma weight residual 114.56 110.58 3.98 1.27e+00 6.20e-01 9.84e+00 angle pdb=" N VAL D 16 " pdb=" CA VAL D 16 " pdb=" C VAL D 16 " ideal model delta sigma weight residual 111.91 109.18 2.73 8.90e-01 1.26e+00 9.43e+00 ... (remaining 47125 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.13: 19557 22.13 - 44.26: 665 44.26 - 66.38: 42 66.38 - 88.51: 14 88.51 - 110.64: 4 Dihedral angle restraints: 20282 sinusoidal: 5106 harmonic: 15176 Sorted by residual: dihedral pdb=" O1B ADP A 701 " pdb=" O3A ADP A 701 " pdb=" PB ADP A 701 " pdb=" PA ADP A 701 " ideal model delta sinusoidal sigma weight residual -60.00 -170.64 110.64 1 2.00e+01 2.50e-03 3.25e+01 dihedral pdb=" CA PHE B 208 " pdb=" C PHE B 208 " pdb=" N SER B 209 " pdb=" CA SER B 209 " ideal model delta harmonic sigma weight residual 180.00 157.52 22.48 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA GLY C 282 " pdb=" C GLY C 282 " pdb=" N CYS C 283 " pdb=" CA CYS C 283 " ideal model delta harmonic sigma weight residual -180.00 -158.57 -21.43 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 20279 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 3799 0.034 - 0.067: 1470 0.067 - 0.101: 455 0.101 - 0.135: 179 0.135 - 0.169: 15 Chirality restraints: 5918 Sorted by residual: chirality pdb=" CA MET C 485 " pdb=" N MET C 485 " pdb=" C MET C 485 " pdb=" CB MET C 485 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.10e-01 chirality pdb=" CB ILE B 170 " pdb=" CA ILE B 170 " pdb=" CG1 ILE B 170 " pdb=" CG2 ILE B 170 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 6.92e-01 chirality pdb=" CA ILE E 254 " pdb=" N ILE E 254 " pdb=" C ILE E 254 " pdb=" CB ILE E 254 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.33e-01 ... (remaining 5915 not shown) Planarity restraints: 6176 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS G 118 " -0.034 5.00e-02 4.00e+02 5.00e-02 4.00e+00 pdb=" N PRO G 119 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO G 119 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO G 119 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 344 " -0.032 5.00e-02 4.00e+02 4.76e-02 3.63e+00 pdb=" N PRO B 345 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 345 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 345 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU F 266 " -0.008 2.00e-02 2.50e+03 1.70e-02 2.88e+00 pdb=" C LEU F 266 " 0.029 2.00e-02 2.50e+03 pdb=" O LEU F 266 " -0.011 2.00e-02 2.50e+03 pdb=" N ALA F 267 " -0.010 2.00e-02 2.50e+03 ... (remaining 6173 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2426 2.74 - 3.28: 35924 3.28 - 3.82: 58954 3.82 - 4.36: 63110 4.36 - 4.90: 113964 Nonbonded interactions: 274378 Sorted by model distance: nonbonded pdb=" O ILE D 52 " pdb=" OG1 THR D 96 " model vdw 2.195 2.440 nonbonded pdb=" O LEU F 266 " pdb=" OG1 THR F 270 " model vdw 2.207 2.440 nonbonded pdb=" O SER B 163 " pdb=" OG SER B 380 " model vdw 2.207 2.440 nonbonded pdb=" NZ LYS A 262 " pdb=" O1B ADP A 701 " model vdw 2.209 2.520 nonbonded pdb=" O GLU D 296 " pdb=" NE2 GLN M 207 " model vdw 2.218 2.520 ... (remaining 274373 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 24 through 54 or (resid 55 and (name N or name CA or name \ C or name O or name CB )) or resid 56 through 70 or (resid 71 and (name N or nam \ e CA or name C or name O or name CB )) or resid 72 through 109 or (resid 110 and \ (name N or name CA or name C or name O or name CB )) or resid 111 through 112 o \ r (resid 113 through 114 and (name N or name CA or name C or name O or name CB ) \ ) or resid 115 through 116 or (resid 117 through 121 and (name N or name CA or n \ ame C or name O or name CB )) or resid 122 through 129 or (resid 130 and (name N \ or name CA or name C or name O or name CB )) or resid 131 through 135 or (resid \ 136 and (name N or name CA or name C or name O or name CB )) or resid 137 or (r \ esid 138 and (name N or name CA or name C or name O or name CB )) or resid 139 t \ hrough 147 or (resid 148 and (name N or name CA or name C or name O or name CB ) \ ) or resid 149 through 161 or (resid 162 and (name N or name CA or name C or nam \ e O or name CB )) or resid 163 or (resid 164 through 165 and (name N or name CA \ or name C or name O or name CB )) or resid 166 through 167 or (resid 168 through \ 169 and (name N or name CA or name C or name O or name CB )) or resid 170 throu \ gh 180 or (resid 181 and (name N or name CA or name C or name O or name CB )) or \ resid 182 or (resid 183 and (name N or name CA or name C or name O or name CB ) \ ) or resid 184 through 189 or (resid 190 and (name N or name CA or name C or nam \ e O or name CB )) or resid 191 through 196 or (resid 197 and (name N or name CA \ or name C or name O or name CB )) or resid 198 through 201 or (resid 202 through \ 203 and (name N or name CA or name C or name O or name CB )) or (resid 204 thro \ ugh 208 and (name N or name CA or name C or name O or name CB )) or resid 209 or \ (resid 210 and (name N or name CA or name C or name O or name CB )) or resid 21 \ 1 through 217 or (resid 218 and (name N or name CA or name C or name O or name C \ B )) or resid 219 through 223 or (resid 224 through 225 and (name N or name CA o \ r name C or name O or name CB )) or resid 226 through 234 or (resid 235 and (nam \ e N or name CA or name C or name O or name CB )) or resid 236 through 240 or (re \ sid 241 through 242 and (name N or name CA or name C or name O or name CB )) or \ resid 243 through 255 or (resid 264 through 277 and (name N or name CA or name C \ or name O or name CB )) or resid 278 through 289 or (resid 290 through 292 and \ (name N or name CA or name C or name O or name CB )) or resid 293 through 294 or \ (resid 295 through 296 and (name N or name CA or name C or name O or name CB )) \ or resid 297 through 299 or (resid 300 through 305 and (name N or name CA or na \ me C or name O or name CB )) or resid 306 through 310 or (resid 311 and (name N \ or name CA or name C or name O or name CB )) or resid 312 through 314 or (resid \ 315 and (name N or name CA or name C or name O or name CB )) or resid 316 throug \ h 329 or (resid 330 through 332 and (name N or name CA or name C or name O or na \ me CB )) or resid 333 through 361 or (resid 362 through 363 and (name N or name \ CA or name C or name O or name CB )) or resid 364 through 367 or (resid 368 and \ (name N or name CA or name C or name O or name CB )) or resid 369 through 386 or \ (resid 387 and (name N or name CA or name C or name O or name CB )) or resid 38 \ 8 through 389 or (resid 390 and (name N or name CA or name C or name O or name C \ B )) or resid 391 through 406 or (resid 407 and (name N or name CA or name C or \ name O or name CB )) or resid 408 through 416 or (resid 417 and (name N or name \ CA or name C or name O or name CB )) or resid 424 through 440 or (resid 441 thro \ ugh 444 and (name N or name CA or name C or name O or name CB )) or resid 445 th \ rough 446 or (resid 447 through 449 and (name N or name CA or name C or name O o \ r name CB )) or resid 450 or (resid 451 and (name N or name CA or name C or name \ O or name CB )) or resid 452 or (resid 453 and (name N or name CA or name C or \ name O or name CB )) or resid 454 or (resid 455 through 459 and (name N or name \ CA or name C or name O or name CB )) or resid 460 through 479 or (resid 480 and \ (name N or name CA or name C or name O or name CB )) or resid 481 through 482 or \ (resid 483 and (name N or name CA or name C or name O or name CB )) or resid 48 \ 4 through 486 or (resid 487 and (name N or name CA or name C or name O or name C \ B )) or resid 488 through 489 or (resid 490 through 502 and (name N or name CA o \ r name C or name O or name CB )) or (resid 503 through 518 and (name N or name C \ A or name C or name O or name CB )) or resid 519 through 528 or (resid 529 and ( \ name N or name CA or name C or name O or name CB )) or resid 530 or (resid 531 t \ hrough 536 and (name N or name CA or name C or name O or name CB )) or resid 537 \ or (resid 538 and (name N or name CA or name C or name O or name CB )) or resid \ 539 through 551 or (resid 552 and (name N or name CA or name C or name O or nam \ e CB )) or resid 553 through 557 or (resid 558 through 563 and (name N or name C \ A or name C or name O or name CB )) or (resid 564 through 574 and (name N or nam \ e CA or name C or name O or name CB )) or (resid 575 through 580 and (name N or \ name CA or name C or name O or name CB )) or resid 581 or (resid 582 through 584 \ and (name N or name CA or name C or name O or name CB )) or resid 585 through 5 \ 86 or (resid 587 through 588 and (name N or name CA or name C or name O or name \ CB )) or resid 589 through 590 or (resid 591 and (name N or name CA or name C or \ name O or name CB )) or resid 592 through 602 or (resid 603 through 613 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 'C' and (resid 24 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 35 or (resid 36 through 39 and (na \ me N or name CA or name C or name O or name CB )) or resid 40 or (resid 41 and ( \ name N or name CA or name C or name O or name CB )) or resid 42 or (resid 43 thr \ ough 44 and (name N or name CA or name C or name O or name CB )) or resid 45 thr \ ough 50 or (resid 51 and (name N or name CA or name C or name O or name CB )) or \ resid 52 through 61 or (resid 62 and (name N or name CA or name C or name O or \ name CB )) or resid 63 through 66 or (resid 67 through 68 and (name N or name CA \ or name C or name O or name CB )) or resid 69 through 85 or (resid 86 and (name \ N or name CA or name C or name O or name CB )) or resid 87 through 92 or (resid \ 93 and (name N or name CA or name C or name O or name CB )) or resid 94 through \ 109 or (resid 110 and (name N or name CA or name C or name O or name CB )) or r \ esid 111 through 129 or (resid 130 and (name N or name CA or name C or name O or \ name CB )) or resid 131 through 137 or (resid 138 and (name N or name CA or nam \ e C or name O or name CB )) or resid 139 or (resid 140 and (name N or name CA or \ name C or name O or name CB )) or resid 141 through 147 or (resid 148 and (name \ N or name CA or name C or name O or name CB )) or (resid 149 through 151 and (n \ ame N or name CA or name C or name O or name CB )) or resid 152 through 164 or ( \ resid 165 and (name N or name CA or name C or name O or name CB )) or resid 166 \ or (resid 167 through 169 and (name N or name CA or name C or name O or name CB \ )) or resid 170 through 180 or (resid 181 and (name N or name CA or name C or na \ me O or name CB )) or resid 182 or (resid 183 and (name N or name CA or name C o \ r name O or name CB )) or resid 184 through 189 or (resid 190 and (name N or nam \ e CA or name C or name O or name CB )) or resid 191 through 194 or (resid 195 th \ rough 197 and (name N or name CA or name C or name O or name CB )) or resid 198 \ or (resid 199 and (name N or name CA or name C or name O or name CB )) or resid \ 200 through 223 or (resid 224 through 225 and (name N or name CA or name C or na \ me O or name CB )) or resid 226 through 234 or (resid 235 and (name N or name CA \ or name C or name O or name CB )) or resid 236 through 250 or (resid 251 and (n \ ame N or name CA or name C or name O or name CB )) or resid 252 through 255 or ( \ resid 264 through 277 and (name N or name CA or name C or name O or name CB )) o \ r resid 278 through 289 or (resid 290 through 292 and (name N or name CA or name \ C or name O or name CB )) or resid 293 through 299 or (resid 300 through 305 an \ d (name N or name CA or name C or name O or name CB )) or resid 306 through 408 \ or (resid 409 and (name N or name CA or name C or name O or name CB )) or resid \ 410 or (resid 411 and (name N or name CA or name C or name O or name CB )) or re \ sid 412 through 415 or (resid 416 through 417 and (name N or name CA or name C o \ r name O or name CB )) or resid 424 through 440 or (resid 441 through 444 and (n \ ame N or name CA or name C or name O or name CB )) or resid 445 through 457 or ( \ resid 458 through 459 and (name N or name CA or name C or name O or name CB )) o \ r resid 460 through 461 or (resid 462 and (name N or name CA or name C or name O \ or name CB )) or resid 463 through 464 or (resid 465 and (name N or name CA or \ name C or name O or name CB )) or resid 466 through 489 or (resid 490 through 50 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 503 through \ 537 or (resid 538 and (name N or name CA or name C or name O or name CB )) or re \ sid 539 through 577 or (resid 578 through 580 and (name N or name CA or name C o \ r name O or name CB )) or resid 581 through 603 or (resid 604 through 613 and (n \ ame N or name CA or name C or name O or name CB )))) selection = (chain 'E' and ((resid 24 and (name N or name CA or name C or name O or name CB \ )) or resid 25 through 28 or (resid 29 and (name N or name CA or name C or name \ O or name CB )) or resid 30 or (resid 31 and (name N or name CA or name C or nam \ e O or name CB )) or resid 32 through 35 or (resid 36 through 39 and (name N or \ name CA or name C or name O or name CB )) or resid 40 through 42 or (resid 43 th \ rough 44 and (name N or name CA or name C or name O or name CB )) or resid 45 th \ rough 50 or (resid 51 and (name N or name CA or name C or name O or name CB )) o \ r resid 52 through 54 or (resid 55 and (name N or name CA or name C or name O or \ name CB )) or resid 56 through 61 or (resid 62 and (name N or name CA or name C \ or name O or name CB )) or resid 63 through 66 or (resid 67 through 68 and (nam \ e N or name CA or name C or name O or name CB )) or resid 69 through 70 or (resi \ d 71 and (name N or name CA or name C or name O or name CB )) or resid 72 throug \ h 79 or (resid 80 and (name N or name CA or name C or name O or name CB )) or re \ sid 81 through 82 or (resid 83 and (name N or name CA or name C or name O or nam \ e CB )) or resid 84 through 85 or (resid 86 and (name N or name CA or name C or \ name O or name CB )) or resid 87 through 92 or (resid 93 and (name N or name CA \ or name C or name O or name CB )) or resid 94 through 107 or (resid 108 and (nam \ e N or name CA or name C or name O or name CB )) or resid 109 through 133 or (re \ sid 134 and (name N or name CA or name C or name O or name CB )) or resid 135 th \ rough 150 or (resid 151 and (name N or name CA or name C or name O or name CB )) \ or resid 152 through 161 or (resid 162 and (name N or name CA or name C or name \ O or name CB )) or resid 163 or (resid 164 through 165 and (name N or name CA o \ r name C or name O or name CB )) or resid 166 or (resid 167 through 169 and (nam \ e N or name CA or name C or name O or name CB )) or resid 170 through 195 or (re \ sid 196 through 197 and (name N or name CA or name C or name O or name CB )) or \ resid 198 through 205 or (resid 206 through 208 and (name N or name CA or name C \ or name O or name CB )) or resid 209 or (resid 210 and (name N or name CA or na \ me C or name O or name CB )) or resid 211 through 217 or (resid 218 and (name N \ or name CA or name C or name O or name CB )) or resid 219 through 250 or (resid \ 251 and (name N or name CA or name C or name O or name CB )) or resid 252 throug \ h 275 or (resid 276 through 277 and (name N or name CA or name C or name O or na \ me CB )) or resid 278 through 284 or (resid 285 and (name N or name CA or name C \ or name O or name CB )) or resid 286 through 288 or (resid 289 through 292 and \ (name N or name CA or name C or name O or name CB )) or resid 293 through 301 or \ (resid 302 through 305 and (name N or name CA or name C or name O or name CB )) \ or resid 306 through 310 or (resid 311 and (name N or name CA or name C or name \ O or name CB )) or resid 312 through 314 or (resid 315 and (name N or name CA o \ r name C or name O or name CB )) or resid 316 through 329 or (resid 330 through \ 332 and (name N or name CA or name C or name O or name CB )) or resid 333 throug \ h 361 or (resid 362 through 363 and (name N or name CA or name C or name O or na \ me CB )) or resid 364 through 365 or (resid 366 and (name N or name CA or name C \ or name O or name CB )) or resid 367 or (resid 368 and (name N or name CA or na \ me C or name O or name CB )) or resid 369 through 386 or (resid 387 and (name N \ or name CA or name C or name O or name CB )) or resid 388 through 406 or (resid \ 407 and (name N or name CA or name C or name O or name CB )) or resid 408 throug \ h 415 or (resid 416 through 425 and (name N or name CA or name C or name O or na \ me CB )) or resid 426 through 446 or (resid 447 through 449 and (name N or name \ CA or name C or name O or name CB )) or resid 450 or (resid 451 and (name N or n \ ame CA or name C or name O or name CB )) or resid 452 through 454 or (resid 455 \ through 459 and (name N or name CA or name C or name O or name CB )) or resid 46 \ 0 through 461 or (resid 462 and (name N or name CA or name C or name O or name C \ B )) or resid 463 through 479 or (resid 480 and (name N or name CA or name C or \ name O or name CB )) or resid 481 through 482 or (resid 483 and (name N or name \ CA or name C or name O or name CB )) or resid 484 through 490 or (resid 491 thro \ ugh 502 and (name N or name CA or name C or name O or name CB )) or (resid 503 t \ hrough 518 and (name N or name CA or name C or name O or name CB )) or resid 519 \ through 530 or (resid 531 through 536 and (name N or name CA or name C or name \ O or name CB )) or resid 537 through 551 or (resid 552 and (name N or name CA or \ name C or name O or name CB )) or resid 553 through 555 or (resid 556 through 5 \ 63 and (name N or name CA or name C or name O or name CB )) or (resid 564 throug \ h 574 and (name N or name CA or name C or name O or name CB )) or (resid 575 thr \ ough 580 and (name N or name CA or name C or name O or name CB )) or resid 581 o \ r (resid 582 through 584 and (name N or name CA or name C or name O or name CB ) \ ) or resid 585 through 586 or (resid 587 through 588 and (name N or name CA or n \ ame C or name O or name CB )) or resid 589 through 590 or (resid 591 and (name N \ or name CA or name C or name O or name CB )) or resid 592 through 602 or (resid \ 603 through 613 and (name N or name CA or name C or name O or name CB )))) } ncs_group { reference = (chain 'B' and (resid 15 through 60 or (resid 61 and (name N or name CA or name \ C or name O or name CB )) or resid 62 through 80 or (resid 81 and (name N or nam \ e CA or name C or name O or name CB )) or resid 82 through 93 or (resid 94 and ( \ name N or name CA or name C or name O or name CB )) or resid 95 through 104 or ( \ resid 105 through 107 and (name N or name CA or name C or name O or name CB )) o \ r resid 108 through 115 or (resid 116 and (name N or name CA or name C or name O \ or name CB )) or resid 117 through 121 or (resid 122 and (name N or name CA or \ name C or name O or name CB )) or resid 123 through 128 or (resid 129 through 13 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 131 through \ 136 or (resid 137 and (name N or name CA or name C or name O or name CB )) or re \ sid 138 through 147 or (resid 148 through 149 and (name N or name CA or name C o \ r name O or name CB )) or resid 150 through 155 or (resid 156 through 157 and (n \ ame N or name CA or name C or name O or name CB )) or resid 158 through 159 or ( \ resid 160 and (name N or name CA or name C or name O or name CB )) or resid 161 \ through 173 or (resid 174 through 176 and (name N or name CA or name C or name O \ or name CB )) or resid 177 through 180 or (resid 181 through 182 and (name N or \ name CA or name C or name O or name CB )) or resid 183 through 193 or (resid 19 \ 4 and (name N or name CA or name C or name O or name CB )) or (resid 207 and (na \ me N or name CA or name C or name O or name CB )) or resid 208 through 217 or (r \ esid 218 and (name N or name CA or name C or name O or name CB )) or resid 219 t \ hrough 220 or (resid 221 through 223 and (name N or name CA or name C or name O \ or name CB )) or resid 224 through 225 or (resid 226 through 228 and (name N or \ name CA or name C or name O or name CB )) or resid 229 through 230 or (resid 231 \ through 232 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 33 or (resid 234 and (name N or name CA or name C or name O or name CB )) or res \ id 235 through 237 or (resid 238 through 239 and (name N or name CA or name C or \ name O or name CB )) or resid 240 through 245 or (resid 246 through 247 and (na \ me N or name CA or name C or name O or name CB )) or resid 248 through 250 or (r \ esid 251 and (name N or name CA or name C or name O or name CB )) or resid 252 t \ hrough 253 or (resid 254 and (name N or name CA or name C or name O or name CB ) \ ) or resid 255 through 270 or (resid 271 and (name N or name CA or name C or nam \ e O or name CB )) or resid 272 through 281 or (resid 282 through 283 and (name N \ or name CA or name C or name O or name CB )) or resid 284 through 296 or (resid \ 297 and (name N or name CA or name C or name O or name CB )) or resid 298 throu \ gh 300 or (resid 301 and (name N or name CA or name C or name O or name CB )) or \ resid 302 through 312 or (resid 313 and (name N or name CA or name C or name O \ or name CB )) or resid 314 through 316 or (resid 317 and (name N or name CA or n \ ame C or name O or name CB )) or resid 318 through 325 or (resid 326 and (name N \ or name CA or name C or name O or name CB )) or resid 327 through 356 or (resid \ 357 and (name N or name CA or name C or name O or name CB )) or resid 358 throu \ gh 375 or (resid 376 and (name N or name CA or name C or name O or name CB )) or \ resid 377 or (resid 378 and (name N or name CA or name C or name O or name CB ) \ ) or resid 379 or (resid 380 and (name N or name CA or name C or name O or name \ CB )) or resid 381 through 383 or (resid 384 through 387 and (name N or name CA \ or name C or name O or name CB )) or (resid 388 through 392 and (name N or name \ CA or name C or name O or name CB )) or resid 393 through 399 or (resid 400 thro \ ugh 401 and (name N or name CA or name C or name O or name CB )) or resid 402 th \ rough 416 or (resid 417 through 420 and (name N or name CA or name C or name O o \ r name CB )) or (resid 421 through 430 and (name N or name CA or name C or name \ O or name CB )) or resid 431 through 437 or (resid 438 and (name N or name CA or \ name C or name O or name CB )) or resid 439 or (resid 440 through 442 and (name \ N or name CA or name C or name O or name CB )) or resid 443 through 444 or (res \ id 445 and (name N or name CA or name C or name O or name CB )) or resid 446 thr \ ough 448 or (resid 449 and (name N or name CA or name C or name O or name CB )) \ or resid 450 or (resid 451 and (name N or name CA or name C or name O or name CB \ )) or resid 452 through 456 or (resid 457 and (name N or name CA or name C or n \ ame O or name CB )) or resid 458 or (resid 459 through 461 and (name N or name C \ A or name C or name O or name CB )) or resid 462 through 485)) selection = (chain 'D' and (resid 15 through 20 or (resid 21 and (name N or name CA or name \ C or name O or name CB )) or resid 22 through 31 or (resid 32 and (name N or nam \ e CA or name C or name O or name CB )) or resid 33 through 39 or (resid 40 and ( \ name N or name CA or name C or name O or name CB )) or resid 41 through 51 or (r \ esid 52 and (name N or name CA or name C or name O or name CB )) or resid 53 thr \ ough 55 or (resid 56 and (name N or name CA or name C or name O or name CB )) or \ resid 57 through 70 or (resid 71 and (name N or name CA or name C or name O or \ name CB )) or resid 72 through 132 or (resid 133 and (name N or name CA or name \ C or name O or name CB )) or resid 134 through 136 or (resid 137 and (name N or \ name CA or name C or name O or name CB )) or resid 138 through 155 or (resid 156 \ through 157 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 58 through 173 or (resid 174 through 176 and (name N or name CA or name C or nam \ e O or name CB )) or resid 177 through 193 or (resid 194 through 207 and (name N \ or name CA or name C or name O or name CB )) or resid 208 through 220 or (resid \ 221 through 223 and (name N or name CA or name C or name O or name CB )) or res \ id 224 through 231 or (resid 232 and (name N or name CA or name C or name O or n \ ame CB )) or resid 233 through 253 or (resid 254 and (name N or name CA or name \ C or name O or name CB )) or resid 255 through 263 or (resid 264 and (name N or \ name CA or name C or name O or name CB )) or resid 265 through 316 or (resid 317 \ and (name N or name CA or name C or name O or name CB )) or resid 318 through 3 \ 90 or (resid 391 through 392 and (name N or name CA or name C or name O or name \ CB )) or resid 393 or (resid 394 through 395 and (name N or name CA or name C or \ name O or name CB )) or resid 396 through 415 or (resid 416 through 420 and (na \ me N or name CA or name C or name O or name CB )) or (resid 421 through 430 and \ (name N or name CA or name C or name O or name CB )) or resid 431 or (resid 432 \ and (name N or name CA or name C or name O or name CB )) or resid 433 through 43 \ 9 or (resid 440 through 442 and (name N or name CA or name C or name O or name C \ B )) or resid 443 through 448 or (resid 449 and (name N or name CA or name C or \ name O or name CB )) or resid 450 through 455 or (resid 456 through 457 and (nam \ e N or name CA or name C or name O or name CB )) or resid 458 through 459 or (re \ sid 460 through 461 and (name N or name CA or name C or name O or name CB )) or \ resid 462 through 485)) selection = (chain 'F' and (resid 15 through 20 or (resid 21 and (name N or name CA or name \ C or name O or name CB )) or resid 22 or (resid 23 and (name N or name CA or nam \ e C or name O or name CB )) or resid 24 through 31 or (resid 32 and (name N or n \ ame CA or name C or name O or name CB )) or resid 33 through 34 or (resid 35 and \ (name N or name CA or name C or name O or name CB )) or resid 36 through 39 or \ (resid 40 and (name N or name CA or name C or name O or name CB )) or resid 41 t \ hrough 42 or (resid 43 and (name N or name CA or name C or name O or name CB )) \ or resid 44 through 50 or (resid 51 through 52 and (name N or name CA or name C \ or name O or name CB )) or resid 53 through 55 or (resid 56 and (name N or name \ CA or name C or name O or name CB )) or resid 57 through 60 or (resid 61 and (na \ me N or name CA or name C or name O or name CB )) or resid 62 through 83 or (res \ id 84 and (name N or name CA or name C or name O or name CB )) or resid 85 throu \ gh 93 or (resid 94 and (name N or name CA or name C or name O or name CB )) or r \ esid 95 through 128 or (resid 129 through 130 and (name N or name CA or name C o \ r name O or name CB )) or resid 131 through 180 or (resid 181 through 182 and (n \ ame N or name CA or name C or name O or name CB )) or resid 183 through 217 or ( \ resid 218 and (name N or name CA or name C or name O or name CB )) or resid 219 \ through 225 or (resid 226 through 228 and (name N or name CA or name C or name O \ or name CB )) or resid 229 through 237 or (resid 238 through 239 and (name N or \ name CA or name C or name O or name CB )) or resid 240 through 250 or (resid 25 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 252 through \ 263 or (resid 264 and (name N or name CA or name C or name O or name CB )) or re \ sid 265 through 281 or (resid 282 through 283 and (name N or name CA or name C o \ r name O or name CB )) or resid 284 through 312 or (resid 313 and (name N or nam \ e CA or name C or name O or name CB )) or resid 314 through 338 or (resid 339 th \ rough 341 and (name N or name CA or name C or name O or name CB )) or resid 342 \ through 347 or (resid 348 and (name N or name CA or name C or name O or name CB \ )) or resid 349 through 356 or (resid 357 and (name N or name CA or name C or na \ me O or name CB )) or resid 358 through 375 or (resid 376 and (name N or name CA \ or name C or name O or name CB )) or resid 377 through 391 or (resid 392 and (n \ ame N or name CA or name C or name O or name CB )) or resid 393 through 397 or ( \ resid 398 and (name N or name CA or name C or name O or name CB )) or resid 399 \ or (resid 400 through 401 and (name N or name CA or name C or name O or name CB \ )) or resid 402 through 444 or (resid 445 and (name N or name CA or name C or na \ me O or name CB )) or resid 446 through 455 or (resid 456 through 457 and (name \ N or name CA or name C or name O or name CB )) or resid 458 or (resid 459 throug \ h 461 and (name N or name CA or name C or name O or name CB )) or resid 462 or ( \ resid 463 and (name N or name CA or name C or name O or name CB )) or resid 464 \ through 473 or (resid 474 and (name N or name CA or name C or name O or name CB \ )) or resid 475 through 476 or (resid 477 and (name N or name CA or name C or na \ me O or name CB )) or resid 478 through 485)) } ncs_group { reference = (chain 'G' and ((resid 21 through 85 and (name N or name CA or name C or name O \ or name CB )) or resid 86 through 89 or (resid 90 through 91 and (name N or name \ CA or name C or name O or name CB )) or resid 92 through 94 or (resid 95 and (n \ ame N or name CA or name C or name O or name CB )) or resid 96 through 102 or (r \ esid 103 through 105 and (name N or name CA or name C or name O or name CB )) or \ resid 106 through 109 or (resid 110 through 116 and (name N or name CA or name \ C or name O or name CB )) or resid 117 through 122 or (resid 123 and (name N or \ name CA or name C or name O or name CB )) or resid 124 through 131 or (resid 132 \ and (name N or name CA or name C or name O or name CB )) or resid 133 through 1 \ 37 or (resid 138 and (name N or name CA or name C or name O or name CB )) or res \ id 139 or (resid 140 through 141 and (name N or name CA or name C or name O or n \ ame CB )) or resid 142 through 145 or (resid 146 through 148 and (name N or name \ CA or name C or name O or name CB )) or resid 149 through 162 or (resid 163 thr \ ough 167 and (name N or name CA or name C or name O or name CB )) or resid 168 t \ hrough 183 or (resid 184 through 185 and (name N or name CA or name C or name O \ or name CB )) or resid 186 through 193 or (resid 194 through 196 and (name N or \ name CA or name C or name O or name CB )) or resid 197 or (resid 198 and (name N \ or name CA or name C or name O or name CB )) or resid 199 through 231)) selection = (chain 'I' and (resid 21 through 89 or (resid 90 through 91 and (name N or name \ CA or name C or name O or name CB )) or resid 92 through 100 or (resid 101 throu \ gh 105 and (name N or name CA or name C or name O or name CB )) or resid 106 thr \ ough 121 or (resid 122 through 123 and (name N or name CA or name C or name O or \ name CB )) or resid 124 through 137 or (resid 138 and (name N or name CA or nam \ e C or name O or name CB )) or resid 139 or (resid 140 through 141 and (name N o \ r name CA or name C or name O or name CB )) or resid 142 through 143 or (resid 1 \ 44 through 148 and (name N or name CA or name C or name O or name CB )) or resid \ 149 through 191 or (resid 192 through 196 and (name N or name CA or name C or n \ ame O or name CB )) or resid 197 or (resid 198 and (name N or name CA or name C \ or name O or name CB )) or resid 199 through 219 or (resid 220 through 221 and ( \ name N or name CA or name C or name O or name CB )) or resid 222 through 227 or \ (resid 228 and (name N or name CA or name C or name O or name CB )) or resid 229 \ through 231)) selection = (chain 'K' and ((resid 21 through 85 and (name N or name CA or name C or name O \ or name CB )) or resid 86 through 94 or (resid 95 and (name N or name CA or name \ C or name O or name CB )) or resid 96 through 131 or (resid 132 and (name N or \ name CA or name C or name O or name CB )) or resid 133 through 135 or (resid 136 \ through 138 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 39 through 143 or (resid 144 through 148 and (name N or name CA or name C or nam \ e O or name CB )) or resid 149 through 152 or (resid 153 through 155 and (name N \ or name CA or name C or name O or name CB )) or resid 156 through 158 or (resid \ 159 and (name N or name CA or name C or name O or name CB )) or resid 160 throu \ gh 162 or (resid 163 through 167 and (name N or name CA or name C or name O or n \ ame CB )) or resid 168 through 219 or (resid 220 through 221 and (name N or name \ CA or name C or name O or name CB )) or resid 222 through 230 or (resid 231 and \ (name N or name CA or name C or name O or name CB )))) } ncs_group { reference = (chain 'H' and ((resid 14 through 77 and (name N or name CA or name C or name O \ or name CB )) or resid 78 or (resid 79 through 93 and (name N or name CA or name \ C or name O or name CB )) or resid 94 through 102 or (resid 103 through 104 and \ (name N or name CA or name C or name O or name CB )) or resid 105 through 112)) \ selection = (chain 'J' and ((resid 14 through 93 and (name N or name CA or name C or name O \ or name CB )) or resid 94 or (resid 95 through 97 and (name N or name CA or name \ C or name O or name CB )) or resid 98 or (resid 99 through 100 and (name N or n \ ame CA or name C or name O or name CB )) or resid 101 through 102 or (resid 103 \ through 104 and (name N or name CA or name C or name O or name CB )) or resid 10 \ 5 through 108 or (resid 109 and (name N or name CA or name C or name O or name C \ B )) or resid 110 or (resid 111 through 112 and (name N or name CA or name C or \ name O or name CB )))) selection = (chain 'L' and ((resid 14 through 93 and (name N or name CA or name C or name O \ or name CB )) or resid 94 or (resid 95 through 97 and (name N or name CA or name \ C or name O or name CB )) or resid 98 or (resid 99 through 100 and (name N or n \ ame CA or name C or name O or name CB )) or resid 101 through 108 or (resid 109 \ and (name N or name CA or name C or name O or name CB )) or resid 110 through 11 \ 2)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.410 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: 14.760 Check model and map are aligned: 0.490 Set scattering table: 0.300 Process input model: 93.160 Find NCS groups from input model: 2.560 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 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 : 0.005 0.053 34274 Z= 0.316 Angle : 0.539 10.487 47130 Z= 0.279 Chirality : 0.042 0.169 5918 Planarity : 0.004 0.056 6176 Dihedral : 11.398 110.640 10462 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.04 % Allowed : 0.36 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.12), residues: 5188 helix: 2.50 (0.10), residues: 2624 sheet: -1.94 (0.21), residues: 550 loop : -0.09 (0.15), residues: 2014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 541 HIS 0.004 0.001 HIS A 213 PHE 0.022 0.001 PHE A 451 TYR 0.019 0.001 TYR C 272 ARG 0.008 0.000 ARG E 344 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10376 Ramachandran restraints generated. 5188 Oldfield, 0 Emsley, 5188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10376 Ramachandran restraints generated. 5188 Oldfield, 0 Emsley, 5188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 4521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 363 time to evaluate : 4.004 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 363 average time/residue: 0.4420 time to fit residues: 266.6233 Evaluate side-chains 304 residues out of total 4521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 304 time to evaluate : 4.278 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.5626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 435 optimal weight: 0.0980 chunk 391 optimal weight: 5.9990 chunk 217 optimal weight: 0.9990 chunk 133 optimal weight: 3.9990 chunk 263 optimal weight: 1.9990 chunk 208 optimal weight: 0.7980 chunk 404 optimal weight: 0.9980 chunk 156 optimal weight: 0.0010 chunk 245 optimal weight: 0.6980 chunk 301 optimal weight: 0.8980 chunk 468 optimal weight: 10.0000 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 ASN ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 GLN ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 366 ASN E 349 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.0738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 34274 Z= 0.179 Angle : 0.478 9.577 47130 Z= 0.248 Chirality : 0.041 0.164 5918 Planarity : 0.004 0.044 6176 Dihedral : 4.130 92.603 5536 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.93 % Allowed : 8.21 % Favored : 90.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.12), residues: 5188 helix: 2.56 (0.10), residues: 2605 sheet: -1.80 (0.21), residues: 559 loop : 0.00 (0.15), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 541 HIS 0.006 0.001 HIS B 273 PHE 0.019 0.001 PHE A 451 TYR 0.014 0.001 TYR E 463 ARG 0.011 0.000 ARG M 42 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10376 Ramachandran restraints generated. 5188 Oldfield, 0 Emsley, 5188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10376 Ramachandran restraints generated. 5188 Oldfield, 0 Emsley, 5188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 4521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 355 time to evaluate : 3.977 Fit side-chains outliers start: 21 outliers final: 10 residues processed: 362 average time/residue: 0.4590 time to fit residues: 274.7624 Evaluate side-chains 329 residues out of total 4521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 319 time to evaluate : 3.839 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.3012 time to fit residues: 10.8320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 260 optimal weight: 0.7980 chunk 145 optimal weight: 0.9980 chunk 389 optimal weight: 3.9990 chunk 319 optimal weight: 1.9990 chunk 129 optimal weight: 0.6980 chunk 469 optimal weight: 40.0000 chunk 507 optimal weight: 30.0000 chunk 418 optimal weight: 6.9990 chunk 465 optimal weight: 20.0000 chunk 160 optimal weight: 5.9990 chunk 376 optimal weight: 40.0000 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 HIS ** B 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 ASN ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 ASN E 349 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.0852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 34274 Z= 0.398 Angle : 0.548 10.176 47130 Z= 0.281 Chirality : 0.044 0.161 5918 Planarity : 0.004 0.048 6176 Dihedral : 4.261 81.132 5536 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.22 % Allowed : 11.63 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.12), residues: 5188 helix: 2.48 (0.10), residues: 2596 sheet: -1.90 (0.21), residues: 558 loop : -0.06 (0.15), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 541 HIS 0.007 0.001 HIS A 213 PHE 0.025 0.001 PHE A 451 TYR 0.015 0.001 TYR E 463 ARG 0.010 0.000 ARG E 344 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10376 Ramachandran restraints generated. 5188 Oldfield, 0 Emsley, 5188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10376 Ramachandran restraints generated. 5188 Oldfield, 0 Emsley, 5188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 4521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 327 time to evaluate : 4.020 Fit side-chains outliers start: 50 outliers final: 33 residues processed: 358 average time/residue: 0.4476 time to fit residues: 264.7951 Evaluate side-chains 344 residues out of total 4521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 311 time to evaluate : 3.580 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.3246 time to fit residues: 25.5770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 463 optimal weight: 8.9990 chunk 352 optimal weight: 2.9990 chunk 243 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 224 optimal weight: 1.9990 chunk 315 optimal weight: 40.0000 chunk 471 optimal weight: 30.0000 chunk 498 optimal weight: 40.0000 chunk 246 optimal weight: 1.9990 chunk 446 optimal weight: 7.9990 chunk 134 optimal weight: 0.6980 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 ASN ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 349 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 34274 Z= 0.441 Angle : 0.560 11.129 47130 Z= 0.287 Chirality : 0.044 0.165 5918 Planarity : 0.004 0.049 6176 Dihedral : 4.335 72.243 5536 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.60 % Allowed : 14.34 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.12), residues: 5188 helix: 2.41 (0.10), residues: 2587 sheet: -1.99 (0.21), residues: 544 loop : -0.15 (0.15), residues: 2057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 541 HIS 0.007 0.001 HIS A 213 PHE 0.022 0.002 PHE C 297 TYR 0.014 0.001 TYR E 534 ARG 0.009 0.000 ARG E 344 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10376 Ramachandran restraints generated. 5188 Oldfield, 0 Emsley, 5188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10376 Ramachandran restraints generated. 5188 Oldfield, 0 Emsley, 5188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 4521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 320 time to evaluate : 4.227 Fit side-chains outliers start: 36 outliers final: 22 residues processed: 341 average time/residue: 0.4893 time to fit residues: 277.4457 Evaluate side-chains 323 residues out of total 4521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 301 time to evaluate : 3.699 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.3028 time to fit residues: 17.8576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 415 optimal weight: 7.9990 chunk 283 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 371 optimal weight: 30.0000 chunk 205 optimal weight: 1.9990 chunk 425 optimal weight: 2.9990 chunk 344 optimal weight: 30.0000 chunk 0 optimal weight: 1.9990 chunk 254 optimal weight: 0.7980 chunk 447 optimal weight: 4.9990 chunk 125 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 ASN C 323 ASN ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 349 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 34274 Z= 0.254 Angle : 0.486 9.803 47130 Z= 0.248 Chirality : 0.041 0.155 5918 Planarity : 0.004 0.047 6176 Dihedral : 4.132 68.650 5536 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.29 % Allowed : 15.63 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.12), residues: 5188 helix: 2.52 (0.10), residues: 2589 sheet: -1.94 (0.21), residues: 538 loop : -0.08 (0.14), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 541 HIS 0.004 0.001 HIS A 213 PHE 0.017 0.001 PHE A 451 TYR 0.011 0.001 TYR O 296 ARG 0.007 0.000 ARG E 344 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10376 Ramachandran restraints generated. 5188 Oldfield, 0 Emsley, 5188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10376 Ramachandran restraints generated. 5188 Oldfield, 0 Emsley, 5188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 4521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 324 time to evaluate : 4.272 Fit side-chains outliers start: 29 outliers final: 14 residues processed: 341 average time/residue: 0.4710 time to fit residues: 263.6537 Evaluate side-chains 319 residues out of total 4521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 305 time to evaluate : 3.889 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.3070 time to fit residues: 13.3191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 167 optimal weight: 0.7980 chunk 449 optimal weight: 30.0000 chunk 98 optimal weight: 3.9990 chunk 292 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 499 optimal weight: 10.0000 chunk 414 optimal weight: 8.9990 chunk 231 optimal weight: 0.0020 chunk 41 optimal weight: 2.9990 chunk 165 optimal weight: 2.9990 chunk 262 optimal weight: 9.9990 overall best weight: 1.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 ASN ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 349 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 34274 Z= 0.404 Angle : 0.541 10.213 47130 Z= 0.276 Chirality : 0.043 0.163 5918 Planarity : 0.004 0.048 6176 Dihedral : 4.225 64.448 5536 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.42 % Allowed : 16.21 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.12), residues: 5188 helix: 2.46 (0.10), residues: 2597 sheet: -2.03 (0.21), residues: 545 loop : -0.12 (0.15), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 541 HIS 0.007 0.001 HIS A 213 PHE 0.017 0.001 PHE A 451 TYR 0.014 0.001 TYR O 296 ARG 0.009 0.000 ARG E 344 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10376 Ramachandran restraints generated. 5188 Oldfield, 0 Emsley, 5188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10376 Ramachandran restraints generated. 5188 Oldfield, 0 Emsley, 5188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 4521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 319 time to evaluate : 3.810 Fit side-chains outliers start: 32 outliers final: 20 residues processed: 333 average time/residue: 0.4715 time to fit residues: 258.6533 Evaluate side-chains 328 residues out of total 4521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 308 time to evaluate : 4.302 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.3265 time to fit residues: 18.1448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 481 optimal weight: 9.9990 chunk 56 optimal weight: 1.9990 chunk 284 optimal weight: 0.9980 chunk 364 optimal weight: 2.9990 chunk 282 optimal weight: 0.5980 chunk 420 optimal weight: 2.9990 chunk 278 optimal weight: 1.9990 chunk 497 optimal weight: 30.0000 chunk 311 optimal weight: 30.0000 chunk 303 optimal weight: 1.9990 chunk 229 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 ASN ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 349 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 34274 Z= 0.357 Angle : 0.526 10.050 47130 Z= 0.268 Chirality : 0.043 0.173 5918 Planarity : 0.004 0.048 6176 Dihedral : 4.203 59.530 5536 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.89 % Allowed : 17.41 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.12), residues: 5188 helix: 2.46 (0.10), residues: 2590 sheet: -2.00 (0.21), residues: 560 loop : -0.14 (0.15), residues: 2038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 541 HIS 0.006 0.001 HIS A 213 PHE 0.017 0.001 PHE A 451 TYR 0.013 0.001 TYR O 296 ARG 0.008 0.000 ARG E 344 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10376 Ramachandran restraints generated. 5188 Oldfield, 0 Emsley, 5188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10376 Ramachandran restraints generated. 5188 Oldfield, 0 Emsley, 5188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 4521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 314 time to evaluate : 4.039 Fit side-chains outliers start: 20 outliers final: 11 residues processed: 325 average time/residue: 0.4733 time to fit residues: 251.7031 Evaluate side-chains 320 residues out of total 4521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 309 time to evaluate : 3.893 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.3136 time to fit residues: 11.8183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 307 optimal weight: 1.9990 chunk 198 optimal weight: 1.9990 chunk 297 optimal weight: 0.0170 chunk 149 optimal weight: 0.4980 chunk 97 optimal weight: 1.9990 chunk 96 optimal weight: 0.2980 chunk 316 optimal weight: 5.9990 chunk 338 optimal weight: 30.0000 chunk 245 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 390 optimal weight: 0.0980 overall best weight: 0.3820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 ASN C 346 GLN ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 ASN E 349 ASN ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 34274 Z= 0.156 Angle : 0.453 7.824 47130 Z= 0.232 Chirality : 0.040 0.153 5918 Planarity : 0.003 0.046 6176 Dihedral : 3.865 48.970 5536 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.53 % Allowed : 17.90 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.12), residues: 5188 helix: 2.64 (0.10), residues: 2578 sheet: -1.89 (0.21), residues: 562 loop : 0.07 (0.15), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 567 HIS 0.005 0.001 HIS B 396 PHE 0.012 0.001 PHE M 156 TYR 0.011 0.001 TYR O 296 ARG 0.004 0.000 ARG K 144 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10376 Ramachandran restraints generated. 5188 Oldfield, 0 Emsley, 5188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10376 Ramachandran restraints generated. 5188 Oldfield, 0 Emsley, 5188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 4521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 340 time to evaluate : 3.960 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 345 average time/residue: 0.4756 time to fit residues: 269.9434 Evaluate side-chains 319 residues out of total 4521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 311 time to evaluate : 3.844 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.3594 time to fit residues: 10.6783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 452 optimal weight: 6.9990 chunk 476 optimal weight: 4.9990 chunk 434 optimal weight: 3.9990 chunk 463 optimal weight: 7.9990 chunk 278 optimal weight: 2.9990 chunk 201 optimal weight: 2.9990 chunk 363 optimal weight: 2.9990 chunk 142 optimal weight: 4.9990 chunk 418 optimal weight: 9.9990 chunk 438 optimal weight: 7.9990 chunk 461 optimal weight: 50.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 GLN ** B 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 ASN ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 ASN E 349 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.126 34274 Z= 0.772 Angle : 0.738 17.358 47130 Z= 0.377 Chirality : 0.050 0.205 5918 Planarity : 0.005 0.066 6176 Dihedral : 4.640 46.220 5536 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.93 % Allowed : 18.03 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.12), residues: 5188 helix: 2.20 (0.11), residues: 2587 sheet: -2.19 (0.21), residues: 545 loop : -0.35 (0.14), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 541 HIS 0.010 0.002 HIS A 213 PHE 0.027 0.003 PHE F 439 TYR 0.021 0.002 TYR E 158 ARG 0.009 0.001 ARG B 475 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10376 Ramachandran restraints generated. 5188 Oldfield, 0 Emsley, 5188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10376 Ramachandran restraints generated. 5188 Oldfield, 0 Emsley, 5188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 4521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 302 time to evaluate : 4.803 Fit side-chains outliers start: 21 outliers final: 14 residues processed: 316 average time/residue: 0.4994 time to fit residues: 261.2664 Evaluate side-chains 304 residues out of total 4521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 290 time to evaluate : 4.032 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.3152 time to fit residues: 13.6617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 304 optimal weight: 0.6980 chunk 490 optimal weight: 30.0000 chunk 299 optimal weight: 0.5980 chunk 232 optimal weight: 0.6980 chunk 340 optimal weight: 1.9990 chunk 514 optimal weight: 1.9990 chunk 473 optimal weight: 20.0000 chunk 409 optimal weight: 0.8980 chunk 42 optimal weight: 0.4980 chunk 316 optimal weight: 6.9990 chunk 251 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 ASN E 349 ASN M 207 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 34274 Z= 0.219 Angle : 0.500 11.898 47130 Z= 0.254 Chirality : 0.041 0.164 5918 Planarity : 0.004 0.049 6176 Dihedral : 4.149 38.725 5536 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.22 % Allowed : 17.94 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.12), residues: 5188 helix: 2.46 (0.11), residues: 2572 sheet: -2.01 (0.21), residues: 560 loop : -0.08 (0.15), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 360 HIS 0.004 0.001 HIS A 213 PHE 0.017 0.001 PHE A 451 TYR 0.014 0.001 TYR E 463 ARG 0.005 0.000 ARG M 197 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10376 Ramachandran restraints generated. 5188 Oldfield, 0 Emsley, 5188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10376 Ramachandran restraints generated. 5188 Oldfield, 0 Emsley, 5188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 4521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 321 time to evaluate : 3.936 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 322 average time/residue: 0.4789 time to fit residues: 254.1036 Evaluate side-chains 315 residues out of total 4521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 312 time to evaluate : 3.993 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3295 time to fit residues: 6.9412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 325 optimal weight: 4.9990 chunk 436 optimal weight: 9.9990 chunk 125 optimal weight: 0.1980 chunk 377 optimal weight: 30.0000 chunk 60 optimal weight: 0.9980 chunk 113 optimal weight: 0.7980 chunk 410 optimal weight: 3.9990 chunk 171 optimal weight: 2.9990 chunk 421 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 349 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.133272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.098479 restraints weight = 50184.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.098335 restraints weight = 23650.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.099850 restraints weight = 18685.846| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 34274 Z= 0.218 Angle : 0.480 11.923 47130 Z= 0.243 Chirality : 0.041 0.149 5918 Planarity : 0.003 0.046 6176 Dihedral : 3.905 39.055 5536 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.31 % Allowed : 18.96 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.12), residues: 5188 helix: 2.56 (0.11), residues: 2578 sheet: -1.98 (0.20), residues: 580 loop : 0.02 (0.15), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 360 HIS 0.004 0.001 HIS B 396 PHE 0.016 0.001 PHE A 451 TYR 0.015 0.001 TYR E 463 ARG 0.005 0.000 ARG M 197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6216.88 seconds wall clock time: 113 minutes 34.43 seconds (6814.43 seconds total)