Starting phenix.real_space_refine on Sun Mar 24 23:44:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qum_4640/03_2024/6qum_4640_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qum_4640/03_2024/6qum_4640.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qum_4640/03_2024/6qum_4640.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qum_4640/03_2024/6qum_4640.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qum_4640/03_2024/6qum_4640_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qum_4640/03_2024/6qum_4640_neut_updated.pdb" } resolution = 3.25 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= 0.004 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4 5.49 5 Mg 1 5.21 5 S 128 5.16 5 C 28654 2.51 5 N 7834 2.21 5 O 8279 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 41": "NH1" <-> "NH2" Residue "A ARG 93": "NH1" <-> "NH2" Residue "A ARG 113": "NH1" <-> "NH2" Residue "A ARG 284": "NH1" <-> "NH2" Residue "A ARG 329": "NH1" <-> "NH2" Residue "A TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A TYR 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 488": "NH1" <-> "NH2" Residue "A ARG 532": "NH1" <-> "NH2" Residue "A ARG 547": "NH1" <-> "NH2" Residue "A ARG 550": "NH1" <-> "NH2" Residue "B ARG 41": "NH1" <-> "NH2" Residue "B ARG 93": "NH1" <-> "NH2" Residue "B ARG 95": "NH1" <-> "NH2" Residue "B ARG 130": "NH1" <-> "NH2" Residue "B ARG 284": "NH1" <-> "NH2" Residue "B ARG 314": "NH1" <-> "NH2" Residue "B ARG 329": "NH1" <-> "NH2" Residue "B TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B TYR 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 532": "NH1" <-> "NH2" Residue "B ARG 547": "NH1" <-> "NH2" Residue "C ARG 41": "NH1" <-> "NH2" Residue "C ARG 93": "NH1" <-> "NH2" Residue "C ARG 156": "NH1" <-> "NH2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C ARG 335": "NH1" <-> "NH2" Residue "C TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 408": "NH1" <-> "NH2" Residue "C TYR 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 460": "NH1" <-> "NH2" Residue "C ARG 481": "NH1" <-> "NH2" Residue "C ARG 488": "NH1" <-> "NH2" Residue "C ARG 491": "NH1" <-> "NH2" Residue "C ARG 550": "NH1" <-> "NH2" Residue "D ARG 41": "NH1" <-> "NH2" Residue "D ARG 43": "NH1" <-> "NH2" Residue "D ARG 91": "NH1" <-> "NH2" Residue "D ARG 125": "NH1" <-> "NH2" Residue "D ARG 146": "NH1" <-> "NH2" Residue "D ARG 174": "NH1" <-> "NH2" Residue "D ARG 199": "NH1" <-> "NH2" Residue "D ARG 231": "NH1" <-> "NH2" Residue "D ARG 236": "NH1" <-> "NH2" Residue "D ARG 274": "NH1" <-> "NH2" Residue "D ARG 321": "NH1" <-> "NH2" Residue "D ARG 453": "NH1" <-> "NH2" Residue "E ARG 43": "NH1" <-> "NH2" Residue "E TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 146": "NH1" <-> "NH2" Residue "E ARG 169": "NH1" <-> "NH2" Residue "E ARG 174": "NH1" <-> "NH2" Residue "E ARG 280": "NH1" <-> "NH2" Residue "E ARG 281": "NH1" <-> "NH2" Residue "E TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 360": "NH1" <-> "NH2" Residue "E ARG 372": "NH1" <-> "NH2" Residue "E ARG 393": "NH1" <-> "NH2" Residue "E ARG 409": "NH1" <-> "NH2" Residue "E ARG 410": "NH1" <-> "NH2" Residue "E ARG 420": "NH1" <-> "NH2" Residue "F ARG 41": "NH1" <-> "NH2" Residue "F ARG 81": "NH1" <-> "NH2" Residue "F ARG 91": "NH1" <-> "NH2" Residue "F ARG 92": "NH1" <-> "NH2" Residue "F ARG 169": "NH1" <-> "NH2" Residue "F ARG 174": "NH1" <-> "NH2" Residue "F ARG 236": "NH1" <-> "NH2" Residue "F ARG 280": "NH1" <-> "NH2" Residue "F ARG 297": "NH1" <-> "NH2" Residue "F ARG 372": "NH1" <-> "NH2" Residue "F ARG 409": "NH1" <-> "NH2" Residue "F ARG 410": "NH1" <-> "NH2" Residue "G ARG 8": "NH1" <-> "NH2" Residue "G ARG 103": "NH1" <-> "NH2" Residue "G ARG 132": "NH1" <-> "NH2" Residue "G ARG 139": "NH1" <-> "NH2" Residue "G ARG 146": "NH1" <-> "NH2" Residue "G ARG 160": "NH1" <-> "NH2" Residue "G ARG 173": "NH1" <-> "NH2" Residue "G ARG 188": "NH1" <-> "NH2" Residue "G ARG 196": "NH1" <-> "NH2" Residue "G ARG 204": "NH1" <-> "NH2" Residue "H ARG 14": "NH1" <-> "NH2" Residue "H ARG 61": "NH1" <-> "NH2" Residue "H ARG 64": "NH1" <-> "NH2" Residue "H ARG 66": "NH1" <-> "NH2" Residue "H ARG 91": "NH1" <-> "NH2" Residue "I ARG 87": "NH1" <-> "NH2" Residue "I ARG 91": "NH1" <-> "NH2" Residue "J ARG 105": "NH1" <-> "NH2" Residue "J ARG 136": "NH1" <-> "NH2" Residue "J ARG 173": "NH1" <-> "NH2" Residue "K ARG 78": "NH1" <-> "NH2" Residue "K ARG 89": "NH1" <-> "NH2" Residue "L ARG 45": "NH1" <-> "NH2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L ARG 58": "NH1" <-> "NH2" Residue "L ARG 59": "NH1" <-> "NH2" Residue "L ARG 72": "NH1" <-> "NH2" Residue "L ARG 76": "NH1" <-> "NH2" Residue "L ARG 84": "NH1" <-> "NH2" Residue "L ARG 86": "NH1" <-> "NH2" Residue "L ARG 136": "NH1" <-> "NH2" Residue "M ARG 11": "NH1" <-> "NH2" Residue "M ARG 16": "NH1" <-> "NH2" Residue "M ARG 156": "NH1" <-> "NH2" Residue "M ARG 171": "NH1" <-> "NH2" Residue "M ARG 189": "NH1" <-> "NH2" Residue "M ARG 202": "NH1" <-> "NH2" Residue "M ARG 227": "NH1" <-> "NH2" Residue "M ARG 301": "NH1" <-> "NH2" Residue "N ARG 50": "NH1" <-> "NH2" Residue "N ARG 124": "NH1" <-> "NH2" Residue "N ARG 229": "NH1" <-> "NH2" Residue "N ARG 273": "NH1" <-> "NH2" Residue "N ARG 296": "NH1" <-> "NH2" Residue "N ARG 385": "NH1" <-> "NH2" Residue "N ARG 482": "NH1" <-> "NH2" Residue "N ARG 588": "NH1" <-> "NH2" Residue "N ARG 622": "NH1" <-> "NH2" Residue "N ARG 640": "NH1" <-> "NH2" Residue "N ARG 643": "NH1" <-> "NH2" Residue "P ARG 36": "NH1" <-> "NH2" Residue "P ARG 79": "NH1" <-> "NH2" Residue "Q ARG 79": "NH1" <-> "NH2" Residue "S ARG 79": "NH1" <-> "NH2" Residue "T ARG 79": "NH1" <-> "NH2" Residue "U ARG 49": "NH1" <-> "NH2" Residue "U ARG 79": "NH1" <-> "NH2" Residue "V ARG 36": "NH1" <-> "NH2" Residue "V ARG 49": "NH1" <-> "NH2" Residue "V ARG 79": "NH1" <-> "NH2" Residue "W ARG 12": "NH1" <-> "NH2" Residue "W ARG 36": "NH1" <-> "NH2" Residue "W ARG 49": "NH1" <-> "NH2" Residue "X ARG 79": "NH1" <-> "NH2" Residue "Y ARG 79": "NH1" <-> "NH2" Residue "Z ARG 79": "NH1" <-> "NH2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 44900 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 4477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4477 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "B" Number of atoms: 4477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4477 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "C" Number of atoms: 4477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4477 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "D" Number of atoms: 3682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3682 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 442} Chain: "E" Number of atoms: 3682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3682 Classifications: {'peptide': 469} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 442} Chain: "F" Number of atoms: 3686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3686 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 443} Chain: "G" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1628 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 9, 'TRANS': 197} Chain: "H" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 792 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "I" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 808 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 1, 'TRANS': 101} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "J" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1437 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 7, 'TRANS': 178} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "K" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 788 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 1, 'TRANS': 97} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "L" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1441 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 7, 'TRANS': 179} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "M" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2514 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 12, 'TRANS': 307} Chain: "N" Number of atoms: 4858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 649, 4858 Classifications: {'peptide': 649} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 36, 'TRANS': 612} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 309 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 3, 'TYR:plan': 2, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 120 Chain: "O" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 508 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "P" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 508 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "Q" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "R" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 508 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "S" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 508 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "T" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 508 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "U" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 508 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "V" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 508 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "W" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 508 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "X" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 504 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "Y" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 508 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "Z" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 508 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "A" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 55 Unusual residues: {' MG': 1, 'ADP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 23.24, per 1000 atoms: 0.52 Number of scatterers: 44900 At special positions: 0 Unit cell: (149.73, 151.9, 254.975, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 128 16.00 P 4 15.00 Mg 1 11.99 O 8279 8.00 N 7834 7.00 C 28654 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS M 267 " - pdb=" SG CYS M 322 " distance=2.02 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: 16.83 Conformation dependent library (CDL) restraints added in 9.2 seconds 11644 Ramachandran restraints generated. 5822 Oldfield, 0 Emsley, 5822 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10590 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 185 helices and 36 sheets defined 51.5% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.11 Creating SS restraints... Processing helix chain 'A' and resid 91 through 97 Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'A' and resid 234 through 244 Processing helix chain 'A' and resid 260 through 268 removed outlier: 4.322A pdb=" N VAL A 265 " --> pdb=" O GLU A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 284 Processing helix chain 'A' and resid 296 through 316 removed outlier: 4.322A pdb=" N GLU A 300 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL A 305 " --> pdb=" O SER A 302 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLY A 306 " --> pdb=" O ILE A 303 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN A 316 " --> pdb=" O PHE A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 340 removed outlier: 3.817A pdb=" N ARG A 340 " --> pdb=" O GLU A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 349 No H-bonds generated for 'chain 'A' and resid 347 through 349' Processing helix chain 'A' and resid 354 through 364 removed outlier: 4.154A pdb=" N ARG A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 402 removed outlier: 4.762A pdb=" N ARG A 401 " --> pdb=" O GLN A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 415 No H-bonds generated for 'chain 'A' and resid 412 through 415' Processing helix chain 'A' and resid 436 through 442 Processing helix chain 'A' and resid 447 through 470 removed outlier: 4.665A pdb=" N GLU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ILE A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 493 Processing helix chain 'A' and resid 509 through 532 removed outlier: 3.604A pdb=" N ARG A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 552 removed outlier: 3.520A pdb=" N ARG A 550 " --> pdb=" O ARG A 547 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ARG A 552 " --> pdb=" O GLY A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 576 removed outlier: 4.255A pdb=" N GLU A 565 " --> pdb=" O ALA A 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 98 Processing helix chain 'B' and resid 234 through 243 Processing helix chain 'B' and resid 259 through 262 No H-bonds generated for 'chain 'B' and resid 259 through 262' Processing helix chain 'B' and resid 269 through 271 No H-bonds generated for 'chain 'B' and resid 269 through 271' Processing helix chain 'B' and resid 281 through 284 Processing helix chain 'B' and resid 296 through 315 removed outlier: 5.854A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N TYR B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 340 Processing helix chain 'B' and resid 354 through 362 Processing helix chain 'B' and resid 394 through 402 Processing helix chain 'B' and resid 411 through 415 Processing helix chain 'B' and resid 430 through 432 No H-bonds generated for 'chain 'B' and resid 430 through 432' Processing helix chain 'B' and resid 436 through 442 Processing helix chain 'B' and resid 447 through 463 removed outlier: 3.737A pdb=" N ALA B 462 " --> pdb=" O LEU B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 470 Processing helix chain 'B' and resid 473 through 475 No H-bonds generated for 'chain 'B' and resid 473 through 475' Processing helix chain 'B' and resid 479 through 493 Processing helix chain 'B' and resid 509 through 532 removed outlier: 4.496A pdb=" N ALA B 528 " --> pdb=" O LYS B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 540 Processing helix chain 'B' and resid 543 through 551 removed outlier: 3.547A pdb=" N GLU B 546 " --> pdb=" O PRO B 543 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG B 550 " --> pdb=" O ARG B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 561 No H-bonds generated for 'chain 'B' and resid 559 through 561' Processing helix chain 'B' and resid 563 through 575 removed outlier: 3.511A pdb=" N GLN B 571 " --> pdb=" O MET B 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'C' and resid 236 through 243 Processing helix chain 'C' and resid 259 through 268 Processing helix chain 'C' and resid 281 through 284 removed outlier: 3.558A pdb=" N ARG C 284 " --> pdb=" O LEU C 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 281 through 284' Processing helix chain 'C' and resid 298 through 316 removed outlier: 3.896A pdb=" N ILE C 303 " --> pdb=" O ARG C 299 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR C 304 " --> pdb=" O GLU C 300 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN C 316 " --> pdb=" O TYR C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 340 Processing helix chain 'C' and resid 354 through 364 removed outlier: 4.288A pdb=" N ARG C 364 " --> pdb=" O ALA C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 399 Processing helix chain 'C' and resid 436 through 442 Processing helix chain 'C' and resid 447 through 471 removed outlier: 4.335A pdb=" N GLU C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ILE C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 493 removed outlier: 3.673A pdb=" N ILE C 484 " --> pdb=" O GLU C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 527 Processing helix chain 'C' and resid 536 through 539 No H-bonds generated for 'chain 'C' and resid 536 through 539' Processing helix chain 'C' and resid 544 through 549 Processing helix chain 'C' and resid 551 through 553 No H-bonds generated for 'chain 'C' and resid 551 through 553' Processing helix chain 'C' and resid 559 through 572 removed outlier: 3.751A pdb=" N GLU C 565 " --> pdb=" O ALA C 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 123 No H-bonds generated for 'chain 'D' and resid 121 through 123' Processing helix chain 'D' and resid 136 through 139 No H-bonds generated for 'chain 'D' and resid 136 through 139' Processing helix chain 'D' and resid 160 through 168 Processing helix chain 'D' and resid 175 through 177 No H-bonds generated for 'chain 'D' and resid 175 through 177' Processing helix chain 'D' and resid 198 through 210 Processing helix chain 'D' and resid 228 through 248 Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 260 through 273 Processing helix chain 'D' and resid 285 through 295 removed outlier: 4.620A pdb=" N TYR D 288 " --> pdb=" O GLY D 285 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR D 289 " --> pdb=" O TYR D 286 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP D 290 " --> pdb=" O MET D 287 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N THR D 293 " --> pdb=" O ASP D 290 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR D 295 " --> pdb=" O ALA D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 332 Processing helix chain 'D' and resid 341 through 346 Processing helix chain 'D' and resid 375 through 397 removed outlier: 4.247A pdb=" N ASP D 391 " --> pdb=" O ALA D 387 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE D 392 " --> pdb=" O ASN D 388 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ALA D 397 " --> pdb=" O ARG D 393 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 421 removed outlier: 3.791A pdb=" N ARG D 420 " --> pdb=" O ASP D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 443 Processing helix chain 'D' and resid 456 through 462 Processing helix chain 'D' and resid 467 through 470 No H-bonds generated for 'chain 'D' and resid 467 through 470' Processing helix chain 'E' and resid 86 through 88 No H-bonds generated for 'chain 'E' and resid 86 through 88' Processing helix chain 'E' and resid 136 through 140 Processing helix chain 'E' and resid 161 through 167 Processing helix chain 'E' and resid 175 through 177 No H-bonds generated for 'chain 'E' and resid 175 through 177' Processing helix chain 'E' and resid 198 through 210 Processing helix chain 'E' and resid 213 through 216 removed outlier: 3.737A pdb=" N ARG E 216 " --> pdb=" O ALA E 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 213 through 216' Processing helix chain 'E' and resid 228 through 248 Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 260 through 271 Processing helix chain 'E' and resid 287 through 295 removed outlier: 3.836A pdb=" N ILE E 294 " --> pdb=" O ASP E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 330 Processing helix chain 'E' and resid 341 through 346 removed outlier: 4.019A pdb=" N LYS E 346 " --> pdb=" O GLU E 342 " (cutoff:3.500A) Processing helix chain 'E' and resid 375 through 396 Processing helix chain 'E' and resid 406 through 421 Processing helix chain 'E' and resid 432 through 445 removed outlier: 4.063A pdb=" N MET E 445 " --> pdb=" O ALA E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 461 Processing helix chain 'E' and resid 467 through 470 No H-bonds generated for 'chain 'E' and resid 467 through 470' Processing helix chain 'F' and resid 136 through 140 Processing helix chain 'F' and resid 160 through 170 Processing helix chain 'F' and resid 175 through 178 No H-bonds generated for 'chain 'F' and resid 175 through 178' Processing helix chain 'F' and resid 199 through 211 Processing helix chain 'F' and resid 231 through 247 Proline residue: F 235 - end of helix removed outlier: 3.625A pdb=" N VAL F 241 " --> pdb=" O MET F 237 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 272 Processing helix chain 'F' and resid 287 through 295 Processing helix chain 'F' and resid 324 through 332 Processing helix chain 'F' and resid 341 through 344 No H-bonds generated for 'chain 'F' and resid 341 through 344' Processing helix chain 'F' and resid 360 through 364 removed outlier: 4.660A pdb=" N ASN F 363 " --> pdb=" O ARG F 360 " (cutoff:3.500A) Processing helix chain 'F' and resid 375 through 399 removed outlier: 3.902A pdb=" N LYS F 394 " --> pdb=" O VAL F 390 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU F 395 " --> pdb=" O ASP F 391 " (cutoff:3.500A) Processing helix chain 'F' and resid 408 through 421 removed outlier: 3.756A pdb=" N ASP F 416 " --> pdb=" O LEU F 412 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 445 removed outlier: 4.123A pdb=" N MET F 445 " --> pdb=" O ALA F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 456 through 461 Processing helix chain 'G' and resid 8 through 70 removed outlier: 3.909A pdb=" N ASP G 26 " --> pdb=" O GLN G 22 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA G 37 " --> pdb=" O ASP G 33 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG G 44 " --> pdb=" O PHE G 40 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU G 45 " --> pdb=" O GLY G 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 82 Processing helix chain 'G' and resid 96 through 98 No H-bonds generated for 'chain 'G' and resid 96 through 98' Processing helix chain 'G' and resid 123 through 168 removed outlier: 4.185A pdb=" N ARG G 146 " --> pdb=" O ASN G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 170 through 208 removed outlier: 3.628A pdb=" N LYS G 195 " --> pdb=" O THR G 191 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG G 204 " --> pdb=" O LYS G 200 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLU G 205 " --> pdb=" O ILE G 201 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA G 206 " --> pdb=" O GLU G 202 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 15 Processing helix chain 'H' and resid 26 through 38 Processing helix chain 'H' and resid 56 through 61 Processing helix chain 'H' and resid 77 through 79 No H-bonds generated for 'chain 'H' and resid 77 through 79' Processing helix chain 'H' and resid 86 through 98 Processing helix chain 'I' and resid 19 through 103 removed outlier: 3.770A pdb=" N GLU I 45 " --> pdb=" O LYS I 41 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS I 102 " --> pdb=" O ALA I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 118 Processing helix chain 'J' and resid 3 through 94 removed outlier: 3.968A pdb=" N GLU J 33 " --> pdb=" O ALA J 29 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA J 34 " --> pdb=" O VAL J 30 " (cutoff:3.500A) Processing helix chain 'J' and resid 100 through 114 removed outlier: 3.896A pdb=" N ARG J 105 " --> pdb=" O PRO J 101 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N LYS J 106 " --> pdb=" O GLU J 102 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU J 107 " --> pdb=" O VAL J 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 128 through 134 removed outlier: 4.312A pdb=" N ALA J 133 " --> pdb=" O PRO J 129 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU J 134 " --> pdb=" O HIS J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 157 through 159 No H-bonds generated for 'chain 'J' and resid 157 through 159' Processing helix chain 'J' and resid 167 through 186 removed outlier: 5.176A pdb=" N ASP J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ALA J 177 " --> pdb=" O ARG J 173 " (cutoff:3.500A) Processing helix chain 'K' and resid 23 through 106 removed outlier: 3.894A pdb=" N ARG K 87 " --> pdb=" O ALA K 83 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA K 105 " --> pdb=" O GLU K 101 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG K 106 " --> pdb=" O LYS K 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 118 removed outlier: 3.635A pdb=" N LEU K 113 " --> pdb=" O GLU K 109 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 92 removed outlier: 5.502A pdb=" N GLN L 43 " --> pdb=" O LYS L 39 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU L 46 " --> pdb=" O LEU L 42 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU L 78 " --> pdb=" O GLN L 74 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL L 79 " --> pdb=" O ALA L 75 " (cutoff:3.500A) Processing helix chain 'L' and resid 100 through 114 Processing helix chain 'L' and resid 129 through 135 removed outlier: 5.471A pdb=" N ALA L 133 " --> pdb=" O HIS L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 187 removed outlier: 5.278A pdb=" N ASP L 176 " --> pdb=" O ASP L 172 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N ALA L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLN L 184 " --> pdb=" O SER L 180 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 17 removed outlier: 3.646A pdb=" N ARG M 11 " --> pdb=" O TYR M 7 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 27 Processing helix chain 'M' and resid 34 through 40 Processing helix chain 'M' and resid 44 through 47 removed outlier: 3.628A pdb=" N GLY M 47 " --> pdb=" O VAL M 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 44 through 47' Processing helix chain 'M' and resid 54 through 68 Processing helix chain 'M' and resid 79 through 84 Processing helix chain 'M' and resid 90 through 105 Processing helix chain 'M' and resid 121 through 128 removed outlier: 3.947A pdb=" N TYR M 128 " --> pdb=" O TRP M 124 " (cutoff:3.500A) Processing helix chain 'M' and resid 133 through 139 Processing helix chain 'M' and resid 146 through 150 Processing helix chain 'M' and resid 163 through 181 Processing helix chain 'M' and resid 189 through 206 Processing helix chain 'M' and resid 227 through 234 Processing helix chain 'M' and resid 239 through 243 Processing helix chain 'M' and resid 258 through 278 removed outlier: 3.572A pdb=" N LYS M 275 " --> pdb=" O LYS M 271 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N GLY M 276 " --> pdb=" O GLU M 272 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N VAL M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N GLN M 278 " --> pdb=" O LYS M 274 " (cutoff:3.500A) Processing helix chain 'M' and resid 284 through 309 removed outlier: 3.827A pdb=" N GLU M 292 " --> pdb=" O ALA M 288 " (cutoff:3.500A) Processing helix chain 'M' and resid 313 through 315 No H-bonds generated for 'chain 'M' and resid 313 through 315' Processing helix chain 'M' and resid 317 through 319 No H-bonds generated for 'chain 'M' and resid 317 through 319' Processing helix chain 'N' and resid 14 through 26 Processing helix chain 'N' and resid 47 through 70 Processing helix chain 'N' and resid 84 through 118 Proline residue: N 93 - end of helix removed outlier: 3.811A pdb=" N GLN N 106 " --> pdb=" O THR N 102 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA N 117 " --> pdb=" O ALA N 113 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N TYR N 118 " --> pdb=" O LEU N 114 " (cutoff:3.500A) Processing helix chain 'N' and resid 120 through 128 Processing helix chain 'N' and resid 150 through 159 removed outlier: 5.167A pdb=" N ALA N 156 " --> pdb=" O LEU N 152 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LEU N 157 " --> pdb=" O VAL N 153 " (cutoff:3.500A) Processing helix chain 'N' and resid 185 through 196 Processing helix chain 'N' and resid 208 through 210 No H-bonds generated for 'chain 'N' and resid 208 through 210' Processing helix chain 'N' and resid 213 through 243 Proline residue: N 228 - end of helix Processing helix chain 'N' and resid 246 through 266 Processing helix chain 'N' and resid 284 through 294 removed outlier: 3.561A pdb=" N LYS N 287 " --> pdb=" O VAL N 284 " (cutoff:3.500A) Proline residue: N 288 - end of helix removed outlier: 3.572A pdb=" N LEU N 294 " --> pdb=" O GLU N 291 " (cutoff:3.500A) Processing helix chain 'N' and resid 328 through 335 removed outlier: 4.803A pdb=" N LEU N 332 " --> pdb=" O PRO N 329 " (cutoff:3.500A) Processing helix chain 'N' and resid 347 through 362 removed outlier: 3.760A pdb=" N VAL N 350 " --> pdb=" O PRO N 347 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL N 351 " --> pdb=" O THR N 348 " (cutoff:3.500A) Proline residue: N 352 - end of helix removed outlier: 4.638A pdb=" N PHE N 355 " --> pdb=" O PRO N 352 " (cutoff:3.500A) Proline residue: N 356 - end of helix removed outlier: 3.741A pdb=" N GLY N 360 " --> pdb=" O PHE N 357 " (cutoff:3.500A) Processing helix chain 'N' and resid 366 through 385 Processing helix chain 'N' and resid 400 through 424 removed outlier: 4.547A pdb=" N TRP N 416 " --> pdb=" O TRP N 412 " (cutoff:3.500A) Processing helix chain 'N' and resid 460 through 488 removed outlier: 3.726A pdb=" N GLY N 471 " --> pdb=" O SER N 467 " (cutoff:3.500A) Processing helix chain 'N' and resid 492 through 515 Processing helix chain 'N' and resid 524 through 540 Processing helix chain 'N' and resid 548 through 587 removed outlier: 4.450A pdb=" N PHE N 552 " --> pdb=" O ILE N 548 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N THR N 553 " --> pdb=" O PRO N 549 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N HIS N 561 " --> pdb=" O HIS N 557 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE N 562 " --> pdb=" O ILE N 558 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ARG N 563 " --> pdb=" O LEU N 559 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ILE N 564 " --> pdb=" O SER N 560 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N TYR N 565 " --> pdb=" O HIS N 561 " (cutoff:3.500A) Processing helix chain 'N' and resid 594 through 631 removed outlier: 5.402A pdb=" N LEU N 614 " --> pdb=" O LEU N 610 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N GLY N 615 " --> pdb=" O LEU N 611 " (cutoff:3.500A) Proline residue: N 620 - end of helix removed outlier: 4.566A pdb=" N PHE N 629 " --> pdb=" O TRP N 625 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N THR N 630 " --> pdb=" O VAL N 626 " (cutoff:3.500A) Processing helix chain 'O' and resid 10 through 47 removed outlier: 3.520A pdb=" N LEU O 14 " --> pdb=" O LEU O 10 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ARG O 36 " --> pdb=" O VAL O 32 " (cutoff:3.500A) Processing helix chain 'O' and resid 52 through 79 Proline residue: O 62 - end of helix removed outlier: 5.351A pdb=" N LEU O 65 " --> pdb=" O LEU O 61 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N VAL O 66 " --> pdb=" O PRO O 62 " (cutoff:3.500A) Processing helix chain 'P' and resid 11 through 47 removed outlier: 3.998A pdb=" N ARG P 36 " --> pdb=" O VAL P 32 " (cutoff:3.500A) Processing helix chain 'P' and resid 52 through 78 Proline residue: P 62 - end of helix removed outlier: 5.188A pdb=" N LEU P 65 " --> pdb=" O LEU P 61 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N VAL P 66 " --> pdb=" O PRO P 62 " (cutoff:3.500A) Processing helix chain 'Q' and resid 11 through 47 removed outlier: 3.905A pdb=" N ALA Q 16 " --> pdb=" O ARG Q 12 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ARG Q 36 " --> pdb=" O VAL Q 32 " (cutoff:3.500A) Processing helix chain 'Q' and resid 52 through 78 Proline residue: Q 62 - end of helix removed outlier: 5.595A pdb=" N LEU Q 65 " --> pdb=" O LEU Q 61 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N VAL Q 66 " --> pdb=" O PRO Q 62 " (cutoff:3.500A) Processing helix chain 'R' and resid 11 through 47 removed outlier: 4.021A pdb=" N ARG R 36 " --> pdb=" O VAL R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 79 removed outlier: 3.942A pdb=" N PHE R 52 " --> pdb=" O ARG R 49 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N GLY R 53 " --> pdb=" O SER R 50 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ALA R 55 " --> pdb=" O PHE R 52 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N LEU R 56 " --> pdb=" O GLY R 53 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE R 58 " --> pdb=" O ALA R 55 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU R 60 " --> pdb=" O ILE R 57 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU R 61 " --> pdb=" O PHE R 58 " (cutoff:3.500A) Proline residue: R 62 - end of helix removed outlier: 3.619A pdb=" N LEU R 65 " --> pdb=" O PRO R 62 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU R 70 " --> pdb=" O ILE R 67 " (cutoff:3.500A) Processing helix chain 'S' and resid 12 through 47 removed outlier: 4.061A pdb=" N ARG S 36 " --> pdb=" O VAL S 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 49 through 79 removed outlier: 3.556A pdb=" N PHE S 52 " --> pdb=" O ARG S 49 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N GLY S 53 " --> pdb=" O SER S 50 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N THR S 54 " --> pdb=" O ASN S 51 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE S 58 " --> pdb=" O ALA S 55 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU S 60 " --> pdb=" O ILE S 57 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU S 61 " --> pdb=" O PHE S 58 " (cutoff:3.500A) Proline residue: S 62 - end of helix removed outlier: 3.768A pdb=" N LEU S 65 " --> pdb=" O PRO S 62 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG S 79 " --> pdb=" O LEU S 76 " (cutoff:3.500A) Processing helix chain 'T' and resid 11 through 47 removed outlier: 4.068A pdb=" N ILE T 15 " --> pdb=" O ASP T 11 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ALA T 16 " --> pdb=" O ARG T 12 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL T 17 " --> pdb=" O GLY T 13 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU T 25 " --> pdb=" O LEU T 21 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ARG T 36 " --> pdb=" O VAL T 32 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ILE T 37 " --> pdb=" O ALA T 33 " (cutoff:3.500A) Processing helix chain 'T' and resid 52 through 79 Proline residue: T 62 - end of helix removed outlier: 5.379A pdb=" N LEU T 65 " --> pdb=" O LEU T 61 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N VAL T 66 " --> pdb=" O PRO T 62 " (cutoff:3.500A) Processing helix chain 'U' and resid 11 through 47 removed outlier: 3.990A pdb=" N ARG U 36 " --> pdb=" O VAL U 32 " (cutoff:3.500A) Processing helix chain 'U' and resid 52 through 79 Proline residue: U 62 - end of helix removed outlier: 5.103A pdb=" N LEU U 65 " --> pdb=" O LEU U 61 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL U 66 " --> pdb=" O PRO U 62 " (cutoff:3.500A) Processing helix chain 'V' and resid 11 through 47 removed outlier: 4.263A pdb=" N ARG V 36 " --> pdb=" O VAL V 32 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE V 37 " --> pdb=" O ALA V 33 " (cutoff:3.500A) Processing helix chain 'V' and resid 52 through 60 Processing helix chain 'V' and resid 62 through 78 removed outlier: 3.529A pdb=" N LEU V 70 " --> pdb=" O ILE V 67 " (cutoff:3.500A) Processing helix chain 'W' and resid 12 through 47 removed outlier: 4.071A pdb=" N ARG W 36 " --> pdb=" O VAL W 32 " (cutoff:3.500A) Processing helix chain 'W' and resid 52 through 79 Proline residue: W 62 - end of helix removed outlier: 5.311A pdb=" N LEU W 65 " --> pdb=" O LEU W 61 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N VAL W 66 " --> pdb=" O PRO W 62 " (cutoff:3.500A) Processing helix chain 'X' and resid 14 through 47 removed outlier: 3.910A pdb=" N ARG X 36 " --> pdb=" O VAL X 32 " (cutoff:3.500A) Processing helix chain 'X' and resid 49 through 79 removed outlier: 5.554A pdb=" N GLY X 53 " --> pdb=" O SER X 50 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N THR X 54 " --> pdb=" O ASN X 51 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE X 58 " --> pdb=" O ALA X 55 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU X 61 " --> pdb=" O PHE X 58 " (cutoff:3.500A) Proline residue: X 62 - end of helix removed outlier: 3.639A pdb=" N LEU X 65 " --> pdb=" O PRO X 62 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ARG X 79 " --> pdb=" O LEU X 76 " (cutoff:3.500A) Processing helix chain 'Y' and resid 12 through 45 removed outlier: 4.042A pdb=" N ARG Y 36 " --> pdb=" O VAL Y 32 " (cutoff:3.500A) Processing helix chain 'Y' and resid 53 through 78 removed outlier: 4.938A pdb=" N PHE Y 58 " --> pdb=" O THR Y 54 " (cutoff:3.500A) Proline residue: Y 62 - end of helix removed outlier: 6.004A pdb=" N LEU Y 65 " --> pdb=" O LEU Y 61 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N VAL Y 66 " --> pdb=" O PRO Y 62 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ILE Y 67 " --> pdb=" O GLU Y 63 " (cutoff:3.500A) Processing helix chain 'Z' and resid 10 through 47 removed outlier: 3.647A pdb=" N ALA Z 16 " --> pdb=" O ARG Z 12 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL Z 17 " --> pdb=" O GLY Z 13 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA Z 22 " --> pdb=" O GLY Z 18 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARG Z 36 " --> pdb=" O VAL Z 32 " (cutoff:3.500A) Processing helix chain 'Z' and resid 52 through 60 removed outlier: 3.990A pdb=" N ILE Z 57 " --> pdb=" O GLY Z 53 " (cutoff:3.500A) Processing helix chain 'Z' and resid 64 through 79 Processing sheet with id= A, first strand: chain 'A' and resid 3 through 5 removed outlier: 3.553A pdb=" N PHE A 48 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N LYS A 17 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ILE A 6 " --> pdb=" O LYS A 17 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 72 through 75 Processing sheet with id= C, first strand: chain 'A' and resid 82 through 84 removed outlier: 3.879A pdb=" N GLY A 82 " --> pdb=" O THR A 285 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL A 250 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N ILE A 288 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N TYR A 252 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N ASN A 290 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N GLY A 254 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL A 249 " --> pdb=" O SER A 319 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N CYS A 255 " --> pdb=" O ASP A 325 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ALA A 377 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N LEU A 322 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THR A 379 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N ALA A 324 " --> pdb=" O THR A 379 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL A 381 " --> pdb=" O ALA A 324 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 117 through 119 Processing sheet with id= E, first strand: chain 'A' and resid 134 through 140 removed outlier: 6.697A pdb=" N ILE A 147 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N THR A 137 " --> pdb=" O HIS A 145 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N HIS A 145 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N PHE A 143 " --> pdb=" O PRO A 139 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 157 through 160 removed outlier: 6.778A pdb=" N VAL A 174 " --> pdb=" O LYS A 158 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 64 through 66 removed outlier: 5.500A pdb=" N LYS B 17 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ILE B 6 " --> pdb=" O LYS B 17 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 72 through 75 Processing sheet with id= I, first strand: chain 'B' and resid 82 through 84 removed outlier: 3.971A pdb=" N GLY B 82 " --> pdb=" O THR B 285 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VAL B 250 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N ILE B 288 " --> pdb=" O VAL B 250 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR B 252 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N ASN B 290 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N GLY B 254 " --> pdb=" O ASN B 290 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N CYS B 255 " --> pdb=" O ASP B 325 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ALA B 377 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU B 322 " --> pdb=" O ALA B 377 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N THR B 379 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ALA B 324 " --> pdb=" O THR B 379 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 116 through 118 Processing sheet with id= K, first strand: chain 'B' and resid 119 through 121 removed outlier: 6.524A pdb=" N ILE B 147 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N THR B 137 " --> pdb=" O HIS B 145 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N HIS B 145 " --> pdb=" O THR B 137 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 49 through 51 removed outlier: 3.947A pdb=" N ILE C 2 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE C 15 " --> pdb=" O GLN C 7 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ILE C 9 " --> pdb=" O ALA C 13 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ALA C 13 " --> pdb=" O ILE C 9 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 72 through 75 Processing sheet with id= N, first strand: chain 'C' and resid 82 through 84 removed outlier: 3.762A pdb=" N GLY C 82 " --> pdb=" O THR C 285 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL C 250 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ILE C 288 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N TYR C 252 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N ASN C 290 " --> pdb=" O TYR C 252 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLY C 254 " --> pdb=" O ASN C 290 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N VAL C 251 " --> pdb=" O SER C 319 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ALA C 321 " --> pdb=" O VAL C 251 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N VAL C 253 " --> pdb=" O ALA C 321 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N MET C 323 " --> pdb=" O VAL C 253 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N CYS C 255 " --> pdb=" O MET C 323 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ASP C 325 " --> pdb=" O CYS C 255 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ALA C 377 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N LEU C 322 " --> pdb=" O ALA C 377 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N THR C 379 " --> pdb=" O LEU C 322 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ALA C 324 " --> pdb=" O THR C 379 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N VAL C 381 " --> pdb=" O ALA C 324 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 119 through 121 removed outlier: 6.962A pdb=" N ILE C 147 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N THR C 137 " --> pdb=" O HIS C 145 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N HIS C 145 " --> pdb=" O THR C 137 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 366 through 369 Processing sheet with id= Q, first strand: chain 'C' and resid 157 through 160 removed outlier: 6.813A pdb=" N VAL C 174 " --> pdb=" O LYS C 158 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 71 through 76 removed outlier: 3.674A pdb=" N ILE D 32 " --> pdb=" O VAL D 76 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N TYR D 13 " --> pdb=" O PHE D 20 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N GLU D 22 " --> pdb=" O ILE D 11 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ILE D 11 " --> pdb=" O GLU D 22 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 81 through 84 Processing sheet with id= T, first strand: chain 'D' and resid 336 through 338 Processing sheet with id= U, first strand: chain 'D' and resid 217 through 221 removed outlier: 8.775A pdb=" N VAL D 218 " --> pdb=" O PHE D 187 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL D 189 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N PHE D 220 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N PHE D 191 " --> pdb=" O PHE D 220 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N HIS D 252 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N VAL D 190 " --> pdb=" O HIS D 252 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N LEU D 254 " --> pdb=" O VAL D 190 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ALA D 192 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ILE D 256 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N SER D 307 " --> pdb=" O VAL D 253 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N VAL D 255 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N THR D 309 " --> pdb=" O VAL D 255 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N LEU D 257 " --> pdb=" O THR D 309 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ILE D 311 " --> pdb=" O LEU D 257 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'E' and resid 32 through 36 removed outlier: 3.993A pdb=" N TYR E 13 " --> pdb=" O PHE E 20 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N GLU E 22 " --> pdb=" O ILE E 11 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE E 11 " --> pdb=" O GLU E 22 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 81 through 84 Processing sheet with id= X, first strand: chain 'E' and resid 336 through 338 Processing sheet with id= Y, first strand: chain 'E' and resid 217 through 219 removed outlier: 6.638A pdb=" N VAL E 189 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N VAL E 190 " --> pdb=" O HIS E 252 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LEU E 254 " --> pdb=" O VAL E 190 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ALA E 192 " --> pdb=" O LEU E 254 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ILE E 256 " --> pdb=" O ALA E 192 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N SER E 307 " --> pdb=" O VAL E 253 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N VAL E 255 " --> pdb=" O SER E 307 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N THR E 309 " --> pdb=" O VAL E 255 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N LEU E 257 " --> pdb=" O THR E 309 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE E 311 " --> pdb=" O LEU E 257 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'F' and resid 11 through 15 removed outlier: 6.669A pdb=" N PHE F 20 " --> pdb=" O THR F 12 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ILE F 14 " --> pdb=" O LEU F 18 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LEU F 18 " --> pdb=" O ILE F 14 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU F 49 " --> pdb=" O VAL F 56 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLN F 58 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N VAL F 47 " --> pdb=" O GLN F 58 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE F 32 " --> pdb=" O VAL F 76 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'F' and resid 81 through 84 Processing sheet with id= AB, first strand: chain 'F' and resid 336 through 338 Processing sheet with id= AC, first strand: chain 'F' and resid 307 through 312 Processing sheet with id= AD, first strand: chain 'G' and resid 90 through 96 Processing sheet with id= AE, first strand: chain 'H' and resid 2 through 4 removed outlier: 5.529A pdb=" N VAL H 70 " --> pdb=" O VAL H 45 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N VAL H 47 " --> pdb=" O VAL H 70 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N LEU H 72 " --> pdb=" O VAL H 47 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'J' and resid 141 through 143 Processing sheet with id= AG, first strand: chain 'L' and resid 141 through 144 removed outlier: 3.764A pdb=" N VAL L 152 " --> pdb=" O ASN L 165 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'N' and resid 304 through 306 Processing sheet with id= AI, first strand: chain 'N' and resid 140 through 145 Processing sheet with id= AJ, first strand: chain 'N' and resid 389 through 391 2331 hydrogen bonds defined for protein. 6570 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: 15.59 Time building geometry restraints manager: 18.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 7725 1.32 - 1.44: 11005 1.44 - 1.57: 26688 1.57 - 1.69: 8 1.69 - 1.81: 242 Bond restraints: 45668 Sorted by residual: bond pdb=" C PHE B 559 " pdb=" N PRO B 560 " ideal model delta sigma weight residual 1.334 1.383 -0.049 8.40e-03 1.42e+04 3.41e+01 bond pdb=" CG LEU O 60 " pdb=" CD1 LEU O 60 " ideal model delta sigma weight residual 1.521 1.406 0.115 3.30e-02 9.18e+02 1.21e+01 bond pdb=" C LYS L 39 " pdb=" O LYS L 39 " ideal model delta sigma weight residual 1.234 1.194 0.040 1.40e-02 5.10e+03 8.03e+00 bond pdb=" CB VAL A 218 " pdb=" CG2 VAL A 218 " ideal model delta sigma weight residual 1.521 1.436 0.085 3.30e-02 9.18e+02 6.70e+00 bond pdb=" C LYS L 39 " pdb=" N ALA L 40 " ideal model delta sigma weight residual 1.332 1.300 0.033 1.40e-02 5.10e+03 5.46e+00 ... (remaining 45663 not shown) Histogram of bond angle deviations from ideal: 97.14 - 105.01: 932 105.01 - 112.88: 23583 112.88 - 120.74: 23175 120.74 - 128.61: 13889 128.61 - 136.48: 258 Bond angle restraints: 61837 Sorted by residual: angle pdb=" N GLY A 366 " pdb=" CA GLY A 366 " pdb=" C GLY A 366 " ideal model delta sigma weight residual 113.18 126.56 -13.38 2.37e+00 1.78e-01 3.19e+01 angle pdb=" C TRP N 545 " pdb=" N LEU N 546 " pdb=" CA LEU N 546 " ideal model delta sigma weight residual 122.74 130.77 -8.03 1.44e+00 4.82e-01 3.11e+01 angle pdb=" C GLU F 406 " pdb=" N ASN F 407 " pdb=" CA ASN F 407 " ideal model delta sigma weight residual 121.54 132.01 -10.47 1.91e+00 2.74e-01 3.00e+01 angle pdb=" N THR N 348 " pdb=" CA THR N 348 " pdb=" C THR N 348 " ideal model delta sigma weight residual 109.81 121.50 -11.69 2.21e+00 2.05e-01 2.80e+01 angle pdb=" C ASP F 318 " pdb=" N ASP F 319 " pdb=" CA ASP F 319 " ideal model delta sigma weight residual 121.54 131.60 -10.06 1.91e+00 2.74e-01 2.78e+01 ... (remaining 61832 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.65: 26461 20.65 - 41.29: 1044 41.29 - 61.94: 55 61.94 - 82.58: 16 82.58 - 103.23: 2 Dihedral angle restraints: 27578 sinusoidal: 10985 harmonic: 16593 Sorted by residual: dihedral pdb=" CA ARG N 36 " pdb=" C ARG N 36 " pdb=" N PRO N 37 " pdb=" CA PRO N 37 " ideal model delta harmonic sigma weight residual -180.00 -142.23 -37.77 0 5.00e+00 4.00e-02 5.71e+01 dihedral pdb=" CA HIS N 297 " pdb=" C HIS N 297 " pdb=" N LYS N 298 " pdb=" CA LYS N 298 " ideal model delta harmonic sigma weight residual -180.00 -142.40 -37.60 0 5.00e+00 4.00e-02 5.66e+01 dihedral pdb=" CA VAL N 301 " pdb=" C VAL N 301 " pdb=" N VAL N 302 " pdb=" CA VAL N 302 " ideal model delta harmonic sigma weight residual -180.00 -149.11 -30.89 0 5.00e+00 4.00e-02 3.82e+01 ... (remaining 27575 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 6036 0.085 - 0.170: 960 0.170 - 0.256: 73 0.256 - 0.341: 7 0.341 - 0.426: 3 Chirality restraints: 7079 Sorted by residual: chirality pdb=" CB ILE N 544 " pdb=" CA ILE N 544 " pdb=" CG1 ILE N 544 " pdb=" CG2 ILE N 544 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.43 2.00e-01 2.50e+01 4.54e+00 chirality pdb=" CB ILE A 226 " pdb=" CA ILE A 226 " pdb=" CG1 ILE A 226 " pdb=" CG2 ILE A 226 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.37e+00 chirality pdb=" CG LEU N 231 " pdb=" CB LEU N 231 " pdb=" CD1 LEU N 231 " pdb=" CD2 LEU N 231 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.16e+00 ... (remaining 7076 not shown) Planarity restraints: 8046 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 378 " -0.018 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C VAL B 378 " 0.061 2.00e-02 2.50e+03 pdb=" O VAL B 378 " -0.023 2.00e-02 2.50e+03 pdb=" N THR B 379 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE C 226 " 0.055 5.00e-02 4.00e+02 8.21e-02 1.08e+01 pdb=" N PRO C 227 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO C 227 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO C 227 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA L 40 " 0.016 2.00e-02 2.50e+03 3.23e-02 1.04e+01 pdb=" C ALA L 40 " -0.056 2.00e-02 2.50e+03 pdb=" O ALA L 40 " 0.020 2.00e-02 2.50e+03 pdb=" N LEU L 41 " 0.019 2.00e-02 2.50e+03 ... (remaining 8043 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 555 2.66 - 3.22: 39797 3.22 - 3.78: 70439 3.78 - 4.34: 92535 4.34 - 4.90: 154119 Nonbonded interactions: 357445 Sorted by model distance: nonbonded pdb=" O GLU L 36 " pdb=" O LYS L 39 " model vdw 2.095 2.432 nonbonded pdb=" OG1 THR A 235 " pdb="MG MG A 601 " model vdw 2.158 2.170 nonbonded pdb=" O ALA N 538 " pdb=" OG SER N 542 " model vdw 2.193 2.440 nonbonded pdb=" O LEU E 446 " pdb=" OH TYR E 463 " model vdw 2.224 2.440 nonbonded pdb=" OE1 GLU C 38 " pdb=" OH TYR C 52 " model vdw 2.248 2.440 ... (remaining 357440 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 1 through 578) selection = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and resid 5 through 471) selection = (chain 'E' and resid 5 through 471) selection = (chain 'F' and resid 5 through 471) } ncs_group { reference = (chain 'I' and resid 22 through 120) selection = chain 'K' } ncs_group { reference = chain 'J' selection = (chain 'L' and resid 2 through 187) } ncs_group { reference = (chain 'O' and resid 9 through 80) selection = (chain 'P' and resid 9 through 80) selection = (chain 'Q' and resid 9 through 80) selection = (chain 'R' and resid 9 through 80) selection = (chain 'S' and resid 9 through 80) selection = (chain 'T' and resid 9 through 80) selection = (chain 'U' and resid 9 through 80) selection = (chain 'V' and resid 9 through 80) selection = (chain 'W' and resid 9 through 80) selection = chain 'X' selection = (chain 'Y' and resid 9 through 80) selection = (chain 'Z' and resid 9 through 80) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.220 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: 0.050 Extract box with map and model: 3.750 Check model and map are aligned: 0.640 Set scattering table: 0.390 Process input model: 110.520 Find NCS groups from input model: 2.960 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 121.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 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 : 0.007 0.115 45668 Z= 0.479 Angle : 1.097 17.551 61837 Z= 0.565 Chirality : 0.061 0.426 7079 Planarity : 0.008 0.082 8046 Dihedral : 10.752 103.230 16985 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.72 % Favored : 93.25 % Rotamer: Outliers : 0.82 % Allowed : 6.33 % Favored : 92.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.19 % Cis-general : 0.00 % Twisted Proline : 0.36 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.78 (0.09), residues: 5822 helix: -2.18 (0.07), residues: 3120 sheet: -2.05 (0.20), residues: 574 loop : -2.92 (0.11), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP A 330 HIS 0.016 0.002 HIS N 561 PHE 0.047 0.003 PHE N 274 TYR 0.035 0.003 TYR D 411 ARG 0.017 0.001 ARG F 360 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11644 Ramachandran restraints generated. 5822 Oldfield, 0 Emsley, 5822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11644 Ramachandran restraints generated. 5822 Oldfield, 0 Emsley, 5822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1352 residues out of total 4601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 1315 time to evaluate : 4.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO L 146 " (corrupted residue). Skipping it. Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 303, in __init__ self.caller(self.optimize_sidechains) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 609, in optimize_sidechains log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 83, in __init__ rotatable_hd = self.rotatable_hd) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 189, in run_one pdb_hierarchy = self.run_one_one(args=args) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 133, in run_one_one log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 108, in __init__ self.loop(function = self.one_residue_iteration) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 284, in loop function(residue = residue) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 271, in one_residue_iteration log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 172, in __init__ self.fit_proline() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 217, in fit_proline for rotamer, sites_cart in rotamer_iterator: TypeError: 'NoneType' object is not iterable