Starting phenix.real_space_refine on Mon Mar 18 20:15:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jpb_9869/03_2024/6jpb_9869_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jpb_9869/03_2024/6jpb_9869.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jpb_9869/03_2024/6jpb_9869.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jpb_9869/03_2024/6jpb_9869.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jpb_9869/03_2024/6jpb_9869_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jpb_9869/03_2024/6jpb_9869_updated.pdb" } resolution = 2.9 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= 0.000 sd= 0.005 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 Ca 3 9.91 5 P 5 5.49 5 S 127 5.16 5 C 14226 2.51 5 N 3592 2.21 5 O 4036 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 PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 174": "NH1" <-> "NH2" Residue "A ARG 262": "NH1" <-> "NH2" Residue "A ARG 347": "NH1" <-> "NH2" Residue "A ARG 354": "NH1" <-> "NH2" Residue "A ARG 498": "NH1" <-> "NH2" Residue "A ARG 584": "NH1" <-> "NH2" Residue "A PHE 656": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 794": "NH1" <-> "NH2" Residue "A ARG 910": "NH1" <-> "NH2" Residue "A ARG 1022": "NH1" <-> "NH2" Residue "A ASP 1082": "OD1" <-> "OD2" Residue "A ARG 1099": "NH1" <-> "NH2" Residue "A TYR 1119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1236": "NH1" <-> "NH2" Residue "A ARG 1242": "NH1" <-> "NH2" Residue "A ARG 1389": "NH1" <-> "NH2" Residue "A ARG 1427": "NH1" <-> "NH2" Residue "A ARG 1428": "NH1" <-> "NH2" Residue "A PHE 1438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1442": "NH1" <-> "NH2" Residue "A ARG 1447": "NH1" <-> "NH2" Residue "A ARG 1472": "NH1" <-> "NH2" Residue "F TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 93": "NH1" <-> "NH2" Residue "F ARG 158": "NH1" <-> "NH2" Residue "F ARG 199": "NH1" <-> "NH2" Residue "F GLU 200": "OE1" <-> "OE2" Residue "F ARG 230": "NH1" <-> "NH2" Residue "F ARG 241": "NH1" <-> "NH2" Residue "F ARG 243": "NH1" <-> "NH2" Residue "F ARG 275": "NH1" <-> "NH2" Residue "F ARG 315": "NH1" <-> "NH2" Residue "F TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 544": "NH1" <-> "NH2" Residue "F ARG 546": "NH1" <-> "NH2" Residue "F GLU 567": "OE1" <-> "OE2" Residue "F ARG 591": "NH1" <-> "NH2" Residue "F ARG 607": "NH1" <-> "NH2" Residue "F GLU 658": "OE1" <-> "OE2" Residue "F ARG 692": "NH1" <-> "NH2" Residue "F PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 745": "NH1" <-> "NH2" Residue "F ARG 1004": "NH1" <-> "NH2" Residue "F GLU 1022": "OE1" <-> "OE2" Residue "F GLU 1069": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 21989 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 10219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1274, 10219 Classifications: {'peptide': 1274} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 38, 'TRANS': 1235} Chain breaks: 6 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 57 Chain: "E" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1326 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain breaks: 4 Chain: "B" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 710 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 8, 'TRANS': 91} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "C" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1367 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 12, 'TRANS': 165} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "F" Number of atoms: 7804 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 973, 7796 Classifications: {'peptide': 973} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 927} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 973, 7796 Classifications: {'peptide': 973} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 927} Chain breaks: 2 bond proxies already assigned to first conformer: 7954 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 228 Unusual residues: {' CA': 2, '3PE': 4, 'C9F': 1, 'NAG': 1, 'PC1': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 103 Unusual residues: {' CA': 1, 'ETA': 1, 'NAG': 7} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 15.32, per 1000 atoms: 0.70 Number of scatterers: 21989 At special positions: 0 Unit cell: (171.287, 183.288, 165.832, 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) Ca 3 19.99 S 127 16.00 P 5 15.00 O 4036 8.00 N 3592 7.00 C 14226 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 226 " - pdb=" SG CYS A 254 " distance=1.35 Simple disulfide: pdb=" SG CYS A 245 " - pdb=" SG CYS A 261 " distance=2.98 Simple disulfide: pdb=" SG CYS A 957 " - pdb=" SG CYS A 968 " distance=2.02 Simple disulfide: pdb=" SG CYS A1338 " - pdb=" SG CYS A1352 " distance=1.92 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 80 " distance=2.05 Simple disulfide: pdb=" SG CYS F 305 " - pdb=" SG CYS F1047 " distance=2.03 Simple disulfide: pdb=" SG CYS F 356 " - pdb=" SG CYS F1062 " distance=2.77 Simple disulfide: pdb=" SG CYS F 406 " - pdb=" SG CYS F1074 " distance=2.27 Simple disulfide: pdb=" SG CYS F 670 " - pdb=" SG CYS F 700 " distance=2.02 Simple disulfide: pdb=" SG CYS F 844 " - pdb=" SG CYS F 853 " distance=1.57 Simple disulfide: pdb=" SG CYS F 907 " - pdb=" SG CYS F 977 " distance=2.03 Simple disulfide: pdb=" SG CYS F 999 " - pdb=" SG CYS F1029 " distance=2.03 Simple disulfide: pdb=" SG CYS F1002 " - pdb=" SG CYS F1027 " 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 Atom "HETATM21903 O5 NAG F1105 .*. O " rejected from bonding due to valence issues. Atom "HETATM21931 O5 NAG F1115 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-3 " NAG D 1 " - " NAG D 2 " " NAG K 1 " - " NAG K 2 " " NAG L 2 " - " NAG L 3 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A1901 " - " ASN A 257 " " NAG F1105 " - " ASN F 326 " " NAG F1108 " - " ASN F 891 " " NAG F1115 " - " ASN F 92 " " NAG F1116 " - " ASN F 606 " " NAG F1121 " - " ASN F 784 " " NAG F1122 " - " ASN F1001 " " NAG F1123 " - " ASN F 988 " " NAG G 1 " - " ASN F 615 " " NAG H 1 " - " ASN F 186 " " NAG I 1 " - " ASN F 470 " " NAG J 1 " - " ASN F 898 " " NAG K 1 " - " ASN F 678 " " NAG L 1 " - " ASN F 827 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.23 Conformation dependent library (CDL) restraints added in 4.8 seconds 5318 Ramachandran restraints generated. 2659 Oldfield, 0 Emsley, 2659 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5110 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 107 helices and 13 sheets defined 45.4% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.41 Creating SS restraints... Processing helix chain 'A' and resid 40 through 48 removed outlier: 5.357A pdb=" N ILE A 45 " --> pdb=" O ARG A 41 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N SER A 46 " --> pdb=" O LYS A 42 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ILE A 47 " --> pdb=" O ALA A 43 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL A 48 " --> pdb=" O CYS A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 69 removed outlier: 3.592A pdb=" N ILE A 57 " --> pdb=" O PHE A 53 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE A 62 " --> pdb=" O LEU A 58 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA A 63 " --> pdb=" O LEU A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 84 No H-bonds generated for 'chain 'A' and resid 81 through 84' Processing helix chain 'A' and resid 87 through 100 removed outlier: 3.580A pdb=" N TYR A 91 " --> pdb=" O GLU A 87 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL A 96 " --> pdb=" O PHE A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 119 removed outlier: 3.596A pdb=" N LEU A 118 " --> pdb=" O GLN A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 142 removed outlier: 3.931A pdb=" N LEU A 125 " --> pdb=" O TRP A 122 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ASP A 126 " --> pdb=" O ASN A 123 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ILE A 129 " --> pdb=" O ASP A 126 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE A 131 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY A 133 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL A 134 " --> pdb=" O PHE A 131 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE A 135 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE A 138 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N LEU A 139 " --> pdb=" O THR A 136 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLU A 140 " --> pdb=" O ALA A 137 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL A 142 " --> pdb=" O LEU A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 178 removed outlier: 4.070A pdb=" N ARG A 171 " --> pdb=" O ARG A 168 " (cutoff:3.500A) Proline residue: A 172 - end of helix removed outlier: 3.612A pdb=" N LEU A 175 " --> pdb=" O PRO A 172 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER A 177 " --> pdb=" O ARG A 174 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY A 178 " --> pdb=" O LEU A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 188 removed outlier: 3.551A pdb=" N SER A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 192 No H-bonds generated for 'chain 'A' and resid 190 through 192' Processing helix chain 'A' and resid 197 through 207 removed outlier: 3.924A pdb=" N LEU A 202 " --> pdb=" O HIS A 198 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N MET A 206 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 218 Processing helix chain 'A' and resid 278 through 289 removed outlier: 3.598A pdb=" N THR A 284 " --> pdb=" O PHE A 280 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N CYS A 288 " --> pdb=" O THR A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 301 removed outlier: 3.665A pdb=" N TYR A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 321 Processing helix chain 'A' and resid 325 through 336 removed outlier: 4.383A pdb=" N SER A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 345 No H-bonds generated for 'chain 'A' and resid 342 through 345' Processing helix chain 'A' and resid 352 through 371 removed outlier: 3.602A pdb=" N LYS A 356 " --> pdb=" O LYS A 352 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLN A 357 " --> pdb=" O LEU A 353 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER A 368 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TRP A 369 " --> pdb=" O GLY A 365 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE A 370 " --> pdb=" O TYR A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 427 removed outlier: 3.900A pdb=" N CYS A 425 " --> pdb=" O PHE A 421 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N HIS A 426 " --> pdb=" O ARG A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 449 removed outlier: 3.514A pdb=" N ALA A 443 " --> pdb=" O ILE A 439 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN A 445 " --> pdb=" O ILE A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 484 removed outlier: 3.637A pdb=" N ASP A 465 " --> pdb=" O THR A 461 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE A 466 " --> pdb=" O HIS A 462 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER A 473 " --> pdb=" O ARG A 469 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE A 475 " --> pdb=" O LEU A 471 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU A 478 " --> pdb=" O LEU A 474 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS A 482 " --> pdb=" O GLU A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 493 removed outlier: 3.717A pdb=" N PHE A 492 " --> pdb=" O LEU A 488 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N MET A 493 " --> pdb=" O ARG A 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 488 through 493' Processing helix chain 'A' and resid 497 through 513 removed outlier: 3.801A pdb=" N PHE A 502 " --> pdb=" O ARG A 498 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLU A 510 " --> pdb=" O SER A 506 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU A 511 " --> pdb=" O GLY A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 541 removed outlier: 4.019A pdb=" N ARG A 528 " --> pdb=" O ILE A 524 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG A 531 " --> pdb=" O LEU A 527 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU A 532 " --> pdb=" O ARG A 528 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LEU A 533 " --> pdb=" O CYS A 529 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ARG A 534 " --> pdb=" O ILE A 530 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N LEU A 535 " --> pdb=" O ARG A 531 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N PHE A 536 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS A 537 " --> pdb=" O LEU A 533 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ILE A 538 " --> pdb=" O ARG A 534 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N THR A 539 " --> pdb=" O LEU A 535 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LYS A 540 " --> pdb=" O PHE A 536 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N TYR A 541 " --> pdb=" O LYS A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 555 removed outlier: 3.617A pdb=" N LEU A 553 " --> pdb=" O VAL A 549 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N SER A 555 " --> pdb=" O SER A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 563 Processing helix chain 'A' and resid 565 through 580 removed outlier: 3.698A pdb=" N ILE A 571 " --> pdb=" O PHE A 567 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE A 573 " --> pdb=" O PHE A 569 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY A 577 " --> pdb=" O PHE A 573 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N MET A 578 " --> pdb=" O ALA A 574 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN A 579 " --> pdb=" O LEU A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 612 Processing helix chain 'A' and resid 616 through 626 removed outlier: 3.568A pdb=" N GLY A 623 " --> pdb=" O VAL A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 649 removed outlier: 3.535A pdb=" N VAL A 637 " --> pdb=" O GLY A 634 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE A 641 " --> pdb=" O CYS A 638 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE A 642 " --> pdb=" O ILE A 639 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LEU A 644 " --> pdb=" O PHE A 641 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL A 646 " --> pdb=" O ILE A 643 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N CYS A 647 " --> pdb=" O LEU A 644 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLY A 648 " --> pdb=" O PHE A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 686 removed outlier: 3.623A pdb=" N GLU A 666 " --> pdb=" O ASP A 662 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N THR A 671 " --> pdb=" O ALA A 667 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA A 676 " --> pdb=" O SER A 672 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU A 680 " --> pdb=" O ALA A 676 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG A 681 " --> pdb=" O LYS A 677 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG A 683 " --> pdb=" O GLU A 679 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG A 684 " --> pdb=" O GLU A 680 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS A 685 " --> pdb=" O ARG A 681 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET A 686 " --> pdb=" O LYS A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 795 removed outlier: 4.055A pdb=" N ARG A 794 " --> pdb=" O VAL A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 809 removed outlier: 3.692A pdb=" N PHE A 808 " --> pdb=" O PHE A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 817 Processing helix chain 'A' and resid 827 through 839 removed outlier: 4.288A pdb=" N PHE A 835 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASP A 836 " --> pdb=" O LEU A 832 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE A 837 " --> pdb=" O GLY A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 853 removed outlier: 4.312A pdb=" N ILE A 847 " --> pdb=" O PHE A 843 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL A 848 " --> pdb=" O THR A 844 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR A 852 " --> pdb=" O VAL A 848 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N THR A 853 " --> pdb=" O LEU A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 881 removed outlier: 3.787A pdb=" N ASP A 872 " --> pdb=" O PHE A 868 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 873 " --> pdb=" O ASN A 869 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL A 876 " --> pdb=" O ASP A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 903 removed outlier: 3.865A pdb=" N VAL A 898 " --> pdb=" O LYS A 894 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU A 899 " --> pdb=" O ILE A 895 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG A 900 " --> pdb=" O LEU A 896 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL A 901 " --> pdb=" O ARG A 897 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N LEU A 902 " --> pdb=" O VAL A 898 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ARG A 903 " --> pdb=" O LEU A 899 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 894 through 903' Processing helix chain 'A' and resid 905 through 907 No H-bonds generated for 'chain 'A' and resid 905 through 907' Processing helix chain 'A' and resid 914 through 926 removed outlier: 3.736A pdb=" N VAL A 918 " --> pdb=" O LEU A 914 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG A 926 " --> pdb=" O PHE A 922 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 949 removed outlier: 4.849A pdb=" N VAL A 932 " --> pdb=" O GLY A 929 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU A 933 " --> pdb=" O ASN A 930 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N THR A 935 " --> pdb=" O VAL A 932 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR A 936 " --> pdb=" O LEU A 933 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLN A 939 " --> pdb=" O THR A 936 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE A 942 " --> pdb=" O GLN A 939 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA A 943 " --> pdb=" O PHE A 940 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE A 945 " --> pdb=" O PHE A 942 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY A 946 " --> pdb=" O ALA A 943 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL A 947 " --> pdb=" O CYS A 944 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU A 949 " --> pdb=" O GLY A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 978 No H-bonds generated for 'chain 'A' and resid 976 through 978' Processing helix chain 'A' and resid 1000 through 1012 removed outlier: 3.741A pdb=" N THR A1009 " --> pdb=" O MET A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1024 removed outlier: 3.686A pdb=" N ARG A1022 " --> pdb=" O GLN A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1039 through 1042 removed outlier: 3.772A pdb=" N ALA A1042 " --> pdb=" O VAL A1039 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1039 through 1042' Processing helix chain 'A' and resid 1044 through 1051 removed outlier: 3.640A pdb=" N ILE A1049 " --> pdb=" O PHE A1045 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1067 Processing helix chain 'A' and resid 1083 through 1093 Processing helix chain 'A' and resid 1106 through 1115 removed outlier: 3.764A pdb=" N VAL A1111 " --> pdb=" O TYR A1107 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N VAL A1114 " --> pdb=" O GLN A1110 " (cutoff:3.500A) Processing helix chain 'A' and resid 1118 through 1136 removed outlier: 4.056A pdb=" N LEU A1123 " --> pdb=" O TYR A1119 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N MET A1129 " --> pdb=" O PHE A1125 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE A1133 " --> pdb=" O MET A1129 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A1135 " --> pdb=" O ASN A1131 " (cutoff:3.500A) Processing helix chain 'A' and resid 1144 through 1170 removed outlier: 4.032A pdb=" N ILE A1149 " --> pdb=" O GLU A1145 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR A1158 " --> pdb=" O ASN A1154 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE A1160 " --> pdb=" O ALA A1156 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N MET A1165 " --> pdb=" O PHE A1161 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU A1167 " --> pdb=" O LEU A1163 " (cutoff:3.500A) Processing helix chain 'A' and resid 1181 through 1204 removed outlier: 3.579A pdb=" N PHE A1185 " --> pdb=" O PRO A1181 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASP A1203 " --> pdb=" O LEU A1199 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR A1204 " --> pdb=" O SER A1200 " (cutoff:3.500A) Processing helix chain 'A' and resid 1233 through 1238 removed outlier: 3.648A pdb=" N PHE A1238 " --> pdb=" O PHE A1235 " (cutoff:3.500A) Processing helix chain 'A' and resid 1241 through 1248 removed outlier: 3.519A pdb=" N ILE A1244 " --> pdb=" O MET A1241 " (cutoff:3.500A) Processing helix chain 'A' and resid 1251 through 1265 removed outlier: 3.512A pdb=" N THR A1255 " --> pdb=" O GLU A1251 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU A1256 " --> pdb=" O GLY A1252 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE A1260 " --> pdb=" O LEU A1256 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER A1263 " --> pdb=" O THR A1259 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE A1264 " --> pdb=" O PHE A1260 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN A1265 " --> pdb=" O ILE A1261 " (cutoff:3.500A) Processing helix chain 'A' and resid 1270 through 1288 removed outlier: 3.683A pdb=" N ILE A1274 " --> pdb=" O VAL A1270 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL A1275 " --> pdb=" O ALA A1271 " (cutoff:3.500A) Processing helix chain 'A' and resid 1309 through 1321 Processing helix chain 'A' and resid 1325 through 1332 removed outlier: 3.773A pdb=" N ALA A1331 " --> pdb=" O GLU A1327 " (cutoff:3.500A) Processing helix chain 'A' and resid 1357 through 1380 removed outlier: 3.655A pdb=" N LEU A1375 " --> pdb=" O LEU A1371 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL A1379 " --> pdb=" O LEU A1375 " (cutoff:3.500A) Processing helix chain 'A' and resid 1396 through 1409 removed outlier: 4.039A pdb=" N GLU A1401 " --> pdb=" O HIS A1397 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE A1402 " --> pdb=" O HIS A1398 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYS A1403 " --> pdb=" O LEU A1399 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TYR A1409 " --> pdb=" O ILE A1405 " (cutoff:3.500A) Processing helix chain 'A' and resid 1419 through 1428 removed outlier: 3.833A pdb=" N VAL A1423 " --> pdb=" O HIS A1419 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR A1424 " --> pdb=" O LEU A1420 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A1426 " --> pdb=" O VAL A1422 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ARG A1427 " --> pdb=" O VAL A1423 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ARG A1428 " --> pdb=" O THR A1424 " (cutoff:3.500A) Processing helix chain 'A' and resid 1444 through 1447 No H-bonds generated for 'chain 'A' and resid 1444 through 1447' Processing helix chain 'A' and resid 1464 through 1474 removed outlier: 3.512A pdb=" N VAL A1471 " --> pdb=" O LEU A1467 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR A1473 " --> pdb=" O ALA A1469 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA A1474 " --> pdb=" O LEU A1470 " (cutoff:3.500A) Processing helix chain 'A' and resid 1489 through 1492 No H-bonds generated for 'chain 'A' and resid 1489 through 1492' Processing helix chain 'A' and resid 1499 through 1503 removed outlier: 3.663A pdb=" N SER A1502 " --> pdb=" O LYS A1499 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 26 removed outlier: 3.546A pdb=" N THR E 12 " --> pdb=" O LYS E 8 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY E 19 " --> pdb=" O CYS E 15 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N VAL E 21 " --> pdb=" O LEU E 17 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU E 22 " --> pdb=" O VAL E 18 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA E 23 " --> pdb=" O GLY E 19 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N MET E 24 " --> pdb=" O ILE E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 127 removed outlier: 3.976A pdb=" N SER E 111 " --> pdb=" O ALA E 107 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE E 113 " --> pdb=" O ALA E 109 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU E 118 " --> pdb=" O SER E 114 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR E 122 " --> pdb=" O LEU E 118 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N CYS E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA E 125 " --> pdb=" O GLY E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 163 Proline residue: E 139 - end of helix removed outlier: 3.655A pdb=" N PHE E 143 " --> pdb=" O ALA E 140 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR E 144 " --> pdb=" O SER E 141 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU E 149 " --> pdb=" O PHE E 146 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE E 152 " --> pdb=" O LEU E 149 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU E 155 " --> pdb=" O PHE E 152 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL E 157 " --> pdb=" O SER E 154 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N SER E 161 " --> pdb=" O MET E 158 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS E 163 " --> pdb=" O GLN E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 201 removed outlier: 3.730A pdb=" N ALA E 187 " --> pdb=" O ALA E 183 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N VAL E 190 " --> pdb=" O CYS E 186 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU E 194 " --> pdb=" O VAL E 190 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE E 197 " --> pdb=" O PHE E 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 96 removed outlier: 4.066A pdb=" N GLU B 84 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU B 86 " --> pdb=" O ARG B 82 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG B 87 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA B 96 " --> pdb=" O GLN B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 173 removed outlier: 3.541A pdb=" N LEU B 170 " --> pdb=" O ASP B 166 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLU B 173 " --> pdb=" O ARG B 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 303 removed outlier: 3.648A pdb=" N MET C 292 " --> pdb=" O GLU C 288 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA C 296 " --> pdb=" O MET C 292 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU C 297 " --> pdb=" O MET C 293 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP C 299 " --> pdb=" O LYS C 295 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE C 300 " --> pdb=" O ALA C 296 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU C 301 " --> pdb=" O LEU C 297 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N HIS C 303 " --> pdb=" O ASP C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 357 removed outlier: 3.925A pdb=" N GLU C 350 " --> pdb=" O GLU C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 377 No H-bonds generated for 'chain 'C' and resid 375 through 377' Processing helix chain 'C' and resid 394 through 401 removed outlier: 3.794A pdb=" N GLN C 398 " --> pdb=" O PRO C 394 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ARG C 399 " --> pdb=" O LYS C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 410 No H-bonds generated for 'chain 'C' and resid 408 through 410' Processing helix chain 'C' and resid 412 through 424 removed outlier: 4.029A pdb=" N ILE C 416 " --> pdb=" O LEU C 412 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA C 418 " --> pdb=" O VAL C 414 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA C 423 " --> pdb=" O SER C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 429 No H-bonds generated for 'chain 'C' and resid 427 through 429' Processing helix chain 'C' and resid 439 through 457 removed outlier: 3.951A pdb=" N HIS C 445 " --> pdb=" O ASP C 441 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU C 450 " --> pdb=" O LEU C 446 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA C 456 " --> pdb=" O ALA C 452 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 37 Processing helix chain 'F' and resid 42 through 52 Processing helix chain 'F' and resid 54 through 64 removed outlier: 3.652A pdb=" N TYR F 64 " --> pdb=" O ILE F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 109 removed outlier: 3.725A pdb=" N SER F 94 " --> pdb=" O LEU F 90 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA F 96 " --> pdb=" O ASN F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 201 removed outlier: 3.920A pdb=" N GLU F 184 " --> pdb=" O ILE F 180 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER F 189 " --> pdb=" O LEU F 185 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ALA F 190 " --> pdb=" O ASN F 186 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N LEU F 191 " --> pdb=" O TRP F 187 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ASP F 192 " --> pdb=" O THR F 188 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ASP F 193 " --> pdb=" O SER F 189 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL F 194 " --> pdb=" O ALA F 190 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG F 199 " --> pdb=" O PHE F 195 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU F 201 " --> pdb=" O LYS F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 250 removed outlier: 3.862A pdb=" N GLY F 249 " --> pdb=" O TRP F 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 264 through 266 No H-bonds generated for 'chain 'F' and resid 264 through 266' Processing helix chain 'F' and resid 269 through 283 removed outlier: 3.617A pdb=" N ARG F 275 " --> pdb=" O LEU F 271 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N THR F 276 " --> pdb=" O LYS F 272 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER F 279 " --> pdb=" O ARG F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 323 Processing helix chain 'F' and resid 335 through 346 Processing helix chain 'F' and resid 372 through 378 removed outlier: 3.939A pdb=" N LYS F 377 " --> pdb=" O GLU F 373 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 407 Processing helix chain 'F' and resid 427 through 432 removed outlier: 3.836A pdb=" N LEU F 432 " --> pdb=" O LEU F 429 " (cutoff:3.500A) Processing helix chain 'F' and resid 434 through 437 No H-bonds generated for 'chain 'F' and resid 434 through 437' Processing helix chain 'F' and resid 440 through 443 Processing helix chain 'F' and resid 496 through 499 No H-bonds generated for 'chain 'F' and resid 496 through 499' Processing helix chain 'F' and resid 543 through 545 No H-bonds generated for 'chain 'F' and resid 543 through 545' Processing helix chain 'F' and resid 563 through 566 No H-bonds generated for 'chain 'F' and resid 563 through 566' Processing helix chain 'F' and resid 574 through 581 Processing helix chain 'F' and resid 641 through 646 Processing helix chain 'F' and resid 679 through 692 removed outlier: 3.686A pdb=" N PHE F 689 " --> pdb=" O ASN F 685 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE F 690 " --> pdb=" O PHE F 686 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP F 691 " --> pdb=" O ASN F 687 " (cutoff:3.500A) Processing helix chain 'F' and resid 702 through 721 removed outlier: 3.839A pdb=" N GLU F 717 " --> pdb=" O GLY F 713 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU F 718 " --> pdb=" O PHE F 714 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL F 719 " --> pdb=" O THR F 715 " (cutoff:3.500A) Processing helix chain 'F' and resid 749 through 753 removed outlier: 3.533A pdb=" N GLU F 753 " --> pdb=" O LYS F 749 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 749 through 753' Processing helix chain 'F' and resid 765 through 772 removed outlier: 3.561A pdb=" N LEU F 771 " --> pdb=" O TYR F 767 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP F 772 " --> pdb=" O LYS F 768 " (cutoff:3.500A) Processing helix chain 'F' and resid 821 through 829 removed outlier: 3.506A pdb=" N GLU F 826 " --> pdb=" O ASN F 822 " (cutoff:3.500A) Processing helix chain 'F' and resid 878 through 880 No H-bonds generated for 'chain 'F' and resid 878 through 880' Processing helix chain 'F' and resid 883 through 891 removed outlier: 3.561A pdb=" N ASN F 891 " --> pdb=" O ARG F 887 " (cutoff:3.500A) Processing helix chain 'F' and resid 1024 through 1026 No H-bonds generated for 'chain 'F' and resid 1024 through 1026' Processing helix chain 'F' and resid 1046 through 1052 removed outlier: 4.334A pdb=" N LYS F1051 " --> pdb=" O CYS F1047 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLN F1052 " --> pdb=" O ASP F1048 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 225 through 228 Processing sheet with id= B, first strand: chain 'A' and resid 971 through 975 Processing sheet with id= C, first strand: chain 'E' and resid 48 through 51 Processing sheet with id= D, first strand: chain 'B' and resid 103 through 106 removed outlier: 3.704A pdb=" N PHE B 103 " --> pdb=" O ILE B 136 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE B 146 " --> pdb=" O LYS B 137 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N LYS B 139 " --> pdb=" O TRP B 144 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N TRP B 144 " --> pdb=" O LYS B 139 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 432 through 434 removed outlier: 3.990A pdb=" N ILE C 389 " --> pdb=" O VAL C 280 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL C 364 " --> pdb=" O ILE C 277 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N LEU C 279 " --> pdb=" O VAL C 364 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N LEU C 366 " --> pdb=" O LEU C 279 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 68 through 72 Processing sheet with id= G, first strand: chain 'F' and resid 167 through 170 removed outlier: 4.289A pdb=" N LEU F 216 " --> pdb=" O SER F 212 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N VAL F 468 " --> pdb=" O LEU F 487 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N VAL F 489 " --> pdb=" O LEU F 466 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU F 466 " --> pdb=" O VAL F 489 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLY F 491 " --> pdb=" O GLY F 464 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLY F 464 " --> pdb=" O GLY F 491 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ASP F 493 " --> pdb=" O ILE F 462 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE F 462 " --> pdb=" O ASP F 493 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 411 through 415 removed outlier: 3.642A pdb=" N TYR F 411 " --> pdb=" O VAL F 386 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE F 359 " --> pdb=" O ASP F 255 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N PHE F 290 " --> pdb=" O MET F 256 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ILE F 258 " --> pdb=" O PHE F 290 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ASN F 292 " --> pdb=" O ILE F 258 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N VAL F 260 " --> pdb=" O ASN F 292 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ALA F 294 " --> pdb=" O VAL F 260 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 513 through 517 Processing sheet with id= J, first strand: chain 'F' and resid 777 through 779 Processing sheet with id= K, first strand: chain 'F' and resid 992 through 994 removed outlier: 3.618A pdb=" N MET F 864 " --> pdb=" O ILE F 855 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 896 through 902 removed outlier: 3.618A pdb=" N GLN F 983 " --> pdb=" O ASN F 898 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 905 through 907 removed outlier: 3.574A pdb=" N SER F 905 " --> pdb=" O CYS F 977 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN F 975 " --> pdb=" O CYS F 907 " (cutoff:3.500A) 693 hydrogen bonds defined for protein. 1886 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: 7.02 Time building geometry restraints manager: 10.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3540 1.30 - 1.43: 6083 1.43 - 1.56: 12635 1.56 - 1.69: 12 1.69 - 1.82: 196 Bond restraints: 22466 Sorted by residual: bond pdb=" C21 3PE A1904 " pdb=" O21 3PE A1904 " ideal model delta sigma weight residual 1.316 1.453 -0.137 2.00e-02 2.50e+03 4.68e+01 bond pdb=" C02 C9F A1909 " pdb=" N03 C9F A1909 " ideal model delta sigma weight residual 1.358 1.483 -0.125 2.00e-02 2.50e+03 3.91e+01 bond pdb=" C31 3PE A1904 " pdb=" O31 3PE A1904 " ideal model delta sigma weight residual 1.331 1.455 -0.124 2.00e-02 2.50e+03 3.87e+01 bond pdb=" C04 C9F A1909 " pdb=" N03 C9F A1909 " ideal model delta sigma weight residual 1.414 1.531 -0.117 2.00e-02 2.50e+03 3.42e+01 bond pdb=" C ALA F 665 " pdb=" N PRO F 666 " ideal model delta sigma weight residual 1.334 1.207 0.127 2.34e-02 1.83e+03 2.95e+01 ... (remaining 22461 not shown) Histogram of bond angle deviations from ideal: 96.81 - 105.14: 463 105.14 - 113.47: 12283 113.47 - 121.80: 13139 121.80 - 130.13: 4401 130.13 - 138.46: 141 Bond angle restraints: 30427 Sorted by residual: angle pdb=" N HIS F 867 " pdb=" CA HIS F 867 " pdb=" C HIS F 867 " ideal model delta sigma weight residual 111.28 122.20 -10.92 1.09e+00 8.42e-01 1.00e+02 angle pdb=" N LYS F 478 " pdb=" CA LYS F 478 " pdb=" C LYS F 478 " ideal model delta sigma weight residual 111.28 121.92 -10.64 1.09e+00 8.42e-01 9.53e+01 angle pdb=" N SER E 181 " pdb=" CA SER E 181 " pdb=" C SER E 181 " ideal model delta sigma weight residual 111.28 121.14 -9.86 1.09e+00 8.42e-01 8.18e+01 angle pdb=" N LYS F 991 " pdb=" CA LYS F 991 " pdb=" C LYS F 991 " ideal model delta sigma weight residual 111.28 120.02 -8.74 1.09e+00 8.42e-01 6.42e+01 angle pdb=" N ASN F 325 " pdb=" CA ASN F 325 " pdb=" C ASN F 325 " ideal model delta sigma weight residual 111.71 120.82 -9.11 1.15e+00 7.56e-01 6.28e+01 ... (remaining 30422 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.40: 13114 27.40 - 54.80: 572 54.80 - 82.20: 84 82.20 - 109.60: 26 109.60 - 136.99: 18 Dihedral angle restraints: 13814 sinusoidal: 5915 harmonic: 7899 Sorted by residual: dihedral pdb=" CB CYS F 406 " pdb=" SG CYS F 406 " pdb=" SG CYS F1074 " pdb=" CB CYS F1074 " ideal model delta sinusoidal sigma weight residual -86.00 0.15 -86.15 1 1.00e+01 1.00e-02 8.96e+01 dihedral pdb=" CB CYS F 907 " pdb=" SG CYS F 907 " pdb=" SG CYS F 977 " pdb=" CB CYS F 977 " ideal model delta sinusoidal sigma weight residual 93.00 174.00 -81.00 1 1.00e+01 1.00e-02 8.10e+01 dihedral pdb=" CB CYS F 844 " pdb=" SG CYS F 844 " pdb=" SG CYS F 853 " pdb=" CB CYS F 853 " ideal model delta sinusoidal sigma weight residual -86.00 -162.03 76.03 1 1.00e+01 1.00e-02 7.28e+01 ... (remaining 13811 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.765: 3480 0.765 - 1.530: 3 1.530 - 2.295: 0 2.295 - 3.059: 1 3.059 - 3.824: 1 Chirality restraints: 3485 Sorted by residual: chirality pdb=" C1 NAG L 3 " pdb=" O3 NAG L 2 " pdb=" C2 NAG L 3 " pdb=" O5 NAG L 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.76 -0.64 2.00e-02 2.50e+03 1.04e+03 chirality pdb=" C1 NAG F1121 " pdb=" ND2 ASN F 784 " pdb=" C2 NAG F1121 " pdb=" O5 NAG F1121 " both_signs ideal model delta sigma weight residual False -2.40 1.42 -3.82 2.00e-01 2.50e+01 3.66e+02 chirality pdb=" C1 NAG D 2 " pdb=" O3 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.68 0.28 2.00e-02 2.50e+03 1.91e+02 ... (remaining 3482 not shown) Planarity restraints: 3819 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG L 1 " 0.347 2.00e-02 2.50e+03 3.00e-01 1.13e+03 pdb=" C7 NAG L 1 " -0.081 2.00e-02 2.50e+03 pdb=" C8 NAG L 1 " 0.104 2.00e-02 2.50e+03 pdb=" N2 NAG L 1 " -0.534 2.00e-02 2.50e+03 pdb=" O7 NAG L 1 " 0.165 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " -0.344 2.00e-02 2.50e+03 2.99e-01 1.11e+03 pdb=" C7 NAG D 1 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " -0.116 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " 0.533 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " -0.153 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F1105 " -0.315 2.00e-02 2.50e+03 2.66e-01 8.87e+02 pdb=" C7 NAG F1105 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG F1105 " -0.186 2.00e-02 2.50e+03 pdb=" N2 NAG F1105 " 0.461 2.00e-02 2.50e+03 pdb=" O7 NAG F1105 " -0.042 2.00e-02 2.50e+03 ... (remaining 3816 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.37: 58 2.37 - 3.00: 11685 3.00 - 3.64: 31750 3.64 - 4.27: 49672 4.27 - 4.90: 81017 Nonbonded interactions: 174182 Sorted by model distance: nonbonded pdb=" SG CYS A1079 " pdb=" CD1 LEU A1081 " model vdw 1.739 3.820 nonbonded pdb=" ND2 ASN A 38 " pdb=" CD PRO A 39 " model vdw 1.865 3.520 nonbonded pdb=" O ASN F 480 " pdb=" ND2 ASN F 480 " model vdw 1.921 2.520 nonbonded pdb=" O TYR A1334 " pdb=" O CYS A1352 " model vdw 2.033 3.040 nonbonded pdb=" OD1 ASN F 891 " pdb=" O5 NAG F1108 " model vdw 2.082 3.040 ... (remaining 174177 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 'D' selection = chain 'G' selection = chain 'J' selection = chain 'K' } ncs_group { reference = (chain 'H' and resid 1 through 2) selection = (chain 'I' and resid 1 through 2) selection = (chain 'L' and resid 1 through 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=0.50 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: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 8.250 Check model and map are aligned: 0.310 Set scattering table: 0.220 Process input model: 63.380 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.150 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: 0.000 Load rotamer database and sin/cos tables:11.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.154 22466 Z= 0.964 Angle : 1.481 15.224 30427 Z= 0.844 Chirality : 0.121 3.824 3485 Planarity : 0.014 0.300 3805 Dihedral : 16.402 136.994 8665 Min Nonbonded Distance : 1.739 Molprobity Statistics. All-atom Clashscore : 21.16 Ramachandran Plot: Outliers : 0.41 % Allowed : 8.50 % Favored : 91.08 % Rotamer: Outliers : 4.38 % Allowed : 7.41 % Favored : 88.21 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 1.82 % 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: -4.25 (0.14), residues: 2659 helix: -3.32 (0.11), residues: 1269 sheet: -1.70 (0.32), residues: 237 loop : -2.27 (0.17), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.005 TRP A 265 HIS 0.023 0.003 HIS A 274 PHE 0.043 0.004 PHE F 663 TYR 0.060 0.005 TYR F 762 ARG 0.021 0.002 ARG F 275 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5318 Ramachandran restraints generated. 2659 Oldfield, 0 Emsley, 2659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5318 Ramachandran restraints generated. 2659 Oldfield, 0 Emsley, 2659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 2378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 491 time to evaluate : 2.555 Fit side-chains revert: symmetry clash 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