Starting phenix.real_space_refine (version: 1.21rc1) on Fri May 5 06:34:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ar8_11876/05_2023/7ar8_11876_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ar8_11876/05_2023/7ar8_11876.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ar8_11876/05_2023/7ar8_11876_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ar8_11876/05_2023/7ar8_11876_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ar8_11876/05_2023/7ar8_11876_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ar8_11876/05_2023/7ar8_11876.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ar8_11876/05_2023/7ar8_11876.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ar8_11876/05_2023/7ar8_11876_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ar8_11876/05_2023/7ar8_11876_updated.pdb" } resolution = 3.53 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.001 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: 7 Type Number sf(0) Gaussians Fe 29 7.16 5 Zn 2 6.06 5 P 14 5.49 5 S 420 5.16 5 C 39719 2.51 5 N 10271 2.21 5 O 11006 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 74": "OD1" <-> "OD2" Residue "B ASP 211": "OD1" <-> "OD2" Residue "C ASP 36": "OD1" <-> "OD2" Residue "C ASP 58": "OD1" <-> "OD2" Residue "C GLU 112": "OE1" <-> "OE2" Residue "C TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 158": "OD1" <-> "OD2" Residue "C ASP 159": "OD1" <-> "OD2" Residue "C GLU 174": "OE1" <-> "OE2" Residue "C ASP 179": "OD1" <-> "OD2" Residue "C GLU 185": "OE1" <-> "OE2" Residue "D ASP 205": "OD1" <-> "OD2" Residue "D ASP 240": "OD1" <-> "OD2" Residue "D ASP 367": "OD1" <-> "OD2" Residue "E ASP 161": "OD1" <-> "OD2" Residue "E PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 185": "OD1" <-> "OD2" Residue "E TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 102": "OE1" <-> "OE2" Residue "F GLU 144": "OE1" <-> "OE2" Residue "F ASP 150": "OD1" <-> "OD2" Residue "F TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 123": "OE1" <-> "OE2" Residue "G ASP 169": "OD1" <-> "OD2" Residue "G ASP 204": "OD1" <-> "OD2" Residue "G GLU 326": "OE1" <-> "OE2" Residue "G ASP 389": "OD1" <-> "OD2" Residue "G GLU 435": "OE1" <-> "OE2" Residue "G TYR 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 599": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 649": "OD1" <-> "OD2" Residue "G TYR 670": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 169": "OE1" <-> "OE2" Residue "H TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 219": "OE1" <-> "OE2" Residue "H PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 89": "OD1" <-> "OD2" Residue "I GLU 143": "OE1" <-> "OE2" Residue "I TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 156": "OD1" <-> "OD2" Residue "I GLU 218": "OE1" <-> "OE2" Residue "K TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 55": "OD1" <-> "OD2" Residue "K PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 71": "OD1" <-> "OD2" Residue "L TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 70": "OE1" <-> "OE2" Residue "M PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 210": "OE1" <-> "OE2" Residue "M GLU 243": "OE1" <-> "OE2" Residue "M PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 22": "OE1" <-> "OE2" Residue "N ASP 90": "OD1" <-> "OD2" Residue "N GLU 170": "OE1" <-> "OE2" Residue "N PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 376": "OD1" <-> "OD2" Residue "N GLU 459": "OE1" <-> "OE2" Residue "O ASP 79": "OD1" <-> "OD2" Residue "O GLU 101": "OE1" <-> "OE2" Residue "O GLU 152": "OE1" <-> "OE2" Residue "P GLU 148": "OE1" <-> "OE2" Residue "P GLU 226": "OE1" <-> "OE2" Residue "P TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 112": "OE1" <-> "OE2" Residue "Q GLU 119": "OE1" <-> "OE2" Residue "T GLU 96": "OE1" <-> "OE2" Residue "T GLU 113": "OE1" <-> "OE2" Residue "U ASP 46": "OD1" <-> "OD2" Residue "U PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 94": "OE1" <-> "OE2" Residue "U PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 100": "OE1" <-> "OE2" Residue "V PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 116": "OE1" <-> "OE2" Residue "W PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 47": "OE1" <-> "OE2" Residue "X GLU 74": "OE1" <-> "OE2" Residue "X TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 90": "OD1" <-> "OD2" Residue "Z GLU 93": "OE1" <-> "OE2" Residue "Z ASP 94": "OD1" <-> "OD2" Residue "Z GLU 95": "OE1" <-> "OE2" Residue "Z GLU 100": "OE1" <-> "OE2" Residue "Z TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 106": "OE1" <-> "OE2" Residue "a GLU 7": "OE1" <-> "OE2" Residue "a TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 43": "OD1" <-> "OD2" Residue "c GLU 85": "OE1" <-> "OE2" Residue "d ASP 59": "OD1" <-> "OD2" Residue "d ASP 61": "OD1" <-> "OD2" Residue "d GLU 72": "OE1" <-> "OE2" Residue "g GLU 38": "OE1" <-> "OE2" Residue "g GLU 60": "OE1" <-> "OE2" Residue "i GLU 17": "OE1" <-> "OE2" Residue "i GLU 20": "OE1" <-> "OE2" Residue "j TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 15": "OE1" <-> "OE2" Residue "o TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 11": "OE1" <-> "OE2" Residue "p PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ASP 19": "OD1" <-> "OD2" Residue "p ASP 26": "OD1" <-> "OD2" Residue "p GLU 53": "OE1" <-> "OE2" Residue "p TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ASP 79": "OD1" <-> "OD2" Residue "x PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y GLU 226": "OE1" <-> "OE2" Residue "y GLU 251": "OE1" <-> "OE2" Residue "z TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 61461 Number of models: 1 Model: "" Number of chains: 64 Chain: "A" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 785 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 3, 'TRANS': 88} Chain breaks: 1 Chain: "B" Number of atoms: 1244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1244 Classifications: {'peptide': 157} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 146} Chain: "C" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1581 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 9, 'TRANS': 175} Chain: "D" Number of atoms: 3077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3077 Classifications: {'peptide': 385} Link IDs: {'PTRANS': 17, 'TRANS': 367} Chain: "E" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1500 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 12, 'TRANS': 179} Chain: "F" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3368 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 21, 'TRANS': 412} Chain: "G" Number of atoms: 5252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5252 Classifications: {'peptide': 688} Link IDs: {'PTRANS': 35, 'TRANS': 652} Chain: "H" Number of atoms: 2536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2536 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 18, 'TRANS': 305} Chain: "I" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1381 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 8, 'TRANS': 160} Chain: "J" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1093 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 3, 'TRANS': 134} Chain breaks: 1 Chain: "K" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 707 Classifications: {'peptide': 90} Link IDs: {'TRANS': 89} Chain: "L" Number of atoms: 4807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4807 Classifications: {'peptide': 615} Link IDs: {'PTRANS': 20, 'TRANS': 594} Chain: "M" Number of atoms: 3887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3887 Classifications: {'peptide': 487} Link IDs: {'PTRANS': 17, 'TRANS': 469} Chain: "N" Number of atoms: 3820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3820 Classifications: {'peptide': 488} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 471} Chain: "O" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 956 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 6, 'TRANS': 115} Chain: "P" Number of atoms: 2560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2560 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 21, 'TRANS': 310} Chain: "Q" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 939 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 8, 'TRANS': 110} Chain: "R" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 482 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 6, 'TRANS': 55} Chain: "S" Number of atoms: 727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 727 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain: "T" Number of atoms: 667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 667 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 5, 'TRANS': 78} Chain: "U" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 616 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "V" Number of atoms: 1123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1123 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 10, 'TRANS': 129} Chain: "W" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 893 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain breaks: 1 Chain: "X" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 767 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 6, 'TRANS': 90} Chain: "Z" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 990 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 10, 'TRANS': 113} Chain: "a" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 469 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "b" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 288 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 3, 'TRANS': 35} Chain: "c" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 595 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 7, 'TRANS': 65} Chain: "d" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 574 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "e" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 546 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 1, 'TRANS': 62} Chain: "f" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 734 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "g" Number of atoms: 615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 615 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 7, 'TRANS': 67} Chain: "i" Number of atoms: 721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 721 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "j" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 415 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "k" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 374 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "l" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 384 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 4, 'TRANS': 45} Chain: "m" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "n" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 911 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 7, 'TRANS': 101} Chain: "o" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 631 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "p" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 778 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain: "q" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 536 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "r" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 88 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "u" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 150 Classifications: {'peptide': 30} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'TRANS': 29} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'UNK:plan-1': 30} Unresolved non-hydrogen planarities: 30 Chain: "v" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 226 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "x" Number of atoms: 1637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1637 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 14, 'TRANS': 196} Chain: "y" Number of atoms: 2001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2001 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 9, 'TRANS': 253} Chain: "z" Number of atoms: 1763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1763 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 225} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Unusual residues: {'FES': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 85 Unusual residues: {'PTY': 1, 'UQ9': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'UQ9:plan-8': 1, 'UQ9:plan-9': 1, 'UQ9:plan-10': 1, 'UQ9:plan-7': 1, 'UQ9:plan-2': 1} Unresolved non-hydrogen planarities: 23 Chain: "I" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'PC7': 1, 'PTY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'PGT': 1, 'PTY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'LMN': 1} Classifications: {'undetermined': 1} Chain: "n" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Chain: "v" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PC7': 1} Classifications: {'undetermined': 1} Chain: "y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "z" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'PSF': 1, 'T7X': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1538 SG CYS B 158 71.669 91.878 100.906 1.00 34.25 S ATOM 1038 SG CYS B 94 73.127 90.421 94.358 1.00 29.73 S ATOM 1768 SG CYS B 188 70.975 86.321 98.702 1.00 39.14 S ATOM 1032 SG CYS B 93 76.333 88.301 97.592 1.00 15.62 S ATOM 7523 SG CYS E 135 36.568 26.070 124.140 1.00 99.60 S ATOM 7796 SG CYS E 171 36.554 27.579 129.763 1.00106.96 S ATOM 10912 SG CYS F 405 50.973 49.459 133.719 1.00 47.51 S ATOM 10932 SG CYS F 408 49.161 45.440 130.763 1.00 34.27 S ATOM 10893 SG CYS F 402 44.306 47.591 134.501 1.00 31.97 S ATOM 11257 SG CYS F 448 48.785 44.238 137.001 1.00 24.66 S ATOM 11933 SG CYS G 106 51.693 59.849 136.600 1.00 47.51 S ATOM 12017 SG CYS G 117 52.923 59.007 133.627 1.00 47.51 S ATOM 12042 SG CYS G 120 57.308 58.718 138.495 1.00 47.51 S ATOM 12144 SG CYS G 134 54.175 59.158 140.144 1.00 28.85 S ATOM 12478 SG CYS G 179 53.339 67.253 123.223 1.00 30.26 S ATOM 12417 SG CYS G 170 54.172 66.215 116.632 1.00 47.51 S ATOM 12438 SG CYS G 173 48.824 68.943 119.239 1.00 47.51 S ATOM 12830 SG CYS G 224 41.064 64.293 131.399 1.00 37.89 S ATOM 12783 SG CYS G 218 43.687 61.468 126.411 1.00 38.93 S ATOM 12806 SG CYS G 221 47.512 62.767 131.480 1.00 47.51 S ATOM 13151 SG CYS G 268 45.603 67.161 127.530 1.00 32.51 S ATOM 20279 SG CYS I 168 60.717 78.626 101.523 1.00 47.51 S ATOM 20232 SG CYS I 162 62.768 84.107 99.579 1.00 47.51 S ATOM 20258 SG CYS I 165 66.756 80.225 102.925 1.00 39.24 S ATOM 20000 SG CYS I 133 62.476 83.531 105.882 1.00 45.18 S ATOM 20308 SG CYS I 172 55.972 73.912 103.553 1.00 40.93 S ATOM 19931 SG CYS I 123 49.993 76.996 104.667 1.00 47.51 S ATOM 19973 SG CYS I 129 56.034 78.766 106.175 1.00 47.51 S ATOM 19950 SG CYS I 126 53.951 73.727 109.111 1.00 47.51 S ATOM 35451 SG CYS O 91 125.544 147.077 112.188 1.00 69.90 S ATOM 35477 SG CYS O 95 121.982 145.169 113.836 1.00 77.18 S ATOM 39683 SG CYS R 72 43.635 60.822 103.331 1.00 39.81 S ATOM 39869 SG CYS R 97 43.361 63.576 106.074 1.00 32.48 S ATOM 39896 SG CYS R 100 44.889 64.387 102.568 1.00 35.75 S Time building chain proxies: 24.20, per 1000 atoms: 0.39 Number of scatterers: 61461 At special positions: 0 Unit cell: (216.783, 261.144, 192.51, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 Fe 29 26.01 S 420 16.00 P 14 15.00 O 11006 8.00 N 10271 7.00 C 39719 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS E 174 " - pdb=" SG CYS F 148 " distance=2.03 Simple disulfide: pdb=" SG CYS N 336 " - pdb=" SG CYS N 420 " distance=2.03 Simple disulfide: pdb=" SG CYS X 29 " - pdb=" SG CYS X 59 " distance=2.04 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=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 20.26 Conformation dependent library (CDL) restraints added in 7.5 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 500 " pdb="FE1 FES E 500 " - pdb=" SG CYS E 135 " pdb="FE2 FES E 500 " - pdb=" SG CYS E 171 " pdb=" FES G 801 " pdb="FE2 FES G 801 " - pdb=" SG CYS G 120 " pdb="FE1 FES G 801 " - pdb=" SG CYS G 106 " pdb="FE2 FES G 801 " - pdb=" SG CYS G 134 " pdb="FE1 FES G 801 " - pdb=" SG CYS G 117 " pdb=" SF4 B 500 " pdb="FE4 SF4 B 500 " - pdb=" SG CYS B 93 " pdb="FE1 SF4 B 500 " - pdb=" SG CYS B 158 " pdb="FE3 SF4 B 500 " - pdb=" SG CYS B 188 " pdb="FE2 SF4 B 500 " - pdb=" SG CYS B 94 " pdb=" SF4 F 501 " pdb="FE4 SF4 F 501 " - pdb=" SG CYS F 448 " pdb="FE1 SF4 F 501 " - pdb=" SG CYS F 405 " pdb="FE3 SF4 F 501 " - pdb=" SG CYS F 402 " pdb="FE2 SF4 F 501 " - pdb=" SG CYS F 408 " pdb=" SF4 G 802 " pdb="FE2 SF4 G 802 " - pdb=" NE2 HIS G 166 " pdb="FE1 SF4 G 802 " - pdb=" SG CYS G 179 " pdb="FE4 SF4 G 802 " - pdb=" SG CYS G 173 " pdb="FE3 SF4 G 802 " - pdb=" SG CYS G 170 " pdb=" SF4 G 803 " pdb="FE2 SF4 G 803 " - pdb=" SG CYS G 218 " pdb="FE4 SF4 G 803 " - pdb=" SG CYS G 268 " pdb="FE3 SF4 G 803 " - pdb=" SG CYS G 221 " pdb="FE1 SF4 G 803 " - pdb=" SG CYS G 224 " pdb=" SF4 I 500 " pdb="FE2 SF4 I 500 " - pdb=" SG CYS I 162 " pdb="FE4 SF4 I 500 " - pdb=" SG CYS I 133 " pdb="FE1 SF4 I 500 " - pdb=" SG CYS I 168 " pdb="FE3 SF4 I 500 " - pdb=" SG CYS I 165 " pdb=" SF4 I 501 " pdb="FE1 SF4 I 501 " - pdb=" SG CYS I 172 " pdb="FE4 SF4 I 501 " - pdb=" SG CYS I 126 " pdb="FE2 SF4 I 501 " - pdb=" SG CYS I 123 " pdb="FE3 SF4 I 501 " - pdb=" SG CYS I 129 " Number of angles added : 77 Zn2+ tetrahedral coordination pdb=" ZN R 200 " pdb="ZN ZN R 200 " - pdb=" NE2 HIS R 82 " pdb="ZN ZN R 200 " - pdb=" SG CYS R 72 " pdb="ZN ZN R 200 " - pdb=" SG CYS R 100 " pdb="ZN ZN R 200 " - pdb=" SG CYS R 97 " pdb=" ZN y 300 " pdb="ZN ZN y 300 " - pdb=" NE2 HIS y 135 " pdb="ZN ZN y 300 " - pdb=" NE2 HIS z 130 " pdb="ZN ZN y 300 " - pdb=" ND1 HIS y 107 " Number of angles added : 3 15156 Ramachandran restraints generated. 7578 Oldfield, 0 Emsley, 7578 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14274 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 298 helices and 37 sheets defined 48.5% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.71 Creating SS restraints... Processing helix chain 'A' and resid 2 through 4 No H-bonds generated for 'chain 'A' and resid 2 through 4' Processing helix chain 'A' and resid 6 through 28 removed outlier: 3.542A pdb=" N LEU A 23 " --> pdb=" O SER A 19 " (cutoff:3.500A) Proline residue: A 26 - end of helix Processing helix chain 'A' and resid 60 through 83 Proline residue: A 80 - end of helix Processing helix chain 'A' and resid 92 through 112 removed outlier: 3.557A pdb=" N PHE A 99 " --> pdb=" O SER A 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 82 Processing helix chain 'B' and resid 93 through 101 removed outlier: 3.599A pdb=" N GLU B 97 " --> pdb=" O CYS B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 111 Processing helix chain 'B' and resid 136 through 145 Processing helix chain 'B' and resid 192 through 208 removed outlier: 3.724A pdb=" N ARG B 208 " --> pdb=" O LYS B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 217 Processing helix chain 'C' and resid 3 through 12 Processing helix chain 'C' and resid 38 through 47 Processing helix chain 'C' and resid 106 through 118 removed outlier: 3.737A pdb=" N TRP C 110 " --> pdb=" O SER C 107 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLU C 112 " --> pdb=" O GLY C 109 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET C 118 " --> pdb=" O VAL C 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 22 No H-bonds generated for 'chain 'D' and resid 20 through 22' Processing helix chain 'D' and resid 51 through 57 removed outlier: 4.222A pdb=" N GLU D 56 " --> pdb=" O GLU D 52 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N TYR D 57 " --> pdb=" O LYS D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 69 removed outlier: 3.820A pdb=" N ASP D 68 " --> pdb=" O LEU D 64 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG D 69 " --> pdb=" O PRO D 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 64 through 69' Processing helix chain 'D' and resid 75 through 90 removed outlier: 3.535A pdb=" N HIS D 80 " --> pdb=" O MET D 76 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ALA D 81 " --> pdb=" O ALA D 77 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR D 82 " --> pdb=" O GLN D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 125 Processing helix chain 'D' and resid 129 through 148 removed outlier: 3.606A pdb=" N TRP D 133 " --> pdb=" O THR D 129 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LYS D 140 " --> pdb=" O GLU D 136 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU D 141 " --> pdb=" O GLU D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 191 removed outlier: 3.917A pdb=" N GLN D 181 " --> pdb=" O SER D 177 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ALA D 183 " --> pdb=" O THR D 179 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N SER D 184 " --> pdb=" O GLN D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 203 Processing helix chain 'D' and resid 211 through 217 Processing helix chain 'D' and resid 222 through 227 removed outlier: 3.724A pdb=" N SER D 227 " --> pdb=" O MET D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 236 No H-bonds generated for 'chain 'D' and resid 233 through 236' Processing helix chain 'D' and resid 257 through 280 Processing helix chain 'D' and resid 306 through 316 Processing helix chain 'D' and resid 358 through 369 removed outlier: 3.511A pdb=" N HIS D 362 " --> pdb=" O PRO D 358 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU D 366 " --> pdb=" O HIS D 362 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ASP D 367 " --> pdb=" O SER D 363 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N PHE D 368 " --> pdb=" O GLN D 364 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET D 369 " --> pdb=" O GLY D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 385 removed outlier: 4.146A pdb=" N THR D 380 " --> pdb=" O ALA D 376 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE D 381 " --> pdb=" O ASP D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 392 No H-bonds generated for 'chain 'D' and resid 389 through 392' Processing helix chain 'E' and resid 53 through 61 Processing helix chain 'E' and resid 66 through 84 removed outlier: 3.569A pdb=" N LYS E 69 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N GLN E 70 " --> pdb=" O ASN E 67 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA E 72 " --> pdb=" O LYS E 69 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ILE E 74 " --> pdb=" O SER E 71 " (cutoff:3.500A) Proline residue: E 75 - end of helix Processing helix chain 'E' and resid 90 through 100 Processing helix chain 'E' and resid 104 through 113 removed outlier: 3.857A pdb=" N VAL E 110 " --> pdb=" O ARG E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 138 No H-bonds generated for 'chain 'E' and resid 136 through 138' Processing helix chain 'E' and resid 140 through 149 removed outlier: 3.705A pdb=" N GLU E 144 " --> pdb=" O ARG E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 215 removed outlier: 3.591A pdb=" N VAL E 207 " --> pdb=" O PRO E 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 82 Processing helix chain 'F' and resid 88 through 93 Processing helix chain 'F' and resid 97 through 106 Processing helix chain 'F' and resid 118 through 124 removed outlier: 3.540A pdb=" N PHE F 124 " --> pdb=" O LEU F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 151 through 156 Processing helix chain 'F' and resid 158 through 171 removed outlier: 3.548A pdb=" N LEU F 166 " --> pdb=" O LEU F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 202 Processing helix chain 'F' and resid 209 through 211 No H-bonds generated for 'chain 'F' and resid 209 through 211' Processing helix chain 'F' and resid 227 through 230 Processing helix chain 'F' and resid 234 through 239 Processing helix chain 'F' and resid 258 through 260 No H-bonds generated for 'chain 'F' and resid 258 through 260' Processing helix chain 'F' and resid 268 through 272 Processing helix chain 'F' and resid 275 through 278 No H-bonds generated for 'chain 'F' and resid 275 through 278' Processing helix chain 'F' and resid 283 through 286 No H-bonds generated for 'chain 'F' and resid 283 through 286' Processing helix chain 'F' and resid 319 through 325 Processing helix chain 'F' and resid 352 through 355 No H-bonds generated for 'chain 'F' and resid 352 through 355' Processing helix chain 'F' and resid 362 through 368 Processing helix chain 'F' and resid 386 through 399 Processing helix chain 'F' and resid 406 through 423 removed outlier: 4.462A pdb=" N GLY F 413 " --> pdb=" O ARG F 409 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TRP F 416 " --> pdb=" O THR F 412 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 442 Processing helix chain 'F' and resid 450 through 464 Proline residue: F 457 - end of helix Processing helix chain 'F' and resid 466 through 482 Processing helix chain 'G' and resid 60 through 62 No H-bonds generated for 'chain 'G' and resid 60 through 62' Processing helix chain 'G' and resid 91 through 98 Processing helix chain 'G' and resid 149 through 164 Processing helix chain 'G' and resid 180 through 187 Processing helix chain 'G' and resid 215 through 217 No H-bonds generated for 'chain 'G' and resid 215 through 217' Processing helix chain 'G' and resid 223 through 230 Processing helix chain 'G' and resid 261 through 267 removed outlier: 3.748A pdb=" N VAL G 264 " --> pdb=" O SER G 261 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE G 267 " --> pdb=" O VAL G 264 " (cutoff:3.500A) Processing helix chain 'G' and resid 330 through 333 No H-bonds generated for 'chain 'G' and resid 330 through 333' Processing helix chain 'G' and resid 361 through 371 Processing helix chain 'G' and resid 390 through 403 removed outlier: 3.836A pdb=" N MET G 403 " --> pdb=" O PHE G 399 " (cutoff:3.500A) Processing helix chain 'G' and resid 432 through 436 removed outlier: 3.573A pdb=" N GLU G 435 " --> pdb=" O SER G 432 " (cutoff:3.500A) Processing helix chain 'G' and resid 452 through 465 removed outlier: 3.529A pdb=" N ARG G 457 " --> pdb=" O MET G 453 " (cutoff:3.500A) Processing helix chain 'G' and resid 489 through 496 Processing helix chain 'G' and resid 501 through 507 Processing helix chain 'G' and resid 518 through 522 removed outlier: 3.887A pdb=" N ASN G 522 " --> pdb=" O GLY G 519 " (cutoff:3.500A) Processing helix chain 'G' and resid 526 through 540 Processing helix chain 'G' and resid 557 through 565 removed outlier: 4.742A pdb=" N ALA G 561 " --> pdb=" O ALA G 557 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA G 562 " --> pdb=" O ALA G 558 " (cutoff:3.500A) Processing helix chain 'G' and resid 653 through 664 Processing helix chain 'G' and resid 673 through 682 removed outlier: 3.785A pdb=" N SER G 682 " --> pdb=" O SER G 678 " (cutoff:3.500A) Processing helix chain 'G' and resid 685 through 688 removed outlier: 3.644A pdb=" N VAL G 688 " --> pdb=" O PRO G 685 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 685 through 688' Processing helix chain 'G' and resid 727 through 730 No H-bonds generated for 'chain 'G' and resid 727 through 730' Processing helix chain 'G' and resid 733 through 740 removed outlier: 4.262A pdb=" N ALA G 740 " --> pdb=" O ALA G 736 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 34 Proline residue: H 15 - end of helix removed outlier: 3.664A pdb=" N LEU H 25 " --> pdb=" O ALA H 21 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA H 32 " --> pdb=" O ARG H 28 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL H 34 " --> pdb=" O VAL H 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 59 Processing helix chain 'H' and resid 73 through 90 Proline residue: H 78 - end of helix removed outlier: 3.903A pdb=" N ALA H 88 " --> pdb=" O LEU H 84 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N TRP H 89 " --> pdb=" O SER H 85 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ALA H 90 " --> pdb=" O LEU H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 121 removed outlier: 4.869A pdb=" N VAL H 118 " --> pdb=" O SER H 114 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N TYR H 119 " --> pdb=" O SER H 115 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N GLY H 120 " --> pdb=" O LEU H 116 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE H 121 " --> pdb=" O GLY H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 123 through 127 Processing helix chain 'H' and resid 131 through 162 removed outlier: 4.031A pdb=" N VAL H 149 " --> pdb=" O VAL H 145 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N SER H 150 " --> pdb=" O SER H 146 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N CYS H 161 " --> pdb=" O THR H 157 " (cutoff:3.500A) Processing helix chain 'H' and resid 167 through 174 removed outlier: 3.746A pdb=" N VAL H 171 " --> pdb=" O LEU H 167 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET H 172 " --> pdb=" O SER H 168 " (cutoff:3.500A) Processing helix chain 'H' and resid 179 through 182 No H-bonds generated for 'chain 'H' and resid 179 through 182' Processing helix chain 'H' and resid 184 through 197 Processing helix chain 'H' and resid 201 through 203 No H-bonds generated for 'chain 'H' and resid 201 through 203' Processing helix chain 'H' and resid 205 through 207 No H-bonds generated for 'chain 'H' and resid 205 through 207' Processing helix chain 'H' and resid 222 through 246 Processing helix chain 'H' and resid 260 through 262 No H-bonds generated for 'chain 'H' and resid 260 through 262' Processing helix chain 'H' and resid 266 through 284 removed outlier: 3.637A pdb=" N SER H 270 " --> pdb=" O SER H 266 " (cutoff:3.500A) Processing helix chain 'H' and resid 292 through 301 Processing helix chain 'H' and resid 304 through 320 Processing helix chain 'I' and resid 62 through 72 Processing helix chain 'I' and resid 74 through 84 removed outlier: 3.884A pdb=" N GLY I 79 " --> pdb=" O GLU I 75 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU I 84 " --> pdb=" O LEU I 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 128 through 132 Processing helix chain 'I' and resid 167 through 171 Processing helix chain 'I' and resid 190 through 193 No H-bonds generated for 'chain 'I' and resid 190 through 193' Processing helix chain 'I' and resid 197 through 206 Processing helix chain 'I' and resid 208 through 219 removed outlier: 3.965A pdb=" N GLU I 213 " --> pdb=" O THR I 209 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 17 Processing helix chain 'J' and resid 23 through 44 removed outlier: 3.546A pdb=" N PHE J 34 " --> pdb=" O PHE J 30 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLY J 39 " --> pdb=" O CYS J 35 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU J 40 " --> pdb=" O ASP J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 48 through 56 removed outlier: 3.590A pdb=" N LEU J 54 " --> pdb=" O ALA J 50 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 70 Processing helix chain 'J' and resid 136 through 144 removed outlier: 4.680A pdb=" N LEU J 143 " --> pdb=" O THR J 139 " (cutoff:3.500A) Processing helix chain 'J' and resid 149 through 168 removed outlier: 3.809A pdb=" N ILE J 167 " --> pdb=" O MET J 163 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 22 removed outlier: 3.766A pdb=" N PHE K 9 " --> pdb=" O LYS K 5 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 53 removed outlier: 4.074A pdb=" N ILE K 35 " --> pdb=" O MET K 31 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU K 36 " --> pdb=" O LEU K 32 " (cutoff:3.500A) Processing helix chain 'K' and resid 58 through 84 removed outlier: 3.670A pdb=" N LEU K 66 " --> pdb=" O ALA K 62 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N THR K 67 " --> pdb=" O LEU K 63 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL K 68 " --> pdb=" O LEU K 64 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE K 84 " --> pdb=" O PHE K 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 18 removed outlier: 4.145A pdb=" N VAL L 6 " --> pdb=" O TYR L 2 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU L 8 " --> pdb=" O LEU L 4 " (cutoff:3.500A) Proline residue: L 9 - end of helix Processing helix chain 'L' and resid 27 through 50 removed outlier: 3.608A pdb=" N THR L 33 " --> pdb=" O ALA L 29 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR L 34 " --> pdb=" O ILE L 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 105 removed outlier: 3.671A pdb=" N VAL L 84 " --> pdb=" O SER L 80 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET L 85 " --> pdb=" O LEU L 81 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE L 101 " --> pdb=" O HIS L 97 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N SER L 102 " --> pdb=" O LEU L 98 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR L 103 " --> pdb=" O TYR L 99 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 129 Processing helix chain 'L' and resid 133 through 153 removed outlier: 4.074A pdb=" N GLY L 139 " --> pdb=" O GLN L 135 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY L 144 " --> pdb=" O TRP L 140 " (cutoff:3.500A) Processing helix chain 'L' and resid 158 through 189 removed outlier: 4.458A pdb=" N GLY L 177 " --> pdb=" O VAL L 173 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LEU L 178 " --> pdb=" O GLY L 174 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU L 183 " --> pdb=" O ALA L 179 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU L 188 " --> pdb=" O GLY L 184 " (cutoff:3.500A) Processing helix chain 'L' and resid 218 through 231 removed outlier: 3.674A pdb=" N GLY L 231 " --> pdb=" O ILE L 227 " (cutoff:3.500A) Processing helix chain 'L' and resid 240 through 244 removed outlier: 4.232A pdb=" N ASP L 244 " --> pdb=" O THR L 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 240 through 244' Processing helix chain 'L' and resid 250 through 256 removed outlier: 3.929A pdb=" N LEU L 255 " --> pdb=" O PRO L 251 " (cutoff:3.500A) Processing helix chain 'L' and resid 261 through 271 removed outlier: 4.010A pdb=" N GLY L 265 " --> pdb=" O VAL L 262 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL L 266 " --> pdb=" O THR L 263 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG L 271 " --> pdb=" O MET L 268 " (cutoff:3.500A) Processing helix chain 'L' and resid 273 through 276 No H-bonds generated for 'chain 'L' and resid 273 through 276' Processing helix chain 'L' and resid 280 through 300 removed outlier: 3.507A pdb=" N VAL L 285 " --> pdb=" O THR L 281 " (cutoff:3.500A) Processing helix chain 'L' and resid 307 through 327 removed outlier: 3.679A pdb=" N ILE L 311 " --> pdb=" O LEU L 307 " (cutoff:3.500A) Processing helix chain 'L' and resid 331 through 344 removed outlier: 3.621A pdb=" N PHE L 343 " --> pdb=" O MET L 339 " (cutoff:3.500A) Processing helix chain 'L' and resid 346 through 357 Processing helix chain 'L' and resid 372 through 374 No H-bonds generated for 'chain 'L' and resid 372 through 374' Processing helix chain 'L' and resid 377 through 390 Processing helix chain 'L' and resid 398 through 410 removed outlier: 4.391A pdb=" N VAL L 403 " --> pdb=" O TYR L 399 " (cutoff:3.500A) Processing helix chain 'L' and resid 414 through 440 removed outlier: 3.889A pdb=" N PHE L 418 " --> pdb=" O ILE L 414 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU L 428 " --> pdb=" O SER L 424 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE L 429 " --> pdb=" O VAL L 425 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE L 435 " --> pdb=" O SER L 431 " (cutoff:3.500A) Processing helix chain 'L' and resid 450 through 454 removed outlier: 4.061A pdb=" N SER L 454 " --> pdb=" O GLY L 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 450 through 454' Processing helix chain 'L' and resid 461 through 485 Proline residue: L 466 - end of helix removed outlier: 3.701A pdb=" N LEU L 475 " --> pdb=" O ALA L 471 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE L 476 " --> pdb=" O LEU L 472 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLY L 478 " --> pdb=" O SER L 474 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N TYR L 479 " --> pdb=" O LEU L 475 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ASP L 483 " --> pdb=" O TYR L 479 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N MET L 484 " --> pdb=" O LEU L 480 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET L 485 " --> pdb=" O ALA L 481 " (cutoff:3.500A) Processing helix chain 'L' and resid 507 through 509 No H-bonds generated for 'chain 'L' and resid 507 through 509' Processing helix chain 'L' and resid 520 through 537 Processing helix chain 'L' and resid 553 through 560 removed outlier: 3.584A pdb=" N PHE L 559 " --> pdb=" O LEU L 555 " (cutoff:3.500A) Processing helix chain 'L' and resid 562 through 583 removed outlier: 5.739A pdb=" N ASP L 566 " --> pdb=" O TRP L 563 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL L 568 " --> pdb=" O PHE L 565 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N LEU L 569 " --> pdb=" O ASP L 566 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP L 571 " --> pdb=" O VAL L 568 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE L 572 " --> pdb=" O LEU L 569 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N VAL L 574 " --> pdb=" O ASP L 571 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ARG L 575 " --> pdb=" O PHE L 572 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER L 576 " --> pdb=" O LEU L 573 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY L 581 " --> pdb=" O LEU L 578 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLU L 583 " --> pdb=" O PHE L 580 " (cutoff:3.500A) Processing helix chain 'L' and resid 594 through 597 Processing helix chain 'L' and resid 605 through 607 No H-bonds generated for 'chain 'L' and resid 605 through 607' Processing helix chain 'L' and resid 611 through 613 No H-bonds generated for 'chain 'L' and resid 611 through 613' Processing helix chain 'M' and resid 12 through 28 Proline residue: M 19 - end of helix removed outlier: 3.843A pdb=" N PHE M 28 " --> pdb=" O ILE M 24 " (cutoff:3.500A) Processing helix chain 'M' and resid 34 through 57 removed outlier: 3.740A pdb=" N ARG M 38 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU M 39 " --> pdb=" O ARG M 35 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU M 55 " --> pdb=" O TYR M 51 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TRP M 56 " --> pdb=" O SER M 52 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE M 57 " --> pdb=" O LEU M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 90 through 107 removed outlier: 3.550A pdb=" N ILE M 101 " --> pdb=" O THR M 97 " (cutoff:3.500A) Proline residue: M 102 - end of helix Processing helix chain 'M' and resid 112 through 115 No H-bonds generated for 'chain 'M' and resid 112 through 115' Processing helix chain 'M' and resid 117 through 134 removed outlier: 3.516A pdb=" N ILE M 121 " --> pdb=" O GLU M 118 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA M 122 " --> pdb=" O TYR M 119 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE M 134 " --> pdb=" O ILE M 131 " (cutoff:3.500A) Processing helix chain 'M' and resid 139 through 159 removed outlier: 3.996A pdb=" N VAL M 149 " --> pdb=" O PHE M 145 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N LEU M 150 " --> pdb=" O PHE M 146 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N ILE M 151 " --> pdb=" O GLU M 147 " (cutoff:3.500A) Proline residue: M 152 - end of helix Processing helix chain 'M' and resid 164 through 195 removed outlier: 3.885A pdb=" N ILE M 167 " --> pdb=" O GLN M 164 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA M 170 " --> pdb=" O ILE M 167 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR M 171 " --> pdb=" O LYS M 168 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN M 172 " --> pdb=" O ALA M 169 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N TYR M 176 " --> pdb=" O PHE M 173 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU M 179 " --> pdb=" O TYR M 176 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU M 186 " --> pdb=" O PHE M 183 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE M 193 " --> pdb=" O LEU M 190 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR M 195 " --> pdb=" O LEU M 192 " (cutoff:3.500A) Processing helix chain 'M' and resid 200 through 205 removed outlier: 3.987A pdb=" N THR M 205 " --> pdb=" O GLN M 201 " (cutoff:3.500A) Processing helix chain 'M' and resid 210 through 227 removed outlier: 3.713A pdb=" N PHE M 215 " --> pdb=" O ARG M 211 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N SER M 223 " --> pdb=" O ALA M 219 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N VAL M 226 " --> pdb=" O ALA M 222 " (cutoff:3.500A) Processing helix chain 'M' and resid 235 through 239 removed outlier: 3.666A pdb=" N GLU M 239 " --> pdb=" O ILE M 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 235 through 239' Processing helix chain 'M' and resid 246 through 252 removed outlier: 4.678A pdb=" N ILE M 251 " --> pdb=" O ALA M 247 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU M 252 " --> pdb=" O GLY M 248 " (cutoff:3.500A) Processing helix chain 'M' and resid 258 through 267 removed outlier: 3.704A pdb=" N LEU M 265 " --> pdb=" O THR M 261 " (cutoff:3.500A) Processing helix chain 'M' and resid 273 through 278 removed outlier: 3.977A pdb=" N LEU M 277 " --> pdb=" O PRO M 273 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N CYS M 278 " --> pdb=" O GLU M 274 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 273 through 278' Processing helix chain 'M' and resid 280 through 299 removed outlier: 3.945A pdb=" N ILE M 289 " --> pdb=" O THR M 285 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE M 292 " --> pdb=" O ALA M 288 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER M 295 " --> pdb=" O ILE M 291 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU M 299 " --> pdb=" O SER M 295 " (cutoff:3.500A) Processing helix chain 'M' and resid 304 through 324 removed outlier: 4.108A pdb=" N ILE M 308 " --> pdb=" O LEU M 304 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE M 321 " --> pdb=" O ASN M 317 " (cutoff:3.500A) Processing helix chain 'M' and resid 328 through 359 removed outlier: 3.908A pdb=" N GLY M 332 " --> pdb=" O ILE M 328 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER M 346 " --> pdb=" O GLY M 342 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU M 355 " --> pdb=" O CYS M 351 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR M 356 " --> pdb=" O VAL M 352 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG M 358 " --> pdb=" O VAL M 354 " (cutoff:3.500A) Processing helix chain 'M' and resid 375 through 388 Processing helix chain 'M' and resid 395 through 410 removed outlier: 3.830A pdb=" N LEU M 402 " --> pdb=" O ILE M 398 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE M 403 " --> pdb=" O GLY M 399 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG M 410 " --> pdb=" O GLY M 406 " (cutoff:3.500A) Processing helix chain 'M' and resid 412 through 436 removed outlier: 3.657A pdb=" N THR M 416 " --> pdb=" O SER M 412 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N MET M 422 " --> pdb=" O ALA M 418 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA M 426 " --> pdb=" O MET M 422 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ALA M 427 " --> pdb=" O ILE M 423 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TYR M 428 " --> pdb=" O LEU M 424 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER M 429 " --> pdb=" O GLY M 425 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LEU M 430 " --> pdb=" O ALA M 426 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N TRP M 431 " --> pdb=" O ALA M 427 " (cutoff:3.500A) Processing helix chain 'M' and resid 454 through 472 removed outlier: 3.518A pdb=" N PHE M 460 " --> pdb=" O GLU M 456 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE M 461 " --> pdb=" O VAL M 457 " (cutoff:3.500A) Proline residue: M 462 - end of helix Processing helix chain 'M' and resid 475 through 489 removed outlier: 3.854A pdb=" N MET M 481 " --> pdb=" O PHE M 477 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N THR M 483 " --> pdb=" O ASP M 479 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N SER M 484 " --> pdb=" O CYS M 480 " (cutoff:3.500A) Processing helix chain 'N' and resid 14 through 17 Processing helix chain 'N' and resid 20 through 38 Processing helix chain 'N' and resid 52 through 71 Processing helix chain 'N' and resid 91 through 115 removed outlier: 3.538A pdb=" N PHE N 99 " --> pdb=" O PHE N 95 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU N 102 " --> pdb=" O ILE N 98 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N PHE N 112 " --> pdb=" O ILE N 108 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ASP N 113 " --> pdb=" O SER N 109 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N PHE N 114 " --> pdb=" O MET N 110 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N PHE N 115 " --> pdb=" O CYS N 111 " (cutoff:3.500A) Processing helix chain 'N' and resid 123 through 140 removed outlier: 3.595A pdb=" N ILE N 140 " --> pdb=" O LEU N 137 " (cutoff:3.500A) Processing helix chain 'N' and resid 147 through 163 removed outlier: 3.672A pdb=" N CYS N 158 " --> pdb=" O LEU N 154 " (cutoff:3.500A) Processing helix chain 'N' and resid 171 through 201 removed outlier: 3.822A pdb=" N SER N 200 " --> pdb=" O MET N 196 " (cutoff:3.500A) Processing helix chain 'N' and resid 206 through 209 No H-bonds generated for 'chain 'N' and resid 206 through 209' Processing helix chain 'N' and resid 224 through 241 Processing helix chain 'N' and resid 250 through 256 Processing helix chain 'N' and resid 259 through 265 Processing helix chain 'N' and resid 268 through 281 Processing helix chain 'N' and resid 291 through 309 Processing helix chain 'N' and resid 316 through 336 removed outlier: 3.724A pdb=" N GLY N 333 " --> pdb=" O TYR N 329 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE N 334 " --> pdb=" O ILE N 330 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N CYS N 336 " --> pdb=" O ILE N 332 " (cutoff:3.500A) Processing helix chain 'N' and resid 339 through 369 removed outlier: 4.156A pdb=" N GLN N 368 " --> pdb=" O LEU N 364 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N THR N 369 " --> pdb=" O ALA N 365 " (cutoff:3.500A) Processing helix chain 'N' and resid 380 through 383 No H-bonds generated for 'chain 'N' and resid 380 through 383' Processing helix chain 'N' and resid 385 through 399 Processing helix chain 'N' and resid 407 through 419 Processing helix chain 'N' and resid 423 through 448 removed outlier: 3.790A pdb=" N LEU N 443 " --> pdb=" O TYR N 439 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL N 444 " --> pdb=" O TYR N 440 " (cutoff:3.500A) Processing helix chain 'N' and resid 463 through 479 Processing helix chain 'N' and resid 484 through 497 Processing helix chain 'O' and resid 41 through 44 Processing helix chain 'O' and resid 68 through 75 removed outlier: 3.577A pdb=" N HIS O 74 " --> pdb=" O ARG O 70 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N THR O 75 " --> pdb=" O ALA O 71 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 103 No H-bonds generated for 'chain 'O' and resid 101 through 103' Processing helix chain 'O' and resid 114 through 120 removed outlier: 3.761A pdb=" N LEU O 118 " --> pdb=" O GLU O 114 " (cutoff:3.500A) Processing helix chain 'P' and resid 81 through 91 removed outlier: 4.073A pdb=" N GLN P 86 " --> pdb=" O ARG P 82 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N MET P 91 " --> pdb=" O GLN P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 105 through 111 removed outlier: 4.613A pdb=" N HIS P 108 " --> pdb=" O SER P 105 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU P 109 " --> pdb=" O PRO P 106 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU P 111 " --> pdb=" O HIS P 108 " (cutoff:3.500A) Processing helix chain 'P' and resid 131 through 134 Processing helix chain 'P' and resid 157 through 160 No H-bonds generated for 'chain 'P' and resid 157 through 160' Processing helix chain 'P' and resid 162 through 174 Processing helix chain 'P' and resid 195 through 210 removed outlier: 3.646A pdb=" N ALA P 199 " --> pdb=" O ARG P 195 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU P 208 " --> pdb=" O GLU P 204 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ASN P 209 " --> pdb=" O GLU P 205 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA P 210 " --> pdb=" O ALA P 206 " (cutoff:3.500A) Processing helix chain 'P' and resid 231 through 239 Processing helix chain 'P' and resid 258 through 270 Processing helix chain 'P' and resid 290 through 301 removed outlier: 4.679A pdb=" N MET P 300 " --> pdb=" O ILE P 296 " (cutoff:3.500A) Processing helix chain 'P' and resid 312 through 323 Proline residue: P 321 - end of helix Processing helix chain 'P' and resid 341 through 348 removed outlier: 4.008A pdb=" N ASN P 345 " --> pdb=" O LEU P 341 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N THR P 348 " --> pdb=" O ILE P 344 " (cutoff:3.500A) Processing helix chain 'P' and resid 361 through 363 No H-bonds generated for 'chain 'P' and resid 361 through 363' Processing helix chain 'P' and resid 377 through 380 Processing helix chain 'Q' and resid 37 through 42 Processing helix chain 'Q' and resid 47 through 51 removed outlier: 3.697A pdb=" N SER Q 51 " --> pdb=" O GLU Q 48 " (cutoff:3.500A) Processing helix chain 'Q' and resid 101 through 104 No H-bonds generated for 'chain 'Q' and resid 101 through 104' Processing helix chain 'Q' and resid 111 through 121 Processing helix chain 'R' and resid 53 through 57 Processing helix chain 'R' and resid 78 through 80 No H-bonds generated for 'chain 'R' and resid 78 through 80' Processing helix chain 'S' and resid 7 through 10 No H-bonds generated for 'chain 'S' and resid 7 through 10' Processing helix chain 'S' and resid 23 through 34 Proline residue: S 27 - end of helix Processing helix chain 'S' and resid 37 through 40 No H-bonds generated for 'chain 'S' and resid 37 through 40' Processing helix chain 'S' and resid 79 through 92 Processing helix chain 'T' and resid 43 through 55 removed outlier: 4.728A pdb=" N ASP T 48 " --> pdb=" O GLU T 44 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ARG T 49 " --> pdb=" O ALA T 45 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU T 51 " --> pdb=" O VAL T 47 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL T 53 " --> pdb=" O ARG T 49 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N VAL T 54 " --> pdb=" O VAL T 50 " (cutoff:3.500A) Processing helix chain 'T' and resid 82 through 90 removed outlier: 3.964A pdb=" N VAL T 86 " --> pdb=" O THR T 82 " (cutoff:3.500A) Processing helix chain 'T' and resid 99 through 102 No H-bonds generated for 'chain 'T' and resid 99 through 102' Processing helix chain 'T' and resid 108 through 117 Processing helix chain 'U' and resid 47 through 60 removed outlier: 3.545A pdb=" N ASP U 52 " --> pdb=" O SER U 48 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ARG U 53 " --> pdb=" O GLU U 49 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N SER U 56 " --> pdb=" O ASP U 52 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL U 57 " --> pdb=" O ARG U 53 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL U 58 " --> pdb=" O VAL U 54 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS U 59 " --> pdb=" O LEU U 55 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ASN U 60 " --> pdb=" O SER U 56 " (cutoff:3.500A) Processing helix chain 'U' and resid 66 through 68 No H-bonds generated for 'chain 'U' and resid 66 through 68' Processing helix chain 'U' and resid 83 through 96 Processing helix chain 'U' and resid 105 through 107 No H-bonds generated for 'chain 'U' and resid 105 through 107' Processing helix chain 'U' and resid 112 through 120 Processing helix chain 'V' and resid 29 through 46 removed outlier: 4.600A pdb=" N GLN V 45 " --> pdb=" O LEU V 41 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ALA V 46 " --> pdb=" O LYS V 42 " (cutoff:3.500A) Processing helix chain 'V' and resid 52 through 70 removed outlier: 3.908A pdb=" N SER V 59 " --> pdb=" O LYS V 55 " (cutoff:3.500A) Processing helix chain 'V' and resid 74 through 81 removed outlier: 3.922A pdb=" N LYS V 79 " --> pdb=" O GLU V 75 " (cutoff:3.500A) Processing helix chain 'V' and resid 88 through 106 Processing helix chain 'V' and resid 140 through 150 removed outlier: 4.222A pdb=" N LEU V 146 " --> pdb=" O PHE V 142 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU V 147 " --> pdb=" O TYR V 143 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY V 148 " --> pdb=" O LYS V 144 " (cutoff:3.500A) Processing helix chain 'W' and resid 19 through 43 removed outlier: 3.720A pdb=" N ARG W 24 " --> pdb=" O THR W 20 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG W 25 " --> pdb=" O GLU W 21 " (cutoff:3.500A) Proline residue: W 38 - end of helix removed outlier: 3.551A pdb=" N MET W 41 " --> pdb=" O ILE W 37 " (cutoff:3.500A) Processing helix chain 'W' and resid 52 through 65 removed outlier: 3.632A pdb=" N ARG W 56 " --> pdb=" O PRO W 52 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR W 57 " --> pdb=" O SER W 53 " (cutoff:3.500A) Processing helix chain 'W' and resid 72 through 90 Processing helix chain 'W' and resid 99 through 102 No H-bonds generated for 'chain 'W' and resid 99 through 102' Processing helix chain 'W' and resid 122 through 129 Processing helix chain 'X' and resid 15 through 20 Processing helix chain 'X' and resid 22 through 27 removed outlier: 4.161A pdb=" N MET X 27 " --> pdb=" O LYS X 23 " (cutoff:3.500A) Processing helix chain 'X' and resid 30 through 42 Processing helix chain 'X' and resid 46 through 48 No H-bonds generated for 'chain 'X' and resid 46 through 48' Processing helix chain 'X' and resid 51 through 53 No H-bonds generated for 'chain 'X' and resid 51 through 53' Processing helix chain 'X' and resid 55 through 70 Processing helix chain 'X' and resid 76 through 84 Processing helix chain 'X' and resid 95 through 102 Processing helix chain 'Z' and resid 48 through 83 removed outlier: 3.942A pdb=" N ALA Z 56 " --> pdb=" O ALA Z 52 " (cutoff:3.500A) Processing helix chain 'Z' and resid 86 through 112 removed outlier: 3.608A pdb=" N SER Z 99 " --> pdb=" O GLU Z 95 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU Z 100 " --> pdb=" O ARG Z 96 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL Z 111 " --> pdb=" O TYR Z 107 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET Z 112 " --> pdb=" O GLU Z 108 " (cutoff:3.500A) Processing helix chain 'Z' and resid 140 through 142 No H-bonds generated for 'chain 'Z' and resid 140 through 142' Processing helix chain 'a' and resid 5 through 28 Proline residue: a 11 - end of helix removed outlier: 3.506A pdb=" N MET a 18 " --> pdb=" O ILE a 15 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER a 25 " --> pdb=" O MET a 22 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLN a 26 " --> pdb=" O GLY a 23 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR a 28 " --> pdb=" O SER a 25 " (cutoff:3.500A) Processing helix chain 'a' and resid 30 through 34 Processing helix chain 'a' and resid 44 through 59 Processing helix chain 'b' and resid 6 through 13 Processing helix chain 'b' and resid 15 through 39 Proline residue: b 31 - end of helix removed outlier: 4.486A pdb=" N ARG b 35 " --> pdb=" O PRO b 31 " (cutoff:3.500A) Proline residue: b 36 - end of helix Processing helix chain 'c' and resid 33 through 57 Proline residue: c 50 - end of helix removed outlier: 4.310A pdb=" N LYS c 57 " --> pdb=" O LYS c 53 " (cutoff:3.500A) Processing helix chain 'd' and resid 7 through 24 removed outlier: 3.700A pdb=" N ARG d 24 " --> pdb=" O SER d 20 " (cutoff:3.500A) Processing helix chain 'd' and resid 32 through 74 removed outlier: 3.595A pdb=" N VAL d 62 " --> pdb=" O GLU d 58 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N MET d 63 " --> pdb=" O ASP d 59 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS d 66 " --> pdb=" O VAL d 62 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ARG d 74 " --> pdb=" O ALA d 70 " (cutoff:3.500A) Processing helix chain 'e' and resid 15 through 27 removed outlier: 3.956A pdb=" N HIS e 27 " --> pdb=" O GLU e 23 " (cutoff:3.500A) Processing helix chain 'e' and resid 35 through 46 removed outlier: 3.619A pdb=" N ASP e 40 " --> pdb=" O LEU e 36 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N HIS e 46 " --> pdb=" O LEU e 42 " (cutoff:3.500A) Processing helix chain 'e' and resid 50 through 64 removed outlier: 4.243A pdb=" N LYS e 64 " --> pdb=" O GLU e 60 " (cutoff:3.500A) Processing helix chain 'f' and resid 22 through 27 Processing helix chain 'f' and resid 31 through 53 removed outlier: 3.655A pdb=" N ILE f 40 " --> pdb=" O ARG f 36 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR f 41 " --> pdb=" O PHE f 37 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ILE f 53 " --> pdb=" O TYR f 49 " (cutoff:3.500A) Processing helix chain 'f' and resid 60 through 86 Processing helix chain 'g' and resid 45 through 47 No H-bonds generated for 'chain 'g' and resid 45 through 47' Processing helix chain 'g' and resid 61 through 79 Proline residue: g 65 - end of helix Processing helix chain 'g' and resid 91 through 101 Processing helix chain 'i' and resid 4 through 15 removed outlier: 4.324A pdb=" N ASN i 10 " --> pdb=" O GLU i 6 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LEU i 11 " --> pdb=" O PHE i 7 " (cutoff:3.500A) Processing helix chain 'i' and resid 19 through 44 removed outlier: 3.591A pdb=" N LYS i 38 " --> pdb=" O HIS i 34 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS i 39 " --> pdb=" O GLU i 35 " (cutoff:3.500A) Processing helix chain 'i' and resid 66 through 69 No H-bonds generated for 'chain 'i' and resid 66 through 69' Processing helix chain 'i' and resid 80 through 83 No H-bonds generated for 'chain 'i' and resid 80 through 83' Processing helix chain 'j' and resid 22 through 24 No H-bonds generated for 'chain 'j' and resid 22 through 24' Processing helix chain 'j' and resid 26 through 44 removed outlier: 4.066A pdb=" N VAL j 34 " --> pdb=" O GLY j 30 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET j 35 " --> pdb=" O LEU j 31 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU j 40 " --> pdb=" O TRP j 36 " (cutoff:3.500A) Processing helix chain 'j' and resid 49 through 51 No H-bonds generated for 'chain 'j' and resid 49 through 51' Processing helix chain 'k' and resid 9 through 15 Processing helix chain 'k' and resid 17 through 19 No H-bonds generated for 'chain 'k' and resid 17 through 19' Processing helix chain 'k' and resid 22 through 24 No H-bonds generated for 'chain 'k' and resid 22 through 24' Processing helix chain 'k' and resid 33 through 48 removed outlier: 4.174A pdb=" N GLY k 36 " --> pdb=" O PRO k 33 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE k 37 " --> pdb=" O GLY k 34 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N VAL k 39 " --> pdb=" O GLY k 36 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL k 47 " --> pdb=" O VAL k 44 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLY k 48 " --> pdb=" O TYR k 45 " (cutoff:3.500A) Processing helix chain 'l' and resid 77 through 98 removed outlier: 3.528A pdb=" N GLY l 84 " --> pdb=" O ALA l 80 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE l 89 " --> pdb=" O GLY l 85 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL l 97 " --> pdb=" O GLY l 93 " (cutoff:3.500A) Processing helix chain 'l' and resid 113 through 117 Processing helix chain 'm' and resid 11 through 20 removed outlier: 3.614A pdb=" N ASP m 15 " --> pdb=" O LYS m 11 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N TRP m 16 " --> pdb=" O PHE m 12 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG m 20 " --> pdb=" O TRP m 16 " (cutoff:3.500A) Processing helix chain 'm' and resid 31 through 40 Processing helix chain 'm' and resid 43 through 63 Processing helix chain 'n' and resid 10 through 34 removed outlier: 3.795A pdb=" N ARG n 21 " --> pdb=" O LYS n 17 " (cutoff:3.500A) Processing helix chain 'n' and resid 41 through 53 Processing helix chain 'n' and resid 65 through 77 Processing helix chain 'o' and resid 15 through 19 Processing helix chain 'o' and resid 32 through 43 removed outlier: 3.976A pdb=" N ILE o 35 " --> pdb=" O HIS o 32 " (cutoff:3.500A) Proline residue: o 36 - end of helix removed outlier: 3.550A pdb=" N CYS o 40 " --> pdb=" O LEU o 37 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG o 41 " --> pdb=" O ASN o 38 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLN o 42 " --> pdb=" O LYS o 39 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA o 43 " --> pdb=" O CYS o 40 " (cutoff:3.500A) Processing helix chain 'o' and resid 55 through 83 removed outlier: 3.752A pdb=" N LYS o 75 " --> pdb=" O LEU o 71 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE o 76 " --> pdb=" O ALA o 72 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ALA o 81 " --> pdb=" O ARG o 77 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N LEU o 82 " --> pdb=" O GLU o 78 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ALA o 83 " --> pdb=" O GLU o 79 " (cutoff:3.500A) Processing helix chain 'p' and resid 20 through 22 No H-bonds generated for 'chain 'p' and resid 20 through 22' Processing helix chain 'p' and resid 27 through 59 removed outlier: 3.836A pdb=" N VAL p 31 " --> pdb=" O PRO p 27 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLU p 32 " --> pdb=" O VAL p 28 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL p 38 " --> pdb=" O ARG p 34 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE p 43 " --> pdb=" O ARG p 39 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN p 44 " --> pdb=" O GLU p 40 " (cutoff:3.500A) Processing helix chain 'p' and resid 71 through 81 removed outlier: 3.888A pdb=" N GLN p 76 " --> pdb=" O HIS p 72 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP p 79 " --> pdb=" O GLN p 75 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER p 80 " --> pdb=" O GLN p 76 " (cutoff:3.500A) Processing helix chain 'q' and resid 83 through 85 No H-bonds generated for 'chain 'q' and resid 83 through 85' Processing helix chain 'q' and resid 91 through 97 removed outlier: 4.202A pdb=" N GLY q 95 " --> pdb=" O ALA q 91 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N TRP q 96 " --> pdb=" O GLU q 92 " (cutoff:3.500A) Processing helix chain 'q' and resid 106 through 109 No H-bonds generated for 'chain 'q' and resid 106 through 109' Processing helix chain 'u' and resid 2 through 25 removed outlier: 3.671A pdb=" N UNK u 24 " --> pdb=" O UNK u 20 " (cutoff:3.500A) Processing helix chain 'v' and resid 82 through 102 Processing helix chain 'x' and resid 211 through 214 No H-bonds generated for 'chain 'x' and resid 211 through 214' Processing helix chain 'x' and resid 216 through 234 removed outlier: 4.188A pdb=" N GLU x 234 " --> pdb=" O ASP x 230 " (cutoff:3.500A) Processing helix chain 'x' and resid 240 through 251 Processing helix chain 'y' and resid 3 through 30 Processing helix chain 'y' and resid 194 through 219 removed outlier: 4.242A pdb=" N GLN y 212 " --> pdb=" O ILE y 208 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N ILE y 213 " --> pdb=" O ASN y 209 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N HIS y 214 " --> pdb=" O LEU y 210 " (cutoff:3.500A) Processing helix chain 'y' and resid 222 through 234 removed outlier: 4.054A pdb=" N VAL y 227 " --> pdb=" O GLU y 223 " (cutoff:3.500A) Processing helix chain 'y' and resid 240 through 245 Processing helix chain 'y' and resid 254 through 256 No H-bonds generated for 'chain 'y' and resid 254 through 256' Processing helix chain 'z' and resid 3 through 29 Processing helix chain 'z' and resid 34 through 36 No H-bonds generated for 'chain 'z' and resid 34 through 36' Processing helix chain 'z' and resid 194 through 218 removed outlier: 3.859A pdb=" N SER z 201 " --> pdb=" O ILE z 197 " (cutoff:3.500A) Processing helix chain 'z' and resid 224 through 231 Processing sheet with id= A, first strand: chain 'B' and resid 86 through 90 removed outlier: 7.143A pdb=" N CYS B 124 " --> pdb=" O MET B 87 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N PHE B 89 " --> pdb=" O CYS B 124 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ILE B 126 " --> pdb=" O PHE B 89 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N TRP B 151 " --> pdb=" O MET B 125 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N VAL B 127 " --> pdb=" O TRP B 151 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ILE B 153 " --> pdb=" O VAL B 127 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'C' and resid 55 through 59 removed outlier: 6.896A pdb=" N ASN C 76 " --> pdb=" O ILE C 57 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ILE C 59 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N VAL C 74 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE C 86 " --> pdb=" O LEU C 77 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 153 through 158 removed outlier: 3.907A pdb=" N ASP C 158 " --> pdb=" O ARG C 163 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ARG C 163 " --> pdb=" O ASP C 158 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 12 through 14 removed outlier: 3.968A pdb=" N LEU D 13 " --> pdb=" O LEU D 30 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU D 30 " --> pdb=" O LEU D 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'D' and resid 326 through 328 removed outlier: 3.501A pdb=" N GLY D 339 " --> pdb=" O ARG D 356 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 125 through 128 removed outlier: 3.576A pdb=" N SER E 165 " --> pdb=" O TYR E 125 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 180 through 184 removed outlier: 3.578A pdb=" N VAL E 183 " --> pdb=" O ASN E 196 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN E 196 " --> pdb=" O VAL E 183 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 263 through 267 removed outlier: 7.153A pdb=" N TYR F 135 " --> pdb=" O THR F 264 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N THR F 266 " --> pdb=" O TYR F 135 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL F 137 " --> pdb=" O THR F 266 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ALA F 176 " --> pdb=" O LEU F 136 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N VAL F 138 " --> pdb=" O ALA F 176 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N TYR F 178 " --> pdb=" O VAL F 138 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 339 through 341 removed outlier: 3.586A pdb=" N ILE F 378 " --> pdb=" O ILE F 341 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'G' and resid 74 through 77 Processing sheet with id= K, first strand: chain 'G' and resid 211 through 213 Processing sheet with id= L, first strand: chain 'G' and resid 288 through 293 removed outlier: 6.241A pdb=" N ARG G 308 " --> pdb=" O VAL G 312 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N VAL G 312 " --> pdb=" O ARG G 308 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 348 through 350 Processing sheet with id= N, first strand: chain 'G' and resid 514 through 517 Processing sheet with id= O, first strand: chain 'G' and resid 601 through 604 removed outlier: 6.039A pdb=" N VAL G 616 " --> pdb=" O TYR G 602 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N GLY G 604 " --> pdb=" O VAL G 616 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N LEU G 618 " --> pdb=" O GLY G 604 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'I' and resid 111 through 113 Processing sheet with id= Q, first strand: chain 'I' and resid 138 through 144 removed outlier: 6.501A pdb=" N GLU I 143 " --> pdb=" O THR I 152 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N THR I 152 " --> pdb=" O GLU I 143 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'L' and resid 57 through 59 removed outlier: 3.633A pdb=" N LEU L 59 " --> pdb=" O PHE L 76 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'M' and resid 71 through 73 Processing sheet with id= T, first strand: chain 'O' and resid 45 through 48 Processing sheet with id= U, first strand: chain 'O' and resid 131 through 133 Processing sheet with id= V, first strand: chain 'P' and resid 72 through 74 removed outlier: 6.443A pdb=" N ARG P 179 " --> pdb=" O VAL P 141 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N ASN P 143 " --> pdb=" O ARG P 179 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE P 181 " --> pdb=" O ASN P 143 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N THR P 215 " --> pdb=" O GLN P 182 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N SER P 184 " --> pdb=" O THR P 215 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N MET P 217 " --> pdb=" O SER P 184 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'Q' and resid 124 through 128 removed outlier: 4.590A pdb=" N SER Q 58 " --> pdb=" O LYS Q 128 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'Q' and resid 83 through 85 Processing sheet with id= Y, first strand: chain 'R' and resid 63 through 65 Processing sheet with id= Z, first strand: chain 'R' and resid 69 through 72 Processing sheet with id= AA, first strand: chain 'S' and resid 48 through 51 removed outlier: 6.382A pdb=" N LEU S 14 " --> pdb=" O LEU S 49 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ARG S 51 " --> pdb=" O LEU S 14 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ILE S 16 " --> pdb=" O ARG S 51 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'q' and resid 50 through 52 removed outlier: 3.537A pdb=" N THR q 50 " --> pdb=" O GLN q 63 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN q 63 " --> pdb=" O THR q 50 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N TYR q 61 " --> pdb=" O VAL q 52 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TRP q 75 " --> pdb=" O TYR q 62 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'x' and resid 62 through 64 removed outlier: 6.609A pdb=" N LEU x 84 " --> pdb=" O ILE x 63 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'x' and resid 109 through 111 removed outlier: 6.799A pdb=" N THR x 137 " --> pdb=" O THR x 110 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD Processing sheet with id= AE, first strand: chain 'x' and resid 197 through 199 removed outlier: 5.931A pdb=" N GLY x 199 " --> pdb=" O PHE x 205 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N PHE x 205 " --> pdb=" O GLY x 199 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'y' and resid 66 through 69 Processing sheet with id= AG, first strand: chain 'y' and resid 71 through 73 removed outlier: 6.338A pdb=" N ILE y 92 " --> pdb=" O GLN y 72 " (cutoff:3.500A) No H-bonds generated for sheet with id= AG Processing sheet with id= AH, first strand: chain 'y' and resid 105 through 107 Processing sheet with id= AI, first strand: chain 'y' and resid 179 through 181 removed outlier: 4.034A pdb=" N ARG y 190 " --> pdb=" O VAL y 180 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'z' and resid 68 through 73 removed outlier: 8.173A pdb=" N VAL z 89 " --> pdb=" O ASP z 70 " (cutoff:3.500A) removed outlier: 11.496A pdb=" N HIS z 72 " --> pdb=" O VAL z 89 " (cutoff:3.500A) removed outlier: 9.368A pdb=" N THR z 91 " --> pdb=" O HIS z 72 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'z' and resid 179 through 182 removed outlier: 4.276A pdb=" N ARG z 190 " --> pdb=" O VAL z 180 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLY z 182 " --> pdb=" O PHE z 188 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N PHE z 188 " --> pdb=" O GLY z 182 " (cutoff:3.500A) 2327 hydrogen bonds defined for protein. 6498 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: 16.40 Time building geometry restraints manager: 22.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.40: 25428 1.40 - 1.62: 36764 1.62 - 1.84: 655 1.84 - 2.06: 0 2.06 - 2.28: 80 Bond restraints: 62927 Sorted by residual: bond pdb=" C PRO r 83 " pdb=" N ILE r 84 " ideal model delta sigma weight residual 1.330 1.512 -0.182 1.23e-02 6.61e+03 2.19e+02 bond pdb=" C1 UQ9 H 401 " pdb=" C6 UQ9 H 401 " ideal model delta sigma weight residual 1.345 1.540 -0.195 2.00e-02 2.50e+03 9.52e+01 bond pdb=" C3 UQ9 H 401 " pdb=" C4 UQ9 H 401 " ideal model delta sigma weight residual 1.340 1.533 -0.193 2.00e-02 2.50e+03 9.34e+01 bond pdb=" C1 LMN d 101 " pdb=" O5 LMN d 101 " ideal model delta sigma weight residual 1.403 1.535 -0.132 2.00e-02 2.50e+03 4.33e+01 bond pdb=" CBS LMN d 101 " pdb=" CCM LMN d 101 " ideal model delta sigma weight residual 1.529 1.633 -0.104 2.00e-02 2.50e+03 2.70e+01 ... (remaining 62922 not shown) Histogram of bond angle deviations from ideal: 73.56 - 86.49: 76 86.49 - 99.41: 17 99.41 - 112.34: 32901 112.34 - 125.26: 51110 125.26 - 138.18: 1105 Bond angle restraints: 85209 Sorted by residual: angle pdb=" C PRO r 83 " pdb=" N ILE r 84 " pdb=" CA ILE r 84 " ideal model delta sigma weight residual 123.10 90.96 32.14 1.33e+00 5.65e-01 5.84e+02 angle pdb=" O PRO r 83 " pdb=" C PRO r 83 " pdb=" N ILE r 84 " ideal model delta sigma weight residual 123.00 138.18 -15.18 1.60e+00 3.91e-01 9.01e+01 angle pdb=" CA PRO r 83 " pdb=" C PRO r 83 " pdb=" N ILE r 84 " ideal model delta sigma weight residual 116.20 98.25 17.95 2.00e+00 2.50e-01 8.06e+01 angle pdb=" CA PRO r 83 " pdb=" N PRO r 83 " pdb=" CD PRO r 83 " ideal model delta sigma weight residual 112.00 99.51 12.49 1.40e+00 5.10e-01 7.96e+01 angle pdb=" O11 PTY N 502 " pdb=" P1 PTY N 502 " pdb=" O14 PTY N 502 " ideal model delta sigma weight residual 92.90 109.76 -16.86 3.00e+00 1.11e-01 3.16e+01 ... (remaining 85204 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.51: 36445 34.51 - 69.02: 821 69.02 - 103.53: 84 103.53 - 138.04: 1 138.04 - 172.55: 3 Dihedral angle restraints: 37354 sinusoidal: 15150 harmonic: 22204 Sorted by residual: dihedral pdb=" C10 FMN F 500 " pdb=" C1' FMN F 500 " pdb=" N10 FMN F 500 " pdb=" C2' FMN F 500 " ideal model delta sinusoidal sigma weight residual 257.59 85.04 172.55 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" CA VAL P 329 " pdb=" C VAL P 329 " pdb=" N PRO P 330 " pdb=" CA PRO P 330 " ideal model delta harmonic sigma weight residual -180.00 -153.90 -26.10 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA GLU i 17 " pdb=" C GLU i 17 " pdb=" N ASN i 18 " pdb=" CA ASN i 18 " ideal model delta harmonic sigma weight residual 180.00 154.66 25.34 0 5.00e+00 4.00e-02 2.57e+01 ... (remaining 37351 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.974: 9448 0.974 - 1.949: 0 1.949 - 2.923: 0 2.923 - 3.897: 0 3.897 - 4.871: 1 Chirality restraints: 9449 Sorted by residual: chirality pdb=" C1 T7X z 302 " pdb=" C2 T7X z 302 " pdb=" C6 T7X z 302 " pdb=" O1 T7X z 302 " both_signs ideal model delta sigma weight residual False -2.42 2.45 -4.87 2.00e-01 2.50e+01 5.93e+02 chirality pdb=" C5 PGT N 501 " pdb=" C4 PGT N 501 " pdb=" C6 PGT N 501 " pdb=" O5 PGT N 501 " both_signs ideal model delta sigma weight residual False -2.30 -2.51 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA THR E 133 " pdb=" N THR E 133 " pdb=" C THR E 133 " pdb=" CB THR E 133 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 9446 not shown) Planarity restraints: 10724 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU L 500 " 0.059 5.00e-02 4.00e+02 8.93e-02 1.28e+01 pdb=" N PRO L 501 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO L 501 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO L 501 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO x 237 " -0.016 2.00e-02 2.50e+03 3.19e-02 1.01e+01 pdb=" C PRO x 237 " 0.055 2.00e-02 2.50e+03 pdb=" O PRO x 237 " -0.021 2.00e-02 2.50e+03 pdb=" N TYR x 238 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE P 312 " 0.045 5.00e-02 4.00e+02 6.78e-02 7.35e+00 pdb=" N PRO P 313 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO P 313 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO P 313 " 0.038 5.00e-02 4.00e+02 ... (remaining 10721 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 577 2.58 - 3.16: 52779 3.16 - 3.74: 97534 3.74 - 4.32: 132882 4.32 - 4.90: 222554 Nonbonded interactions: 506326 Sorted by model distance: nonbonded pdb=" NE2 HIS O 83 " pdb="FE FE O 200 " model vdw 2.002 2.340 nonbonded pdb=" O PHE A 77 " pdb=" OH TYR J 145 " model vdw 2.023 2.440 nonbonded pdb=" OH TYR x 148 " pdb=" O ASN z 103 " model vdw 2.098 2.440 nonbonded pdb=" OD1 ASP G 294 " pdb=" OG1 THR G 332 " model vdw 2.138 2.440 nonbonded pdb=" OG1 THR S 30 " pdb=" NZ LYS S 34 " model vdw 2.138 2.520 ... (remaining 506321 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.370 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: 44.530 Check model and map are aligned: 0.700 Set scattering table: 0.420 Process input model: 129.410 Find NCS groups from input model: 1.670 Set up NCS constraints: 0.180 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 187.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 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 : 0.004 0.195 62927 Z= 0.287 Angle : 0.727 32.135 85209 Z= 0.353 Chirality : 0.066 4.871 9449 Planarity : 0.004 0.089 10724 Dihedral : 14.855 172.551 23071 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.26 % Favored : 92.72 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.82 % 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: -0.59 (0.10), residues: 7578 helix: 0.86 (0.09), residues: 3704 sheet: -1.37 (0.26), residues: 412 loop : -1.69 (0.11), residues: 3462 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15156 Ramachandran restraints generated. 7578 Oldfield, 0 Emsley, 7578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15156 Ramachandran restraints generated. 7578 Oldfield, 0 Emsley, 7578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1354 residues out of total 6530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1352 time to evaluate : 5.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 1353 average time/residue: 0.5946 time to fit residues: 1354.0879 Evaluate side-chains 1113 residues out of total 6530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1113 time to evaluate : 6.277 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.2799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 750 random chunks: chunk 633 optimal weight: 0.9990 chunk 568 optimal weight: 0.9990 chunk 315 optimal weight: 0.6980 chunk 194 optimal weight: 0.8980 chunk 383 optimal weight: 3.9990 chunk 303 optimal weight: 0.9980 chunk 587 optimal weight: 0.7980 chunk 227 optimal weight: 0.6980 chunk 357 optimal weight: 3.9990 chunk 437 optimal weight: 4.9990 chunk 681 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 HIS D 10 ASN ** E 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 221 HIS ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 446 GLN G 716 GLN L 457 HIS ** M 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 464 ASN Q 65 GLN S 43 ASN ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 131 ASN ** X 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 126 ASN a 30 HIS e 52 GLN g 47 ASN ** g 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 8 ASN q 88 GLN y 101 GLN ** z 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.0931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.067 62927 Z= 0.217 Angle : 0.591 10.780 85209 Z= 0.294 Chirality : 0.043 0.202 9449 Planarity : 0.004 0.068 10724 Dihedral : 8.192 172.607 8725 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.43 % Favored : 92.54 % Rotamer Outliers : 1.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.82 % 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: -0.54 (0.10), residues: 7578 helix: 0.89 (0.09), residues: 3731 sheet: -1.29 (0.25), residues: 430 loop : -1.68 (0.11), residues: 3417 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15156 Ramachandran restraints generated. 7578 Oldfield, 0 Emsley, 7578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15156 Ramachandran restraints generated. 7578 Oldfield, 0 Emsley, 7578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1337 residues out of total 6530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 1216 time to evaluate : 5.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 121 outliers final: 89 residues processed: 1266 average time/residue: 0.5973 time to fit residues: 1275.1641 Evaluate side-chains 1190 residues out of total 6530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 1101 time to evaluate : 5.439 Switching outliers to nearest non-outliers outliers start: 89 outliers final: 0 residues processed: 89 average time/residue: 0.4392 time to fit residues: 82.1629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 750 random chunks: chunk 378 optimal weight: 0.8980 chunk 211 optimal weight: 0.9990 chunk 566 optimal weight: 6.9990 chunk 463 optimal weight: 10.0000 chunk 187 optimal weight: 0.0570 chunk 682 optimal weight: 0.9980 chunk 737 optimal weight: 3.9990 chunk 607 optimal weight: 3.9990 chunk 676 optimal weight: 10.0000 chunk 232 optimal weight: 0.6980 chunk 547 optimal weight: 0.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 33 ASN ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 457 HIS M 329 GLN M 409 GLN ** M 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 98 GLN ** P 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 131 ASN e 52 GLN ** g 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 88 GLN ** v 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 101 GLN ** z 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 62927 Z= 0.201 Angle : 0.570 10.820 85209 Z= 0.284 Chirality : 0.042 0.197 9449 Planarity : 0.004 0.067 10724 Dihedral : 7.922 172.506 8725 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.48 % Favored : 92.49 % Rotamer Outliers : 1.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.82 % 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: -0.51 (0.10), residues: 7578 helix: 0.88 (0.09), residues: 3746 sheet: -1.25 (0.25), residues: 437 loop : -1.64 (0.11), residues: 3395 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15156 Ramachandran restraints generated. 7578 Oldfield, 0 Emsley, 7578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15156 Ramachandran restraints generated. 7578 Oldfield, 0 Emsley, 7578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1257 residues out of total 6530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 1180 time to evaluate : 5.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 77 outliers final: 41 residues processed: 1217 average time/residue: 0.5973 time to fit residues: 1229.6803 Evaluate side-chains 1142 residues out of total 6530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 1101 time to evaluate : 5.410 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.4495 time to fit residues: 42.1090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 750 random chunks: chunk 674 optimal weight: 9.9990 chunk 512 optimal weight: 0.5980 chunk 354 optimal weight: 0.0870 chunk 75 optimal weight: 0.9980 chunk 325 optimal weight: 8.9990 chunk 458 optimal weight: 0.7980 chunk 684 optimal weight: 0.8980 chunk 724 optimal weight: 0.8980 chunk 357 optimal weight: 2.9990 chunk 648 optimal weight: 4.9990 chunk 195 optimal weight: 10.0000 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 4 GLN D 78 GLN E 221 HIS F 436 GLN ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 686 ASN ** H 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 73 HIS L 132 ASN L 457 HIS M 329 GLN ** M 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 98 GLN S 57 GLN ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 131 ASN e 52 GLN ** g 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 88 GLN ** v 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 101 GLN ** z 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 62927 Z= 0.186 Angle : 0.558 10.851 85209 Z= 0.277 Chirality : 0.042 0.200 9449 Planarity : 0.004 0.066 10724 Dihedral : 7.645 172.433 8725 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.21 % Favored : 92.77 % Rotamer Outliers : 1.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.82 % 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: -0.45 (0.10), residues: 7578 helix: 0.92 (0.09), residues: 3741 sheet: -1.15 (0.25), residues: 431 loop : -1.60 (0.11), residues: 3406 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15156 Ramachandran restraints generated. 7578 Oldfield, 0 Emsley, 7578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15156 Ramachandran restraints generated. 7578 Oldfield, 0 Emsley, 7578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1278 residues out of total 6530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 1181 time to evaluate : 5.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 97 outliers final: 58 residues processed: 1220 average time/residue: 0.6071 time to fit residues: 1248.9294 Evaluate side-chains 1154 residues out of total 6530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 1096 time to evaluate : 6.660 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 0 residues processed: 58 average time/residue: 0.4614 time to fit residues: 57.8697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 750 random chunks: chunk 603 optimal weight: 1.9990 chunk 411 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 539 optimal weight: 0.5980 chunk 299 optimal weight: 3.9990 chunk 618 optimal weight: 2.9990 chunk 501 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 370 optimal weight: 4.9990 chunk 650 optimal weight: 9.9990 chunk 182 optimal weight: 1.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 HIS C 4 GLN D 62 GLN ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 457 HIS M 490 GLN N 53 ASN ** N 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 368 GLN O 98 GLN O 141 GLN ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 131 ASN X 45 ASN Z 66 GLN ** a 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 52 GLN ** f 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 8 ASN v 83 ASN ** x 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.063 62927 Z= 0.373 Angle : 0.650 15.019 85209 Z= 0.324 Chirality : 0.045 0.192 9449 Planarity : 0.005 0.066 10724 Dihedral : 7.770 174.285 8725 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.47 % Favored : 91.49 % Rotamer Outliers : 2.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.82 % 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: -0.73 (0.10), residues: 7578 helix: 0.68 (0.09), residues: 3785 sheet: -1.47 (0.25), residues: 445 loop : -1.73 (0.11), residues: 3348 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15156 Ramachandran restraints generated. 7578 Oldfield, 0 Emsley, 7578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15156 Ramachandran restraints generated. 7578 Oldfield, 0 Emsley, 7578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1282 residues out of total 6530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 1145 time to evaluate : 5.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 137 outliers final: 74 residues processed: 1229 average time/residue: 0.5906 time to fit residues: 1227.8599 Evaluate side-chains 1144 residues out of total 6530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 1070 time to evaluate : 5.504 Switching outliers to nearest non-outliers outliers start: 74 outliers final: 0 residues processed: 74 average time/residue: 0.4650 time to fit residues: 72.5061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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-1.21rc1-4953/modules/cctbx_project/iotbx/cli_parser.py", line 872, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.9925 > 50: distance: 19 - 36: 4.877 distance: 23 - 44: 5.254 distance: 28 - 53: 10.985 distance: 32 - 36: 5.189 distance: 36 - 37: 4.217 distance: 37 - 38: 3.189 distance: 38 - 39: 5.542 distance: 38 - 44: 7.001 distance: 40 - 41: 19.115 distance: 41 - 42: 34.915 distance: 41 - 43: 25.367 distance: 44 - 45: 6.719 distance: 45 - 46: 10.644 distance: 45 - 48: 11.340 distance: 46 - 47: 14.986 distance: 46 - 53: 12.358 distance: 48 - 49: 13.156 distance: 49 - 50: 12.879 distance: 50 - 51: 13.392 distance: 50 - 52: 13.286 distance: 53 - 54: 11.065 distance: 54 - 55: 7.948 distance: 54 - 57: 11.895 distance: 55 - 56: 12.631 distance: 55 - 62: 14.881 distance: 57 - 58: 16.603 distance: 58 - 59: 21.720 distance: 59 - 60: 13.748 distance: 59 - 61: 4.566 distance: 62 - 63: 10.631 distance: 63 - 64: 6.492 distance: 63 - 66: 9.742 distance: 64 - 65: 7.717 distance: 64 - 70: 6.643 distance: 66 - 67: 10.667 distance: 67 - 68: 15.053 distance: 68 - 69: 16.434 distance: 70 - 71: 7.305 distance: 71 - 72: 21.774 distance: 71 - 74: 14.451 distance: 72 - 73: 10.003 distance: 72 - 78: 36.276 distance: 74 - 75: 16.078 distance: 75 - 76: 14.756 distance: 75 - 77: 6.616 distance: 78 - 79: 13.262 distance: 79 - 80: 20.948 distance: 79 - 82: 8.370 distance: 80 - 81: 4.716 distance: 80 - 85: 13.585 distance: 82 - 83: 14.695 distance: 82 - 84: 15.895 distance: 85 - 86: 34.862 distance: 86 - 87: 12.533 distance: 87 - 88: 21.529 distance: 87 - 89: 7.796 distance: 89 - 90: 12.862 distance: 90 - 91: 11.192 distance: 90 - 93: 15.736 distance: 91 - 92: 44.647 distance: 91 - 97: 17.591 distance: 93 - 94: 49.694 distance: 94 - 95: 6.624 distance: 94 - 96: 38.198 distance: 97 - 98: 13.153 distance: 98 - 99: 23.468 distance: 98 - 101: 18.363 distance: 99 - 100: 34.473 distance: 99 - 108: 19.842 distance: 100 - 138: 29.656 distance: 101 - 102: 7.448 distance: 102 - 103: 17.631 distance: 103 - 104: 20.736 distance: 104 - 105: 37.635 distance: 105 - 106: 15.021 distance: 105 - 107: 9.282 distance: 108 - 109: 17.098 distance: 109 - 110: 7.787 distance: 109 - 112: 13.276 distance: 110 - 111: 24.954 distance: 110 - 116: 20.468 distance: 111 - 147: 10.686 distance: 112 - 113: 22.138 distance: 112 - 114: 24.148 distance: 113 - 115: 10.242