Starting phenix.real_space_refine on Sat Jan 20 07:59:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g2j_4345/01_2024/6g2j_4345_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g2j_4345/01_2024/6g2j_4345.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g2j_4345/01_2024/6g2j_4345_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g2j_4345/01_2024/6g2j_4345_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g2j_4345/01_2024/6g2j_4345_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g2j_4345/01_2024/6g2j_4345.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g2j_4345/01_2024/6g2j_4345.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g2j_4345/01_2024/6g2j_4345_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g2j_4345/01_2024/6g2j_4345_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.013 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 28 7.16 5 Zn 1 6.06 5 P 32 5.49 5 S 492 5.16 5 C 43196 2.51 5 N 11078 2.21 5 O 11984 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 48": "NH1" <-> "NH2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 35": "NH1" <-> "NH2" Residue "B ARG 52": "NH1" <-> "NH2" Residue "B TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 189": "NH1" <-> "NH2" Residue "C TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 182": "NH1" <-> "NH2" Residue "D ARG 2": "NH1" <-> "NH2" Residue "D TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 133": "NH1" <-> "NH2" Residue "D ARG 174": "NH1" <-> "NH2" Residue "D ARG 221": "NH1" <-> "NH2" Residue "D ARG 290": "NH1" <-> "NH2" Residue "D TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 10": "NH1" <-> "NH2" Residue "F PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 28": "NH1" <-> "NH2" Residue "F ARG 139": "NH1" <-> "NH2" Residue "F ARG 339": "NH1" <-> "NH2" Residue "F ARG 349": "NH1" <-> "NH2" Residue "F ARG 378": "NH1" <-> "NH2" Residue "G ARG 135": "NH1" <-> "NH2" Residue "G ARG 218": "NH1" <-> "NH2" Residue "G ARG 243": "NH1" <-> "NH2" Residue "G ARG 249": "NH1" <-> "NH2" Residue "G ARG 253": "NH1" <-> "NH2" Residue "G ARG 268": "NH1" <-> "NH2" Residue "G TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 285": "NH1" <-> "NH2" Residue "G ARG 359": "NH1" <-> "NH2" Residue "G TYR 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 62": "NH1" <-> "NH2" Residue "H TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 25": "NH1" <-> "NH2" Residue "I ARG 62": "NH1" <-> "NH2" Residue "L PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 116": "NH1" <-> "NH2" Residue "L TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 161": "NH1" <-> "NH2" Residue "L PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 262": "NH1" <-> "NH2" Residue "L TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 436": "NH1" <-> "NH2" Residue "L PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 535": "NH1" <-> "NH2" Residue "M TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 145": "NH1" <-> "NH2" Residue "P ARG 50": "NH1" <-> "NH2" Residue "P ARG 76": "NH1" <-> "NH2" Residue "P ARG 102": "NH1" <-> "NH2" Residue "P ARG 186": "NH1" <-> "NH2" Residue "P ARG 251": "NH1" <-> "NH2" Residue "P ARG 320": "NH1" <-> "NH2" Residue "P ARG 322": "NH1" <-> "NH2" Residue "Q TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 31": "NH1" <-> "NH2" Residue "S ARG 55": "NH1" <-> "NH2" Residue "V ARG 44": "NH1" <-> "NH2" Residue "W ARG 32": "NH1" <-> "NH2" Residue "W ARG 33": "NH1" <-> "NH2" Residue "W ARG 79": "NH1" <-> "NH2" Residue "W ARG 107": "NH1" <-> "NH2" Residue "X ARG 54": "NH1" <-> "NH2" Residue "X ARG 118": "NH1" <-> "NH2" Residue "X ARG 144": "NH1" <-> "NH2" Residue "X ARG 146": "NH1" <-> "NH2" Residue "Y ARG 103": "NH1" <-> "NH2" Residue "Z ARG 22": "NH1" <-> "NH2" Residue "Z ARG 26": "NH1" <-> "NH2" Residue "Z ARG 27": "NH1" <-> "NH2" Residue "Z ARG 48": "NH1" <-> "NH2" Residue "Z ARG 67": "NH1" <-> "NH2" Residue "Z ARG 81": "NH1" <-> "NH2" Residue "Z TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 40": "NH1" <-> "NH2" Residue "a ARG 52": "NH1" <-> "NH2" Residue "a ARG 53": "NH1" <-> "NH2" Residue "a TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 5": "NH1" <-> "NH2" Residue "c ARG 45": "NH1" <-> "NH2" Residue "e PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 50": "NH1" <-> "NH2" Residue "e ARG 68": "NH1" <-> "NH2" Residue "e ARG 100": "NH1" <-> "NH2" Residue "e ARG 104": "NH1" <-> "NH2" Residue "g ARG 57": "NH1" <-> "NH2" Residue "g ARG 89": "NH1" <-> "NH2" Residue "g ARG 93": "NH1" <-> "NH2" Residue "h ARG 20": "NH1" <-> "NH2" Residue "h ARG 115": "NH1" <-> "NH2" Residue "i ARG 10": "NH1" <-> "NH2" Residue "k ARG 44": "NH1" <-> "NH2" Residue "k ARG 52": "NH1" <-> "NH2" Residue "l ARG 85": "NH1" <-> "NH2" Residue "m ARG 29": "NH1" <-> "NH2" Residue "m ARG 30": "NH1" <-> "NH2" Residue "m ARG 44": "NH1" <-> "NH2" Residue "m ARG 80": "NH1" <-> "NH2" Residue "n ARG 33": "NH1" <-> "NH2" Residue "n ARG 92": "NH1" <-> "NH2" Residue "n ARG 157": "NH1" <-> "NH2" Residue "n ARG 158": "NH1" <-> "NH2" Residue "o ARG 36": "NH1" <-> "NH2" Residue "o PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 97": "NH1" <-> "NH2" Residue "o ARG 105": "NH1" <-> "NH2" Residue "o ARG 106": "NH1" <-> "NH2" Residue "p ARG 15": "NH1" <-> "NH2" Residue "p ARG 48": "NH1" <-> "NH2" Residue "p ARG 65": "NH1" <-> "NH2" Residue "p ARG 68": "NH1" <-> "NH2" Residue "p ARG 92": "NH1" <-> "NH2" Residue "p TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 60": "NH1" <-> "NH2" Residue "q PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 5": "NH1" <-> "NH2" Residue "r ARG 26": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 66811 Number of models: 1 Model: "" Number of chains: 60 Chain: "A" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 933 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1241 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 10, 'TRANS': 144} Chain: "C" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1712 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 15, 'TRANS': 190} Chain: "D" Number of atoms: 3452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3452 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 26, 'TRANS': 403} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1, '2MR:plan-2': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 1648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1648 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 21, 'TRANS': 190} Chain: "F" Number of atoms: 3301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3301 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 21, 'TRANS': 406} Chain: "G" Number of atoms: 5296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5296 Classifications: {'peptide': 688} Link IDs: {'PTRANS': 31, 'TRANS': 656} Chain: "H" Number of atoms: 2540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2540 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 22, 'TRANS': 295} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1408 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 9, 'TRANS': 168} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 16 Chain: "J" Number of atoms: 1300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1300 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 3, 'TRANS': 167} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 737 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 4800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4800 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 26, 'TRANS': 579} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3632 Classifications: {'peptide': 459} Link IDs: {'PTRANS': 20, 'TRANS': 438} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 2696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2696 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 20, 'TRANS': 323} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2607 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 16, 'TRANS': 303} Chain: "P" Number of atoms: 2748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2748 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 19, 'TRANS': 322} Chain: "Q" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1015 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "R" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 748 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "S" Number of atoms: 667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 667 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} Chain: "T" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 604 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "U" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 706 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain: "V" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 915 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 8, 'TRANS': 103} Chain: "W" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 970 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "X" Number of atoms: 1396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1396 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 11, 'TRANS': 159} Chain: "Y" Number of atoms: 1037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1037 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain: "Z" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1152 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 9, 'TRANS': 129} Chain: "a" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 548 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "b" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 651 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 11, 'TRANS': 71} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "c" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 389 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "d" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 985 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 12, 'TRANS': 106} Chain: "e" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 870 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "f" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 433 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "g" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 850 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 8, 'TRANS': 92} Chain: "h" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1154 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 11, 'TRANS': 125} Chain: "i" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 820 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 11, 'TRANS': 89} Chain breaks: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'GLN:plan1': 1, 'SAC:plan-2': 1, 'ASP:plan': 1, 'TYR:plan': 1, 'HIS:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "j" Number of atoms: 525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 525 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 4, 'TRANS': 55} Chain: "k" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 582 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 4, 'TRANS': 67} Chain: "l" Number of atoms: 1274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1274 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 18, 'TRANS': 133} Chain: "m" Number of atoms: 1035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1035 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 11, 'TRANS': 112} Chain: "n" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1527 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 15, 'TRANS': 160} Chain: "o" Number of atoms: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 898 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "p" Number of atoms: 1438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1438 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 10, 'TRANS': 159} Chain: "q" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1204 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 11, 'TRANS': 132} Chain: "r" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 796 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 11, 'TRANS': 87} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "s" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 336 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 3, 'TRANS': 36} Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 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: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 283 Unusual residues: {'3PE': 2, 'CDL': 1, 'PC1': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 81 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: "L" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 241 Unusual residues: {'3PE': 2, 'CDL': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 61 Chain: "M" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 344 Unusual residues: {'3PE': 6, 'CDL': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 64 Chain: "N" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'NDP': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 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: "T" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'EHZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Chain: "U" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'EHZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1682 SG CYS B 129 95.645 92.068 198.611 1.00 28.96 S ATOM 1185 SG CYS B 65 89.776 94.517 200.168 1.00 30.11 S ATOM 1179 SG CYS B 64 89.801 88.850 197.115 1.00 29.52 S ATOM 1912 SG CYS B 159 92.408 89.154 202.981 1.00 29.28 S ATOM 8140 SG CYS E 103 112.379 42.870 252.522 1.00 56.01 S ATOM 8174 SG CYS E 108 111.396 39.725 253.878 1.00 56.50 S ATOM 8458 SG CYS E 144 115.715 40.548 248.920 1.00 54.42 S ATOM 8481 SG CYS E 148 114.643 37.474 249.947 1.00 57.95 S ATOM 11682 SG CYS F 362 119.365 49.764 229.257 1.00 40.29 S ATOM 11702 SG CYS F 365 115.488 49.525 233.799 1.00 39.95 S ATOM 12024 SG CYS F 405 119.357 44.728 233.247 1.00 45.60 S ATOM 11663 SG CYS F 359 121.785 50.934 234.697 1.00 43.09 S ATOM 13112 SG CYS G 114 114.320 68.352 219.891 1.00 33.13 S ATOM 13051 SG CYS G 105 108.717 71.098 222.547 1.00 30.26 S ATOM 13072 SG CYS G 108 114.613 72.967 223.845 1.00 31.31 S ATOM 13444 SG CYS G 156 123.005 62.516 225.095 1.00 35.62 S ATOM 13421 SG CYS G 153 120.184 64.738 230.811 1.00 34.05 S ATOM 13468 SG CYS G 159 126.314 65.510 229.483 1.00 36.31 S ATOM 13797 SG CYS G 203 121.828 68.412 225.656 1.00 34.31 S ATOM 12558 SG CYS G 41 123.841 55.936 221.863 1.00 35.53 S ATOM 12644 SG CYS G 52 119.658 55.806 221.488 1.00 36.47 S ATOM 12669 SG CYS G 55 121.406 52.238 217.852 1.00 36.76 S ATOM 12770 SG CYS G 69 124.257 53.976 218.077 1.00 39.04 S ATOM 21071 SG CYS I 121 96.352 83.749 208.893 1.00 27.04 S ATOM 21045 SG CYS I 118 96.656 90.574 210.402 1.00 27.39 S ATOM 21092 SG CYS I 124 97.767 85.898 214.507 1.00 26.60 S ATOM 20819 SG CYS I 89 101.652 87.009 209.366 1.00 27.30 S ATOM 21121 SG CYS I 128 100.266 82.743 221.857 1.00 28.07 S ATOM 20791 SG CYS I 85 104.136 85.061 217.017 1.00 28.85 S ATOM 20749 SG CYS I 79 105.246 87.137 222.791 1.00 28.61 S ATOM 20768 SG CYS I 82 106.100 81.023 221.845 1.00 29.24 S ATOM 41546 SG CYS R 59 102.269 78.266 236.723 1.00 32.60 S ATOM 41722 SG CYS R 84 105.065 79.765 235.368 1.00 32.49 S ATOM 41744 SG CYS R 87 101.936 81.410 234.312 1.00 30.78 S Time building chain proxies: 26.30, per 1000 atoms: 0.39 Number of scatterers: 66811 At special positions: 0 Unit cell: (185.85, 190.05, 285.6, 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 1 29.99 Fe 28 26.01 S 492 16.00 P 32 15.00 O 11984 8.00 N 11078 7.00 C 43196 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS X 35 " - pdb=" SG CYS X 65 " distance=2.03 Simple disulfide: pdb=" SG CYS X 45 " - pdb=" SG CYS X 55 " distance=2.03 Simple disulfide: pdb=" SG CYS X 77 " - pdb=" SG CYS X 109 " distance=2.04 Simple disulfide: pdb=" SG CYS X 87 " - pdb=" SG CYS X 99 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 17 " - pdb=" SG CYS Y 74 " distance=2.03 Simple disulfide: pdb=" SG CYS e 32 " - pdb=" SG CYS e 65 " distance=2.04 Simple disulfide: pdb=" SG CYS e 42 " - pdb=" SG CYS e 55 " distance=2.05 Simple disulfide: pdb=" SG CYS o 58 " - pdb=" SG CYS o 89 " distance=2.03 Simple disulfide: pdb=" SG CYS o 68 " - pdb=" SG CYS o 79 " distance=2.03 Simple disulfide: pdb=" SG CYS p 76 " - pdb=" SG CYS p 83 " distance=2.05 Simple disulfide: pdb=" SG CYS p 112 " - pdb=" SG CYS p 124 " 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 20.44 Conformation dependent library (CDL) restraints added in 9.4 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 103 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 108 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 148 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 144 " pdb=" FES G 803 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 41 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 55 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 69 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 52 " pdb=" SF4 B 201 " pdb="FE1 SF4 B 201 " - pdb=" SG CYS B 129 " pdb="FE4 SF4 B 201 " - pdb=" SG CYS B 159 " pdb="FE3 SF4 B 201 " - pdb=" SG CYS B 64 " pdb="FE2 SF4 B 201 " - pdb=" SG CYS B 65 " pdb=" SF4 F 502 " pdb="FE2 SF4 F 502 " - pdb=" SG CYS F 365 " pdb="FE3 SF4 F 502 " - pdb=" SG CYS F 405 " pdb="FE1 SF4 F 502 " - pdb=" SG CYS F 362 " pdb="FE4 SF4 F 502 " - pdb=" SG CYS F 359 " pdb=" SF4 G 801 " pdb="FE3 SF4 G 801 " - pdb=" NE2 HIS G 101 " pdb="FE4 SF4 G 801 " - pdb=" SG CYS G 108 " pdb="FE1 SF4 G 801 " - pdb=" SG CYS G 114 " pdb="FE2 SF4 G 801 " - pdb=" SG CYS G 105 " pdb=" SF4 G 802 " pdb="FE4 SF4 G 802 " - pdb=" SG CYS G 203 " pdb="FE1 SF4 G 802 " - pdb=" SG CYS G 156 " pdb="FE3 SF4 G 802 " - pdb=" SG CYS G 159 " pdb="FE2 SF4 G 802 " - pdb=" SG CYS G 153 " pdb=" SF4 I 201 " pdb="FE1 SF4 I 201 " - pdb=" SG CYS I 121 " pdb="FE3 SF4 I 201 " - pdb=" SG CYS I 124 " pdb="FE4 SF4 I 201 " - pdb=" SG CYS I 89 " pdb="FE2 SF4 I 201 " - pdb=" SG CYS I 118 " pdb="FE2 SF4 I 201 " - pdb=" NE2 HIS I 67 " pdb=" SF4 I 202 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 82 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 128 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 79 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 85 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" NE2 HIS R 68 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 84 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 59 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 87 " Number of angles added : 3 16112 Ramachandran restraints generated. 8056 Oldfield, 0 Emsley, 8056 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15372 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 327 helices and 22 sheets defined 42.8% alpha, 1.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.28 Creating SS restraints... Processing helix chain 'A' and resid 4 through 22 removed outlier: 4.696A pdb=" N ILE A 9 " --> pdb=" O THR A 5 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN A 10 " --> pdb=" O VAL A 6 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 17 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL A 20 " --> pdb=" O THR A 16 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA A 21 " --> pdb=" O LEU A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 80 removed outlier: 3.732A pdb=" N ILE A 60 " --> pdb=" O PHE A 56 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LEU A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) Proline residue: A 74 - end of helix removed outlier: 5.551A pdb=" N TRP A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N GLN A 80 " --> pdb=" O PRO A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 107 removed outlier: 3.612A pdb=" N GLU A 105 " --> pdb=" O GLY A 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 53 removed outlier: 3.851A pdb=" N ASN B 48 " --> pdb=" O ASP B 44 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TRP B 49 " --> pdb=" O ASP B 45 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ALA B 50 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG B 51 " --> pdb=" O ILE B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 72 Processing helix chain 'B' and resid 80 through 82 No H-bonds generated for 'chain 'B' and resid 80 through 82' Processing helix chain 'B' and resid 104 through 116 Proline residue: B 108 - end of helix removed outlier: 3.819A pdb=" N VAL B 113 " --> pdb=" O ALA B 109 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLN B 116 " --> pdb=" O LYS B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 131 No H-bonds generated for 'chain 'B' and resid 128 through 131' Processing helix chain 'B' and resid 146 through 148 No H-bonds generated for 'chain 'B' and resid 146 through 148' Processing helix chain 'B' and resid 163 through 166 No H-bonds generated for 'chain 'B' and resid 163 through 166' Processing helix chain 'B' and resid 173 through 176 No H-bonds generated for 'chain 'B' and resid 173 through 176' Processing helix chain 'B' and resid 184 through 187 No H-bonds generated for 'chain 'B' and resid 184 through 187' Processing helix chain 'C' and resid 16 through 31 removed outlier: 3.554A pdb=" N HIS C 19 " --> pdb=" O ASP C 16 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N GLN C 21 " --> pdb=" O THR C 18 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU C 22 " --> pdb=" O HIS C 19 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER C 23 " --> pdb=" O LYS C 20 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA C 24 " --> pdb=" O GLN C 21 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU C 27 " --> pdb=" O ALA C 24 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR C 28 " --> pdb=" O PHE C 25 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU C 31 " --> pdb=" O TYR C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 56 No H-bonds generated for 'chain 'C' and resid 54 through 56' Processing helix chain 'C' and resid 58 through 60 No H-bonds generated for 'chain 'C' and resid 58 through 60' Processing helix chain 'C' and resid 62 through 65 No H-bonds generated for 'chain 'C' and resid 62 through 65' Processing helix chain 'C' and resid 125 through 137 removed outlier: 3.777A pdb=" N TRP C 129 " --> pdb=" O ALA C 126 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TYR C 130 " --> pdb=" O ALA C 127 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N GLU C 131 " --> pdb=" O ASN C 128 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU C 133 " --> pdb=" O TYR C 130 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N MET C 137 " --> pdb=" O VAL C 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 93 No H-bonds generated for 'chain 'D' and resid 91 through 93' Processing helix chain 'D' and resid 100 through 106 removed outlier: 3.635A pdb=" N LEU D 106 " --> pdb=" O PHE D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.824A pdb=" N ILE D 120 " --> pdb=" O GLN D 116 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLU D 123 " --> pdb=" O SER D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 142 Processing helix chain 'D' and resid 145 through 154 removed outlier: 3.558A pdb=" N ILE D 151 " --> pdb=" O ILE D 147 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N MET D 152 " --> pdb=" O LEU D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 159 No H-bonds generated for 'chain 'D' and resid 156 through 159' Processing helix chain 'D' and resid 165 through 173 removed outlier: 3.760A pdb=" N GLU D 173 " --> pdb=" O TRP D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 182 removed outlier: 4.211A pdb=" N PHE D 180 " --> pdb=" O LYS D 176 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR D 181 " --> pdb=" O MET D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 229 removed outlier: 3.852A pdb=" N GLU D 213 " --> pdb=" O ASP D 209 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N ASN D 217 " --> pdb=" O GLU D 213 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N SER D 219 " --> pdb=" O SER D 215 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N LEU D 220 " --> pdb=" O LYS D 216 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP D 223 " --> pdb=" O SER D 219 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N MET D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 238 Processing helix chain 'D' and resid 247 through 253 removed outlier: 3.747A pdb=" N LEU D 251 " --> pdb=" O ALA D 247 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN D 252 " --> pdb=" O GLU D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 263 No H-bonds generated for 'chain 'D' and resid 261 through 263' Processing helix chain 'D' and resid 295 through 316 removed outlier: 3.528A pdb=" N GLU D 303 " --> pdb=" O CYS D 299 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N MET D 304 " --> pdb=" O ARG D 300 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG D 305 " --> pdb=" O VAL D 301 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU D 312 " --> pdb=" O LEU D 308 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN D 313 " --> pdb=" O ARG D 309 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASN D 316 " --> pdb=" O GLU D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 340 No H-bonds generated for 'chain 'D' and resid 337 through 340' Processing helix chain 'D' and resid 343 through 351 Processing helix chain 'D' and resid 400 through 402 No H-bonds generated for 'chain 'D' and resid 400 through 402' Processing helix chain 'D' and resid 411 through 417 removed outlier: 3.671A pdb=" N VAL D 415 " --> pdb=" O LEU D 411 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ALA D 416 " --> pdb=" O ALA D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 421 No H-bonds generated for 'chain 'D' and resid 419 through 421' Processing helix chain 'E' and resid 25 through 35 removed outlier: 3.743A pdb=" N GLU E 32 " --> pdb=" O TYR E 28 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ALA E 33 " --> pdb=" O LYS E 29 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE E 34 " --> pdb=" O ARG E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 57 removed outlier: 3.573A pdb=" N VAL E 47 " --> pdb=" O ALA E 44 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LEU E 48 " --> pdb=" O ALA E 45 " (cutoff:3.500A) Proline residue: E 49 - end of helix removed outlier: 4.019A pdb=" N ALA E 54 " --> pdb=" O LEU E 51 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN E 57 " --> pdb=" O ALA E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 73 removed outlier: 4.343A pdb=" N ALA E 70 " --> pdb=" O MET E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 86 removed outlier: 3.862A pdb=" N VAL E 83 " --> pdb=" O ARG E 79 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA E 84 " --> pdb=" O VAL E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 109 No H-bonds generated for 'chain 'E' and resid 106 through 109' Processing helix chain 'E' and resid 115 through 124 removed outlier: 3.797A pdb=" N LEU E 120 " --> pdb=" O ILE E 116 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG E 122 " --> pdb=" O GLU E 118 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS E 123 " --> pdb=" O THR E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 177 removed outlier: 4.079A pdb=" N GLU E 170 " --> pdb=" O PRO E 166 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLU E 171 " --> pdb=" O LYS E 167 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE E 172 " --> pdb=" O ASP E 168 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP E 174 " --> pdb=" O GLU E 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 19 No H-bonds generated for 'chain 'F' and resid 17 through 19' Processing helix chain 'F' and resid 45 through 50 removed outlier: 3.541A pdb=" N LEU F 49 " --> pdb=" O THR F 45 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU F 50 " --> pdb=" O LYS F 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 45 through 50' Processing helix chain 'F' and resid 53 through 61 Processing helix chain 'F' and resid 79 through 82 Processing helix chain 'F' and resid 105 through 107 No H-bonds generated for 'chain 'F' and resid 105 through 107' Processing helix chain 'F' and resid 115 through 129 removed outlier: 3.534A pdb=" N GLY F 121 " --> pdb=" O LYS F 117 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N CYS F 122 " --> pdb=" O LEU F 118 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU F 123 " --> pdb=" O VAL F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 158 removed outlier: 3.542A pdb=" N GLU F 155 " --> pdb=" O VAL F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 187 No H-bonds generated for 'chain 'F' and resid 185 through 187' Processing helix chain 'F' and resid 191 through 196 Processing helix chain 'F' and resid 215 through 217 No H-bonds generated for 'chain 'F' and resid 215 through 217' Processing helix chain 'F' and resid 225 through 229 Processing helix chain 'F' and resid 232 through 235 No H-bonds generated for 'chain 'F' and resid 232 through 235' Processing helix chain 'F' and resid 241 through 244 No H-bonds generated for 'chain 'F' and resid 241 through 244' Processing helix chain 'F' and resid 276 through 279 No H-bonds generated for 'chain 'F' and resid 276 through 279' Processing helix chain 'F' and resid 312 through 314 No H-bonds generated for 'chain 'F' and resid 312 through 314' Processing helix chain 'F' and resid 319 through 324 removed outlier: 3.857A pdb=" N VAL F 323 " --> pdb=" O PHE F 319 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLN F 324 " --> pdb=" O ASP F 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 319 through 324' Processing helix chain 'F' and resid 343 through 355 Processing helix chain 'F' and resid 363 through 366 No H-bonds generated for 'chain 'F' and resid 363 through 366' Processing helix chain 'F' and resid 369 through 380 removed outlier: 3.531A pdb=" N LYS F 374 " --> pdb=" O ASP F 370 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL F 375 " --> pdb=" O TRP F 371 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG F 378 " --> pdb=" O LYS F 374 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 398 removed outlier: 4.333A pdb=" N ASP F 390 " --> pdb=" O ALA F 387 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU F 392 " --> pdb=" O ILE F 389 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N TRP F 393 " --> pdb=" O ASP F 390 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE F 395 " --> pdb=" O LEU F 392 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS F 397 " --> pdb=" O GLU F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 420 Proline residue: F 414 - end of helix Processing helix chain 'F' and resid 423 through 435 Processing helix chain 'G' and resid 26 through 31 Processing helix chain 'G' and resid 84 through 88 removed outlier: 3.699A pdb=" N LYS G 88 " --> pdb=" O GLU G 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 84 through 88' Processing helix chain 'G' and resid 94 through 97 No H-bonds generated for 'chain 'G' and resid 94 through 97' Processing helix chain 'G' and resid 117 through 122 Processing helix chain 'G' and resid 198 through 202 Processing helix chain 'G' and resid 219 through 221 No H-bonds generated for 'chain 'G' and resid 219 through 221' Processing helix chain 'G' and resid 266 through 275 removed outlier: 6.403A pdb=" N TYR G 271 " --> pdb=" O THR G 267 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ASP G 272 " --> pdb=" O ARG G 268 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N GLY G 273 " --> pdb=" O PHE G 269 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU G 274 " --> pdb=" O ALA G 270 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LYS G 275 " --> pdb=" O TYR G 271 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 306 removed outlier: 3.956A pdb=" N SER G 301 " --> pdb=" O GLU G 297 " (cutoff:3.500A) Processing helix chain 'G' and resid 327 through 336 removed outlier: 3.692A pdb=" N LEU G 335 " --> pdb=" O LEU G 331 " (cutoff:3.500A) Processing helix chain 'G' and resid 369 through 371 No H-bonds generated for 'chain 'G' and resid 369 through 371' Processing helix chain 'G' and resid 391 through 400 removed outlier: 3.589A pdb=" N ILE G 395 " --> pdb=" O PHE G 391 " (cutoff:3.500A) Processing helix chain 'G' and resid 427 through 434 Processing helix chain 'G' and resid 438 through 444 removed outlier: 3.554A pdb=" N LEU G 443 " --> pdb=" O CYS G 440 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS G 444 " --> pdb=" O GLU G 441 " (cutoff:3.500A) Processing helix chain 'G' and resid 464 through 480 removed outlier: 3.524A pdb=" N VAL G 468 " --> pdb=" O ALA G 464 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS G 476 " --> pdb=" O ASN G 472 " (cutoff:3.500A) Processing helix chain 'G' and resid 497 through 505 removed outlier: 3.982A pdb=" N VAL G 500 " --> pdb=" O ALA G 497 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ALA G 501 " --> pdb=" O SER G 498 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ALA G 502 " --> pdb=" O GLN G 499 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU G 503 " --> pdb=" O VAL G 500 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP G 504 " --> pdb=" O ALA G 501 " (cutoff:3.500A) Processing helix chain 'G' and resid 512 through 516 Processing helix chain 'G' and resid 597 through 606 removed outlier: 3.702A pdb=" N ARG G 601 " --> pdb=" O TRP G 597 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ALA G 602 " --> pdb=" O LYS G 598 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU G 605 " --> pdb=" O ARG G 601 " (cutoff:3.500A) Processing helix chain 'G' and resid 616 through 626 removed outlier: 3.829A pdb=" N ARG G 620 " --> pdb=" O LEU G 616 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG G 622 " --> pdb=" O GLN G 618 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU G 625 " --> pdb=" O ASN G 621 " (cutoff:3.500A) Processing helix chain 'G' and resid 643 through 649 Processing helix chain 'G' and resid 682 through 691 removed outlier: 3.635A pdb=" N CYS G 687 " --> pdb=" O THR G 683 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 32 removed outlier: 3.535A pdb=" N THR H 8 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL H 11 " --> pdb=" O LEU H 7 " (cutoff:3.500A) Proline residue: H 12 - end of helix removed outlier: 4.397A pdb=" N ALA H 16 " --> pdb=" O PRO H 12 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE H 19 " --> pdb=" O ILE H 15 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG H 25 " --> pdb=" O THR H 21 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LEU H 28 " --> pdb=" O GLU H 24 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 55 Processing helix chain 'H' and resid 68 through 86 removed outlier: 3.715A pdb=" N ILE H 72 " --> pdb=" O MET H 68 " (cutoff:3.500A) Proline residue: H 75 - end of helix removed outlier: 4.567A pdb=" N TRP H 86 " --> pdb=" O ALA H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 122 removed outlier: 3.558A pdb=" N SER H 112 " --> pdb=" O THR H 108 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE H 116 " --> pdb=" O SER H 112 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER H 119 " --> pdb=" O SER H 115 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY H 120 " --> pdb=" O ILE H 116 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 142 removed outlier: 4.423A pdb=" N GLY H 131 " --> pdb=" O TYR H 127 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN H 138 " --> pdb=" O ARG H 134 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER H 141 " --> pdb=" O ALA H 137 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 155 removed outlier: 4.048A pdb=" N LEU H 150 " --> pdb=" O MET H 146 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL H 153 " --> pdb=" O ILE H 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 162 through 168 Processing helix chain 'H' and resid 174 through 177 No H-bonds generated for 'chain 'H' and resid 174 through 177' Processing helix chain 'H' and resid 179 through 191 Processing helix chain 'H' and resid 217 through 236 removed outlier: 4.495A pdb=" N LEU H 222 " --> pdb=" O GLY H 218 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N PHE H 223 " --> pdb=" O PRO H 219 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE H 224 " --> pdb=" O PHE H 220 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR H 229 " --> pdb=" O MET H 225 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ILE H 232 " --> pdb=" O TYR H 228 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU H 233 " --> pdb=" O THR H 229 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN H 235 " --> pdb=" O ILE H 231 " (cutoff:3.500A) Processing helix chain 'H' and resid 238 through 241 No H-bonds generated for 'chain 'H' and resid 238 through 241' Processing helix chain 'H' and resid 253 through 274 removed outlier: 3.837A pdb=" N LEU H 265 " --> pdb=" O MET H 261 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE H 270 " --> pdb=" O LEU H 266 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU H 271 " --> pdb=" O SER H 267 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TRP H 272 " --> pdb=" O SER H 268 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE H 273 " --> pdb=" O THR H 269 " (cutoff:3.500A) Processing helix chain 'H' and resid 284 through 287 No H-bonds generated for 'chain 'H' and resid 284 through 287' Processing helix chain 'H' and resid 293 through 308 removed outlier: 3.513A pdb=" N ILE H 305 " --> pdb=" O CYS H 301 " (cutoff:3.500A) Proline residue: H 308 - end of helix Processing helix chain 'I' and resid 16 through 23 removed outlier: 3.596A pdb=" N THR I 20 " --> pdb=" O MET I 16 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN I 22 " --> pdb=" O SER I 18 " (cutoff:3.500A) Processing helix chain 'I' and resid 30 through 43 removed outlier: 3.867A pdb=" N GLY I 35 " --> pdb=" O GLU I 31 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N MET I 38 " --> pdb=" O ARG I 34 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N TYR I 42 " --> pdb=" O MET I 38 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU I 43 " --> pdb=" O THR I 39 " (cutoff:3.500A) Processing helix chain 'I' and resid 123 through 127 Processing helix chain 'I' and resid 147 through 149 No H-bonds generated for 'chain 'I' and resid 147 through 149' Processing helix chain 'I' and resid 154 through 160 removed outlier: 3.510A pdb=" N ASN I 158 " --> pdb=" O GLU I 154 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASN I 159 " --> pdb=" O LYS I 155 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY I 160 " --> pdb=" O LEU I 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 154 through 160' Processing helix chain 'I' and resid 163 through 172 removed outlier: 3.748A pdb=" N ILE I 167 " --> pdb=" O GLU I 164 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ALA I 168 " --> pdb=" O ALA I 165 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA I 169 " --> pdb=" O GLU I 166 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN I 172 " --> pdb=" O ALA I 169 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 15 Processing helix chain 'J' and resid 18 through 21 No H-bonds generated for 'chain 'J' and resid 18 through 21' Processing helix chain 'J' and resid 25 through 45 removed outlier: 3.522A pdb=" N GLY J 31 " --> pdb=" O TYR J 27 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER J 35 " --> pdb=" O GLY J 31 " (cutoff:3.500A) Processing helix chain 'J' and resid 49 through 61 removed outlier: 3.547A pdb=" N LEU J 53 " --> pdb=" O SER J 49 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL J 55 " --> pdb=" O LEU J 51 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N LEU J 60 " --> pdb=" O PHE J 56 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY J 61 " --> pdb=" O LEU J 57 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 70 removed outlier: 3.517A pdb=" N GLY J 68 " --> pdb=" O LEU J 64 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR J 70 " --> pdb=" O VAL J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 105 removed outlier: 3.829A pdb=" N PHE J 91 " --> pdb=" O LEU J 87 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLY J 95 " --> pdb=" O PHE J 91 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL J 96 " --> pdb=" O LEU J 92 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N CYS J 104 " --> pdb=" O VAL J 100 " (cutoff:3.500A) Processing helix chain 'J' and resid 141 through 144 Processing helix chain 'J' and resid 150 through 165 removed outlier: 3.646A pdb=" N SER J 158 " --> pdb=" O VAL J 154 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE J 164 " --> pdb=" O PHE J 160 " (cutoff:3.500A) Processing helix chain 'J' and resid 167 through 170 No H-bonds generated for 'chain 'J' and resid 167 through 170' Processing helix chain 'K' and resid 5 through 18 removed outlier: 3.517A pdb=" N LEU K 14 " --> pdb=" O MET K 10 " (cutoff:3.500A) Processing helix chain 'K' and resid 29 through 45 removed outlier: 3.704A pdb=" N GLU K 34 " --> pdb=" O LEU K 30 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLY K 35 " --> pdb=" O LEU K 31 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET K 36 " --> pdb=" O CYS K 32 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU K 40 " --> pdb=" O MET K 36 " (cutoff:3.500A) Processing helix chain 'K' and resid 47 through 50 No H-bonds generated for 'chain 'K' and resid 47 through 50' Processing helix chain 'K' and resid 54 through 56 No H-bonds generated for 'chain 'K' and resid 54 through 56' Processing helix chain 'K' and resid 59 through 85 removed outlier: 4.178A pdb=" N LEU K 64 " --> pdb=" O PRO K 60 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE K 66 " --> pdb=" O THR K 62 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA K 67 " --> pdb=" O ILE K 63 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA K 68 " --> pdb=" O LEU K 64 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU K 70 " --> pdb=" O PHE K 66 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA K 71 " --> pdb=" O ALA K 67 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU K 77 " --> pdb=" O VAL K 73 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU K 78 " --> pdb=" O GLY K 74 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL K 79 " --> pdb=" O LEU K 75 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS K 80 " --> pdb=" O ALA K 76 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N THR K 84 " --> pdb=" O LYS K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 92 No H-bonds generated for 'chain 'K' and resid 90 through 92' Processing helix chain 'L' and resid 3 through 15 removed outlier: 3.646A pdb=" N SER L 7 " --> pdb=" O ILE L 3 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU L 10 " --> pdb=" O THR L 6 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N PHE L 12 " --> pdb=" O ILE L 8 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE L 13 " --> pdb=" O LEU L 9 " (cutoff:3.500A) Processing helix chain 'L' and resid 17 through 20 No H-bonds generated for 'chain 'L' and resid 17 through 20' Processing helix chain 'L' and resid 32 through 57 removed outlier: 3.624A pdb=" N SER L 43 " --> pdb=" O SER L 39 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE L 45 " --> pdb=" O LYS L 41 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU L 49 " --> pdb=" O ILE L 45 " (cutoff:3.500A) Proline residue: L 50 - end of helix removed outlier: 4.131A pdb=" N HIS L 56 " --> pdb=" O LEU L 52 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN L 57 " --> pdb=" O MET L 53 " (cutoff:3.500A) Processing helix chain 'L' and resid 95 through 101 Processing helix chain 'L' and resid 103 through 106 No H-bonds generated for 'chain 'L' and resid 103 through 106' Processing helix chain 'L' and resid 115 through 133 removed outlier: 3.533A pdb=" N TYR L 120 " --> pdb=" O ARG L 116 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU L 131 " --> pdb=" O THR L 127 " (cutoff:3.500A) Processing helix chain 'L' and resid 139 through 148 removed outlier: 3.842A pdb=" N GLY L 143 " --> pdb=" O GLN L 139 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL L 147 " --> pdb=" O GLY L 143 " (cutoff:3.500A) Processing helix chain 'L' and resid 150 through 155 Processing helix chain 'L' and resid 162 through 190 removed outlier: 3.725A pdb=" N TYR L 174 " --> pdb=" O GLN L 170 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE L 180 " --> pdb=" O ARG L 176 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLY L 181 " --> pdb=" O ILE L 177 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TRP L 188 " --> pdb=" O LEU L 184 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER L 190 " --> pdb=" O MET L 186 " (cutoff:3.500A) Processing helix chain 'L' and resid 198 through 204 removed outlier: 4.279A pdb=" N PHE L 203 " --> pdb=" O GLN L 199 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER L 204 " --> pdb=" O GLN L 200 " (cutoff:3.500A) Processing helix chain 'L' and resid 211 through 223 removed outlier: 3.689A pdb=" N LEU L 217 " --> pdb=" O LEU L 213 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY L 222 " --> pdb=" O ILE L 218 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS L 223 " --> pdb=" O ALA L 219 " (cutoff:3.500A) Processing helix chain 'L' and resid 231 through 237 removed outlier: 3.645A pdb=" N SER L 235 " --> pdb=" O PRO L 231 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N MET L 237 " --> pdb=" O LEU L 233 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 246 Processing helix chain 'L' and resid 253 through 262 removed outlier: 4.091A pdb=" N GLY L 256 " --> pdb=" O VAL L 253 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE L 257 " --> pdb=" O VAL L 254 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE L 258 " --> pdb=" O ALA L 255 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU L 260 " --> pdb=" O ILE L 257 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL L 261 " --> pdb=" O PHE L 258 " (cutoff:3.500A) Processing helix chain 'L' and resid 264 through 267 No H-bonds generated for 'chain 'L' and resid 264 through 267' Processing helix chain 'L' and resid 273 through 293 removed outlier: 4.279A pdb=" N LEU L 278 " --> pdb=" O LEU L 274 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA L 289 " --> pdb=" O THR L 285 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 318 removed outlier: 3.510A pdb=" N THR L 306 " --> pdb=" O ILE L 302 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER L 307 " --> pdb=" O ALA L 303 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N MET L 313 " --> pdb=" O GLN L 309 " (cutoff:3.500A) Processing helix chain 'L' and resid 322 through 334 removed outlier: 3.977A pdb=" N CYS L 330 " --> pdb=" O PHE L 326 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR L 331 " --> pdb=" O LEU L 327 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ALA L 333 " --> pdb=" O ILE L 329 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N PHE L 334 " --> pdb=" O CYS L 330 " (cutoff:3.500A) Processing helix chain 'L' and resid 336 through 347 removed outlier: 3.515A pdb=" N PHE L 340 " --> pdb=" O LYS L 336 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N MET L 341 " --> pdb=" O ALA L 337 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N SER L 345 " --> pdb=" O MET L 341 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE L 346 " --> pdb=" O CYS L 342 " (cutoff:3.500A) Processing helix chain 'L' and resid 362 through 365 No H-bonds generated for 'chain 'L' and resid 362 through 365' Processing helix chain 'L' and resid 369 through 381 removed outlier: 4.396A pdb=" N VAL L 374 " --> pdb=" O SER L 370 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE L 375 " --> pdb=" O SER L 371 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA L 379 " --> pdb=" O ILE L 375 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR L 381 " --> pdb=" O SER L 377 " (cutoff:3.500A) Processing helix chain 'L' and resid 392 through 399 Processing helix chain 'L' and resid 407 through 416 removed outlier: 3.745A pdb=" N THR L 412 " --> pdb=" O ALA L 408 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA L 415 " --> pdb=" O ILE L 411 " (cutoff:3.500A) Processing helix chain 'L' and resid 421 through 429 removed outlier: 3.553A pdb=" N TYR L 428 " --> pdb=" O MET L 424 " (cutoff:3.500A) Processing helix chain 'L' and resid 448 through 471 Proline residue: L 453 - end of helix removed outlier: 6.051A pdb=" N GLY L 465 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N PHE L 466 " --> pdb=" O ILE L 462 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR L 470 " --> pdb=" O PHE L 466 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN L 471 " --> pdb=" O VAL L 467 " (cutoff:3.500A) Processing helix chain 'L' and resid 484 through 504 removed outlier: 3.695A pdb=" N THR L 488 " --> pdb=" O TRP L 484 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N THR L 489 " --> pdb=" O PHE L 485 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ALA L 490 " --> pdb=" O LEU L 486 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N LEU L 491 " --> pdb=" O LYS L 487 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY L 497 " --> pdb=" O ILE L 493 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE L 498 " --> pdb=" O SER L 494 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU L 499 " --> pdb=" O VAL L 495 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE L 500 " --> pdb=" O LEU L 496 " (cutoff:3.500A) Processing helix chain 'L' and resid 522 through 525 No H-bonds generated for 'chain 'L' and resid 522 through 525' Processing helix chain 'L' and resid 529 through 532 No H-bonds generated for 'chain 'L' and resid 529 through 532' Processing helix chain 'L' and resid 537 through 540 No H-bonds generated for 'chain 'L' and resid 537 through 540' Processing helix chain 'L' and resid 558 through 561 No H-bonds generated for 'chain 'L' and resid 558 through 561' Processing helix chain 'L' and resid 563 through 577 removed outlier: 3.678A pdb=" N HIS L 570 " --> pdb=" O THR L 566 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N MET L 573 " --> pdb=" O LEU L 569 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N THR L 574 " --> pdb=" O HIS L 570 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N THR L 575 " --> pdb=" O THR L 571 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU L 576 " --> pdb=" O ASN L 572 " (cutoff:3.500A) Processing helix chain 'L' and resid 584 through 605 removed outlier: 3.726A pdb=" N MET L 589 " --> pdb=" O LYS L 585 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE L 593 " --> pdb=" O MET L 589 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE L 604 " --> pdb=" O ILE L 600 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN L 605 " --> pdb=" O LEU L 601 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 16 removed outlier: 4.076A pdb=" N LEU M 12 " --> pdb=" O SER M 8 " (cutoff:3.500A) Proline residue: M 13 - end of helix removed outlier: 3.779A pdb=" N TRP M 16 " --> pdb=" O LEU M 12 " (cutoff:3.500A) Processing helix chain 'M' and resid 20 through 42 removed outlier: 4.471A pdb=" N TRP M 24 " --> pdb=" O PRO M 20 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N THR M 25 " --> pdb=" O LYS M 21 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN M 26 " --> pdb=" O LYS M 22 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER M 31 " --> pdb=" O VAL M 27 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE M 32 " --> pdb=" O THR M 28 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU M 33 " --> pdb=" O SER M 29 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU M 36 " --> pdb=" O PHE M 32 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR M 37 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR M 40 " --> pdb=" O LEU M 36 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LEU M 41 " --> pdb=" O THR M 37 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N LEU M 42 " --> pdb=" O SER M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 79 removed outlier: 3.800A pdb=" N LEU M 73 " --> pdb=" O THR M 69 " (cutoff:3.500A) Proline residue: M 74 - end of helix Processing helix chain 'M' and resid 89 through 99 removed outlier: 4.694A pdb=" N ILE M 96 " --> pdb=" O GLN M 92 " (cutoff:3.500A) Processing helix chain 'M' and resid 101 through 110 Processing helix chain 'M' and resid 116 through 136 removed outlier: 3.504A pdb=" N THR M 125 " --> pdb=" O LEU M 121 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N LEU M 126 " --> pdb=" O PHE M 122 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE M 127 " --> pdb=" O GLU M 123 " (cutoff:3.500A) Proline residue: M 128 - end of helix removed outlier: 4.080A pdb=" N ILE M 132 " --> pdb=" O PRO M 128 " (cutoff:3.500A) Processing helix chain 'M' and resid 140 through 171 removed outlier: 4.352A pdb=" N LEU M 143 " --> pdb=" O THR M 140 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA M 145 " --> pdb=" O ARG M 142 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE M 147 " --> pdb=" O ASN M 144 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE M 149 " --> pdb=" O GLY M 146 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N TYR M 152 " --> pdb=" O PHE M 149 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N THR M 153 " --> pdb=" O LEU M 150 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU M 154 " --> pdb=" O PHE M 151 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE M 155 " --> pdb=" O TYR M 152 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ILE M 158 " --> pdb=" O ILE M 155 " (cutoff:3.500A) Proline residue: M 159 - end of helix removed outlier: 4.506A pdb=" N LEU M 164 " --> pdb=" O LEU M 161 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE M 165 " --> pdb=" O ILE M 162 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE M 167 " --> pdb=" O LEU M 164 " (cutoff:3.500A) Processing helix chain 'M' and resid 190 through 192 No H-bonds generated for 'chain 'M' and resid 190 through 192' Processing helix chain 'M' and resid 194 through 206 removed outlier: 4.701A pdb=" N ALA M 202 " --> pdb=" O ALA M 198 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N PHE M 203 " --> pdb=" O CYS M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 212 through 222 removed outlier: 3.865A pdb=" N TRP M 215 " --> pdb=" O VAL M 212 " (cutoff:3.500A) Proline residue: M 217 - end of helix removed outlier: 4.091A pdb=" N VAL M 221 " --> pdb=" O LYS M 218 " (cutoff:3.500A) Processing helix chain 'M' and resid 229 through 233 Processing helix chain 'M' and resid 235 through 250 removed outlier: 3.838A pdb=" N GLY M 239 " --> pdb=" O LEU M 235 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N SER M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLY M 242 " --> pdb=" O LEU M 238 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET M 243 " --> pdb=" O GLY M 239 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N ILE M 248 " --> pdb=" O ILE M 244 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ILE M 249 " --> pdb=" O ARG M 245 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU M 250 " --> pdb=" O ILE M 246 " (cutoff:3.500A) Processing helix chain 'M' and resid 263 through 277 removed outlier: 3.737A pdb=" N GLY M 268 " --> pdb=" O LEU M 264 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE M 270 " --> pdb=" O LEU M 266 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N SER M 273 " --> pdb=" O MET M 269 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU M 277 " --> pdb=" O SER M 273 " (cutoff:3.500A) Processing helix chain 'M' and resid 283 through 301 removed outlier: 4.063A pdb=" N ALA M 287 " --> pdb=" O LYS M 283 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TYR M 288 " --> pdb=" O SER M 284 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU M 296 " --> pdb=" O SER M 292 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL M 297 " --> pdb=" O HIS M 293 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 337 removed outlier: 3.703A pdb=" N LEU M 315 " --> pdb=" O GLY M 311 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA M 318 " --> pdb=" O MET M 314 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER M 324 " --> pdb=" O GLY M 320 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASN M 333 " --> pdb=" O LEU M 329 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ARG M 336 " --> pdb=" O SER M 332 " (cutoff:3.500A) Processing helix chain 'M' and resid 353 through 366 removed outlier: 3.813A pdb=" N THR M 357 " --> pdb=" O PRO M 353 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TRP M 358 " --> pdb=" O LEU M 354 " (cutoff:3.500A) Processing helix chain 'M' and resid 374 through 388 removed outlier: 3.653A pdb=" N ILE M 381 " --> pdb=" O GLY M 377 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N THR M 382 " --> pdb=" O GLU M 378 " (cutoff:3.500A) Processing helix chain 'M' and resid 393 through 415 removed outlier: 4.040A pdb=" N ILE M 398 " --> pdb=" O ILE M 394 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N MET M 405 " --> pdb=" O ILE M 401 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR M 406 " --> pdb=" O ILE M 402 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER M 407 " --> pdb=" O THR M 403 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N MET M 408 " --> pdb=" O GLY M 404 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ILE M 411 " --> pdb=" O SER M 407 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR M 414 " --> pdb=" O MET M 410 " (cutoff:3.500A) Processing helix chain 'M' and resid 438 through 447 Proline residue: M 443 - end of helix Processing helix chain 'N' and resid 3 through 21 removed outlier: 4.141A pdb=" N ILE N 8 " --> pdb=" O ILE N 4 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE N 14 " --> pdb=" O TYR N 10 " (cutoff:3.500A) Proline residue: N 17 - end of helix Processing helix chain 'N' and resid 28 through 44 removed outlier: 4.203A pdb=" N LEU N 33 " --> pdb=" O MET N 29 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU N 34 " --> pdb=" O TRP N 30 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU N 37 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ILE N 40 " --> pdb=" O SER N 36 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ILE N 41 " --> pdb=" O LEU N 37 " (cutoff:3.500A) Proline residue: N 42 - end of helix Processing helix chain 'N' and resid 52 through 79 removed outlier: 4.201A pdb=" N THR N 62 " --> pdb=" O LYS N 58 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN N 63 " --> pdb=" O TYR N 59 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR N 65 " --> pdb=" O VAL N 61 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ALA N 66 " --> pdb=" O THR N 62 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER N 67 " --> pdb=" O GLN N 63 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA N 73 " --> pdb=" O ILE N 69 " (cutoff:3.500A) Processing helix chain 'N' and resid 92 through 106 Processing helix chain 'N' and resid 115 through 119 Processing helix chain 'N' and resid 128 through 132 Processing helix chain 'N' and resid 134 through 144 Proline residue: N 138 - end of helix removed outlier: 3.594A pdb=" N LEU N 142 " --> pdb=" O PRO N 138 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN N 144 " --> pdb=" O SER N 140 " (cutoff:3.500A) Processing helix chain 'N' and resid 153 through 170 removed outlier: 3.812A pdb=" N ALA N 158 " --> pdb=" O ILE N 154 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY N 168 " --> pdb=" O MET N 164 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLY N 169 " --> pdb=" O GLY N 165 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU N 170 " --> pdb=" O ALA N 166 " (cutoff:3.500A) Processing helix chain 'N' and resid 175 through 192 removed outlier: 3.629A pdb=" N TYR N 181 " --> pdb=" O LYS N 177 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY N 188 " --> pdb=" O ILE N 184 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N TRP N 189 " --> pdb=" O ALA N 185 " (cutoff:3.500A) Processing helix chain 'N' and resid 201 through 220 removed outlier: 3.616A pdb=" N ILE N 210 " --> pdb=" O MET N 206 " (cutoff:3.500A) Proline residue: N 214 - end of helix Processing helix chain 'N' and resid 227 through 231 Processing helix chain 'N' and resid 238 through 251 removed outlier: 4.100A pdb=" N THR N 242 " --> pdb=" O ALA N 239 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE N 244 " --> pdb=" O LEU N 241 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N SER N 245 " --> pdb=" O THR N 242 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET N 247 " --> pdb=" O ILE N 244 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LEU N 248 " --> pdb=" O SER N 245 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU N 249 " --> pdb=" O LEU N 246 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N SER N 250 " --> pdb=" O MET N 247 " (cutoff:3.500A) Processing helix chain 'N' and resid 258 through 273 Proline residue: N 262 - end of helix removed outlier: 3.781A pdb=" N ILE N 265 " --> pdb=" O PRO N 262 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ILE N 266 " --> pdb=" O LYS N 263 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS N 272 " --> pdb=" O GLU N 269 " (cutoff:3.500A) Processing helix chain 'N' and resid 278 through 283 Processing helix chain 'N' and resid 288 through 300 removed outlier: 4.115A pdb=" N PHE N 292 " --> pdb=" O LEU N 288 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N TYR N 293 " --> pdb=" O ASN N 289 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU N 296 " --> pdb=" O PHE N 292 " (cutoff:3.500A) Processing helix chain 'N' and resid 310 through 316 removed outlier: 3.523A pdb=" N MET N 313 " --> pdb=" O ASN N 310 " (cutoff:3.500A) Processing helix chain 'N' and resid 327 through 331 Processing helix chain 'N' and resid 337 through 343 Proline residue: N 341 - end of helix Processing helix chain 'O' and resid 6 through 11 Processing helix chain 'O' and resid 43 through 46 No H-bonds generated for 'chain 'O' and resid 43 through 46' Processing helix chain 'O' and resid 58 through 61 No H-bonds generated for 'chain 'O' and resid 58 through 61' Processing helix chain 'O' and resid 79 through 84 removed outlier: 3.594A pdb=" N TYR O 83 " --> pdb=" O LEU O 79 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASP O 84 " --> pdb=" O GLU O 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 79 through 84' Processing helix chain 'O' and resid 95 through 115 removed outlier: 3.824A pdb=" N LEU O 100 " --> pdb=" O LEU O 96 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N HIS O 114 " --> pdb=" O ASP O 110 " (cutoff:3.500A) Processing helix chain 'O' and resid 128 through 130 No H-bonds generated for 'chain 'O' and resid 128 through 130' Processing helix chain 'O' and resid 132 through 140 Processing helix chain 'O' and resid 146 through 159 removed outlier: 3.692A pdb=" N ASP O 150 " --> pdb=" O LYS O 146 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N HIS O 151 " --> pdb=" O GLN O 147 " (cutoff:3.500A) Processing helix chain 'O' and resid 176 through 184 removed outlier: 3.573A pdb=" N SER O 181 " --> pdb=" O PRO O 177 " (cutoff:3.500A) Processing helix chain 'O' and resid 204 through 207 No H-bonds generated for 'chain 'O' and resid 204 through 207' Processing helix chain 'O' and resid 210 through 214 Processing helix chain 'O' and resid 233 through 239 removed outlier: 3.523A pdb=" N ASP O 237 " --> pdb=" O LYS O 233 " (cutoff:3.500A) Processing helix chain 'O' and resid 253 through 264 removed outlier: 3.736A pdb=" N TYR O 258 " --> pdb=" O TRP O 254 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU O 259 " --> pdb=" O THR O 255 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU O 262 " --> pdb=" O TYR O 258 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL O 263 " --> pdb=" O LEU O 259 " (cutoff:3.500A) Processing helix chain 'O' and resid 266 through 273 removed outlier: 5.719A pdb=" N TYR O 272 " --> pdb=" O GLU O 268 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N THR O 273 " --> pdb=" O VAL O 269 " (cutoff:3.500A) Processing helix chain 'O' and resid 287 through 297 removed outlier: 3.560A pdb=" N ARG O 291 " --> pdb=" O HIS O 287 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE O 292 " --> pdb=" O GLN O 288 " (cutoff:3.500A) Processing helix chain 'O' and resid 310 through 312 No H-bonds generated for 'chain 'O' and resid 310 through 312' Processing helix chain 'P' and resid 31 through 39 Processing helix chain 'P' and resid 106 through 110 Processing helix chain 'P' and resid 112 through 124 removed outlier: 3.843A pdb=" N ALA P 124 " --> pdb=" O ALA P 120 " (cutoff:3.500A) Processing helix chain 'P' and resid 146 through 155 removed outlier: 3.765A pdb=" N ALA P 150 " --> pdb=" O LEU P 146 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N VAL P 151 " --> pdb=" O ARG P 147 " (cutoff:3.500A) Processing helix chain 'P' and resid 179 through 187 removed outlier: 3.874A pdb=" N ASN P 184 " --> pdb=" O ASN P 180 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR P 185 " --> pdb=" O HIS P 181 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ARG P 186 " --> pdb=" O PHE P 182 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N TRP P 187 " --> pdb=" O ALA P 183 " (cutoff:3.500A) Processing helix chain 'P' and resid 194 through 197 Processing helix chain 'P' and resid 207 through 217 Processing helix chain 'P' and resid 238 through 248 removed outlier: 3.512A pdb=" N ILE P 245 " --> pdb=" O LEU P 241 " (cutoff:3.500A) Processing helix chain 'P' and resid 260 through 263 No H-bonds generated for 'chain 'P' and resid 260 through 263' Processing helix chain 'P' and resid 266 through 270 Processing helix chain 'P' and resid 283 through 289 removed outlier: 4.128A pdb=" N ILE P 287 " --> pdb=" O LYS P 283 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N HIS P 288 " --> pdb=" O VAL P 284 " (cutoff:3.500A) Processing helix chain 'P' and resid 315 through 318 No H-bonds generated for 'chain 'P' and resid 315 through 318' Processing helix chain 'Q' and resid 89 through 91 No H-bonds generated for 'chain 'Q' and resid 89 through 91' Processing helix chain 'Q' and resid 93 through 96 No H-bonds generated for 'chain 'Q' and resid 93 through 96' Processing helix chain 'Q' and resid 119 through 122 Processing helix chain 'R' and resid 26 through 28 No H-bonds generated for 'chain 'R' and resid 26 through 28' Processing helix chain 'R' and resid 40 through 43 No H-bonds generated for 'chain 'R' and resid 40 through 43' Processing helix chain 'S' and resid 27 through 29 No H-bonds generated for 'chain 'S' and resid 27 through 29' Processing helix chain 'S' and resid 32 through 45 removed outlier: 3.736A pdb=" N VAL S 37 " --> pdb=" O ARG S 33 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR S 40 " --> pdb=" O ILE S 36 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N VAL S 41 " --> pdb=" O VAL S 37 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N GLU S 42 " --> pdb=" O GLN S 38 " (cutoff:3.500A) Processing helix chain 'S' and resid 83 through 91 removed outlier: 3.704A pdb=" N THR S 87 " --> pdb=" O ALA S 83 " (cutoff:3.500A) Processing helix chain 'T' and resid 9 through 20 removed outlier: 3.610A pdb=" N LEU T 16 " --> pdb=" O LYS T 12 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR T 17 " --> pdb=" O ASP T 13 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL T 18 " --> pdb=" O ARG T 14 " (cutoff:3.500A) Processing helix chain 'T' and resid 46 through 58 removed outlier: 3.616A pdb=" N ILE T 50 " --> pdb=" O ASP T 46 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N MET T 52 " --> pdb=" O VAL T 48 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA T 53 " --> pdb=" O GLU T 49 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N MET T 54 " --> pdb=" O ILE T 50 " (cutoff:3.500A) Processing helix chain 'T' and resid 67 through 69 No H-bonds generated for 'chain 'T' and resid 67 through 69' Processing helix chain 'T' and resid 75 through 81 removed outlier: 3.520A pdb=" N ALA T 81 " --> pdb=" O VAL T 77 " (cutoff:3.500A) Processing helix chain 'U' and resid 9 through 21 removed outlier: 4.250A pdb=" N ARG U 14 " --> pdb=" O GLY U 10 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N TYR U 17 " --> pdb=" O ASP U 13 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU U 21 " --> pdb=" O TYR U 17 " (cutoff:3.500A) Processing helix chain 'U' and resid 45 through 58 removed outlier: 3.534A pdb=" N GLU U 49 " --> pdb=" O LEU U 45 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE U 50 " --> pdb=" O ASP U 46 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N MET U 52 " --> pdb=" O VAL U 48 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA U 53 " --> pdb=" O GLU U 49 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET U 54 " --> pdb=" O ILE U 50 " (cutoff:3.500A) Processing helix chain 'U' and resid 64 through 67 No H-bonds generated for 'chain 'U' and resid 64 through 67' Processing helix chain 'U' and resid 73 through 84 removed outlier: 3.703A pdb=" N ALA U 81 " --> pdb=" O VAL U 77 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASP U 82 " --> pdb=" O ASP U 78 " (cutoff:3.500A) Processing helix chain 'V' and resid 22 through 33 removed outlier: 3.676A pdb=" N TYR V 27 " --> pdb=" O LEU V 23 " (cutoff:3.500A) Processing helix chain 'V' and resid 42 through 59 removed outlier: 3.600A pdb=" N GLU V 48 " --> pdb=" O ARG V 44 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN V 49 " --> pdb=" O LYS V 45 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLU V 53 " --> pdb=" O GLN V 49 " (cutoff:3.500A) Processing helix chain 'V' and resid 64 through 67 No H-bonds generated for 'chain 'V' and resid 64 through 67' Processing helix chain 'V' and resid 76 through 95 removed outlier: 3.553A pdb=" N ILE V 80 " --> pdb=" O GLU V 77 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU V 81 " --> pdb=" O GLU V 78 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA V 83 " --> pdb=" O ILE V 80 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLU V 84 " --> pdb=" O LEU V 81 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU V 86 " --> pdb=" O ALA V 83 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LEU V 87 " --> pdb=" O GLU V 84 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA V 90 " --> pdb=" O LEU V 87 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ARG V 91 " --> pdb=" O SER V 88 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS V 95 " --> pdb=" O LYS V 92 " (cutoff:3.500A) Processing helix chain 'W' and resid 27 through 41 removed outlier: 4.012A pdb=" N LYS W 31 " --> pdb=" O ASN W 28 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ARG W 32 " --> pdb=" O GLU W 29 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ARG W 33 " --> pdb=" O ALA W 30 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLU W 36 " --> pdb=" O ARG W 33 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG W 39 " --> pdb=" O GLU W 36 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TRP W 41 " --> pdb=" O TYR W 38 " (cutoff:3.500A) Processing helix chain 'W' and resid 45 through 51 removed outlier: 3.718A pdb=" N HIS W 50 " --> pdb=" O PRO W 46 " (cutoff:3.500A) Processing helix chain 'W' and resid 59 through 69 removed outlier: 4.117A pdb=" N LYS W 64 " --> pdb=" O GLN W 60 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL W 65 " --> pdb=" O GLY W 61 " (cutoff:3.500A) Processing helix chain 'W' and resid 78 through 96 removed outlier: 4.014A pdb=" N ILE W 86 " --> pdb=" O ASP W 82 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR W 95 " --> pdb=" O GLU W 91 " (cutoff:3.500A) Processing helix chain 'W' and resid 102 through 107 Processing helix chain 'W' and resid 120 through 124 removed outlier: 3.788A pdb=" N PHE W 124 " --> pdb=" O PHE W 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 120 through 124' Processing helix chain 'X' and resid 21 through 26 Processing helix chain 'X' and resid 28 through 33 Processing helix chain 'X' and resid 37 through 48 removed outlier: 3.678A pdb=" N GLU X 41 " --> pdb=" O LYS X 37 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N PHE X 42 " --> pdb=" O THR X 38 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU X 48 " --> pdb=" O LEU X 44 " (cutoff:3.500A) Processing helix chain 'X' and resid 52 through 54 No H-bonds generated for 'chain 'X' and resid 52 through 54' Processing helix chain 'X' and resid 57 through 75 removed outlier: 3.623A pdb=" N LEU X 61 " --> pdb=" O LYS X 57 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N LEU X 67 " --> pdb=" O ASN X 63 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN X 72 " --> pdb=" O ASN X 68 " (cutoff:3.500A) Processing helix chain 'X' and resid 79 through 90 removed outlier: 3.946A pdb=" N CYS X 87 " --> pdb=" O GLU X 83 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N TYR X 90 " --> pdb=" O THR X 86 " (cutoff:3.500A) Processing helix chain 'X' and resid 101 through 112 removed outlier: 3.596A pdb=" N CYS X 109 " --> pdb=" O LYS X 105 " (cutoff:3.500A) Processing helix chain 'X' and resid 140 through 142 No H-bonds generated for 'chain 'X' and resid 140 through 142' Processing helix chain 'Y' and resid 2 through 8 removed outlier: 3.799A pdb=" N TYR Y 8 " --> pdb=" O PHE Y 4 " (cutoff:3.500A) Processing helix chain 'Y' and resid 19 through 40 removed outlier: 3.811A pdb=" N THR Y 24 " --> pdb=" O LYS Y 20 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU Y 27 " --> pdb=" O ILE Y 23 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY Y 28 " --> pdb=" O THR Y 24 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR Y 38 " --> pdb=" O ILE Y 34 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N SER Y 39 " --> pdb=" O GLY Y 35 " (cutoff:3.500A) Processing helix chain 'Y' and resid 49 through 78 removed outlier: 3.689A pdb=" N ILE Y 65 " --> pdb=" O THR Y 61 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR Y 72 " --> pdb=" O MET Y 68 " (cutoff:3.500A) Processing helix chain 'Y' and resid 86 through 103 removed outlier: 3.599A pdb=" N PHE Y 90 " --> pdb=" O LEU Y 87 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE Y 91 " --> pdb=" O ASN Y 88 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N CYS Y 94 " --> pdb=" O ILE Y 91 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU Y 98 " --> pdb=" O ALA Y 95 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLY Y 101 " --> pdb=" O LEU Y 98 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ARG Y 103 " --> pdb=" O LEU Y 100 " (cutoff:3.500A) Processing helix chain 'Y' and resid 108 through 130 removed outlier: 3.658A pdb=" N VAL Y 115 " --> pdb=" O ALA Y 111 " (cutoff:3.500A) Processing helix chain 'Z' and resid 33 through 85 removed outlier: 3.546A pdb=" N GLY Z 45 " --> pdb=" O ALA Z 41 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TYR Z 46 " --> pdb=" O LEU Z 42 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET Z 49 " --> pdb=" O GLY Z 45 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU Z 55 " --> pdb=" O ARG Z 51 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA Z 66 " --> pdb=" O GLU Z 62 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG Z 67 " --> pdb=" O ASP Z 63 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU Z 70 " --> pdb=" O ALA Z 66 " (cutoff:3.500A) Proline residue: Z 72 - end of helix Processing helix chain 'Z' and resid 90 through 94 Processing helix chain 'Z' and resid 129 through 132 No H-bonds generated for 'chain 'Z' and resid 129 through 132' Processing helix chain 'a' and resid 2 through 10 Proline residue: a 7 - end of helix removed outlier: 3.764A pdb=" N ALA a 10 " --> pdb=" O PRO a 7 " (cutoff:3.500A) Processing helix chain 'a' and resid 18 through 31 removed outlier: 3.965A pdb=" N THR a 23 " --> pdb=" O PRO a 19 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA a 24 " --> pdb=" O GLY a 20 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N HIS a 27 " --> pdb=" O THR a 23 " (cutoff:3.500A) Processing helix chain 'a' and resid 42 through 53 removed outlier: 3.954A pdb=" N ARG a 53 " --> pdb=" O GLU a 49 " (cutoff:3.500A) Processing helix chain 'b' and resid 7 through 13 Processing helix chain 'b' and resid 18 through 26 Processing helix chain 'b' and resid 32 through 34 No H-bonds generated for 'chain 'b' and resid 32 through 34' Processing helix chain 'b' and resid 38 through 47 removed outlier: 3.745A pdb=" N SER b 42 " --> pdb=" O LYS b 39 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ILE b 44 " --> pdb=" O ALA b 41 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ASN b 45 " --> pdb=" O SER b 42 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA b 47 " --> pdb=" O ILE b 44 " (cutoff:3.500A) Processing helix chain 'c' and resid 14 through 44 removed outlier: 3.502A pdb=" N ALA c 23 " --> pdb=" O LEU c 19 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP c 38 " --> pdb=" O THR c 34 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU c 41 " --> pdb=" O GLU c 37 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ARG c 44 " --> pdb=" O LEU c 40 " (cutoff:3.500A) Processing helix chain 'd' and resid 2 through 4 No H-bonds generated for 'chain 'd' and resid 2 through 4' Processing helix chain 'd' and resid 31 through 48 removed outlier: 3.801A pdb=" N THR d 41 " --> pdb=" O LEU d 37 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN d 46 " --> pdb=" O GLY d 42 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N MET d 47 " --> pdb=" O LEU d 43 " (cutoff:3.500A) Processing helix chain 'd' and resid 61 through 96 removed outlier: 4.305A pdb=" N THR d 66 " --> pdb=" O LEU d 62 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL d 69 " --> pdb=" O VAL d 65 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA d 71 " --> pdb=" O SER d 67 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE d 74 " --> pdb=" O PHE d 70 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N TYR d 81 " --> pdb=" O LYS d 77 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N MET d 90 " --> pdb=" O LYS d 86 " (cutoff:3.500A) Processing helix chain 'd' and resid 98 through 100 No H-bonds generated for 'chain 'd' and resid 98 through 100' Processing helix chain 'e' and resid 33 through 40 removed outlier: 3.590A pdb=" N GLU e 38 " --> pdb=" O ALA e 34 " (cutoff:3.500A) Processing helix chain 'e' and resid 48 through 50 No H-bonds generated for 'chain 'e' and resid 48 through 50' Processing helix chain 'e' and resid 57 through 65 removed outlier: 3.639A pdb=" N GLU e 64 " --> pdb=" O ASP e 60 " (cutoff:3.500A) Processing helix chain 'e' and resid 70 through 85 removed outlier: 4.240A pdb=" N ILE e 78 " --> pdb=" O ARG e 74 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS e 79 " --> pdb=" O MET e 75 " (cutoff:3.500A) Processing helix chain 'e' and resid 95 through 97 No H-bonds generated for 'chain 'e' and resid 95 through 97' Processing helix chain 'f' and resid 11 through 33 removed outlier: 3.697A pdb=" N LEU f 14 " --> pdb=" O VAL f 11 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N VAL f 15 " --> pdb=" O HIS f 12 " (cutoff:3.500A) Proline residue: f 16 - end of helix removed outlier: 3.507A pdb=" N VAL f 20 " --> pdb=" O ALA f 17 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY f 22 " --> pdb=" O PHE f 19 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP f 26 " --> pdb=" O CYS f 23 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG f 27 " --> pdb=" O TYR f 24 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP f 29 " --> pdb=" O ASP f 26 " (cutoff:3.500A) Processing helix chain 'g' and resid 49 through 56 removed outlier: 3.853A pdb=" N VAL g 53 " --> pdb=" O PRO g 49 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N TRP g 54 " --> pdb=" O VAL g 50 " (cutoff:3.500A) Processing helix chain 'g' and resid 59 through 64 Processing helix chain 'g' and resid 70 through 77 removed outlier: 3.858A pdb=" N TYR g 77 " --> pdb=" O THR g 73 " (cutoff:3.500A) Processing helix chain 'g' and resid 81 through 100 removed outlier: 3.715A pdb=" N GLN g 84 " --> pdb=" O TYR g 81 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N GLU g 85 " --> pdb=" O ARG g 82 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TRP g 86 " --> pdb=" O MET g 83 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ALA g 87 " --> pdb=" O GLN g 84 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ARG g 88 " --> pdb=" O GLU g 85 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU g 90 " --> pdb=" O ALA g 87 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ALA g 91 " --> pdb=" O ARG g 88 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL g 95 " --> pdb=" O GLU g 92 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LYS g 96 " --> pdb=" O ARG g 93 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TYR g 97 " --> pdb=" O LEU g 94 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL g 100 " --> pdb=" O TYR g 97 " (cutoff:3.500A) Processing helix chain 'h' and resid 17 through 45 removed outlier: 3.845A pdb=" N PHE h 21 " --> pdb=" O TYR h 17 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N LEU h 22 " --> pdb=" O ASP h 18 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE h 27 " --> pdb=" O ARG h 23 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET h 30 " --> pdb=" O LYS h 26 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR h 32 " --> pdb=" O TYR h 28 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE h 34 " --> pdb=" O MET h 30 " (cutoff:3.500A) Proline residue: h 35 - end of helix removed outlier: 3.697A pdb=" N ASN h 44 " --> pdb=" O ILE h 40 " (cutoff:3.500A) Processing helix chain 'h' and resid 70 through 78 removed outlier: 4.112A pdb=" N ALA h 76 " --> pdb=" O SER h 72 " (cutoff:3.500A) Processing helix chain 'h' and resid 83 through 85 No H-bonds generated for 'chain 'h' and resid 83 through 85' Processing helix chain 'h' and resid 87 through 116 removed outlier: 4.615A pdb=" N ALA h 101 " --> pdb=" O GLU h 97 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU h 107 " --> pdb=" O LEU h 103 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARG h 115 " --> pdb=" O ARG h 111 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA h 116 " --> pdb=" O ARG h 112 " (cutoff:3.500A) Processing helix chain 'h' and resid 130 through 132 No H-bonds generated for 'chain 'h' and resid 130 through 132' Processing helix chain 'i' and resid 5 through 7 No H-bonds generated for 'chain 'i' and resid 5 through 7' Processing helix chain 'i' and resid 13 through 21 Processing helix chain 'i' and resid 69 through 73 Processing helix chain 'i' and resid 76 through 85 Processing helix chain 'j' and resid 21 through 42 removed outlier: 3.592A pdb=" N MET j 32 " --> pdb=" O LEU j 28 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TRP j 33 " --> pdb=" O SER j 29 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE j 34 " --> pdb=" O SER j 30 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N HIS j 42 " --> pdb=" O TRP j 38 " (cutoff:3.500A) Processing helix chain 'k' and resid 38 through 42 Processing helix chain 'k' and resid 76 through 88 removed outlier: 4.125A pdb=" N VAL k 85 " --> pdb=" O ALA k 81 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA k 86 " --> pdb=" O ALA k 82 " (cutoff:3.500A) Processing helix chain 'l' and resid 5 through 7 No H-bonds generated for 'chain 'l' and resid 5 through 7' Processing helix chain 'l' and resid 17 through 25 removed outlier: 3.867A pdb=" N LYS l 24 " --> pdb=" O ALA l 20 " (cutoff:3.500A) Processing helix chain 'l' and resid 30 through 32 No H-bonds generated for 'chain 'l' and resid 30 through 32' Processing helix chain 'l' and resid 97 through 120 removed outlier: 3.522A pdb=" N LYS l 102 " --> pdb=" O ASP l 98 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N PHE l 105 " --> pdb=" O CYS l 101 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N PHE l 115 " --> pdb=" O MET l 111 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TRP l 116 " --> pdb=" O VAL l 112 " (cutoff:3.500A) Processing helix chain 'm' and resid 28 through 50 removed outlier: 4.012A pdb=" N GLN m 32 " --> pdb=" O THR m 28 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ARG m 39 " --> pdb=" O ARG m 35 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG m 44 " --> pdb=" O ALA m 40 " (cutoff:3.500A) Processing helix chain 'm' and resid 62 through 72 removed outlier: 3.546A pdb=" N TRP m 67 " --> pdb=" O ALA m 63 " (cutoff:3.500A) Processing helix chain 'm' and resid 76 through 78 No H-bonds generated for 'chain 'm' and resid 76 through 78' Processing helix chain 'm' and resid 95 through 99 Processing helix chain 'm' and resid 101 through 117 removed outlier: 4.341A pdb=" N THR m 106 " --> pdb=" O TYR m 102 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP m 107 " --> pdb=" O VAL m 103 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU m 117 " --> pdb=" O ARG m 113 " (cutoff:3.500A) Processing helix chain 'n' and resid 12 through 16 Processing helix chain 'n' and resid 18 through 27 removed outlier: 3.877A pdb=" N LEU n 23 " --> pdb=" O TYR n 19 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU n 27 " --> pdb=" O LEU n 23 " (cutoff:3.500A) Processing helix chain 'n' and resid 34 through 39 Processing helix chain 'n' and resid 41 through 48 removed outlier: 3.630A pdb=" N ARG n 46 " --> pdb=" O LEU n 42 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE n 47 " --> pdb=" O MET n 43 " (cutoff:3.500A) Processing helix chain 'n' and resid 56 through 73 removed outlier: 3.958A pdb=" N GLU n 65 " --> pdb=" O GLN n 61 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU n 67 " --> pdb=" O LEU n 63 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU n 68 " --> pdb=" O ARG n 64 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU n 69 " --> pdb=" O GLU n 65 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TRP n 71 " --> pdb=" O GLU n 67 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N GLN n 72 " --> pdb=" O GLU n 68 " (cutoff:3.500A) Processing helix chain 'n' and resid 92 through 94 No H-bonds generated for 'chain 'n' and resid 92 through 94' Processing helix chain 'n' and resid 102 through 104 No H-bonds generated for 'chain 'n' and resid 102 through 104' Processing helix chain 'n' and resid 115 through 131 removed outlier: 4.664A pdb=" N GLN n 123 " --> pdb=" O SER n 119 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER n 131 " --> pdb=" O LEU n 127 " (cutoff:3.500A) Processing helix chain 'n' and resid 133 through 140 removed outlier: 3.692A pdb=" N GLN n 138 " --> pdb=" O ARG n 134 " (cutoff:3.500A) Processing helix chain 'o' and resid 42 through 48 removed outlier: 3.506A pdb=" N ASP o 47 " --> pdb=" O GLN o 43 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA o 48 " --> pdb=" O GLU o 44 " (cutoff:3.500A) Processing helix chain 'o' and resid 60 through 71 removed outlier: 4.137A pdb=" N ARG o 64 " --> pdb=" O HIS o 60 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS o 69 " --> pdb=" O LEU o 65 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASP o 71 " --> pdb=" O LYS o 67 " (cutoff:3.500A) Processing helix chain 'o' and resid 80 through 113 removed outlier: 4.035A pdb=" N ASP o 85 " --> pdb=" O HIS o 81 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N CYS o 89 " --> pdb=" O ASP o 85 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR o 94 " --> pdb=" O GLU o 90 " (cutoff:3.500A) Processing helix chain 'p' and resid 30 through 38 removed outlier: 3.746A pdb=" N LYS p 34 " --> pdb=" O THR p 30 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ALA p 35 " --> pdb=" O TYR p 31 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N LEU p 38 " --> pdb=" O LYS p 34 " (cutoff:3.500A) Processing helix chain 'p' and resid 41 through 57 removed outlier: 3.583A pdb=" N LEU p 46 " --> pdb=" O TRP p 42 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU p 49 " --> pdb=" O THR p 45 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN p 54 " --> pdb=" O PHE p 50 " (cutoff:3.500A) Processing helix chain 'p' and resid 81 through 115 removed outlier: 3.562A pdb=" N TRP p 91 " --> pdb=" O ALA p 87 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN p 99 " --> pdb=" O PHE p 95 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE p 101 " --> pdb=" O VAL p 97 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N MET p 102 " --> pdb=" O ASP p 98 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS p 110 " --> pdb=" O GLN p 106 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA p 111 " --> pdb=" O GLU p 107 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N CYS p 112 " --> pdb=" O ARG p 108 " (cutoff:3.500A) Processing helix chain 'p' and resid 128 through 140 removed outlier: 4.324A pdb=" N ALA p 137 " --> pdb=" O LYS p 133 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP p 140 " --> pdb=" O LYS p 136 " (cutoff:3.500A) Processing helix chain 'p' and resid 151 through 167 removed outlier: 3.719A pdb=" N ARG p 161 " --> pdb=" O LYS p 157 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU p 163 " --> pdb=" O LYS p 159 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLU p 164 " --> pdb=" O GLN p 160 " (cutoff:3.500A) Processing helix chain 'q' and resid 3 through 10 removed outlier: 4.297A pdb=" N LEU q 7 " --> pdb=" O LEU q 3 " (cutoff:3.500A) Processing helix chain 'q' and resid 14 through 16 No H-bonds generated for 'chain 'q' and resid 14 through 16' Processing helix chain 'q' and resid 20 through 30 removed outlier: 3.691A pdb=" N ARG q 25 " --> pdb=" O ARG q 21 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE q 28 " --> pdb=" O LEU q 24 " (cutoff:3.500A) Processing helix chain 'q' and resid 87 through 90 No H-bonds generated for 'chain 'q' and resid 87 through 90' Processing helix chain 'r' and resid 7 through 15 removed outlier: 3.663A pdb=" N SER r 15 " --> pdb=" O ARG r 11 " (cutoff:3.500A) Processing helix chain 'r' and resid 53 through 55 No H-bonds generated for 'chain 'r' and resid 53 through 55' Processing helix chain 'r' and resid 58 through 60 No H-bonds generated for 'chain 'r' and resid 58 through 60' Processing helix chain 's' and resid 35 through 39 Processing helix chain 's' and resid 44 through 53 removed outlier: 3.813A pdb=" N LEU s 48 " --> pdb=" O THR s 44 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 95 through 99 removed outlier: 6.617A pdb=" N TYR B 122 " --> pdb=" O MET B 96 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N VAL B 98 " --> pdb=" O TYR B 122 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL B 124 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ILE B 154 " --> pdb=" O SER B 125 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'C' and resid 104 through 109 removed outlier: 3.512A pdb=" N ILE C 105 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN C 95 " --> pdb=" O ASP C 77 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP C 77 " --> pdb=" O ASN C 95 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU C 97 " --> pdb=" O LEU C 75 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N LEU C 75 " --> pdb=" O LEU C 97 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 172 through 177 removed outlier: 3.736A pdb=" N GLU C 173 " --> pdb=" O GLU C 186 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU C 186 " --> pdb=" O GLU C 173 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 65 through 68 removed outlier: 3.610A pdb=" N LYS D 75 " --> pdb=" O GLU D 67 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 101 through 103 removed outlier: 6.165A pdb=" N ILE E 140 " --> pdb=" O VAL E 102 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'F' and resid 219 through 224 removed outlier: 3.770A pdb=" N THR F 221 " --> pdb=" O TYR F 92 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL F 94 " --> pdb=" O THR F 221 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ALA F 133 " --> pdb=" O LEU F 93 " (cutoff:3.500A) removed outlier: 8.707A pdb=" N VAL F 95 " --> pdb=" O ALA F 133 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N TYR F 135 " --> pdb=" O VAL F 95 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ASP F 174 " --> pdb=" O ALA F 134 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 257 through 259 Processing sheet with id= H, first strand: chain 'G' and resid 9 through 11 Processing sheet with id= I, first strand: chain 'G' and resid 146 through 148 Processing sheet with id= J, first strand: chain 'G' and resid 223 through 228 removed outlier: 3.508A pdb=" N SER G 241 " --> pdb=" O ARG G 249 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG G 249 " --> pdb=" O SER G 241 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 283 through 285 Processing sheet with id= L, first strand: chain 'G' and resid 315 through 317 removed outlier: 6.523A pdb=" N MET G 521 " --> pdb=" O ALA G 316 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'G' and resid 376 through 380 removed outlier: 6.937A pdb=" N LYS G 405 " --> pdb=" O VAL G 377 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N LEU G 379 " --> pdb=" O LYS G 405 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ALA G 407 " --> pdb=" O LEU G 379 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'G' and resid 572 through 574 Processing sheet with id= O, first strand: chain 'I' and resid 67 through 69 Processing sheet with id= P, first strand: chain 'I' and resid 98 through 100 removed outlier: 3.516A pdb=" N ARG I 107 " --> pdb=" O GLU I 99 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'O' and resid 26 through 28 Processing sheet with id= R, first strand: chain 'P' and resid 21 through 23 removed outlier: 6.895A pdb=" N VAL P 90 " --> pdb=" O THR P 22 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ARG P 128 " --> pdb=" O VAL P 91 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'P' and resid 45 through 49 removed outlier: 4.112A pdb=" N THR P 69 " --> pdb=" O VAL P 45 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU P 71 " --> pdb=" O ILE P 47 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'P' and resid 131 through 134 Processing sheet with id= U, first strand: chain 'R' and resid 56 through 59 removed outlier: 3.671A pdb=" N ILE R 57 " --> pdb=" O ILE R 73 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N VAL R 71 " --> pdb=" O CYS R 59 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'S' and resid 52 through 57 removed outlier: 7.037A pdb=" N ILE S 18 " --> pdb=" O LEU S 53 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N ARG S 55 " --> pdb=" O ILE S 18 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL S 20 " --> pdb=" O ARG S 55 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N CYS S 57 " --> pdb=" O VAL S 20 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU S 22 " --> pdb=" O CYS S 57 " (cutoff:3.500A) 1649 hydrogen bonds defined for protein. 4557 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: 17.42 Time building geometry restraints manager: 22.56 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: 27595 1.40 - 1.63: 39958 1.63 - 1.85: 857 1.85 - 2.08: 0 2.08 - 2.30: 80 Bond restraints: 68490 Sorted by residual: bond pdb=" CA AME q 1 " pdb=" C AME q 1 " ideal model delta sigma weight residual 1.527 1.334 0.193 2.00e-02 2.50e+03 9.33e+01 bond pdb=" CA7 CDL M 507 " pdb=" OA8 CDL M 507 " ideal model delta sigma weight residual 1.334 1.402 -0.068 1.10e-02 8.26e+03 3.87e+01 bond pdb=" CA7 CDL L 702 " pdb=" OA8 CDL L 702 " ideal model delta sigma weight residual 1.334 1.401 -0.067 1.10e-02 8.26e+03 3.76e+01 bond pdb=" CB7 CDL L 702 " pdb=" OB8 CDL L 702 " ideal model delta sigma weight residual 1.334 1.401 -0.067 1.10e-02 8.26e+03 3.75e+01 bond pdb=" CA7 CDL H 405 " pdb=" OA8 CDL H 405 " ideal model delta sigma weight residual 1.334 1.401 -0.067 1.10e-02 8.26e+03 3.73e+01 ... (remaining 68485 not shown) Histogram of bond angle deviations from ideal: 73.13 - 85.87: 76 85.87 - 98.61: 47 98.61 - 111.35: 28804 111.35 - 124.09: 61473 124.09 - 136.83: 2332 Bond angle restraints: 92732 Sorted by residual: angle pdb=" C51 CDL M 507 " pdb=" CB5 CDL M 507 " pdb=" OB6 CDL M 507 " ideal model delta sigma weight residual 111.33 121.42 -10.09 1.32e+00 5.72e-01 5.82e+01 angle pdb=" C51 CDL L 702 " pdb=" CB5 CDL L 702 " pdb=" OB6 CDL L 702 " ideal model delta sigma weight residual 111.33 120.85 -9.52 1.32e+00 5.72e-01 5.18e+01 angle pdb=" C11 CDL L 702 " pdb=" CA5 CDL L 702 " pdb=" OA6 CDL L 702 " ideal model delta sigma weight residual 111.33 120.82 -9.49 1.32e+00 5.72e-01 5.15e+01 angle pdb=" C31 CDL M 507 " pdb=" CA7 CDL M 507 " pdb=" OA8 CDL M 507 " ideal model delta sigma weight residual 111.64 122.59 -10.95 1.65e+00 3.69e-01 4.42e+01 angle pdb=" C51 CDL H 405 " pdb=" CB5 CDL H 405 " pdb=" OB6 CDL H 405 " ideal model delta sigma weight residual 111.33 119.81 -8.48 1.32e+00 5.72e-01 4.12e+01 ... (remaining 92727 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.34: 40729 35.34 - 70.69: 648 70.69 - 106.03: 51 106.03 - 141.37: 4 141.37 - 176.72: 3 Dihedral angle restraints: 41435 sinusoidal: 17613 harmonic: 23822 Sorted by residual: dihedral pdb=" CA GLU i 114 " pdb=" C GLU i 114 " pdb=" N VAL i 115 " pdb=" CA VAL i 115 " ideal model delta harmonic sigma weight residual -180.00 -130.10 -49.90 0 5.00e+00 4.00e-02 9.96e+01 dihedral pdb=" CA ILE G 258 " pdb=" C ILE G 258 " pdb=" N ASN G 259 " pdb=" CA ASN G 259 " ideal model delta harmonic sigma weight residual 180.00 -132.23 -47.77 0 5.00e+00 4.00e-02 9.13e+01 dihedral pdb=" CA TYR a 61 " pdb=" C TYR a 61 " pdb=" N VAL a 62 " pdb=" CA VAL a 62 " ideal model delta harmonic sigma weight residual 180.00 -132.36 -47.64 0 5.00e+00 4.00e-02 9.08e+01 ... (remaining 41432 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.266: 10099 4.266 - 8.532: 0 8.532 - 12.798: 0 12.798 - 17.064: 0 17.064 - 21.330: 24 Chirality restraints: 10123 Sorted by residual: chirality pdb="FE2 SF4 B 201 " pdb=" S1 SF4 B 201 " pdb=" S3 SF4 B 201 " pdb=" S4 SF4 B 201 " both_signs ideal model delta sigma weight residual False 10.55 -10.78 21.33 2.00e-01 2.50e+01 1.14e+04 chirality pdb="FE2 SF4 I 201 " pdb=" S1 SF4 I 201 " pdb=" S3 SF4 I 201 " pdb=" S4 SF4 I 201 " both_signs ideal model delta sigma weight residual False 10.55 -10.68 21.23 2.00e-01 2.50e+01 1.13e+04 chirality pdb="FE3 SF4 B 201 " pdb=" S1 SF4 B 201 " pdb=" S2 SF4 B 201 " pdb=" S4 SF4 B 201 " both_signs ideal model delta sigma weight residual False -10.55 10.67 -21.22 2.00e-01 2.50e+01 1.13e+04 ... (remaining 10120 not shown) Planarity restraints: 11611 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR J 170 " 0.036 2.00e-02 2.50e+03 7.22e-02 5.21e+01 pdb=" C THR J 170 " -0.125 2.00e-02 2.50e+03 pdb=" O THR J 170 " 0.047 2.00e-02 2.50e+03 pdb=" N ARG J 171 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE L 598 " 0.036 2.00e-02 2.50e+03 7.07e-02 5.00e+01 pdb=" C ILE L 598 " -0.122 2.00e-02 2.50e+03 pdb=" O ILE L 598 " 0.046 2.00e-02 2.50e+03 pdb=" N ILE L 599 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG f 48 " -0.093 5.00e-02 4.00e+02 1.43e-01 3.25e+01 pdb=" N PRO f 49 " 0.247 5.00e-02 4.00e+02 pdb=" CA PRO f 49 " -0.080 5.00e-02 4.00e+02 pdb=" CD PRO f 49 " -0.074 5.00e-02 4.00e+02 ... (remaining 11608 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.18: 74 2.18 - 2.86: 23263 2.86 - 3.54: 96313 3.54 - 4.22: 162979 4.22 - 4.90: 276623 Nonbonded interactions: 559252 Sorted by model distance: nonbonded pdb=" OXT AME q 1 " pdb=" CA GLU q 2 " model vdw 1.499 2.776 nonbonded pdb=" OH TYR l 46 " pdb=" O ILE l 76 " model vdw 2.023 2.440 nonbonded pdb=" OG SER L 371 " pdb=" OG SER j 29 " model vdw 2.024 2.440 nonbonded pdb=" OG1 THR P 27 " pdb=" O3B NDP P 501 " model vdw 2.030 2.440 nonbonded pdb=" O PHE H 104 " pdb=" OG1 THR H 108 " model vdw 2.038 2.440 ... (remaining 559247 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'T' selection = (chain 'U' and (resid 8 through 82 or (resid 201 and (name C1 or name C10 or nam \ e C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or \ name C18 or name C19 or name C2 or name C20 or name C21 or name C22 or name C3 \ or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 or name N1 or \ name N2 or name O1 or name O2 or name O3 or name O4 or name O5 or name O6 or nam \ e O7 or name O9 or name P1 or name S1 )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.080 Extract box with map and model: 20.550 Check model and map are aligned: 0.730 Set scattering table: 0.450 Process input model: 148.100 Find NCS groups from input model: 2.010 Set up NCS constraints: 0.260 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: 0.020 Load rotamer database and sin/cos tables:2.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 179.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 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 : 0.009 0.193 68490 Z= 0.592 Angle : 1.169 17.101 92732 Z= 0.590 Chirality : 1.032 21.330 10123 Planarity : 0.007 0.143 11611 Dihedral : 13.010 176.716 26030 Min Nonbonded Distance : 1.499 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.37 % Allowed : 14.88 % Favored : 84.74 % Rotamer: Outliers : 0.06 % Allowed : 5.88 % Favored : 94.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.08 % Twisted General : 0.56 % 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: -5.96 (0.07), residues: 8056 helix: -4.09 (0.05), residues: 3738 sheet: -3.99 (0.21), residues: 376 loop : -3.82 (0.09), residues: 3942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP V 113 HIS 0.018 0.002 HIS L 534 PHE 0.041 0.003 PHE G 523 TYR 0.049 0.003 TYR a 61 ARG 0.020 0.002 ARG P 186 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16112 Ramachandran restraints generated. 8056 Oldfield, 0 Emsley, 8056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16112 Ramachandran restraints generated. 8056 Oldfield, 0 Emsley, 8056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2272 residues out of total 7156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 2268 time to evaluate : 5.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 11 VAL cc_start: 0.8253 (m) cc_final: 0.7888 (t) REVERT: C 27 GLU cc_start: 0.7620 (mt-10) cc_final: 0.7397 (mt-10) REVERT: D 23 LYS cc_start: 0.7322 (pmmt) cc_final: 0.6941 (pttt) REVERT: D 28 TRP cc_start: 0.8109 (m-10) cc_final: 0.7883 (m-10) REVERT: D 152 MET cc_start: 0.8235 (tpt) cc_final: 0.7821 (tpt) REVERT: E 211 PHE cc_start: 0.7738 (t80) cc_final: 0.7378 (t80) REVERT: F 272 MET cc_start: 0.7020 (ttp) cc_final: 0.6794 (ttt) REVERT: G 82 ASN cc_start: 0.7355 (t0) cc_final: 0.7123 (t0) REVERT: G 121 MET cc_start: 0.7922 (tpt) cc_final: 0.7709 (tpt) REVERT: G 306 MET cc_start: 0.6118 (mmm) cc_final: 0.5754 (mmp) REVERT: H 67 SER cc_start: 0.8517 (m) cc_final: 0.7918 (t) REVERT: H 68 MET cc_start: 0.7849 (mmm) cc_final: 0.7464 (mmt) REVERT: J 123 TRP cc_start: 0.8209 (m100) cc_final: 0.7958 (m100) REVERT: K 39 SER cc_start: 0.8378 (p) cc_final: 0.8080 (p) REVERT: L 290 ILE cc_start: 0.8141 (tt) cc_final: 0.7922 (tp) REVERT: L 358 LYS cc_start: 0.8492 (tppp) cc_final: 0.8257 (mptt) REVERT: L 555 LEU cc_start: 0.7295 (tt) cc_final: 0.7064 (tt) REVERT: M 108 MET cc_start: 0.7848 (mtt) cc_final: 0.7632 (mtp) REVERT: M 139 GLN cc_start: 0.7775 (mm110) cc_final: 0.7541 (mm-40) REVERT: M 205 ILE cc_start: 0.8630 (mm) cc_final: 0.8171 (mt) REVERT: M 340 ARG cc_start: 0.7703 (mpp80) cc_final: 0.7424 (mtm-85) REVERT: O 268 GLU cc_start: 0.7262 (mt-10) cc_final: 0.6661 (mm-30) REVERT: P 296 ASP cc_start: 0.6072 (p0) cc_final: 0.5593 (t0) REVERT: Q 132 THR cc_start: 0.8055 (p) cc_final: 0.7687 (p) REVERT: S 63 LYS cc_start: 0.8415 (mmtp) cc_final: 0.8084 (mptt) REVERT: U 9 ASP cc_start: 0.6833 (m-30) cc_final: 0.6214 (m-30) REVERT: U 13 ASP cc_start: 0.7410 (t70) cc_final: 0.6993 (p0) REVERT: V 84 GLU cc_start: 0.7516 (pp20) cc_final: 0.7257 (tp30) REVERT: W 20 LYS cc_start: 0.8531 (ttmt) cc_final: 0.8257 (ttpp) REVERT: X 11 GLU cc_start: 0.7128 (mt-10) cc_final: 0.6597 (tp30) REVERT: X 73 ILE cc_start: 0.8822 (mm) cc_final: 0.8610 (mm) REVERT: X 170 THR cc_start: 0.8126 (p) cc_final: 0.7917 (p) REVERT: Y 13 ASP cc_start: 0.5692 (t0) cc_final: 0.5130 (t0) REVERT: d 100 ASP cc_start: 0.7153 (p0) cc_final: 0.6460 (p0) REVERT: e 13 LEU cc_start: 0.8491 (tm) cc_final: 0.8045 (tp) REVERT: g 117 GLN cc_start: 0.7035 (mp10) cc_final: 0.6769 (tt0) REVERT: k 77 LYS cc_start: 0.8495 (tppt) cc_final: 0.8128 (ttpt) REVERT: m 74 ASN cc_start: 0.7704 (t160) cc_final: 0.7503 (t0) REVERT: n 73 ASN cc_start: 0.7114 (m110) cc_final: 0.6880 (m110) REVERT: o 79 CYS cc_start: 0.4656 (m) cc_final: 0.4000 (m) REVERT: o 107 LEU cc_start: 0.6241 (tt) cc_final: 0.5809 (tp) REVERT: p 136 LYS cc_start: 0.7091 (tptp) cc_final: 0.6322 (ttpt) REVERT: q 75 TRP cc_start: 0.7585 (m100) cc_final: 0.7329 (m-90) REVERT: q 124 TYR cc_start: 0.8743 (t80) cc_final: 0.8404 (t80) REVERT: r 101 LYS cc_start: 0.5552 (pmmt) cc_final: 0.4689 (pttp) outliers start: 4 outliers final: 2 residues processed: 2272 average time/residue: 0.7292 time to fit residues: 2737.1703 Evaluate side-chains 1342 residues out of total 7156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1340 time to evaluate : 5.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain M residue 434 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 797 random chunks: chunk 673 optimal weight: 0.9990 chunk 604 optimal weight: 3.9990 chunk 335 optimal weight: 2.9990 chunk 206 optimal weight: 9.9990 chunk 407 optimal weight: 4.9990 chunk 322 optimal weight: 3.9990 chunk 624 optimal weight: 0.8980 chunk 241 optimal weight: 0.8980 chunk 379 optimal weight: 2.9990 chunk 464 optimal weight: 4.9990 chunk 723 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN ** B 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 GLN C 128 ASN C 200 ASN D 46 ASN D 79 HIS D 84 HIS ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 201 GLN D 232 ASN D 237 ASN D 409 HIS E 15 ASN E 27 ASN E 43 GLN ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 326 GLN G 51 ASN G 437 HIS G 472 ASN G 499 GLN G 548 HIS H 230 ASN H 235 ASN I 138 ASN I 146 HIS L 25 ASN ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 135 ASN ** L 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 175 ASN ** L 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 320 ASN L 332 HIS L 403 ASN L 444 ASN ** L 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 572 ASN L 605 ASN M 44 GLN M 48 ASN M 366 ASN N 2 ASN ** N 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 150 ASN N 317 GLN N 323 ASN N 342 GLN O 30 ASN O 97 GLN O 184 GLN O 251 GLN P 2 HIS P 3 HIS P 37 HIS P 93 ASN P 136 ASN P 203 GLN P 216 ASN Q 29 HIS Q 43 ASN ** R 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 74 ASN R 94 HIS S 79 ASN V 49 GLN W 60 GLN W 128 HIS X 101 GLN X 123 GLN X 139 ASN Y 16 GLN Y 18 HIS Z 54 GLN a 42 GLN ** b 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 59 HIS d 117 HIS ** e 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 25 GLN g 34 ASN h 44 ASN h 86 ASN h 124 GLN i 73 HIS j 42 HIS k 38 GLN k 65 ASN l 62 GLN l 65 HIS l 103 HIS l 154 HIS m 74 ASN m 78 ASN ** n 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 109 GLN ** p 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 113 GLN q 17 HIS q 31 ASN q 113 HIS ** q 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 89 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.276 68490 Z= 0.562 Angle : 1.683 51.237 92732 Z= 1.058 Chirality : 0.316 6.725 10123 Planarity : 0.007 0.120 11611 Dihedral : 12.978 173.048 9954 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.21 % Allowed : 12.48 % Favored : 87.31 % Rotamer: Outliers : 2.82 % Allowed : 12.58 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.34 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.60 (0.08), residues: 8056 helix: -2.79 (0.07), residues: 3824 sheet: -3.22 (0.24), residues: 380 loop : -3.31 (0.10), residues: 3852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP V 113 HIS 0.028 0.002 HIS I 67 PHE 0.024 0.002 PHE H 211 TYR 0.035 0.002 TYR N 146 ARG 0.011 0.001 ARG C 106 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16112 Ramachandran restraints generated. 8056 Oldfield, 0 Emsley, 8056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16112 Ramachandran restraints generated. 8056 Oldfield, 0 Emsley, 8056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1730 residues out of total 7156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 1529 time to evaluate : 5.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 23 LYS cc_start: 0.7284 (pmmt) cc_final: 0.6865 (pttt) REVERT: D 152 MET cc_start: 0.8361 (tpt) cc_final: 0.8076 (tpt) REVERT: D 311 ILE cc_start: 0.8669 (mm) cc_final: 0.8434 (mt) REVERT: E 118 GLU cc_start: 0.6019 (mm-30) cc_final: 0.5436 (mm-30) REVERT: E 211 PHE cc_start: 0.7652 (t80) cc_final: 0.7399 (t80) REVERT: F 376 MET cc_start: 0.7938 (mmm) cc_final: 0.7717 (mmm) REVERT: G 121 MET cc_start: 0.8045 (tpt) cc_final: 0.7691 (tpt) REVERT: G 271 TYR cc_start: 0.7824 (p90) cc_final: 0.7432 (p90) REVERT: G 521 MET cc_start: 0.7029 (ttp) cc_final: 0.6748 (ttp) REVERT: G 556 MET cc_start: 0.7988 (ttp) cc_final: 0.7689 (ptm) REVERT: G 673 MET cc_start: 0.8661 (mmt) cc_final: 0.8451 (mmt) REVERT: H 17 MET cc_start: 0.7483 (tmm) cc_final: 0.7257 (tmm) REVERT: H 53 MET cc_start: 0.8439 (ttp) cc_final: 0.8156 (ttm) REVERT: H 67 SER cc_start: 0.8484 (m) cc_final: 0.7973 (t) REVERT: H 68 MET cc_start: 0.7858 (mmm) cc_final: 0.7481 (mmt) REVERT: I 31 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7329 (pm20) REVERT: J 152 MET cc_start: 0.7938 (tpt) cc_final: 0.7685 (tpt) REVERT: K 17 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7846 (tp) REVERT: L 319 MET cc_start: 0.7951 (mpp) cc_final: 0.7630 (mpp) REVERT: M 108 MET cc_start: 0.8217 (mtt) cc_final: 0.8013 (mtt) REVERT: M 139 GLN cc_start: 0.7982 (mm110) cc_final: 0.7667 (mm-40) REVERT: M 247 SER cc_start: 0.8698 (t) cc_final: 0.8477 (m) REVERT: M 294 MET cc_start: 0.7459 (mmm) cc_final: 0.7093 (mmm) REVERT: M 340 ARG cc_start: 0.7539 (mpp80) cc_final: 0.7305 (mtm-85) REVERT: N 179 MET cc_start: 0.7873 (mmp) cc_final: 0.7513 (mmt) REVERT: N 191 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8232 (tm) REVERT: N 289 ASN cc_start: 0.8711 (m110) cc_final: 0.8275 (m-40) REVERT: O 163 TYR cc_start: 0.7454 (m-80) cc_final: 0.7132 (m-80) REVERT: O 268 GLU cc_start: 0.7178 (mt-10) cc_final: 0.6643 (mm-30) REVERT: O 294 ASN cc_start: 0.8817 (m-40) cc_final: 0.8449 (m-40) REVERT: P 220 ASP cc_start: 0.5688 (OUTLIER) cc_final: 0.5271 (m-30) REVERT: R 21 LYS cc_start: 0.7512 (ttmm) cc_final: 0.6814 (tppt) REVERT: S 63 LYS cc_start: 0.8394 (mmtp) cc_final: 0.8150 (mptt) REVERT: S 72 GLN cc_start: 0.7502 (mm-40) cc_final: 0.7233 (mp10) REVERT: T 55 GLU cc_start: 0.7049 (mt-10) cc_final: 0.6382 (mm-30) REVERT: U 6 LEU cc_start: 0.7207 (OUTLIER) cc_final: 0.6805 (pp) REVERT: U 74 GLN cc_start: 0.8541 (tp40) cc_final: 0.8328 (tp-100) REVERT: W 20 LYS cc_start: 0.8597 (ttmt) cc_final: 0.8259 (ttpp) REVERT: W 28 ASN cc_start: 0.7066 (t0) cc_final: 0.6837 (t0) REVERT: W 52 MET cc_start: 0.8422 (ptt) cc_final: 0.8217 (ptt) REVERT: W 69 PHE cc_start: 0.8869 (m-10) cc_final: 0.8442 (m-80) REVERT: Y 13 ASP cc_start: 0.5699 (t0) cc_final: 0.5326 (t0) REVERT: Y 60 PHE cc_start: 0.8258 (t80) cc_final: 0.7919 (t80) REVERT: Y 129 LEU cc_start: 0.8718 (tp) cc_final: 0.8485 (mt) REVERT: Z 49 MET cc_start: 0.7156 (tpp) cc_final: 0.6933 (mmt) REVERT: e 13 LEU cc_start: 0.8711 (tm) cc_final: 0.8496 (tp) REVERT: i 7 GLU cc_start: 0.6942 (pt0) cc_final: 0.6736 (pt0) REVERT: k 77 LYS cc_start: 0.8354 (tppt) cc_final: 0.8012 (ttpt) REVERT: n 73 ASN cc_start: 0.7598 (m110) cc_final: 0.7331 (m110) REVERT: o 43 GLN cc_start: 0.7983 (tm-30) cc_final: 0.7659 (tm-30) REVERT: o 45 MET cc_start: 0.8531 (tmm) cc_final: 0.8252 (ttt) REVERT: o 79 CYS cc_start: 0.4542 (m) cc_final: 0.4080 (m) REVERT: p 73 ILE cc_start: 0.8973 (mm) cc_final: 0.8753 (mm) REVERT: p 113 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.8491 (pp30) REVERT: p 136 LYS cc_start: 0.7407 (tptp) cc_final: 0.6565 (ttpt) REVERT: q 124 TYR cc_start: 0.8732 (t80) cc_final: 0.8224 (t80) outliers start: 201 outliers final: 98 residues processed: 1652 average time/residue: 0.6414 time to fit residues: 1797.3558 Evaluate side-chains 1396 residues out of total 7156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 1292 time to evaluate : 5.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain D residue 279 ASP Chi-restraints excluded: chain D residue 314 CYS Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 114 ASP Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 114 ASP Chi-restraints excluded: chain F residue 250 ASN Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 303 SER Chi-restraints excluded: chain F residue 316 LEU Chi-restraints excluded: chain F residue 367 GLU Chi-restraints excluded: chain F residue 392 LEU Chi-restraints excluded: chain F residue 396 SER Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 187 ILE Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 238 ILE Chi-restraints excluded: chain G residue 258 ILE Chi-restraints excluded: chain G residue 307 LEU Chi-restraints excluded: chain G residue 467 LEU Chi-restraints excluded: chain G residue 524 LEU Chi-restraints excluded: chain G residue 536 ASP Chi-restraints excluded: chain G residue 544 VAL Chi-restraints excluded: chain G residue 558 ASP Chi-restraints excluded: chain G residue 674 THR Chi-restraints excluded: chain H residue 265 LEU Chi-restraints excluded: chain I residue 31 GLU Chi-restraints excluded: chain I residue 82 CYS Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain J residue 104 CYS Chi-restraints excluded: chain J residue 106 LEU Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain K residue 17 LEU Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 241 THR Chi-restraints excluded: chain L residue 278 LEU Chi-restraints excluded: chain L residue 370 SER Chi-restraints excluded: chain L residue 403 ASN Chi-restraints excluded: chain L residue 417 SER Chi-restraints excluded: chain L residue 440 LEU Chi-restraints excluded: chain M residue 176 LEU Chi-restraints excluded: chain M residue 250 LEU Chi-restraints excluded: chain N residue 191 LEU Chi-restraints excluded: chain N residue 232 LEU Chi-restraints excluded: chain N residue 236 LYS Chi-restraints excluded: chain N residue 290 LEU Chi-restraints excluded: chain P residue 95 ILE Chi-restraints excluded: chain P residue 108 ASP Chi-restraints excluded: chain P residue 140 LYS Chi-restraints excluded: chain P residue 220 ASP Chi-restraints excluded: chain P residue 222 ASP Chi-restraints excluded: chain P residue 320 ARG Chi-restraints excluded: chain P residue 327 LEU Chi-restraints excluded: chain Q residue 47 SER Chi-restraints excluded: chain Q residue 81 ASN Chi-restraints excluded: chain Q residue 123 SER Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain T residue 76 ILE Chi-restraints excluded: chain U residue 6 LEU Chi-restraints excluded: chain V residue 89 LEU Chi-restraints excluded: chain X residue 109 CYS Chi-restraints excluded: chain X residue 117 VAL Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Z residue 8 ASP Chi-restraints excluded: chain b residue 21 SER Chi-restraints excluded: chain b residue 82 ASN Chi-restraints excluded: chain d residue 114 GLU Chi-restraints excluded: chain e residue 66 LEU Chi-restraints excluded: chain f residue 8 GLU Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain i residue 22 LEU Chi-restraints excluded: chain i residue 97 VAL Chi-restraints excluded: chain i residue 115 VAL Chi-restraints excluded: chain k residue 87 LEU Chi-restraints excluded: chain l residue 61 TYR Chi-restraints excluded: chain n residue 52 ASN Chi-restraints excluded: chain n residue 80 ILE Chi-restraints excluded: chain o residue 23 SER Chi-restraints excluded: chain o residue 37 VAL Chi-restraints excluded: chain o residue 77 LEU Chi-restraints excluded: chain o residue 100 GLU Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain p residue 113 GLN Chi-restraints excluded: chain q residue 66 THR Chi-restraints excluded: chain q residue 77 VAL Chi-restraints excluded: chain r residue 105 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 797 random chunks: chunk 402 optimal weight: 1.9990 chunk 224 optimal weight: 3.9990 chunk 602 optimal weight: 6.9990 chunk 492 optimal weight: 0.7980 chunk 199 optimal weight: 9.9990 chunk 725 optimal weight: 10.0000 chunk 783 optimal weight: 0.2980 chunk 645 optimal weight: 7.9990 chunk 719 optimal weight: 9.9990 chunk 247 optimal weight: 3.9990 chunk 581 optimal weight: 0.0770 overall best weight: 1.4342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 237 ASN E 43 GLN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 165 ASN F 250 ASN ** F 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 326 GLN G 277 GLN G 499 GLN ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 172 GLN ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 321 GLN M 168 GLN M 293 HIS M 374 ASN ** N 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 150 ASN ** N 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 167 HIS ** O 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 89 ASN P 288 HIS ** Q 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 74 ASN S 92 ASN V 49 GLN W 101 GLN X 101 GLN Y 16 GLN ** Y 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 75 GLN d 117 HIS e 24 GLN e 76 HIS e 96 HIS e 97 HIS l 62 GLN l 86 ASN m 58 HIS ** n 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 54 GLN ** o 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 109 GLN p 54 GLN p 90 GLN p 99 GLN q 17 HIS q 101 ASN ** q 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.281 68490 Z= 0.574 Angle : 1.645 51.397 92732 Z= 1.044 Chirality : 0.311 6.591 10123 Planarity : 0.006 0.109 11611 Dihedral : 12.185 175.281 9951 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.22 % Allowed : 11.90 % Favored : 87.87 % Rotamer: Outliers : 3.66 % Allowed : 14.40 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.44 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.82 (0.09), residues: 8056 helix: -2.03 (0.07), residues: 3807 sheet: -2.69 (0.25), residues: 385 loop : -3.05 (0.10), residues: 3864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP V 113 HIS 0.021 0.001 HIS I 67 PHE 0.026 0.002 PHE H 211 TYR 0.031 0.002 TYR N 146 ARG 0.006 0.001 ARG q 88 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16112 Ramachandran restraints generated. 8056 Oldfield, 0 Emsley, 8056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16112 Ramachandran restraints generated. 8056 Oldfield, 0 Emsley, 8056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1663 residues out of total 7156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 261 poor density : 1402 time to evaluate : 5.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 GLU cc_start: 0.5862 (mt-10) cc_final: 0.5569 (mp0) REVERT: C 102 ASN cc_start: 0.8294 (t0) cc_final: 0.8092 (m-40) REVERT: C 176 TYR cc_start: 0.8705 (t80) cc_final: 0.8302 (t80) REVERT: D 3 GLN cc_start: 0.8790 (tp-100) cc_final: 0.8555 (tp-100) REVERT: D 23 LYS cc_start: 0.7254 (pmmt) cc_final: 0.6871 (pttt) REVERT: D 123 GLU cc_start: 0.7386 (mt-10) cc_final: 0.7177 (mt-10) REVERT: D 207 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8060 (tm) REVERT: D 302 GLU cc_start: 0.7242 (tp30) cc_final: 0.6982 (tp30) REVERT: E 211 PHE cc_start: 0.7671 (t80) cc_final: 0.7381 (t80) REVERT: F 352 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7882 (mm-30) REVERT: F 381 LYS cc_start: 0.7899 (mmmt) cc_final: 0.7590 (mtpt) REVERT: G 271 TYR cc_start: 0.8009 (p90) cc_final: 0.7580 (p90) REVERT: G 467 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7027 (tt) REVERT: G 521 MET cc_start: 0.7001 (ttp) cc_final: 0.6692 (ttp) REVERT: G 535 GLN cc_start: 0.6688 (mm-40) cc_final: 0.6342 (mm-40) REVERT: G 556 MET cc_start: 0.8002 (ttp) cc_final: 0.7719 (ptm) REVERT: G 673 MET cc_start: 0.8703 (mmt) cc_final: 0.8465 (mmt) REVERT: H 68 MET cc_start: 0.7782 (mmm) cc_final: 0.7473 (mmt) REVERT: H 260 MET cc_start: 0.8095 (tmm) cc_final: 0.7263 (tmm) REVERT: I 17 LYS cc_start: 0.8074 (tptt) cc_final: 0.7819 (tptt) REVERT: J 134 MET cc_start: 0.7392 (tpp) cc_final: 0.7149 (mmt) REVERT: J 152 MET cc_start: 0.7963 (tpt) cc_final: 0.7747 (tpt) REVERT: K 31 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8422 (tp) REVERT: K 93 LEU cc_start: 0.8594 (pt) cc_final: 0.8246 (pp) REVERT: L 319 MET cc_start: 0.7987 (mpp) cc_final: 0.7655 (mpp) REVERT: L 424 MET cc_start: 0.8301 (tpt) cc_final: 0.7918 (tpp) REVERT: L 482 MET cc_start: 0.6962 (mtp) cc_final: 0.6717 (mtm) REVERT: L 517 ASN cc_start: 0.7837 (OUTLIER) cc_final: 0.7386 (p0) REVERT: M 9 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8080 (mp) REVERT: M 108 MET cc_start: 0.8214 (mtt) cc_final: 0.7977 (mtt) REVERT: M 139 GLN cc_start: 0.8232 (mm110) cc_final: 0.7945 (mm-40) REVERT: M 161 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8882 (tp) REVERT: M 247 SER cc_start: 0.8764 (t) cc_final: 0.8502 (m) REVERT: M 294 MET cc_start: 0.7629 (mmm) cc_final: 0.7292 (mmm) REVERT: M 354 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8466 (tp) REVERT: N 54 GLU cc_start: 0.7782 (tt0) cc_final: 0.7420 (tt0) REVERT: N 129 ILE cc_start: 0.8150 (OUTLIER) cc_final: 0.7798 (mp) REVERT: N 187 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.7637 (mpp) REVERT: N 191 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8208 (tm) REVERT: N 221 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8106 (tm) REVERT: N 289 ASN cc_start: 0.8680 (m110) cc_final: 0.8252 (m-40) REVERT: O 163 TYR cc_start: 0.7575 (m-80) cc_final: 0.7252 (m-80) REVERT: O 268 GLU cc_start: 0.7198 (mt-10) cc_final: 0.6650 (mm-30) REVERT: Q 19 ILE cc_start: 0.8571 (mm) cc_final: 0.8266 (mt) REVERT: R 92 LYS cc_start: 0.8217 (mttp) cc_final: 0.7932 (mttm) REVERT: S 63 LYS cc_start: 0.8387 (mmtp) cc_final: 0.8077 (mptt) REVERT: U 6 LEU cc_start: 0.7177 (OUTLIER) cc_final: 0.6731 (pp) REVERT: U 22 TYR cc_start: 0.6926 (t80) cc_final: 0.6597 (t80) REVERT: U 52 MET cc_start: 0.7454 (mtt) cc_final: 0.7112 (mtp) REVERT: Y 13 ASP cc_start: 0.6016 (t0) cc_final: 0.5668 (t0) REVERT: Y 15 THR cc_start: 0.7872 (m) cc_final: 0.7612 (m) REVERT: Y 16 GLN cc_start: 0.7552 (mt0) cc_final: 0.6593 (mm-40) REVERT: Y 60 PHE cc_start: 0.8247 (t80) cc_final: 0.7903 (t80) REVERT: Z 51 ARG cc_start: 0.7407 (mmt180) cc_final: 0.7150 (mmt180) REVERT: b 31 MET cc_start: 0.7134 (mmm) cc_final: 0.6820 (mmm) REVERT: b 45 ASN cc_start: 0.9072 (t0) cc_final: 0.8799 (m-40) REVERT: d 19 ARG cc_start: 0.7527 (mtp180) cc_final: 0.7286 (mtp180) REVERT: d 54 MET cc_start: 0.7226 (tpp) cc_final: 0.6976 (tpp) REVERT: h 22 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8835 (mm) REVERT: i 7 GLU cc_start: 0.6926 (pt0) cc_final: 0.6619 (pt0) REVERT: j 32 MET cc_start: 0.7866 (ttp) cc_final: 0.7623 (ttp) REVERT: k 77 LYS cc_start: 0.8284 (tppt) cc_final: 0.7929 (ttpt) REVERT: l 102 LYS cc_start: 0.8126 (mtpt) cc_final: 0.7846 (mtmt) REVERT: m 61 ASP cc_start: 0.7636 (t0) cc_final: 0.7324 (t0) REVERT: m 105 LYS cc_start: 0.7706 (ttmm) cc_final: 0.7400 (ttmm) REVERT: n 73 ASN cc_start: 0.7653 (m110) cc_final: 0.7350 (m110) REVERT: o 43 GLN cc_start: 0.8007 (tm-30) cc_final: 0.7521 (tm-30) REVERT: o 47 ASP cc_start: 0.6264 (t70) cc_final: 0.6017 (t0) REVERT: o 49 GLN cc_start: 0.8808 (mm-40) cc_final: 0.8480 (mm-40) REVERT: o 81 HIS cc_start: 0.6732 (t70) cc_final: 0.6502 (t-170) REVERT: o 108 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7499 (mp) REVERT: p 90 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.8254 (tt0) REVERT: p 136 LYS cc_start: 0.7567 (tptp) cc_final: 0.6651 (ttpt) REVERT: p 143 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8120 (tm) REVERT: q 124 TYR cc_start: 0.8674 (t80) cc_final: 0.8281 (t80) outliers start: 261 outliers final: 141 residues processed: 1563 average time/residue: 0.6700 time to fit residues: 1805.0917 Evaluate side-chains 1420 residues out of total 7156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 1263 time to evaluate : 5.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain D residue 7 ASP Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 237 ASN Chi-restraints excluded: chain D residue 279 ASP Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 114 ASP Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 250 ASN Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 303 SER Chi-restraints excluded: chain F residue 307 ILE Chi-restraints excluded: chain F residue 316 LEU Chi-restraints excluded: chain F residue 367 GLU Chi-restraints excluded: chain F residue 392 LEU Chi-restraints excluded: chain F residue 396 SER Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 238 ILE Chi-restraints excluded: chain G residue 258 ILE Chi-restraints excluded: chain G residue 307 LEU Chi-restraints excluded: chain G residue 436 ARG Chi-restraints excluded: chain G residue 467 LEU Chi-restraints excluded: chain G residue 525 LEU Chi-restraints excluded: chain G residue 536 ASP Chi-restraints excluded: chain G residue 543 ILE Chi-restraints excluded: chain G residue 544 VAL Chi-restraints excluded: chain G residue 558 ASP Chi-restraints excluded: chain G residue 674 THR Chi-restraints excluded: chain H residue 146 MET Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 311 THR Chi-restraints excluded: chain I residue 1 THR Chi-restraints excluded: chain I residue 82 CYS Chi-restraints excluded: chain I residue 172 GLN Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain J residue 42 MET Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain J residue 104 CYS Chi-restraints excluded: chain J residue 106 LEU Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain K residue 31 LEU Chi-restraints excluded: chain K residue 53 SER Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 137 MET Chi-restraints excluded: chain L residue 241 THR Chi-restraints excluded: chain L residue 247 LEU Chi-restraints excluded: chain L residue 269 ASN Chi-restraints excluded: chain L residue 278 LEU Chi-restraints excluded: chain L residue 370 SER Chi-restraints excluded: chain L residue 417 SER Chi-restraints excluded: chain L residue 440 LEU Chi-restraints excluded: chain L residue 517 ASN Chi-restraints excluded: chain M residue 6 LEU Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain M residue 126 LEU Chi-restraints excluded: chain M residue 161 LEU Chi-restraints excluded: chain M residue 234 ILE Chi-restraints excluded: chain M residue 250 LEU Chi-restraints excluded: chain M residue 354 LEU Chi-restraints excluded: chain M residue 369 LEU Chi-restraints excluded: chain M residue 424 ILE Chi-restraints excluded: chain M residue 459 MET Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 97 MET Chi-restraints excluded: chain N residue 129 ILE Chi-restraints excluded: chain N residue 187 MET Chi-restraints excluded: chain N residue 191 LEU Chi-restraints excluded: chain N residue 221 LEU Chi-restraints excluded: chain N residue 290 LEU Chi-restraints excluded: chain N residue 324 LEU Chi-restraints excluded: chain O residue 25 ILE Chi-restraints excluded: chain O residue 32 CYS Chi-restraints excluded: chain O residue 96 LEU Chi-restraints excluded: chain O residue 167 HIS Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 108 ASP Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain P residue 220 ASP Chi-restraints excluded: chain P residue 222 ASP Chi-restraints excluded: chain P residue 302 ASP Chi-restraints excluded: chain P residue 327 LEU Chi-restraints excluded: chain Q residue 47 SER Chi-restraints excluded: chain Q residue 81 ASN Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain Q residue 123 SER Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain U residue 6 LEU Chi-restraints excluded: chain V residue 89 LEU Chi-restraints excluded: chain V residue 94 LEU Chi-restraints excluded: chain W residue 112 THR Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 58 GLU Chi-restraints excluded: chain X residue 117 VAL Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Z residue 8 ASP Chi-restraints excluded: chain Z residue 86 LEU Chi-restraints excluded: chain b residue 10 ASN Chi-restraints excluded: chain b residue 21 SER Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain b residue 82 ASN Chi-restraints excluded: chain d residue 37 LEU Chi-restraints excluded: chain d residue 96 LEU Chi-restraints excluded: chain e residue 66 LEU Chi-restraints excluded: chain f residue 8 GLU Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain h residue 22 LEU Chi-restraints excluded: chain h residue 79 PHE Chi-restraints excluded: chain i residue 22 LEU Chi-restraints excluded: chain i residue 115 VAL Chi-restraints excluded: chain j residue 30 SER Chi-restraints excluded: chain j residue 43 ASP Chi-restraints excluded: chain k residue 21 LEU Chi-restraints excluded: chain k residue 87 LEU Chi-restraints excluded: chain l residue 4 THR Chi-restraints excluded: chain l residue 61 TYR Chi-restraints excluded: chain n residue 52 ASN Chi-restraints excluded: chain n residue 88 THR Chi-restraints excluded: chain n residue 98 VAL Chi-restraints excluded: chain o residue 23 SER Chi-restraints excluded: chain o residue 37 VAL Chi-restraints excluded: chain o residue 77 LEU Chi-restraints excluded: chain o residue 108 LEU Chi-restraints excluded: chain p residue 31 TYR Chi-restraints excluded: chain p residue 60 THR Chi-restraints excluded: chain p residue 90 GLN Chi-restraints excluded: chain p residue 143 LEU Chi-restraints excluded: chain q residue 38 LEU Chi-restraints excluded: chain q residue 66 THR Chi-restraints excluded: chain q residue 77 VAL Chi-restraints excluded: chain r residue 6 VAL Chi-restraints excluded: chain r residue 63 VAL Chi-restraints excluded: chain r residue 105 LEU Chi-restraints excluded: chain s residue 30 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 797 random chunks: chunk 716 optimal weight: 9.9990 chunk 545 optimal weight: 0.6980 chunk 376 optimal weight: 0.0270 chunk 80 optimal weight: 1.9990 chunk 346 optimal weight: 2.9990 chunk 486 optimal weight: 0.7980 chunk 727 optimal weight: 0.3980 chunk 770 optimal weight: 4.9990 chunk 380 optimal weight: 0.0370 chunk 689 optimal weight: 10.0000 chunk 207 optimal weight: 1.9990 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: