Starting phenix.real_space_refine on Mon Nov 20 17:00:29 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yal_10760/11_2023/6yal_10760_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yal_10760/11_2023/6yal_10760.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yal_10760/11_2023/6yal_10760_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yal_10760/11_2023/6yal_10760_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yal_10760/11_2023/6yal_10760_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yal_10760/11_2023/6yal_10760.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yal_10760/11_2023/6yal_10760.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yal_10760/11_2023/6yal_10760_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yal_10760/11_2023/6yal_10760_updated.pdb" } resolution = 3.0 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= 0.006 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 8 7.16 5 P 1861 5.49 5 Mg 1 5.21 5 S 260 5.16 5 C 49556 2.51 5 N 16464 2.21 5 O 21935 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "l ARG 9": "NH1" <-> "NH2" Residue "D ARG 82": "NH1" <-> "NH2" Residue "D ARG 151": "NH1" <-> "NH2" Residue "D ARG 162": "NH1" <-> "NH2" Residue "D ARG 165": "NH1" <-> "NH2" Residue "D ARG 213": "NH1" <-> "NH2" Residue "E ARG 108": "NH1" <-> "NH2" Residue "E ARG 151": "NH1" <-> "NH2" Residue "E ARG 152": "NH1" <-> "NH2" Residue "E ARG 185": "NH1" <-> "NH2" Residue "E TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 94": "NH1" <-> "NH2" Residue "G ARG 11": "NH1" <-> "NH2" Residue "G ARG 49": "NH1" <-> "NH2" Residue "G ARG 68": "NH1" <-> "NH2" Residue "G ARG 191": "NH1" <-> "NH2" Residue "G ARG 198": "NH1" <-> "NH2" Residue "G ARG 221": "NH1" <-> "NH2" Residue "G ARG 252": "NH1" <-> "NH2" Residue "H ARG 62": "NH1" <-> "NH2" Residue "H ARG 71": "NH1" <-> "NH2" Residue "H ARG 81": "NH1" <-> "NH2" Residue "H ARG 91": "NH1" <-> "NH2" Residue "H ARG 164": "NH1" <-> "NH2" Residue "I ARG 131": "NH1" <-> "NH2" Residue "I ARG 132": "NH1" <-> "NH2" Residue "I ARG 178": "NH1" <-> "NH2" Residue "J ARG 57": "NH1" <-> "NH2" Residue "J ARG 78": "NH1" <-> "NH2" Residue "J ARG 81": "NH1" <-> "NH2" Residue "J ARG 99": "NH1" <-> "NH2" Residue "J ARG 143": "NH1" <-> "NH2" Residue "K ARG 25": "NH1" <-> "NH2" Residue "K ARG 41": "NH1" <-> "NH2" Residue "L ARG 54": "NH1" <-> "NH2" Residue "L ARG 69": "NH1" <-> "NH2" Residue "L ARG 169": "NH1" <-> "NH2" Residue "N ARG 97": "NH1" <-> "NH2" Residue "P ARG 104": "NH1" <-> "NH2" Residue "P ARG 114": "NH1" <-> "NH2" Residue "P ARG 121": "NH1" <-> "NH2" Residue "Q ARG 55": "NH1" <-> "NH2" Residue "Q ARG 117": "NH1" <-> "NH2" Residue "Q ARG 141": "NH1" <-> "NH2" Residue "Q ARG 150": "NH1" <-> "NH2" Residue "S PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 126": "NH1" <-> "NH2" Residue "S ARG 140": "NH1" <-> "NH2" Residue "S ARG 146": "NH1" <-> "NH2" Residue "T ARG 3": "NH1" <-> "NH2" Residue "T ARG 5": "NH1" <-> "NH2" Residue "T PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 62": "NH1" <-> "NH2" Residue "V ARG 84": "NH1" <-> "NH2" Residue "V ARG 102": "NH1" <-> "NH2" Residue "V ARG 121": "NH1" <-> "NH2" Residue "W ARG 21": "NH1" <-> "NH2" Residue "W ARG 62": "NH1" <-> "NH2" Residue "W ARG 87": "NH1" <-> "NH2" Residue "Y PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 5": "NH1" <-> "NH2" Residue "Z ARG 8": "NH1" <-> "NH2" Residue "Z ARG 17": "NH1" <-> "NH2" Residue "Z ARG 67": "NH1" <-> "NH2" Residue "Z ARG 107": "NH1" <-> "NH2" Residue "a ARG 20": "NH1" <-> "NH2" Residue "a ARG 61": "NH1" <-> "NH2" Residue "a GLU 98": "OE1" <-> "OE2" Residue "b ARG 10": "NH1" <-> "NH2" Residue "b ARG 85": "NH1" <-> "NH2" Residue "b ARG 87": "NH1" <-> "NH2" Residue "b ARG 89": "NH1" <-> "NH2" Residue "d ARG 13": "NH1" <-> "NH2" Residue "d ARG 40": "NH1" <-> "NH2" Residue "d ARG 44": "NH1" <-> "NH2" Residue "d ARG 63": "NH1" <-> "NH2" Residue "e ARG 27": "NH1" <-> "NH2" Residue "f TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 80": "NH1" <-> "NH2" Residue "i ARG 105": "NH1" <-> "NH2" Residue "A ARG 25": "NH1" <-> "NH2" Residue "A GLU 38": "OE1" <-> "OE2" Residue "A ARG 53": "NH1" <-> "NH2" Residue "A ARG 54": "NH1" <-> "NH2" Residue "A ARG 64": "NH1" <-> "NH2" Residue "A ARG 67": "NH1" <-> "NH2" Residue "A ARG 88": "NH1" <-> "NH2" Residue "A ARG 133": "NH1" <-> "NH2" Residue "A ARG 144": "NH1" <-> "NH2" Residue "A ARG 173": "NH1" <-> "NH2" Residue "A ARG 183": "NH1" <-> "NH2" Residue "A ARG 213": "NH1" <-> "NH2" Residue "A ARG 234": "NH1" <-> "NH2" Residue "A ARG 244": "NH1" <-> "NH2" Residue "A ARG 266": "NH1" <-> "NH2" Residue "B GLU 85": "OE1" <-> "OE2" Residue "B GLU 125": "OE1" <-> "OE2" Residue "B GLU 176": "OE1" <-> "OE2" Residue "B GLU 185": "OE1" <-> "OE2" Residue "B GLU 210": "OE1" <-> "OE2" Residue "B GLU 230": "OE1" <-> "OE2" Residue "B GLU 250": "OE1" <-> "OE2" Residue "B GLU 266": "OE1" <-> "OE2" Residue "B GLU 283": "OE1" <-> "OE2" Residue "B GLU 306": "OE1" <-> "OE2" Residue "B GLU 308": "OE1" <-> "OE2" Residue "B GLU 319": "OE1" <-> "OE2" Residue "B GLU 383": "OE1" <-> "OE2" Residue "B GLU 452": "OE1" <-> "OE2" Residue "j ARG 12": "NH1" <-> "NH2" Residue "j ARG 14": "NH1" <-> "NH2" Residue "j GLU 34": "OE1" <-> "OE2" Residue "j GLU 48": "OE1" <-> "OE2" Residue "j ASP 83": "OD1" <-> "OD2" Residue "j GLU 99": "OE1" <-> "OE2" Residue "k GLU 24": "OE1" <-> "OE2" Residue "k ARG 33": "NH1" <-> "NH2" Residue "k GLU 40": "OE1" <-> "OE2" Residue "k ARG 96": "NH1" <-> "NH2" Residue "k ARG 101": "NH1" <-> "NH2" Residue "k ASP 135": "OD1" <-> "OD2" Residue "k ASP 136": "OD1" <-> "OD2" Residue "k GLU 151": "OE1" <-> "OE2" Residue "k TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 190": "NH1" <-> "NH2" Residue "k ASP 192": "OD1" <-> "OD2" Residue "k GLU 193": "OE1" <-> "OE2" Residue "k ARG 267": "NH1" <-> "NH2" Residue "k TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 306": "NH1" <-> "NH2" Residue "k GLU 320": "OE1" <-> "OE2" Residue "k ARG 325": "NH1" <-> "NH2" Residue "k GLU 335": "OE1" <-> "OE2" Residue "k GLU 340": "OE1" <-> "OE2" Residue "k GLU 341": "OE1" <-> "OE2" Residue "k GLU 359": "OE1" <-> "OE2" Residue "k ARG 390": "NH1" <-> "NH2" Residue "k ARG 395": "NH1" <-> "NH2" Residue "k ARG 502": "NH1" <-> "NH2" Residue "k ARG 531": "NH1" <-> "NH2" Residue "k PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 563": "OE1" <-> "OE2" Residue "k ARG 567": "NH1" <-> "NH2" Residue "k ASP 585": "OD1" <-> "OD2" Residue "U ARG 39": "NH1" <-> "NH2" Residue "U ARG 55": "NH1" <-> "NH2" Residue "U ARG 86": "NH1" <-> "NH2" Residue "U ARG 142": "NH1" <-> "NH2" Residue "R ARG 13": "NH1" <-> "NH2" Residue "R ARG 61": "NH1" <-> "NH2" Residue "R PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 140": "NH1" <-> "NH2" Residue "R PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 90085 Number of models: 1 Model: "" Number of chains: 42 Chain: "1" Number of atoms: 1614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1614 Classifications: {'RNA': 75} Modifications used: {'5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 3, 'rna3p': 1, 'rna3p_pur': 33, 'rna3p_pyr': 30} Link IDs: {'rna2p': 11, 'rna3p': 63} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "l" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 240 Classifications: {'peptide': 25} Modifications used: {'COO': 1} Link IDs: {'TRANS': 24} Chain: "C" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1643 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 195} Chain: "D" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1741 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 5, 'TRANS': 209} Chain: "E" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1743 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 214} Chain: "F" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1764 Classifications: {'peptide': 227} Link IDs: {'CIS': 3, 'PTRANS': 11, 'TRANS': 212} Chain: "G" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2083 Classifications: {'peptide': 263} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 248} Chain: "H" Number of atoms: 1509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1509 Classifications: {'peptide': 191} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 184} Chain: "I" Number of atoms: 1924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1924 Classifications: {'peptide': 237} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 226} Chain: "J" Number of atoms: 1530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1530 Classifications: {'peptide': 190} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 180} Chain: "K" Number of atoms: 1680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1680 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 197} Chain: "L" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1499 Classifications: {'peptide': 182} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 175} Chain: "M" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 828 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 89} Chain: "N" Number of atoms: 1296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1296 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 151} Chain: "O" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 958 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "P" Number of atoms: 1208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1208 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 141} Chain: "Q" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1016 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain: "S" Number of atoms: 1124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1124 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "T" Number of atoms: 1019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1019 Classifications: {'peptide': 126} Link IDs: {'CIS': 2, 'PTRANS': 5, 'TRANS': 118} Chain: "V" Number of atoms: 1113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1113 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 136} Chain: "W" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 822 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "X" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 620 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 78} Chain: "Y" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1034 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 1, 'TRANS': 125} Chain: "Z" Number of atoms: 1106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1106 Classifications: {'peptide': 142} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 136} Chain: "a" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1021 Classifications: {'peptide': 126} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 120} Chain: "b" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 789 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 6, 'TRANS': 92} Chain: "c" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 659 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 76} Chain: "d" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 506 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "e" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 445 Classifications: {'peptide': 53} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 51} Chain: "f" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 582 Classifications: {'peptide': 71} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 67} Chain: "g" Number of atoms: 2437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2437 Classifications: {'peptide': 313} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 10, 'TRANS': 300} Chain: "n" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 598 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "i" Number of atoms: 473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 473 Classifications: {'peptide': 59} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 55} Chain: "2" Number of atoms: 37204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1744, 37204 Inner-chain residues flagged as termini: ['pdbres=" C 2 139 "', 'pdbres=" G 2 270 "', 'pdbres=" G 21765 "'] Classifications: {'RNA': 1744} Modifications used: {'5*END': 4, 'rna2p_pur': 149, 'rna2p_pyr': 121, 'rna3p': 1, 'rna3p_pur': 764, 'rna3p_pyr': 709} Link IDs: {'rna2p': 270, 'rna3p': 1473} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 2146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2146 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 8, 'TRANS': 257} Chain: "B" Number of atoms: 3214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3214 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Link IDs: {'CIS': 5, 'PTRANS': 22, 'TRANS': 394} Chain: "j" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 883 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 107} Chain: "k" Number of atoms: 4693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4693 Classifications: {'peptide': 595} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 30, 'TRANS': 561} Chain: "U" Number of atoms: 1194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1194 Classifications: {'peptide': 145} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 141} Chain: "R" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1154 Classifications: {'peptide': 140} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 130} Chain: "3" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 892 Classifications: {'RNA': 42} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 5, 'rna3p_pur': 18, 'rna3p_pyr': 14} Link IDs: {'rna2p': 10, 'rna3p': 31} Chain: "k" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 81 Unusual residues: {' MG': 1, 'GNP': 2, 'SF4': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 82280 SG CYS k 29 115.408 103.943 83.360 1.00 0.82 S ATOM 82480 SG CYS k 55 120.157 104.747 78.929 1.00 0.73 S ATOM 82516 SG CYS k 61 119.622 100.345 83.113 1.00 0.77 S ATOM 82498 SG CYS k 58 120.701 105.562 84.131 1.00 0.73 S ATOM 82250 SG CYS k 25 116.202 95.464 83.596 1.00 0.79 S ATOM 82215 SG CYS k 21 113.020 90.370 84.839 1.00 0.76 S ATOM 82548 SG CYS k 65 118.119 92.647 84.559 1.00 0.68 S ATOM 82175 SG CYS k 16 116.823 90.324 78.692 1.00 0.73 S Residues with excluded nonbonded symmetry interactions: 413 residue: pdb=" N GLN B 52 " occ=0.00 ... (7 atoms not shown) pdb=" NE2 GLN B 52 " occ=0.00 residue: pdb=" N ALA B 53 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA B 53 " occ=0.00 residue: pdb=" N THR B 54 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 THR B 54 " occ=0.00 residue: pdb=" N ILE B 55 " occ=0.00 ... (6 atoms not shown) pdb=" CD1 ILE B 55 " occ=0.00 residue: pdb=" N ASN B 56 " occ=0.00 ... (6 atoms not shown) pdb=" ND2 ASN B 56 " occ=0.00 residue: pdb=" N ILE B 57 " occ=0.00 ... (6 atoms not shown) pdb=" CD1 ILE B 57 " occ=0.00 residue: pdb=" N GLY B 58 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY B 58 " occ=0.00 residue: pdb=" N THR B 59 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 THR B 59 " occ=0.00 residue: pdb=" N ILE B 60 " occ=0.00 ... (6 atoms not shown) pdb=" CD1 ILE B 60 " occ=0.00 residue: pdb=" N GLY B 61 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY B 61 " occ=0.00 residue: pdb=" N HIS B 62 " occ=0.00 ... (8 atoms not shown) pdb=" NE2 HIS B 62 " occ=0.00 residue: pdb=" N VAL B 63 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 VAL B 63 " occ=0.00 ... (remaining 401 not shown) Time building chain proxies: 35.12, per 1000 atoms: 0.39 Number of scatterers: 90085 At special positions: 0 Unit cell: (232.1, 234.3, 227.7, 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) Fe 8 26.01 S 260 16.00 P 1861 15.00 Mg 1 11.99 O 21935 8.00 N 16464 7.00 C 49556 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS b 26 " - pdb=" SG CYS b 77 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 31.45 Conformation dependent library (CDL) restraints added in 7.0 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 k 701 " pdb="FE3 SF4 k 701 " - pdb=" SG CYS k 61 " pdb="FE2 SF4 k 701 " - pdb=" SG CYS k 55 " pdb="FE4 SF4 k 701 " - pdb=" SG CYS k 58 " pdb="FE1 SF4 k 701 " - pdb=" SG CYS k 29 " pdb=" SF4 k 702 " pdb="FE3 SF4 k 702 " - pdb=" SG CYS k 65 " pdb="FE2 SF4 k 702 " - pdb=" SG CYS k 21 " pdb="FE1 SF4 k 702 " - pdb=" SG CYS k 25 " pdb="FE4 SF4 k 702 " - pdb=" SG CYS k 16 " Number of angles added : 24 12456 Ramachandran restraints generated. 6228 Oldfield, 0 Emsley, 6228 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11728 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 175 helices and 72 sheets defined 26.8% alpha, 14.0% beta 506 base pairs and 893 stacking pairs defined. Time for finding SS restraints: 34.79 Creating SS restraints... Processing helix chain 'l' and resid 2 through 24 removed outlier: 3.573A pdb=" N MET l 10 " --> pdb=" O ARG l 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 20 removed outlier: 3.990A pdb=" N LEU C 16 " --> pdb=" O GLU C 12 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS C 17 " --> pdb=" O GLU C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 67 removed outlier: 3.775A pdb=" N LYS C 57 " --> pdb=" O ARG C 53 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU C 59 " --> pdb=" O TRP C 55 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU C 60 " --> pdb=" O GLU C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 93 removed outlier: 4.347A pdb=" N ARG C 85 " --> pdb=" O THR C 82 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ALA C 86 " --> pdb=" O GLY C 83 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL C 87 " --> pdb=" O GLN C 84 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA C 91 " --> pdb=" O LEU C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 139 removed outlier: 3.670A pdb=" N SER C 138 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N TYR C 139 " --> pdb=" O THR C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 185 removed outlier: 3.589A pdb=" N MET C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL C 182 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU C 183 " --> pdb=" O ALA C 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 61 No H-bonds generated for 'chain 'D' and resid 59 through 61' Processing helix chain 'D' and resid 72 through 75 No H-bonds generated for 'chain 'D' and resid 72 through 75' Processing helix chain 'D' and resid 108 through 112 Processing helix chain 'D' and resid 158 through 177 removed outlier: 3.617A pdb=" N ILE D 171 " --> pdb=" O LYS D 167 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N MET D 172 " --> pdb=" O MET D 168 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL D 176 " --> pdb=" O MET D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 189 removed outlier: 3.577A pdb=" N VAL D 185 " --> pdb=" O LEU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 200 removed outlier: 3.571A pdb=" N ILE D 197 " --> pdb=" O ILE D 193 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS D 199 " --> pdb=" O LYS D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 231 removed outlier: 3.784A pdb=" N GLU D 230 " --> pdb=" O GLY D 226 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU D 231 " --> pdb=" O LYS D 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 56 removed outlier: 3.521A pdb=" N VAL E 55 " --> pdb=" O LEU E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 69 Processing helix chain 'E' and resid 79 through 82 No H-bonds generated for 'chain 'E' and resid 79 through 82' Processing helix chain 'E' and resid 132 through 145 removed outlier: 3.760A pdb=" N LYS E 144 " --> pdb=" O ILE E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 202 removed outlier: 3.633A pdb=" N LYS E 197 " --> pdb=" O PRO E 193 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU E 198 " --> pdb=" O VAL E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 233 removed outlier: 3.572A pdb=" N LYS E 231 " --> pdb=" O ASP E 227 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N THR E 232 " --> pdb=" O ALA E 228 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N TYR E 233 " --> pdb=" O ILE E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 241 Processing helix chain 'E' and resid 250 through 253 No H-bonds generated for 'chain 'E' and resid 250 through 253' Processing helix chain 'E' and resid 255 through 258 Processing helix chain 'F' and resid 7 through 27 removed outlier: 3.764A pdb=" N PHE F 11 " --> pdb=" O LYS F 7 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL F 12 " --> pdb=" O LYS F 8 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP F 14 " --> pdb=" O LYS F 10 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU F 21 " --> pdb=" O PHE F 17 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASN F 22 " --> pdb=" O LYS F 18 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N THR F 26 " --> pdb=" O ASN F 22 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG F 27 " --> pdb=" O GLU F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 32 No H-bonds generated for 'chain 'F' and resid 30 through 32' Processing helix chain 'F' and resid 55 through 59 Processing helix chain 'F' and resid 64 through 76 Processing helix chain 'F' and resid 98 through 110 removed outlier: 3.679A pdb=" N TYR F 107 " --> pdb=" O GLU F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 128 removed outlier: 3.746A pdb=" N PHE F 125 " --> pdb=" O GLY F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 167 removed outlier: 4.311A pdb=" N TYR F 167 " --> pdb=" O VAL F 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'G' and resid 58 through 67 removed outlier: 3.964A pdb=" N MET G 66 " --> pdb=" O LYS G 62 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLN G 67 " --> pdb=" O LYS G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 222 through 224 No H-bonds generated for 'chain 'G' and resid 222 through 224' Processing helix chain 'G' and resid 248 through 258 removed outlier: 3.529A pdb=" N ARG G 255 " --> pdb=" O GLU G 251 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 68 through 76 Processing helix chain 'H' and resid 86 through 103 removed outlier: 3.823A pdb=" N ILE H 92 " --> pdb=" O MET H 88 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL H 93 " --> pdb=" O THR H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 119 removed outlier: 3.835A pdb=" N LEU H 112 " --> pdb=" O PRO H 108 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER H 119 " --> pdb=" O ALA H 115 " (cutoff:3.500A) Processing helix chain 'H' and resid 143 through 163 removed outlier: 3.586A pdb=" N LEU H 154 " --> pdb=" O ALA H 150 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N CYS H 155 " --> pdb=" O ILE H 151 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY H 157 " --> pdb=" O LEU H 153 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA H 158 " --> pdb=" O LEU H 154 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N PHE H 163 " --> pdb=" O ARG H 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 169 through 181 Processing helix chain 'H' and resid 188 through 202 removed outlier: 3.537A pdb=" N LYS H 192 " --> pdb=" O TYR H 188 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP H 194 " --> pdb=" O ILE H 190 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER H 202 " --> pdb=" O ARG H 198 " (cutoff:3.500A) Processing helix chain 'I' and resid 21 through 25 Processing helix chain 'I' and resid 39 through 41 No H-bonds generated for 'chain 'I' and resid 39 through 41' Processing helix chain 'I' and resid 138 through 145 Processing helix chain 'I' and resid 182 through 236 removed outlier: 3.561A pdb=" N HIS I 187 " --> pdb=" O ARG I 183 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE I 192 " --> pdb=" O LYS I 188 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS I 195 " --> pdb=" O ARG I 191 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA I 206 " --> pdb=" O ASN I 202 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N MET I 217 " --> pdb=" O LEU I 213 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LYS I 218 " --> pdb=" O ALA I 214 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU I 219 " --> pdb=" O LYS I 215 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS I 221 " --> pdb=" O MET I 217 " (cutoff:3.500A) Processing helix chain 'J' and resid 18 through 32 removed outlier: 4.154A pdb=" N ALA J 26 " --> pdb=" O GLY J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 68 through 75 Processing helix chain 'J' and resid 78 through 86 Processing helix chain 'J' and resid 123 through 133 removed outlier: 3.867A pdb=" N LEU J 130 " --> pdb=" O HIS J 126 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP J 132 " --> pdb=" O ALA J 128 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU J 133 " --> pdb=" O ILE J 129 " (cutoff:3.500A) Processing helix chain 'J' and resid 135 through 137 No H-bonds generated for 'chain 'J' and resid 135 through 137' Processing helix chain 'J' and resid 172 through 180 removed outlier: 3.638A pdb=" N VAL J 176 " --> pdb=" O THR J 172 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR J 177 " --> pdb=" O PHE J 173 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS J 179 " --> pdb=" O GLY J 175 " (cutoff:3.500A) Processing helix chain 'K' and resid 89 through 92 No H-bonds generated for 'chain 'K' and resid 89 through 92' Processing helix chain 'K' and resid 107 through 116 removed outlier: 3.519A pdb=" N GLN K 111 " --> pdb=" O THR K 107 " (cutoff:3.500A) Processing helix chain 'K' and resid 127 through 131 Proline residue: K 131 - end of helix No H-bonds generated for 'chain 'K' and resid 127 through 131' Processing helix chain 'K' and resid 149 through 151 No H-bonds generated for 'chain 'K' and resid 149 through 151' Processing helix chain 'K' and resid 160 through 168 removed outlier: 4.265A pdb=" N GLN K 165 " --> pdb=" O LEU K 161 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE K 166 " --> pdb=" O LEU K 162 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLN K 167 " --> pdb=" O GLU K 163 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLN K 168 " --> pdb=" O GLU K 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 179 through 182 No H-bonds generated for 'chain 'K' and resid 179 through 182' Processing helix chain 'K' and resid 192 through 205 removed outlier: 3.546A pdb=" N GLU K 196 " --> pdb=" O GLY K 192 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU K 199 " --> pdb=" O LEU K 195 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG K 200 " --> pdb=" O GLU K 196 " (cutoff:3.500A) Processing helix chain 'L' and resid 22 through 35 removed outlier: 3.608A pdb=" N ASP L 26 " --> pdb=" O LYS L 22 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN L 27 " --> pdb=" O SER L 23 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR L 35 " --> pdb=" O LEU L 31 " (cutoff:3.500A) Processing helix chain 'L' and resid 40 through 60 removed outlier: 4.105A pdb=" N TRP L 44 " --> pdb=" O ARG L 41 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ARG L 45 " --> pdb=" O GLU L 42 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU L 50 " --> pdb=" O LYS L 47 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG L 54 " --> pdb=" O ALA L 51 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA L 56 " --> pdb=" O ILE L 53 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ALA L 57 " --> pdb=" O ARG L 54 " (cutoff:3.500A) Processing helix chain 'L' and resid 68 through 84 removed outlier: 3.554A pdb=" N ARG L 79 " --> pdb=" O ASN L 75 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG L 80 " --> pdb=" O ALA L 76 " (cutoff:3.500A) Processing helix chain 'L' and resid 94 through 97 Processing helix chain 'L' and resid 102 through 108 removed outlier: 3.907A pdb=" N LEU L 106 " --> pdb=" O ILE L 102 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ARG L 108 " --> pdb=" O ASP L 104 " (cutoff:3.500A) Processing helix chain 'L' and resid 110 through 117 Processing helix chain 'L' and resid 123 through 131 removed outlier: 4.146A pdb=" N VAL L 128 " --> pdb=" O HIS L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 151 through 155 removed outlier: 4.068A pdb=" N LYS L 155 " --> pdb=" O ASP L 152 " (cutoff:3.500A) Processing helix chain 'L' and resid 174 through 180 Processing helix chain 'M' and resid 6 through 18 removed outlier: 3.616A pdb=" N ILE M 11 " --> pdb=" O ASN M 7 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU M 14 " --> pdb=" O ALA M 10 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE M 16 " --> pdb=" O TYR M 12 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 55 removed outlier: 3.843A pdb=" N SER M 51 " --> pdb=" O LYS M 47 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG M 55 " --> pdb=" O SER M 51 " (cutoff:3.500A) Processing helix chain 'M' and resid 73 through 82 Processing helix chain 'N' and resid 48 through 52 Processing helix chain 'O' and resid 14 through 28 removed outlier: 3.731A pdb=" N LEU O 18 " --> pdb=" O VAL O 14 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN O 19 " --> pdb=" O ASN O 15 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU O 22 " --> pdb=" O LEU O 18 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS O 23 " --> pdb=" O GLN O 19 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N THR O 24 " --> pdb=" O GLU O 20 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ILE O 27 " --> pdb=" O LYS O 23 " (cutoff:3.500A) Processing helix chain 'O' and resid 35 through 43 Processing helix chain 'O' and resid 61 through 71 removed outlier: 4.072A pdb=" N GLU O 66 " --> pdb=" O VAL O 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 82 through 88 Processing helix chain 'O' and resid 121 through 131 removed outlier: 3.782A pdb=" N GLU O 125 " --> pdb=" O LYS O 121 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE O 128 " --> pdb=" O ILE O 124 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYS O 130 " --> pdb=" O GLU O 126 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LYS O 131 " --> pdb=" O TYR O 127 " (cutoff:3.500A) Processing helix chain 'P' and resid 30 through 43 removed outlier: 3.580A pdb=" N GLU P 35 " --> pdb=" O ASP P 31 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS P 39 " --> pdb=" O GLU P 35 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU P 40 " --> pdb=" O GLN P 36 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS P 42 " --> pdb=" O TYR P 38 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS P 43 " --> pdb=" O LYS P 39 " (cutoff:3.500A) Processing helix chain 'P' and resid 47 through 55 Processing helix chain 'P' and resid 71 through 78 removed outlier: 3.608A pdb=" N LEU P 75 " --> pdb=" O ILE P 71 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS P 78 " --> pdb=" O ILE P 74 " (cutoff:3.500A) Processing helix chain 'P' and resid 86 through 104 removed outlier: 3.556A pdb=" N VAL P 96 " --> pdb=" O ILE P 92 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ALA P 97 " --> pdb=" O LYS P 93 " (cutoff:3.500A) Processing helix chain 'P' and resid 109 through 129 removed outlier: 3.616A pdb=" N ILE P 116 " --> pdb=" O LYS P 112 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU P 117 " --> pdb=" O PHE P 113 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N HIS P 123 " --> pdb=" O GLU P 119 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR P 128 " --> pdb=" O ARG P 124 " (cutoff:3.500A) Processing helix chain 'P' and resid 143 through 150 Processing helix chain 'Q' and resid 58 through 61 No H-bonds generated for 'chain 'Q' and resid 58 through 61' Processing helix chain 'Q' and resid 71 through 88 removed outlier: 3.679A pdb=" N ASP Q 80 " --> pdb=" O LEU Q 76 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLN Q 83 " --> pdb=" O GLN Q 79 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG Q 84 " --> pdb=" O ASP Q 80 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS Q 86 " --> pdb=" O ALA Q 82 " (cutoff:3.500A) Processing helix chain 'Q' and resid 113 through 122 removed outlier: 3.575A pdb=" N ARG Q 117 " --> pdb=" O GLN Q 113 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG Q 121 " --> pdb=" O ARG Q 117 " (cutoff:3.500A) Processing helix chain 'S' and resid 39 through 41 No H-bonds generated for 'chain 'S' and resid 39 through 41' Processing helix chain 'S' and resid 48 through 51 No H-bonds generated for 'chain 'S' and resid 48 through 51' Processing helix chain 'S' and resid 53 through 58 Processing helix chain 'S' and resid 77 through 99 removed outlier: 4.043A pdb=" N ILE S 81 " --> pdb=" O HIS S 77 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR S 82 " --> pdb=" O VAL S 78 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL S 93 " --> pdb=" O SER S 89 " (cutoff:3.500A) Processing helix chain 'S' and resid 102 through 114 removed outlier: 3.804A pdb=" N GLU S 107 " --> pdb=" O ALA S 103 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE S 108 " --> pdb=" O SER S 104 " (cutoff:3.500A) Processing helix chain 'T' and resid 7 through 19 removed outlier: 3.784A pdb=" N ALA T 12 " --> pdb=" O THR T 8 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG T 14 " --> pdb=" O LYS T 10 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL T 15 " --> pdb=" O LYS T 11 " (cutoff:3.500A) Processing helix chain 'T' and resid 28 through 37 Processing helix chain 'T' and resid 45 through 61 removed outlier: 3.911A pdb=" N GLY T 52 " --> pdb=" O ASN T 48 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ARG T 60 " --> pdb=" O HIS T 56 " (cutoff:3.500A) Processing helix chain 'T' and resid 72 through 81 Processing helix chain 'T' and resid 103 through 109 removed outlier: 3.532A pdb=" N LEU T 108 " --> pdb=" O GLU T 104 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU T 109 " --> pdb=" O MET T 105 " (cutoff:3.500A) Processing helix chain 'V' and resid 11 through 24 removed outlier: 3.991A pdb=" N ARG V 16 " --> pdb=" O GLN V 12 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ALA V 20 " --> pdb=" O ARG V 16 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS V 23 " --> pdb=" O ALA V 19 " (cutoff:3.500A) Processing helix chain 'V' and resid 52 through 66 removed outlier: 3.612A pdb=" N ALA V 58 " --> pdb=" O TYR V 54 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER V 59 " --> pdb=" O THR V 55 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU V 64 " --> pdb=" O THR V 60 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU V 66 " --> pdb=" O ARG V 62 " (cutoff:3.500A) Processing helix chain 'V' and resid 72 through 79 removed outlier: 3.625A pdb=" N THR V 76 " --> pdb=" O VAL V 72 " (cutoff:3.500A) Processing helix chain 'V' and resid 98 through 109 removed outlier: 3.769A pdb=" N GLN V 105 " --> pdb=" O ARG V 101 " (cutoff:3.500A) Processing helix chain 'V' and resid 125 through 141 removed outlier: 3.749A pdb=" N GLY V 136 " --> pdb=" O ASP V 132 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLN V 137 " --> pdb=" O ARG V 133 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA V 139 " --> pdb=" O ALA V 135 " (cutoff:3.500A) Processing helix chain 'W' and resid 29 through 44 removed outlier: 3.848A pdb=" N VAL W 35 " --> pdb=" O SER W 31 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU W 39 " --> pdb=" O VAL W 35 " (cutoff:3.500A) Processing helix chain 'W' and resid 95 through 102 Processing helix chain 'X' and resid 57 through 62 Processing helix chain 'X' and resid 65 through 74 Processing helix chain 'Y' and resid 6 through 20 removed outlier: 4.302A pdb=" N LYS Y 12 " --> pdb=" O ALA Y 8 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N SER Y 13 " --> pdb=" O ASP Y 9 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE Y 14 " --> pdb=" O ALA Y 10 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS Y 19 " --> pdb=" O ASN Y 15 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG Y 20 " --> pdb=" O ASN Y 16 " (cutoff:3.500A) Processing helix chain 'Y' and resid 32 through 43 Processing helix chain 'Y' and resid 86 through 93 removed outlier: 3.644A pdb=" N ASN Y 92 " --> pdb=" O LYS Y 88 " (cutoff:3.500A) Processing helix chain 'Y' and resid 113 through 118 removed outlier: 4.230A pdb=" N ARG Y 118 " --> pdb=" O GLU Y 114 " (cutoff:3.500A) Processing helix chain 'Z' and resid 10 through 14 Processing helix chain 'Z' and resid 17 through 20 No H-bonds generated for 'chain 'Z' and resid 17 through 20' Processing helix chain 'Z' and resid 25 through 32 removed outlier: 3.521A pdb=" N LYS Z 29 " --> pdb=" O LYS Z 25 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU Z 32 " --> pdb=" O LYS Z 28 " (cutoff:3.500A) Processing helix chain 'Z' and resid 34 through 38 Processing helix chain 'Z' and resid 130 through 135 Processing helix chain 'a' and resid 37 through 48 removed outlier: 3.532A pdb=" N GLU a 42 " --> pdb=" O THR a 38 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS a 43 " --> pdb=" O GLU a 39 " (cutoff:3.500A) Processing helix chain 'a' and resid 79 through 84 Processing helix chain 'a' and resid 88 through 91 No H-bonds generated for 'chain 'a' and resid 88 through 91' Processing helix chain 'a' and resid 108 through 116 removed outlier: 3.669A pdb=" N ARG a 113 " --> pdb=" O GLU a 109 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS a 116 " --> pdb=" O ASN a 112 " (cutoff:3.500A) Processing helix chain 'a' and resid 122 through 126 Processing helix chain 'b' and resid 50 through 56 removed outlier: 4.479A pdb=" N VAL b 56 " --> pdb=" O ASP b 52 " (cutoff:3.500A) Processing helix chain 'b' and resid 75 through 81 removed outlier: 3.617A pdb=" N ILE b 79 " --> pdb=" O VAL b 75 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER b 81 " --> pdb=" O CYS b 77 " (cutoff:3.500A) Processing helix chain 'e' and resid 40 through 43 No H-bonds generated for 'chain 'e' and resid 40 through 43' Processing helix chain 'n' and resid 52 through 64 removed outlier: 3.599A pdb=" N CYS n 59 " --> pdb=" O TYR n 55 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS n 60 " --> pdb=" O ASP n 56 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL n 62 " --> pdb=" O LEU n 58 " (cutoff:3.500A) Proline residue: n 63 - end of helix Processing helix chain 'n' and resid 70 through 76 removed outlier: 3.842A pdb=" N GLU n 75 " --> pdb=" O ALA n 71 " (cutoff:3.500A) Processing helix chain 'n' and resid 82 through 94 removed outlier: 3.628A pdb=" N ALA n 86 " --> pdb=" O SER n 82 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU n 91 " --> pdb=" O ALA n 87 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER n 93 " --> pdb=" O GLN n 89 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS n 94 " --> pdb=" O GLU n 90 " (cutoff:3.500A) Processing helix chain 'i' and resid 104 through 115 removed outlier: 4.103A pdb=" N ARG i 108 " --> pdb=" O GLY i 104 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG i 115 " --> pdb=" O GLN i 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 51 No H-bonds generated for 'chain 'A' and resid 49 through 51' Processing helix chain 'A' and resid 92 through 118 removed outlier: 3.702A pdb=" N HIS A 114 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL A 115 " --> pdb=" O ILE A 111 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ALA A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N VAL A 118 " --> pdb=" O HIS A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 143 removed outlier: 3.741A pdb=" N LEU A 127 " --> pdb=" O ASP A 124 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN A 132 " --> pdb=" O SER A 129 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG A 133 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR A 134 " --> pdb=" O PHE A 131 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ALA A 135 " --> pdb=" O GLN A 132 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N TRP A 136 " --> pdb=" O ARG A 133 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL A 137 " --> pdb=" O THR A 134 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ASP A 140 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LYS A 141 " --> pdb=" O PHE A 138 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS A 143 " --> pdb=" O ASP A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 158 removed outlier: 3.553A pdb=" N SER A 158 " --> pdb=" O LYS A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 183 Processing helix chain 'A' and resid 204 through 213 removed outlier: 3.677A pdb=" N LYS A 209 " --> pdb=" O ILE A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 263 removed outlier: 3.839A pdb=" N ALA A 254 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N MET A 255 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA A 256 " --> pdb=" O ASN A 252 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL A 257 " --> pdb=" O GLN A 253 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE A 258 " --> pdb=" O ALA A 254 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS A 259 " --> pdb=" O MET A 255 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU A 263 " --> pdb=" O LYS A 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 74 Processing helix chain 'B' and resid 153 through 164 removed outlier: 4.654A pdb=" N ALA B 156 " --> pdb=" O ILE B 153 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU B 159 " --> pdb=" O ALA B 156 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY B 161 " --> pdb=" O MET B 158 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL B 164 " --> pdb=" O GLY B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 193 Processing helix chain 'B' and resid 210 through 223 Processing helix chain 'B' and resid 245 through 254 removed outlier: 3.692A pdb=" N GLU B 250 " --> pdb=" O GLU B 246 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL B 253 " --> pdb=" O CYS B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 360 No H-bonds generated for 'chain 'B' and resid 358 through 360' Processing helix chain 'j' and resid 65 through 68 No H-bonds generated for 'chain 'j' and resid 65 through 68' Processing helix chain 'j' and resid 97 through 106 Processing helix chain 'k' and resid 24 through 27 No H-bonds generated for 'chain 'k' and resid 24 through 27' Processing helix chain 'k' and resid 31 through 33 No H-bonds generated for 'chain 'k' and resid 31 through 33' Processing helix chain 'k' and resid 60 through 63 No H-bonds generated for 'chain 'k' and resid 60 through 63' Processing helix chain 'k' and resid 116 through 123 Processing helix chain 'k' and resid 142 through 146 Processing helix chain 'k' and resid 151 through 160 removed outlier: 3.791A pdb=" N PHE k 156 " --> pdb=" O GLN k 153 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR k 157 " --> pdb=" O ASN k 154 " (cutoff:3.500A) Processing helix chain 'k' and resid 186 through 191 Processing helix chain 'k' and resid 194 through 203 removed outlier: 3.784A pdb=" N ALA k 198 " --> pdb=" O THR k 194 " (cutoff:3.500A) Processing helix chain 'k' and resid 214 through 216 No H-bonds generated for 'chain 'k' and resid 214 through 216' Processing helix chain 'k' and resid 219 through 232 Processing helix chain 'k' and resid 249 through 262 removed outlier: 3.604A pdb=" N LEU k 253 " --> pdb=" O VAL k 249 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LEU k 262 " --> pdb=" O THR k 258 " (cutoff:3.500A) Processing helix chain 'k' and resid 279 through 282 No H-bonds generated for 'chain 'k' and resid 279 through 282' Processing helix chain 'k' and resid 305 through 313 removed outlier: 3.901A pdb=" N ASN k 310 " --> pdb=" O ARG k 306 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE k 311 " --> pdb=" O GLU k 307 " (cutoff:3.500A) Processing helix chain 'k' and resid 386 through 393 Processing helix chain 'k' and resid 424 through 430 removed outlier: 3.558A pdb=" N HIS k 429 " --> pdb=" O ARG k 425 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLU k 430 " --> pdb=" O GLN k 426 " (cutoff:3.500A) Processing helix chain 'k' and resid 441 through 444 No H-bonds generated for 'chain 'k' and resid 441 through 444' Processing helix chain 'k' and resid 452 through 455 No H-bonds generated for 'chain 'k' and resid 452 through 455' Processing helix chain 'k' and resid 464 through 474 Processing helix chain 'k' and resid 494 through 510 removed outlier: 4.102A pdb=" N MET k 499 " --> pdb=" O GLU k 495 " (cutoff:3.500A) Processing helix chain 'k' and resid 522 through 526 Processing helix chain 'k' and resid 551 through 561 removed outlier: 3.634A pdb=" N GLN k 561 " --> pdb=" O LYS k 557 " (cutoff:3.500A) Processing helix chain 'k' and resid 587 through 590 No H-bonds generated for 'chain 'k' and resid 587 through 590' Processing helix chain 'U' and resid 26 through 32 removed outlier: 3.506A pdb=" N THR U 31 " --> pdb=" O ALA U 27 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ALA U 32 " --> pdb=" O PHE U 28 " (cutoff:3.500A) Processing helix chain 'U' and resid 39 through 47 removed outlier: 3.995A pdb=" N VAL U 43 " --> pdb=" O ARG U 39 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL U 44 " --> pdb=" O TYR U 40 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ARG U 46 " --> pdb=" O HIS U 42 " (cutoff:3.500A) Processing helix chain 'U' and resid 56 through 58 No H-bonds generated for 'chain 'U' and resid 56 through 58' Processing helix chain 'U' and resid 61 through 72 removed outlier: 3.647A pdb=" N ARG U 66 " --> pdb=" O ASP U 62 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE U 68 " --> pdb=" O VAL U 64 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N THR U 69 " --> pdb=" O GLU U 65 " (cutoff:3.500A) Processing helix chain 'U' and resid 74 through 76 No H-bonds generated for 'chain 'U' and resid 74 through 76' Processing helix chain 'U' and resid 81 through 83 No H-bonds generated for 'chain 'U' and resid 81 through 83' Processing helix chain 'U' and resid 100 through 116 removed outlier: 3.865A pdb=" N ASP U 104 " --> pdb=" O ALA U 100 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN U 105 " --> pdb=" O ASN U 101 " (cutoff:3.500A) Processing helix chain 'U' and resid 120 through 127 Processing helix chain 'R' and resid 17 through 19 No H-bonds generated for 'chain 'R' and resid 17 through 19' Processing helix chain 'R' and resid 22 through 25 No H-bonds generated for 'chain 'R' and resid 22 through 25' Processing helix chain 'R' and resid 30 through 34 Processing helix chain 'R' and resid 39 through 46 removed outlier: 3.665A pdb=" N LEU R 45 " --> pdb=" O ARG R 42 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER R 46 " --> pdb=" O ARG R 43 " (cutoff:3.500A) Processing helix chain 'R' and resid 54 through 66 removed outlier: 3.971A pdb=" N ARG R 59 " --> pdb=" O SER R 55 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG R 61 " --> pdb=" O LEU R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 116 through 118 No H-bonds generated for 'chain 'R' and resid 116 through 118' Processing sheet with id= A, first strand: chain 'C' and resid 97 through 100 removed outlier: 3.701A pdb=" N THR C 97 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER C 78 " --> pdb=" O ILE C 99 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU C 121 " --> pdb=" O SER C 75 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N ILE C 77 " --> pdb=" O LEU C 121 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N VAL C 123 " --> pdb=" O ILE C 77 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE C 145 " --> pdb=" O VAL C 124 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 38 through 41 removed outlier: 7.059A pdb=" N ILE C 48 " --> pdb=" O TYR C 39 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 28 through 30 Processing sheet with id= D, first strand: chain 'D' and resid 32 through 34 Processing sheet with id= E, first strand: chain 'D' and resid 120 through 128 removed outlier: 4.056A pdb=" N ALA D 123 " --> pdb=" O CYS D 139 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 84 through 88 removed outlier: 3.879A pdb=" N GLY D 102 " --> pdb=" O LYS D 85 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N ILE D 87 " --> pdb=" O PHE D 100 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N PHE D 100 " --> pdb=" O ILE D 87 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 121 through 129 removed outlier: 4.010A pdb=" N HIS E 121 " --> pdb=" O ASP E 117 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS E 93 " --> pdb=" O PHE E 112 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ALA E 114 " --> pdb=" O VAL E 91 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N VAL E 91 " --> pdb=" O ALA E 114 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N GLY E 116 " --> pdb=" O ASP E 89 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N ASP E 89 " --> pdb=" O GLY E 116 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 169 through 172 removed outlier: 3.646A pdb=" N GLY E 171 " --> pdb=" O VAL E 178 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 38 through 42 removed outlier: 3.516A pdb=" N ILE F 48 " --> pdb=" O GLU F 85 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU F 89 " --> pdb=" O ILE F 50 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 147 through 155 removed outlier: 4.412A pdb=" N GLY F 133 " --> pdb=" O MET F 189 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS F 185 " --> pdb=" O VAL F 137 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LYS F 141 " --> pdb=" O VAL F 181 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N VAL F 181 " --> pdb=" O LYS F 141 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 41 through 43 removed outlier: 3.877A pdb=" N ALA G 84 " --> pdb=" O LEU G 42 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 70 through 72 removed outlier: 3.560A pdb=" N SER G 91 " --> pdb=" O LYS G 71 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE G 90 " --> pdb=" O PHE G 99 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 121 through 125 removed outlier: 3.729A pdb=" N THR G 159 " --> pdb=" O ILE G 173 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ASP G 171 " --> pdb=" O GLN G 161 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 192 through 194 removed outlier: 5.763A pdb=" N MET G 182 " --> pdb=" O VAL G 227 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N VAL G 227 " --> pdb=" O MET G 182 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 207 through 211 Processing sheet with id= P, first strand: chain 'G' and resid 126 through 132 removed outlier: 6.889A pdb=" N VAL G 140 " --> pdb=" O ARG G 127 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N ILE G 129 " --> pdb=" O HIS G 138 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N HIS G 138 " --> pdb=" O ILE G 129 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N VAL G 131 " --> pdb=" O ILE G 136 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE G 136 " --> pdb=" O VAL G 131 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'H' and resid 124 through 130 removed outlier: 3.783A pdb=" N ARG H 135 " --> pdb=" O ILE H 128 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ARG H 130 " --> pdb=" O THR H 133 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 12 through 17 removed outlier: 3.593A pdb=" N ILE I 16 " --> pdb=" O LEU I 3 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL I 49 " --> pdb=" O VAL I 114 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'I' and resid 72 through 77 removed outlier: 3.609A pdb=" N LYS I 95 " --> pdb=" O LEU I 75 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'I' and resid 54 through 57 removed outlier: 4.068A pdb=" N GLY I 54 " --> pdb=" O ASN I 110 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL I 108 " --> pdb=" O ASN I 56 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'J' and resid 48 through 52 removed outlier: 6.322A pdb=" N HIS J 91 " --> pdb=" O ILE J 60 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N ILE J 62 " --> pdb=" O HIS J 91 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N VAL J 93 " --> pdb=" O ILE J 62 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'J' and resid 141 through 146 Processing sheet with id= W, first strand: chain 'K' and resid 42 through 46 Processing sheet with id= X, first strand: chain 'K' and resid 62 through 67 removed outlier: 3.775A pdb=" N PHE K 65 " --> pdb=" O ARG K 74 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG K 74 " --> pdb=" O PHE K 65 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'K' and resid 101 through 103 Processing sheet with id= Z, first strand: chain 'L' and resid 135 through 137 removed outlier: 3.675A pdb=" N ASP L 158 " --> pdb=" O ARG L 136 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'M' and resid 20 through 24 removed outlier: 3.763A pdb=" N ALA M 23 " --> pdb=" O PHE M 67 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'N' and resid 102 through 111 removed outlier: 3.951A pdb=" N LYS N 79 " --> pdb=" O VAL N 87 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ARG N 89 " --> pdb=" O VAL N 77 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N VAL N 77 " --> pdb=" O ARG N 89 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ASP N 91 " --> pdb=" O GLY N 75 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N GLY N 75 " --> pdb=" O ASP N 91 " (cutoff:3.500A) removed outlier: 15.839A pdb=" N LEU N 93 " --> pdb=" O LEU N 73 " (cutoff:3.500A) removed outlier: 16.896A pdb=" N LEU N 73 " --> pdb=" O LEU N 93 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL N 126 " --> pdb=" O GLY N 75 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS N 144 " --> pdb=" O THR N 127 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N GLY N 129 " --> pdb=" O VAL N 142 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N VAL N 142 " --> pdb=" O GLY N 129 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'O' and resid 49 through 52 Processing sheet with id= AD, first strand: chain 'Q' and resid 28 through 30 removed outlier: 6.664A pdb=" N ALA Q 92 " --> pdb=" O GLY Q 29 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD Processing sheet with id= AE, first strand: chain 'Q' and resid 41 through 43 Processing sheet with id= AF, first strand: chain 'S' and resid 9 through 15 removed outlier: 3.730A pdb=" N ARG S 69 " --> pdb=" O HIS S 24 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'V' and resid 81 through 83 removed outlier: 3.575A pdb=" N GLY V 81 " --> pdb=" O SER V 93 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'V' and resid 113 through 116 removed outlier: 3.564A pdb=" N ASP V 116 " --> pdb=" O GLY V 120 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLY V 120 " --> pdb=" O ASP V 116 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'W' and resid 111 through 115 removed outlier: 3.622A pdb=" N THR W 25 " --> pdb=" O GLU W 111 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG W 21 " --> pdb=" O THR W 115 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ASP W 90 " --> pdb=" O GLY W 52 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N GLY W 52 " --> pdb=" O ASP W 90 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'W' and resid 59 through 66 removed outlier: 3.827A pdb=" N LYS W 59 " --> pdb=" O ILE W 84 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE W 84 " --> pdb=" O LYS W 59 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR W 65 " --> pdb=" O ASP W 78 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'Y' and resid 50 through 53 Processing sheet with id= AL, first strand: chain 'Y' and resid 71 through 74 removed outlier: 4.402A pdb=" N LYS Y 71 " --> pdb=" O PHE Y 130 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE Y 130 " --> pdb=" O LYS Y 71 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'Y' and resid 103 through 106 Processing sheet with id= AN, first strand: chain 'Z' and resid 80 through 83 removed outlier: 3.775A pdb=" N ALA Z 47 " --> pdb=" O VAL Z 102 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS Z 124 " --> pdb=" O LEU Z 101 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ALA Z 103 " --> pdb=" O VAL Z 122 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N VAL Z 122 " --> pdb=" O ALA Z 103 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'a' and resid 6 through 8 Processing sheet with id= AP, first strand: chain 'a' and resid 13 through 15 Processing sheet with id= AQ, first strand: chain 'b' and resid 20 through 22 Processing sheet with id= AR, first strand: chain 'b' and resid 36 through 43 removed outlier: 3.783A pdb=" N VAL b 69 " --> pdb=" O VAL b 40 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'c' and resid 32 through 35 Processing sheet with id= AT, first strand: chain 'd' and resid 55 through 58 removed outlier: 3.841A pdb=" N ALA d 12 " --> pdb=" O LEU d 56 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N ARG d 31 " --> pdb=" O THR d 15 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N VAL d 17 " --> pdb=" O GLN d 29 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N GLN d 29 " --> pdb=" O VAL d 17 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'd' and resid 19 through 21 removed outlier: 3.674A pdb=" N GLY d 19 " --> pdb=" O GLN d 29 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'g' and resid 99 through 102 removed outlier: 3.812A pdb=" N ARG g 99 " --> pdb=" O LEU g 89 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU g 87 " --> pdb=" O PHE g 101 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR g 86 " --> pdb=" O SER g 82 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG g 88 " --> pdb=" O SER g 80 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA g 78 " --> pdb=" O TRP g 90 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'g' and resid 140 through 142 removed outlier: 3.916A pdb=" N TYR g 140 " --> pdb=" O LEU g 131 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE g 129 " --> pdb=" O VAL g 142 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA g 112 " --> pdb=" O VAL g 121 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'g' and resid 151 through 156 removed outlier: 6.951A pdb=" N CYS g 168 " --> pdb=" O SER g 152 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N VAL g 154 " --> pdb=" O VAL g 166 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL g 166 " --> pdb=" O VAL g 154 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N PHE g 156 " --> pdb=" O ILE g 164 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ILE g 164 " --> pdb=" O PHE g 156 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY g 169 " --> pdb=" O LEU g 173 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LEU g 173 " --> pdb=" O GLY g 169 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL g 176 " --> pdb=" O THR g 186 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR g 186 " --> pdb=" O VAL g 176 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ASN g 178 " --> pdb=" O LEU g 184 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU g 184 " --> pdb=" O ASN g 178 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'g' and resid 195 through 200 removed outlier: 7.241A pdb=" N GLY g 210 " --> pdb=" O ASN g 196 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N VAL g 198 " --> pdb=" O ALA g 208 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ALA g 208 " --> pdb=" O VAL g 198 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N VAL g 200 " --> pdb=" O LEU g 206 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LEU g 206 " --> pdb=" O VAL g 200 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N GLY g 211 " --> pdb=" O GLN g 215 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N GLN g 215 " --> pdb=" O GLY g 211 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N TYR g 228 " --> pdb=" O LEU g 218 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ASP g 220 " --> pdb=" O HIS g 226 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N HIS g 226 " --> pdb=" O ASP g 220 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'g' and resid 238 through 241 removed outlier: 4.493A pdb=" N ALA g 238 " --> pdb=" O ALA g 251 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N CYS g 240 " --> pdb=" O CYS g 249 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASP g 268 " --> pdb=" O ILE g 258 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ASP g 260 " --> pdb=" O ILE g 266 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ILE g 266 " --> pdb=" O ASP g 260 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'g' and resid 4 through 12 removed outlier: 6.772A pdb=" N VAL g 309 " --> pdb=" O ARG g 8 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N THR g 10 " --> pdb=" O VAL g 307 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL g 307 " --> pdb=" O THR g 10 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N LEU g 306 " --> pdb=" O TYR g 302 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR g 302 " --> pdb=" O LEU g 306 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG g 308 " --> pdb=" O ALA g 300 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER g 288 " --> pdb=" O GLY g 301 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'g' and resid 39 through 44 removed outlier: 3.502A pdb=" N ILE g 40 " --> pdb=" O LEU g 59 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N LYS g 44 " --> pdb=" O PRO g 55 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'n' and resid 98 through 102 removed outlier: 3.798A pdb=" N VAL n 100 " --> pdb=" O ILE n 108 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ILE n 108 " --> pdb=" O VAL n 100 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'A' and resid 68 through 72 removed outlier: 6.743A pdb=" N ILE A 83 " --> pdb=" O MET A 45 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N LEU A 47 " --> pdb=" O ILE A 83 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N LEU A 85 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR A 82 " --> pdb=" O ASP A 77 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG A 75 " --> pdb=" O ASP A 84 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N SER A 86 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N VAL A 73 " --> pdb=" O SER A 86 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'A' and resid 226 through 229 Processing sheet with id= BF, first strand: chain 'B' and resid 234 through 236 removed outlier: 8.767A pdb=" N ILE B 235 " --> pdb=" O ILE B 198 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ILE B 200 " --> pdb=" O ILE B 235 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ALA B 168 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N LEU B 201 " --> pdb=" O ALA B 168 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N LEU B 170 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ASN B 203 " --> pdb=" O LEU B 170 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ILE B 172 " --> pdb=" O ASN B 203 " (cutoff:3.500A) removed outlier: 8.846A pdb=" N ILE B 57 " --> pdb=" O HIS B 142 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N SER B 144 " --> pdb=" O ILE B 57 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N THR B 59 " --> pdb=" O SER B 144 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VAL B 146 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ILE B 101 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N HIS B 142 " --> pdb=" O ALA B 99 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA B 99 " --> pdb=" O HIS B 142 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N SER B 144 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ALA B 97 " --> pdb=" O SER B 144 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N VAL B 146 " --> pdb=" O GLY B 95 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N GLY B 95 " --> pdb=" O VAL B 146 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'B' and resid 369 through 372 removed outlier: 4.017A pdb=" N LYS B 298 " --> pdb=" O ARG B 268 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE B 270 " --> pdb=" O ILE B 296 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ILE B 296 " --> pdb=" O ILE B 270 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY B 348 " --> pdb=" O ILE B 296 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'B' and resid 306 through 309 Processing sheet with id= BI, first strand: chain 'B' and resid 379 through 381 removed outlier: 3.893A pdb=" N GLU B 379 " --> pdb=" O THR B 448 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'B' and resid 438 through 441 removed outlier: 7.065A pdb=" N LEU B 456 " --> pdb=" O ILE B 467 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N TRP B 469 " --> pdb=" O ILE B 454 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE B 454 " --> pdb=" O TRP B 469 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET B 418 " --> pdb=" O SER B 457 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N ARG B 459 " --> pdb=" O VAL B 416 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N VAL B 416 " --> pdb=" O ARG B 459 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LYS B 439 " --> pdb=" O SER B 431 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL B 433 " --> pdb=" O LEU B 437 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LEU B 437 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'j' and resid 33 through 37 Processing sheet with id= BL, first strand: chain 'j' and resid 58 through 60 Processing sheet with id= BM, first strand: chain 'k' and resid 8 through 10 Processing sheet with id= BN, first strand: chain 'k' and resid 285 through 288 removed outlier: 6.927A pdb=" N PHE k 238 " --> pdb=" O ILE k 270 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N VAL k 272 " --> pdb=" O PHE k 238 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N PHE k 240 " --> pdb=" O VAL k 272 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'k' and resid 289 through 292 Processing sheet with id= BP, first strand: chain 'k' and resid 354 through 356 removed outlier: 4.096A pdb=" N VAL k 534 " --> pdb=" O ASN k 546 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'k' and resid 375 through 377 Processing sheet with id= BR, first strand: chain 'k' and resid 566 through 569 removed outlier: 3.676A pdb=" N ARG k 574 " --> pdb=" O ASP k 569 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'U' and resid 13 through 15 removed outlier: 3.652A pdb=" N VAL U 15 " --> pdb=" O THR U 18 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR U 18 " --> pdb=" O VAL U 15 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain 'R' and resid 76 through 78 1237 hydrogen bonds defined for protein. 3405 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1263 hydrogen bonds 2016 hydrogen bond angles 0 basepair planarities 506 basepair parallelities 893 stacking parallelities Total time for adding SS restraints: 64.06 Time building geometry restraints manager: 34.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.44 - 0.95: 7 0.95 - 1.46: 54513 1.46 - 1.97: 41080 1.97 - 2.48: 30 2.48 - 2.98: 4 Warning: very small bond lengths. Bond restraints: 95634 Sorted by residual: bond pdb=" C ASP k 521 " pdb=" N PHE k 522 " ideal model delta sigma weight residual 1.335 2.984 -1.649 1.25e-02 6.40e+03 1.74e+04 bond pdb=" C ARG U 142 " pdb=" N GLY U 143 " ideal model delta sigma weight residual 1.329 2.920 -1.591 1.40e-02 5.10e+03 1.29e+04 bond pdb=" C ILE k 451 " pdb=" N GLU k 452 " ideal model delta sigma weight residual 1.332 2.788 -1.455 1.40e-02 5.10e+03 1.08e+04 bond pdb=" C GLU k 373 " pdb=" N ILE k 374 " ideal model delta sigma weight residual 1.329 2.704 -1.375 1.63e-02 3.76e+03 7.11e+03 bond pdb=" C THR k 550 " pdb=" N LEU k 551 " ideal model delta sigma weight residual 1.335 2.350 -1.015 1.27e-02 6.20e+03 6.39e+03 ... (remaining 95629 not shown) Histogram of bond angle deviations from ideal: 35.77 - 64.36: 5 64.36 - 92.95: 53 92.95 - 121.54: 110868 121.54 - 150.14: 27106 150.14 - 178.73: 4 Bond angle restraints: 138036 Sorted by residual: angle pdb=" C ARG k 531 " pdb=" N VAL k 532 " pdb=" CA VAL k 532 " ideal model delta sigma weight residual 122.37 35.77 86.60 1.29e+00 6.01e-01 4.51e+03 angle pdb=" O LEU k 160 " pdb=" C LEU k 160 " pdb=" N GLU k 161 " ideal model delta sigma weight residual 122.12 178.73 -56.61 1.06e+00 8.90e-01 2.85e+03 angle pdb=" CA ARG k 531 " pdb=" C ARG k 531 " pdb=" N VAL k 532 " ideal model delta sigma weight residual 116.37 43.46 72.91 1.45e+00 4.76e-01 2.53e+03 angle pdb=" CA LEU k 160 " pdb=" C LEU k 160 " pdb=" N GLU k 161 " ideal model delta sigma weight residual 117.30 61.22 56.08 1.16e+00 7.43e-01 2.34e+03 angle pdb=" C LEU k 160 " pdb=" N GLU k 161 " pdb=" CA GLU k 161 " ideal model delta sigma weight residual 122.65 59.19 63.46 1.66e+00 3.63e-01 1.46e+03 ... (remaining 138031 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 52434 35.99 - 71.98: 1400 71.98 - 107.98: 139 107.98 - 143.97: 23 143.97 - 179.96: 30 Dihedral angle restraints: 54026 sinusoidal: 35836 harmonic: 18190 Sorted by residual: dihedral pdb=" CA LEU B 322 " pdb=" C LEU B 322 " pdb=" N MET B 323 " pdb=" CA MET B 323 " ideal model delta harmonic sigma weight residual 180.00 48.43 131.57 0 5.00e+00 4.00e-02 6.92e+02 dihedral pdb=" CA ASN j 19 " pdb=" C ASN j 19 " pdb=" N GLU j 20 " pdb=" CA GLU j 20 " ideal model delta harmonic sigma weight residual 180.00 53.32 126.68 0 5.00e+00 4.00e-02 6.42e+02 dihedral pdb=" CA ALA B 373 " pdb=" C ALA B 373 " pdb=" N VAL B 374 " pdb=" CA VAL B 374 " ideal model delta harmonic sigma weight residual -180.00 -60.62 -119.38 0 5.00e+00 4.00e-02 5.70e+02 ... (remaining 54023 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.914: 16946 0.914 - 1.827: 5 1.827 - 2.741: 0 2.741 - 3.655: 0 3.655 - 4.569: 3 Chirality restraints: 16954 Sorted by residual: chirality pdb=" C2' C 1 17 " pdb=" C3' C 1 17 " pdb=" O2' C 1 17 " pdb=" C1' C 1 17 " both_signs ideal model delta sigma weight residual False -2.52 2.05 -4.57 2.00e-01 2.50e+01 5.22e+02 chirality pdb=" C3' G 1 18 " pdb=" C4' G 1 18 " pdb=" O3' G 1 18 " pdb=" C2' G 1 18 " both_signs ideal model delta sigma weight residual False -2.48 1.89 -4.37 2.00e-01 2.50e+01 4.77e+02 chirality pdb=" C3' C 1 17 " pdb=" C4' C 1 17 " pdb=" O3' C 1 17 " pdb=" C2' C 1 17 " both_signs ideal model delta sigma weight residual False -2.74 1.01 -3.75 2.00e-01 2.50e+01 3.52e+02 ... (remaining 16951 not shown) Planarity restraints: 10627 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' T6A 1 37 " -0.089 2.00e-02 2.50e+03 5.43e-01 6.62e+03 pdb=" C4' T6A 1 37 " 0.459 2.00e-02 2.50e+03 pdb=" O4' T6A 1 37 " 0.680 2.00e-02 2.50e+03 pdb=" C3' T6A 1 37 " -0.524 2.00e-02 2.50e+03 pdb=" O3' T6A 1 37 " -0.448 2.00e-02 2.50e+03 pdb=" C2' T6A 1 37 " -0.223 2.00e-02 2.50e+03 pdb=" O2' T6A 1 37 " 0.755 2.00e-02 2.50e+03 pdb=" C1' T6A 1 37 " 0.282 2.00e-02 2.50e+03 pdb=" N9 T6A 1 37 " -0.892 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' C4J 21244 " 0.005 2.00e-02 2.50e+03 5.08e-01 5.80e+03 pdb=" C4' C4J 21244 " -0.379 2.00e-02 2.50e+03 pdb=" O4' C4J 21244 " -0.466 2.00e-02 2.50e+03 pdb=" C3' C4J 21244 " 0.608 2.00e-02 2.50e+03 pdb=" O3' C4J 21244 " 0.451 2.00e-02 2.50e+03 pdb=" C2' C4J 21244 " 0.205 2.00e-02 2.50e+03 pdb=" O2' C4J 21244 " -0.939 2.00e-02 2.50e+03 pdb=" C1' C4J 21244 " -0.148 2.00e-02 2.50e+03 pdb=" C5 C4J 21244 " 0.665 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE k 451 " -0.184 2.00e-02 2.50e+03 2.66e-01 7.07e+02 pdb=" C ILE k 451 " 0.440 2.00e-02 2.50e+03 pdb=" O ILE k 451 " -0.233 2.00e-02 2.50e+03 pdb=" N GLU k 452 " -0.023 2.00e-02 2.50e+03 ... (remaining 10624 not shown) Histogram of nonbonded interaction distances: 0.81 - 1.62: 23 1.62 - 2.44: 353 2.44 - 3.26: 84881 3.26 - 4.08: 253271 4.08 - 4.90: 407293 Warning: very small nonbonded interaction distances. Nonbonded interactions: 745821 Sorted by model distance: nonbonded pdb=" C ILE k 451 " pdb=" N ASN k 453 " model vdw 0.805 3.350 nonbonded pdb=" O ILE k 455 " pdb=" CA ASP k 456 " model vdw 0.861 2.776 nonbonded pdb=" CE1 HIS k 208 " pdb=" OG SER k 540 " model vdw 0.877 3.260 nonbonded pdb=" OD2 ASP k 174 " pdb=" CB SER k 417 " model vdw 0.937 3.440 nonbonded pdb=" N2 G 2 686 " pdb=" N4 C 2 729 " model vdw 0.950 3.200 ... (remaining 745816 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.96 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: 3.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 15.470 Check model and map are aligned: 0.970 Set scattering table: 0.620 Process input model: 242.160 Find NCS groups from input model: 1.990 Set up NCS constraints: 0.220 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:9.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 274.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6263 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 : 0.022 1.649 95634 Z= 1.312 Angle : 2.097 86.597 138036 Z= 1.280 Chirality : 0.117 4.569 16954 Planarity : 0.021 0.543 10627 Dihedral : 14.863 179.960 42295 Min Nonbonded Distance : 0.805 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 3.89 % Allowed : 10.02 % Favored : 86.10 % Rotamer: Outliers : 2.62 % Allowed : 5.35 % Favored : 92.02 % Cbeta Deviations : 0.78 % Peptide Plane: Cis-proline : 1.95 % Cis-general : 0.33 % Twisted Proline : 3.12 % Twisted General : 1.03 % 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: -4.12 (0.09), residues: 6228 helix: -2.79 (0.09), residues: 1679 sheet: -2.46 (0.15), residues: 996 loop : -2.86 (0.09), residues: 3553 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12456 Ramachandran restraints generated. 6228 Oldfield, 0 Emsley, 6228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12456 Ramachandran restraints generated. 6228 Oldfield, 0 Emsley, 6228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1719 residues out of total 5454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 1576 time to evaluate : 5.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 143 outliers final: 23 residues processed: 1692 average time/residue: 1.8613 time to fit residues: 4150.9505 Evaluate side-chains 845 residues out of total 5454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 822 time to evaluate : 4.589 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 21 residues processed: 3 average time/residue: 0.5597 time to fit residues: 9.0916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 800 random chunks: chunk 675 optimal weight: 6.9990 chunk 606 optimal weight: 0.9990 chunk 336 optimal weight: 0.9990 chunk 207 optimal weight: 5.9990 chunk 409 optimal weight: 7.9990 chunk 323 optimal weight: 5.9990 chunk 627 optimal weight: 0.8980 chunk 242 optimal weight: 6.9990 chunk 381 optimal weight: 1.9990 chunk 466 optimal weight: 0.8980 chunk 726 optimal weight: 9.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 165 ASN D 95 ASN D 202 GLN E 100 GLN F 145 GLN G 8 HIS ** G 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 161 GLN H 74 ASN J 76 GLN J 91 HIS J 186 ASN K 7 ASN K 22 HIS L 113 GLN L 132 GLN L 156 HIS M 84 HIS P 123 HIS V 11 GLN V 85 ASN W 81 GLN Y 56 HIS Z 31 HIS a 29 HIS a 106 GLN a 124 ASN f 111 ASN g 15 ASN g 119 GLN g 147 HIS g 159 ASN n 46 ASN i 132 ASN j 37 GLN j 44 ASN j 60 HIS j 72 ASN k 85 HIS k 208 HIS k 520 HIS k 556 ASN U 120 HIS R 53 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6526 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 95634 Z= 0.197 Angle : 0.754 21.003 138036 Z= 0.386 Chirality : 0.042 0.489 16954 Planarity : 0.006 0.154 10627 Dihedral : 14.013 179.749 29334 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.83 % Allowed : 7.72 % Favored : 91.45 % Rotamer: Outliers : 5.19 % Allowed : 18.34 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.95 % Cis-general : 0.38 % Twisted Proline : 1.95 % Twisted General : 0.50 % 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: -2.91 (0.09), residues: 6246 helix: -1.15 (0.11), residues: 1695 sheet: -1.51 (0.15), residues: 1111 loop : -2.56 (0.09), residues: 3440 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12492 Ramachandran restraints generated. 6246 Oldfield, 0 Emsley, 6246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12492 Ramachandran restraints generated. 6246 Oldfield, 0 Emsley, 6246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1236 residues out of total 5454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 283 poor density : 953 time to evaluate : 5.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 283 outliers final: 66 residues processed: 1138 average time/residue: 1.6765 time to fit residues: 2588.4206 Evaluate side-chains 827 residues out of total 5454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 761 time to evaluate : 5.340 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 48 residues processed: 20 average time/residue: 0.8412 time to fit residues: 35.3621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 800 random chunks: chunk 403 optimal weight: 0.7980 chunk 225 optimal weight: 0.9990 chunk 604 optimal weight: 10.0000 chunk 494 optimal weight: 10.0000 chunk 200 optimal weight: 4.9990 chunk 727 optimal weight: 4.9990 chunk 786 optimal weight: 9.9990 chunk 648 optimal weight: 8.9990 chunk 721 optimal weight: 20.0000 chunk 248 optimal weight: 0.0570 chunk 583 optimal weight: 10.0000 overall best weight: 2.3704 ------------------------------------------------------------------------------- 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: