Starting phenix.real_space_refine on Fri Mar 15 20:23:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sw9_10320/03_2024/6sw9_10320_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sw9_10320/03_2024/6sw9_10320.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sw9_10320/03_2024/6sw9_10320_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sw9_10320/03_2024/6sw9_10320_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sw9_10320/03_2024/6sw9_10320_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sw9_10320/03_2024/6sw9_10320.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sw9_10320/03_2024/6sw9_10320.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sw9_10320/03_2024/6sw9_10320_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sw9_10320/03_2024/6sw9_10320_updated.pdb" } resolution = 4.2 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= 0.003 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 Zn 6 6.06 5 P 1596 5.49 5 Mg 34 5.21 5 S 132 5.16 5 C 38369 2.51 5 N 13000 2.21 5 O 17524 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 12": "OD1" <-> "OD2" Residue "A TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 42": "OE1" <-> "OE2" Residue "A TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 111": "OE1" <-> "OE2" Residue "B ASP 113": "OD1" <-> "OD2" Residue "B TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 31": "OD1" <-> "OD2" Residue "D TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 86": "OD1" <-> "OD2" Residue "D ASP 91": "OD1" <-> "OD2" Residue "D TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 28": "OE1" <-> "OE2" Residue "F GLU 56": "OE1" <-> "OE2" Residue "F ASP 93": "OD1" <-> "OD2" Residue "F TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 25": "OE1" <-> "OE2" Residue "G ASP 68": "OD1" <-> "OD2" Residue "H PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 24": "OE1" <-> "OE2" Residue "H PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 112": "OE1" <-> "OE2" Residue "H GLU 134": "OE1" <-> "OE2" Residue "H ASP 151": "OD1" <-> "OD2" Residue "H GLU 186": "OE1" <-> "OE2" Residue "H TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 206": "OE1" <-> "OE2" Residue "I TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 54": "OD1" <-> "OD2" Residue "I PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 135": "NH1" <-> "NH2" Residue "L GLU 28": "OE1" <-> "OE2" Residue "L GLU 92": "OE1" <-> "OE2" Residue "L GLU 99": "OE1" <-> "OE2" Residue "N PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 39": "OE1" <-> "OE2" Residue "N PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 143": "OE1" <-> "OE2" Residue "O ASP 3": "OD1" <-> "OD2" Residue "O PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 68": "OD1" <-> "OD2" Residue "Q PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 29": "OE1" <-> "OE2" Residue "T TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 14": "OE1" <-> "OE2" Residue "T TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 93": "OE1" <-> "OE2" Residue "T TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 124": "NH1" <-> "NH2" Residue "U TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 141": "OE1" <-> "OE2" Residue "U TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 2": "OE1" <-> "OE2" Residue "V PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 59": "OE1" <-> "OE2" Residue "X GLU 63": "OE1" <-> "OE2" Residue "Y ARG 42": "NH1" <-> "NH2" Residue "Z GLU 4": "OE1" <-> "OE2" Residue "Z GLU 19": "OE1" <-> "OE2" Residue "Z TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 70": "OE1" <-> "OE2" Residue "Z TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 129": "OE1" <-> "OE2" Residue "Z PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 10": "OE1" <-> "OE2" Residue "3 ASP 56": "OD1" <-> "OD2" Residue "3 GLU 61": "OE1" <-> "OE2" Residue "3 GLU 93": "OE1" <-> "OE2" Residue "3 ASP 109": "OD1" <-> "OD2" Residue "6 ASP 92": "OD1" <-> "OD2" Residue "6 GLU 103": "OE1" <-> "OE2" Residue "7 GLU 9": "OE1" <-> "OE2" Residue "7 GLU 60": "OE1" <-> "OE2" Residue "7 GLU 71": "OE1" <-> "OE2" Residue "7 ARG 87": "NH1" <-> "NH2" Residue "7 ARG 88": "NH1" <-> "NH2" Residue "7 ASP 93": "OD1" <-> "OD2" Residue "7 GLU 98": "OE1" <-> "OE2" Residue "7 GLU 158": "OE1" <-> "OE2" Residue "7 GLU 199": "OE1" <-> "OE2" Residue "7 GLU 200": "OE1" <-> "OE2" Residue "7 ARG 207": "NH1" <-> "NH2" Residue "7 PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 252": "OE1" <-> "OE2" Residue "7 TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 270": "OE1" <-> "OE2" Residue "7 PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 284": "OE1" <-> "OE2" Residue "7 GLU 285": "OE1" <-> "OE2" Residue "7 PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 288": "OE1" <-> "OE2" Residue "7 ASP 302": "OD1" <-> "OD2" Residue "7 ASP 309": "OD1" <-> "OD2" Residue "7 GLU 322": "OE1" <-> "OE2" Residue "7 TYR 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 355": "OE1" <-> "OE2" Residue "7 ARG 384": "NH1" <-> "NH2" Residue "7 ARG 394": "NH1" <-> "NH2" Residue "7 GLU 414": "OE1" <-> "OE2" Residue "8 ASP 113": "OD1" <-> "OD2" Residue "8 GLU 119": "OE1" <-> "OE2" Residue "8 TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 13": "OE1" <-> "OE2" Residue "9 ASP 24": "OD1" <-> "OD2" Residue "9 TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 108": "OE1" <-> "OE2" Residue "9 GLU 118": "OE1" <-> "OE2" Residue "9 GLU 166": "OE1" <-> "OE2" Residue "9 GLU 205": "OE1" <-> "OE2" Residue "9 TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 238": "OE1" <-> "OE2" Residue "9 GLU 241": "OE1" <-> "OE2" Residue "9 GLU 257": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 70661 Number of models: 1 Model: "" Number of chains: 47 Chain: "2" Number of atoms: 32291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1497, 32291 Classifications: {'RNA': 1497} Modifications used: {'rna2p': 2, 'rna2p_pur': 116, 'rna2p_pyr': 82, 'rna3p': 40, 'rna3p_pur': 722, 'rna3p_pyr': 534} Link IDs: {'rna2p': 200, 'rna3p': 1296} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 5 Chain: "A" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1533 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 5, 'TRANS': 182} Chain: "B" Number of atoms: 1571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1571 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 11, 'TRANS': 184} Chain: "C" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 482 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 6, 'TRANS': 54} Chain: "D" Number of atoms: 1470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1470 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 9, 'TRANS': 165} Chain: "E" Number of atoms: 1983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1983 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 18, 'TRANS': 223} Chain: "F" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1808 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 9, 'TRANS': 219} Chain: "G" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 977 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 113} Chain: "H" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1720 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 202} Chain: "I" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1034 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "J" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 996 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "K" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1065 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 126} Chain: "L" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 817 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain: "M" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 964 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 119} Chain: "N" Number of atoms: 1148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1148 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 137} Chain: "O" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1116 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "P" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 455 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 51} Chain: "Q" Number of atoms: 1262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1262 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 12, 'TRANS': 139} Chain: "R" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 900 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 8, 'TRANS': 100} Chain: "S" Number of atoms: 558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 558 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 64} Chain: "T" Number of atoms: 1018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1018 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 8, 'TRANS': 116} Chain: "U" Number of atoms: 1223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1223 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 11, 'TRANS': 137} Chain: "V" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 790 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain: "W" Number of atoms: 481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 481 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 5, 'TRANS': 57} Chain: "X" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 536 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "Y" Number of atoms: 408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 408 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "Z" Number of atoms: 1550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1550 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 8, 'TRANS': 188} Chain: "0" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 343 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "3" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 941 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 114} Chain: "5" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 430 Classifications: {'RNA': 20} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 11, 'rna3p_pyr': 6} Link IDs: {'rna2p': 3, 'rna3p': 16} Chain: "4" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1622 Classifications: {'RNA': 76} Modifications used: {'rna2p': 1, 'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p': 4, 'rna3p_pur': 32, 'rna3p_pyr': 28} Link IDs: {'rna2p': 12, 'rna3p': 63} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 3 Chain: "6" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 777 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "7" Number of atoms: 3213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3213 Classifications: {'peptide': 414} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 392} Chain: "8" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1032 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "9" Number of atoms: 2025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 2025 Classifications: {'peptide': 253} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 244} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "2" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Unusual residues: {' MG': 31} Classifications: {'undetermined': 31} Link IDs: {None: 30} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 41 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Chain: "2" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 35634 SG CYS C 32 66.354 173.594 137.534 1.00 87.69 S ATOM 35655 SG CYS C 35 64.461 176.200 138.933 1.00 94.99 S ATOM 35817 SG CYS C 55 65.516 174.146 141.336 1.00113.75 S ATOM 35839 SG CYS C 58 63.857 175.910 140.060 1.00115.32 S ATOM 35493 SG CYS C 14 72.560 161.283 139.436 1.00 64.73 S ATOM 35512 SG CYS C 17 73.804 158.628 140.977 1.00 74.18 S ATOM 35720 SG CYS C 43 73.962 159.182 138.274 1.00 63.84 S ATOM 35742 SG CYS C 46 73.193 157.814 137.909 1.00 64.11 S ATOM 40352 SG CYS F 128 97.079 150.225 156.661 1.00 42.92 S ATOM 40391 SG CYS F 133 98.550 150.113 157.909 1.00 45.74 S ATOM 40408 SG CYS F 135 98.979 151.605 158.951 1.00 48.80 S ATOM 51139 SG CYS P 21 138.464 149.344 80.561 1.00 77.69 S ATOM 51164 SG CYS P 24 135.531 148.085 82.830 1.00 79.16 S ATOM 51279 SG CYS P 39 136.012 147.040 80.480 1.00 74.85 S ATOM 51306 SG CYS P 42 134.348 148.959 82.420 1.00 76.84 S ATOM 52809 SG CYS R 16 59.467 92.357 187.096 1.00 87.57 S ATOM 52847 SG CYS R 21 61.499 92.711 187.691 1.00 79.08 S ATOM 53335 SG CYS R 77 58.786 93.049 186.922 1.00 67.36 S ATOM 57337 SG CYS W 20 10.607 137.986 137.752 1.00130.27 S ATOM 57359 SG CYS W 23 8.293 135.136 138.133 1.00134.10 S ATOM 57485 SG CYS W 39 11.425 135.335 139.670 1.00117.80 S ATOM 57506 SG CYS W 42 9.058 133.803 137.272 1.00125.98 S Time building chain proxies: 28.41, per 1000 atoms: 0.40 Number of scatterers: 70661 At special positions: 0 Unit cell: (219.09, 208.19, 248.52, 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 6 29.99 S 132 16.00 P 1596 15.00 Mg 34 11.99 O 17524 8.00 N 13000 7.00 C 38369 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS 7 59 " - pdb=" SG CYS 7 74 " distance=2.02 Simple disulfide: pdb=" SG CYS 7 62 " - pdb=" SG CYS 7 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 33.48 Conformation dependent library (CDL) restraints added in 5.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 101 " pdb="ZN ZN C 101 " - pdb=" SG CYS C 55 " pdb="ZN ZN C 101 " - pdb=" SG CYS C 35 " pdb="ZN ZN C 101 " - pdb=" SG CYS C 32 " pdb="ZN ZN C 101 " - pdb=" SG CYS C 58 " pdb=" ZN C 102 " pdb="ZN ZN C 102 " - pdb=" SG CYS C 17 " pdb="ZN ZN C 102 " - pdb=" SG CYS C 43 " pdb="ZN ZN C 102 " - pdb=" SG CYS C 14 " pdb="ZN ZN C 102 " - pdb=" SG CYS C 46 " pdb=" ZN F 301 " pdb="ZN ZN F 301 " - pdb=" NE2 HIS F 139 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 128 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 135 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 133 " pdb=" ZN P 101 " pdb="ZN ZN P 101 " - pdb=" SG CYS P 39 " pdb="ZN ZN P 101 " - pdb=" SG CYS P 24 " pdb="ZN ZN P 101 " - pdb=" SG CYS P 21 " pdb="ZN ZN P 101 " - pdb=" SG CYS P 42 " pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 16 " pdb="ZN ZN R 201 " - pdb=" ND1 HIS R 24 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 21 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 77 " pdb=" ZN W 101 " pdb="ZN ZN W 101 " - pdb=" SG CYS W 42 " pdb="ZN ZN W 101 " - pdb=" SG CYS W 20 " pdb="ZN ZN W 101 " - pdb=" SG CYS W 23 " pdb="ZN ZN W 101 " - pdb=" SG CYS W 39 " Number of angles added : 30 8874 Ramachandran restraints generated. 4437 Oldfield, 0 Emsley, 4437 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8326 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 139 helices and 46 sheets defined 26.8% alpha, 12.7% beta 401 base pairs and 578 stacking pairs defined. Time for finding SS restraints: 28.27 Creating SS restraints... Processing helix chain 'A' and resid 12 through 15 No H-bonds generated for 'chain 'A' and resid 12 through 15' Processing helix chain 'A' and resid 26 through 28 No H-bonds generated for 'chain 'A' and resid 26 through 28' Processing helix chain 'A' and resid 90 through 95 Processing helix chain 'A' and resid 132 through 134 No H-bonds generated for 'chain 'A' and resid 132 through 134' Processing helix chain 'A' and resid 136 through 151 removed outlier: 4.331A pdb=" N LYS A 149 " --> pdb=" O ILE A 145 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 164 removed outlier: 3.618A pdb=" N VAL A 163 " --> pdb=" O VAL A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 174 removed outlier: 3.516A pdb=" N ILE A 171 " --> pdb=" O ALA A 168 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ALA A 172 " --> pdb=" O ALA A 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 14 removed outlier: 3.794A pdb=" N ALA B 14 " --> pdb=" O ASP B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 30 removed outlier: 3.532A pdb=" N LYS B 29 " --> pdb=" O LYS B 26 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LYS B 30 " --> pdb=" O ASP B 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 26 through 30' Processing helix chain 'B' and resid 46 through 57 removed outlier: 3.560A pdb=" N LYS B 53 " --> pdb=" O ASP B 49 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL B 54 " --> pdb=" O GLU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 66 No H-bonds generated for 'chain 'B' and resid 64 through 66' Processing helix chain 'B' and resid 78 through 86 removed outlier: 3.997A pdb=" N PHE B 83 " --> pdb=" O PRO B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 131 Processing helix chain 'B' and resid 164 through 179 removed outlier: 3.774A pdb=" N TYR B 168 " --> pdb=" O LEU B 164 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASN B 178 " --> pdb=" O GLU B 174 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG B 179 " --> pdb=" O ILE B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 195 No H-bonds generated for 'chain 'B' and resid 192 through 195' Processing helix chain 'C' and resid 44 through 48 Processing helix chain 'D' and resid 20 through 32 removed outlier: 5.817A pdb=" N VAL D 28 " --> pdb=" O ASP D 24 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LEU D 29 " --> pdb=" O ARG D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 59 removed outlier: 5.249A pdb=" N LYS D 43 " --> pdb=" O GLU D 40 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASN D 50 " --> pdb=" O GLN D 47 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ARG D 56 " --> pdb=" O ARG D 53 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG D 57 " --> pdb=" O ARG D 54 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU D 58 " --> pdb=" O ALA D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 79 removed outlier: 3.691A pdb=" N ILE D 68 " --> pdb=" O LYS D 64 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU D 73 " --> pdb=" O GLU D 69 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU D 74 " --> pdb=" O ARG D 70 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ALA D 75 " --> pdb=" O GLU D 71 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ARG D 76 " --> pdb=" O GLN D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 93 Processing helix chain 'D' and resid 97 through 103 removed outlier: 3.834A pdb=" N ARG D 103 " --> pdb=" O ASP D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 111 Processing helix chain 'D' and resid 118 through 126 removed outlier: 4.679A pdb=" N GLN D 123 " --> pdb=" O ARG D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 174 removed outlier: 3.915A pdb=" N GLU D 172 " --> pdb=" O ARG D 168 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LYS D 173 " --> pdb=" O MET D 169 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA D 174 " --> pdb=" O MET D 170 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 168 through 174' Processing helix chain 'E' and resid 12 through 14 No H-bonds generated for 'chain 'E' and resid 12 through 14' Processing helix chain 'E' and resid 45 through 50 removed outlier: 4.216A pdb=" N ARG E 50 " --> pdb=" O TYR E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 62 No H-bonds generated for 'chain 'E' and resid 59 through 62' Processing helix chain 'E' and resid 73 through 75 No H-bonds generated for 'chain 'E' and resid 73 through 75' Processing helix chain 'E' and resid 152 through 154 No H-bonds generated for 'chain 'E' and resid 152 through 154' Processing helix chain 'F' and resid 4 through 13 removed outlier: 5.660A pdb=" N ALA F 9 " --> pdb=" O TRP F 5 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS F 10 " --> pdb=" O LYS F 6 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 27 Processing helix chain 'F' and resid 34 through 36 No H-bonds generated for 'chain 'F' and resid 34 through 36' Processing helix chain 'F' and resid 49 through 53 Processing helix chain 'F' and resid 106 through 118 removed outlier: 3.777A pdb=" N LYS F 118 " --> pdb=" O ILE F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 177 Processing helix chain 'F' and resid 194 through 209 removed outlier: 4.774A pdb=" N ASN F 209 " --> pdb=" O LEU F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 216 through 221 removed outlier: 3.954A pdb=" N TYR F 221 " --> pdb=" O ILE F 218 " (cutoff:3.500A) Processing helix chain 'G' and resid 11 through 13 No H-bonds generated for 'chain 'G' and resid 11 through 13' Processing helix chain 'G' and resid 25 through 27 No H-bonds generated for 'chain 'G' and resid 25 through 27' Processing helix chain 'G' and resid 40 through 43 No H-bonds generated for 'chain 'G' and resid 40 through 43' Processing helix chain 'H' and resid 5 through 8 No H-bonds generated for 'chain 'H' and resid 5 through 8' Processing helix chain 'H' and resid 31 through 36 Proline residue: H 35 - end of helix Processing helix chain 'H' and resid 57 through 59 No H-bonds generated for 'chain 'H' and resid 57 through 59' Processing helix chain 'H' and resid 63 through 71 removed outlier: 3.733A pdb=" N LYS H 70 " --> pdb=" O ARG H 66 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE H 71 " --> pdb=" O LEU H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 114 Processing helix chain 'H' and resid 119 through 128 Processing helix chain 'H' and resid 154 through 171 Processing helix chain 'H' and resid 180 through 193 removed outlier: 4.096A pdb=" N GLU H 187 " --> pdb=" O ALA H 183 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEU H 190 " --> pdb=" O GLU H 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 200 through 214 removed outlier: 3.860A pdb=" N ILE H 210 " --> pdb=" O GLU H 206 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N SER H 214 " --> pdb=" O ILE H 210 " (cutoff:3.500A) Processing helix chain 'I' and resid 8 through 20 removed outlier: 4.000A pdb=" N ARG I 19 " --> pdb=" O THR I 15 " (cutoff:3.500A) Processing helix chain 'I' and resid 32 through 43 Processing helix chain 'I' and resid 86 through 90 Processing helix chain 'I' and resid 113 through 119 removed outlier: 5.020A pdb=" N GLU I 118 " --> pdb=" O LYS I 114 " (cutoff:3.500A) Processing helix chain 'J' and resid 49 through 51 No H-bonds generated for 'chain 'J' and resid 49 through 51' Processing helix chain 'J' and resid 114 through 117 No H-bonds generated for 'chain 'J' and resid 114 through 117' Processing helix chain 'K' and resid 39 through 42 No H-bonds generated for 'chain 'K' and resid 39 through 42' Processing helix chain 'K' and resid 48 through 51 No H-bonds generated for 'chain 'K' and resid 48 through 51' Processing helix chain 'K' and resid 56 through 58 No H-bonds generated for 'chain 'K' and resid 56 through 58' Processing helix chain 'K' and resid 73 through 89 removed outlier: 3.710A pdb=" N ALA K 77 " --> pdb=" O GLY K 73 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU K 88 " --> pdb=" O ARG K 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 94 through 101 removed outlier: 3.866A pdb=" N PHE K 99 " --> pdb=" O LEU K 95 " (cutoff:3.500A) Processing helix chain 'K' and resid 105 through 108 No H-bonds generated for 'chain 'K' and resid 105 through 108' Processing helix chain 'L' and resid 14 through 29 removed outlier: 3.810A pdb=" N GLU L 18 " --> pdb=" O ARG L 14 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N VAL L 19 " --> pdb=" O SER L 15 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 82 No H-bonds generated for 'chain 'L' and resid 79 through 82' Processing helix chain 'M' and resid 57 through 74 removed outlier: 4.135A pdb=" N ALA M 68 " --> pdb=" O ALA M 64 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLU M 73 " --> pdb=" O GLU M 69 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS M 74 " --> pdb=" O GLU M 70 " (cutoff:3.500A) Processing helix chain 'M' and resid 98 through 108 removed outlier: 3.504A pdb=" N ARG M 103 " --> pdb=" O GLN M 99 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA M 104 " --> pdb=" O ALA M 100 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA M 106 " --> pdb=" O ILE M 102 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG M 107 " --> pdb=" O ARG M 103 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 23 Processing helix chain 'N' and resid 31 through 34 No H-bonds generated for 'chain 'N' and resid 31 through 34' Processing helix chain 'N' and resid 93 through 95 No H-bonds generated for 'chain 'N' and resid 93 through 95' Processing helix chain 'N' and resid 111 through 113 No H-bonds generated for 'chain 'N' and resid 111 through 113' Processing helix chain 'N' and resid 134 through 139 Processing helix chain 'O' and resid 21 through 27 removed outlier: 4.333A pdb=" N LEU O 25 " --> pdb=" O LEU O 21 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N THR O 26 " --> pdb=" O ARG O 22 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ALA O 27 " --> pdb=" O TRP O 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 21 through 27' Processing helix chain 'O' and resid 33 through 43 removed outlier: 4.885A pdb=" N MET O 38 " --> pdb=" O ASN O 34 " (cutoff:3.500A) Processing helix chain 'O' and resid 56 through 67 Processing helix chain 'O' and resid 70 through 72 No H-bonds generated for 'chain 'O' and resid 70 through 72' Processing helix chain 'O' and resid 95 through 112 removed outlier: 4.419A pdb=" N ASP O 99 " --> pdb=" O THR O 95 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N MET O 100 " --> pdb=" O ALA O 96 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LEU O 109 " --> pdb=" O ASP O 105 " (cutoff:3.500A) Processing helix chain 'O' and resid 116 through 121 removed outlier: 3.838A pdb=" N HIS O 120 " --> pdb=" O ARG O 116 " (cutoff:3.500A) Processing helix chain 'P' and resid 16 through 18 No H-bonds generated for 'chain 'P' and resid 16 through 18' Processing helix chain 'P' and resid 42 through 45 Processing helix chain 'Q' and resid 30 through 43 removed outlier: 3.675A pdb=" N LEU Q 36 " --> pdb=" O ASP Q 32 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS Q 42 " --> pdb=" O VAL Q 38 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N GLU Q 43 " --> pdb=" O LYS Q 39 " (cutoff:3.500A) Processing helix chain 'Q' and resid 50 through 58 Processing helix chain 'Q' and resid 78 through 85 removed outlier: 3.671A pdb=" N GLU Q 83 " --> pdb=" O THR Q 79 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N LYS Q 84 " --> pdb=" O ARG Q 80 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N HIS Q 85 " --> pdb=" O ILE Q 81 " (cutoff:3.500A) Processing helix chain 'Q' and resid 93 through 111 removed outlier: 4.465A pdb=" N ASN Q 104 " --> pdb=" O LYS Q 100 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N LEU Q 105 " --> pdb=" O ARG Q 101 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ARG Q 106 " --> pdb=" O ALA Q 102 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N GLU Q 110 " --> pdb=" O ARG Q 106 " (cutoff:3.500A) Processing helix chain 'Q' and resid 116 through 138 removed outlier: 5.468A pdb=" N GLY Q 121 " --> pdb=" O HIS Q 117 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU Q 122 " --> pdb=" O SER Q 118 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR Q 135 " --> pdb=" O ARG Q 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 78 No H-bonds generated for 'chain 'R' and resid 76 through 78' Processing helix chain 'S' and resid 7 through 16 removed outlier: 3.626A pdb=" N VAL S 12 " --> pdb=" O PHE S 8 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLU S 15 " --> pdb=" O ARG S 11 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 38 removed outlier: 3.515A pdb=" N VAL S 35 " --> pdb=" O ASN S 31 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N GLU S 36 " --> pdb=" O LYS S 32 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLU S 37 " --> pdb=" O LYS S 33 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LEU S 38 " --> pdb=" O LYS S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 45 through 62 removed outlier: 4.013A pdb=" N ARG S 49 " --> pdb=" O LYS S 45 " (cutoff:3.500A) Processing helix chain 'T' and resid 23 through 27 Processing helix chain 'T' and resid 30 through 35 Processing helix chain 'T' and resid 42 through 56 removed outlier: 4.139A pdb=" N LYS T 50 " --> pdb=" O LYS T 46 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU T 53 " --> pdb=" O ARG T 49 " (cutoff:3.500A) Processing helix chain 'T' and resid 104 through 106 No H-bonds generated for 'chain 'T' and resid 104 through 106' Processing helix chain 'U' and resid 4 through 6 No H-bonds generated for 'chain 'U' and resid 4 through 6' Processing helix chain 'U' and resid 9 through 21 removed outlier: 3.616A pdb=" N GLN U 18 " --> pdb=" O GLU U 14 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ARG U 19 " --> pdb=" O ARG U 15 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N LYS U 21 " --> pdb=" O ALA U 17 " (cutoff:3.500A) Processing helix chain 'U' and resid 52 through 65 removed outlier: 3.825A pdb=" N ARG U 61 " --> pdb=" O SER U 57 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL U 62 " --> pdb=" O ILE U 58 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR U 63 " --> pdb=" O LEU U 59 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU U 64 " --> pdb=" O ARG U 60 " (cutoff:3.500A) Processing helix chain 'U' and resid 73 through 76 No H-bonds generated for 'chain 'U' and resid 73 through 76' Processing helix chain 'U' and resid 96 through 108 Processing helix chain 'U' and resid 123 through 142 removed outlier: 3.673A pdb=" N ILE U 132 " --> pdb=" O PHE U 128 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU U 139 " --> pdb=" O GLU U 135 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N GLU U 142 " --> pdb=" O LYS U 138 " (cutoff:3.500A) Processing helix chain 'V' and resid 33 through 43 Processing helix chain 'V' and resid 78 through 81 No H-bonds generated for 'chain 'V' and resid 78 through 81' Processing helix chain 'V' and resid 84 through 89 Processing helix chain 'Z' and resid 4 through 24 removed outlier: 4.184A pdb=" N ARG Z 9 " --> pdb=" O ARG Z 5 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N LYS Z 13 " --> pdb=" O ARG Z 9 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU Z 14 " --> pdb=" O GLU Z 10 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N MET Z 15 " --> pdb=" O ALA Z 11 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU Z 16 " --> pdb=" O VAL Z 12 " (cutoff:3.500A) Processing helix chain 'Z' and resid 51 through 55 Processing helix chain 'Z' and resid 62 through 72 Processing helix chain 'Z' and resid 92 through 105 removed outlier: 4.207A pdb=" N VAL Z 97 " --> pdb=" O LYS Z 93 " (cutoff:3.500A) Processing helix chain 'Z' and resid 109 through 123 removed outlier: 4.006A pdb=" N ALA Z 113 " --> pdb=" O PHE Z 109 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR Z 114 " --> pdb=" O ARG Z 110 " (cutoff:3.500A) Processing helix chain 'Z' and resid 157 through 160 No H-bonds generated for 'chain 'Z' and resid 157 through 160' Processing helix chain '0' and resid 17 through 32 removed outlier: 4.814A pdb=" N ARG 0 22 " --> pdb=" O TRP 0 18 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG 0 25 " --> pdb=" O LYS 0 21 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU 0 26 " --> pdb=" O ARG 0 22 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLN 0 29 " --> pdb=" O ARG 0 25 " (cutoff:3.500A) Processing helix chain '3' and resid 13 through 20 Processing helix chain '3' and resid 24 through 27 No H-bonds generated for 'chain '3' and resid 24 through 27' Processing helix chain '3' and resid 36 through 38 No H-bonds generated for 'chain '3' and resid 36 through 38' Processing helix chain '3' and resid 40 through 45 Processing helix chain '3' and resid 67 through 72 removed outlier: 4.566A pdb=" N GLU 3 71 " --> pdb=" O PRO 3 67 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N GLU 3 72 " --> pdb=" O PRO 3 68 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 67 through 72' Processing helix chain '3' and resid 84 through 87 No H-bonds generated for 'chain '3' and resid 84 through 87' Processing helix chain '3' and resid 108 through 121 removed outlier: 5.204A pdb=" N MET 3 116 " --> pdb=" O GLU 3 112 " (cutoff:3.500A) Processing helix chain '6' and resid 55 through 58 No H-bonds generated for 'chain '6' and resid 55 through 58' Processing helix chain '6' and resid 88 through 91 No H-bonds generated for 'chain '6' and resid 88 through 91' Processing helix chain '6' and resid 93 through 96 No H-bonds generated for 'chain '6' and resid 93 through 96' Processing helix chain '7' and resid 22 through 30 Processing helix chain '7' and resid 38 through 43 Processing helix chain '7' and resid 102 through 110 Processing helix chain '7' and resid 127 through 139 removed outlier: 3.997A pdb=" N GLU 7 131 " --> pdb=" O PRO 7 127 " (cutoff:3.500A) Processing helix chain '7' and resid 158 through 170 Processing helix chain '7' and resid 191 through 200 Processing helix chain '7' and resid 307 through 309 No H-bonds generated for 'chain '7' and resid 307 through 309' Processing helix chain '8' and resid 4 through 17 removed outlier: 4.579A pdb=" N VAL 8 8 " --> pdb=" O GLU 8 4 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ARG 8 13 " --> pdb=" O GLU 8 9 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR 8 15 " --> pdb=" O LEU 8 11 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SER 8 16 " --> pdb=" O ASP 8 12 " (cutoff:3.500A) Processing helix chain '8' and resid 45 through 54 removed outlier: 4.376A pdb=" N ALA 8 48 " --> pdb=" O ARG 8 45 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG 8 53 " --> pdb=" O TYR 8 50 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE 8 54 " --> pdb=" O CYS 8 51 " (cutoff:3.500A) Processing helix chain '8' and resid 58 through 69 Processing helix chain '8' and resid 89 through 103 Processing helix chain '9' and resid 43 through 45 No H-bonds generated for 'chain '9' and resid 43 through 45' Processing helix chain '9' and resid 54 through 56 No H-bonds generated for 'chain '9' and resid 54 through 56' Processing helix chain '9' and resid 87 through 114 removed outlier: 4.201A pdb=" N ARG 9 91 " --> pdb=" O ASP 9 87 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LYS 9 92 " --> pdb=" O ASP 9 88 " (cutoff:3.500A) Processing helix chain '9' and resid 118 through 123 removed outlier: 3.788A pdb=" N TRP 9 122 " --> pdb=" O GLU 9 118 " (cutoff:3.500A) Processing helix chain '9' and resid 126 through 129 No H-bonds generated for 'chain '9' and resid 126 through 129' Processing helix chain '9' and resid 136 through 145 removed outlier: 3.763A pdb=" N LYS 9 145 " --> pdb=" O GLU 9 141 " (cutoff:3.500A) Processing helix chain '9' and resid 149 through 153 Processing helix chain '9' and resid 159 through 166 Proline residue: 9 163 - end of helix Processing helix chain '9' and resid 192 through 203 Processing helix chain '9' and resid 207 through 210 No H-bonds generated for 'chain '9' and resid 207 through 210' Processing helix chain '9' and resid 239 through 256 removed outlier: 4.493A pdb=" N GLN 9 245 " --> pdb=" O GLU 9 241 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ILE 9 246 " --> pdb=" O ALA 9 242 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE 9 247 " --> pdb=" O LEU 9 243 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ILE 9 253 " --> pdb=" O ASN 9 249 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLU 9 256 " --> pdb=" O LYS 9 252 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 19 through 21 Processing sheet with id= B, first strand: chain 'A' and resid 48 through 52 removed outlier: 3.641A pdb=" N GLY A 85 " --> pdb=" O TYR A 68 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N GLN A 70 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N PHE A 83 " --> pdb=" O GLN A 70 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 103 through 111 removed outlier: 3.808A pdb=" N LYS A 188 " --> pdb=" O MET A 121 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N MET A 123 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N ILE A 186 " --> pdb=" O MET A 123 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 34 through 36 removed outlier: 3.837A pdb=" N ARG B 34 " --> pdb=" O VAL B 42 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 90 through 93 removed outlier: 4.161A pdb=" N SER B 71 " --> pdb=" O ILE B 92 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL B 114 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N VAL B 70 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ILE B 116 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE B 154 " --> pdb=" O ALA B 139 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.528A pdb=" N THR C 28 " --> pdb=" O ARG C 42 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 91 through 93 removed outlier: 4.143A pdb=" N GLU E 98 " --> pdb=" O ILE E 93 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 123 through 126 removed outlier: 3.526A pdb=" N LYS E 123 " --> pdb=" O MET E 166 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU E 165 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLU E 172 " --> pdb=" O LYS E 167 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 222 through 226 removed outlier: 3.784A pdb=" N GLU E 201 " --> pdb=" O THR E 214 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N GLU E 216 " --> pdb=" O ILE E 199 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N ILE E 199 " --> pdb=" O GLU E 216 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 127 through 133 removed outlier: 6.679A pdb=" N ASN E 141 " --> pdb=" O ARG E 128 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N LYS E 130 " --> pdb=" O GLN E 139 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLN E 139 " --> pdb=" O LYS E 130 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N MET E 132 " --> pdb=" O LYS E 137 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LYS E 137 " --> pdb=" O MET E 132 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 97 through 99 removed outlier: 3.938A pdb=" N ASP F 67 " --> pdb=" O LEU F 86 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ALA F 88 " --> pdb=" O ILE F 65 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ILE F 65 " --> pdb=" O ALA F 88 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 145 through 149 removed outlier: 3.526A pdb=" N LYS F 155 " --> pdb=" O GLN F 186 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN F 186 " --> pdb=" O LYS F 155 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 16 through 21 removed outlier: 3.767A pdb=" N ILE G 21 " --> pdb=" O PHE G 4 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL G 121 " --> pdb=" O VAL G 7 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLN G 118 " --> pdb=" O THR G 67 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LYS G 122 " --> pdb=" O ILE G 63 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE G 63 " --> pdb=" O LYS G 122 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 83 through 88 removed outlier: 3.539A pdb=" N LYS G 105 " --> pdb=" O ILE G 86 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 135 through 140 Processing sheet with id= P, first strand: chain 'J' and resid 45 through 47 Processing sheet with id= Q, first strand: chain 'J' and resid 77 through 81 removed outlier: 3.956A pdb=" N ILE J 78 " --> pdb=" O GLU J 102 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N GLU J 102 " --> pdb=" O ILE J 78 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N VAL J 80 " --> pdb=" O ILE J 100 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ILE J 100 " --> pdb=" O VAL J 80 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'K' and resid 14 through 21 removed outlier: 6.452A pdb=" N ARG K 25 " --> pdb=" O ILE K 62 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N VAL K 64 " --> pdb=" O ARG K 25 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ARG K 27 " --> pdb=" O VAL K 64 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N VAL K 66 " --> pdb=" O ARG K 27 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'L' and resid 94 through 100 removed outlier: 3.605A pdb=" N THR L 95 " --> pdb=" O ALA L 9 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU L 97 " --> pdb=" O LYS L 7 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE L 73 " --> pdb=" O ILE L 6 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU L 8 " --> pdb=" O ARG L 71 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'L' and resid 43 through 47 removed outlier: 3.610A pdb=" N LEU L 66 " --> pdb=" O ILE L 45 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'M' and resid 38 through 42 removed outlier: 6.773A pdb=" N ILE M 30 " --> pdb=" O ILE M 39 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ARG M 41 " --> pdb=" O ILE M 28 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ILE M 28 " --> pdb=" O ARG M 41 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLY M 78 " --> pdb=" O GLY M 15 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N ALA M 17 " --> pdb=" O GLY M 78 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N HIS M 80 " --> pdb=" O ALA M 17 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ILE M 19 " --> pdb=" O HIS M 80 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ARG M 82 " --> pdb=" O ILE M 19 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU M 116 " --> pdb=" O ILE M 81 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'N' and resid 103 through 105 Processing sheet with id= W, first strand: chain 'N' and resid 58 through 61 Processing sheet with id= X, first strand: chain 'O' and resid 7 through 9 Processing sheet with id= Y, first strand: chain 'R' and resid 69 through 73 removed outlier: 3.983A pdb=" N SER R 40 " --> pdb=" O THR R 48 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N GLU R 50 " --> pdb=" O VAL R 38 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N VAL R 38 " --> pdb=" O GLU R 50 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'R' and resid 53 through 56 Processing sheet with id= AA, first strand: chain 'R' and resid 85 through 90 removed outlier: 3.866A pdb=" N ALA R 104 " --> pdb=" O LEU R 87 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ALA R 89 " --> pdb=" O VAL R 102 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N VAL R 102 " --> pdb=" O ALA R 89 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'T' and resid 80 through 84 Processing sheet with id= AC, first strand: chain 'U' and resid 111 through 114 removed outlier: 3.648A pdb=" N GLU U 112 " --> pdb=" O VAL U 120 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'V' and resid 3 through 11 removed outlier: 6.250A pdb=" N TYR V 20 " --> pdb=" O THR V 6 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL V 8 " --> pdb=" O GLU V 18 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N GLU V 18 " --> pdb=" O VAL V 8 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N GLU V 10 " --> pdb=" O ARG V 16 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ARG V 16 " --> pdb=" O GLU V 10 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS V 17 " --> pdb=" O TYR V 71 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR V 71 " --> pdb=" O LYS V 17 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE V 21 " --> pdb=" O GLY V 67 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY V 67 " --> pdb=" O PHE V 21 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LYS V 70 " --> pdb=" O ILE V 53 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ILE V 53 " --> pdb=" O LYS V 70 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N TYR V 72 " --> pdb=" O THR V 51 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N THR V 51 " --> pdb=" O TYR V 72 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'X' and resid 54 through 56 removed outlier: 3.650A pdb=" N ILE X 12 " --> pdb=" O LYS X 28 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LYS X 28 " --> pdb=" O ILE X 12 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ILE X 14 " --> pdb=" O GLN X 26 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N GLN X 26 " --> pdb=" O ILE X 14 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'Z' and resid 33 through 35 Processing sheet with id= AG, first strand: chain 'Z' and resid 128 through 134 removed outlier: 3.514A pdb=" N ARG Z 131 " --> pdb=" O LYS Z 179 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS Z 179 " --> pdb=" O ARG Z 131 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER Z 133 " --> pdb=" O GLY Z 177 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLY Z 177 " --> pdb=" O SER Z 133 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain '3' and resid 31 through 33 removed outlier: 3.808A pdb=" N LYS 3 31 " --> pdb=" O ILE 3 102 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG 3 33 " --> pdb=" O ALA 3 100 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA 3 100 " --> pdb=" O ARG 3 33 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain '6' and resid 24 through 26 Processing sheet with id= AJ, first strand: chain '6' and resid 37 through 40 Processing sheet with id= AK, first strand: chain '7' and resid 12 through 14 removed outlier: 6.929A pdb=" N ILE 7 56 " --> pdb=" O LEU 7 86 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ARG 7 88 " --> pdb=" O THR 7 54 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N THR 7 54 " --> pdb=" O ARG 7 88 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N SER 7 90 " --> pdb=" O ALA 7 52 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ALA 7 52 " --> pdb=" O SER 7 90 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE 7 92 " --> pdb=" O GLY 7 50 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N GLY 7 50 " --> pdb=" O ILE 7 92 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain '7' and resid 115 through 119 removed outlier: 5.796A pdb=" N ILE 7 145 " --> pdb=" O LEU 7 116 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N VAL 7 118 " --> pdb=" O ILE 7 145 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL 7 147 " --> pdb=" O VAL 7 118 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N GLN 7 148 " --> pdb=" O PRO 7 179 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N ILE 7 181 " --> pdb=" O GLN 7 148 " (cutoff:3.500A) No H-bonds generated for sheet with id= AL Processing sheet with id= AM, first strand: chain '7' and resid 219 through 222 removed outlier: 3.968A pdb=" N GLY 7 236 " --> pdb=" O THR 7 299 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain '7' and resid 272 through 274 Processing sheet with id= AO, first strand: chain '7' and resid 259 through 261 removed outlier: 3.503A pdb=" N LEU 7 259 " --> pdb=" O GLU 7 270 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER 7 268 " --> pdb=" O VAL 7 261 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain '7' and resid 377 through 381 removed outlier: 6.785A pdb=" N ILE 7 397 " --> pdb=" O ILE 7 408 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N TRP 7 410 " --> pdb=" O THR 7 395 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N THR 7 395 " --> pdb=" O TRP 7 410 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LEU 7 412 " --> pdb=" O ILE 7 393 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N ILE 7 393 " --> pdb=" O LEU 7 412 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain '8' and resid 35 through 37 removed outlier: 3.821A pdb=" N GLU 8 80 " --> pdb=" O ASP 8 76 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain '8' and resid 114 through 118 Processing sheet with id= AS, first strand: chain '9' and resid 37 through 39 removed outlier: 3.853A pdb=" N VAL 9 29 " --> pdb=" O ALA 9 39 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N SER 9 30 " --> pdb=" O VAL 9 19 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N VAL 9 19 " --> pdb=" O SER 9 30 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ASP 9 79 " --> pdb=" O ILE 9 69 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N VAL 9 71 " --> pdb=" O THR 9 77 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N THR 9 77 " --> pdb=" O VAL 9 71 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain '9' and resid 259 through 263 840 hydrogen bonds defined for protein. 2295 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1085 hydrogen bonds 1904 hydrogen bond angles 0 basepair planarities 401 basepair parallelities 578 stacking parallelities Total time for adding SS restraints: 41.05 Time building geometry restraints manager: 35.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 7474 1.29 - 1.42: 29091 1.42 - 1.56: 35323 1.56 - 1.69: 3191 1.69 - 1.83: 220 Bond restraints: 75299 Sorted by residual: bond pdb=" C4 B8H 2 938 " pdb=" C5 B8H 2 938 " ideal model delta sigma weight residual 1.834 1.380 0.454 2.00e-02 2.50e+03 5.15e+02 bond pdb=" N1 B8H 2 938 " pdb=" C6 B8H 2 938 " ideal model delta sigma weight residual 1.682 1.352 0.330 2.00e-02 2.50e+03 2.73e+02 bond pdb=" C4 5MU 4 54 " pdb=" C5 5MU 4 54 " ideal model delta sigma weight residual 1.802 1.480 0.322 2.00e-02 2.50e+03 2.59e+02 bond pdb=" N1 5MU 4 54 " pdb=" C6 5MU 4 54 " ideal model delta sigma weight residual 1.635 1.337 0.298 2.00e-02 2.50e+03 2.21e+02 bond pdb=" N3 B8H 2 938 " pdb=" C4 B8H 2 938 " ideal model delta sigma weight residual 1.136 1.402 -0.266 2.00e-02 2.50e+03 1.77e+02 ... (remaining 75294 not shown) Histogram of bond angle deviations from ideal: 98.22 - 105.97: 9826 105.97 - 113.72: 45664 113.72 - 121.47: 35583 121.47 - 129.22: 16751 129.22 - 136.97: 1683 Bond angle restraints: 109507 Sorted by residual: angle pdb=" C1' A2M 2 373 " pdb=" N9 A2M 2 373 " pdb=" C8 A2M 2 373 " ideal model delta sigma weight residual 88.50 122.14 -33.64 3.00e+00 1.11e-01 1.26e+02 angle pdb=" N6 A2M 2 373 " pdb=" C6 A2M 2 373 " pdb=" N1 A2M 2 373 " ideal model delta sigma weight residual 92.14 122.63 -30.49 3.00e+00 1.11e-01 1.03e+02 angle pdb=" C GLU N 143 " pdb=" N LYS N 144 " pdb=" CA LYS N 144 " ideal model delta sigma weight residual 122.70 107.21 15.49 1.98e+00 2.55e-01 6.12e+01 angle pdb=" N VAL P 46 " pdb=" CA VAL P 46 " pdb=" C VAL P 46 " ideal model delta sigma weight residual 113.20 106.43 6.77 9.60e-01 1.09e+00 4.97e+01 angle pdb=" N ILE Z 3 " pdb=" CA ILE Z 3 " pdb=" C ILE Z 3 " ideal model delta sigma weight residual 113.47 107.06 6.41 1.01e+00 9.80e-01 4.03e+01 ... (remaining 109502 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.89: 42027 31.89 - 63.77: 4852 63.77 - 95.66: 1169 95.66 - 127.55: 25 127.55 - 159.44: 6 Dihedral angle restraints: 48079 sinusoidal: 35136 harmonic: 12943 Sorted by residual: dihedral pdb=" O4' C 2 721 " pdb=" C1' C 2 721 " pdb=" N1 C 2 721 " pdb=" C2 C 2 721 " ideal model delta sinusoidal sigma weight residual 200.00 45.59 154.41 1 1.50e+01 4.44e-03 8.11e+01 dihedral pdb=" O4' C 21132 " pdb=" C1' C 21132 " pdb=" N1 C 21132 " pdb=" C2 C 21132 " ideal model delta sinusoidal sigma weight residual 200.00 49.85 150.15 1 1.50e+01 4.44e-03 7.97e+01 dihedral pdb=" O4' C 4 17 " pdb=" C1' C 4 17 " pdb=" N1 C 4 17 " pdb=" C2 C 4 17 " ideal model delta sinusoidal sigma weight residual 200.00 71.19 128.81 1 1.50e+01 4.44e-03 6.94e+01 ... (remaining 48076 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 11770 0.089 - 0.179: 1463 0.179 - 0.268: 92 0.268 - 0.357: 14 0.357 - 0.447: 2 Chirality restraints: 13341 Sorted by residual: chirality pdb=" C1' C 2 870 " pdb=" O4' C 2 870 " pdb=" C2' C 2 870 " pdb=" N1 C 2 870 " both_signs ideal model delta sigma weight residual False 2.47 2.02 0.45 2.00e-01 2.50e+01 4.99e+00 chirality pdb=" C1' G 2 857 " pdb=" O4' G 2 857 " pdb=" C2' G 2 857 " pdb=" N9 G 2 857 " both_signs ideal model delta sigma weight residual False 2.46 2.07 0.39 2.00e-01 2.50e+01 3.75e+00 chirality pdb=" C3' B8H 2 938 " pdb=" C4' B8H 2 938 " pdb=" O3' B8H 2 938 " pdb=" C2' B8H 2 938 " both_signs ideal model delta sigma weight residual False -2.74 -2.41 -0.34 2.00e-01 2.50e+01 2.83e+00 ... (remaining 13338 not shown) Planarity restraints: 7930 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 5MU 4 54 " -0.072 2.00e-02 2.50e+03 6.13e-01 8.45e+03 pdb=" C4' 5MU 4 54 " -0.444 2.00e-02 2.50e+03 pdb=" O4' 5MU 4 54 " -0.634 2.00e-02 2.50e+03 pdb=" C3' 5MU 4 54 " 0.595 2.00e-02 2.50e+03 pdb=" O3' 5MU 4 54 " 0.674 2.00e-02 2.50e+03 pdb=" C2' 5MU 4 54 " 0.161 2.00e-02 2.50e+03 pdb=" O2' 5MU 4 54 " -1.005 2.00e-02 2.50e+03 pdb=" C1' 5MU 4 54 " -0.216 2.00e-02 2.50e+03 pdb=" N1 5MU 4 54 " 0.941 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMC 4 32 " -0.070 2.00e-02 2.50e+03 5.54e-01 6.91e+03 pdb=" C4' OMC 4 32 " -0.409 2.00e-02 2.50e+03 pdb=" O4' OMC 4 32 " -0.495 2.00e-02 2.50e+03 pdb=" C3' OMC 4 32 " 0.613 2.00e-02 2.50e+03 pdb=" O3' OMC 4 32 " 0.590 2.00e-02 2.50e+03 pdb=" C2' OMC 4 32 " 0.191 2.00e-02 2.50e+03 pdb=" O2' OMC 4 32 " -0.959 2.00e-02 2.50e+03 pdb=" C1' OMC 4 32 " -0.240 2.00e-02 2.50e+03 pdb=" N1 OMC 4 32 " 0.779 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMC 21376 " -0.018 2.00e-02 2.50e+03 5.53e-01 6.89e+03 pdb=" C4' OMC 21376 " 0.438 2.00e-02 2.50e+03 pdb=" O4' OMC 21376 " 0.767 2.00e-02 2.50e+03 pdb=" C3' OMC 21376 " -0.576 2.00e-02 2.50e+03 pdb=" O3' OMC 21376 " -0.448 2.00e-02 2.50e+03 pdb=" C2' OMC 21376 " -0.298 2.00e-02 2.50e+03 pdb=" O2' OMC 21376 " 0.776 2.00e-02 2.50e+03 pdb=" C1' OMC 21376 " 0.202 2.00e-02 2.50e+03 pdb=" N1 OMC 21376 " -0.843 2.00e-02 2.50e+03 ... (remaining 7927 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.40: 616 2.40 - 3.02: 44084 3.02 - 3.65: 123856 3.65 - 4.27: 169937 4.27 - 4.90: 249446 Nonbonded interactions: 587939 Sorted by model distance: nonbonded pdb=" OP1 G 2 28 " pdb="MG MG 21601 " model vdw 1.769 2.170 nonbonded pdb=" OP2 C 2 952 " pdb="MG MG 21627 " model vdw 1.773 2.170 nonbonded pdb=" OP1 A 2 587 " pdb="MG MG 21606 " model vdw 1.775 2.170 nonbonded pdb=" OP2 G 21278 " pdb="MG MG 21630 " model vdw 1.780 2.170 nonbonded pdb=" OP2 C 2 106 " pdb="MG MG 21610 " model vdw 1.785 2.170 ... (remaining 587934 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 11.100 Check model and map are aligned: 0.810 Set scattering table: 0.500 Process input model: 196.350 Find NCS groups from input model: 1.500 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 214.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 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 : 0.014 0.454 75299 Z= 0.819 Angle : 1.258 33.636 109507 Z= 0.632 Chirality : 0.058 0.447 13341 Planarity : 0.017 0.613 7930 Dihedral : 23.521 159.436 39747 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 31.76 Ramachandran Plot: Outliers : 0.16 % Allowed : 19.04 % Favored : 80.80 % Rotamer: Outliers : 0.80 % Allowed : 13.50 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.60 (0.10), residues: 4437 helix: -3.75 (0.10), residues: 1181 sheet: -2.88 (0.17), residues: 733 loop : -4.14 (0.10), residues: 2523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP R 23 HIS 0.015 0.003 HIS T 115 PHE 0.032 0.003 PHE Q 66 TYR 0.032 0.003 TYR A 116 ARG 0.015 0.001 ARG 0 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8874 Ramachandran restraints generated. 4437 Oldfield, 0 Emsley, 4437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8874 Ramachandran restraints generated. 4437 Oldfield, 0 Emsley, 4437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 3861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 432 time to evaluate : 4.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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 Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 303, in __init__ self.caller(self.optimize_sidechains) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 609, in optimize_sidechains log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 83, in __init__ rotatable_hd = self.rotatable_hd) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 189, in run_one pdb_hierarchy = self.run_one_one(args=args) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 133, in run_one_one log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 108, in __init__ self.loop(function = self.one_residue_iteration) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 284, in loop function(residue = residue) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 271, in one_residue_iteration log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 172, in __init__ self.fit_proline() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 217, in fit_proline for rotamer, sites_cart in rotamer_iterator: TypeError: 'NoneType' object is not iterable