Starting phenix.real_space_refine on Sat Jan 20 07:45:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s6b_10102/01_2024/6s6b_10102.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s6b_10102/01_2024/6s6b_10102.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s6b_10102/01_2024/6s6b_10102.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s6b_10102/01_2024/6s6b_10102.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s6b_10102/01_2024/6s6b_10102.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s6b_10102/01_2024/6s6b_10102.pdb" } resolution = 2.75 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= 0.004 sd= 0.609 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 50 5.49 5 S 111 5.16 5 C 42809 2.51 5 N 11023 2.21 5 O 12920 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 101": "NH1" <-> "NH2" Residue "A GLU 105": "OE1" <-> "OE2" Residue "A ARG 155": "NH1" <-> "NH2" Residue "B TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 65": "OD1" <-> "OD2" Residue "B ARG 101": "NH1" <-> "NH2" Residue "B ARG 155": "NH1" <-> "NH2" Residue "C TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 101": "NH1" <-> "NH2" Residue "C ASP 121": "OD1" <-> "OD2" Residue "C ARG 155": "NH1" <-> "NH2" Residue "D GLU 28": "OE1" <-> "OE2" Residue "D PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 270": "OE1" <-> "OE2" Residue "E PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 76": "OE1" <-> "OE2" Residue "E GLU 116": "OE1" <-> "OE2" Residue "E GLU 167": "OE1" <-> "OE2" Residue "F PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 27": "OE1" <-> "OE2" Residue "F PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 75": "OD1" <-> "OD2" Residue "F GLU 200": "OE1" <-> "OE2" Residue "F GLU 246": "OE1" <-> "OE2" Residue "G GLU 74": "OE1" <-> "OE2" Residue "G PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 200": "OE1" <-> "OE2" Residue "G ARG 259": "NH1" <-> "NH2" Residue "G GLU 270": "OE1" <-> "OE2" Residue "H ARG 15": "NH1" <-> "NH2" Residue "H ARG 113": "NH1" <-> "NH2" Residue "H ARG 114": "NH1" <-> "NH2" Residue "H ASP 124": "OD1" <-> "OD2" Residue "H GLU 191": "OE1" <-> "OE2" Residue "H TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 243": "OD1" <-> "OD2" Residue "I TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 68": "OD1" <-> "OD2" Residue "I ASP 199": "OD1" <-> "OD2" Residue "I PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 280": "OE1" <-> "OE2" Residue "J GLU 78": "OE1" <-> "OE2" Residue "J ARG 97": "NH1" <-> "NH2" Residue "J ARG 113": "NH1" <-> "NH2" Residue "J TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 246": "NH1" <-> "NH2" Residue "J ARG 335": "NH1" <-> "NH2" Residue "J TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 367": "NH1" <-> "NH2" Residue "J PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 420": "OD1" <-> "OD2" Residue "J ARG 433": "NH1" <-> "NH2" Residue "J TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 469": "OE1" <-> "OE2" Residue "K GLU 67": "OE1" <-> "OE2" Residue "K ASP 120": "OD1" <-> "OD2" Residue "K ASP 125": "OD1" <-> "OD2" Residue "K GLU 130": "OE1" <-> "OE2" Residue "K TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 164": "OE1" <-> "OE2" Residue "K ARG 171": "NH1" <-> "NH2" Residue "K ARG 218": "NH1" <-> "NH2" Residue "K PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 281": "OE1" <-> "OE2" Residue "K ARG 355": "NH1" <-> "NH2" Residue "K ARG 360": "NH1" <-> "NH2" Residue "K GLU 399": "OE1" <-> "OE2" Residue "K ARG 510": "NH1" <-> "NH2" Residue "K ASP 535": "OD1" <-> "OD2" Residue "K TYR 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 549": "NH1" <-> "NH2" Residue "K ASP 656": "OD1" <-> "OD2" Residue "K GLU 690": "OE1" <-> "OE2" Residue "K TYR 726": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 736": "NH1" <-> "NH2" Residue "K GLU 746": "OE1" <-> "OE2" Residue "K ARG 763": "NH1" <-> "NH2" Residue "K GLU 785": "OE1" <-> "OE2" Residue "K GLU 819": "OE1" <-> "OE2" Residue "K ARG 821": "NH1" <-> "NH2" Residue "K PHE 872": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 891": "NH1" <-> "NH2" Residue "K ARG 923": "NH1" <-> "NH2" Residue "K GLU 944": "OE1" <-> "OE2" Residue "K GLU 974": "OE1" <-> "OE2" Residue "K GLU 1001": "OE1" <-> "OE2" Residue "K GLU 1011": "OE1" <-> "OE2" Residue "M ARG 118": "NH1" <-> "NH2" Residue "R PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 118": "NH1" <-> "NH2" Residue "R GLU 173": "OE1" <-> "OE2" Residue "S ASP 64": "OD1" <-> "OD2" Residue "S TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 118": "NH1" <-> "NH2" Residue "Q ARG 118": "NH1" <-> "NH2" Residue "Q ASP 131": "OD1" <-> "OD2" Residue "Q ASP 162": "OD1" <-> "OD2" Residue "Q PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 6": "OE1" <-> "OE2" Residue "P ASP 19": "OD1" <-> "OD2" Residue "P ASP 50": "OD1" <-> "OD2" Residue "P ASP 82": "OD1" <-> "OD2" Residue "P TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 118": "NH1" <-> "NH2" Residue "W TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 19": "OD1" <-> "OD2" Residue "W ASP 34": "OD1" <-> "OD2" Residue "W ARG 118": "NH1" <-> "NH2" Residue "W ASP 143": "OD1" <-> "OD2" Residue "W TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 104": "OD1" <-> "OD2" Residue "T TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 118": "NH1" <-> "NH2" Residue "T ASP 131": "OD1" <-> "OD2" Residue "T GLU 140": "OE1" <-> "OE2" Residue "T GLU 165": "OE1" <-> "OE2" Residue "Z ASP 28": "OD1" <-> "OD2" Residue "Z ASP 34": "OD1" <-> "OD2" Residue "Z ASP 61": "OD1" <-> "OD2" Residue "Z ASP 64": "OD1" <-> "OD2" Residue "Z ASP 104": "OD1" <-> "OD2" Residue "Z ARG 118": "NH1" <-> "NH2" Residue "Z PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 157": "OE1" <-> "OE2" Residue "Z GLU 161": "OE1" <-> "OE2" Residue "Y PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 118": "NH1" <-> "NH2" Residue "Y ASP 143": "OD1" <-> "OD2" Residue "Y TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ASP 104": "OD1" <-> "OD2" Residue "r TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 50": "OD1" <-> "OD2" Residue "s GLU 51": "OE1" <-> "OE2" Residue "s ASP 64": "OD1" <-> "OD2" Residue "s TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 161": "OE1" <-> "OE2" Residue "s GLU 173": "OE1" <-> "OE2" Residue "q ASP 19": "OD1" <-> "OD2" Residue "q PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 6": "OE1" <-> "OE2" Residue "p PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w ASP 50": "OD1" <-> "OD2" Residue "t TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ASP 130": "OD1" <-> "OD2" Residue "t GLU 152": "OE1" <-> "OE2" Residue "z ASP 34": "OD1" <-> "OD2" Residue "z GLU 35": "OE1" <-> "OE2" Residue "z TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ASP 50": "OD1" <-> "OD2" Residue "z TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ASP 131": "OD1" <-> "OD2" Residue "z GLU 152": "OE1" <-> "OE2" Residue "z GLU 165": "OE1" <-> "OE2" Residue "y PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y ASP 50": "OD1" <-> "OD2" Residue "y TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y ASP 104": "OD1" <-> "OD2" Residue "y TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y ASP 143": "OD1" <-> "OD2" Residue "y ASP 162": "OD1" <-> "OD2" Residue "y TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 118": "NH1" <-> "NH2" Residue "m ASP 131": "OD1" <-> "OD2" Residue "m PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 105": "OD1" <-> "OD2" Residue "L ARG 118": "NH1" <-> "NH2" Residue "L PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 162": "OD1" <-> "OD2" Residue "l ASP 82": "OD1" <-> "OD2" Residue "l ASP 116": "OD1" <-> "OD2" Residue "l ARG 118": "NH1" <-> "NH2" Residue "l ASP 131": "OD1" <-> "OD2" Residue "l PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 34": "OD1" <-> "OD2" Residue "O ASP 50": "OD1" <-> "OD2" Residue "O ASP 104": "OD1" <-> "OD2" Residue "O TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 118": "NH1" <-> "NH2" Residue "O PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 161": "OE1" <-> "OE2" Residue "O GLU 165": "OE1" <-> "OE2" Residue "o PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ASP 19": "OD1" <-> "OD2" Residue "o ASP 116": "OD1" <-> "OD2" Residue "o ARG 118": "NH1" <-> "NH2" Residue "o PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 161": "OE1" <-> "OE2" Residue "o PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 105": "OD1" <-> "OD2" Residue "N ASP 116": "OD1" <-> "OD2" Residue "N ARG 118": "NH1" <-> "NH2" Residue "N ASP 131": "OD1" <-> "OD2" Residue "N GLU 140": "OE1" <-> "OE2" Residue "N PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 162": "OD1" <-> "OD2" Residue "N GLU 165": "OE1" <-> "OE2" Residue "n GLU 6": "OE1" <-> "OE2" Residue "n ASP 34": "OD1" <-> "OD2" Residue "n GLU 35": "OE1" <-> "OE2" Residue "n TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 118": "NH1" <-> "NH2" Residue "n ASP 131": "OD1" <-> "OD2" Residue "x TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ASP 34": "OD1" <-> "OD2" Residue "x GLU 51": "OE1" <-> "OE2" Residue "x ASP 105": "OD1" <-> "OD2" Residue "x ASP 116": "OD1" <-> "OD2" Residue "x ARG 118": "NH1" <-> "NH2" Residue "x TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ASP 162": "OD1" <-> "OD2" Residue "X ASP 34": "OD1" <-> "OD2" Residue "X ASP 82": "OD1" <-> "OD2" Residue "X TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 118": "NH1" <-> "NH2" Residue "X GLU 161": "OE1" <-> "OE2" Residue "X PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.19s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 66914 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 1253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1253 Classifications: {'peptide': 153} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 150} Chain: "B" Number of atoms: 1261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1261 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} Chain: "C" Number of atoms: 1261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1261 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} Chain: "D" Number of atoms: 2276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2276 Classifications: {'peptide': 285} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 274} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 2276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2276 Classifications: {'peptide': 285} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 274} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "F" Number of atoms: 2277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2277 Classifications: {'peptide': 285} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain: "G" Number of atoms: 2276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2276 Classifications: {'peptide': 285} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 274} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "H" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2528 Classifications: {'peptide': 312} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 302} Chain: "I" Number of atoms: 2282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2282 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 12, 'TRANS': 271} Chain: "J" Number of atoms: 3890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3890 Classifications: {'peptide': 475} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 469} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "K" Number of atoms: 8418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 8418 Classifications: {'peptide': 1024} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 988} Chain breaks: 1 Chain: "V" Number of atoms: 1087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1087 Classifications: {'RNA': 51} Modifications used: {'5*END': 1, 'rna2p_pur': 12, 'rna2p_pyr': 7, 'rna3p_pur': 18, 'rna3p_pyr': 14} Link IDs: {'rna2p': 19, 'rna3p': 31} Chain: "M" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "R" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "S" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "Q" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "P" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "W" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "T" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "Z" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "Y" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "r" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "s" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "q" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "p" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "w" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "t" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "z" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "y" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "m" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "L" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "l" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "O" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "o" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "N" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "n" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "x" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "X" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 25350 SG CYS K 464 77.258 109.508 44.952 1.00 46.72 S ATOM 25369 SG CYS K 467 77.322 104.938 43.645 1.00 50.19 S ATOM 25717 SG CYS K 512 76.875 107.935 41.252 1.00 50.77 S ATOM 25744 SG CYS K 515 74.777 107.005 43.927 1.00 52.11 S Time building chain proxies: 31.07, per 1000 atoms: 0.46 Number of scatterers: 66914 At special positions: 0 Unit cell: (153.92, 173.056, 252.096, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 111 16.00 P 50 15.00 O 12920 8.00 N 11023 7.00 C 42809 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 115 " - pdb=" SG CYS R 63 " distance=2.06 Simple disulfide: pdb=" SG CYS B 115 " - pdb=" SG CYS Q 63 " distance=2.03 Simple disulfide: pdb=" SG CYS C 115 " - pdb=" SG CYS S 63 " distance=2.02 Simple disulfide: pdb=" SG CYS E 256 " - pdb=" SG CYS l 63 " distance=2.04 Simple disulfide: pdb=" SG CYS F 256 " - pdb=" SG CYS m 63 " distance=2.04 Simple disulfide: pdb=" SG CYS H 304 " - pdb=" SG CYS X 63 " distance=2.04 Simple disulfide: pdb=" SG CYS J 111 " - pdb=" SG CYS t 63 " distance=2.04 Simple disulfide: pdb=" SG CYS J 262 " - pdb=" SG CYS J 268 " distance=2.02 Simple disulfide: pdb=" SG CYS J 356 " - pdb=" SG CYS J 474 " distance=2.03 Simple disulfide: pdb=" SG CYS J 396 " - pdb=" SG CYS J 399 " distance=2.03 Simple disulfide: pdb=" SG CYS J 466 " - pdb=" SG CYS w 63 " distance=2.05 Simple disulfide: pdb=" SG CYS K 578 " - pdb=" SG CYS K 587 " distance=2.05 Simple disulfide: pdb=" SG CYS K 711 " - pdb=" SG CYS K 721 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 25.14 Conformation dependent library (CDL) restraints added in 9.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K1101 " pdb="ZN ZN K1101 " - pdb=" SG CYS K 515 " pdb="ZN ZN K1101 " - pdb=" SG CYS K 512 " pdb="ZN ZN K1101 " - pdb=" SG CYS K 464 " pdb="ZN ZN K1101 " - pdb=" SG CYS K 467 " Number of angles added : 6 16236 Ramachandran restraints generated. 8118 Oldfield, 0 Emsley, 8118 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15614 Finding SS restraints... Secondary structure from input PDB file: 226 helices and 0 sheets defined 29.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.97 Creating SS restraints... Processing helix chain 'A' and resid 4 through 21 Processing helix chain 'A' and resid 23 through 44 removed outlier: 3.500A pdb=" N SER A 32 " --> pdb=" O GLN A 28 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG A 35 " --> pdb=" O ARG A 31 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL A 38 " --> pdb=" O ALA A 34 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU A 39 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 58 removed outlier: 4.072A pdb=" N GLU A 58 " --> pdb=" O ILE A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 73 removed outlier: 4.024A pdb=" N SER A 72 " --> pdb=" O ILE A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 100 removed outlier: 3.525A pdb=" N TYR A 97 " --> pdb=" O ILE A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 115 removed outlier: 4.399A pdb=" N CYS A 115 " --> pdb=" O GLN A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 129 removed outlier: 3.592A pdb=" N ASP A 121 " --> pdb=" O LYS A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 137 removed outlier: 3.627A pdb=" N ALA A 135 " --> pdb=" O PRO A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 152 Processing helix chain 'B' and resid 5 through 20 removed outlier: 3.579A pdb=" N LEU B 11 " --> pdb=" O TYR B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 42 removed outlier: 3.853A pdb=" N VAL B 38 " --> pdb=" O ALA B 34 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU B 39 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N TYR B 42 " --> pdb=" O VAL B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 58 Processing helix chain 'B' and resid 61 through 71 removed outlier: 3.686A pdb=" N ASP B 65 " --> pdb=" O SER B 61 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 101 Processing helix chain 'B' and resid 105 through 113 Processing helix chain 'B' and resid 115 through 129 removed outlier: 4.491A pdb=" N LEU B 120 " --> pdb=" O GLU B 116 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ASP B 121 " --> pdb=" O LYS B 117 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASN B 128 " --> pdb=" O ASP B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 152 removed outlier: 3.915A pdb=" N ARG B 138 " --> pdb=" O SER B 134 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N THR B 139 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N TYR B 140 " --> pdb=" O LYS B 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 21 removed outlier: 3.816A pdb=" N ASN C 19 " --> pdb=" O LYS C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 44 removed outlier: 4.058A pdb=" N VAL C 38 " --> pdb=" O ALA C 34 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLU C 39 " --> pdb=" O ARG C 35 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TYR C 42 " --> pdb=" O VAL C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 57 removed outlier: 3.627A pdb=" N THR C 49 " --> pdb=" O GLY C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 73 removed outlier: 3.697A pdb=" N PHE C 71 " --> pdb=" O LEU C 67 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N SER C 72 " --> pdb=" O ILE C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 101 Processing helix chain 'C' and resid 105 through 115 Processing helix chain 'C' and resid 116 through 129 removed outlier: 3.933A pdb=" N LEU C 120 " --> pdb=" O GLU C 116 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASP C 121 " --> pdb=" O LYS C 117 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR C 127 " --> pdb=" O ILE C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 152 removed outlier: 3.633A pdb=" N ALA C 135 " --> pdb=" O PRO C 131 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS C 136 " --> pdb=" O ILE C 132 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ARG C 138 " --> pdb=" O SER C 134 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N THR C 139 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N TYR C 140 " --> pdb=" O LYS C 136 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU C 142 " --> pdb=" O ARG C 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 61 removed outlier: 3.653A pdb=" N LYS D 59 " --> pdb=" O SER D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 70 Processing helix chain 'D' and resid 115 through 131 Processing helix chain 'D' and resid 136 through 148 Processing helix chain 'D' and resid 194 through 204 removed outlier: 4.167A pdb=" N GLU D 200 " --> pdb=" O SER D 196 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN D 203 " --> pdb=" O ARG D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 256 Processing helix chain 'D' and resid 269 through 273 Processing helix chain 'D' and resid 282 through 286 Processing helix chain 'E' and resid 45 through 61 removed outlier: 3.809A pdb=" N LYS E 59 " --> pdb=" O SER E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 73 Processing helix chain 'E' and resid 115 through 129 removed outlier: 3.549A pdb=" N VAL E 121 " --> pdb=" O LEU E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 149 removed outlier: 3.579A pdb=" N LYS E 142 " --> pdb=" O ASN E 138 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LYS E 149 " --> pdb=" O THR E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 168 No H-bonds generated for 'chain 'E' and resid 166 through 168' Processing helix chain 'E' and resid 194 through 205 removed outlier: 3.896A pdb=" N GLU E 200 " --> pdb=" O SER E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 257 Processing helix chain 'E' and resid 269 through 273 Processing helix chain 'E' and resid 283 through 285 No H-bonds generated for 'chain 'E' and resid 283 through 285' Processing helix chain 'F' and resid 45 through 61 removed outlier: 3.590A pdb=" N LYS F 59 " --> pdb=" O SER F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 72 Processing helix chain 'F' and resid 115 through 131 Processing helix chain 'F' and resid 136 through 147 Processing helix chain 'F' and resid 148 through 150 No H-bonds generated for 'chain 'F' and resid 148 through 150' Processing helix chain 'F' and resid 194 through 206 removed outlier: 3.801A pdb=" N GLU F 200 " --> pdb=" O SER F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 256 Processing helix chain 'F' and resid 257 through 261 removed outlier: 3.690A pdb=" N LEU F 261 " --> pdb=" O LEU F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 273 Processing helix chain 'G' and resid 45 through 56 Processing helix chain 'G' and resid 61 through 63 No H-bonds generated for 'chain 'G' and resid 61 through 63' Processing helix chain 'G' and resid 64 through 73 Processing helix chain 'G' and resid 115 through 130 removed outlier: 3.658A pdb=" N ILE G 128 " --> pdb=" O TYR G 124 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLN G 130 " --> pdb=" O ASP G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 149 removed outlier: 4.357A pdb=" N LYS G 142 " --> pdb=" O ASN G 138 " (cutoff:3.500A) Processing helix chain 'G' and resid 194 through 206 removed outlier: 3.708A pdb=" N GLU G 200 " --> pdb=" O SER G 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 247 through 257 removed outlier: 3.789A pdb=" N ALA G 251 " --> pdb=" O SER G 247 " (cutoff:3.500A) Processing helix chain 'G' and resid 269 through 273 Processing helix chain 'H' and resid 38 through 50 Processing helix chain 'H' and resid 98 through 100 No H-bonds generated for 'chain 'H' and resid 98 through 100' Processing helix chain 'H' and resid 102 through 107 Processing helix chain 'H' and resid 110 through 123 Processing helix chain 'H' and resid 225 through 231 Processing helix chain 'H' and resid 271 through 279 removed outlier: 4.131A pdb=" N ASP H 275 " --> pdb=" O ARG H 271 " (cutoff:3.500A) Processing helix chain 'H' and resid 282 through 295 removed outlier: 3.840A pdb=" N TYR H 287 " --> pdb=" O ASN H 283 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ARG H 288 " --> pdb=" O ASP H 284 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS H 291 " --> pdb=" O TYR H 287 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 7 Processing helix chain 'I' and resid 8 through 17 removed outlier: 3.523A pdb=" N ILE I 13 " --> pdb=" O ILE I 9 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS I 14 " --> pdb=" O LEU I 10 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS I 16 " --> pdb=" O LEU I 12 " (cutoff:3.500A) Processing helix chain 'I' and resid 21 through 35 removed outlier: 3.691A pdb=" N ILE I 31 " --> pdb=" O SER I 27 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL I 32 " --> pdb=" O LEU I 28 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 41 removed outlier: 3.593A pdb=" N LEU I 40 " --> pdb=" O GLY I 37 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 57 Processing helix chain 'I' and resid 64 through 88 removed outlier: 3.505A pdb=" N VAL I 69 " --> pdb=" O LYS I 65 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU I 71 " --> pdb=" O LYS I 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 92 through 109 Processing helix chain 'I' and resid 153 through 169 Processing helix chain 'I' and resid 169 through 175 removed outlier: 4.156A pdb=" N GLU I 173 " --> pdb=" O LEU I 169 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA I 174 " --> pdb=" O GLY I 170 " (cutoff:3.500A) Processing helix chain 'I' and resid 244 through 246 No H-bonds generated for 'chain 'I' and resid 244 through 246' Processing helix chain 'I' and resid 247 through 261 removed outlier: 3.900A pdb=" N ILE I 251 " --> pdb=" O VAL I 247 " (cutoff:3.500A) Proline residue: I 256 - end of helix removed outlier: 3.868A pdb=" N ILE I 260 " --> pdb=" O PRO I 256 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG I 261 " --> pdb=" O ILE I 257 " (cutoff:3.500A) Processing helix chain 'I' and resid 266 through 270 Processing helix chain 'J' and resid 34 through 55 removed outlier: 3.574A pdb=" N LEU J 49 " --> pdb=" O TRP J 45 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN J 51 " --> pdb=" O ARG J 47 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 76 removed outlier: 3.833A pdb=" N ARG J 69 " --> pdb=" O GLU J 65 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N ASP J 73 " --> pdb=" O ARG J 69 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N VAL J 74 " --> pdb=" O LEU J 70 " (cutoff:3.500A) Processing helix chain 'J' and resid 106 through 111 Processing helix chain 'J' and resid 150 through 159 Processing helix chain 'J' and resid 159 through 170 removed outlier: 3.827A pdb=" N LEU J 167 " --> pdb=" O SER J 163 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N GLY J 168 " --> pdb=" O PHE J 164 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N PHE J 169 " --> pdb=" O GLU J 165 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 198 Processing helix chain 'J' and resid 199 through 201 No H-bonds generated for 'chain 'J' and resid 199 through 201' Processing helix chain 'J' and resid 223 through 242 removed outlier: 3.790A pdb=" N LYS J 229 " --> pdb=" O GLU J 225 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR J 233 " --> pdb=" O LYS J 229 " (cutoff:3.500A) Processing helix chain 'J' and resid 247 through 251 Processing helix chain 'J' and resid 264 through 277 removed outlier: 7.241A pdb=" N LYS J 270 " --> pdb=" O SER J 266 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ILE J 271 " --> pdb=" O ILE J 267 " (cutoff:3.500A) Processing helix chain 'J' and resid 283 through 297 Processing helix chain 'J' and resid 338 through 346 Processing helix chain 'J' and resid 346 through 351 Processing helix chain 'J' and resid 356 through 361 Processing helix chain 'J' and resid 364 through 375 Processing helix chain 'J' and resid 391 through 396 Processing helix chain 'J' and resid 416 through 422 Processing helix chain 'J' and resid 460 through 475 Processing helix chain 'K' and resid 13 through 19 removed outlier: 3.712A pdb=" N ALA K 17 " --> pdb=" O TYR K 13 " (cutoff:3.500A) Processing helix chain 'K' and resid 24 through 29 Processing helix chain 'K' and resid 48 through 56 removed outlier: 3.877A pdb=" N VAL K 52 " --> pdb=" O LYS K 48 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE K 56 " --> pdb=" O VAL K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 77 removed outlier: 4.233A pdb=" N SER K 77 " --> pdb=" O ASP K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 81 Processing helix chain 'K' and resid 84 through 89 removed outlier: 3.754A pdb=" N LYS K 89 " --> pdb=" O SER K 85 " (cutoff:3.500A) Processing helix chain 'K' and resid 120 through 136 removed outlier: 4.105A pdb=" N ASN K 126 " --> pdb=" O SER K 122 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU K 127 " --> pdb=" O LYS K 123 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE K 128 " --> pdb=" O LEU K 124 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLU K 130 " --> pdb=" O ASN K 126 " (cutoff:3.500A) Processing helix chain 'K' and resid 142 through 161 removed outlier: 5.160A pdb=" N GLU K 155 " --> pdb=" O TYR K 151 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU K 156 " --> pdb=" O LEU K 152 " (cutoff:3.500A) Processing helix chain 'K' and resid 176 through 196 removed outlier: 4.096A pdb=" N ASN K 189 " --> pdb=" O ALA K 185 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N TRP K 190 " --> pdb=" O ALA K 186 " (cutoff:3.500A) Processing helix chain 'K' and resid 209 through 215 Processing helix chain 'K' and resid 219 through 246 removed outlier: 3.650A pdb=" N VAL K 230 " --> pdb=" O SER K 226 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER K 231 " --> pdb=" O SER K 227 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL K 237 " --> pdb=" O LEU K 233 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N TRP K 240 " --> pdb=" O TYR K 236 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N PHE K 241 " --> pdb=" O VAL K 237 " (cutoff:3.500A) Processing helix chain 'K' and resid 254 through 257 removed outlier: 4.031A pdb=" N PHE K 257 " --> pdb=" O SER K 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 254 through 257' Processing helix chain 'K' and resid 258 through 271 Processing helix chain 'K' and resid 282 through 290 Processing helix chain 'K' and resid 295 through 301 Processing helix chain 'K' and resid 331 through 334 Processing helix chain 'K' and resid 335 through 361 removed outlier: 3.694A pdb=" N GLY K 346 " --> pdb=" O ARG K 342 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TRP K 347 " --> pdb=" O TYR K 343 " (cutoff:3.500A) Processing helix chain 'K' and resid 366 through 377 Processing helix chain 'K' and resid 377 through 382 Processing helix chain 'K' and resid 409 through 411 No H-bonds generated for 'chain 'K' and resid 409 through 411' Processing helix chain 'K' and resid 412 through 429 Processing helix chain 'K' and resid 435 through 439 Processing helix chain 'K' and resid 441 through 447 Processing helix chain 'K' and resid 482 through 487 Processing helix chain 'K' and resid 497 through 502 Processing helix chain 'K' and resid 512 through 524 Processing helix chain 'K' and resid 525 through 527 No H-bonds generated for 'chain 'K' and resid 525 through 527' Processing helix chain 'K' and resid 528 through 534 removed outlier: 3.526A pdb=" N GLY K 534 " --> pdb=" O ILE K 530 " (cutoff:3.500A) Processing helix chain 'K' and resid 538 through 548 removed outlier: 3.590A pdb=" N ILE K 546 " --> pdb=" O ILE K 542 " (cutoff:3.500A) Processing helix chain 'K' and resid 557 through 562 Processing helix chain 'K' and resid 563 through 571 Processing helix chain 'K' and resid 573 through 579 removed outlier: 3.698A pdb=" N GLU K 579 " --> pdb=" O ASN K 575 " (cutoff:3.500A) Processing helix chain 'K' and resid 614 through 618 Processing helix chain 'K' and resid 624 through 635 removed outlier: 3.661A pdb=" N HIS K 635 " --> pdb=" O VAL K 631 " (cutoff:3.500A) Processing helix chain 'K' and resid 653 through 659 removed outlier: 3.609A pdb=" N GLU K 659 " --> pdb=" O GLY K 655 " (cutoff:3.500A) Processing helix chain 'K' and resid 671 through 680 removed outlier: 4.573A pdb=" N ILE K 678 " --> pdb=" O TYR K 675 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N SER K 679 " --> pdb=" O ALA K 676 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU K 680 " --> pdb=" O ASN K 677 " (cutoff:3.500A) Processing helix chain 'K' and resid 681 through 696 removed outlier: 3.526A pdb=" N LYS K 687 " --> pdb=" O GLU K 683 " (cutoff:3.500A) Processing helix chain 'K' and resid 701 through 711 removed outlier: 3.573A pdb=" N THR K 707 " --> pdb=" O ASP K 703 " (cutoff:3.500A) Processing helix chain 'K' and resid 721 through 734 removed outlier: 3.878A pdb=" N SER K 727 " --> pdb=" O GLU K 723 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASN K 728 " --> pdb=" O LYS K 724 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS K 732 " --> pdb=" O ASN K 728 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N MET K 734 " --> pdb=" O VAL K 730 " (cutoff:3.500A) Processing helix chain 'K' and resid 743 through 762 removed outlier: 3.977A pdb=" N LYS K 749 " --> pdb=" O GLU K 745 " (cutoff:3.500A) Processing helix chain 'K' and resid 767 through 792 Processing helix chain 'K' and resid 812 through 825 Processing helix chain 'K' and resid 869 through 881 removed outlier: 3.855A pdb=" N LEU K 881 " --> pdb=" O SER K 877 " (cutoff:3.500A) Processing helix chain 'K' and resid 928 through 935 removed outlier: 3.668A pdb=" N PHE K 932 " --> pdb=" O VAL K 929 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ASN K 933 " --> pdb=" O SER K 930 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU K 934 " --> pdb=" O ASP K 931 " (cutoff:3.500A) Processing helix chain 'K' and resid 936 through 951 removed outlier: 3.909A pdb=" N ASP K 940 " --> pdb=" O ALA K 936 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL K 941 " --> pdb=" O SER K 937 " (cutoff:3.500A) Processing helix chain 'K' and resid 957 through 972 removed outlier: 3.578A pdb=" N TYR K 962 " --> pdb=" O LEU K 958 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N GLU K 963 " --> pdb=" O LEU K 959 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N LYS K 964 " --> pdb=" O TYR K 960 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR K 965 " --> pdb=" O ASP K 961 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N HIS K 967 " --> pdb=" O GLU K 963 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LEU K 968 " --> pdb=" O LYS K 964 " (cutoff:3.500A) Processing helix chain 'K' and resid 974 through 989 removed outlier: 4.084A pdb=" N PHE K 980 " --> pdb=" O TYR K 976 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS K 983 " --> pdb=" O GLU K 979 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASN K 989 " --> pdb=" O TRP K 985 " (cutoff:3.500A) Processing helix chain 'K' and resid 1020 through 1035 Processing helix chain 'M' and resid 89 through 93 Processing helix chain 'M' and resid 130 through 146 removed outlier: 3.847A pdb=" N ASN M 135 " --> pdb=" O ASP M 131 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ASN M 136 " --> pdb=" O THR M 132 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS M 139 " --> pdb=" O ASN M 135 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N PHE M 142 " --> pdb=" O ILE M 138 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ASP M 143 " --> pdb=" O LYS M 139 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS M 144 " --> pdb=" O GLU M 140 " (cutoff:3.500A) Processing helix chain 'M' and resid 148 through 153 removed outlier: 3.575A pdb=" N GLU M 152 " --> pdb=" O ILE M 148 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS M 153 " --> pdb=" O THR M 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 148 through 153' Processing helix chain 'M' and resid 155 through 167 removed outlier: 3.793A pdb=" N VAL M 159 " --> pdb=" O LYS M 155 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LYS M 164 " --> pdb=" O LYS M 160 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLU M 165 " --> pdb=" O GLU M 161 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE M 167 " --> pdb=" O ILE M 163 " (cutoff:3.500A) Processing helix chain 'R' and resid 130 through 141 removed outlier: 3.628A pdb=" N ILE R 138 " --> pdb=" O VAL R 134 " (cutoff:3.500A) Processing helix chain 'R' and resid 141 through 146 removed outlier: 3.877A pdb=" N TYR R 146 " --> pdb=" O PHE R 142 " (cutoff:3.500A) Processing helix chain 'R' and resid 155 through 164 removed outlier: 3.895A pdb=" N ILE R 163 " --> pdb=" O VAL R 159 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LYS R 164 " --> pdb=" O LYS R 160 " (cutoff:3.500A) Processing helix chain 'S' and resid 135 through 147 removed outlier: 3.540A pdb=" N PHE S 142 " --> pdb=" O ILE S 138 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYS S 144 " --> pdb=" O GLU S 140 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ILE S 145 " --> pdb=" O VAL S 141 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASN S 147 " --> pdb=" O ASP S 143 " (cutoff:3.500A) Processing helix chain 'S' and resid 158 through 166 removed outlier: 3.949A pdb=" N LYS S 164 " --> pdb=" O LYS S 160 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU S 165 " --> pdb=" O GLU S 161 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 83 removed outlier: 3.744A pdb=" N ASP Q 82 " --> pdb=" O GLN Q 79 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE Q 83 " --> pdb=" O SER Q 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 79 through 83' Processing helix chain 'Q' and resid 133 through 141 removed outlier: 3.649A pdb=" N LYS Q 139 " --> pdb=" O ASN Q 135 " (cutoff:3.500A) Processing helix chain 'Q' and resid 155 through 163 removed outlier: 3.761A pdb=" N ASP Q 162 " --> pdb=" O LYS Q 158 " (cutoff:3.500A) Processing helix chain 'P' and resid 79 through 83 removed outlier: 3.501A pdb=" N ASP P 82 " --> pdb=" O GLN P 79 " (cutoff:3.500A) Processing helix chain 'P' and resid 130 through 141 removed outlier: 3.737A pdb=" N ASN P 135 " --> pdb=" O ASP P 131 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ASN P 136 " --> pdb=" O THR P 132 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE P 137 " --> pdb=" O ILE P 133 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE P 138 " --> pdb=" O VAL P 134 " (cutoff:3.500A) Processing helix chain 'P' and resid 141 through 146 removed outlier: 3.713A pdb=" N TYR P 146 " --> pdb=" O PHE P 142 " (cutoff:3.500A) Processing helix chain 'P' and resid 162 through 167 Processing helix chain 'W' and resid 133 through 141 removed outlier: 3.945A pdb=" N LYS W 139 " --> pdb=" O ASN W 135 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU W 140 " --> pdb=" O ASN W 136 " (cutoff:3.500A) Processing helix chain 'W' and resid 155 through 167 removed outlier: 4.100A pdb=" N GLU W 161 " --> pdb=" O GLU W 157 " (cutoff:3.500A) Processing helix chain 'T' and resid 130 through 140 removed outlier: 3.852A pdb=" N ASN T 135 " --> pdb=" O ASP T 131 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN T 136 " --> pdb=" O THR T 132 " (cutoff:3.500A) Processing helix chain 'T' and resid 141 through 146 Processing helix chain 'T' and resid 155 through 167 removed outlier: 4.697A pdb=" N GLU T 161 " --> pdb=" O GLU T 157 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS T 164 " --> pdb=" O LYS T 160 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU T 166 " --> pdb=" O ASP T 162 " (cutoff:3.500A) Processing helix chain 'Z' and resid 132 through 139 removed outlier: 4.035A pdb=" N ASN Z 136 " --> pdb=" O THR Z 132 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE Z 137 " --> pdb=" O ILE Z 133 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS Z 139 " --> pdb=" O ASN Z 135 " (cutoff:3.500A) Processing helix chain 'Z' and resid 154 through 156 No H-bonds generated for 'chain 'Z' and resid 154 through 156' Processing helix chain 'Z' and resid 157 through 165 removed outlier: 3.563A pdb=" N GLU Z 161 " --> pdb=" O GLU Z 157 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE Z 163 " --> pdb=" O VAL Z 159 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLU Z 165 " --> pdb=" O GLU Z 161 " (cutoff:3.500A) Processing helix chain 'Y' and resid 130 through 136 removed outlier: 3.624A pdb=" N VAL Y 134 " --> pdb=" O ASP Y 130 " (cutoff:3.500A) Processing helix chain 'Y' and resid 136 through 141 Processing helix chain 'Y' and resid 142 through 145 Processing helix chain 'Y' and resid 155 through 160 Processing helix chain 'Y' and resid 161 through 166 Processing helix chain 'r' and resid 130 through 141 removed outlier: 3.523A pdb=" N VAL r 134 " --> pdb=" O ASP r 130 " (cutoff:3.500A) Processing helix chain 'r' and resid 159 through 166 removed outlier: 3.861A pdb=" N ILE r 163 " --> pdb=" O VAL r 159 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS r 164 " --> pdb=" O LYS r 160 " (cutoff:3.500A) Processing helix chain 's' and resid 130 through 140 removed outlier: 3.668A pdb=" N VAL s 134 " --> pdb=" O ASP s 130 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE s 138 " --> pdb=" O VAL s 134 " (cutoff:3.500A) Processing helix chain 's' and resid 159 through 164 Processing helix chain 'q' and resid 79 through 83 removed outlier: 4.616A pdb=" N ASP q 82 " --> pdb=" O GLN q 79 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE q 83 " --> pdb=" O SER q 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 79 through 83' Processing helix chain 'q' and resid 131 through 141 Processing helix chain 'q' and resid 156 through 166 removed outlier: 3.661A pdb=" N GLU q 161 " --> pdb=" O GLU q 157 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP q 162 " --> pdb=" O LYS q 158 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LYS q 164 " --> pdb=" O LYS q 160 " (cutoff:3.500A) Processing helix chain 'p' and resid 134 through 142 removed outlier: 3.850A pdb=" N LYS p 139 " --> pdb=" O ASN p 135 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N GLU p 140 " --> pdb=" O ASN p 136 " (cutoff:3.500A) Processing helix chain 'p' and resid 156 through 163 removed outlier: 3.553A pdb=" N ASP p 162 " --> pdb=" O LYS p 158 " (cutoff:3.500A) Processing helix chain 'w' and resid 75 through 83 removed outlier: 3.521A pdb=" N ALA w 78 " --> pdb=" O PRO w 75 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N SER w 80 " --> pdb=" O GLN w 77 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ASN w 81 " --> pdb=" O ALA w 78 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASP w 82 " --> pdb=" O GLN w 79 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N PHE w 83 " --> pdb=" O SER w 80 " (cutoff:3.500A) Processing helix chain 'w' and resid 130 through 141 removed outlier: 4.138A pdb=" N LYS w 139 " --> pdb=" O ASN w 135 " (cutoff:3.500A) Processing helix chain 'w' and resid 141 through 146 Processing helix chain 'w' and resid 158 through 167 removed outlier: 3.571A pdb=" N PHE w 167 " --> pdb=" O ILE w 163 " (cutoff:3.500A) Processing helix chain 't' and resid 131 through 138 removed outlier: 4.375A pdb=" N ASN t 135 " --> pdb=" O ASP t 131 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN t 136 " --> pdb=" O THR t 132 " (cutoff:3.500A) Processing helix chain 't' and resid 156 through 163 Processing helix chain 'z' and resid 131 through 140 removed outlier: 3.564A pdb=" N ASN z 135 " --> pdb=" O ASP z 131 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASN z 136 " --> pdb=" O THR z 132 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ILE z 138 " --> pdb=" O VAL z 134 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLU z 140 " --> pdb=" O ASN z 136 " (cutoff:3.500A) Processing helix chain 'z' and resid 158 through 166 removed outlier: 4.371A pdb=" N LYS z 164 " --> pdb=" O LYS z 160 " (cutoff:3.500A) Processing helix chain 'y' and resid 13 through 17 removed outlier: 3.931A pdb=" N ILE y 16 " --> pdb=" O THR y 13 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N THR y 17 " --> pdb=" O ASN y 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 13 through 17' Processing helix chain 'y' and resid 130 through 142 removed outlier: 3.675A pdb=" N VAL y 134 " --> pdb=" O ASP y 130 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLU y 140 " --> pdb=" O ASN y 136 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE y 142 " --> pdb=" O ILE y 138 " (cutoff:3.500A) Processing helix chain 'y' and resid 156 through 167 removed outlier: 3.780A pdb=" N LYS y 160 " --> pdb=" O ILE y 156 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU y 161 " --> pdb=" O GLU y 157 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU y 165 " --> pdb=" O GLU y 161 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU y 166 " --> pdb=" O ASP y 162 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE y 167 " --> pdb=" O ILE y 163 " (cutoff:3.500A) Processing helix chain 'm' and resid 130 through 141 removed outlier: 4.007A pdb=" N ASN m 136 " --> pdb=" O THR m 132 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE m 138 " --> pdb=" O VAL m 134 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LYS m 139 " --> pdb=" O ASN m 135 " (cutoff:3.500A) Processing helix chain 'm' and resid 146 through 150 Processing helix chain 'm' and resid 155 through 165 removed outlier: 3.600A pdb=" N GLU m 161 " --> pdb=" O GLU m 157 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LYS m 164 " --> pdb=" O LYS m 160 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU m 165 " --> pdb=" O GLU m 161 " (cutoff:3.500A) Processing helix chain 'L' and resid 89 through 93 Processing helix chain 'L' and resid 130 through 141 removed outlier: 3.515A pdb=" N ASN L 135 " --> pdb=" O ASP L 131 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASN L 136 " --> pdb=" O THR L 132 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS L 139 " --> pdb=" O ASN L 135 " (cutoff:3.500A) Processing helix chain 'L' and resid 146 through 151 Processing helix chain 'L' and resid 155 through 167 removed outlier: 3.842A pdb=" N VAL L 159 " --> pdb=" O LYS L 155 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS L 164 " --> pdb=" O LYS L 160 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU L 166 " --> pdb=" O ASP L 162 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE L 167 " --> pdb=" O ILE L 163 " (cutoff:3.500A) Processing helix chain 'l' and resid 132 through 141 removed outlier: 4.001A pdb=" N ILE l 138 " --> pdb=" O VAL l 134 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS l 139 " --> pdb=" O ASN l 135 " (cutoff:3.500A) Processing helix chain 'l' and resid 141 through 146 Processing helix chain 'l' and resid 147 through 150 Processing helix chain 'l' and resid 155 through 162 Processing helix chain 'O' and resid 13 through 17 removed outlier: 3.675A pdb=" N ILE O 16 " --> pdb=" O THR O 13 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR O 17 " --> pdb=" O ASN O 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 13 through 17' Processing helix chain 'O' and resid 89 through 93 Processing helix chain 'O' and resid 133 through 146 removed outlier: 3.513A pdb=" N ILE O 138 " --> pdb=" O VAL O 134 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE O 142 " --> pdb=" O ILE O 138 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASP O 143 " --> pdb=" O LYS O 139 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LYS O 144 " --> pdb=" O GLU O 140 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE O 145 " --> pdb=" O VAL O 141 " (cutoff:3.500A) Processing helix chain 'O' and resid 148 through 153 removed outlier: 3.895A pdb=" N GLU O 152 " --> pdb=" O ILE O 148 " (cutoff:3.500A) Processing helix chain 'O' and resid 156 through 166 removed outlier: 3.580A pdb=" N GLU O 161 " --> pdb=" O GLU O 157 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS O 164 " --> pdb=" O LYS O 160 " (cutoff:3.500A) Processing helix chain 'o' and resid 89 through 93 Processing helix chain 'o' and resid 132 through 141 removed outlier: 3.939A pdb=" N ASN o 136 " --> pdb=" O THR o 132 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE o 138 " --> pdb=" O VAL o 134 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS o 139 " --> pdb=" O ASN o 135 " (cutoff:3.500A) Processing helix chain 'o' and resid 147 through 152 removed outlier: 3.682A pdb=" N LYS o 151 " --> pdb=" O ASN o 147 " (cutoff:3.500A) Processing helix chain 'o' and resid 155 through 167 removed outlier: 3.899A pdb=" N VAL o 159 " --> pdb=" O LYS o 155 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE o 163 " --> pdb=" O VAL o 159 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N LYS o 164 " --> pdb=" O LYS o 160 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU o 165 " --> pdb=" O GLU o 161 " (cutoff:3.500A) Processing helix chain 'N' and resid 130 through 141 removed outlier: 3.935A pdb=" N ASN N 135 " --> pdb=" O ASP N 131 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ASN N 136 " --> pdb=" O THR N 132 " (cutoff:3.500A) Processing helix chain 'N' and resid 157 through 166 removed outlier: 4.164A pdb=" N LYS N 164 " --> pdb=" O LYS N 160 " (cutoff:3.500A) Processing helix chain 'n' and resid 132 through 141 removed outlier: 4.146A pdb=" N ASN n 136 " --> pdb=" O THR n 132 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE n 137 " --> pdb=" O ILE n 133 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE n 138 " --> pdb=" O VAL n 134 " (cutoff:3.500A) Processing helix chain 'n' and resid 146 through 151 Processing helix chain 'n' and resid 155 through 166 removed outlier: 5.313A pdb=" N GLU n 161 " --> pdb=" O GLU n 157 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE n 163 " --> pdb=" O VAL n 159 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N LYS n 164 " --> pdb=" O LYS n 160 " (cutoff:3.500A) Processing helix chain 'x' and resid 13 through 17 removed outlier: 3.846A pdb=" N ILE x 16 " --> pdb=" O THR x 13 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N THR x 17 " --> pdb=" O ASN x 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'x' and resid 13 through 17' Processing helix chain 'x' and resid 130 through 141 removed outlier: 4.009A pdb=" N ASN x 135 " --> pdb=" O ASP x 131 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ASN x 136 " --> pdb=" O THR x 132 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS x 139 " --> pdb=" O ASN x 135 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL x 141 " --> pdb=" O ILE x 137 " (cutoff:3.500A) Processing helix chain 'x' and resid 141 through 146 removed outlier: 3.566A pdb=" N ILE x 145 " --> pdb=" O VAL x 141 " (cutoff:3.500A) Processing helix chain 'x' and resid 146 through 153 removed outlier: 4.163A pdb=" N GLN x 150 " --> pdb=" O TYR x 146 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS x 151 " --> pdb=" O ASN x 147 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU x 152 " --> pdb=" O ILE x 148 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LYS x 153 " --> pdb=" O THR x 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'x' and resid 146 through 153' Processing helix chain 'x' and resid 159 through 164 Processing helix chain 'X' and resid 89 through 93 Processing helix chain 'X' and resid 130 through 141 removed outlier: 3.813A pdb=" N ASN X 136 " --> pdb=" O THR X 132 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE X 137 " --> pdb=" O ILE X 133 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE X 138 " --> pdb=" O VAL X 134 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS X 139 " --> pdb=" O ASN X 135 " (cutoff:3.500A) Processing helix chain 'X' and resid 155 through 167 removed outlier: 4.780A pdb=" N GLU X 161 " --> pdb=" O GLU X 157 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LYS X 164 " --> pdb=" O LYS X 160 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU X 165 " --> pdb=" O GLU X 161 " (cutoff:3.500A) 1245 hydrogen bonds defined for protein. 3591 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 15.50 Time building geometry restraints manager: 27.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 20085 1.33 - 1.46: 13647 1.46 - 1.58: 34192 1.58 - 1.71: 100 1.71 - 1.83: 162 Bond restraints: 68186 Sorted by residual: bond pdb=" N ALA G 104 " pdb=" CA ALA G 104 " ideal model delta sigma weight residual 1.457 1.483 -0.025 1.29e-02 6.01e+03 3.83e+00 bond pdb=" C ILE s 10 " pdb=" N PRO s 11 " ideal model delta sigma weight residual 1.334 1.378 -0.044 2.34e-02 1.83e+03 3.60e+00 bond pdb=" CA TYR x 169 " pdb=" CB TYR x 169 " ideal model delta sigma weight residual 1.535 1.504 0.031 1.93e-02 2.68e+03 2.63e+00 bond pdb=" C TYR J 14 " pdb=" O TYR J 14 " ideal model delta sigma weight residual 1.235 1.227 0.008 4.70e-03 4.53e+04 2.61e+00 bond pdb=" CA LYS K 902 " pdb=" CB LYS K 902 " ideal model delta sigma weight residual 1.522 1.542 -0.020 1.27e-02 6.20e+03 2.55e+00 ... (remaining 68181 not shown) Histogram of bond angle deviations from ideal: 99.17 - 106.15: 1559 106.15 - 113.12: 38061 113.12 - 120.10: 23712 120.10 - 127.07: 28581 127.07 - 134.05: 570 Bond angle restraints: 92483 Sorted by residual: angle pdb=" N VAL W 154 " pdb=" CA VAL W 154 " pdb=" C VAL W 154 " ideal model delta sigma weight residual 113.20 107.33 5.87 9.60e-01 1.09e+00 3.74e+01 angle pdb=" N ILE s 12 " pdb=" CA ILE s 12 " pdb=" C ILE s 12 " ideal model delta sigma weight residual 106.21 112.71 -6.50 1.07e+00 8.73e-01 3.69e+01 angle pdb=" N VAL Y 49 " pdb=" CA VAL Y 49 " pdb=" C VAL Y 49 " ideal model delta sigma weight residual 113.71 108.34 5.37 9.50e-01 1.11e+00 3.19e+01 angle pdb=" N ALA X 78 " pdb=" CA ALA X 78 " pdb=" C ALA X 78 " ideal model delta sigma weight residual 113.23 106.57 6.66 1.24e+00 6.50e-01 2.89e+01 angle pdb=" N VAL D 26 " pdb=" CA VAL D 26 " pdb=" C VAL D 26 " ideal model delta sigma weight residual 112.96 107.64 5.32 1.00e+00 1.00e+00 2.83e+01 ... (remaining 92478 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.80: 41096 35.80 - 71.60: 759 71.60 - 107.41: 57 107.41 - 143.21: 2 143.21 - 179.01: 4 Dihedral angle restraints: 41918 sinusoidal: 17719 harmonic: 24199 Sorted by residual: dihedral pdb=" CA ILE P 22 " pdb=" C ILE P 22 " pdb=" N THR P 23 " pdb=" CA THR P 23 " ideal model delta harmonic sigma weight residual -180.00 -115.86 -64.14 0 5.00e+00 4.00e-02 1.65e+02 dihedral pdb=" CA LYS P 21 " pdb=" C LYS P 21 " pdb=" N ILE P 22 " pdb=" CA ILE P 22 " ideal model delta harmonic sigma weight residual -180.00 -120.00 -60.00 0 5.00e+00 4.00e-02 1.44e+02 dihedral pdb=" CA THR r 17 " pdb=" C THR r 17 " pdb=" N ILE r 18 " pdb=" CA ILE r 18 " ideal model delta harmonic sigma weight residual -180.00 -129.84 -50.16 0 5.00e+00 4.00e-02 1.01e+02 ... (remaining 41915 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 9069 0.068 - 0.137: 1645 0.137 - 0.205: 77 0.205 - 0.274: 6 0.274 - 0.342: 1 Chirality restraints: 10798 Sorted by residual: chirality pdb=" CB ILE P 22 " pdb=" CA ILE P 22 " pdb=" CG1 ILE P 22 " pdb=" CG2 ILE P 22 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" CG LEU K 93 " pdb=" CB LEU K 93 " pdb=" CD1 LEU K 93 " pdb=" CD2 LEU K 93 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CB VAL D 232 " pdb=" CA VAL D 232 " pdb=" CG1 VAL D 232 " pdb=" CG2 VAL D 232 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 10795 not shown) Planarity restraints: 11493 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE N 10 " -0.045 5.00e-02 4.00e+02 6.83e-02 7.47e+00 pdb=" N PRO N 11 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO N 11 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO N 11 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE M 10 " -0.045 5.00e-02 4.00e+02 6.70e-02 7.19e+00 pdb=" N PRO M 11 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO M 11 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO M 11 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE m 10 " 0.042 5.00e-02 4.00e+02 6.40e-02 6.56e+00 pdb=" N PRO m 11 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO m 11 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO m 11 " 0.035 5.00e-02 4.00e+02 ... (remaining 11490 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 806 2.55 - 3.14: 57215 3.14 - 3.72: 105523 3.72 - 4.31: 158243 4.31 - 4.90: 249618 Nonbonded interactions: 571405 Sorted by model distance: nonbonded pdb=" OH TYR Z 7 " pdb=" O LEU Z 42 " model vdw 1.961 2.440 nonbonded pdb=" OG SER J 438 " pdb=" O ASN J 443 " model vdw 2.081 2.440 nonbonded pdb=" OH TYR q 65 " pdb=" OG SER q 168 " model vdw 2.099 2.440 nonbonded pdb=" O THR Q 31 " pdb=" OH TYR Q 146 " model vdw 2.111 2.440 nonbonded pdb=" O GLU K 244 " pdb=" OH TYR K 326 " model vdw 2.114 2.440 ... (remaining 571400 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 3 through 155) selection = (chain 'C' and resid 3 through 155) } ncs_group { reference = chain 'D' selection = chain 'E' selection = (chain 'F' and (resid 2 through 157 or (resid 158 and (name N or name CA or name \ C or name O or name CB )) or resid 159 through 286)) selection = chain 'G' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'w' selection = chain 'x' selection = chain 'y' selection = chain 'z' } 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=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.540 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: 0.060 Extract box with map and model: 27.140 Check model and map are aligned: 0.790 Set scattering table: 0.450 Process input model: 148.690 Find NCS groups from input model: 3.310 Set up NCS constraints: 0.680 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:10.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 197.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 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 : 0.005 0.074 68186 Z= 0.333 Angle : 0.764 13.574 92483 Z= 0.435 Chirality : 0.049 0.342 10798 Planarity : 0.004 0.068 11493 Dihedral : 14.857 179.010 26265 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 19.06 Ramachandran Plot: Outliers : 0.41 % Allowed : 15.29 % Favored : 84.31 % Rotamer: Outliers : 0.15 % Allowed : 6.80 % Favored : 93.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -5.13 (0.07), residues: 8118 helix: -3.69 (0.07), residues: 2089 sheet: -2.54 (0.13), residues: 1305 loop : -3.68 (0.07), residues: 4724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 281 HIS 0.007 0.001 HIS n 29 PHE 0.028 0.002 PHE G 136 TYR 0.026 0.002 TYR F 111 ARG 0.016 0.000 ARG C 101 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16236 Ramachandran restraints generated. 8118 Oldfield, 0 Emsley, 8118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16236 Ramachandran restraints generated. 8118 Oldfield, 0 Emsley, 8118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1711 residues out of total 7465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 1700 time to evaluate : 6.354 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: G 116 GLU cc_start: 0.7145 (mt-10) cc_final: 0.6693 (mt-10) REVERT: J 131 GLU cc_start: 0.7762 (tm-30) cc_final: 0.7429 (tm-30) REVERT: J 296 ASP cc_start: 0.8486 (m-30) cc_final: 0.8192 (m-30) REVERT: J 361 ILE cc_start: 0.9013 (OUTLIER) cc_final: 0.8771 (pt) REVERT: J 445 TYR cc_start: 0.8148 (m-80) cc_final: 0.7767 (m-80) REVERT: K 90 GLU cc_start: 0.8110 (tp30) cc_final: 0.7771 (tp30) REVERT: K 91 ARG cc_start: 0.7940 (ptt180) cc_final: 0.7499 (ptt180) REVERT: K 164 GLU cc_start: 0.7416 (mt-10) cc_final: 0.7213 (mt-10) REVERT: K 677 ASN cc_start: 0.7664 (t0) cc_final: 0.7320 (t0) REVERT: K 748 VAL cc_start: 0.9063 (m) cc_final: 0.8727 (t) REVERT: K 886 GLU cc_start: 0.7359 (tp30) cc_final: 0.7137 (tm-30) REVERT: M 146 TYR cc_start: 0.7864 (m-80) cc_final: 0.7661 (m-80) REVERT: R 112 TYR cc_start: 0.8539 (t80) cc_final: 0.8189 (t80) REVERT: R 131 ASP cc_start: 0.8230 (m-30) cc_final: 0.7976 (t0) REVERT: R 172 LEU cc_start: 0.7278 (mp) cc_final: 0.6582 (mp) REVERT: S 6 GLU cc_start: 0.6036 (mp0) cc_final: 0.5728 (mp0) REVERT: S 7 TYR cc_start: 0.8037 (t80) cc_final: 0.7820 (t80) REVERT: S 32 ASN cc_start: 0.6622 (m-40) cc_final: 0.5917 (t0) REVERT: S 38 ILE cc_start: 0.8046 (mp) cc_final: 0.7755 (mm) REVERT: S 112 TYR cc_start: 0.8046 (t80) cc_final: 0.7351 (t80) REVERT: S 150 GLN cc_start: 0.6957 (mm110) cc_final: 0.6459 (mm-40) REVERT: S 151 LYS cc_start: 0.6029 (pttp) cc_final: 0.5189 (pptt) REVERT: S 162 ASP cc_start: 0.7903 (m-30) cc_final: 0.7453 (m-30) REVERT: P 160 LYS cc_start: 0.7397 (pptt) cc_final: 0.7021 (tttp) REVERT: W 56 LEU cc_start: 0.8369 (mt) cc_final: 0.8062 (mm) REVERT: W 69 ILE cc_start: 0.6922 (pt) cc_final: 0.6663 (pp) REVERT: W 142 PHE cc_start: 0.8686 (m-80) cc_final: 0.8022 (m-80) REVERT: T 79 GLN cc_start: 0.6495 (tm-30) cc_final: 0.6113 (tm-30) REVERT: T 81 ASN cc_start: 0.7249 (m110) cc_final: 0.6499 (p0) REVERT: T 144 LYS cc_start: 0.8221 (mtpt) cc_final: 0.7847 (ttpt) REVERT: Y 53 ASN cc_start: 0.6296 (t0) cc_final: 0.6047 (t0) REVERT: r 52 LYS cc_start: 0.7738 (ttmt) cc_final: 0.7481 (mppt) REVERT: r 79 GLN cc_start: 0.7887 (tt0) cc_final: 0.7300 (tm-30) REVERT: r 82 ASP cc_start: 0.7664 (m-30) cc_final: 0.6453 (m-30) REVERT: r 149 THR cc_start: 0.5946 (p) cc_final: 0.5714 (t) REVERT: r 168 SER cc_start: 0.8918 (m) cc_final: 0.8292 (p) REVERT: s 5 ARG cc_start: 0.4828 (tpp80) cc_final: 0.3957 (tpp80) REVERT: s 69 ILE cc_start: 0.8817 (mm) cc_final: 0.8550 (pp) REVERT: s 112 TYR cc_start: 0.7776 (t80) cc_final: 0.7560 (t80) REVERT: q 9 PHE cc_start: 0.6884 (p90) cc_final: 0.6465 (p90) REVERT: q 79 GLN cc_start: 0.6555 (mt0) cc_final: 0.6079 (tm-30) REVERT: q 147 ASN cc_start: 0.7433 (m110) cc_final: 0.6951 (m-40) REVERT: q 157 GLU cc_start: 0.7419 (pm20) cc_final: 0.7210 (pm20) REVERT: p 86 LEU cc_start: 0.8608 (tt) cc_final: 0.8227 (tt) REVERT: t 97 ARG cc_start: 0.8038 (mtt180) cc_final: 0.7589 (mtm180) REVERT: t 169 TYR cc_start: 0.6178 (p90) cc_final: 0.5866 (p90) REVERT: t 170 TYR cc_start: 0.7730 (m-10) cc_final: 0.7412 (m-10) REVERT: y 88 LEU cc_start: 0.6933 (pp) cc_final: 0.6523 (tp) REVERT: m 124 LYS cc_start: 0.7989 (mptt) cc_final: 0.7737 (mttm) REVERT: l 21 LYS cc_start: 0.7305 (mmtm) cc_final: 0.6997 (pptt) REVERT: n 79 GLN cc_start: 0.6774 (tm-30) cc_final: 0.5625 (mt0) REVERT: n 169 TYR cc_start: 0.7308 (p90) cc_final: 0.7106 (p90) outliers start: 11 outliers final: 9 residues processed: 1709 average time/residue: 1.3026 time to fit residues: 2977.0004 Evaluate side-chains 1086 residues out of total 7465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 1076 time to evaluate : 5.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain H residue 111 TYR Chi-restraints excluded: chain J residue 361 ILE Chi-restraints excluded: chain s residue 24 ILE Chi-restraints excluded: chain y residue 163 ILE Chi-restraints excluded: chain m residue 152 GLU Chi-restraints excluded: chain O residue 32 ASN Chi-restraints excluded: chain o residue 38 ILE Chi-restraints excluded: chain N residue 119 ASN Chi-restraints excluded: chain X residue 156 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 812 random chunks: chunk 685 optimal weight: 4.9990 chunk 615 optimal weight: 8.9990 chunk 341 optimal weight: 2.9990 chunk 210 optimal weight: 1.9990 chunk 415 optimal weight: 10.0000 chunk 328 optimal weight: 5.9990 chunk 636 optimal weight: 0.6980 chunk 246 optimal weight: 0.0170 chunk 386 optimal weight: 1.9990 chunk 473 optimal weight: 0.8980 chunk 737 optimal weight: 10.0000 overall best weight: 1.1222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 ASN D 17 HIS D 185 ASN E 19 HIS E 130 GLN E 133 ASN ** F 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 141 ASN F 153 ASN F 203 ASN G 19 HIS G 141 ASN G 185 ASN H 28 HIS H 32 GLN H 97 GLN ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 135 GLN H 253 ASN I 8 ASN I 19 ASN I 21 ASN ** I 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 158 ASN J 220 HIS J 223 ASN J 265 ASN J 310 ASN J 440 ASN K 20 HIS ** K 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 ASN ** K 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 175 HIS K 344 ASN K 416 ASN K 604 ASN ** K 635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 738 ASN K 779 ASN K 845 ASN K1024 ASN M 29 HIS ** M 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 53 ASN M 101 ASN M 119 ASN M 174 GLN ** S 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 174 GLN Q 40 ASN Q 119 ASN Q 150 GLN ** P 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 40 ASN P 91 ASN W 53 ASN ** T 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 77 GLN Z 135 ASN Y 79 GLN ** Y 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 39 HIS s 150 GLN q 39 HIS p 101 ASN ** p 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 136 ASN w 29 HIS w 119 ASN ** w 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 76 GLN t 79 GLN t 101 ASN y 40 ASN y 101 ASN m 14 ASN m 32 ASN ** m 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 40 ASN m 76 GLN L 101 ASN l 39 HIS l 53 ASN ** l 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 40 ASN ** O 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 81 ASN O 119 ASN O 174 GLN o 174 GLN N 29 HIS N 40 ASN N 53 ASN N 119 ASN N 174 GLN n 135 ASN n 147 ASN ** x 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 32 ASN x 174 GLN X 4 GLN ** X 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 85 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 68186 Z= 0.232 Angle : 0.726 11.574 92483 Z= 0.379 Chirality : 0.048 0.358 10798 Planarity : 0.005 0.076 11493 Dihedral : 9.714 179.223 9673 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 18.65 Ramachandran Plot: Outliers : 0.22 % Allowed : 14.67 % Favored : 85.11 % Rotamer: Outliers : 3.58 % Allowed : 17.80 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -4.11 (0.08), residues: 8118 helix: -2.21 (0.09), residues: 2202 sheet: -2.12 (0.13), residues: 1314 loop : -3.32 (0.08), residues: 4602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP K 770 HIS 0.009 0.001 HIS n 29 PHE 0.020 0.002 PHE n 9 TYR 0.026 0.002 TYR O 109 ARG 0.010 0.001 ARG x 5 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16236 Ramachandran restraints generated. 8118 Oldfield, 0 Emsley, 8118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16236 Ramachandran restraints generated. 8118 Oldfield, 0 Emsley, 8118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1586 residues out of total 7465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 267 poor density : 1319 time to evaluate : 6.060 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: A 127 TYR cc_start: 0.8278 (t80) cc_final: 0.7797 (t80) REVERT: C 5 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6893 (pm20) REVERT: E 65 ARG cc_start: 0.7542 (mmt90) cc_final: 0.7269 (mmt-90) REVERT: F 28 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7465 (tt0) REVERT: F 206 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8593 (mp) REVERT: F 286 ILE cc_start: 0.7002 (OUTLIER) cc_final: 0.6666 (pt) REVERT: G 136 PHE cc_start: 0.8011 (OUTLIER) cc_final: 0.7421 (p90) REVERT: I 275 GLU cc_start: 0.6984 (OUTLIER) cc_final: 0.6661 (tt0) REVERT: J 445 TYR cc_start: 0.8046 (m-80) cc_final: 0.7656 (m-80) REVERT: K 90 GLU cc_start: 0.8041 (tp30) cc_final: 0.7643 (tp30) REVERT: K 91 ARG cc_start: 0.7747 (ptt180) cc_final: 0.7544 (ptt180) REVERT: K 116 LEU cc_start: 0.7583 (OUTLIER) cc_final: 0.7373 (mp) REVERT: K 164 GLU cc_start: 0.7413 (mt-10) cc_final: 0.7037 (mt-10) REVERT: K 656 ASP cc_start: 0.7840 (t0) cc_final: 0.7614 (t0) REVERT: K 724 LYS cc_start: 0.8970 (mmmm) cc_final: 0.8747 (mmmm) REVERT: K 749 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8267 (tmmm) REVERT: K 886 GLU cc_start: 0.7361 (tp30) cc_final: 0.7129 (tm-30) REVERT: K 976 TYR cc_start: 0.7268 (p90) cc_final: 0.6965 (p90) REVERT: M 7 TYR cc_start: 0.8051 (t80) cc_final: 0.7822 (t80) REVERT: M 8 VAL cc_start: 0.8794 (OUTLIER) cc_final: 0.8553 (m) REVERT: R 4 GLN cc_start: 0.7330 (pm20) cc_final: 0.6987 (pp30) REVERT: R 112 TYR cc_start: 0.8560 (t80) cc_final: 0.8251 (t80) REVERT: R 131 ASP cc_start: 0.8214 (m-30) cc_final: 0.7878 (t0) REVERT: S 7 TYR cc_start: 0.8148 (t80) cc_final: 0.7917 (t80) REVERT: S 32 ASN cc_start: 0.6762 (m-40) cc_final: 0.6173 (t0) REVERT: S 33 ILE cc_start: 0.5922 (OUTLIER) cc_final: 0.5588 (mp) REVERT: S 53 ASN cc_start: 0.7927 (t0) cc_final: 0.7724 (t0) REVERT: S 146 TYR cc_start: 0.7141 (t80) cc_final: 0.6933 (t80) REVERT: S 151 LYS cc_start: 0.5982 (pttp) cc_final: 0.5129 (pptt) REVERT: S 162 ASP cc_start: 0.7640 (m-30) cc_final: 0.7408 (m-30) REVERT: Q 108 ILE cc_start: 0.8967 (OUTLIER) cc_final: 0.8737 (tp) REVERT: Q 112 TYR cc_start: 0.8508 (t80) cc_final: 0.8185 (t80) REVERT: Q 166 LEU cc_start: 0.9201 (mt) cc_final: 0.8842 (mt) REVERT: P 84 LEU cc_start: 0.8032 (tp) cc_final: 0.7493 (tm) REVERT: P 86 LEU cc_start: 0.7777 (mm) cc_final: 0.7387 (mm) REVERT: P 160 LYS cc_start: 0.7318 (pptt) cc_final: 0.6936 (tttp) REVERT: W 6 GLU cc_start: 0.7293 (tm-30) cc_final: 0.6900 (tm-30) REVERT: T 6 GLU cc_start: 0.6931 (tp30) cc_final: 0.5384 (pp20) REVERT: T 79 GLN cc_start: 0.6500 (tm-30) cc_final: 0.6132 (tm-30) REVERT: T 81 ASN cc_start: 0.7326 (m110) cc_final: 0.6544 (p0) REVERT: T 142 PHE cc_start: 0.7835 (m-80) cc_final: 0.7588 (m-80) REVERT: T 144 LYS cc_start: 0.7850 (mtpt) cc_final: 0.7368 (tttt) REVERT: Y 53 ASN cc_start: 0.6327 (t0) cc_final: 0.6036 (t0) REVERT: Y 166 LEU cc_start: 0.6644 (mm) cc_final: 0.6414 (mm) REVERT: Y 167 PHE cc_start: 0.6516 (m-80) cc_final: 0.6257 (m-80) REVERT: Y 170 TYR cc_start: 0.6717 (m-80) cc_final: 0.6499 (m-80) REVERT: r 52 LYS cc_start: 0.7725 (ttmt) cc_final: 0.7478 (mppt) REVERT: r 79 GLN cc_start: 0.7922 (tt0) cc_final: 0.7412 (tm-30) REVERT: r 82 ASP cc_start: 0.7634 (m-30) cc_final: 0.6755 (m-30) REVERT: r 84 LEU cc_start: 0.7867 (mt) cc_final: 0.7514 (mt) REVERT: r 149 THR cc_start: 0.5867 (p) cc_final: 0.5305 (t) REVERT: r 168 SER cc_start: 0.8864 (m) cc_final: 0.8217 (p) REVERT: s 140 GLU cc_start: 0.6124 (tp30) cc_final: 0.5815 (tp30) REVERT: q 9 PHE cc_start: 0.6802 (p90) cc_final: 0.6381 (p90) REVERT: q 35 GLU cc_start: 0.7200 (pt0) cc_final: 0.6973 (mm-30) REVERT: q 79 GLN cc_start: 0.6578 (mt0) cc_final: 0.6121 (tm-30) REVERT: q 94 TYR cc_start: 0.8356 (t80) cc_final: 0.8027 (t80) REVERT: q 147 ASN cc_start: 0.7353 (m110) cc_final: 0.6931 (m-40) REVERT: p 97 ARG cc_start: 0.8191 (mtp85) cc_final: 0.7472 (mtp180) REVERT: p 115 PRO cc_start: 0.8484 (Cg_endo) cc_final: 0.8134 (Cg_exo) REVERT: w 97 ARG cc_start: 0.8075 (mmt-90) cc_final: 0.7837 (mmt-90) REVERT: w 112 TYR cc_start: 0.7525 (t80) cc_final: 0.7277 (t80) REVERT: t 88 LEU cc_start: 0.8637 (mm) cc_final: 0.8401 (mm) REVERT: t 97 ARG cc_start: 0.7961 (mtt180) cc_final: 0.7552 (mtm180) REVERT: t 121 MET cc_start: 0.6288 (mpt) cc_final: 0.5800 (mpt) REVERT: y 88 LEU cc_start: 0.6692 (pp) cc_final: 0.6375 (tp) REVERT: l 160 LYS cc_start: 0.8500 (pttp) cc_final: 0.8227 (pmtt) REVERT: O 114 SER cc_start: 0.7987 (OUTLIER) cc_final: 0.7670 (t) REVERT: o 155 LYS cc_start: 0.6982 (OUTLIER) cc_final: 0.6485 (mmtp) outliers start: 267 outliers final: 87 residues processed: 1475 average time/residue: 1.2216 time to fit residues: 2459.0525 Evaluate side-chains 1182 residues out of total 7465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 1082 time to evaluate : 5.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain C residue 5 GLU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 28 GLU Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain G residue 136 PHE Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 129 SER Chi-restraints excluded: chain I residue 275 GLU Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 103 VAL Chi-restraints excluded: chain J residue 138 ILE Chi-restraints excluded: chain J residue 171 SER Chi-restraints excluded: chain J residue 195 ASN Chi-restraints excluded: chain J residue 329 ASP Chi-restraints excluded: chain J residue 466 CYS Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 749 LYS Chi-restraints excluded: chain K residue 929 VAL Chi-restraints excluded: chain K residue 933 ASN Chi-restraints excluded: chain M residue 8 VAL Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 31 THR Chi-restraints excluded: chain S residue 33 ILE Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 63 CYS Chi-restraints excluded: chain S residue 172 LEU Chi-restraints excluded: chain Q residue 108 ILE Chi-restraints excluded: chain P residue 12 ILE Chi-restraints excluded: chain P residue 57 VAL Chi-restraints excluded: chain P residue 81 ASN Chi-restraints excluded: chain P residue 130 ASP Chi-restraints excluded: chain P residue 135 ASN Chi-restraints excluded: chain W residue 16 ILE Chi-restraints excluded: chain W residue 17 THR Chi-restraints excluded: chain W residue 103 SER Chi-restraints excluded: chain W residue 127 SER Chi-restraints excluded: chain T residue 112 TYR Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 118 ARG Chi-restraints excluded: chain Y residue 34 ASP Chi-restraints excluded: chain Y residue 43 VAL Chi-restraints excluded: chain r residue 31 THR Chi-restraints excluded: chain r residue 59 THR Chi-restraints excluded: chain r residue 74 THR Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain q residue 8 VAL Chi-restraints excluded: chain q residue 114 SER Chi-restraints excluded: chain q residue 168 SER Chi-restraints excluded: chain p residue 40 ASN Chi-restraints excluded: chain p residue 55 ARG Chi-restraints excluded: chain p residue 134 VAL Chi-restraints excluded: chain w residue 3 THR Chi-restraints excluded: chain t residue 81 ASN Chi-restraints excluded: chain t residue 95 LEU Chi-restraints excluded: chain z residue 134 VAL Chi-restraints excluded: chain y residue 8 VAL Chi-restraints excluded: chain y residue 30 ILE Chi-restraints excluded: chain y residue 92 LYS Chi-restraints excluded: chain y residue 105 ASP Chi-restraints excluded: chain m residue 152 GLU Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain L residue 108 ILE Chi-restraints excluded: chain l residue 66 VAL Chi-restraints excluded: chain O residue 32 ASN Chi-restraints excluded: chain O residue 63 CYS Chi-restraints excluded: chain O residue 114 SER Chi-restraints excluded: chain o residue 108 ILE Chi-restraints excluded: chain o residue 120 SER Chi-restraints excluded: chain o residue 155 LYS Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 96 ILE Chi-restraints excluded: chain N residue 113 SER Chi-restraints excluded: chain N residue 149 THR Chi-restraints excluded: chain n residue 60 LEU Chi-restraints excluded: chain n residue 141 VAL Chi-restraints excluded: chain x residue 70 LEU Chi-restraints excluded: chain X residue 38 ILE Chi-restraints excluded: chain X residue 60 LEU Chi-restraints excluded: chain X residue 74 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 812 random chunks: chunk 409 optimal weight: 7.9990 chunk 228 optimal weight: 0.6980 chunk 613 optimal weight: 5.9990 chunk 502 optimal weight: 10.0000 chunk 203 optimal weight: 0.8980 chunk 738 optimal weight: 10.0000 chunk 798 optimal weight: 20.0000 chunk 657 optimal weight: 10.0000 chunk 732 optimal weight: 1.9990 chunk 251 optimal weight: 0.9990 chunk 592 optimal weight: 0.0770 overall best weight: 0.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN A 43 ASN B 28 GLN D 185 ASN E 141 ASN ** F 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 185 ASN H 135 GLN H 187 ASN H 192 ASN ** I 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 157 HIS ** K 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 635 HIS ** K 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 29 HIS M 32 ASN R 135 ASN ** S 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 76 GLN Q 150 GLN ** P 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 53 ASN ** T 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 29 HIS s 91 ASN ** p 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 101 ASN p 135 ASN p 136 ASN ** w 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 79 GLN ** z 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 81 ASN m 4 GLN ** m 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 76 GLN ** l 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 39 HIS ** N 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 53 ASN ** N 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 76 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 68186 Z= 0.212 Angle : 0.692 15.952 92483 Z= 0.359 Chirality : 0.047 0.326 10798 Planarity : 0.004 0.066 11493 Dihedral : 9.609 178.948 9656 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 17.92 Ramachandran Plot: Outliers : 0.20 % Allowed : 13.93 % Favored : 85.87 % Rotamer: Outliers : 4.20 % Allowed : 20.56 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.59 (0.08), residues: 8118 helix: -1.58 (0.10), residues: 2211 sheet: -1.88 (0.14), residues: 1291 loop : -3.07 (0.08), residues: 4616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 770 HIS 0.007 0.001 HIS J 157 PHE 0.024 0.001 PHE t 167 TYR 0.042 0.002 TYR t 112 ARG 0.013 0.000 ARG m 118 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16236 Ramachandran restraints generated. 8118 Oldfield, 0 Emsley, 8118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16236 Ramachandran restraints generated. 8118 Oldfield, 0 Emsley, 8118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1545 residues out of total 7465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 313 poor density : 1232 time to evaluate : 5.988 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: A 127 TYR cc_start: 0.8209 (t80) cc_final: 0.7734 (t80) REVERT: C 5 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6909 (pm20) REVERT: C 105 GLU cc_start: 0.7561 (tt0) cc_final: 0.7127 (tt0) REVERT: E 65 ARG cc_start: 0.7508 (mmt90) cc_final: 0.7277 (mmt-90) REVERT: F 206 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8566 (mp) REVERT: H 125 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8465 (mmpt) REVERT: I 85 SER cc_start: 0.8651 (m) cc_final: 0.8450 (p) REVERT: I 175 GLU cc_start: 0.7328 (mt-10) cc_final: 0.7056 (mt-10) REVERT: I 275 GLU cc_start: 0.6961 (OUTLIER) cc_final: 0.6584 (tt0) REVERT: J 417 PHE cc_start: 0.8095 (t80) cc_final: 0.7764 (t80) REVERT: J 445 TYR cc_start: 0.8025 (m-80) cc_final: 0.7753 (m-80) REVERT: K 49 HIS cc_start: 0.6488 (p90) cc_final: 0.6171 (p-80) REVERT: K 90 GLU cc_start: 0.7934 (tp30) cc_final: 0.7527 (tp30) REVERT: K 91 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.7202 (ptp-170) REVERT: K 164 GLU cc_start: 0.7412 (mt-10) cc_final: 0.7176 (mt-10) REVERT: K 169 ASP cc_start: 0.8068 (t0) cc_final: 0.7820 (t0) REVERT: K 656 ASP cc_start: 0.7880 (t0) cc_final: 0.7655 (t0) REVERT: K 724 LYS cc_start: 0.8978 (mmmm) cc_final: 0.8697 (mmmm) REVERT: K 885 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8224 (pttt) REVERT: K 886 GLU cc_start: 0.7306 (tp30) cc_final: 0.7091 (tm-30) REVERT: K 988 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.7466 (ttm-80) REVERT: M 10 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.7886 (pt) REVERT: R 4 GLN cc_start: 0.7428 (pm20) cc_final: 0.7058 (pp30) REVERT: R 9 PHE cc_start: 0.8314 (OUTLIER) cc_final: 0.7940 (p90) REVERT: R 112 TYR cc_start: 0.8571 (t80) cc_final: 0.8304 (t80) REVERT: R 131 ASP cc_start: 0.8130 (m-30) cc_final: 0.7882 (t0) REVERT: S 32 ASN cc_start: 0.7023 (m-40) cc_final: 0.6374 (t0) REVERT: S 33 ILE cc_start: 0.6284 (OUTLIER) cc_final: 0.5764 (mp) REVERT: S 93 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8417 (pt) REVERT: S 122 LYS cc_start: 0.7178 (tppt) cc_final: 0.6713 (mttm) REVERT: S 151 LYS cc_start: 0.5911 (pttp) cc_final: 0.5046 (pptt) REVERT: S 162 ASP cc_start: 0.7525 (m-30) cc_final: 0.7324 (m-30) REVERT: Q 112 TYR cc_start: 0.8539 (t80) cc_final: 0.8238 (t80) REVERT: Q 124 LYS cc_start: 0.7888 (mptt) cc_final: 0.7432 (mptt) REVERT: P 5 ARG cc_start: 0.8515 (tpp-160) cc_final: 0.8270 (tpp-160) REVERT: P 84 LEU cc_start: 0.7897 (tp) cc_final: 0.7417 (tp) REVERT: P 86 LEU cc_start: 0.7780 (mm) cc_final: 0.7555 (OUTLIER) REVERT: W 6 GLU cc_start: 0.7324 (tm-30) cc_final: 0.6923 (tm-30) REVERT: W 161 GLU cc_start: 0.8600 (tt0) cc_final: 0.8386 (tm-30) REVERT: T 79 GLN cc_start: 0.6440 (tm-30) cc_final: 0.6145 (tm-30) REVERT: T 81 ASN cc_start: 0.7363 (m110) cc_final: 0.6651 (p0) REVERT: T 142 PHE cc_start: 0.7754 (m-80) cc_final: 0.7531 (m-80) REVERT: T 144 LYS cc_start: 0.7815 (mtpt) cc_final: 0.7323 (tttt) REVERT: Z 137 ILE cc_start: 0.6471 (mp) cc_final: 0.6241 (pp) REVERT: Y 38 ILE cc_start: 0.6772 (mt) cc_final: 0.6504 (mm) REVERT: Y 53 ASN cc_start: 0.6342 (t0) cc_final: 0.6032 (t0) REVERT: Y 131 ASP cc_start: 0.5917 (OUTLIER) cc_final: 0.5677 (m-30) REVERT: Y 170 TYR cc_start: 0.6694 (m-80) cc_final: 0.6489 (m-80) REVERT: r 36 ARG cc_start: 0.8139 (mpp-170) cc_final: 0.7767 (mpp-170) REVERT: r 52 LYS cc_start: 0.7696 (ttmt) cc_final: 0.7454 (mppt) REVERT: r 79 GLN cc_start: 0.7952 (tt0) cc_final: 0.7439 (tm-30) REVERT: r 82 ASP cc_start: 0.7655 (m-30) cc_final: 0.6775 (m-30) REVERT: r 149 THR cc_start: 0.5624 (p) cc_final: 0.5401 (t) REVERT: r 168 SER cc_start: 0.8859 (m) cc_final: 0.8207 (p) REVERT: s 99 LYS cc_start: 0.7249 (OUTLIER) cc_final: 0.6671 (ptmm) REVERT: s 109 TYR cc_start: 0.7123 (OUTLIER) cc_final: 0.6780 (m-80) REVERT: q 9 PHE cc_start: 0.6730 (p90) cc_final: 0.6374 (p90) REVERT: q 79 GLN cc_start: 0.6511 (mt0) cc_final: 0.6247 (tm-30) REVERT: q 147 ASN cc_start: 0.7405 (m110) cc_final: 0.6981 (m-40) REVERT: p 39 HIS cc_start: 0.7343 (m-70) cc_final: 0.7139 (m-70) REVERT: p 97 ARG cc_start: 0.8148 (mtp85) cc_final: 0.7330 (mtp180) REVERT: w 55 ARG cc_start: 0.5881 (mmt180) cc_final: 0.5635 (mmt180) REVERT: t 88 LEU cc_start: 0.8614 (mm) cc_final: 0.8368 (mm) REVERT: t 97 ARG cc_start: 0.7999 (mtt180) cc_final: 0.7557 (mtm180) REVERT: t 121 MET cc_start: 0.6351 (OUTLIER) cc_final: 0.5885 (mpt) REVERT: t 169 TYR cc_start: 0.6020 (p90) cc_final: 0.5775 (p90) REVERT: z 79 GLN cc_start: 0.2033 (OUTLIER) cc_final: 0.1737 (pm20) REVERT: y 88 LEU cc_start: 0.6673 (pp) cc_final: 0.6393 (tp) REVERT: L 104 ASP cc_start: 0.8232 (OUTLIER) cc_final: 0.7874 (m-30) REVERT: l 160 LYS cc_start: 0.8563 (pttp) cc_final: 0.8247 (pttt) REVERT: O 114 SER cc_start: 0.7868 (OUTLIER) cc_final: 0.7629 (t) REVERT: o 55 ARG cc_start: 0.6787 (pmm-80) cc_final: 0.6532 (mpp80) REVERT: N 12 ILE cc_start: 0.6924 (OUTLIER) cc_final: 0.6544 (pp) REVERT: X 106 LEU cc_start: 0.6412 (OUTLIER) cc_final: 0.6054 (tm) outliers start: 313 outliers final: 133 residues processed: 1429 average time/residue: 1.1861 time to fit residues: 2318.8466 Evaluate side-chains 1200 residues out of total 7465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 1048 time to evaluate : 5.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain C residue 5 GLU Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 31 ASP Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 127 SER Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 105 LYS Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain F residue 205 SER Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain G residue 250 SER Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 111 TYR Chi-restraints excluded: chain H residue 125 LYS Chi-restraints excluded: chain H residue 147 ARG Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 129 SER Chi-restraints excluded: chain I residue 275 GLU Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 103 VAL Chi-restraints excluded: chain J residue 123 PHE Chi-restraints excluded: chain J residue 171 SER Chi-restraints excluded: chain J residue 283 SER Chi-restraints excluded: chain J residue 357 ILE Chi-restraints excluded: chain J residue 362 THR Chi-restraints excluded: chain J residue 466 CYS Chi-restraints excluded: chain J residue 475 VAL Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain K residue 91 ARG Chi-restraints excluded: chain K residue 282 ILE Chi-restraints excluded: chain K residue 284 GLU Chi-restraints excluded: chain K residue 386 LEU Chi-restraints excluded: chain K residue 594 VAL Chi-restraints excluded: chain K residue 803 ASP Chi-restraints excluded: chain K residue 885 LYS Chi-restraints excluded: chain K residue 915 SER Chi-restraints excluded: chain K residue 929 VAL Chi-restraints excluded: chain K residue 933 ASN Chi-restraints excluded: chain K residue 988 ARG Chi-restraints excluded: chain M residue 8 VAL Chi-restraints excluded: chain M residue 10 ILE Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 159 VAL Chi-restraints excluded: chain M residue 168 SER Chi-restraints excluded: chain R residue 9 PHE Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 132 THR Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 31 THR Chi-restraints excluded: chain S residue 33 ILE Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 63 CYS Chi-restraints excluded: chain S residue 93 LEU Chi-restraints excluded: chain S residue 114 SER Chi-restraints excluded: chain S residue 172 LEU Chi-restraints excluded: chain P residue 12 ILE Chi-restraints excluded: chain P residue 81 ASN Chi-restraints excluded: chain P residue 130 ASP Chi-restraints excluded: chain P residue 135 ASN Chi-restraints excluded: chain W residue 16 ILE Chi-restraints excluded: chain W residue 43 VAL Chi-restraints excluded: chain W residue 127 SER Chi-restraints excluded: chain T residue 8 VAL Chi-restraints excluded: chain T residue 42 LEU Chi-restraints excluded: chain Z residue 8 VAL Chi-restraints excluded: chain Y residue 74 THR Chi-restraints excluded: chain Y residue 131 ASP Chi-restraints excluded: chain r residue 31 THR Chi-restraints excluded: chain r residue 59 THR Chi-restraints excluded: chain r residue 74 THR Chi-restraints excluded: chain r residue 131 ASP Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain s residue 99 LYS Chi-restraints excluded: chain s residue 109 TYR Chi-restraints excluded: chain s residue 119 ASN Chi-restraints excluded: chain s residue 123 THR Chi-restraints excluded: chain q residue 8 VAL Chi-restraints excluded: chain q residue 16 ILE Chi-restraints excluded: chain q residue 17 THR Chi-restraints excluded: chain q residue 168 SER Chi-restraints excluded: chain p residue 40 ASN Chi-restraints excluded: chain p residue 55 ARG Chi-restraints excluded: chain p residue 104 ASP Chi-restraints excluded: chain p residue 134 VAL Chi-restraints excluded: chain w residue 3 THR Chi-restraints excluded: chain w residue 4 GLN Chi-restraints excluded: chain t residue 81 ASN Chi-restraints excluded: chain t residue 95 LEU Chi-restraints excluded: chain t residue 108 ILE Chi-restraints excluded: chain t residue 121 MET Chi-restraints excluded: chain z residue 16 ILE Chi-restraints excluded: chain z residue 45 THR Chi-restraints excluded: chain z residue 79 GLN Chi-restraints excluded: chain z residue 134 VAL Chi-restraints excluded: chain y residue 8 VAL Chi-restraints excluded: chain y residue 30 ILE Chi-restraints excluded: chain y residue 105 ASP Chi-restraints excluded: chain m residue 152 GLU Chi-restraints excluded: chain m residue 153 LYS Chi-restraints excluded: chain L residue 104 ASP Chi-restraints excluded: chain L residue 108 ILE Chi-restraints excluded: chain L residue 156 ILE Chi-restraints excluded: chain l residue 66 VAL Chi-restraints excluded: chain l residue 154 VAL Chi-restraints excluded: chain l residue 163 ILE Chi-restraints excluded: chain O residue 32 ASN Chi-restraints excluded: chain O residue 53 ASN Chi-restraints excluded: chain O residue 63 CYS Chi-restraints excluded: chain O residue 114 SER Chi-restraints excluded: chain O residue 123 THR Chi-restraints excluded: chain o residue 12 ILE Chi-restraints excluded: chain o residue 38 ILE Chi-restraints excluded: chain o residue 94 TYR Chi-restraints excluded: chain o residue 108 ILE Chi-restraints excluded: chain o residue 155 LYS Chi-restraints excluded: chain N residue 12 ILE Chi-restraints excluded: chain N residue 29 HIS Chi-restraints excluded: chain N residue 113 SER Chi-restraints excluded: chain N residue 127 SER Chi-restraints excluded: chain N residue 149 THR Chi-restraints excluded: chain N residue 163 ILE Chi-restraints excluded: chain n residue 141 VAL Chi-restraints excluded: chain n residue 150 GLN Chi-restraints excluded: chain x residue 8 VAL Chi-restraints excluded: chain x residue 42 LEU Chi-restraints excluded: chain x residue 70 LEU Chi-restraints excluded: chain x residue 141 VAL Chi-restraints excluded: chain X residue 24 ILE Chi-restraints excluded: chain X residue 38 ILE Chi-restraints excluded: chain X residue 74 THR Chi-restraints excluded: chain X residue 106 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 812 random chunks: chunk 729 optimal weight: 0.2980 chunk 555 optimal weight: 0.0070 chunk 383 optimal weight: 9.9990 chunk 81 optimal weight: 0.0000 chunk 352 optimal weight: 5.9990 chunk 496 optimal weight: 9.9990 chunk 741 optimal weight: 3.9990 chunk 784 optimal weight: 0.9990 chunk 387 optimal weight: 5.9990 chunk 702 optimal weight: 7.9990 chunk 211 optimal weight: 2.9990 overall best weight: 0.8606 ------------------------------------------------------------------------------- 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: