Starting phenix.real_space_refine on Mon Mar 25 18:53:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxt_23574/03_2024/7lxt_23574_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxt_23574/03_2024/7lxt_23574.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxt_23574/03_2024/7lxt_23574.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxt_23574/03_2024/7lxt_23574.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxt_23574/03_2024/7lxt_23574_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxt_23574/03_2024/7lxt_23574_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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: 5 Type Number sf(0) Gaussians S 272 5.16 5 B 6 2.79 5 C 32182 2.51 5 N 8432 2.21 5 O 9644 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 11": "NH1" <-> "NH2" Residue "A ARG 187": "NH1" <-> "NH2" Residue "A ASP 202": "OD1" <-> "OD2" Residue "A GLU 203": "OE1" <-> "OE2" Residue "A ARG 259": "NH1" <-> "NH2" Residue "B PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 82": "OD1" <-> "OD2" Residue "B TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 177": "NH1" <-> "NH2" Residue "B ASP 181": "OD1" <-> "OD2" Residue "B GLU 205": "OE1" <-> "OE2" Residue "B TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 233": "OE1" <-> "OE2" Residue "C ARG 3": "NH1" <-> "NH2" Residue "C TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 22": "OE1" <-> "OE2" Residue "C ASP 41": "OD1" <-> "OD2" Residue "C ASP 57": "OD1" <-> "OD2" Residue "C TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 140": "OD1" <-> "OD2" Residue "C ASP 182": "OD1" <-> "OD2" Residue "C GLU 186": "OE1" <-> "OE2" Residue "C GLU 208": "OE1" <-> "OE2" Residue "C GLU 211": "OE1" <-> "OE2" Residue "C TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 219": "OD1" <-> "OD2" Residue "C TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 231": "OE1" <-> "OE2" Residue "D TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 181": "OE1" <-> "OE2" Residue "D PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 198": "OE1" <-> "OE2" Residue "D GLU 205": "OE1" <-> "OE2" Residue "D GLU 219": "OE1" <-> "OE2" Residue "E GLU 18": "OE1" <-> "OE2" Residue "E GLU 60": "OE1" <-> "OE2" Residue "E PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 177": "OE1" <-> "OE2" Residue "E PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 7": "OD1" <-> "OD2" Residue "F ASP 42": "OD1" <-> "OD2" Residue "F TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 163": "NH1" <-> "NH2" Residue "F PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 41": "OE1" <-> "OE2" Residue "G TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 228": "OE1" <-> "OE2" Residue "H ARG 32": "NH1" <-> "NH2" Residue "H GLU 39": "OE1" <-> "OE2" Residue "H ARG 75": "NH1" <-> "NH2" Residue "H PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 175": "OE1" <-> "OE2" Residue "H ASP 195": "OD1" <-> "OD2" Residue "H PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 75": "NH1" <-> "NH2" Residue "I ASP 144": "OD1" <-> "OD2" Residue "I ASP 174": "OD1" <-> "OD2" Residue "I TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 83": "OE1" <-> "OE2" Residue "J ASP 85": "OD1" <-> "OD2" Residue "J ASP 172": "OD1" <-> "OD2" Residue "J ASP 189": "OD1" <-> "OD2" Residue "J GLU 199": "OE1" <-> "OE2" Residue "K GLU 59": "OE1" <-> "OE2" Residue "K GLU 99": "OE1" <-> "OE2" Residue "K TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 155": "OE1" <-> "OE2" Residue "L GLU 67": "OE1" <-> "OE2" Residue "L ASP 105": "OD1" <-> "OD2" Residue "L ASP 144": "OD1" <-> "OD2" Residue "L GLU 154": "OE1" <-> "OE2" Residue "L TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 204": "OE1" <-> "OE2" Residue "M GLU 106": "OE1" <-> "OE2" Residue "M PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 178": "OD1" <-> "OD2" Residue "M ARG 180": "NH1" <-> "NH2" Residue "N GLU 57": "OE1" <-> "OE2" Residue "N ASP 60": "OD1" <-> "OD2" Residue "N GLU 83": "OE1" <-> "OE2" Residue "N ARG 97": "NH1" <-> "NH2" Residue "N ASP 124": "OD1" <-> "OD2" Residue "N ASP 157": "OD1" <-> "OD2" Residue "O ARG 11": "NH1" <-> "NH2" Residue "O ARG 187": "NH1" <-> "NH2" Residue "O ASP 202": "OD1" <-> "OD2" Residue "O GLU 203": "OE1" <-> "OE2" Residue "O ARG 259": "NH1" <-> "NH2" Residue "P PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 82": "OD1" <-> "OD2" Residue "P TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 177": "NH1" <-> "NH2" Residue "P ASP 181": "OD1" <-> "OD2" Residue "P GLU 205": "OE1" <-> "OE2" Residue "P TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 233": "OE1" <-> "OE2" Residue "Q ARG 3": "NH1" <-> "NH2" Residue "Q TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 22": "OE1" <-> "OE2" Residue "Q ASP 41": "OD1" <-> "OD2" Residue "Q ASP 57": "OD1" <-> "OD2" Residue "Q TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 140": "OD1" <-> "OD2" Residue "Q ASP 182": "OD1" <-> "OD2" Residue "Q GLU 186": "OE1" <-> "OE2" Residue "Q GLU 208": "OE1" <-> "OE2" Residue "Q GLU 211": "OE1" <-> "OE2" Residue "Q TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 219": "OD1" <-> "OD2" Residue "Q TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 231": "OE1" <-> "OE2" Residue "R TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 181": "OE1" <-> "OE2" Residue "R PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 198": "OE1" <-> "OE2" Residue "R GLU 205": "OE1" <-> "OE2" Residue "R GLU 219": "OE1" <-> "OE2" Residue "S GLU 18": "OE1" <-> "OE2" Residue "S GLU 60": "OE1" <-> "OE2" Residue "S PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 177": "OE1" <-> "OE2" Residue "S PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 7": "OD1" <-> "OD2" Residue "T ASP 42": "OD1" <-> "OD2" Residue "T TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 163": "NH1" <-> "NH2" Residue "T PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 41": "OE1" <-> "OE2" Residue "U TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 228": "OE1" <-> "OE2" Residue "V ARG 32": "NH1" <-> "NH2" Residue "V GLU 39": "OE1" <-> "OE2" Residue "V ARG 75": "NH1" <-> "NH2" Residue "V PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 175": "OE1" <-> "OE2" Residue "V ASP 195": "OD1" <-> "OD2" Residue "V PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 75": "NH1" <-> "NH2" Residue "W ASP 144": "OD1" <-> "OD2" Residue "W ASP 174": "OD1" <-> "OD2" Residue "W TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 83": "OE1" <-> "OE2" Residue "X ASP 85": "OD1" <-> "OD2" Residue "X ASP 172": "OD1" <-> "OD2" Residue "X ASP 189": "OD1" <-> "OD2" Residue "X GLU 199": "OE1" <-> "OE2" Residue "Y GLU 59": "OE1" <-> "OE2" Residue "Y GLU 99": "OE1" <-> "OE2" Residue "Y TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 155": "OE1" <-> "OE2" Residue "Z GLU 67": "OE1" <-> "OE2" Residue "Z ASP 105": "OD1" <-> "OD2" Residue "Z ASP 144": "OD1" <-> "OD2" Residue "Z GLU 154": "OE1" <-> "OE2" Residue "Z TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 204": "OE1" <-> "OE2" Residue "a GLU 106": "OE1" <-> "OE2" Residue "a PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 178": "OD1" <-> "OD2" Residue "a ARG 180": "NH1" <-> "NH2" Residue "b GLU 57": "OE1" <-> "OE2" Residue "b ASP 60": "OD1" <-> "OD2" Residue "b GLU 83": "OE1" <-> "OE2" Residue "b ARG 97": "NH1" <-> "NH2" Residue "b ASP 124": "OD1" <-> "OD2" Residue "b ASP 157": "OD1" <-> "OD2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 50536 Number of models: 1 Model: "" Number of chains: 34 Chain: "A" Number of atoms: 2001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2001 Classifications: {'peptide': 252} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 247} Chain: "B" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1805 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 7, 'TRANS': 219} Chain: "C" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1934 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 5, 'TRANS': 236} Chain: "D" Number of atoms: 1845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1845 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 7, 'TRANS': 225} Chain: "E" Number of atoms: 1802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1802 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 6, 'TRANS': 226} Chain breaks: 1 Chain: "F" Number of atoms: 1866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1866 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 5, 'TRANS': 229} Chain: "G" Number of atoms: 1968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1968 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 5, 'TRANS': 234} Chain: "H" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1772 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 1, 'TRANS': 218} Chain breaks: 1 Chain: "I" Number of atoms: 1664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1664 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 11, 'TRANS': 206} Chain: "J" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1698 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 210} Chain: "K" Number of atoms: 1614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1614 Classifications: {'peptide': 195} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 193} Chain: "L" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1647 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 1, 'TRANS': 207} Chain: "M" Number of atoms: 1696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1696 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 207} Chain: "N" Number of atoms: 1872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1872 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 5, 'TRANS': 221} Chain breaks: 1 Chain: "O" Number of atoms: 2001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2001 Classifications: {'peptide': 252} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 247} Chain: "P" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1805 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 7, 'TRANS': 219} Chain: "Q" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1934 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 5, 'TRANS': 236} Chain: "R" Number of atoms: 1845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1845 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 7, 'TRANS': 225} Chain: "S" Number of atoms: 1802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1802 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 6, 'TRANS': 226} Chain breaks: 1 Chain: "T" Number of atoms: 1866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1866 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 5, 'TRANS': 229} Chain: "U" Number of atoms: 1968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1968 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 5, 'TRANS': 234} Chain: "V" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1772 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 1, 'TRANS': 218} Chain breaks: 1 Chain: "W" Number of atoms: 1664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1664 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 11, 'TRANS': 206} Chain: "X" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1698 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 210} Chain: "Y" Number of atoms: 1614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1614 Classifications: {'peptide': 195} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 193} Chain: "Z" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1647 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 1, 'TRANS': 207} Chain: "a" Number of atoms: 1696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1696 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 207} Chain: "b" Number of atoms: 1872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1872 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 5, 'TRANS': 221} Chain breaks: 1 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Time building chain proxies: 25.57, per 1000 atoms: 0.51 Number of scatterers: 50536 At special positions: 0 Unit cell: (179.47, 145.41, 136.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 272 16.00 O 9644 8.00 N 8432 7.00 C 32182 6.00 B 6 5.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 21.14 Conformation dependent library (CDL) restraints added in 9.3 seconds 12500 Ramachandran restraints generated. 6250 Oldfield, 0 Emsley, 6250 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11856 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 172 helices and 56 sheets defined 33.5% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.10 Creating SS restraints... Processing helix chain 'A' and resid 23 through 35 removed outlier: 3.732A pdb=" N THR A 35 " --> pdb=" O ALA A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 71 No H-bonds generated for 'chain 'A' and resid 69 through 71' Processing helix chain 'A' and resid 90 through 111 removed outlier: 3.658A pdb=" N SER A 105 " --> pdb=" O ARG A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 133 removed outlier: 3.609A pdb=" N TYR A 131 " --> pdb=" O LYS A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 194 removed outlier: 3.646A pdb=" N ILE A 182 " --> pdb=" O GLU A 178 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N SER A 183 " --> pdb=" O GLN A 179 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU A 186 " --> pdb=" O ILE A 182 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU A 190 " --> pdb=" O GLU A 186 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS A 191 " --> pdb=" O ARG A 187 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ARG A 192 " --> pdb=" O LEU A 188 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 206 No H-bonds generated for 'chain 'A' and resid 204 through 206' Processing helix chain 'A' and resid 209 through 219 removed outlier: 3.810A pdb=" N THR A 218 " --> pdb=" O GLU A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 228 No H-bonds generated for 'chain 'A' and resid 226 through 228' Processing helix chain 'A' and resid 246 through 253 removed outlier: 4.249A pdb=" N ASN A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR A 252 " --> pdb=" O GLU A 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 31 removed outlier: 3.537A pdb=" N ARG B 28 " --> pdb=" O TYR B 24 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER B 31 " --> pdb=" O ASN B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 61 No H-bonds generated for 'chain 'B' and resid 59 through 61' Processing helix chain 'B' and resid 80 through 100 removed outlier: 3.607A pdb=" N VAL B 85 " --> pdb=" O GLY B 81 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU B 93 " --> pdb=" O ARG B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 123 removed outlier: 3.900A pdb=" N LYS B 112 " --> pdb=" O LYS B 108 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU B 120 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE B 121 " --> pdb=" O ILE B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 175 Processing helix chain 'B' and resid 184 through 189 removed outlier: 3.641A pdb=" N HIS B 189 " --> pdb=" O GLU B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 198 Processing helix chain 'B' and resid 225 through 228 No H-bonds generated for 'chain 'B' and resid 225 through 228' Processing helix chain 'C' and resid 3 through 5 No H-bonds generated for 'chain 'C' and resid 3 through 5' Processing helix chain 'C' and resid 19 through 29 Processing helix chain 'C' and resid 80 through 101 removed outlier: 3.986A pdb=" N ASN C 84 " --> pdb=" O ASN C 80 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ILE C 85 " --> pdb=" O ALA C 81 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU C 86 " --> pdb=" O ASP C 82 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU C 92 " --> pdb=" O ASN C 88 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU C 98 " --> pdb=" O ALA C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 120 removed outlier: 4.154A pdb=" N VAL C 111 " --> pdb=" O SER C 108 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N VAL C 112 " --> pdb=" O GLN C 109 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N CYS C 115 " --> pdb=" O VAL C 112 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASP C 116 " --> pdb=" O GLN C 113 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE C 117 " --> pdb=" O ILE C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 178 removed outlier: 3.750A pdb=" N GLN C 177 " --> pdb=" O SER C 173 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU C 178 " --> pdb=" O VAL C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 199 removed outlier: 3.935A pdb=" N LEU C 190 " --> pdb=" O GLU C 186 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU C 191 " --> pdb=" O GLU C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 241 removed outlier: 3.958A pdb=" N GLU C 233 " --> pdb=" O GLU C 229 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS C 237 " --> pdb=" O GLU C 233 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR C 240 " --> pdb=" O ILE C 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 28 removed outlier: 3.697A pdb=" N ALA D 22 " --> pdb=" O GLN D 18 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS D 28 " --> pdb=" O GLU D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 98 removed outlier: 4.560A pdb=" N ARG D 81 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N VAL D 82 " --> pdb=" O ASP D 79 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASN D 85 " --> pdb=" O VAL D 82 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ARG D 88 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N CYS D 91 " --> pdb=" O ARG D 88 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N TYR D 94 " --> pdb=" O CYS D 91 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N MET D 98 " --> pdb=" O TYR D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 118 Processing helix chain 'D' and resid 165 through 172 removed outlier: 3.570A pdb=" N PHE D 171 " --> pdb=" O ILE D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 195 removed outlier: 3.947A pdb=" N ILE D 186 " --> pdb=" O GLN D 182 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE D 194 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 233 removed outlier: 3.666A pdb=" N ASP D 230 " --> pdb=" O VAL D 226 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLN D 231 " --> pdb=" O GLU D 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 32 removed outlier: 4.482A pdb=" N GLY E 29 " --> pdb=" O GLU E 25 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ALA E 30 " --> pdb=" O TYR E 26 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LYS E 32 " --> pdb=" O LEU E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 102 removed outlier: 4.033A pdb=" N THR E 87 " --> pdb=" O ALA E 83 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LEU E 88 " --> pdb=" O ASP E 84 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR E 91 " --> pdb=" O THR E 87 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN E 97 " --> pdb=" O ARG E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 120 removed outlier: 3.549A pdb=" N LEU E 119 " --> pdb=" O LEU E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 186 removed outlier: 3.609A pdb=" N LEU E 181 " --> pdb=" O GLU E 177 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU E 182 " --> pdb=" O GLY E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 206 removed outlier: 3.676A pdb=" N ILE E 198 " --> pdb=" O GLU E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 238 Processing helix chain 'E' and resid 240 through 242 No H-bonds generated for 'chain 'E' and resid 240 through 242' Processing helix chain 'F' and resid 20 through 24 Processing helix chain 'F' and resid 29 through 31 No H-bonds generated for 'chain 'F' and resid 29 through 31' Processing helix chain 'F' and resid 78 through 98 removed outlier: 3.800A pdb=" N LEU F 84 " --> pdb=" O ASP F 80 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER F 94 " --> pdb=" O ASN F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 113 removed outlier: 3.506A pdb=" N SER F 111 " --> pdb=" O SER F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 121 removed outlier: 3.854A pdb=" N ASN F 119 " --> pdb=" O LYS F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 172 Processing helix chain 'F' and resid 176 through 179 No H-bonds generated for 'chain 'F' and resid 176 through 179' Processing helix chain 'F' and resid 183 through 197 removed outlier: 3.529A pdb=" N SER F 197 " --> pdb=" O ALA F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 236 removed outlier: 4.578A pdb=" N GLU F 230 " --> pdb=" O LEU F 226 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N TYR F 231 " --> pdb=" O GLN F 227 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER F 233 " --> pdb=" O GLU F 229 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS F 236 " --> pdb=" O LEU F 232 " (cutoff:3.500A) Processing helix chain 'G' and resid 25 through 33 Processing helix chain 'G' and resid 53 through 55 No H-bonds generated for 'chain 'G' and resid 53 through 55' Processing helix chain 'G' and resid 84 through 105 removed outlier: 3.737A pdb=" N ARG G 88 " --> pdb=" O ASP G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 125 removed outlier: 4.749A pdb=" N ASN G 116 " --> pdb=" O HIS G 112 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR G 121 " --> pdb=" O ARG G 117 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR G 125 " --> pdb=" O TYR G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 181 removed outlier: 3.547A pdb=" N THR G 177 " --> pdb=" O GLU G 173 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LYS G 181 " --> pdb=" O THR G 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 189 through 203 removed outlier: 3.786A pdb=" N ILE G 193 " --> pdb=" O VAL G 189 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N GLU G 194 " --> pdb=" O ARG G 190 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ASP G 195 " --> pdb=" O ASP G 191 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N THR G 202 " --> pdb=" O LYS G 198 " (cutoff:3.500A) Processing helix chain 'G' and resid 223 through 225 No H-bonds generated for 'chain 'G' and resid 223 through 225' Processing helix chain 'G' and resid 234 through 240 Proline residue: G 239 - end of helix Processing helix chain 'H' and resid 49 through 67 removed outlier: 3.520A pdb=" N LYS H 54 " --> pdb=" O ALA H 50 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 143 removed outlier: 3.613A pdb=" N ILE H 140 " --> pdb=" O THR H 136 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR H 141 " --> pdb=" O LYS H 137 " (cutoff:3.500A) Processing helix chain 'H' and resid 186 through 188 No H-bonds generated for 'chain 'H' and resid 186 through 188' Processing helix chain 'H' and resid 190 through 196 Processing helix chain 'H' and resid 203 through 219 Processing helix chain 'I' and resid 49 through 69 removed outlier: 3.722A pdb=" N GLU I 64 " --> pdb=" O GLN I 60 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N HIS I 66 " --> pdb=" O ASN I 62 " (cutoff:3.500A) Processing helix chain 'I' and resid 76 through 90 removed outlier: 3.746A pdb=" N SER I 81 " --> pdb=" O SER I 77 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS I 89 " --> pdb=" O GLN I 85 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TYR I 90 " --> pdb=" O GLU I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 129 through 141 removed outlier: 4.044A pdb=" N LEU I 132 " --> pdb=" O SER I 129 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET I 135 " --> pdb=" O LEU I 132 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL I 137 " --> pdb=" O ALA I 134 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA I 140 " --> pdb=" O VAL I 137 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS I 141 " --> pdb=" O LEU I 138 " (cutoff:3.500A) Processing helix chain 'I' and resid 148 through 164 removed outlier: 3.741A pdb=" N ASN I 153 " --> pdb=" O GLU I 149 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE I 164 " --> pdb=" O CYS I 160 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 80 removed outlier: 3.656A pdb=" N GLN J 63 " --> pdb=" O ALA J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 86 through 100 removed outlier: 3.982A pdb=" N TYR J 98 " --> pdb=" O SER J 94 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN J 100 " --> pdb=" O ILE J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 156 through 166 removed outlier: 4.394A pdb=" N GLY J 161 " --> pdb=" O GLU J 157 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N MET J 162 " --> pdb=" O GLN J 158 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER J 165 " --> pdb=" O GLY J 161 " (cutoff:3.500A) Processing helix chain 'J' and resid 173 through 188 removed outlier: 4.263A pdb=" N GLU J 178 " --> pdb=" O ASN J 174 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N CYS J 183 " --> pdb=" O THR J 179 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER J 186 " --> pdb=" O GLN J 182 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ALA J 187 " --> pdb=" O CYS J 183 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 71 removed outlier: 3.878A pdb=" N GLN K 56 " --> pdb=" O GLY K 52 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU K 59 " --> pdb=" O LEU K 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 91 removed outlier: 3.536A pdb=" N LYS K 87 " --> pdb=" O PHE K 83 " (cutoff:3.500A) Processing helix chain 'K' and resid 134 through 146 removed outlier: 3.539A pdb=" N TYR K 137 " --> pdb=" O TYR K 134 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL K 139 " --> pdb=" O ALA K 136 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N SER K 140 " --> pdb=" O TYR K 137 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA K 141 " --> pdb=" O LEU K 138 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS K 145 " --> pdb=" O ILE K 142 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR K 146 " --> pdb=" O LEU K 143 " (cutoff:3.500A) Processing helix chain 'K' and resid 153 through 170 removed outlier: 3.572A pdb=" N GLU K 166 " --> pdb=" O LEU K 162 " (cutoff:3.500A) Processing helix chain 'L' and resid 50 through 69 removed outlier: 4.971A pdb=" N TRP L 55 " --> pdb=" O ASP L 51 " (cutoff:3.500A) Processing helix chain 'L' and resid 76 through 90 removed outlier: 4.395A pdb=" N TYR L 90 " --> pdb=" O ILE L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 140 removed outlier: 4.458A pdb=" N THR L 133 " --> pdb=" O SER L 130 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR L 136 " --> pdb=" O THR L 133 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP L 140 " --> pdb=" O SER L 137 " (cutoff:3.500A) Processing helix chain 'L' and resid 149 through 166 Processing helix chain 'L' and resid 195 through 198 No H-bonds generated for 'chain 'L' and resid 195 through 198' Processing helix chain 'M' and resid 86 through 107 removed outlier: 3.603A pdb=" N LEU M 95 " --> pdb=" O THR M 91 " (cutoff:3.500A) Processing helix chain 'M' and resid 113 through 130 removed outlier: 3.861A pdb=" N ARG M 127 " --> pdb=" O ILE M 123 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG M 128 " --> pdb=" O LEU M 124 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N PHE M 129 " --> pdb=" O TYR M 125 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N PHE M 130 " --> pdb=" O SER M 126 " (cutoff:3.500A) Processing helix chain 'M' and resid 168 through 179 removed outlier: 4.212A pdb=" N GLN M 171 " --> pdb=" O SER M 168 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N LEU M 174 " --> pdb=" O GLN M 171 " (cutoff:3.500A) Proline residue: M 175 - end of helix Processing helix chain 'M' and resid 195 through 212 removed outlier: 4.117A pdb=" N ASN M 200 " --> pdb=" O GLY M 196 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR M 210 " --> pdb=" O ILE M 206 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU M 211 " --> pdb=" O THR M 207 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG M 212 " --> pdb=" O SER M 208 " (cutoff:3.500A) Processing helix chain 'N' and resid 58 through 77 removed outlier: 3.586A pdb=" N GLN N 62 " --> pdb=" O LEU N 58 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR N 63 " --> pdb=" O ALA N 59 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU N 66 " --> pdb=" O GLN N 62 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE N 73 " --> pdb=" O THR N 69 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 84 No H-bonds generated for 'chain 'N' and resid 82 through 84' Processing helix chain 'N' and resid 88 through 104 removed outlier: 3.685A pdb=" N ARG N 97 " --> pdb=" O SER N 93 " (cutoff:3.500A) Processing helix chain 'N' and resid 181 through 183 No H-bonds generated for 'chain 'N' and resid 181 through 183' Processing helix chain 'N' and resid 185 through 192 removed outlier: 3.599A pdb=" N ASP N 191 " --> pdb=" O THR N 187 " (cutoff:3.500A) Processing helix chain 'N' and resid 199 through 216 removed outlier: 4.049A pdb=" N ILE N 212 " --> pdb=" O GLU N 208 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE N 215 " --> pdb=" O ARG N 211 " (cutoff:3.500A) Processing helix chain 'O' and resid 23 through 35 removed outlier: 3.731A pdb=" N THR O 35 " --> pdb=" O ALA O 31 " (cutoff:3.500A) Processing helix chain 'O' and resid 69 through 71 No H-bonds generated for 'chain 'O' and resid 69 through 71' Processing helix chain 'O' and resid 90 through 111 removed outlier: 3.657A pdb=" N SER O 105 " --> pdb=" O ARG O 101 " (cutoff:3.500A) Processing helix chain 'O' and resid 119 through 133 removed outlier: 3.609A pdb=" N TYR O 131 " --> pdb=" O LYS O 127 " (cutoff:3.500A) Processing helix chain 'O' and resid 178 through 194 removed outlier: 3.646A pdb=" N ILE O 182 " --> pdb=" O GLU O 178 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N SER O 183 " --> pdb=" O GLN O 179 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU O 186 " --> pdb=" O ILE O 182 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU O 190 " --> pdb=" O GLU O 186 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS O 191 " --> pdb=" O ARG O 187 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ARG O 192 " --> pdb=" O LEU O 188 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS O 193 " --> pdb=" O LEU O 189 " (cutoff:3.500A) Processing helix chain 'O' and resid 204 through 206 No H-bonds generated for 'chain 'O' and resid 204 through 206' Processing helix chain 'O' and resid 209 through 219 removed outlier: 3.809A pdb=" N THR O 218 " --> pdb=" O GLU O 214 " (cutoff:3.500A) Processing helix chain 'O' and resid 226 through 228 No H-bonds generated for 'chain 'O' and resid 226 through 228' Processing helix chain 'O' and resid 246 through 253 removed outlier: 4.249A pdb=" N ASN O 251 " --> pdb=" O LYS O 247 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR O 252 " --> pdb=" O GLU O 248 " (cutoff:3.500A) Processing helix chain 'P' and resid 20 through 31 removed outlier: 3.536A pdb=" N ARG P 28 " --> pdb=" O TYR P 24 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER P 31 " --> pdb=" O ASN P 27 " (cutoff:3.500A) Processing helix chain 'P' and resid 59 through 61 No H-bonds generated for 'chain 'P' and resid 59 through 61' Processing helix chain 'P' and resid 80 through 100 removed outlier: 3.607A pdb=" N VAL P 85 " --> pdb=" O GLY P 81 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU P 93 " --> pdb=" O ARG P 89 " (cutoff:3.500A) Processing helix chain 'P' and resid 107 through 123 removed outlier: 3.901A pdb=" N LYS P 112 " --> pdb=" O LYS P 108 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU P 120 " --> pdb=" O SER P 116 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE P 121 " --> pdb=" O ILE P 117 " (cutoff:3.500A) Processing helix chain 'P' and resid 167 through 175 Processing helix chain 'P' and resid 184 through 189 removed outlier: 3.642A pdb=" N HIS P 189 " --> pdb=" O GLU P 185 " (cutoff:3.500A) Processing helix chain 'P' and resid 192 through 198 Processing helix chain 'P' and resid 225 through 228 No H-bonds generated for 'chain 'P' and resid 225 through 228' Processing helix chain 'Q' and resid 3 through 5 No H-bonds generated for 'chain 'Q' and resid 3 through 5' Processing helix chain 'Q' and resid 19 through 29 Processing helix chain 'Q' and resid 80 through 101 removed outlier: 3.987A pdb=" N ASN Q 84 " --> pdb=" O ASN Q 80 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ILE Q 85 " --> pdb=" O ALA Q 81 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU Q 86 " --> pdb=" O ASP Q 82 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU Q 92 " --> pdb=" O ASN Q 88 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU Q 98 " --> pdb=" O ALA Q 94 " (cutoff:3.500A) Processing helix chain 'Q' and resid 107 through 120 removed outlier: 4.155A pdb=" N VAL Q 111 " --> pdb=" O SER Q 108 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N VAL Q 112 " --> pdb=" O GLN Q 109 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N CYS Q 115 " --> pdb=" O VAL Q 112 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASP Q 116 " --> pdb=" O GLN Q 113 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE Q 117 " --> pdb=" O ILE Q 114 " (cutoff:3.500A) Processing helix chain 'Q' and resid 168 through 178 removed outlier: 3.749A pdb=" N GLN Q 177 " --> pdb=" O SER Q 173 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU Q 178 " --> pdb=" O VAL Q 174 " (cutoff:3.500A) Processing helix chain 'Q' and resid 185 through 199 removed outlier: 3.934A pdb=" N LEU Q 190 " --> pdb=" O GLU Q 186 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU Q 191 " --> pdb=" O GLU Q 187 " (cutoff:3.500A) Processing helix chain 'Q' and resid 228 through 241 removed outlier: 3.959A pdb=" N GLU Q 233 " --> pdb=" O GLU Q 229 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS Q 237 " --> pdb=" O GLU Q 233 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR Q 240 " --> pdb=" O ILE Q 236 " (cutoff:3.500A) Processing helix chain 'R' and resid 17 through 28 removed outlier: 3.696A pdb=" N ALA R 22 " --> pdb=" O GLN R 18 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS R 28 " --> pdb=" O GLU R 24 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 98 removed outlier: 4.560A pdb=" N ARG R 81 " --> pdb=" O ALA R 78 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N VAL R 82 " --> pdb=" O ASP R 79 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASN R 85 " --> pdb=" O VAL R 82 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ARG R 88 " --> pdb=" O ASN R 85 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N CYS R 91 " --> pdb=" O ARG R 88 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N TYR R 94 " --> pdb=" O CYS R 91 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N MET R 98 " --> pdb=" O TYR R 95 " (cutoff:3.500A) Processing helix chain 'R' and resid 104 through 118 Processing helix chain 'R' and resid 165 through 172 removed outlier: 3.570A pdb=" N PHE R 171 " --> pdb=" O ILE R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 182 through 195 removed outlier: 3.946A pdb=" N ILE R 186 " --> pdb=" O GLN R 182 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE R 194 " --> pdb=" O LEU R 190 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU R 195 " --> pdb=" O LYS R 191 " (cutoff:3.500A) Processing helix chain 'R' and resid 219 through 233 removed outlier: 3.666A pdb=" N ASP R 230 " --> pdb=" O VAL R 226 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLN R 231 " --> pdb=" O GLU R 227 " (cutoff:3.500A) Processing helix chain 'S' and resid 22 through 32 removed outlier: 4.481A pdb=" N GLY S 29 " --> pdb=" O GLU S 25 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA S 30 " --> pdb=" O TYR S 26 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LYS S 32 " --> pdb=" O LEU S 28 " (cutoff:3.500A) Processing helix chain 'S' and resid 82 through 102 removed outlier: 4.034A pdb=" N THR S 87 " --> pdb=" O ALA S 83 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LEU S 88 " --> pdb=" O ASP S 84 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR S 91 " --> pdb=" O THR S 87 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN S 97 " --> pdb=" O ARG S 93 " (cutoff:3.500A) Processing helix chain 'S' and resid 109 through 120 removed outlier: 3.547A pdb=" N LEU S 119 " --> pdb=" O LEU S 115 " (cutoff:3.500A) Processing helix chain 'S' and resid 176 through 186 removed outlier: 3.608A pdb=" N LEU S 181 " --> pdb=" O GLU S 177 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU S 182 " --> pdb=" O GLY S 178 " (cutoff:3.500A) Processing helix chain 'S' and resid 193 through 206 removed outlier: 3.676A pdb=" N ILE S 198 " --> pdb=" O GLU S 194 " (cutoff:3.500A) Processing helix chain 'S' and resid 234 through 238 Processing helix chain 'S' and resid 240 through 242 No H-bonds generated for 'chain 'S' and resid 240 through 242' Processing helix chain 'T' and resid 20 through 24 Processing helix chain 'T' and resid 29 through 31 No H-bonds generated for 'chain 'T' and resid 29 through 31' Processing helix chain 'T' and resid 78 through 98 removed outlier: 3.800A pdb=" N LEU T 84 " --> pdb=" O ASP T 80 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER T 94 " --> pdb=" O ASN T 90 " (cutoff:3.500A) Processing helix chain 'T' and resid 105 through 113 removed outlier: 3.507A pdb=" N SER T 111 " --> pdb=" O SER T 107 " (cutoff:3.500A) Processing helix chain 'T' and resid 115 through 121 removed outlier: 3.853A pdb=" N ASN T 119 " --> pdb=" O LYS T 115 " (cutoff:3.500A) Processing helix chain 'T' and resid 164 through 172 Processing helix chain 'T' and resid 176 through 179 No H-bonds generated for 'chain 'T' and resid 176 through 179' Processing helix chain 'T' and resid 183 through 197 removed outlier: 3.529A pdb=" N SER T 197 " --> pdb=" O ALA T 193 " (cutoff:3.500A) Processing helix chain 'T' and resid 225 through 236 removed outlier: 4.579A pdb=" N GLU T 230 " --> pdb=" O LEU T 226 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N TYR T 231 " --> pdb=" O GLN T 227 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER T 233 " --> pdb=" O GLU T 229 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS T 236 " --> pdb=" O LEU T 232 " (cutoff:3.500A) Processing helix chain 'U' and resid 25 through 33 Processing helix chain 'U' and resid 53 through 55 No H-bonds generated for 'chain 'U' and resid 53 through 55' Processing helix chain 'U' and resid 84 through 105 removed outlier: 3.736A pdb=" N ARG U 88 " --> pdb=" O ASP U 84 " (cutoff:3.500A) Processing helix chain 'U' and resid 111 through 125 removed outlier: 4.749A pdb=" N ASN U 116 " --> pdb=" O HIS U 112 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR U 121 " --> pdb=" O ARG U 117 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR U 125 " --> pdb=" O TYR U 121 " (cutoff:3.500A) Processing helix chain 'U' and resid 172 through 181 removed outlier: 3.547A pdb=" N THR U 177 " --> pdb=" O GLU U 173 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LYS U 181 " --> pdb=" O THR U 177 " (cutoff:3.500A) Processing helix chain 'U' and resid 189 through 203 removed outlier: 3.787A pdb=" N ILE U 193 " --> pdb=" O VAL U 189 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N GLU U 194 " --> pdb=" O ARG U 190 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ASP U 195 " --> pdb=" O ASP U 191 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N THR U 202 " --> pdb=" O LYS U 198 " (cutoff:3.500A) Processing helix chain 'U' and resid 223 through 225 No H-bonds generated for 'chain 'U' and resid 223 through 225' Processing helix chain 'U' and resid 234 through 240 Proline residue: U 239 - end of helix Processing helix chain 'V' and resid 49 through 67 removed outlier: 3.520A pdb=" N LYS V 54 " --> pdb=" O ALA V 50 " (cutoff:3.500A) Processing helix chain 'V' and resid 132 through 143 removed outlier: 3.612A pdb=" N ILE V 140 " --> pdb=" O THR V 136 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR V 141 " --> pdb=" O LYS V 137 " (cutoff:3.500A) Processing helix chain 'V' and resid 186 through 188 No H-bonds generated for 'chain 'V' and resid 186 through 188' Processing helix chain 'V' and resid 190 through 196 Processing helix chain 'V' and resid 203 through 219 Processing helix chain 'W' and resid 49 through 69 removed outlier: 3.723A pdb=" N GLU W 64 " --> pdb=" O GLN W 60 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N HIS W 66 " --> pdb=" O ASN W 62 " (cutoff:3.500A) Processing helix chain 'W' and resid 76 through 90 removed outlier: 3.746A pdb=" N SER W 81 " --> pdb=" O SER W 77 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS W 89 " --> pdb=" O GLN W 85 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TYR W 90 " --> pdb=" O GLU W 86 " (cutoff:3.500A) Processing helix chain 'W' and resid 129 through 141 removed outlier: 4.044A pdb=" N LEU W 132 " --> pdb=" O SER W 129 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N MET W 135 " --> pdb=" O LEU W 132 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL W 137 " --> pdb=" O ALA W 134 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA W 140 " --> pdb=" O VAL W 137 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS W 141 " --> pdb=" O LEU W 138 " (cutoff:3.500A) Processing helix chain 'W' and resid 148 through 164 removed outlier: 3.742A pdb=" N ASN W 153 " --> pdb=" O GLU W 149 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE W 164 " --> pdb=" O CYS W 160 " (cutoff:3.500A) Processing helix chain 'X' and resid 59 through 80 removed outlier: 3.657A pdb=" N GLN X 63 " --> pdb=" O ALA X 59 " (cutoff:3.500A) Processing helix chain 'X' and resid 86 through 100 removed outlier: 3.981A pdb=" N TYR X 98 " --> pdb=" O SER X 94 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN X 100 " --> pdb=" O ILE X 96 " (cutoff:3.500A) Processing helix chain 'X' and resid 156 through 166 removed outlier: 4.395A pdb=" N GLY X 161 " --> pdb=" O GLU X 157 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N MET X 162 " --> pdb=" O GLN X 158 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER X 165 " --> pdb=" O GLY X 161 " (cutoff:3.500A) Processing helix chain 'X' and resid 173 through 188 removed outlier: 4.263A pdb=" N GLU X 178 " --> pdb=" O ASN X 174 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N CYS X 183 " --> pdb=" O THR X 179 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER X 186 " --> pdb=" O GLN X 182 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ALA X 187 " --> pdb=" O CYS X 183 " (cutoff:3.500A) Processing helix chain 'Y' and resid 51 through 71 removed outlier: 3.878A pdb=" N GLN Y 56 " --> pdb=" O GLY Y 52 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU Y 59 " --> pdb=" O LEU Y 55 " (cutoff:3.500A) Processing helix chain 'Y' and resid 78 through 91 removed outlier: 3.536A pdb=" N LYS Y 87 " --> pdb=" O PHE Y 83 " (cutoff:3.500A) Processing helix chain 'Y' and resid 134 through 146 removed outlier: 3.540A pdb=" N TYR Y 137 " --> pdb=" O TYR Y 134 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL Y 139 " --> pdb=" O ALA Y 136 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N SER Y 140 " --> pdb=" O TYR Y 137 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ALA Y 141 " --> pdb=" O LEU Y 138 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS Y 145 " --> pdb=" O ILE Y 142 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR Y 146 " --> pdb=" O LEU Y 143 " (cutoff:3.500A) Processing helix chain 'Y' and resid 153 through 170 removed outlier: 3.571A pdb=" N GLU Y 166 " --> pdb=" O LEU Y 162 " (cutoff:3.500A) Processing helix chain 'Z' and resid 50 through 69 removed outlier: 4.970A pdb=" N TRP Z 55 " --> pdb=" O ASP Z 51 " (cutoff:3.500A) Processing helix chain 'Z' and resid 76 through 90 removed outlier: 4.393A pdb=" N TYR Z 90 " --> pdb=" O ILE Z 86 " (cutoff:3.500A) Processing helix chain 'Z' and resid 130 through 140 removed outlier: 4.459A pdb=" N THR Z 133 " --> pdb=" O SER Z 130 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR Z 136 " --> pdb=" O THR Z 133 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP Z 140 " --> pdb=" O SER Z 137 " (cutoff:3.500A) Processing helix chain 'Z' and resid 149 through 166 Processing helix chain 'Z' and resid 195 through 198 No H-bonds generated for 'chain 'Z' and resid 195 through 198' Processing helix chain 'a' and resid 86 through 107 removed outlier: 3.603A pdb=" N LEU a 95 " --> pdb=" O THR a 91 " (cutoff:3.500A) Processing helix chain 'a' and resid 113 through 130 removed outlier: 3.861A pdb=" N ARG a 127 " --> pdb=" O ILE a 123 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG a 128 " --> pdb=" O LEU a 124 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N PHE a 129 " --> pdb=" O TYR a 125 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N PHE a 130 " --> pdb=" O SER a 126 " (cutoff:3.500A) Processing helix chain 'a' and resid 168 through 179 removed outlier: 4.212A pdb=" N GLN a 171 " --> pdb=" O SER a 168 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N LEU a 174 " --> pdb=" O GLN a 171 " (cutoff:3.500A) Proline residue: a 175 - end of helix Processing helix chain 'a' and resid 195 through 212 removed outlier: 4.117A pdb=" N ASN a 200 " --> pdb=" O GLY a 196 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR a 210 " --> pdb=" O ILE a 206 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU a 211 " --> pdb=" O THR a 207 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG a 212 " --> pdb=" O SER a 208 " (cutoff:3.500A) Processing helix chain 'b' and resid 58 through 77 removed outlier: 3.584A pdb=" N GLN b 62 " --> pdb=" O LEU b 58 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR b 63 " --> pdb=" O ALA b 59 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU b 66 " --> pdb=" O GLN b 62 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE b 73 " --> pdb=" O THR b 69 " (cutoff:3.500A) Processing helix chain 'b' and resid 82 through 84 No H-bonds generated for 'chain 'b' and resid 82 through 84' Processing helix chain 'b' and resid 88 through 104 removed outlier: 3.685A pdb=" N ARG b 97 " --> pdb=" O SER b 93 " (cutoff:3.500A) Processing helix chain 'b' and resid 181 through 183 No H-bonds generated for 'chain 'b' and resid 181 through 183' Processing helix chain 'b' and resid 185 through 192 removed outlier: 3.598A pdb=" N ASP b 191 " --> pdb=" O THR b 187 " (cutoff:3.500A) Processing helix chain 'b' and resid 199 through 216 removed outlier: 4.050A pdb=" N ILE b 212 " --> pdb=" O GLU b 208 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE b 215 " --> pdb=" O ARG b 211 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 47 through 52 removed outlier: 3.747A pdb=" N CYS A 47 " --> pdb=" O GLY A 44 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 83 through 88 removed outlier: 3.548A pdb=" N GLY A 148 " --> pdb=" O GLU A 156 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 160 through 162 Processing sheet with id= D, first strand: chain 'B' and resid 72 through 78 Processing sheet with id= E, first strand: chain 'C' and resid 34 through 38 Processing sheet with id= F, first strand: chain 'C' and resid 72 through 78 removed outlier: 3.679A pdb=" N SER C 133 " --> pdb=" O ALA C 77 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU C 147 " --> pdb=" O TRP C 159 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 32 through 35 Processing sheet with id= H, first strand: chain 'D' and resid 132 through 136 removed outlier: 3.894A pdb=" N ILE D 144 " --> pdb=" O TRP D 156 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA D 154 " --> pdb=" O GLN D 146 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 169 through 172 removed outlier: 3.527A pdb=" N VAL E 46 " --> pdb=" O ILE E 222 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 35 through 39 Processing sheet with id= K, first strand: chain 'F' and resid 132 through 137 removed outlier: 3.565A pdb=" N LEU F 132 " --> pdb=" O THR F 146 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR F 146 " --> pdb=" O LEU F 132 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE F 143 " --> pdb=" O TYR F 155 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 46 through 51 removed outlier: 3.580A pdb=" N THR G 36 " --> pdb=" O ILE G 51 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 70 through 72 removed outlier: 3.571A pdb=" N SER G 81 " --> pdb=" O SER G 137 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER G 137 " --> pdb=" O SER G 81 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE G 151 " --> pdb=" O TYR G 163 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'H' and resid 179 through 182 removed outlier: 3.605A pdb=" N ILE H 3 " --> pdb=" O SER H 182 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY H 11 " --> pdb=" O TYR H 8 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU H 239 " --> pdb=" O ASN H 232 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE H 237 " --> pdb=" O THR H 234 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 41 through 44 removed outlier: 3.521A pdb=" N GLN H 163 " --> pdb=" O GLY H 155 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'I' and resid 2 through 6 Processing sheet with id= Q, first strand: chain 'I' and resid 119 through 121 removed outlier: 3.565A pdb=" N VAL I 99 " --> pdb=" O ALA I 44 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N CYS I 43 " --> pdb=" O TYR I 36 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N TYR I 36 " --> pdb=" O CYS I 43 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'J' and resid 150 through 153 Processing sheet with id= S, first strand: chain 'J' and resid 110 through 112 removed outlier: 6.929A pdb=" N VAL J 53 " --> pdb=" O LYS J 46 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N LYS J 46 " --> pdb=" O VAL J 53 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'K' and resid 129 through 132 removed outlier: 3.502A pdb=" N GLY K 6 " --> pdb=" O GLY K 130 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR K 184 " --> pdb=" O LYS K 187 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'L' and resid 98 through 100 Processing sheet with id= V, first strand: chain 'L' and resid 103 through 105 removed outlier: 3.676A pdb=" N GLY L 103 " --> pdb=" O ASN L 110 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'L' and resid 20 through 22 removed outlier: 6.411A pdb=" N MET L 22 " --> pdb=" O ILE L 26 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ILE L 26 " --> pdb=" O MET L 22 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'L' and resid 175 through 179 removed outlier: 6.967A pdb=" N HIS L 178 " --> pdb=" O LYS L 186 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N LYS L 186 " --> pdb=" O HIS L 178 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'M' and resid 163 through 167 removed outlier: 3.531A pdb=" N VAL M 166 " --> pdb=" O VAL M 40 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N THR M 39 " --> pdb=" O ASP M 54 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'M' and resid 148 through 151 removed outlier: 3.841A pdb=" N CYS M 78 " --> pdb=" O THR M 75 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE M 80 " --> pdb=" O LYS M 73 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N LYS M 73 " --> pdb=" O ILE M 80 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N SER M 82 " --> pdb=" O ILE M 71 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N ILE M 71 " --> pdb=" O SER M 82 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'N' and resid 175 through 178 removed outlier: 3.583A pdb=" N VAL N 12 " --> pdb=" O THR N 178 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'N' and resid 50 through 52 Processing sheet with id= AC, first strand: chain 'O' and resid 47 through 52 removed outlier: 3.747A pdb=" N CYS O 47 " --> pdb=" O GLY O 44 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'O' and resid 83 through 88 removed outlier: 3.549A pdb=" N GLY O 148 " --> pdb=" O GLU O 156 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'P' and resid 160 through 162 Processing sheet with id= AF, first strand: chain 'P' and resid 72 through 78 Processing sheet with id= AG, first strand: chain 'Q' and resid 34 through 38 Processing sheet with id= AH, first strand: chain 'Q' and resid 72 through 78 removed outlier: 3.679A pdb=" N SER Q 133 " --> pdb=" O ALA Q 77 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU Q 147 " --> pdb=" O TRP Q 159 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'R' and resid 32 through 35 Processing sheet with id= AJ, first strand: chain 'R' and resid 132 through 136 removed outlier: 3.893A pdb=" N ILE R 144 " --> pdb=" O TRP R 156 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA R 154 " --> pdb=" O GLN R 146 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'S' and resid 169 through 172 removed outlier: 3.528A pdb=" N VAL S 46 " --> pdb=" O ILE S 222 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'T' and resid 35 through 39 Processing sheet with id= AM, first strand: chain 'T' and resid 132 through 137 removed outlier: 3.565A pdb=" N LEU T 132 " --> pdb=" O THR T 146 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR T 146 " --> pdb=" O LEU T 132 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE T 143 " --> pdb=" O TYR T 155 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'U' and resid 46 through 51 removed outlier: 3.580A pdb=" N THR U 36 " --> pdb=" O ILE U 51 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'U' and resid 70 through 72 removed outlier: 3.570A pdb=" N SER U 81 " --> pdb=" O SER U 137 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER U 137 " --> pdb=" O SER U 81 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE U 151 " --> pdb=" O TYR U 163 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'V' and resid 179 through 182 removed outlier: 3.604A pdb=" N ILE V 3 " --> pdb=" O SER V 182 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY V 11 " --> pdb=" O TYR V 8 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU V 239 " --> pdb=" O ASN V 232 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N PHE V 237 " --> pdb=" O THR V 234 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'V' and resid 41 through 44 removed outlier: 3.520A pdb=" N GLN V 163 " --> pdb=" O GLY V 155 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'W' and resid 2 through 6 Processing sheet with id= AS, first strand: chain 'W' and resid 119 through 121 removed outlier: 3.564A pdb=" N VAL W 99 " --> pdb=" O ALA W 44 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N CYS W 43 " --> pdb=" O TYR W 36 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N TYR W 36 " --> pdb=" O CYS W 43 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'X' and resid 150 through 153 Processing sheet with id= AU, first strand: chain 'X' and resid 110 through 112 removed outlier: 6.930A pdb=" N VAL X 53 " --> pdb=" O LYS X 46 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N LYS X 46 " --> pdb=" O VAL X 53 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'Y' and resid 129 through 132 removed outlier: 3.503A pdb=" N GLY Y 6 " --> pdb=" O GLY Y 130 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR Y 184 " --> pdb=" O LYS Y 187 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'Z' and resid 98 through 100 Processing sheet with id= AX, first strand: chain 'Z' and resid 103 through 105 removed outlier: 3.676A pdb=" N GLY Z 103 " --> pdb=" O ASN Z 110 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'Z' and resid 20 through 22 removed outlier: 6.411A pdb=" N MET Z 22 " --> pdb=" O ILE Z 26 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ILE Z 26 " --> pdb=" O MET Z 22 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'Z' and resid 175 through 179 removed outlier: 6.967A pdb=" N HIS Z 178 " --> pdb=" O LYS Z 186 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N LYS Z 186 " --> pdb=" O HIS Z 178 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'a' and resid 163 through 167 removed outlier: 3.531A pdb=" N VAL a 166 " --> pdb=" O VAL a 40 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N THR a 39 " --> pdb=" O ASP a 54 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'a' and resid 148 through 151 removed outlier: 3.842A pdb=" N CYS a 78 " --> pdb=" O THR a 75 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE a 80 " --> pdb=" O LYS a 73 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N LYS a 73 " --> pdb=" O ILE a 80 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N SER a 82 " --> pdb=" O ILE a 71 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N ILE a 71 " --> pdb=" O SER a 82 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'b' and resid 175 through 178 removed outlier: 3.584A pdb=" N VAL b 12 " --> pdb=" O THR b 178 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'b' and resid 50 through 52 1714 hydrogen bonds defined for protein. 4758 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: 18.96 Time building geometry restraints manager: 22.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 8482 1.30 - 1.43: 13279 1.43 - 1.55: 29305 1.55 - 1.68: 12 1.68 - 1.81: 386 Bond restraints: 51464 Sorted by residual: bond pdb=" C18 BO2 W 301 " pdb=" N20 BO2 W 301 " ideal model delta sigma weight residual 1.342 1.445 -0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" C18 BO2 I 301 " pdb=" N20 BO2 I 301 " ideal model delta sigma weight residual 1.342 1.445 -0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" C7 BO2 H 301 " pdb=" N9 BO2 H 301 " ideal model delta sigma weight residual 1.339 1.441 -0.102 2.00e-02 2.50e+03 2.62e+01 bond pdb=" C7 BO2 W 301 " pdb=" N9 BO2 W 301 " ideal model delta sigma weight residual 1.339 1.441 -0.102 2.00e-02 2.50e+03 2.61e+01 bond pdb=" C7 BO2 V 301 " pdb=" N9 BO2 V 301 " ideal model delta sigma weight residual 1.339 1.441 -0.102 2.00e-02 2.50e+03 2.60e+01 ... (remaining 51459 not shown) Histogram of bond angle deviations from ideal: 96.98 - 104.40: 440 104.40 - 111.82: 24190 111.82 - 119.23: 17677 119.23 - 126.65: 26820 126.65 - 134.07: 357 Bond angle restraints: 69484 Sorted by residual: angle pdb=" CG ARG C 8 " pdb=" CD ARG C 8 " pdb=" NE ARG C 8 " ideal model delta sigma weight residual 112.00 126.83 -14.83 2.20e+00 2.07e-01 4.54e+01 angle pdb=" CG ARG Q 8 " pdb=" CD ARG Q 8 " pdb=" NE ARG Q 8 " ideal model delta sigma weight residual 112.00 126.76 -14.76 2.20e+00 2.07e-01 4.50e+01 angle pdb=" CA LEU N 109 " pdb=" CB LEU N 109 " pdb=" CG LEU N 109 " ideal model delta sigma weight residual 116.30 133.41 -17.11 3.50e+00 8.16e-02 2.39e+01 angle pdb=" CA LEU b 109 " pdb=" CB LEU b 109 " pdb=" CG LEU b 109 " ideal model delta sigma weight residual 116.30 133.41 -17.11 3.50e+00 8.16e-02 2.39e+01 angle pdb=" CD ARG Q 8 " pdb=" NE ARG Q 8 " pdb=" CZ ARG Q 8 " ideal model delta sigma weight residual 124.40 131.01 -6.61 1.40e+00 5.10e-01 2.23e+01 ... (remaining 69479 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 27586 17.99 - 35.97: 2780 35.97 - 53.96: 466 53.96 - 71.95: 104 71.95 - 89.93: 46 Dihedral angle restraints: 30982 sinusoidal: 12446 harmonic: 18536 Sorted by residual: dihedral pdb=" CA ILE Y 22 " pdb=" C ILE Y 22 " pdb=" N ASN Y 23 " pdb=" CA ASN Y 23 " ideal model delta harmonic sigma weight residual -180.00 -149.96 -30.04 0 5.00e+00 4.00e-02 3.61e+01 dihedral pdb=" CA ILE K 22 " pdb=" C ILE K 22 " pdb=" N ASN K 23 " pdb=" CA ASN K 23 " ideal model delta harmonic sigma weight residual -180.00 -149.98 -30.02 0 5.00e+00 4.00e-02 3.61e+01 dihedral pdb=" CA PHE T 160 " pdb=" C PHE T 160 " pdb=" N GLY T 161 " pdb=" CA GLY T 161 " ideal model delta harmonic sigma weight residual 180.00 150.81 29.19 0 5.00e+00 4.00e-02 3.41e+01 ... (remaining 30979 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 5935 0.058 - 0.117: 1639 0.117 - 0.175: 173 0.175 - 0.234: 7 0.234 - 0.292: 10 Chirality restraints: 7764 Sorted by residual: chirality pdb=" C21 BO2 L 301 " pdb=" B26 BO2 L 301 " pdb=" C22 BO2 L 301 " pdb=" N20 BO2 L 301 " both_signs ideal model delta sigma weight residual False 2.49 2.78 -0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" C21 BO2 Z 301 " pdb=" B26 BO2 Z 301 " pdb=" C22 BO2 Z 301 " pdb=" N20 BO2 Z 301 " both_signs ideal model delta sigma weight residual False 2.49 2.78 -0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CG LEU T 158 " pdb=" CB LEU T 158 " pdb=" CD1 LEU T 158 " pdb=" CD2 LEU T 158 " both_signs ideal model delta sigma weight residual False -2.59 -2.88 0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 7761 not shown) Planarity restraints: 8864 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG I 187 " -0.078 5.00e-02 4.00e+02 1.19e-01 2.25e+01 pdb=" N PRO I 188 " 0.205 5.00e-02 4.00e+02 pdb=" CA PRO I 188 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO I 188 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG W 187 " -0.078 5.00e-02 4.00e+02 1.19e-01 2.25e+01 pdb=" N PRO W 188 " 0.205 5.00e-02 4.00e+02 pdb=" CA PRO W 188 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO W 188 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 156 " -0.010 2.00e-02 2.50e+03 2.48e-02 1.23e+01 pdb=" CG TYR H 156 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 TYR H 156 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR H 156 " -0.033 2.00e-02 2.50e+03 pdb=" CE1 TYR H 156 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR H 156 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR H 156 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR H 156 " 0.007 2.00e-02 2.50e+03 ... (remaining 8861 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 565 2.56 - 3.14: 44656 3.14 - 3.73: 75898 3.73 - 4.31: 111933 4.31 - 4.90: 187404 Nonbonded interactions: 420456 Sorted by model distance: nonbonded pdb=" OD1 ASP a 153 " pdb=" OG SER a 157 " model vdw 1.972 2.440 nonbonded pdb=" OD1 ASP M 153 " pdb=" OG SER M 157 " model vdw 1.972 2.440 nonbonded pdb=" OG1 THR E 36 " pdb=" OE2 GLU E 51 " model vdw 2.051 2.440 nonbonded pdb=" OG1 THR S 36 " pdb=" OE2 GLU S 51 " model vdw 2.051 2.440 nonbonded pdb=" O THR X 60 " pdb=" NH2 ARG Y 86 " model vdw 2.088 2.520 ... (remaining 420451 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 'O' } ncs_group { reference = chain 'B' selection = chain 'P' } ncs_group { reference = chain 'C' selection = chain 'Q' } ncs_group { reference = chain 'D' selection = chain 'R' } ncs_group { reference = chain 'E' selection = chain 'S' } ncs_group { reference = chain 'F' selection = chain 'T' } ncs_group { reference = chain 'G' selection = chain 'U' } ncs_group { reference = chain 'H' selection = chain 'V' } ncs_group { reference = chain 'I' selection = chain 'W' } ncs_group { reference = chain 'J' selection = chain 'X' } ncs_group { reference = chain 'K' selection = chain 'Y' } ncs_group { reference = chain 'L' selection = chain 'Z' } ncs_group { reference = chain 'M' selection = chain 'a' } ncs_group { reference = chain 'N' selection = chain 'b' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.920 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: 0.040 Extract box with map and model: 11.810 Check model and map are aligned: 0.790 Set scattering table: 0.460 Process input model: 131.270 Find NCS groups from input model: 5.730 Set up NCS constraints: 0.590 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 156.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.103 51464 Z= 0.594 Angle : 0.854 17.114 69484 Z= 0.456 Chirality : 0.051 0.292 7764 Planarity : 0.005 0.119 8864 Dihedral : 14.932 89.934 19126 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 18.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.70 % Favored : 89.26 % Rotamer: Outliers : 0.79 % Allowed : 0.65 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.10), residues: 6250 helix: -1.36 (0.11), residues: 2066 sheet: -1.88 (0.14), residues: 1346 loop : -2.29 (0.11), residues: 2838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP G 220 HIS 0.014 0.002 HIS N 167 PHE 0.041 0.003 PHE T 178 TYR 0.057 0.002 TYR H 156 ARG 0.013 0.001 ARG a 29 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12500 Ramachandran restraints generated. 6250 Oldfield, 0 Emsley, 6250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12500 Ramachandran restraints generated. 6250 Oldfield, 0 Emsley, 6250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 958 residues out of total 5552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 914 time to evaluate : 5.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 123 GLN cc_start: 0.8112 (tt0) cc_final: 0.7794 (tt0) REVERT: B 159 MET cc_start: 0.8135 (mmt) cc_final: 0.7719 (mmt) REVERT: C 41 ASP cc_start: 0.7774 (t0) cc_final: 0.7573 (t0) REVERT: D 37 SER cc_start: 0.8779 (t) cc_final: 0.8565 (t) REVERT: D 98 MET cc_start: 0.7936 (tpp) cc_final: 0.7446 (mpp) REVERT: E 205 ARG cc_start: 0.8490 (ttm110) cc_final: 0.7991 (ttm170) REVERT: F 159 SER cc_start: 0.8946 (p) cc_final: 0.8728 (p) REVERT: F 223 ILE cc_start: 0.8423 (mm) cc_final: 0.7704 (mm) REVERT: F 227 GLN cc_start: 0.8813 (tm-30) cc_final: 0.8356 (tm-30) REVERT: H 130 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8316 (pm20) REVERT: H 190 GLN cc_start: 0.8606 (tp40) cc_final: 0.8372 (tp40) REVERT: I 141 LYS cc_start: 0.8577 (mtpp) cc_final: 0.8265 (mtpp) REVERT: I 157 GLU cc_start: 0.8154 (tt0) cc_final: 0.7916 (tt0) REVERT: J 201 LEU cc_start: 0.8744 (tt) cc_final: 0.8491 (tt) REVERT: K 20 TYR cc_start: 0.8295 (m-10) cc_final: 0.7692 (m-10) REVERT: K 53 ASP cc_start: 0.8182 (m-30) cc_final: 0.7971 (m-30) REVERT: K 99 GLU cc_start: 0.7586 (tm-30) cc_final: 0.7269 (tm-30) REVERT: K 173 LEU cc_start: 0.8635 (pp) cc_final: 0.8420 (pp) REVERT: L 116 ASP cc_start: 0.7791 (p0) cc_final: 0.7501 (p0) REVERT: L 197 HIS cc_start: 0.8372 (OUTLIER) cc_final: 0.7927 (t-170) REVERT: M 29 ARG cc_start: 0.8303 (mmm160) cc_final: 0.7519 (tpm170) REVERT: M 56 ARG cc_start: 0.8954 (ttm170) cc_final: 0.8699 (ttm170) REVERT: M 59 LEU cc_start: 0.8392 (tp) cc_final: 0.8190 (tp) REVERT: Q 41 ASP cc_start: 0.7768 (t0) cc_final: 0.7544 (t0) REVERT: R 37 SER cc_start: 0.8758 (t) cc_final: 0.8525 (t) REVERT: R 153 TYR cc_start: 0.8625 (p90) cc_final: 0.8259 (p90) REVERT: S 205 ARG cc_start: 0.8439 (ttm110) cc_final: 0.7855 (ttm170) REVERT: T 7 ASP cc_start: 0.8944 (t70) cc_final: 0.8740 (t0) REVERT: T 223 ILE cc_start: 0.8425 (mm) cc_final: 0.7712 (mm) REVERT: T 227 GLN cc_start: 0.8824 (tm-30) cc_final: 0.8356 (tm-30) REVERT: V 36 ARG cc_start: 0.8733 (ttt-90) cc_final: 0.8527 (ttt-90) REVERT: V 130 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8392 (pm20) REVERT: V 190 GLN cc_start: 0.8628 (tp40) cc_final: 0.8421 (tp40) REVERT: W 104 ASP cc_start: 0.7661 (p0) cc_final: 0.6952 (p0) REVERT: Y 20 TYR cc_start: 0.8318 (m-10) cc_final: 0.7729 (m-10) REVERT: Y 53 ASP cc_start: 0.8201 (m-30) cc_final: 0.7960 (m-30) REVERT: Y 59 GLU cc_start: 0.8641 (mm-30) cc_final: 0.8131 (mm-30) REVERT: Y 69 GLN cc_start: 0.8122 (mt0) cc_final: 0.7847 (mt0) REVERT: Y 99 GLU cc_start: 0.7596 (tm-30) cc_final: 0.7326 (tm-30) REVERT: Z 116 ASP cc_start: 0.7509 (p0) cc_final: 0.7176 (p0) REVERT: Z 192 ASP cc_start: 0.6606 (t0) cc_final: 0.6401 (t0) REVERT: Z 197 HIS cc_start: 0.8272 (OUTLIER) cc_final: 0.7961 (t-170) REVERT: a 29 ARG cc_start: 0.8297 (mmm160) cc_final: 0.7584 (tpm170) REVERT: a 56 ARG cc_start: 0.9002 (ttm170) cc_final: 0.8664 (ttm170) outliers start: 44 outliers final: 8 residues processed: 934 average time/residue: 0.6105 time to fit residues: 941.4904 Evaluate side-chains 745 residues out of total 5552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 733 time to evaluate : 5.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain K residue 23 ASN Chi-restraints excluded: chain L residue 194 PHE Chi-restraints excluded: chain L residue 197 HIS Chi-restraints excluded: chain N residue 110 PHE Chi-restraints excluded: chain Q residue 62 TYR Chi-restraints excluded: chain V residue 130 GLU Chi-restraints excluded: chain Y residue 23 ASN Chi-restraints excluded: chain Z residue 194 PHE Chi-restraints excluded: chain Z residue 197 HIS Chi-restraints excluded: chain b residue 110 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 620 random chunks: chunk 523 optimal weight: 0.7980 chunk 469 optimal weight: 0.7980 chunk 260 optimal weight: 0.9980 chunk 160 optimal weight: 0.8980 chunk 316 optimal weight: 1.9990 chunk 251 optimal weight: 2.9990 chunk 485 optimal weight: 0.9990 chunk 188 optimal weight: 0.5980 chunk 295 optimal weight: 4.9990 chunk 361 optimal weight: 1.9990 chunk 563 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 ASN ** E 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN G 74 ASN G 108 ASN ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 185 HIS ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 56 GLN K 148 HIS M 179 ASN M 186 GLN N 111 ASN N 192 HIS ** O 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 73 ASN U 74 ASN U 108 ASN U 116 ASN U 230 GLN ** V 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 109 GLN ** Y 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 56 GLN b 192 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 51464 Z= 0.195 Angle : 0.606 17.065 69484 Z= 0.320 Chirality : 0.045 0.170 7764 Planarity : 0.004 0.076 8864 Dihedral : 7.473 83.188 7052 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.30 % Favored : 92.69 % Rotamer: Outliers : 1.48 % Allowed : 8.50 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.10), residues: 6250 helix: -0.36 (0.11), residues: 2094 sheet: -1.61 (0.14), residues: 1340 loop : -2.12 (0.12), residues: 2816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 220 HIS 0.010 0.001 HIS H 134 PHE 0.022 0.002 PHE H 76 TYR 0.025 0.001 TYR A 255 ARG 0.008 0.001 ARG A 259 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12500 Ramachandran restraints generated. 6250 Oldfield, 0 Emsley, 6250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12500 Ramachandran restraints generated. 6250 Oldfield, 0 Emsley, 6250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1018 residues out of total 5552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 936 time to evaluate : 5.578 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 ARG cc_start: 0.5942 (mpt180) cc_final: 0.5696 (mpt180) REVERT: B 119 GLN cc_start: 0.8112 (tm-30) cc_final: 0.7743 (tm-30) REVERT: B 158 TRP cc_start: 0.8671 (m100) cc_final: 0.8353 (m100) REVERT: B 159 MET cc_start: 0.8305 (mmt) cc_final: 0.7963 (mmt) REVERT: B 184 ILE cc_start: 0.6721 (OUTLIER) cc_final: 0.6090 (mt) REVERT: C 41 ASP cc_start: 0.7711 (t0) cc_final: 0.7444 (t0) REVERT: D 66 ASP cc_start: 0.8408 (m-30) cc_final: 0.8064 (m-30) REVERT: D 99 ASP cc_start: 0.8425 (t0) cc_final: 0.8192 (t0) REVERT: D 153 TYR cc_start: 0.8686 (p90) cc_final: 0.8473 (p90) REVERT: E 114 GLU cc_start: 0.8308 (tp30) cc_final: 0.8005 (tt0) REVERT: E 205 ARG cc_start: 0.8312 (ttm110) cc_final: 0.7825 (ttm170) REVERT: E 230 TYR cc_start: 0.8297 (t80) cc_final: 0.8047 (t80) REVERT: F 68 ASP cc_start: 0.7702 (m-30) cc_final: 0.7351 (m-30) REVERT: F 159 SER cc_start: 0.8737 (p) cc_final: 0.8512 (p) REVERT: F 223 ILE cc_start: 0.8536 (mm) cc_final: 0.7962 (mm) REVERT: F 227 GLN cc_start: 0.8726 (tm-30) cc_final: 0.8503 (tm-30) REVERT: G 57 LYS cc_start: 0.6336 (tmtt) cc_final: 0.5977 (tptp) REVERT: G 97 GLU cc_start: 0.7849 (tp30) cc_final: 0.7621 (tp30) REVERT: H 156 TYR cc_start: 0.8112 (t80) cc_final: 0.7881 (t80) REVERT: I 53 GLU cc_start: 0.7821 (tt0) cc_final: 0.7361 (mt-10) REVERT: I 174 ASP cc_start: 0.8947 (p0) cc_final: 0.8663 (p0) REVERT: J 134 LEU cc_start: 0.8606 (mt) cc_final: 0.8394 (mt) REVERT: J 201 LEU cc_start: 0.8676 (tt) cc_final: 0.8458 (tt) REVERT: K 20 TYR cc_start: 0.7975 (m-10) cc_final: 0.7491 (m-10) REVERT: K 53 ASP cc_start: 0.8034 (m-30) cc_final: 0.7757 (m-30) REVERT: L 3 THR cc_start: 0.9060 (m) cc_final: 0.8733 (m) REVERT: L 115 ASP cc_start: 0.7941 (t70) cc_final: 0.7169 (t0) REVERT: M 29 ARG cc_start: 0.8207 (mmm160) cc_final: 0.7531 (tpm170) REVERT: M 56 ARG cc_start: 0.8851 (ttm170) cc_final: 0.8617 (ttm170) REVERT: N 22 MET cc_start: 0.7942 (tpp) cc_final: 0.7572 (tpp) REVERT: N 52 MET cc_start: 0.8985 (tmm) cc_final: 0.8711 (ttp) REVERT: N 89 GLN cc_start: 0.9246 (tm-30) cc_final: 0.8990 (tm-30) REVERT: O 137 MET cc_start: 0.7735 (mpp) cc_final: 0.7519 (mpp) REVERT: P 119 GLN cc_start: 0.8016 (tm-30) cc_final: 0.7345 (tm-30) REVERT: P 123 GLN cc_start: 0.7505 (tt0) cc_final: 0.7275 (tt0) REVERT: P 209 GLU cc_start: 0.7013 (mm-30) cc_final: 0.6807 (mm-30) REVERT: R 37 SER cc_start: 0.8704 (t) cc_final: 0.8496 (t) REVERT: R 66 ASP cc_start: 0.8596 (m-30) cc_final: 0.8334 (m-30) REVERT: R 153 TYR cc_start: 0.8594 (p90) cc_final: 0.8339 (p90) REVERT: R 176 TYR cc_start: 0.8270 (t80) cc_final: 0.8029 (t80) REVERT: S 205 ARG cc_start: 0.8286 (ttm110) cc_final: 0.7942 (ttm170) REVERT: S 230 TYR cc_start: 0.8362 (t80) cc_final: 0.8133 (t80) REVERT: T 68 ASP cc_start: 0.7782 (m-30) cc_final: 0.7402 (m-30) REVERT: T 223 ILE cc_start: 0.8493 (mm) cc_final: 0.7933 (mm) REVERT: T 227 GLN cc_start: 0.8745 (tm-30) cc_final: 0.8505 (tm-30) REVERT: U 97 GLU cc_start: 0.7936 (tp30) cc_final: 0.7632 (tp30) REVERT: V 53 GLN cc_start: 0.8609 (tp40) cc_final: 0.8351 (tp40) REVERT: V 156 TYR cc_start: 0.8094 (t80) cc_final: 0.7797 (t80) REVERT: V 182 SER cc_start: 0.8698 (p) cc_final: 0.8469 (m) REVERT: W 174 ASP cc_start: 0.8769 (p0) cc_final: 0.8553 (p0) REVERT: Y 20 TYR cc_start: 0.8004 (m-10) cc_final: 0.7468 (m-10) REVERT: Y 53 ASP cc_start: 0.8020 (m-30) cc_final: 0.7619 (m-30) REVERT: Y 69 GLN cc_start: 0.7965 (mt0) cc_final: 0.7681 (mt0) REVERT: Z 3 THR cc_start: 0.9035 (m) cc_final: 0.8674 (m) REVERT: Z 111 MET cc_start: 0.7859 (ttm) cc_final: 0.7653 (ttm) REVERT: Z 115 ASP cc_start: 0.7868 (t70) cc_final: 0.6914 (t0) REVERT: Z 116 ASP cc_start: 0.7556 (p0) cc_final: 0.7347 (p0) REVERT: a 29 ARG cc_start: 0.8166 (mmm160) cc_final: 0.7541 (tpm170) REVERT: a 56 ARG cc_start: 0.8808 (ttm170) cc_final: 0.8585 (ttm170) REVERT: b 22 MET cc_start: 0.7951 (ttm) cc_final: 0.7734 (ttm) REVERT: b 52 MET cc_start: 0.9031 (tmm) cc_final: 0.8735 (ttp) REVERT: b 89 GLN cc_start: 0.9252 (tm-30) cc_final: 0.8994 (tm-30) outliers start: 82 outliers final: 59 residues processed: 973 average time/residue: 0.6054 time to fit residues: 971.7358 Evaluate side-chains 844 residues out of total 5552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 784 time to evaluate : 4.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 68 HIS Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 91 CYS Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 151 ASN Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 142 CYS Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain I residue 209 THR Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 67 GLU Chi-restraints excluded: chain L residue 150 ASP Chi-restraints excluded: chain L residue 180 HIS Chi-restraints excluded: chain L residue 194 PHE Chi-restraints excluded: chain M residue 170 SER Chi-restraints excluded: chain N residue 174 ASP Chi-restraints excluded: chain P residue 48 THR Chi-restraints excluded: chain Q residue 62 TYR Chi-restraints excluded: chain Q residue 117 ILE Chi-restraints excluded: chain R residue 13 ASP Chi-restraints excluded: chain R residue 68 HIS Chi-restraints excluded: chain R residue 70 CYS Chi-restraints excluded: chain R residue 91 CYS Chi-restraints excluded: chain R residue 100 GLU Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain S residue 151 ASN Chi-restraints excluded: chain T residue 226 LEU Chi-restraints excluded: chain U residue 113 ILE Chi-restraints excluded: chain U residue 118 ILE Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain V residue 174 ILE Chi-restraints excluded: chain V residue 178 ASP Chi-restraints excluded: chain V residue 184 SER Chi-restraints excluded: chain W residue 132 LEU Chi-restraints excluded: chain W residue 209 THR Chi-restraints excluded: chain X residue 36 THR Chi-restraints excluded: chain X residue 67 GLU Chi-restraints excluded: chain X residue 81 ASP Chi-restraints excluded: chain Y residue 93 LEU Chi-restraints excluded: chain Z residue 150 ASP Chi-restraints excluded: chain Z residue 180 HIS Chi-restraints excluded: chain Z residue 194 PHE Chi-restraints excluded: chain a residue 170 SER Chi-restraints excluded: chain b residue 73 ILE Chi-restraints excluded: chain b residue 110 PHE Chi-restraints excluded: chain b residue 174 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 620 random chunks: chunk 312 optimal weight: 6.9990 chunk 174 optimal weight: 0.9980 chunk 468 optimal weight: 10.0000 chunk 383 optimal weight: 9.9990 chunk 155 optimal weight: 8.9990 chunk 564 optimal weight: 4.9990 chunk 609 optimal weight: 2.9990 chunk 502 optimal weight: 2.9990 chunk 559 optimal weight: 7.9990 chunk 192 optimal weight: 8.9990 chunk 452 optimal weight: 5.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 32 ASN G 108 ASN G 116 ASN ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 56 GLN N 222 ASN ** P 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 116 ASN U 230 GLN ** V 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 56 GLN a 186 GLN b 222 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 51464 Z= 0.485 Angle : 0.707 17.553 69484 Z= 0.370 Chirality : 0.049 0.181 7764 Planarity : 0.005 0.064 8864 Dihedral : 7.400 70.866 7036 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.81 % Favored : 90.16 % Rotamer: Outliers : 2.45 % Allowed : 15.27 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.10), residues: 6250 helix: -0.44 (0.11), residues: 2116 sheet: -1.71 (0.14), residues: 1366 loop : -2.22 (0.11), residues: 2768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP G 220 HIS 0.013 0.002 HIS b 155 PHE 0.028 0.002 PHE R 194 TYR 0.023 0.002 TYR H 118 ARG 0.006 0.001 ARG Q 8 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12500 Ramachandran restraints generated. 6250 Oldfield, 0 Emsley, 6250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12500 Ramachandran restraints generated. 6250 Oldfield, 0 Emsley, 6250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 970 residues out of total 5552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 834 time to evaluate : 7.099 Fit side-chains revert: symmetry clash REVERT: B 119 GLN cc_start: 0.8205 (tm-30) cc_final: 0.7397 (tm-30) REVERT: D 66 ASP cc_start: 0.8553 (m-30) cc_final: 0.8167 (m-30) REVERT: D 153 TYR cc_start: 0.8915 (p90) cc_final: 0.8491 (p90) REVERT: E 114 GLU cc_start: 0.8361 (tp30) cc_final: 0.8060 (tt0) REVERT: E 205 ARG cc_start: 0.8398 (ttm110) cc_final: 0.8041 (ttm170) REVERT: E 230 TYR cc_start: 0.8374 (t80) cc_final: 0.8060 (t80) REVERT: F 68 ASP cc_start: 0.7746 (m-30) cc_final: 0.7405 (m-30) REVERT: F 223 ILE cc_start: 0.8606 (mm) cc_final: 0.8111 (mm) REVERT: G 55 MET cc_start: 0.7265 (mmm) cc_final: 0.7043 (mmm) REVERT: G 57 LYS cc_start: 0.6211 (tmtt) cc_final: 0.5851 (tptp) REVERT: G 97 GLU cc_start: 0.7874 (tp30) cc_final: 0.7604 (tp30) REVERT: H 32 ARG cc_start: 0.7807 (mmt-90) cc_final: 0.7568 (mmt180) REVERT: H 156 TYR cc_start: 0.8245 (t80) cc_final: 0.7959 (t80) REVERT: I 174 ASP cc_start: 0.8992 (p0) cc_final: 0.8732 (p0) REVERT: K 2 ASP cc_start: 0.7925 (OUTLIER) cc_final: 0.7662 (p0) REVERT: K 20 TYR cc_start: 0.8106 (m-10) cc_final: 0.7577 (m-10) REVERT: K 119 ASP cc_start: 0.7805 (t0) cc_final: 0.7315 (t0) REVERT: L 6 PHE cc_start: 0.8564 (m-10) cc_final: 0.8272 (m-10) REVERT: L 192 ASP cc_start: 0.6836 (t0) cc_final: 0.6282 (t0) REVERT: M 29 ARG cc_start: 0.8336 (mmm160) cc_final: 0.7644 (tpm170) REVERT: M 59 LEU cc_start: 0.8440 (tp) cc_final: 0.8195 (tp) REVERT: N 89 GLN cc_start: 0.9315 (tm-30) cc_final: 0.8885 (tm-30) REVERT: O 11 ARG cc_start: 0.6124 (mpt180) cc_final: 0.5767 (mpt180) REVERT: O 137 MET cc_start: 0.7827 (mpp) cc_final: 0.7526 (mpp) REVERT: O 172 CYS cc_start: 0.8308 (p) cc_final: 0.8074 (p) REVERT: P 119 GLN cc_start: 0.8153 (tm-30) cc_final: 0.7278 (tm-30) REVERT: P 159 MET cc_start: 0.8148 (mmt) cc_final: 0.7846 (mmt) REVERT: P 209 GLU cc_start: 0.6991 (mm-30) cc_final: 0.6720 (mm-30) REVERT: R 37 SER cc_start: 0.8799 (t) cc_final: 0.8571 (t) REVERT: R 66 ASP cc_start: 0.8645 (m-30) cc_final: 0.8276 (m-30) REVERT: R 99 ASP cc_start: 0.8496 (t0) cc_final: 0.8264 (t0) REVERT: R 153 TYR cc_start: 0.8837 (p90) cc_final: 0.8438 (p90) REVERT: R 176 TYR cc_start: 0.8435 (t80) cc_final: 0.8152 (t80) REVERT: S 205 ARG cc_start: 0.8429 (ttm110) cc_final: 0.8014 (ttm170) REVERT: S 230 TYR cc_start: 0.8415 (t80) cc_final: 0.8142 (t80) REVERT: T 67 ASP cc_start: 0.8024 (t0) cc_final: 0.7639 (t0) REVERT: T 68 ASP cc_start: 0.7803 (m-30) cc_final: 0.7260 (m-30) REVERT: T 223 ILE cc_start: 0.8600 (mm) cc_final: 0.8109 (mm) REVERT: U 97 GLU cc_start: 0.7863 (tp30) cc_final: 0.7591 (tp30) REVERT: V 32 ARG cc_start: 0.7747 (mmt-90) cc_final: 0.7469 (mmt180) REVERT: V 156 TYR cc_start: 0.8245 (t80) cc_final: 0.8000 (t80) REVERT: W 174 ASP cc_start: 0.8999 (p0) cc_final: 0.8731 (p0) REVERT: Y 2 ASP cc_start: 0.7902 (OUTLIER) cc_final: 0.7645 (p0) REVERT: Y 20 TYR cc_start: 0.8112 (m-10) cc_final: 0.7567 (m-10) REVERT: Y 53 ASP cc_start: 0.8147 (m-30) cc_final: 0.7921 (m-30) REVERT: Y 69 GLN cc_start: 0.7933 (mt0) cc_final: 0.7676 (mt0) REVERT: Y 119 ASP cc_start: 0.7807 (t0) cc_final: 0.7299 (t0) REVERT: Z 115 ASP cc_start: 0.8129 (t70) cc_final: 0.7511 (t0) REVERT: Z 192 ASP cc_start: 0.6861 (t0) cc_final: 0.6311 (t0) REVERT: a 29 ARG cc_start: 0.8347 (mmm160) cc_final: 0.7665 (tpm170) REVERT: a 83 SER cc_start: 0.8485 (p) cc_final: 0.8205 (t) REVERT: a 173 ILE cc_start: 0.8240 (OUTLIER) cc_final: 0.7921 (mt) REVERT: b 22 MET cc_start: 0.7969 (ttm) cc_final: 0.7709 (ttm) REVERT: b 89 GLN cc_start: 0.9313 (tm-30) cc_final: 0.8877 (tm-30) outliers start: 136 outliers final: 106 residues processed: 902 average time/residue: 0.6513 time to fit residues: 967.7505 Evaluate side-chains 885 residues out of total 5552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 776 time to evaluate : 5.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 134 PHE Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 68 HIS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 91 CYS Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 151 ASN Chi-restraints excluded: chain E residue 208 MET Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 52 CYS Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 176 HIS Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 174 ILE Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 67 GLU Chi-restraints excluded: chain J residue 202 VAL Chi-restraints excluded: chain K residue 2 ASP Chi-restraints excluded: chain K residue 56 GLN Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 150 ASP Chi-restraints excluded: chain L residue 180 HIS Chi-restraints excluded: chain L residue 194 PHE Chi-restraints excluded: chain M residue 41 ILE Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain M residue 170 SER Chi-restraints excluded: chain N residue 33 SER Chi-restraints excluded: chain N residue 77 SER Chi-restraints excluded: chain N residue 110 PHE Chi-restraints excluded: chain N residue 174 ASP Chi-restraints excluded: chain O residue 12 HIS Chi-restraints excluded: chain O residue 173 VAL Chi-restraints excluded: chain O residue 224 LEU Chi-restraints excluded: chain O residue 233 ILE Chi-restraints excluded: chain P residue 16 THR Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 36 LEU Chi-restraints excluded: chain P residue 48 THR Chi-restraints excluded: chain Q residue 62 TYR Chi-restraints excluded: chain Q residue 117 ILE Chi-restraints excluded: chain Q residue 134 PHE Chi-restraints excluded: chain Q residue 174 VAL Chi-restraints excluded: chain R residue 13 ASP Chi-restraints excluded: chain R residue 68 HIS Chi-restraints excluded: chain R residue 91 CYS Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 151 ASN Chi-restraints excluded: chain T residue 12 ILE Chi-restraints excluded: chain T residue 52 CYS Chi-restraints excluded: chain T residue 176 HIS Chi-restraints excluded: chain T residue 226 LEU Chi-restraints excluded: chain U residue 47 ILE Chi-restraints excluded: chain U residue 113 ILE Chi-restraints excluded: chain U residue 118 ILE Chi-restraints excluded: chain U residue 141 SER Chi-restraints excluded: chain U residue 238 THR Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain V residue 59 ILE Chi-restraints excluded: chain V residue 174 ILE Chi-restraints excluded: chain V residue 184 SER Chi-restraints excluded: chain W residue 95 VAL Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 132 LEU Chi-restraints excluded: chain X residue 26 ASP Chi-restraints excluded: chain X residue 36 THR Chi-restraints excluded: chain X residue 67 GLU Chi-restraints excluded: chain X residue 202 VAL Chi-restraints excluded: chain Y residue 2 ASP Chi-restraints excluded: chain Y residue 56 GLN Chi-restraints excluded: chain Y residue 93 LEU Chi-restraints excluded: chain Z residue 150 ASP Chi-restraints excluded: chain Z residue 180 HIS Chi-restraints excluded: chain Z residue 194 PHE Chi-restraints excluded: chain Z residue 201 THR Chi-restraints excluded: chain a residue 63 ILE Chi-restraints excluded: chain a residue 170 SER Chi-restraints excluded: chain a residue 173 ILE Chi-restraints excluded: chain a residue 186 GLN Chi-restraints excluded: chain b residue 33 SER Chi-restraints excluded: chain b residue 73 ILE Chi-restraints excluded: chain b residue 75 ASN Chi-restraints excluded: chain b residue 174 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 620 random chunks: chunk 557 optimal weight: 0.8980 chunk 424 optimal weight: 3.9990 chunk 292 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 269 optimal weight: 0.9990 chunk 378 optimal weight: 1.9990 chunk 566 optimal weight: 3.9990 chunk 599 optimal weight: 1.9990 chunk 295 optimal weight: 5.9990 chunk 536 optimal weight: 0.1980 chunk 161 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 ASN ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 HIS G 230 GLN ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 185 HIS K 56 GLN L 197 HIS ** P 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 97 ASN S 176 GLN T 176 HIS U 108 ASN U 116 ASN ** U 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 177 HIS ** W 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 185 HIS Y 56 GLN Z 197 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 51464 Z= 0.199 Angle : 0.564 15.776 69484 Z= 0.298 Chirality : 0.044 0.183 7764 Planarity : 0.004 0.059 8864 Dihedral : 7.113 74.020 7034 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 2.83 % Allowed : 17.38 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.11), residues: 6250 helix: -0.05 (0.11), residues: 2108 sheet: -1.58 (0.14), residues: 1348 loop : -2.12 (0.12), residues: 2794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP Q 179 HIS 0.019 0.001 HIS N 155 PHE 0.017 0.001 PHE H 25 TYR 0.020 0.001 TYR H 118 ARG 0.006 0.000 ARG R 93 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12500 Ramachandran restraints generated. 6250 Oldfield, 0 Emsley, 6250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12500 Ramachandran restraints generated. 6250 Oldfield, 0 Emsley, 6250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1023 residues out of total 5552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 866 time to evaluate : 6.719 Fit side-chains REVERT: B 119 GLN cc_start: 0.7965 (tm-30) cc_final: 0.7514 (tm-30) REVERT: B 159 MET cc_start: 0.8064 (mmt) cc_final: 0.7351 (mmt) REVERT: B 184 ILE cc_start: 0.6695 (OUTLIER) cc_final: 0.6026 (mt) REVERT: C 48 ASP cc_start: 0.7311 (t0) cc_final: 0.7079 (t0) REVERT: C 62 TYR cc_start: 0.7213 (OUTLIER) cc_final: 0.5830 (p90) REVERT: D 153 TYR cc_start: 0.8821 (p90) cc_final: 0.8510 (p90) REVERT: E 114 GLU cc_start: 0.8402 (tp30) cc_final: 0.8075 (tt0) REVERT: E 205 ARG cc_start: 0.8371 (ttm110) cc_final: 0.7999 (ttm170) REVERT: E 230 TYR cc_start: 0.8449 (t80) cc_final: 0.8112 (t80) REVERT: F 68 ASP cc_start: 0.7729 (m-30) cc_final: 0.7334 (m-30) REVERT: F 223 ILE cc_start: 0.8420 (mm) cc_final: 0.8209 (mm) REVERT: G 57 LYS cc_start: 0.6171 (tmtt) cc_final: 0.5930 (tptp) REVERT: G 97 GLU cc_start: 0.7812 (tp30) cc_final: 0.7590 (tp30) REVERT: H 156 TYR cc_start: 0.8117 (t80) cc_final: 0.7859 (t80) REVERT: I 174 ASP cc_start: 0.8626 (p0) cc_final: 0.8305 (p0) REVERT: K 20 TYR cc_start: 0.7949 (m-10) cc_final: 0.7447 (m-10) REVERT: L 111 MET cc_start: 0.7723 (ttm) cc_final: 0.7473 (ttm) REVERT: L 150 ASP cc_start: 0.7783 (OUTLIER) cc_final: 0.7555 (m-30) REVERT: M 29 ARG cc_start: 0.8269 (mmm160) cc_final: 0.7560 (tpm170) REVERT: M 56 ARG cc_start: 0.8848 (ttm170) cc_final: 0.8455 (ttm170) REVERT: N 89 GLN cc_start: 0.9256 (tm-30) cc_final: 0.8926 (tm-30) REVERT: P 119 GLN cc_start: 0.7897 (tm-30) cc_final: 0.7334 (tm-30) REVERT: P 123 GLN cc_start: 0.7712 (tt0) cc_final: 0.7461 (tt0) REVERT: P 184 ILE cc_start: 0.6721 (OUTLIER) cc_final: 0.6007 (mt) REVERT: Q 62 TYR cc_start: 0.7189 (OUTLIER) cc_final: 0.5763 (p90) REVERT: R 37 SER cc_start: 0.8676 (t) cc_final: 0.8454 (t) REVERT: R 99 ASP cc_start: 0.8387 (t0) cc_final: 0.8148 (t0) REVERT: R 153 TYR cc_start: 0.8761 (p90) cc_final: 0.8434 (p90) REVERT: S 205 ARG cc_start: 0.8419 (ttm110) cc_final: 0.8013 (ttm170) REVERT: S 230 TYR cc_start: 0.8436 (t80) cc_final: 0.8179 (t80) REVERT: T 68 ASP cc_start: 0.7714 (m-30) cc_final: 0.7271 (m-30) REVERT: T 223 ILE cc_start: 0.8413 (mm) cc_final: 0.8207 (mm) REVERT: U 97 GLU cc_start: 0.7791 (tp30) cc_final: 0.7580 (tp30) REVERT: V 32 ARG cc_start: 0.7882 (mmt-90) cc_final: 0.7595 (mmt180) REVERT: V 156 TYR cc_start: 0.8108 (t80) cc_final: 0.7838 (t80) REVERT: V 182 SER cc_start: 0.8629 (p) cc_final: 0.8258 (m) REVERT: W 54 HIS cc_start: 0.7759 (t-90) cc_final: 0.7508 (t-90) REVERT: W 174 ASP cc_start: 0.8700 (p0) cc_final: 0.8378 (p0) REVERT: Y 20 TYR cc_start: 0.7968 (m-10) cc_final: 0.7460 (m-10) REVERT: Y 69 GLN cc_start: 0.8063 (mt0) cc_final: 0.7736 (mt0) REVERT: Z 3 THR cc_start: 0.9116 (m) cc_final: 0.8777 (m) REVERT: Z 115 ASP cc_start: 0.7924 (t70) cc_final: 0.7276 (t0) REVERT: Z 150 ASP cc_start: 0.7778 (OUTLIER) cc_final: 0.7527 (m-30) REVERT: a 29 ARG cc_start: 0.8253 (mmm160) cc_final: 0.7587 (tpm170) REVERT: a 56 ARG cc_start: 0.8857 (ttm170) cc_final: 0.8581 (ttm170) REVERT: a 173 ILE cc_start: 0.8191 (OUTLIER) cc_final: 0.7971 (mt) REVERT: b 22 MET cc_start: 0.7892 (ttm) cc_final: 0.7659 (ttm) REVERT: b 89 GLN cc_start: 0.9254 (tm-30) cc_final: 0.8911 (tm-30) outliers start: 157 outliers final: 99 residues processed: 951 average time/residue: 0.6101 time to fit residues: 960.4329 Evaluate side-chains 883 residues out of total 5552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 777 time to evaluate : 6.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 182 ASP Chi-restraints excluded: chain D residue 68 HIS Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 91 CYS Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 151 ASN Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 176 HIS Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain I residue 209 THR Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 67 GLU Chi-restraints excluded: chain J residue 209 ILE Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain L residue 115 ASP Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 150 ASP Chi-restraints excluded: chain L residue 180 HIS Chi-restraints excluded: chain L residue 194 PHE Chi-restraints excluded: chain M residue 41 ILE Chi-restraints excluded: chain M residue 170 SER Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 33 SER Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain N residue 174 ASP Chi-restraints excluded: chain N residue 206 ILE Chi-restraints excluded: chain O residue 12 HIS Chi-restraints excluded: chain O residue 173 VAL Chi-restraints excluded: chain O residue 233 ILE Chi-restraints excluded: chain P residue 48 THR Chi-restraints excluded: chain P residue 184 ILE Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 62 TYR Chi-restraints excluded: chain Q residue 117 ILE Chi-restraints excluded: chain Q residue 174 VAL Chi-restraints excluded: chain R residue 13 ASP Chi-restraints excluded: chain R residue 68 HIS Chi-restraints excluded: chain R residue 70 CYS Chi-restraints excluded: chain R residue 91 CYS Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain S residue 21 LEU Chi-restraints excluded: chain S residue 151 ASN Chi-restraints excluded: chain S residue 208 MET Chi-restraints excluded: chain S residue 212 LEU Chi-restraints excluded: chain T residue 12 ILE Chi-restraints excluded: chain T residue 176 HIS Chi-restraints excluded: chain T residue 226 LEU Chi-restraints excluded: chain U residue 113 ILE Chi-restraints excluded: chain U residue 141 SER Chi-restraints excluded: chain U residue 238 THR Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain V residue 41 LEU Chi-restraints excluded: chain V residue 58 ILE Chi-restraints excluded: chain V residue 59 ILE Chi-restraints excluded: chain V residue 128 LEU Chi-restraints excluded: chain V residue 178 ASP Chi-restraints excluded: chain V residue 184 SER Chi-restraints excluded: chain W residue 132 LEU Chi-restraints excluded: chain W residue 209 THR Chi-restraints excluded: chain X residue 36 THR Chi-restraints excluded: chain X residue 67 GLU Chi-restraints excluded: chain Y residue 93 LEU Chi-restraints excluded: chain Z residue 137 SER Chi-restraints excluded: chain Z residue 150 ASP Chi-restraints excluded: chain Z residue 180 HIS Chi-restraints excluded: chain Z residue 194 PHE Chi-restraints excluded: chain Z residue 201 THR Chi-restraints excluded: chain a residue 170 SER Chi-restraints excluded: chain a residue 173 ILE Chi-restraints excluded: chain a residue 186 GLN Chi-restraints excluded: chain b residue 6 VAL Chi-restraints excluded: chain b residue 12 VAL Chi-restraints excluded: chain b residue 33 SER Chi-restraints excluded: chain b residue 73 ILE Chi-restraints excluded: chain b residue 174 ASP Chi-restraints excluded: chain b residue 206 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 620 random chunks: chunk 499 optimal weight: 5.9990 chunk 340 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 446 optimal weight: 0.0030 chunk 247 optimal weight: 0.9980 chunk 511 optimal weight: 0.7980 chunk 414 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 306 optimal weight: 3.9990 chunk 537 optimal weight: 0.8980 chunk 151 optimal weight: 4.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 139 ASN ** G 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 109 GLN K 56 GLN L 151 GLN L 197 HIS ** P 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 139 ASN U 74 ASN U 108 ASN U 116 ASN U 157 ASN ** V 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 56 GLN Z 151 GLN Z 197 HIS a 186 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 51464 Z= 0.164 Angle : 0.540 14.878 69484 Z= 0.284 Chirality : 0.043 0.199 7764 Planarity : 0.004 0.059 8864 Dihedral : 6.902 74.532 7034 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 2.88 % Allowed : 18.98 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.11), residues: 6250 helix: 0.21 (0.11), residues: 2140 sheet: -1.42 (0.14), residues: 1358 loop : -2.05 (0.12), residues: 2752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP Q 179 HIS 0.014 0.001 HIS b 155 PHE 0.015 0.001 PHE H 25 TYR 0.022 0.001 TYR H 118 ARG 0.006 0.000 ARG S 86 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12500 Ramachandran restraints generated. 6250 Oldfield, 0 Emsley, 6250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12500 Ramachandran restraints generated. 6250 Oldfield, 0 Emsley, 6250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1042 residues out of total 5552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 882 time to evaluate : 6.340 Fit side-chains REVERT: A 96 MET cc_start: 0.8601 (mmp) cc_final: 0.8336 (tpp) REVERT: B 119 GLN cc_start: 0.7827 (tm-30) cc_final: 0.7330 (tm-30) REVERT: B 159 MET cc_start: 0.7809 (mmt) cc_final: 0.7316 (mmt) REVERT: B 184 ILE cc_start: 0.6633 (OUTLIER) cc_final: 0.5985 (mt) REVERT: C 62 TYR cc_start: 0.7117 (OUTLIER) cc_final: 0.5904 (p90) REVERT: C 93 TYR cc_start: 0.7722 (m-10) cc_final: 0.6852 (m-10) REVERT: D 66 ASP cc_start: 0.8518 (m-30) cc_final: 0.8186 (m-30) REVERT: D 93 ARG cc_start: 0.7976 (tmm-80) cc_final: 0.7623 (tmm-80) REVERT: D 99 ASP cc_start: 0.8307 (t0) cc_final: 0.8090 (t0) REVERT: D 153 TYR cc_start: 0.8750 (p90) cc_final: 0.8533 (p90) REVERT: E 114 GLU cc_start: 0.8402 (tp30) cc_final: 0.8104 (tt0) REVERT: E 205 ARG cc_start: 0.8458 (ttm110) cc_final: 0.8234 (ttm170) REVERT: F 68 ASP cc_start: 0.7689 (m-30) cc_final: 0.7371 (m-30) REVERT: F 223 ILE cc_start: 0.8462 (mm) cc_final: 0.8187 (mm) REVERT: G 68 ARG cc_start: 0.8516 (mtp180) cc_final: 0.8243 (mtp-110) REVERT: G 97 GLU cc_start: 0.7693 (tp30) cc_final: 0.7463 (tp30) REVERT: H 19 ARG cc_start: 0.8343 (ttm170) cc_final: 0.7946 (ttm170) REVERT: H 32 ARG cc_start: 0.7764 (mmt-90) cc_final: 0.7298 (mmm160) REVERT: H 156 TYR cc_start: 0.8128 (t80) cc_final: 0.7863 (t80) REVERT: I 53 GLU cc_start: 0.8103 (tt0) cc_final: 0.7670 (mt-10) REVERT: I 54 HIS cc_start: 0.7624 (t-90) cc_final: 0.7400 (t-90) REVERT: I 174 ASP cc_start: 0.8403 (p0) cc_final: 0.8113 (p0) REVERT: K 20 TYR cc_start: 0.7944 (m-10) cc_final: 0.7457 (m-10) REVERT: L 3 THR cc_start: 0.9008 (m) cc_final: 0.8706 (m) REVERT: L 115 ASP cc_start: 0.7940 (OUTLIER) cc_final: 0.7135 (t0) REVERT: M 29 ARG cc_start: 0.8235 (mmm160) cc_final: 0.7524 (tpm170) REVERT: M 39 THR cc_start: 0.9117 (t) cc_final: 0.8843 (m) REVERT: N 89 GLN cc_start: 0.9212 (tm-30) cc_final: 0.8900 (tm-30) REVERT: O 129 GLN cc_start: 0.8320 (tm-30) cc_final: 0.7921 (tm-30) REVERT: O 137 MET cc_start: 0.7883 (mpp) cc_final: 0.7537 (mpp) REVERT: P 119 GLN cc_start: 0.7818 (tm-30) cc_final: 0.7215 (tm-30) REVERT: P 123 GLN cc_start: 0.7681 (tt0) cc_final: 0.7410 (tt0) REVERT: P 184 ILE cc_start: 0.6683 (OUTLIER) cc_final: 0.6029 (mt) REVERT: Q 93 TYR cc_start: 0.7727 (m-10) cc_final: 0.6885 (m-10) REVERT: R 37 SER cc_start: 0.8754 (t) cc_final: 0.8524 (t) REVERT: R 99 ASP cc_start: 0.8322 (t0) cc_final: 0.8098 (t0) REVERT: R 153 TYR cc_start: 0.8680 (p90) cc_final: 0.8439 (p90) REVERT: S 205 ARG cc_start: 0.8422 (ttm110) cc_final: 0.8150 (ttm170) REVERT: S 230 TYR cc_start: 0.8460 (t80) cc_final: 0.8166 (t80) REVERT: T 68 ASP cc_start: 0.7680 (m-30) cc_final: 0.7347 (m-30) REVERT: T 223 ILE cc_start: 0.8469 (mm) cc_final: 0.7979 (mm) REVERT: T 227 GLN cc_start: 0.8675 (tm-30) cc_final: 0.8467 (tm-30) REVERT: U 97 GLU cc_start: 0.7679 (tp30) cc_final: 0.7474 (tp30) REVERT: V 156 TYR cc_start: 0.8088 (t80) cc_final: 0.7829 (t80) REVERT: V 182 SER cc_start: 0.8699 (p) cc_final: 0.8430 (m) REVERT: W 53 GLU cc_start: 0.8040 (tt0) cc_final: 0.7575 (mt-10) REVERT: W 54 HIS cc_start: 0.7686 (t-90) cc_final: 0.7404 (t-90) REVERT: X 129 ASN cc_start: 0.8048 (p0) cc_final: 0.7717 (p0) REVERT: Y 20 TYR cc_start: 0.7960 (m-10) cc_final: 0.7477 (m-10) REVERT: Y 69 GLN cc_start: 0.8077 (mt0) cc_final: 0.7831 (mt0) REVERT: Z 3 THR cc_start: 0.9058 (m) cc_final: 0.8744 (m) REVERT: Z 115 ASP cc_start: 0.7924 (t70) cc_final: 0.7283 (t0) REVERT: a 39 THR cc_start: 0.9154 (t) cc_final: 0.8877 (m) REVERT: a 233 ASN cc_start: 0.8476 (OUTLIER) cc_final: 0.8008 (p0) REVERT: b 22 MET cc_start: 0.7956 (ttm) cc_final: 0.7743 (ttm) REVERT: b 75 ASN cc_start: 0.8559 (OUTLIER) cc_final: 0.8131 (t0) REVERT: b 89 GLN cc_start: 0.9229 (tm-30) cc_final: 0.8899 (tm-30) outliers start: 160 outliers final: 114 residues processed: 967 average time/residue: 0.6543 time to fit residues: 1064.0047 Evaluate side-chains 906 residues out of total 5552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 786 time to evaluate : 6.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 182 ASP Chi-restraints excluded: chain D residue 68 HIS Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 91 CYS Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 225 MET Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 151 ASN Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 52 CYS Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 163 ARG Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain H residue 172 SER Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 109 GLN Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain I residue 204 ILE Chi-restraints excluded: chain I residue 209 THR Chi-restraints excluded: chain I residue 212 ILE Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 67 GLU Chi-restraints excluded: chain J residue 202 VAL Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 125 ASP Chi-restraints excluded: chain L residue 115 ASP Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 180 HIS Chi-restraints excluded: chain L residue 194 PHE Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 33 SER Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain N residue 174 ASP Chi-restraints excluded: chain N residue 206 ILE Chi-restraints excluded: chain O residue 12 HIS Chi-restraints excluded: chain O residue 174 ILE Chi-restraints excluded: chain O residue 233 ILE Chi-restraints excluded: chain P residue 36 LEU Chi-restraints excluded: chain P residue 48 THR Chi-restraints excluded: chain P residue 184 ILE Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 45 LEU Chi-restraints excluded: chain Q residue 117 ILE Chi-restraints excluded: chain Q residue 134 PHE Chi-restraints excluded: chain Q residue 174 VAL Chi-restraints excluded: chain R residue 13 ASP Chi-restraints excluded: chain R residue 68 HIS Chi-restraints excluded: chain R residue 70 CYS Chi-restraints excluded: chain R residue 91 CYS Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain R residue 225 MET Chi-restraints excluded: chain S residue 21 LEU Chi-restraints excluded: chain S residue 47 ILE Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 148 VAL Chi-restraints excluded: chain S residue 151 ASN Chi-restraints excluded: chain T residue 12 ILE Chi-restraints excluded: chain T residue 52 CYS Chi-restraints excluded: chain T residue 163 ARG Chi-restraints excluded: chain T residue 226 LEU Chi-restraints excluded: chain U residue 113 ILE Chi-restraints excluded: chain U residue 238 THR Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain V residue 41 LEU Chi-restraints excluded: chain V residue 59 ILE Chi-restraints excluded: chain V residue 128 LEU Chi-restraints excluded: chain V residue 140 ILE Chi-restraints excluded: chain V residue 178 ASP Chi-restraints excluded: chain V residue 184 SER Chi-restraints excluded: chain W residue 95 VAL Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 132 LEU Chi-restraints excluded: chain W residue 204 ILE Chi-restraints excluded: chain W residue 209 THR Chi-restraints excluded: chain W residue 212 ILE Chi-restraints excluded: chain X residue 36 THR Chi-restraints excluded: chain X residue 202 VAL Chi-restraints excluded: chain X residue 209 ILE Chi-restraints excluded: chain Y residue 93 LEU Chi-restraints excluded: chain Y residue 173 LEU Chi-restraints excluded: chain Y residue 183 MET Chi-restraints excluded: chain Z residue 125 LEU Chi-restraints excluded: chain Z residue 137 SER Chi-restraints excluded: chain Z residue 180 HIS Chi-restraints excluded: chain Z residue 194 PHE Chi-restraints excluded: chain Z residue 201 THR Chi-restraints excluded: chain a residue 170 SER Chi-restraints excluded: chain a residue 233 ASN Chi-restraints excluded: chain b residue 6 VAL Chi-restraints excluded: chain b residue 12 VAL Chi-restraints excluded: chain b residue 33 SER Chi-restraints excluded: chain b residue 73 ILE Chi-restraints excluded: chain b residue 75 ASN Chi-restraints excluded: chain b residue 174 ASP Chi-restraints excluded: chain b residue 206 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 620 random chunks: chunk 201 optimal weight: 2.9990 chunk 539 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 351 optimal weight: 10.0000 chunk 147 optimal weight: 0.8980 chunk 599 optimal weight: 0.9990 chunk 497 optimal weight: 0.9980 chunk 277 optimal weight: 0.3980 chunk 49 optimal weight: 7.9990 chunk 198 optimal weight: 6.9990 chunk 314 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 GLN ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 139 ASN F 176 HIS ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 197 HIS ** P 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 139 ASN T 176 HIS U 230 GLN ** V 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 197 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 51464 Z= 0.180 Angle : 0.545 14.466 69484 Z= 0.286 Chirality : 0.044 0.377 7764 Planarity : 0.004 0.059 8864 Dihedral : 6.789 74.121 7032 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 3.08 % Allowed : 19.83 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.11), residues: 6250 helix: 0.31 (0.11), residues: 2126 sheet: -1.37 (0.14), residues: 1356 loop : -1.98 (0.12), residues: 2768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 179 HIS 0.010 0.001 HIS b 155 PHE 0.015 0.001 PHE R 194 TYR 0.021 0.001 TYR H 118 ARG 0.006 0.000 ARG a 29 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12500 Ramachandran restraints generated. 6250 Oldfield, 0 Emsley, 6250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12500 Ramachandran restraints generated. 6250 Oldfield, 0 Emsley, 6250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1020 residues out of total 5552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 849 time to evaluate : 6.426 Fit side-chains REVERT: B 100 GLN cc_start: 0.8518 (mt0) cc_final: 0.8145 (mt0) REVERT: B 119 GLN cc_start: 0.7769 (tm-30) cc_final: 0.7238 (tm-30) REVERT: B 158 TRP cc_start: 0.8500 (m100) cc_final: 0.7997 (m100) REVERT: B 159 MET cc_start: 0.7791 (mmt) cc_final: 0.7233 (mmt) REVERT: B 184 ILE cc_start: 0.6612 (OUTLIER) cc_final: 0.6027 (mt) REVERT: C 93 TYR cc_start: 0.7748 (m-10) cc_final: 0.6898 (m-10) REVERT: D 5 ARG cc_start: 0.5870 (ptm160) cc_final: 0.5641 (ptm160) REVERT: D 66 ASP cc_start: 0.8537 (m-30) cc_final: 0.8152 (m-30) REVERT: D 99 ASP cc_start: 0.8315 (t0) cc_final: 0.8062 (t0) REVERT: E 114 GLU cc_start: 0.8387 (tp30) cc_final: 0.8048 (tt0) REVERT: E 205 ARG cc_start: 0.8471 (ttm110) cc_final: 0.8246 (ttm170) REVERT: F 68 ASP cc_start: 0.7695 (m-30) cc_final: 0.7399 (m-30) REVERT: F 139 ASN cc_start: 0.7885 (m-40) cc_final: 0.7650 (m110) REVERT: F 223 ILE cc_start: 0.8450 (mm) cc_final: 0.8161 (mm) REVERT: G 68 ARG cc_start: 0.8559 (mtp180) cc_final: 0.8280 (mtp-110) REVERT: G 97 GLU cc_start: 0.7643 (tp30) cc_final: 0.7436 (tp30) REVERT: H 32 ARG cc_start: 0.7976 (mmt-90) cc_final: 0.7550 (mmm160) REVERT: H 156 TYR cc_start: 0.8132 (t80) cc_final: 0.7868 (t80) REVERT: I 53 GLU cc_start: 0.8083 (tt0) cc_final: 0.7681 (mt-10) REVERT: I 54 HIS cc_start: 0.7658 (t-90) cc_final: 0.7430 (t-90) REVERT: I 174 ASP cc_start: 0.8344 (p0) cc_final: 0.7986 (p0) REVERT: K 2 ASP cc_start: 0.7582 (p0) cc_final: 0.7362 (p0) REVERT: K 20 TYR cc_start: 0.7986 (m-10) cc_final: 0.7519 (m-10) REVERT: L 3 THR cc_start: 0.8968 (m) cc_final: 0.8637 (m) REVERT: M 39 THR cc_start: 0.9090 (t) cc_final: 0.8834 (m) REVERT: M 233 ASN cc_start: 0.8439 (OUTLIER) cc_final: 0.7950 (p0) REVERT: N 89 GLN cc_start: 0.9223 (tm-30) cc_final: 0.8907 (tm-30) REVERT: O 129 GLN cc_start: 0.8251 (tm-30) cc_final: 0.7860 (tm-30) REVERT: O 137 MET cc_start: 0.7901 (mpp) cc_final: 0.7542 (mpp) REVERT: P 119 GLN cc_start: 0.7755 (tm-30) cc_final: 0.7247 (tm-30) REVERT: P 184 ILE cc_start: 0.6662 (OUTLIER) cc_final: 0.6005 (mt) REVERT: Q 93 TYR cc_start: 0.7741 (m-10) cc_final: 0.6913 (m-10) REVERT: Q 155 ASN cc_start: 0.8101 (OUTLIER) cc_final: 0.7839 (p0) REVERT: R 37 SER cc_start: 0.8724 (t) cc_final: 0.8479 (t) REVERT: R 99 ASP cc_start: 0.8319 (t0) cc_final: 0.8042 (t0) REVERT: R 153 TYR cc_start: 0.8651 (p90) cc_final: 0.8449 (p90) REVERT: S 114 GLU cc_start: 0.8346 (tp30) cc_final: 0.8066 (tt0) REVERT: S 230 TYR cc_start: 0.8487 (t80) cc_final: 0.8196 (t80) REVERT: T 68 ASP cc_start: 0.7706 (m-30) cc_final: 0.7382 (m-30) REVERT: T 223 ILE cc_start: 0.8465 (mm) cc_final: 0.8000 (mm) REVERT: T 227 GLN cc_start: 0.8665 (tm-30) cc_final: 0.8410 (tm-30) REVERT: U 31 ILE cc_start: 0.8305 (pt) cc_final: 0.7859 (mt) REVERT: U 97 GLU cc_start: 0.7629 (tp30) cc_final: 0.7429 (tp30) REVERT: U 197 TYR cc_start: 0.8609 (OUTLIER) cc_final: 0.8368 (m-10) REVERT: V 156 TYR cc_start: 0.8111 (t80) cc_final: 0.7839 (t80) REVERT: V 182 SER cc_start: 0.8532 (p) cc_final: 0.8256 (m) REVERT: W 53 GLU cc_start: 0.8035 (tt0) cc_final: 0.7624 (mt-10) REVERT: W 54 HIS cc_start: 0.7589 (t-90) cc_final: 0.7345 (t-90) REVERT: Y 20 TYR cc_start: 0.7995 (m-10) cc_final: 0.7512 (m-10) REVERT: Y 69 GLN cc_start: 0.8100 (mt0) cc_final: 0.7872 (mt0) REVERT: Z 115 ASP cc_start: 0.7994 (t70) cc_final: 0.7166 (t0) REVERT: Z 116 ASP cc_start: 0.7656 (p0) cc_final: 0.7453 (p0) REVERT: a 29 ARG cc_start: 0.8060 (mmm160) cc_final: 0.7345 (tpm170) REVERT: a 39 THR cc_start: 0.9114 (t) cc_final: 0.8841 (m) REVERT: a 233 ASN cc_start: 0.8460 (OUTLIER) cc_final: 0.7987 (p0) REVERT: b 22 MET cc_start: 0.7961 (ttm) cc_final: 0.7736 (ttm) REVERT: b 75 ASN cc_start: 0.8610 (OUTLIER) cc_final: 0.8179 (t0) REVERT: b 89 GLN cc_start: 0.9237 (tm-30) cc_final: 0.8903 (tm-30) outliers start: 171 outliers final: 130 residues processed: 949 average time/residue: 0.5945 time to fit residues: 942.3702 Evaluate side-chains 945 residues out of total 5552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 808 time to evaluate : 5.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 182 ASP Chi-restraints excluded: chain D residue 68 HIS Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 91 CYS Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 225 MET Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 151 ASN Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 52 CYS Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 168 ILE Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 172 SER Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 109 GLN Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain I residue 204 ILE Chi-restraints excluded: chain I residue 209 THR Chi-restraints excluded: chain I residue 212 ILE Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 67 GLU Chi-restraints excluded: chain J residue 202 VAL Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 125 ASP Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain L residue 14 VAL Chi-restraints excluded: chain L residue 115 ASP Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 180 HIS Chi-restraints excluded: chain L residue 194 PHE Chi-restraints excluded: chain M residue 41 ILE Chi-restraints excluded: chain M residue 233 ASN Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 33 SER Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain N residue 109 LEU Chi-restraints excluded: chain N residue 174 ASP Chi-restraints excluded: chain N residue 219 THR Chi-restraints excluded: chain O residue 12 HIS Chi-restraints excluded: chain O residue 173 VAL Chi-restraints excluded: chain O residue 233 ILE Chi-restraints excluded: chain P residue 36 LEU Chi-restraints excluded: chain P residue 48 THR Chi-restraints excluded: chain P residue 184 ILE Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 45 LEU Chi-restraints excluded: chain Q residue 117 ILE Chi-restraints excluded: chain Q residue 134 PHE Chi-restraints excluded: chain Q residue 155 ASN Chi-restraints excluded: chain Q residue 174 VAL Chi-restraints excluded: chain R residue 13 ASP Chi-restraints excluded: chain R residue 68 HIS Chi-restraints excluded: chain R residue 70 CYS Chi-restraints excluded: chain R residue 91 CYS Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 129 ILE Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain R residue 225 MET Chi-restraints excluded: chain S residue 21 LEU Chi-restraints excluded: chain S residue 47 ILE Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 148 VAL Chi-restraints excluded: chain S residue 151 ASN Chi-restraints excluded: chain T residue 12 ILE Chi-restraints excluded: chain T residue 52 CYS Chi-restraints excluded: chain T residue 176 HIS Chi-restraints excluded: chain T residue 226 LEU Chi-restraints excluded: chain U residue 113 ILE Chi-restraints excluded: chain U residue 141 SER Chi-restraints excluded: chain U residue 197 TYR Chi-restraints excluded: chain U residue 232 ILE Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain V residue 41 LEU Chi-restraints excluded: chain V residue 59 ILE Chi-restraints excluded: chain V residue 128 LEU Chi-restraints excluded: chain V residue 140 ILE Chi-restraints excluded: chain V residue 172 SER Chi-restraints excluded: chain V residue 178 ASP Chi-restraints excluded: chain V residue 184 SER Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 95 VAL Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 132 LEU Chi-restraints excluded: chain W residue 204 ILE Chi-restraints excluded: chain W residue 212 ILE Chi-restraints excluded: chain X residue 36 THR Chi-restraints excluded: chain X residue 67 GLU Chi-restraints excluded: chain X residue 202 VAL Chi-restraints excluded: chain Y residue 93 LEU Chi-restraints excluded: chain Y residue 165 GLU Chi-restraints excluded: chain Z residue 14 VAL Chi-restraints excluded: chain Z residue 125 LEU Chi-restraints excluded: chain Z residue 137 SER Chi-restraints excluded: chain Z residue 180 HIS Chi-restraints excluded: chain Z residue 194 PHE Chi-restraints excluded: chain Z residue 201 THR Chi-restraints excluded: chain a residue 63 ILE Chi-restraints excluded: chain a residue 233 ASN Chi-restraints excluded: chain b residue 6 VAL Chi-restraints excluded: chain b residue 12 VAL Chi-restraints excluded: chain b residue 33 SER Chi-restraints excluded: chain b residue 73 ILE Chi-restraints excluded: chain b residue 75 ASN Chi-restraints excluded: chain b residue 109 LEU Chi-restraints excluded: chain b residue 174 ASP Chi-restraints excluded: chain b residue 206 ILE Chi-restraints excluded: chain b residue 219 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 620 random chunks: chunk 578 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 341 optimal weight: 0.5980 chunk 438 optimal weight: 5.9990 chunk 339 optimal weight: 7.9990 chunk 504 optimal weight: 3.9990 chunk 334 optimal weight: 3.9990 chunk 597 optimal weight: 3.9990 chunk 373 optimal weight: 0.9990 chunk 364 optimal weight: 4.9990 chunk 275 optimal weight: 4.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 ASN ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 230 GLN ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 151 GLN L 197 HIS O 114 ASN ** P 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 151 GLN Z 197 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 51464 Z= 0.351 Angle : 0.620 15.644 69484 Z= 0.324 Chirality : 0.046 0.233 7764 Planarity : 0.004 0.060 8864 Dihedral : 6.948 73.992 7030 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 3.57 % Allowed : 20.01 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.11), residues: 6250 helix: 0.17 (0.11), residues: 2138 sheet: -1.49 (0.14), residues: 1368 loop : -2.08 (0.12), residues: 2744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 179 HIS 0.018 0.001 HIS T 176 PHE 0.023 0.002 PHE R 194 TYR 0.023 0.002 TYR H 118 ARG 0.007 0.001 ARG S 20 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12500 Ramachandran restraints generated. 6250 Oldfield, 0 Emsley, 6250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12500 Ramachandran restraints generated. 6250 Oldfield, 0 Emsley, 6250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1012 residues out of total 5552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 814 time to evaluate : 6.565 Fit side-chains REVERT: B 119 GLN cc_start: 0.7928 (tm-30) cc_final: 0.7413 (tm-30) REVERT: B 184 ILE cc_start: 0.6797 (OUTLIER) cc_final: 0.6110 (mt) REVERT: C 62 TYR cc_start: 0.7396 (OUTLIER) cc_final: 0.5413 (p90) REVERT: C 93 TYR cc_start: 0.7852 (m-10) cc_final: 0.6984 (m-10) REVERT: C 130 TYR cc_start: 0.8749 (m-80) cc_final: 0.8517 (m-10) REVERT: D 5 ARG cc_start: 0.5898 (ptm160) cc_final: 0.5690 (ptm160) REVERT: D 66 ASP cc_start: 0.8608 (m-30) cc_final: 0.8214 (m-30) REVERT: D 99 ASP cc_start: 0.8339 (t0) cc_final: 0.8061 (t0) REVERT: E 114 GLU cc_start: 0.8424 (tp30) cc_final: 0.8105 (tt0) REVERT: E 212 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8727 (mm) REVERT: E 230 TYR cc_start: 0.8415 (t80) cc_final: 0.8037 (t80) REVERT: F 68 ASP cc_start: 0.7728 (m-30) cc_final: 0.7434 (m-30) REVERT: F 139 ASN cc_start: 0.8071 (m-40) cc_final: 0.7853 (m110) REVERT: F 223 ILE cc_start: 0.8570 (mm) cc_final: 0.8293 (mm) REVERT: G 97 GLU cc_start: 0.7830 (tp30) cc_final: 0.7550 (tp30) REVERT: H 156 TYR cc_start: 0.8195 (t80) cc_final: 0.7914 (t80) REVERT: I 53 GLU cc_start: 0.8120 (tt0) cc_final: 0.7688 (mt-10) REVERT: I 54 HIS cc_start: 0.7672 (t-90) cc_final: 0.7403 (t-90) REVERT: I 174 ASP cc_start: 0.8526 (p0) cc_final: 0.8165 (p0) REVERT: K 20 TYR cc_start: 0.8083 (m-10) cc_final: 0.7675 (m-10) REVERT: K 72 ASN cc_start: 0.7954 (OUTLIER) cc_final: 0.7741 (m-40) REVERT: L 150 ASP cc_start: 0.7800 (OUTLIER) cc_final: 0.7550 (m-30) REVERT: L 197 HIS cc_start: 0.8454 (OUTLIER) cc_final: 0.8042 (t-170) REVERT: M 29 ARG cc_start: 0.8152 (mmm160) cc_final: 0.7337 (tpm170) REVERT: M 233 ASN cc_start: 0.8474 (OUTLIER) cc_final: 0.8096 (p0) REVERT: N 89 GLN cc_start: 0.9285 (tm-30) cc_final: 0.8892 (tm-30) REVERT: O 129 GLN cc_start: 0.8442 (tm-30) cc_final: 0.7910 (tm-30) REVERT: O 137 MET cc_start: 0.7863 (mpp) cc_final: 0.7467 (mpp) REVERT: P 119 GLN cc_start: 0.7923 (tm-30) cc_final: 0.7440 (tm-30) REVERT: Q 62 TYR cc_start: 0.7384 (OUTLIER) cc_final: 0.5336 (p90) REVERT: Q 93 TYR cc_start: 0.7850 (m-10) cc_final: 0.6970 (m-10) REVERT: Q 155 ASN cc_start: 0.8224 (OUTLIER) cc_final: 0.7997 (p0) REVERT: R 37 SER cc_start: 0.8747 (t) cc_final: 0.8513 (t) REVERT: R 99 ASP cc_start: 0.8363 (t0) cc_final: 0.8089 (t0) REVERT: R 153 TYR cc_start: 0.8768 (p90) cc_final: 0.8470 (p90) REVERT: S 51 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.7176 (mt-10) REVERT: S 114 GLU cc_start: 0.8380 (tp30) cc_final: 0.8070 (tt0) REVERT: S 212 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8799 (mm) REVERT: S 230 TYR cc_start: 0.8483 (t80) cc_final: 0.8102 (t80) REVERT: T 68 ASP cc_start: 0.7743 (m-30) cc_final: 0.7418 (m-30) REVERT: T 139 ASN cc_start: 0.8152 (m110) cc_final: 0.7846 (m110) REVERT: T 223 ILE cc_start: 0.8585 (mm) cc_final: 0.8173 (mm) REVERT: T 227 GLN cc_start: 0.8652 (tm-30) cc_final: 0.8433 (tm-30) REVERT: U 97 GLU cc_start: 0.7888 (tp30) cc_final: 0.7641 (tp30) REVERT: V 156 TYR cc_start: 0.8188 (t80) cc_final: 0.7881 (t80) REVERT: V 182 SER cc_start: 0.8621 (p) cc_final: 0.8243 (m) REVERT: W 53 GLU cc_start: 0.8113 (tt0) cc_final: 0.7700 (mt-10) REVERT: W 54 HIS cc_start: 0.7735 (t-90) cc_final: 0.7451 (t-90) REVERT: Y 2 ASP cc_start: 0.7826 (p0) cc_final: 0.7623 (p0) REVERT: Y 20 TYR cc_start: 0.8109 (m-10) cc_final: 0.7697 (m-10) REVERT: Y 69 GLN cc_start: 0.7940 (mt0) cc_final: 0.7694 (mt0) REVERT: Y 72 ASN cc_start: 0.7857 (OUTLIER) cc_final: 0.7649 (m-40) REVERT: Y 165 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8294 (tt0) REVERT: Z 115 ASP cc_start: 0.8181 (t70) cc_final: 0.7609 (t0) REVERT: Z 150 ASP cc_start: 0.7797 (OUTLIER) cc_final: 0.7542 (m-30) REVERT: Z 197 HIS cc_start: 0.8366 (OUTLIER) cc_final: 0.7934 (t-170) REVERT: a 233 ASN cc_start: 0.8530 (OUTLIER) cc_final: 0.8022 (p0) REVERT: b 22 MET cc_start: 0.7964 (ttm) cc_final: 0.7753 (ttm) REVERT: b 89 GLN cc_start: 0.9275 (tm-30) cc_final: 0.8880 (tm-30) REVERT: b 155 HIS cc_start: 0.7098 (t-170) cc_final: 0.6890 (t-90) outliers start: 198 outliers final: 151 residues processed: 937 average time/residue: 0.6145 time to fit residues: 956.2338 Evaluate side-chains 941 residues out of total 5552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 774 time to evaluate : 6.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 172 CYS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 134 PHE Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 182 ASP Chi-restraints excluded: chain D residue 68 HIS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 91 CYS Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 225 MET Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 151 ASN Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 52 CYS Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 163 ARG Chi-restraints excluded: chain F residue 176 HIS Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 168 ILE Chi-restraints excluded: chain G residue 237 LEU Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 162 GLN Chi-restraints excluded: chain H residue 172 SER Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain I residue 204 ILE Chi-restraints excluded: chain I residue 209 THR Chi-restraints excluded: chain I residue 212 ILE Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 67 GLU Chi-restraints excluded: chain J residue 202 VAL Chi-restraints excluded: chain J residue 209 ILE Chi-restraints excluded: chain K residue 72 ASN Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 125 ASP Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain L residue 14 VAL Chi-restraints excluded: chain L residue 115 ASP Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 150 ASP Chi-restraints excluded: chain L residue 180 HIS Chi-restraints excluded: chain L residue 194 PHE Chi-restraints excluded: chain L residue 197 HIS Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain M residue 41 ILE Chi-restraints excluded: chain M residue 170 SER Chi-restraints excluded: chain M residue 233 ASN Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 33 SER Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain N residue 174 ASP Chi-restraints excluded: chain N residue 206 ILE Chi-restraints excluded: chain N residue 219 THR Chi-restraints excluded: chain O residue 12 HIS Chi-restraints excluded: chain O residue 142 CYS Chi-restraints excluded: chain O residue 173 VAL Chi-restraints excluded: chain O residue 233 ILE Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 36 LEU Chi-restraints excluded: chain P residue 48 THR Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 45 LEU Chi-restraints excluded: chain Q residue 62 TYR Chi-restraints excluded: chain Q residue 117 ILE Chi-restraints excluded: chain Q residue 132 VAL Chi-restraints excluded: chain Q residue 134 PHE Chi-restraints excluded: chain Q residue 155 ASN Chi-restraints excluded: chain Q residue 174 VAL Chi-restraints excluded: chain Q residue 182 ASP Chi-restraints excluded: chain Q residue 183 MET Chi-restraints excluded: chain R residue 13 ASP Chi-restraints excluded: chain R residue 68 HIS Chi-restraints excluded: chain R residue 70 CYS Chi-restraints excluded: chain R residue 91 CYS Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 129 ILE Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain R residue 225 MET Chi-restraints excluded: chain S residue 21 LEU Chi-restraints excluded: chain S residue 47 ILE Chi-restraints excluded: chain S residue 51 GLU Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 148 VAL Chi-restraints excluded: chain S residue 151 ASN Chi-restraints excluded: chain S residue 154 CYS Chi-restraints excluded: chain S residue 212 LEU Chi-restraints excluded: chain T residue 12 ILE Chi-restraints excluded: chain T residue 52 CYS Chi-restraints excluded: chain T residue 98 LEU Chi-restraints excluded: chain T residue 226 LEU Chi-restraints excluded: chain U residue 113 ILE Chi-restraints excluded: chain U residue 118 ILE Chi-restraints excluded: chain U residue 141 SER Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain V residue 41 LEU Chi-restraints excluded: chain V residue 58 ILE Chi-restraints excluded: chain V residue 59 ILE Chi-restraints excluded: chain V residue 128 LEU Chi-restraints excluded: chain V residue 140 ILE Chi-restraints excluded: chain V residue 162 GLN Chi-restraints excluded: chain V residue 172 SER Chi-restraints excluded: chain V residue 178 ASP Chi-restraints excluded: chain V residue 184 SER Chi-restraints excluded: chain V residue 201 MET Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 95 VAL Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 132 LEU Chi-restraints excluded: chain W residue 174 ASP Chi-restraints excluded: chain W residue 212 ILE Chi-restraints excluded: chain X residue 36 THR Chi-restraints excluded: chain X residue 67 GLU Chi-restraints excluded: chain X residue 134 LEU Chi-restraints excluded: chain X residue 202 VAL Chi-restraints excluded: chain X residue 209 ILE Chi-restraints excluded: chain Y residue 72 ASN Chi-restraints excluded: chain Y residue 93 LEU Chi-restraints excluded: chain Y residue 165 GLU Chi-restraints excluded: chain Y residue 183 MET Chi-restraints excluded: chain Z residue 14 VAL Chi-restraints excluded: chain Z residue 125 LEU Chi-restraints excluded: chain Z residue 137 SER Chi-restraints excluded: chain Z residue 150 ASP Chi-restraints excluded: chain Z residue 180 HIS Chi-restraints excluded: chain Z residue 194 PHE Chi-restraints excluded: chain Z residue 197 HIS Chi-restraints excluded: chain Z residue 201 THR Chi-restraints excluded: chain a residue 63 ILE Chi-restraints excluded: chain a residue 170 SER Chi-restraints excluded: chain a residue 233 ASN Chi-restraints excluded: chain b residue 6 VAL Chi-restraints excluded: chain b residue 12 VAL Chi-restraints excluded: chain b residue 33 SER Chi-restraints excluded: chain b residue 73 ILE Chi-restraints excluded: chain b residue 174 ASP Chi-restraints excluded: chain b residue 206 ILE Chi-restraints excluded: chain b residue 219 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 620 random chunks: chunk 369 optimal weight: 0.9980 chunk 238 optimal weight: 0.9990 chunk 356 optimal weight: 0.0570 chunk 180 optimal weight: 3.9990 chunk 117 optimal weight: 8.9990 chunk 115 optimal weight: 10.0000 chunk 379 optimal weight: 1.9990 chunk 407 optimal weight: 3.9990 chunk 295 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 469 optimal weight: 0.9980 overall best weight: 1.0102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 HIS ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 ASN ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 177 HIS ** I 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 151 GLN L 197 HIS M 190 ASN N 155 HIS ** P 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 176 HIS ** U 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 230 GLN ** V 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 151 GLN Z 197 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 51464 Z= 0.197 Angle : 0.559 16.238 69484 Z= 0.293 Chirality : 0.044 0.229 7764 Planarity : 0.004 0.058 8864 Dihedral : 6.821 75.982 7030 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 3.21 % Allowed : 20.59 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.11), residues: 6250 helix: 0.36 (0.11), residues: 2118 sheet: -1.36 (0.14), residues: 1348 loop : -1.99 (0.12), residues: 2784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 179 HIS 0.019 0.001 HIS L 197 PHE 0.014 0.001 PHE D 194 TYR 0.022 0.001 TYR Z 198 ARG 0.007 0.000 ARG a 29 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12500 Ramachandran restraints generated. 6250 Oldfield, 0 Emsley, 6250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12500 Ramachandran restraints generated. 6250 Oldfield, 0 Emsley, 6250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1000 residues out of total 5552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 822 time to evaluate : 6.266 Fit side-chains REVERT: A 77 ASN cc_start: 0.8313 (OUTLIER) cc_final: 0.7879 (p0) REVERT: A 253 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7500 (mm) REVERT: B 100 GLN cc_start: 0.8483 (mt0) cc_final: 0.8151 (mt0) REVERT: B 119 GLN cc_start: 0.7749 (tm-30) cc_final: 0.7206 (tm-30) REVERT: B 159 MET cc_start: 0.7804 (mmt) cc_final: 0.7165 (mmt) REVERT: B 184 ILE cc_start: 0.6635 (OUTLIER) cc_final: 0.6035 (mt) REVERT: C 93 TYR cc_start: 0.7754 (m-10) cc_final: 0.6876 (m-10) REVERT: C 130 TYR cc_start: 0.8723 (m-80) cc_final: 0.8470 (m-10) REVERT: C 224 GLN cc_start: 0.6503 (OUTLIER) cc_final: 0.5627 (mp10) REVERT: D 5 ARG cc_start: 0.5752 (ptm160) cc_final: 0.5542 (ptm160) REVERT: D 66 ASP cc_start: 0.8630 (m-30) cc_final: 0.8365 (m-30) REVERT: D 99 ASP cc_start: 0.8273 (t0) cc_final: 0.7996 (t0) REVERT: E 114 GLU cc_start: 0.8383 (tp30) cc_final: 0.8056 (tt0) REVERT: E 212 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8735 (mm) REVERT: E 230 TYR cc_start: 0.8416 (t80) cc_final: 0.8105 (t80) REVERT: F 68 ASP cc_start: 0.7703 (m-30) cc_final: 0.7414 (m-30) REVERT: F 139 ASN cc_start: 0.7984 (m-40) cc_final: 0.7779 (m110) REVERT: F 223 ILE cc_start: 0.8549 (mm) cc_final: 0.8250 (mm) REVERT: G 97 GLU cc_start: 0.7746 (tp30) cc_final: 0.7515 (tp30) REVERT: H 32 ARG cc_start: 0.7930 (mmt-90) cc_final: 0.7514 (mmm160) REVERT: H 156 TYR cc_start: 0.8154 (t80) cc_final: 0.7884 (t80) REVERT: I 53 GLU cc_start: 0.8086 (tt0) cc_final: 0.7701 (mt-10) REVERT: I 54 HIS cc_start: 0.7727 (t-90) cc_final: 0.7466 (t-90) REVERT: I 174 ASP cc_start: 0.8565 (p0) cc_final: 0.8275 (p0) REVERT: K 20 TYR cc_start: 0.7981 (m-10) cc_final: 0.7536 (m-10) REVERT: L 3 THR cc_start: 0.9023 (m) cc_final: 0.8694 (m) REVERT: M 29 ARG cc_start: 0.8056 (mmm160) cc_final: 0.7623 (tpm170) REVERT: M 233 ASN cc_start: 0.8442 (OUTLIER) cc_final: 0.8238 (p0) REVERT: N 89 GLN cc_start: 0.9249 (tm-30) cc_final: 0.8905 (tm-30) REVERT: O 77 ASN cc_start: 0.8308 (OUTLIER) cc_final: 0.7859 (p0) REVERT: O 129 GLN cc_start: 0.8345 (tm-30) cc_final: 0.7895 (tm-30) REVERT: P 119 GLN cc_start: 0.7777 (tm-30) cc_final: 0.7262 (tm-30) REVERT: P 203 LEU cc_start: 0.6432 (OUTLIER) cc_final: 0.5961 (pt) REVERT: Q 93 TYR cc_start: 0.7752 (m-10) cc_final: 0.6862 (m-10) REVERT: Q 155 ASN cc_start: 0.8104 (OUTLIER) cc_final: 0.7831 (p0) REVERT: Q 224 GLN cc_start: 0.6346 (OUTLIER) cc_final: 0.5454 (mp10) REVERT: R 37 SER cc_start: 0.8724 (t) cc_final: 0.8485 (t) REVERT: R 66 ASP cc_start: 0.8654 (m-30) cc_final: 0.8446 (m-30) REVERT: R 99 ASP cc_start: 0.8263 (t0) cc_final: 0.7966 (t0) REVERT: R 153 TYR cc_start: 0.8727 (p90) cc_final: 0.8472 (p90) REVERT: S 51 GLU cc_start: 0.7361 (mt-10) cc_final: 0.7026 (mt-10) REVERT: S 114 GLU cc_start: 0.8354 (tp30) cc_final: 0.8055 (tt0) REVERT: S 212 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8759 (mm) REVERT: S 230 TYR cc_start: 0.8481 (t80) cc_final: 0.8130 (t80) REVERT: T 68 ASP cc_start: 0.7715 (m-30) cc_final: 0.7403 (m-30) REVERT: T 139 ASN cc_start: 0.8093 (m110) cc_final: 0.7850 (m110) REVERT: T 223 ILE cc_start: 0.8564 (mm) cc_final: 0.8076 (mm) REVERT: U 97 GLU cc_start: 0.7733 (tp30) cc_final: 0.7511 (tp30) REVERT: V 156 TYR cc_start: 0.8144 (t80) cc_final: 0.7856 (t80) REVERT: V 182 SER cc_start: 0.8624 (OUTLIER) cc_final: 0.8278 (m) REVERT: W 53 GLU cc_start: 0.8031 (tt0) cc_final: 0.7660 (mt-10) REVERT: W 54 HIS cc_start: 0.7656 (t-90) cc_final: 0.7370 (t-90) REVERT: Y 2 ASP cc_start: 0.7811 (p0) cc_final: 0.7579 (p0) REVERT: Y 20 TYR cc_start: 0.8013 (m-10) cc_final: 0.7567 (m-10) REVERT: Y 69 GLN cc_start: 0.8113 (mt0) cc_final: 0.7885 (mt0) REVERT: Z 3 THR cc_start: 0.9063 (m) cc_final: 0.8738 (m) REVERT: Z 115 ASP cc_start: 0.8089 (t70) cc_final: 0.7294 (t0) REVERT: a 29 ARG cc_start: 0.8098 (mmm160) cc_final: 0.7289 (tpm170) REVERT: a 233 ASN cc_start: 0.8499 (OUTLIER) cc_final: 0.8037 (p0) REVERT: b 22 MET cc_start: 0.7950 (ttm) cc_final: 0.7725 (ttm) REVERT: b 89 GLN cc_start: 0.9248 (tm-30) cc_final: 0.8900 (tm-30) outliers start: 178 outliers final: 140 residues processed: 927 average time/residue: 0.6039 time to fit residues: 934.7615 Evaluate side-chains 937 residues out of total 5552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 784 time to evaluate : 6.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 77 ASN Chi-restraints excluded: chain A residue 172 CYS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 134 PHE Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 182 ASP Chi-restraints excluded: chain C residue 224 GLN Chi-restraints excluded: chain D residue 68 HIS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 91 CYS Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 225 MET Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain E residue 151 ASN Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 52 CYS Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 163 ARG Chi-restraints excluded: chain F residue 176 HIS Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 168 ILE Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 162 GLN Chi-restraints excluded: chain H residue 172 SER Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain I residue 204 ILE Chi-restraints excluded: chain I residue 209 THR Chi-restraints excluded: chain I residue 212 ILE Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 67 GLU Chi-restraints excluded: chain J residue 202 VAL Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 125 ASP Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain L residue 14 VAL Chi-restraints excluded: chain L residue 115 ASP Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 180 HIS Chi-restraints excluded: chain L residue 194 PHE Chi-restraints excluded: chain M residue 41 ILE Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain M residue 233 ASN Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 33 SER Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain N residue 174 ASP Chi-restraints excluded: chain N residue 206 ILE Chi-restraints excluded: chain N residue 219 THR Chi-restraints excluded: chain O residue 12 HIS Chi-restraints excluded: chain O residue 77 ASN Chi-restraints excluded: chain O residue 142 CYS Chi-restraints excluded: chain O residue 173 VAL Chi-restraints excluded: chain O residue 233 ILE Chi-restraints excluded: chain P residue 36 LEU Chi-restraints excluded: chain P residue 203 LEU Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 45 LEU Chi-restraints excluded: chain Q residue 117 ILE Chi-restraints excluded: chain Q residue 132 VAL Chi-restraints excluded: chain Q residue 134 PHE Chi-restraints excluded: chain Q residue 155 ASN Chi-restraints excluded: chain Q residue 174 VAL Chi-restraints excluded: chain Q residue 182 ASP Chi-restraints excluded: chain Q residue 224 GLN Chi-restraints excluded: chain R residue 13 ASP Chi-restraints excluded: chain R residue 68 HIS Chi-restraints excluded: chain R residue 70 CYS Chi-restraints excluded: chain R residue 91 CYS Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 129 ILE Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain R residue 225 MET Chi-restraints excluded: chain S residue 21 LEU Chi-restraints excluded: chain S residue 47 ILE Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 148 VAL Chi-restraints excluded: chain S residue 151 ASN Chi-restraints excluded: chain S residue 154 CYS Chi-restraints excluded: chain S residue 212 LEU Chi-restraints excluded: chain T residue 12 ILE Chi-restraints excluded: chain T residue 52 CYS Chi-restraints excluded: chain T residue 98 LEU Chi-restraints excluded: chain T residue 226 LEU Chi-restraints excluded: chain U residue 113 ILE Chi-restraints excluded: chain U residue 141 SER Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain V residue 41 LEU Chi-restraints excluded: chain V residue 58 ILE Chi-restraints excluded: chain V residue 59 ILE Chi-restraints excluded: chain V residue 128 LEU Chi-restraints excluded: chain V residue 140 ILE Chi-restraints excluded: chain V residue 172 SER Chi-restraints excluded: chain V residue 178 ASP Chi-restraints excluded: chain V residue 182 SER Chi-restraints excluded: chain V residue 184 SER Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 95 VAL Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 132 LEU Chi-restraints excluded: chain W residue 174 ASP Chi-restraints excluded: chain W residue 212 ILE Chi-restraints excluded: chain X residue 36 THR Chi-restraints excluded: chain X residue 67 GLU Chi-restraints excluded: chain X residue 134 LEU Chi-restraints excluded: chain X residue 202 VAL Chi-restraints excluded: chain X residue 209 ILE Chi-restraints excluded: chain Y residue 93 LEU Chi-restraints excluded: chain Y residue 183 MET Chi-restraints excluded: chain Z residue 14 VAL Chi-restraints excluded: chain Z residue 125 LEU Chi-restraints excluded: chain Z residue 137 SER Chi-restraints excluded: chain Z residue 180 HIS Chi-restraints excluded: chain Z residue 194 PHE Chi-restraints excluded: chain Z residue 201 THR Chi-restraints excluded: chain a residue 63 ILE Chi-restraints excluded: chain a residue 170 SER Chi-restraints excluded: chain a residue 233 ASN Chi-restraints excluded: chain b residue 6 VAL Chi-restraints excluded: chain b residue 12 VAL Chi-restraints excluded: chain b residue 33 SER Chi-restraints excluded: chain b residue 73 ILE Chi-restraints excluded: chain b residue 174 ASP Chi-restraints excluded: chain b residue 206 ILE Chi-restraints excluded: chain b residue 219 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 620 random chunks: chunk 543 optimal weight: 0.9990 chunk 572 optimal weight: 5.9990 chunk 522 optimal weight: 2.9990 chunk 556 optimal weight: 0.2980 chunk 335 optimal weight: 4.9990 chunk 242 optimal weight: 4.9990 chunk 437 optimal weight: 4.9990 chunk 170 optimal weight: 0.8980 chunk 503 optimal weight: 0.8980 chunk 526 optimal weight: 0.4980 chunk 554 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 ASN ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 56 GLN ** P 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 51464 Z= 0.162 Angle : 0.541 15.555 69484 Z= 0.283 Chirality : 0.043 0.240 7764 Planarity : 0.004 0.062 8864 Dihedral : 6.673 75.836 7030 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 2.97 % Allowed : 21.02 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.11), residues: 6250 helix: 0.54 (0.12), residues: 2122 sheet: -1.24 (0.14), residues: 1324 loop : -1.91 (0.12), residues: 2804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 179 HIS 0.006 0.001 HIS V 134 PHE 0.019 0.001 PHE b 110 TYR 0.043 0.001 TYR L 88 ARG 0.007 0.000 ARG S 20 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12500 Ramachandran restraints generated. 6250 Oldfield, 0 Emsley, 6250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12500 Ramachandran restraints generated. 6250 Oldfield, 0 Emsley, 6250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1020 residues out of total 5552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 855 time to evaluate : 6.108 Fit side-chains revert: symmetry clash REVERT: A 77 ASN cc_start: 0.8266 (OUTLIER) cc_final: 0.7792 (p0) REVERT: A 253 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7318 (mm) REVERT: B 119 GLN cc_start: 0.7652 (tm-30) cc_final: 0.7319 (tm-30) REVERT: B 158 TRP cc_start: 0.8467 (m100) cc_final: 0.8113 (m100) REVERT: B 159 MET cc_start: 0.7775 (mmt) cc_final: 0.7123 (mmt) REVERT: B 184 ILE cc_start: 0.6569 (OUTLIER) cc_final: 0.6259 (mt) REVERT: C 62 TYR cc_start: 0.7212 (OUTLIER) cc_final: 0.5397 (p90) REVERT: C 92 LEU cc_start: 0.8637 (mt) cc_final: 0.8296 (mm) REVERT: C 93 TYR cc_start: 0.7727 (m-10) cc_final: 0.6854 (m-10) REVERT: C 130 TYR cc_start: 0.8761 (m-80) cc_final: 0.8506 (m-10) REVERT: C 224 GLN cc_start: 0.6511 (OUTLIER) cc_final: 0.5671 (mp10) REVERT: D 66 ASP cc_start: 0.8625 (m-30) cc_final: 0.8348 (m-30) REVERT: D 99 ASP cc_start: 0.8185 (t0) cc_final: 0.7914 (t0) REVERT: D 215 THR cc_start: 0.7211 (m) cc_final: 0.6903 (p) REVERT: D 225 MET cc_start: 0.7745 (OUTLIER) cc_final: 0.7363 (mmt) REVERT: E 114 GLU cc_start: 0.8353 (tp30) cc_final: 0.8071 (tt0) REVERT: E 212 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8702 (mm) REVERT: E 230 TYR cc_start: 0.8411 (t80) cc_final: 0.8159 (t80) REVERT: F 68 ASP cc_start: 0.7681 (m-30) cc_final: 0.7406 (m-30) REVERT: F 223 ILE cc_start: 0.8452 (mm) cc_final: 0.8137 (mm) REVERT: G 44 ASP cc_start: 0.8178 (m-30) cc_final: 0.7875 (m-30) REVERT: G 57 LYS cc_start: 0.6309 (tptp) cc_final: 0.5876 (pttm) REVERT: G 68 ARG cc_start: 0.8548 (mtp180) cc_final: 0.8277 (mtp-110) REVERT: G 97 GLU cc_start: 0.7651 (tp30) cc_final: 0.7439 (tp30) REVERT: H 32 ARG cc_start: 0.7911 (mmt-90) cc_final: 0.7465 (mmm160) REVERT: H 138 LYS cc_start: 0.7592 (tptp) cc_final: 0.7165 (tptt) REVERT: H 156 TYR cc_start: 0.8123 (t80) cc_final: 0.7868 (t80) REVERT: I 53 GLU cc_start: 0.8025 (tt0) cc_final: 0.7691 (mt-10) REVERT: I 54 HIS cc_start: 0.7631 (t-90) cc_final: 0.7379 (t-90) REVERT: I 174 ASP cc_start: 0.8309 (p0) cc_final: 0.7876 (p0) REVERT: K 20 TYR cc_start: 0.7977 (m-10) cc_final: 0.7543 (m-10) REVERT: K 165 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8222 (mt-10) REVERT: M 29 ARG cc_start: 0.8020 (mmm160) cc_final: 0.7596 (tpm170) REVERT: M 39 THR cc_start: 0.9141 (t) cc_final: 0.8860 (m) REVERT: M 171 GLN cc_start: 0.8440 (mm-40) cc_final: 0.8116 (mt0) REVERT: M 233 ASN cc_start: 0.8448 (OUTLIER) cc_final: 0.8248 (p0) REVERT: N 89 GLN cc_start: 0.9221 (tm-30) cc_final: 0.8898 (tm-30) REVERT: O 77 ASN cc_start: 0.8238 (OUTLIER) cc_final: 0.7779 (p0) REVERT: O 129 GLN cc_start: 0.8316 (tm-30) cc_final: 0.7866 (tm-30) REVERT: O 137 MET cc_start: 0.7855 (mpp) cc_final: 0.7600 (mpp) REVERT: O 224 LEU cc_start: 0.8667 (mm) cc_final: 0.8417 (tp) REVERT: P 119 GLN cc_start: 0.7630 (tm-30) cc_final: 0.7285 (tm-30) REVERT: P 171 MET cc_start: 0.8794 (tpp) cc_final: 0.8589 (mmm) REVERT: Q 92 LEU cc_start: 0.8623 (mt) cc_final: 0.8276 (mm) REVERT: Q 93 TYR cc_start: 0.7734 (m-10) cc_final: 0.6843 (m-10) REVERT: Q 155 ASN cc_start: 0.8056 (OUTLIER) cc_final: 0.7772 (p0) REVERT: Q 224 GLN cc_start: 0.6377 (OUTLIER) cc_final: 0.5563 (mp10) REVERT: R 37 SER cc_start: 0.8740 (t) cc_final: 0.8501 (t) REVERT: R 99 ASP cc_start: 0.8218 (t0) cc_final: 0.7901 (t0) REVERT: R 153 TYR cc_start: 0.8648 (p90) cc_final: 0.8440 (p90) REVERT: S 51 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6917 (mt-10) REVERT: S 114 GLU cc_start: 0.8328 (tp30) cc_final: 0.8075 (tt0) REVERT: S 212 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8642 (mm) REVERT: S 230 TYR cc_start: 0.8427 (t80) cc_final: 0.8099 (t80) REVERT: T 68 ASP cc_start: 0.7692 (m-30) cc_final: 0.7401 (m-30) REVERT: U 57 LYS cc_start: 0.5964 (tptp) cc_final: 0.5723 (pttm) REVERT: V 138 LYS cc_start: 0.7585 (tptp) cc_final: 0.7172 (tptt) REVERT: V 156 TYR cc_start: 0.8119 (t80) cc_final: 0.7840 (t80) REVERT: V 182 SER cc_start: 0.8511 (OUTLIER) cc_final: 0.8285 (m) REVERT: W 53 GLU cc_start: 0.7967 (tt0) cc_final: 0.7688 (mt-10) REVERT: W 54 HIS cc_start: 0.7627 (t-90) cc_final: 0.7357 (t-90) REVERT: Y 2 ASP cc_start: 0.7815 (p0) cc_final: 0.7584 (p0) REVERT: Y 20 TYR cc_start: 0.8010 (m-10) cc_final: 0.7592 (m-10) REVERT: Y 69 GLN cc_start: 0.8095 (mt0) cc_final: 0.7852 (mt0) REVERT: Z 3 THR cc_start: 0.8913 (m) cc_final: 0.8601 (m) REVERT: Z 115 ASP cc_start: 0.8032 (t70) cc_final: 0.7250 (t0) REVERT: a 29 ARG cc_start: 0.8078 (mmm160) cc_final: 0.7314 (tpm170) REVERT: a 233 ASN cc_start: 0.8520 (OUTLIER) cc_final: 0.8033 (p0) REVERT: b 22 MET cc_start: 0.7960 (ttm) cc_final: 0.7738 (ttm) REVERT: b 75 ASN cc_start: 0.8525 (t0) cc_final: 0.8118 (t0) REVERT: b 89 GLN cc_start: 0.9224 (tm-30) cc_final: 0.8892 (tm-30) outliers start: 165 outliers final: 130 residues processed: 955 average time/residue: 0.5982 time to fit residues: 958.5696 Evaluate side-chains 949 residues out of total 5552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 804 time to evaluate : 5.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 77 ASN Chi-restraints excluded: chain A residue 172 CYS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 155 ASN Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 224 GLN Chi-restraints excluded: chain D residue 68 HIS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 91 CYS Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 225 MET Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 151 ASN Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 52 CYS Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 163 ARG Chi-restraints excluded: chain F residue 176 HIS Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 168 ILE Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 172 SER Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain I residue 204 ILE Chi-restraints excluded: chain I residue 209 THR Chi-restraints excluded: chain I residue 212 ILE Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 202 VAL Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain L residue 14 VAL Chi-restraints excluded: chain L residue 115 ASP Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 180 HIS Chi-restraints excluded: chain L residue 194 PHE Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain M residue 233 ASN Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain N residue 174 ASP Chi-restraints excluded: chain N residue 219 THR Chi-restraints excluded: chain O residue 12 HIS Chi-restraints excluded: chain O residue 77 ASN Chi-restraints excluded: chain O residue 173 VAL Chi-restraints excluded: chain O residue 233 ILE Chi-restraints excluded: chain P residue 36 LEU Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 45 LEU Chi-restraints excluded: chain Q residue 117 ILE Chi-restraints excluded: chain Q residue 132 VAL Chi-restraints excluded: chain Q residue 134 PHE Chi-restraints excluded: chain Q residue 155 ASN Chi-restraints excluded: chain Q residue 174 VAL Chi-restraints excluded: chain Q residue 182 ASP Chi-restraints excluded: chain Q residue 224 GLN Chi-restraints excluded: chain R residue 13 ASP Chi-restraints excluded: chain R residue 68 HIS Chi-restraints excluded: chain R residue 70 CYS Chi-restraints excluded: chain R residue 91 CYS Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 129 ILE Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain R residue 225 MET Chi-restraints excluded: chain S residue 47 ILE Chi-restraints excluded: chain S residue 51 GLU Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 151 ASN Chi-restraints excluded: chain S residue 154 CYS Chi-restraints excluded: chain S residue 212 LEU Chi-restraints excluded: chain T residue 12 ILE Chi-restraints excluded: chain T residue 52 CYS Chi-restraints excluded: chain T residue 98 LEU Chi-restraints excluded: chain T residue 226 LEU Chi-restraints excluded: chain U residue 113 ILE Chi-restraints excluded: chain U residue 141 SER Chi-restraints excluded: chain U residue 232 ILE Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain V residue 41 LEU Chi-restraints excluded: chain V residue 58 ILE Chi-restraints excluded: chain V residue 59 ILE Chi-restraints excluded: chain V residue 128 LEU Chi-restraints excluded: chain V residue 140 ILE Chi-restraints excluded: chain V residue 162 GLN Chi-restraints excluded: chain V residue 172 SER Chi-restraints excluded: chain V residue 178 ASP Chi-restraints excluded: chain V residue 182 SER Chi-restraints excluded: chain V residue 184 SER Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 95 VAL Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 132 LEU Chi-restraints excluded: chain W residue 174 ASP Chi-restraints excluded: chain W residue 212 ILE Chi-restraints excluded: chain X residue 36 THR Chi-restraints excluded: chain X residue 67 GLU Chi-restraints excluded: chain X residue 134 LEU Chi-restraints excluded: chain X residue 202 VAL Chi-restraints excluded: chain Y residue 93 LEU Chi-restraints excluded: chain Y residue 165 GLU Chi-restraints excluded: chain Y residue 173 LEU Chi-restraints excluded: chain Z residue 14 VAL Chi-restraints excluded: chain Z residue 125 LEU Chi-restraints excluded: chain Z residue 137 SER Chi-restraints excluded: chain Z residue 180 HIS Chi-restraints excluded: chain Z residue 194 PHE Chi-restraints excluded: chain Z residue 201 THR Chi-restraints excluded: chain a residue 63 ILE Chi-restraints excluded: chain a residue 170 SER Chi-restraints excluded: chain a residue 233 ASN Chi-restraints excluded: chain b residue 6 VAL Chi-restraints excluded: chain b residue 12 VAL Chi-restraints excluded: chain b residue 33 SER Chi-restraints excluded: chain b residue 73 ILE Chi-restraints excluded: chain b residue 174 ASP Chi-restraints excluded: chain b residue 206 ILE Chi-restraints excluded: chain b residue 219 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 620 random chunks: chunk 365 optimal weight: 3.9990 chunk 588 optimal weight: 0.1980 chunk 359 optimal weight: 0.9980 chunk 279 optimal weight: 0.8980 chunk 409 optimal weight: 7.9990 chunk 617 optimal weight: 0.9990 chunk 568 optimal weight: 0.9990 chunk 491 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 chunk 379 optimal weight: 1.9990 chunk 301 optimal weight: 5.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 ASN ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 56 GLN ** K 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 56 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 51464 Z= 0.175 Angle : 0.547 15.578 69484 Z= 0.286 Chirality : 0.043 0.252 7764 Planarity : 0.004 0.067 8864 Dihedral : 6.639 75.372 7030 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 3.01 % Allowed : 21.15 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.11), residues: 6250 helix: 0.66 (0.12), residues: 2110 sheet: -1.21 (0.14), residues: 1332 loop : -1.87 (0.12), residues: 2808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP Q 179 HIS 0.007 0.001 HIS H 134 PHE 0.015 0.001 PHE D 194 TYR 0.045 0.001 TYR L 88 ARG 0.008 0.000 ARG S 20 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12500 Ramachandran restraints generated. 6250 Oldfield, 0 Emsley, 6250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12500 Ramachandran restraints generated. 6250 Oldfield, 0 Emsley, 6250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 993 residues out of total 5552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 826 time to evaluate : 5.584 Fit side-chains revert: symmetry clash REVERT: A 77 ASN cc_start: 0.8277 (OUTLIER) cc_final: 0.7808 (p0) REVERT: A 253 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7315 (mm) REVERT: B 119 GLN cc_start: 0.7630 (tm-30) cc_final: 0.7290 (tm-30) REVERT: B 159 MET cc_start: 0.7775 (mmt) cc_final: 0.7146 (mmt) REVERT: B 184 ILE cc_start: 0.6558 (OUTLIER) cc_final: 0.6261 (mt) REVERT: C 62 TYR cc_start: 0.7135 (OUTLIER) cc_final: 0.5864 (p90) REVERT: C 92 LEU cc_start: 0.8635 (mt) cc_final: 0.8286 (mm) REVERT: C 93 TYR cc_start: 0.7730 (m-10) cc_final: 0.6842 (m-10) REVERT: C 224 GLN cc_start: 0.6522 (OUTLIER) cc_final: 0.5690 (mp10) REVERT: D 66 ASP cc_start: 0.8636 (m-30) cc_final: 0.8351 (m-30) REVERT: D 99 ASP cc_start: 0.8189 (t0) cc_final: 0.7739 (t0) REVERT: D 187 PHE cc_start: 0.7780 (t80) cc_final: 0.7150 (t80) REVERT: D 215 THR cc_start: 0.7210 (m) cc_final: 0.6916 (p) REVERT: D 225 MET cc_start: 0.7748 (OUTLIER) cc_final: 0.7367 (mmt) REVERT: E 114 GLU cc_start: 0.8356 (tp30) cc_final: 0.8071 (tt0) REVERT: E 212 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8719 (mm) REVERT: E 230 TYR cc_start: 0.8452 (t80) cc_final: 0.8153 (t80) REVERT: F 68 ASP cc_start: 0.7727 (m-30) cc_final: 0.7458 (m-30) REVERT: F 223 ILE cc_start: 0.8324 (mm) cc_final: 0.7989 (mm) REVERT: G 44 ASP cc_start: 0.8169 (m-30) cc_final: 0.7863 (m-30) REVERT: G 57 LYS cc_start: 0.6414 (tptp) cc_final: 0.5968 (pttm) REVERT: G 68 ARG cc_start: 0.8539 (mtp180) cc_final: 0.8290 (mtp-110) REVERT: G 97 GLU cc_start: 0.7671 (tp30) cc_final: 0.7089 (mm-30) REVERT: H 32 ARG cc_start: 0.7901 (mmt-90) cc_final: 0.7459 (mmm160) REVERT: H 138 LYS cc_start: 0.7583 (tptp) cc_final: 0.7161 (tptt) REVERT: H 156 TYR cc_start: 0.8304 (t80) cc_final: 0.7974 (t80) REVERT: I 53 GLU cc_start: 0.8012 (tt0) cc_final: 0.7712 (mt-10) REVERT: I 54 HIS cc_start: 0.7628 (t-90) cc_final: 0.7377 (t-90) REVERT: I 174 ASP cc_start: 0.8207 (p0) cc_final: 0.7869 (p0) REVERT: K 20 TYR cc_start: 0.7977 (m-10) cc_final: 0.7545 (m-10) REVERT: K 165 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8221 (mt-10) REVERT: L 122 GLU cc_start: 0.7757 (tm-30) cc_final: 0.7471 (tm-30) REVERT: M 29 ARG cc_start: 0.8028 (mmm160) cc_final: 0.7602 (tpm170) REVERT: M 39 THR cc_start: 0.9179 (t) cc_final: 0.8878 (m) REVERT: M 233 ASN cc_start: 0.8435 (OUTLIER) cc_final: 0.8097 (p0) REVERT: N 89 GLN cc_start: 0.9222 (tm-30) cc_final: 0.8891 (tm-30) REVERT: O 77 ASN cc_start: 0.8234 (OUTLIER) cc_final: 0.7797 (p0) REVERT: O 129 GLN cc_start: 0.8235 (tm-30) cc_final: 0.7799 (tm-30) REVERT: O 224 LEU cc_start: 0.8666 (mm) cc_final: 0.8433 (tp) REVERT: P 119 GLN cc_start: 0.7686 (tm-30) cc_final: 0.7393 (tm-30) REVERT: P 203 LEU cc_start: 0.6563 (OUTLIER) cc_final: 0.6076 (pt) REVERT: Q 92 LEU cc_start: 0.8619 (mt) cc_final: 0.8265 (mm) REVERT: Q 93 TYR cc_start: 0.7737 (m-10) cc_final: 0.6841 (m-10) REVERT: Q 155 ASN cc_start: 0.8064 (OUTLIER) cc_final: 0.7777 (p0) REVERT: Q 224 GLN cc_start: 0.6486 (OUTLIER) cc_final: 0.5641 (mp10) REVERT: R 37 SER cc_start: 0.8735 (t) cc_final: 0.8453 (t) REVERT: R 99 ASP cc_start: 0.8215 (t0) cc_final: 0.7912 (t0) REVERT: R 215 THR cc_start: 0.7277 (m) cc_final: 0.6944 (p) REVERT: S 14 THR cc_start: 0.8076 (p) cc_final: 0.7862 (p) REVERT: S 20 ARG cc_start: 0.8430 (mtm-85) cc_final: 0.8174 (mtp180) REVERT: S 51 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.6927 (mt-10) REVERT: S 114 GLU cc_start: 0.8330 (tp30) cc_final: 0.8075 (tt0) REVERT: S 212 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8643 (mm) REVERT: S 230 TYR cc_start: 0.8453 (t80) cc_final: 0.8116 (t80) REVERT: T 68 ASP cc_start: 0.7629 (m-30) cc_final: 0.7327 (m-30) REVERT: U 31 ILE cc_start: 0.8276 (pt) cc_final: 0.7813 (mt) REVERT: V 138 LYS cc_start: 0.7576 (tptp) cc_final: 0.7168 (tptt) REVERT: V 156 TYR cc_start: 0.8142 (t80) cc_final: 0.7851 (t80) REVERT: V 182 SER cc_start: 0.8506 (OUTLIER) cc_final: 0.8284 (m) REVERT: W 53 GLU cc_start: 0.7992 (tt0) cc_final: 0.7685 (mt-10) REVERT: W 54 HIS cc_start: 0.7628 (t-90) cc_final: 0.7358 (t-90) REVERT: Y 2 ASP cc_start: 0.7774 (p0) cc_final: 0.7509 (p0) REVERT: Y 20 TYR cc_start: 0.8017 (m-10) cc_final: 0.7583 (m-10) REVERT: Y 69 GLN cc_start: 0.8108 (mt0) cc_final: 0.7860 (mt0) REVERT: Z 3 THR cc_start: 0.8923 (m) cc_final: 0.8605 (m) REVERT: a 29 ARG cc_start: 0.8095 (mmm160) cc_final: 0.7334 (tpm170) REVERT: a 233 ASN cc_start: 0.8498 (OUTLIER) cc_final: 0.8042 (p0) REVERT: b 22 MET cc_start: 0.7969 (ttm) cc_final: 0.7730 (ttm) REVERT: b 75 ASN cc_start: 0.8536 (t0) cc_final: 0.8139 (t0) REVERT: b 89 GLN cc_start: 0.9224 (tm-30) cc_final: 0.8890 (tm-30) outliers start: 167 outliers final: 136 residues processed: 926 average time/residue: 0.5966 time to fit residues: 920.9123 Evaluate side-chains 955 residues out of total 5552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 803 time to evaluate : 7.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 77 ASN Chi-restraints excluded: chain A residue 172 CYS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 155 ASN Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 183 MET Chi-restraints excluded: chain C residue 224 GLN Chi-restraints excluded: chain D residue 68 HIS Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 91 CYS Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 225 MET Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 151 ASN Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 52 CYS Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 176 HIS Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 168 ILE Chi-restraints excluded: chain G residue 232 ILE Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 172 SER Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain I residue 204 ILE Chi-restraints excluded: chain I residue 209 THR Chi-restraints excluded: chain I residue 212 ILE Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 202 VAL Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain L residue 14 VAL Chi-restraints excluded: chain L residue 115 ASP Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 180 HIS Chi-restraints excluded: chain L residue 194 PHE Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain M residue 233 ASN Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 33 SER Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain N residue 174 ASP Chi-restraints excluded: chain N residue 206 ILE Chi-restraints excluded: chain N residue 219 THR Chi-restraints excluded: chain O residue 12 HIS Chi-restraints excluded: chain O residue 77 ASN Chi-restraints excluded: chain O residue 173 VAL Chi-restraints excluded: chain O residue 233 ILE Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 36 LEU Chi-restraints excluded: chain P residue 203 LEU Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 45 LEU Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 117 ILE Chi-restraints excluded: chain Q residue 132 VAL Chi-restraints excluded: chain Q residue 134 PHE Chi-restraints excluded: chain Q residue 155 ASN Chi-restraints excluded: chain Q residue 174 VAL Chi-restraints excluded: chain Q residue 182 ASP Chi-restraints excluded: chain Q residue 224 GLN Chi-restraints excluded: chain R residue 13 ASP Chi-restraints excluded: chain R residue 68 HIS Chi-restraints excluded: chain R residue 70 CYS Chi-restraints excluded: chain R residue 91 CYS Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 129 ILE Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain R residue 225 MET Chi-restraints excluded: chain S residue 47 ILE Chi-restraints excluded: chain S residue 51 GLU Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 151 ASN Chi-restraints excluded: chain S residue 154 CYS Chi-restraints excluded: chain S residue 212 LEU Chi-restraints excluded: chain T residue 12 ILE Chi-restraints excluded: chain T residue 52 CYS Chi-restraints excluded: chain T residue 98 LEU Chi-restraints excluded: chain T residue 163 ARG Chi-restraints excluded: chain T residue 226 LEU Chi-restraints excluded: chain U residue 113 ILE Chi-restraints excluded: chain U residue 141 SER Chi-restraints excluded: chain U residue 232 ILE Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain V residue 41 LEU Chi-restraints excluded: chain V residue 58 ILE Chi-restraints excluded: chain V residue 59 ILE Chi-restraints excluded: chain V residue 128 LEU Chi-restraints excluded: chain V residue 140 ILE Chi-restraints excluded: chain V residue 172 SER Chi-restraints excluded: chain V residue 178 ASP Chi-restraints excluded: chain V residue 182 SER Chi-restraints excluded: chain V residue 184 SER Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 95 VAL Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 132 LEU Chi-restraints excluded: chain W residue 174 ASP Chi-restraints excluded: chain W residue 212 ILE Chi-restraints excluded: chain X residue 36 THR Chi-restraints excluded: chain X residue 67 GLU Chi-restraints excluded: chain X residue 83 GLU Chi-restraints excluded: chain X residue 134 LEU Chi-restraints excluded: chain X residue 202 VAL Chi-restraints excluded: chain Y residue 93 LEU Chi-restraints excluded: chain Y residue 165 GLU Chi-restraints excluded: chain Y residue 173 LEU Chi-restraints excluded: chain Z residue 14 VAL Chi-restraints excluded: chain Z residue 125 LEU Chi-restraints excluded: chain Z residue 137 SER Chi-restraints excluded: chain Z residue 180 HIS Chi-restraints excluded: chain Z residue 194 PHE Chi-restraints excluded: chain Z residue 201 THR Chi-restraints excluded: chain a residue 63 ILE Chi-restraints excluded: chain a residue 170 SER Chi-restraints excluded: chain a residue 233 ASN Chi-restraints excluded: chain b residue 6 VAL Chi-restraints excluded: chain b residue 12 VAL Chi-restraints excluded: chain b residue 73 ILE Chi-restraints excluded: chain b residue 174 ASP Chi-restraints excluded: chain b residue 206 ILE Chi-restraints excluded: chain b residue 219 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 64.239 > 50: distance: 70 - 154: 10.291 distance: 82 - 147: 5.749 distance: 85 - 144: 5.179 distance: 93 - 96: 3.080 distance: 94 - 95: 5.947 distance: 94 - 99: 3.593 distance: 96 - 98: 4.583 distance: 99 - 100: 3.256 distance: 100 - 101: 3.576 distance: 100 - 103: 3.028 distance: 101 - 102: 7.741 distance: 101 - 107: 7.901 distance: 107 - 108: 7.769 distance: 107 - 113: 8.515 distance: 108 - 109: 3.872 distance: 108 - 111: 9.603 distance: 109 - 110: 25.505 distance: 109 - 114: 25.018 distance: 111 - 112: 5.434 distance: 112 - 113: 14.128 distance: 114 - 115: 18.325 distance: 115 - 116: 11.233 distance: 115 - 118: 19.997 distance: 116 - 117: 24.079 distance: 116 - 120: 34.115 distance: 118 - 119: 13.653 distance: 120 - 121: 3.051 distance: 121 - 122: 20.279 distance: 122 - 123: 20.862 distance: 122 - 124: 21.058 distance: 124 - 125: 14.161 distance: 125 - 126: 19.959 distance: 125 - 128: 41.189 distance: 126 - 127: 12.113 distance: 126 - 132: 18.178 distance: 128 - 129: 29.960 distance: 129 - 130: 16.385 distance: 129 - 131: 53.746 distance: 132 - 133: 14.137 distance: 133 - 134: 11.275 distance: 133 - 136: 9.724 distance: 134 - 135: 8.052 distance: 134 - 144: 4.004 distance: 136 - 137: 7.440 distance: 137 - 139: 3.756 distance: 138 - 140: 3.232 distance: 144 - 145: 5.758 distance: 145 - 146: 3.109 distance: 145 - 148: 3.440 distance: 146 - 147: 5.671 distance: 146 - 150: 7.202 distance: 148 - 149: 6.701 distance: 150 - 151: 10.222 distance: 151 - 152: 4.969 distance: 152 - 153: 9.832 distance: 152 - 154: 12.045 distance: 154 - 155: 15.094 distance: 155 - 156: 12.640 distance: 155 - 158: 9.745 distance: 156 - 157: 6.141 distance: 156 - 168: 29.257 distance: 158 - 159: 4.432 distance: 159 - 160: 11.105 distance: 159 - 161: 9.605 distance: 160 - 162: 5.175 distance: 161 - 163: 7.577 distance: 161 - 164: 4.425 distance: 163 - 165: 4.976 distance: 164 - 166: 6.760 distance: 166 - 167: 7.179