Starting phenix.real_space_refine on Sat Feb 24 13:50:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ef3_9045/02_2024/6ef3_9045_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ef3_9045/02_2024/6ef3_9045.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ef3_9045/02_2024/6ef3_9045.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ef3_9045/02_2024/6ef3_9045.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ef3_9045/02_2024/6ef3_9045_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ef3_9045/02_2024/6ef3_9045_updated.pdb" } resolution = 4.17 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= 0.001 sd= 0.008 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 P 16 5.49 5 S 164 5.16 5 C 27951 2.51 5 N 7654 2.21 5 O 8486 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1 PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 29": "NH1" <-> "NH2" Residue "1 TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 80": "NH1" <-> "NH2" Residue "3 ARG 99": "NH1" <-> "NH2" Residue "3 PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 23": "NH1" <-> "NH2" Residue "4 PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 121": "NH1" <-> "NH2" Residue "5 TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 182": "NH1" <-> "NH2" Residue "A PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 4": "NH1" <-> "NH2" Residue "B TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 18": "NH1" <-> "NH2" Residue "C TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 113": "NH1" <-> "NH2" Residue "C ARG 143": "NH1" <-> "NH2" Residue "C PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 111": "NH1" <-> "NH2" Residue "D ARG 141": "NH1" <-> "NH2" Residue "D ARG 166": "NH1" <-> "NH2" Residue "E ARG 72": "NH1" <-> "NH2" Residue "E TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 3": "NH1" <-> "NH2" Residue "F PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 190": "NH1" <-> "NH2" Residue "H PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 289": "NH1" <-> "NH2" Residue "H PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 346": "NH1" <-> "NH2" Residue "H TYR 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 212": "NH1" <-> "NH2" Residue "J ARG 231": "NH1" <-> "NH2" Residue "J ARG 257": "NH1" <-> "NH2" Residue "K PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 333": "NH1" <-> "NH2" Residue "L TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 191": "NH1" <-> "NH2" Residue "L TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 299": "NH1" <-> "NH2" Residue "L ARG 303": "NH1" <-> "NH2" Residue "M TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 233": "NH1" <-> "NH2" Residue "M ARG 342": "NH1" <-> "NH2" Residue "M PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 44271 Number of models: 1 Model: "" Number of chains: 30 Chain: "1" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1496 Classifications: {'peptide': 196} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 191} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "2" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1685 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 217} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "3" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1575 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 196} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "4" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1560 Classifications: {'peptide': 195} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 187} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "5" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1644 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 209} Chain: "6" Number of atoms: 1727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1727 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 7, 'TRANS': 212} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "7" Number of atoms: 1598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1598 Classifications: {'peptide': 208} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 199} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 1922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1922 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 236} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 1901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1901 Classifications: {'peptide': 250} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 237} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 1864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1864 Classifications: {'peptide': 242} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 236} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "D" Number of atoms: 1878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1878 Classifications: {'peptide': 241} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 230} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 1918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1918 Classifications: {'peptide': 249} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 244} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 1796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1796 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 227} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 1903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1903 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 236} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 2889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 2889 Classifications: {'peptide': 380} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 21, 'TRANS': 358} Chain breaks: 2 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 5, 'ASP:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 55 Chain: "I" Number of atoms: 2871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2871 Classifications: {'peptide': 384} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 366} Unresolved non-hydrogen bonds: 145 Unresolved non-hydrogen angles: 175 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 91 Chain: "J" Number of atoms: 2918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2918 Classifications: {'peptide': 383} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 367} Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 52 Chain: "K" Number of atoms: 2761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2761 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 352} Chain breaks: 1 Unresolved non-hydrogen bonds: 186 Unresolved non-hydrogen angles: 230 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 10, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 122 Chain: "L" Number of atoms: 2525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2525 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 342} Unresolved non-hydrogen bonds: 321 Unresolved non-hydrogen angles: 396 Unresolved non-hydrogen dihedrals: 259 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 12, 'PHE:plan': 4, 'GLU:plan': 19, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 218 Chain: "M" Number of atoms: 2717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2717 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 355} Chain breaks: 1 Unresolved non-hydrogen bonds: 187 Unresolved non-hydrogen angles: 219 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 10, 'ARG:plan': 7, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 112 Chain: "n" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 14} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "r" Number of atoms: 2088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2088 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 274} Chain breaks: 1 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 4, 'ARG:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 57 Chain: "s" Number of atoms: 253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 253 Classifications: {'peptide': 38} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 4, 'TRANS': 33} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "u" Number of atoms: 481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 481 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ASN:plan1': 1, 'ARG:plan': 3, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 64 Chain: "H" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 23.80, per 1000 atoms: 0.54 Number of scatterers: 44271 At special positions: 0 Unit cell: (174.07, 149.35, 242.05, 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 164 16.00 P 16 15.00 O 8486 8.00 N 7654 7.00 C 27951 6.00 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=0, symmetry=0 Time building additional restraints: 16.27 Conformation dependent library (CDL) restraints added in 8.3 seconds 11532 Ramachandran restraints generated. 5766 Oldfield, 0 Emsley, 5766 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10778 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 200 helices and 60 sheets defined 32.9% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.69 Creating SS restraints... Processing helix chain '1' and resid 50 through 69 removed outlier: 4.026A pdb=" N ALA 1 54 " --> pdb=" O ALA 1 50 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N TYR 1 61 " --> pdb=" O ASP 1 57 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER 1 68 " --> pdb=" O GLU 1 64 " (cutoff:3.500A) Processing helix chain '1' and resid 76 through 86 removed outlier: 3.524A pdb=" N SER 1 80 " --> pdb=" O GLU 1 76 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N GLU 1 84 " --> pdb=" O SER 1 80 " (cutoff:3.500A) Processing helix chain '1' and resid 135 through 139 removed outlier: 3.740A pdb=" N ASP 1 139 " --> pdb=" O TYR 1 135 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 135 through 139' Processing helix chain '1' and resid 148 through 164 removed outlier: 4.071A pdb=" N ASP 1 153 " --> pdb=" O GLU 1 149 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE 1 154 " --> pdb=" O GLU 1 150 " (cutoff:3.500A) Processing helix chain '1' and resid 190 through 194 Processing helix chain '2' and resid 49 through 62 removed outlier: 4.131A pdb=" N VAL 2 55 " --> pdb=" O ASP 2 51 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER 2 61 " --> pdb=" O GLN 2 57 " (cutoff:3.500A) Processing helix chain '2' and resid 64 through 70 Processing helix chain '2' and resid 77 through 81 removed outlier: 3.986A pdb=" N GLN 2 81 " --> pdb=" O SER 2 78 " (cutoff:3.500A) Processing helix chain '2' and resid 83 through 90 removed outlier: 3.586A pdb=" N PHE 2 88 " --> pdb=" O LYS 2 84 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS 2 89 " --> pdb=" O GLN 2 85 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TYR 2 90 " --> pdb=" O HIS 2 86 " (cutoff:3.500A) Processing helix chain '2' and resid 131 through 140 removed outlier: 3.525A pdb=" N MET 2 135 " --> pdb=" O SER 2 131 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU 2 138 " --> pdb=" O ALA 2 134 " (cutoff:3.500A) Processing helix chain '2' and resid 148 through 164 removed outlier: 4.278A pdb=" N LYS 2 153 " --> pdb=" O GLU 2 149 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE 2 159 " --> pdb=" O ALA 2 155 " (cutoff:3.500A) Processing helix chain '3' and resid 4 through 6 No H-bonds generated for 'chain '3' and resid 4 through 6' Processing helix chain '3' and resid 58 through 78 removed outlier: 4.038A pdb=" N LEU 3 63 " --> pdb=" O ASP 3 59 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU 3 65 " --> pdb=" O THR 3 61 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N MET 3 66 " --> pdb=" O THR 3 62 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS 3 70 " --> pdb=" O MET 3 66 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASN 3 72 " --> pdb=" O ARG 3 68 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LEU 3 73 " --> pdb=" O TYR 3 69 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU 3 76 " --> pdb=" O ASN 3 72 " (cutoff:3.500A) Processing helix chain '3' and resid 84 through 98 removed outlier: 4.283A pdb=" N GLN 3 89 " --> pdb=" O GLU 3 85 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER 3 92 " --> pdb=" O THR 3 88 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU 3 97 " --> pdb=" O SER 3 93 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N ARG 3 98 " --> pdb=" O SER 3 94 " (cutoff:3.500A) Processing helix chain '3' and resid 148 through 153 removed outlier: 3.597A pdb=" N SER 3 152 " --> pdb=" O GLY 3 148 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N LEU 3 153 " --> pdb=" O MET 3 149 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 148 through 153' Processing helix chain '3' and resid 160 through 175 removed outlier: 4.224A pdb=" N THR 3 166 " --> pdb=" O ASP 3 162 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN 3 169 " --> pdb=" O GLU 3 165 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA 3 174 " --> pdb=" O ALA 3 170 " (cutoff:3.500A) Processing helix chain '4' and resid 54 through 68 removed outlier: 3.666A pdb=" N GLU 4 58 " --> pdb=" O VAL 4 54 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR 4 59 " --> pdb=" O GLN 4 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU 4 66 " --> pdb=" O ALA 4 62 " (cutoff:3.500A) Processing helix chain '4' and resid 77 through 91 removed outlier: 3.507A pdb=" N SER 4 82 " --> pdb=" O GLN 4 78 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG 4 85 " --> pdb=" O SER 4 81 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLN 4 86 " --> pdb=" O SER 4 82 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU 4 87 " --> pdb=" O PHE 4 83 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU 4 88 " --> pdb=" O VAL 4 84 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS 4 90 " --> pdb=" O GLN 4 86 " (cutoff:3.500A) Processing helix chain '4' and resid 137 through 139 No H-bonds generated for 'chain '4' and resid 137 through 139' Processing helix chain '4' and resid 154 through 161 removed outlier: 4.341A pdb=" N LEU 4 158 " --> pdb=" O THR 4 154 " (cutoff:3.500A) Processing helix chain '4' and resid 164 through 169 removed outlier: 3.532A pdb=" N LEU 4 168 " --> pdb=" O CYS 4 164 " (cutoff:3.500A) Processing helix chain '5' and resid 49 through 65 removed outlier: 4.757A pdb=" N TRP 5 55 " --> pdb=" O ASP 5 51 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR 5 57 " --> pdb=" O GLN 5 53 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER 5 61 " --> pdb=" O THR 5 57 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN 5 62 " --> pdb=" O TRP 5 58 " (cutoff:3.500A) Processing helix chain '5' and resid 67 through 70 No H-bonds generated for 'chain '5' and resid 67 through 70' Processing helix chain '5' and resid 79 through 90 removed outlier: 3.536A pdb=" N LEU 5 83 " --> pdb=" O ALA 5 79 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER 5 84 " --> pdb=" O SER 5 80 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLN 5 89 " --> pdb=" O ASN 5 85 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N TYR 5 90 " --> pdb=" O LEU 5 86 " (cutoff:3.500A) Processing helix chain '5' and resid 133 through 141 removed outlier: 3.724A pdb=" N GLY 5 138 " --> pdb=" O THR 5 134 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N VAL 5 139 " --> pdb=" O PHE 5 135 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU 5 140 " --> pdb=" O ALA 5 136 " (cutoff:3.500A) Processing helix chain '5' and resid 151 through 165 removed outlier: 3.742A pdb=" N LYS 5 158 " --> pdb=" O LEU 5 154 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ALA 5 164 " --> pdb=" O SER 5 160 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ALA 5 165 " --> pdb=" O ILE 5 161 " (cutoff:3.500A) Processing helix chain '5' and resid 193 through 204 removed outlier: 4.560A pdb=" N TRP 5 198 " --> pdb=" O GLY 5 194 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LYS 5 199 " --> pdb=" O GLU 5 195 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU 5 202 " --> pdb=" O TRP 5 198 " (cutoff:3.500A) Processing helix chain '6' and resid 60 through 79 removed outlier: 4.598A pdb=" N VAL 6 65 " --> pdb=" O GLY 6 61 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN 6 70 " --> pdb=" O LYS 6 66 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LYS 6 73 " --> pdb=" O LYS 6 69 " (cutoff:3.500A) Processing helix chain '6' and resid 86 through 98 removed outlier: 3.874A pdb=" N ARG 6 91 " --> pdb=" O ASN 6 87 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE 6 93 " --> pdb=" O ALA 6 89 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN 6 94 " --> pdb=" O ALA 6 90 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N HIS 6 95 " --> pdb=" O ARG 6 91 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU 6 97 " --> pdb=" O ILE 6 93 " (cutoff:3.500A) Processing helix chain '6' and resid 147 through 150 No H-bonds generated for 'chain '6' and resid 147 through 150' Processing helix chain '6' and resid 177 through 187 Processing helix chain '7' and resid 57 through 75 removed outlier: 3.851A pdb=" N HIS 7 62 " --> pdb=" O SER 7 58 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU 7 66 " --> pdb=" O HIS 7 62 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS 7 68 " --> pdb=" O GLU 7 64 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASP 7 69 " --> pdb=" O ARG 7 65 " (cutoff:3.500A) Processing helix chain '7' and resid 89 through 93 removed outlier: 3.993A pdb=" N PHE 7 93 " --> pdb=" O SER 7 90 " (cutoff:3.500A) Processing helix chain '7' and resid 95 through 104 removed outlier: 4.664A pdb=" N MET 7 100 " --> pdb=" O LEU 7 96 " (cutoff:3.500A) Processing helix chain '7' and resid 145 through 150 removed outlier: 3.722A pdb=" N MET 7 150 " --> pdb=" O GLY 7 147 " (cutoff:3.500A) Processing helix chain '7' and resid 152 through 158 removed outlier: 3.542A pdb=" N LYS 7 157 " --> pdb=" O PRO 7 153 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL 7 158 " --> pdb=" O LEU 7 154 " (cutoff:3.500A) Processing helix chain '7' and resid 162 through 165 removed outlier: 4.000A pdb=" N ILE 7 165 " --> pdb=" O GLU 7 162 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 162 through 165' Processing helix chain '7' and resid 170 through 187 removed outlier: 3.613A pdb=" N ALA 7 176 " --> pdb=" O VAL 7 172 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE 7 177 " --> pdb=" O ALA 7 173 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ASN 7 179 " --> pdb=" O GLU 7 175 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL 7 183 " --> pdb=" O ASN 7 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 5 through 9 Processing helix chain 'A' and resid 27 through 34 removed outlier: 3.975A pdb=" N PHE A 32 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N LYS A 33 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ALA A 34 " --> pdb=" O TYR A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 98 removed outlier: 3.549A pdb=" N ASN A 92 " --> pdb=" O PRO A 88 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ALA A 93 " --> pdb=" O ASP A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 107 Processing helix chain 'A' and resid 114 through 120 Processing helix chain 'A' and resid 122 through 125 No H-bonds generated for 'chain 'A' and resid 122 through 125' Processing helix chain 'A' and resid 127 through 129 No H-bonds generated for 'chain 'A' and resid 127 through 129' Processing helix chain 'A' and resid 175 through 189 removed outlier: 5.231A pdb=" N HIS A 185 " --> pdb=" O ASN A 181 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER A 189 " --> pdb=" O HIS A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 212 removed outlier: 3.684A pdb=" N VAL A 203 " --> pdb=" O TRP A 199 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU A 204 " --> pdb=" O GLU A 200 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE A 205 " --> pdb=" O LYS A 201 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR A 208 " --> pdb=" O GLU A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 245 No H-bonds generated for 'chain 'A' and resid 242 through 245' Processing helix chain 'B' and resid 21 through 29 removed outlier: 3.985A pdb=" N THR B 26 " --> pdb=" O ASP B 22 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS B 29 " --> pdb=" O LEU B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 88 removed outlier: 4.407A pdb=" N LEU B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASP B 87 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS B 88 " --> pdb=" O VAL B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 96 Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 108 through 115 Processing helix chain 'B' and resid 120 through 122 No H-bonds generated for 'chain 'B' and resid 120 through 122' Processing helix chain 'B' and resid 168 through 175 removed outlier: 3.535A pdb=" N PHE B 174 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 194 No H-bonds generated for 'chain 'B' and resid 191 through 194' Processing helix chain 'B' and resid 206 through 208 No H-bonds generated for 'chain 'B' and resid 206 through 208' Processing helix chain 'B' and resid 219 through 221 No H-bonds generated for 'chain 'B' and resid 219 through 221' Processing helix chain 'B' and resid 240 through 244 Processing helix chain 'C' and resid 20 through 23 No H-bonds generated for 'chain 'C' and resid 20 through 23' Processing helix chain 'C' and resid 25 through 27 No H-bonds generated for 'chain 'C' and resid 25 through 27' Processing helix chain 'C' and resid 85 through 102 removed outlier: 3.903A pdb=" N THR C 90 " --> pdb=" O ILE C 86 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA C 91 " --> pdb=" O LEU C 87 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASN C 97 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N THR C 101 " --> pdb=" O ASN C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 120 removed outlier: 3.588A pdb=" N ARG C 113 " --> pdb=" O GLU C 109 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS C 119 " --> pdb=" O LEU C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 177 removed outlier: 3.678A pdb=" N LEU C 176 " --> pdb=" O ALA C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 200 removed outlier: 3.745A pdb=" N GLU C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU C 192 " --> pdb=" O ASP C 188 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LYS C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 241 removed outlier: 3.712A pdb=" N LYS C 236 " --> pdb=" O PRO C 232 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASP C 237 " --> pdb=" O GLN C 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 29 removed outlier: 3.674A pdb=" N LEU D 24 " --> pdb=" O VAL D 20 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU D 25 " --> pdb=" O GLU D 21 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA D 26 " --> pdb=" O TYR D 22 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS D 28 " --> pdb=" O LEU D 24 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG D 29 " --> pdb=" O GLU D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 100 removed outlier: 4.739A pdb=" N ILE D 84 " --> pdb=" O ALA D 80 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU D 85 " --> pdb=" O ASP D 81 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N VAL D 91 " --> pdb=" O GLU D 87 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG D 97 " --> pdb=" O ALA D 93 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU D 98 " --> pdb=" O GLN D 94 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N THR D 99 " --> pdb=" O SER D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 113 removed outlier: 3.746A pdb=" N ARG D 111 " --> pdb=" O GLU D 107 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TYR D 112 " --> pdb=" O TYR D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 118 No H-bonds generated for 'chain 'D' and resid 115 through 118' Processing helix chain 'D' and resid 168 through 178 removed outlier: 5.084A pdb=" N GLU D 173 " --> pdb=" O LYS D 169 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE D 174 " --> pdb=" O THR D 170 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN D 178 " --> pdb=" O PHE D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 199 removed outlier: 3.567A pdb=" N SER D 198 " --> pdb=" O LEU D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 240 removed outlier: 3.954A pdb=" N GLN D 231 " --> pdb=" O GLU D 227 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TYR D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN D 235 " --> pdb=" O GLN D 231 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ILE D 236 " --> pdb=" O TYR D 232 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU D 237 " --> pdb=" O VAL D 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 30 removed outlier: 3.810A pdb=" N SER E 27 " --> pdb=" O GLN E 23 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU E 29 " --> pdb=" O GLU E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 86 No H-bonds generated for 'chain 'E' and resid 83 through 86' Processing helix chain 'E' and resid 89 through 102 removed outlier: 4.426A pdb=" N THR E 94 " --> pdb=" O GLU E 90 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA E 96 " --> pdb=" O ALA E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 117 Processing helix chain 'E' and resid 120 through 122 No H-bonds generated for 'chain 'E' and resid 120 through 122' Processing helix chain 'E' and resid 176 through 179 No H-bonds generated for 'chain 'E' and resid 176 through 179' Processing helix chain 'E' and resid 194 through 197 No H-bonds generated for 'chain 'E' and resid 194 through 197' Processing helix chain 'E' and resid 203 through 207 Processing helix chain 'E' and resid 233 through 247 removed outlier: 3.628A pdb=" N LEU E 239 " --> pdb=" O LYS E 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 25 Processing helix chain 'F' and resid 28 through 31 Processing helix chain 'F' and resid 78 through 98 removed outlier: 4.064A pdb=" N ARG F 82 " --> pdb=" O PRO F 79 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N VAL F 83 " --> pdb=" O ASP F 80 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER F 85 " --> pdb=" O ARG F 82 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ARG F 89 " --> pdb=" O ASN F 86 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN F 91 " --> pdb=" O LEU F 88 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N CYS F 92 " --> pdb=" O ARG F 89 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N SER F 95 " --> pdb=" O CYS F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 107 No H-bonds generated for 'chain 'F' and resid 105 through 107' Processing helix chain 'F' and resid 112 through 121 removed outlier: 3.854A pdb=" N GLN F 117 " --> pdb=" O CYS F 113 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN F 119 " --> pdb=" O LYS F 115 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N THR F 120 " --> pdb=" O ALA F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 172 removed outlier: 3.699A pdb=" N TYR F 171 " --> pdb=" O GLY F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 177 No H-bonds generated for 'chain 'F' and resid 175 through 177' Processing helix chain 'F' and resid 186 through 200 removed outlier: 4.227A pdb=" N LYS F 191 " --> pdb=" O ASP F 187 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY F 193 " --> pdb=" O LEU F 189 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU F 195 " --> pdb=" O LYS F 191 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER F 198 " --> pdb=" O VAL F 194 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN F 199 " --> pdb=" O GLU F 195 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N SER F 200 " --> pdb=" O ALA F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 231 through 233 No H-bonds generated for 'chain 'F' and resid 231 through 233' Processing helix chain 'G' and resid 22 through 31 removed outlier: 4.922A pdb=" N LYS G 29 " --> pdb=" O GLU G 25 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA G 30 " --> pdb=" O TYR G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 103 removed outlier: 3.533A pdb=" N ARG G 91 " --> pdb=" O HIS G 87 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N GLU G 94 " --> pdb=" O ASN G 90 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA G 96 " --> pdb=" O GLY G 92 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ALA G 97 " --> pdb=" O ARG G 93 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N LEU G 102 " --> pdb=" O SER G 98 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR G 103 " --> pdb=" O PHE G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 113 No H-bonds generated for 'chain 'G' and resid 110 through 113' Processing helix chain 'G' and resid 120 through 123 No H-bonds generated for 'chain 'G' and resid 120 through 123' Processing helix chain 'G' and resid 169 through 182 removed outlier: 4.360A pdb=" N ALA G 174 " --> pdb=" O GLN G 170 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU G 175 " --> pdb=" O SER G 171 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLU G 177 " --> pdb=" O LYS G 173 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU G 179 " --> pdb=" O GLU G 175 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL G 180 " --> pdb=" O LEU G 176 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP G 181 " --> pdb=" O GLU G 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 192 through 206 removed outlier: 4.094A pdb=" N ILE G 199 " --> pdb=" O GLN G 195 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N GLU G 205 " --> pdb=" O TYR G 201 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ASP G 206 " --> pdb=" O LEU G 202 " (cutoff:3.500A) Processing helix chain 'G' and resid 221 through 224 No H-bonds generated for 'chain 'G' and resid 221 through 224' Processing helix chain 'G' and resid 234 through 246 removed outlier: 3.694A pdb=" N LYS G 245 " --> pdb=" O ASP G 241 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU G 246 " --> pdb=" O PHE G 242 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 64 removed outlier: 3.520A pdb=" N LYS H 50 " --> pdb=" O ALA H 46 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLN H 51 " --> pdb=" O ALA H 47 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASN H 54 " --> pdb=" O LYS H 50 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU H 56 " --> pdb=" O THR H 52 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LYS H 57 " --> pdb=" O GLU H 53 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ASP H 58 " --> pdb=" O ASN H 54 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS H 64 " --> pdb=" O GLU H 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 88 No H-bonds generated for 'chain 'H' and resid 85 through 88' Processing helix chain 'H' and resid 193 through 196 No H-bonds generated for 'chain 'H' and resid 193 through 196' Processing helix chain 'H' and resid 217 through 225 removed outlier: 3.526A pdb=" N GLU H 223 " --> pdb=" O GLU H 219 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL H 224 " --> pdb=" O LYS H 220 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 230 No H-bonds generated for 'chain 'H' and resid 227 through 230' Processing helix chain 'H' and resid 232 through 238 removed outlier: 4.016A pdb=" N THR H 237 " --> pdb=" O GLU H 233 " (cutoff:3.500A) Processing helix chain 'H' and resid 258 through 265 removed outlier: 3.506A pdb=" N VAL H 263 " --> pdb=" O CYS H 259 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA H 264 " --> pdb=" O ALA H 260 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASN H 265 " --> pdb=" O ARG H 261 " (cutoff:3.500A) Processing helix chain 'H' and resid 276 through 278 No H-bonds generated for 'chain 'H' and resid 276 through 278' Processing helix chain 'H' and resid 287 through 300 removed outlier: 3.775A pdb=" N ALA H 298 " --> pdb=" O LEU H 294 " (cutoff:3.500A) Processing helix chain 'H' and resid 327 through 340 removed outlier: 3.624A pdb=" N ARG H 331 " --> pdb=" O ASN H 327 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU H 335 " --> pdb=" O ARG H 331 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU H 336 " --> pdb=" O THR H 332 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN H 339 " --> pdb=" O GLU H 335 " (cutoff:3.500A) Processing helix chain 'H' and resid 363 through 366 Processing helix chain 'H' and resid 382 through 392 removed outlier: 3.710A pdb=" N ASN H 387 " --> pdb=" O GLU H 383 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE H 388 " --> pdb=" O GLY H 384 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE H 389 " --> pdb=" O ARG H 385 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE H 391 " --> pdb=" O ASN H 387 " (cutoff:3.500A) Processing helix chain 'H' and resid 404 through 410 removed outlier: 4.008A pdb=" N ARG H 409 " --> pdb=" O GLU H 405 " (cutoff:3.500A) Processing helix chain 'H' and resid 416 through 431 removed outlier: 3.974A pdb=" N VAL H 422 " --> pdb=" O GLU H 418 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY H 427 " --> pdb=" O CYS H 423 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA H 430 " --> pdb=" O ALA H 426 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE H 431 " --> pdb=" O GLY H 427 " (cutoff:3.500A) Processing helix chain 'H' and resid 441 through 450 removed outlier: 3.979A pdb=" N LYS H 449 " --> pdb=" O LYS H 445 " (cutoff:3.500A) Processing helix chain 'I' and resid 56 through 59 Processing helix chain 'I' and resid 61 through 78 removed outlier: 4.211A pdb=" N ILE I 65 " --> pdb=" O ARG I 61 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS I 66 " --> pdb=" O MET I 62 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE I 75 " --> pdb=" O LEU I 71 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL I 76 " --> pdb=" O GLU I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 92 through 99 removed outlier: 4.485A pdb=" N GLU I 97 " --> pdb=" O LYS I 93 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLU I 98 " --> pdb=" O LYS I 94 " (cutoff:3.500A) Processing helix chain 'I' and resid 166 through 171 Processing helix chain 'I' and resid 190 through 198 removed outlier: 3.986A pdb=" N ILE I 194 " --> pdb=" O GLN I 190 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N SER I 197 " --> pdb=" O GLU I 193 " (cutoff:3.500A) Processing helix chain 'I' and resid 205 through 209 Processing helix chain 'I' and resid 229 through 238 removed outlier: 3.626A pdb=" N VAL I 236 " --> pdb=" O LEU I 232 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASN I 238 " --> pdb=" O LYS I 234 " (cutoff:3.500A) Processing helix chain 'I' and resid 249 through 252 Processing helix chain 'I' and resid 260 through 273 removed outlier: 3.766A pdb=" N ARG I 265 " --> pdb=" O PRO I 261 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE I 268 " --> pdb=" O CYS I 264 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS I 269 " --> pdb=" O ARG I 265 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLY I 272 " --> pdb=" O PHE I 268 " (cutoff:3.500A) Processing helix chain 'I' and resid 284 through 286 No H-bonds generated for 'chain 'I' and resid 284 through 286' Processing helix chain 'I' and resid 299 through 313 removed outlier: 3.680A pdb=" N THR I 305 " --> pdb=" O GLU I 301 " (cutoff:3.500A) Processing helix chain 'I' and resid 355 through 365 removed outlier: 3.587A pdb=" N LYS I 359 " --> pdb=" O LEU I 355 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LYS I 360 " --> pdb=" O SER I 356 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLY I 363 " --> pdb=" O LYS I 359 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ILE I 364 " --> pdb=" O LYS I 360 " (cutoff:3.500A) Processing helix chain 'I' and resid 377 through 379 No H-bonds generated for 'chain 'I' and resid 377 through 379' Processing helix chain 'I' and resid 390 through 406 removed outlier: 3.710A pdb=" N ALA I 394 " --> pdb=" O ALA I 390 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET I 395 " --> pdb=" O ASP I 391 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY I 400 " --> pdb=" O CYS I 396 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA I 403 " --> pdb=" O ALA I 399 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU I 404 " --> pdb=" O GLY I 400 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU I 406 " --> pdb=" O LEU I 402 " (cutoff:3.500A) Processing helix chain 'I' and resid 413 through 426 removed outlier: 3.676A pdb=" N ALA I 419 " --> pdb=" O ASP I 415 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ARG I 422 " --> pdb=" O GLN I 418 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASN I 426 " --> pdb=" O ARG I 422 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 65 removed outlier: 3.896A pdb=" N LEU J 32 " --> pdb=" O GLN J 28 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG J 35 " --> pdb=" O GLU J 31 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ASN J 40 " --> pdb=" O SER J 36 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL J 41 " --> pdb=" O LYS J 37 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LYS J 54 " --> pdb=" O ALA J 50 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL J 55 " --> pdb=" O LEU J 51 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE J 58 " --> pdb=" O LYS J 54 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG J 63 " --> pdb=" O LYS J 59 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU J 64 " --> pdb=" O ASP J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 155 through 163 removed outlier: 3.598A pdb=" N GLU J 159 " --> pdb=" O LYS J 155 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE J 160 " --> pdb=" O GLN J 156 " (cutoff:3.500A) Processing helix chain 'J' and resid 166 through 169 No H-bonds generated for 'chain 'J' and resid 166 through 169' Processing helix chain 'J' and resid 171 through 177 Processing helix chain 'J' and resid 195 through 205 removed outlier: 3.728A pdb=" N ALA J 199 " --> pdb=" O LYS J 195 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG J 200 " --> pdb=" O THR J 196 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA J 203 " --> pdb=" O ALA J 199 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N HIS J 204 " --> pdb=" O ARG J 200 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N HIS J 205 " --> pdb=" O ALA J 201 " (cutoff:3.500A) Processing helix chain 'J' and resid 227 through 238 removed outlier: 3.879A pdb=" N ARG J 231 " --> pdb=" O SER J 227 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL J 235 " --> pdb=" O ARG J 231 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N MET J 236 " --> pdb=" O GLU J 232 " (cutoff:3.500A) Processing helix chain 'J' and resid 266 through 277 removed outlier: 4.029A pdb=" N THR J 271 " --> pdb=" O GLU J 267 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N MET J 272 " --> pdb=" O VAL J 268 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU J 273 " --> pdb=" O GLN J 269 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU J 274 " --> pdb=" O ARG J 270 " (cutoff:3.500A) Processing helix chain 'J' and resid 279 through 284 Processing helix chain 'J' and resid 321 through 331 removed outlier: 4.553A pdb=" N GLU J 326 " --> pdb=" O ALA J 322 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ILE J 327 " --> pdb=" O ALA J 323 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N HIS J 331 " --> pdb=" O ILE J 327 " (cutoff:3.500A) Processing helix chain 'J' and resid 343 through 349 removed outlier: 3.933A pdb=" N ALA J 347 " --> pdb=" O LEU J 343 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLU J 348 " --> pdb=" O ARG J 344 " (cutoff:3.500A) Processing helix chain 'J' and resid 357 through 372 removed outlier: 3.504A pdb=" N THR J 363 " --> pdb=" O LYS J 359 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLY J 366 " --> pdb=" O CYS J 362 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR J 368 " --> pdb=" O GLU J 364 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA J 369 " --> pdb=" O ALA J 365 " (cutoff:3.500A) Processing helix chain 'J' and resid 379 through 383 Processing helix chain 'J' and resid 385 through 389 removed outlier: 3.770A pdb=" N VAL J 389 " --> pdb=" O VAL J 386 " (cutoff:3.500A) Processing helix chain 'J' and resid 391 through 397 removed outlier: 3.605A pdb=" N THR J 396 " --> pdb=" O LYS J 392 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALA J 397 " --> pdb=" O ASN J 393 " (cutoff:3.500A) Processing helix chain 'K' and resid 50 through 83 removed outlier: 3.530A pdb=" N LYS K 56 " --> pdb=" O LYS K 52 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR K 58 " --> pdb=" O LEU K 54 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU K 63 " --> pdb=" O GLU K 59 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN K 64 " --> pdb=" O LEU K 60 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP K 66 " --> pdb=" O THR K 62 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TYR K 67 " --> pdb=" O LEU K 63 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS K 69 " --> pdb=" O GLU K 65 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN K 72 " --> pdb=" O ILE K 68 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ARG K 77 " --> pdb=" O ARG K 73 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLU K 78 " --> pdb=" O HIS K 74 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU K 79 " --> pdb=" O LEU K 75 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS K 80 " --> pdb=" O LYS K 76 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG K 81 " --> pdb=" O ARG K 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 89 removed outlier: 3.753A pdb=" N ILE K 89 " --> pdb=" O GLU K 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 85 through 89' Processing helix chain 'K' and resid 178 through 187 removed outlier: 3.708A pdb=" N ILE K 184 " --> pdb=" O GLN K 180 " (cutoff:3.500A) Processing helix chain 'K' and resid 190 through 193 No H-bonds generated for 'chain 'K' and resid 190 through 193' Processing helix chain 'K' and resid 196 through 201 removed outlier: 3.880A pdb=" N ILE K 201 " --> pdb=" O LEU K 197 " (cutoff:3.500A) Processing helix chain 'K' and resid 219 through 230 Processing helix chain 'K' and resid 239 through 242 No H-bonds generated for 'chain 'K' and resid 239 through 242' Processing helix chain 'K' and resid 251 through 261 removed outlier: 4.113A pdb=" N PHE K 258 " --> pdb=" O VAL K 254 " (cutoff:3.500A) Processing helix chain 'K' and resid 288 through 304 removed outlier: 3.688A pdb=" N VAL K 292 " --> pdb=" O SER K 288 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN K 293 " --> pdb=" O ASP K 289 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU K 298 " --> pdb=" O ARG K 294 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N MET K 303 " --> pdb=" O LEU K 299 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP K 304 " --> pdb=" O LEU K 300 " (cutoff:3.500A) Processing helix chain 'K' and resid 346 through 359 removed outlier: 4.055A pdb=" N ILE K 352 " --> pdb=" O GLU K 348 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N PHE K 353 " --> pdb=" O ARG K 349 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLY K 354 " --> pdb=" O ARG K 350 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N THR K 355 " --> pdb=" O LEU K 351 " (cutoff:3.500A) Processing helix chain 'K' and resid 369 through 372 No H-bonds generated for 'chain 'K' and resid 369 through 372' Processing helix chain 'K' and resid 382 through 390 removed outlier: 3.721A pdb=" N GLU K 389 " --> pdb=" O ALA K 385 " (cutoff:3.500A) Processing helix chain 'K' and resid 393 through 396 No H-bonds generated for 'chain 'K' and resid 393 through 396' Processing helix chain 'K' and resid 405 through 411 removed outlier: 4.157A pdb=" N GLU K 409 " --> pdb=" O SER K 405 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA K 410 " --> pdb=" O ASP K 406 " (cutoff:3.500A) Processing helix chain 'L' and resid 72 through 98 removed outlier: 4.748A pdb=" N ARG L 77 " --> pdb=" O GLN L 73 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG L 78 " --> pdb=" O LEU L 74 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLN L 79 " --> pdb=" O LYS L 75 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU L 87 " --> pdb=" O ASP L 83 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS L 90 " --> pdb=" O LYS L 86 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE L 95 " --> pdb=" O THR L 91 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS L 96 " --> pdb=" O GLU L 92 " (cutoff:3.500A) Processing helix chain 'L' and resid 173 through 175 No H-bonds generated for 'chain 'L' and resid 173 through 175' Processing helix chain 'L' and resid 188 through 197 removed outlier: 3.701A pdb=" N ARG L 194 " --> pdb=" O ILE L 190 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU L 195 " --> pdb=" O ARG L 191 " (cutoff:3.500A) Processing helix chain 'L' and resid 199 through 202 No H-bonds generated for 'chain 'L' and resid 199 through 202' Processing helix chain 'L' and resid 207 through 210 No H-bonds generated for 'chain 'L' and resid 207 through 210' Processing helix chain 'L' and resid 229 through 238 removed outlier: 3.801A pdb=" N ALA L 236 " --> pdb=" O ALA L 232 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA L 237 " --> pdb=" O LYS L 233 " (cutoff:3.500A) Processing helix chain 'L' and resid 250 through 253 No H-bonds generated for 'chain 'L' and resid 250 through 253' Processing helix chain 'L' and resid 260 through 272 removed outlier: 3.632A pdb=" N ALA L 270 " --> pdb=" O MET L 266 " (cutoff:3.500A) Processing helix chain 'L' and resid 283 through 285 No H-bonds generated for 'chain 'L' and resid 283 through 285' Processing helix chain 'L' and resid 299 through 315 removed outlier: 4.601A pdb=" N LEU L 305 " --> pdb=" O ILE L 301 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU L 308 " --> pdb=" O THR L 304 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE L 315 " --> pdb=" O GLN L 311 " (cutoff:3.500A) Processing helix chain 'L' and resid 330 through 332 No H-bonds generated for 'chain 'L' and resid 330 through 332' Processing helix chain 'L' and resid 356 through 367 removed outlier: 4.316A pdb=" N ILE L 363 " --> pdb=" O GLU L 359 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ALA L 366 " --> pdb=" O LYS L 362 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS L 367 " --> pdb=" O ILE L 363 " (cutoff:3.500A) Processing helix chain 'L' and resid 375 through 380 Processing helix chain 'L' and resid 391 through 402 removed outlier: 3.752A pdb=" N THR L 396 " --> pdb=" O ARG L 392 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N PHE L 401 " --> pdb=" O GLU L 397 " (cutoff:3.500A) Processing helix chain 'L' and resid 412 through 416 Processing helix chain 'L' and resid 418 through 427 removed outlier: 3.700A pdb=" N VAL L 422 " --> pdb=" O ALA L 418 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N GLU L 424 " --> pdb=" O ARG L 420 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LYS L 427 " --> pdb=" O ALA L 423 " (cutoff:3.500A) Processing helix chain 'M' and resid 38 through 44 removed outlier: 3.546A pdb=" N ARG M 42 " --> pdb=" O ASP M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 46 through 71 removed outlier: 3.737A pdb=" N HIS M 53 " --> pdb=" O GLN M 49 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE M 62 " --> pdb=" O MET M 58 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS M 63 " --> pdb=" O LEU M 59 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYS M 70 " --> pdb=" O LYS M 66 " (cutoff:3.500A) Processing helix chain 'M' and resid 137 through 139 No H-bonds generated for 'chain 'M' and resid 137 through 139' Processing helix chain 'M' and resid 165 through 170 removed outlier: 5.298A pdb=" N MET M 170 " --> pdb=" O ARG M 166 " (cutoff:3.500A) Processing helix chain 'M' and resid 187 through 196 removed outlier: 3.576A pdb=" N GLU M 195 " --> pdb=" O GLU M 191 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA M 196 " --> pdb=" O GLU M 192 " (cutoff:3.500A) Processing helix chain 'M' and resid 198 through 202 Processing helix chain 'M' and resid 204 through 208 Processing helix chain 'M' and resid 229 through 238 removed outlier: 3.948A pdb=" N ALA M 237 " --> pdb=" O ARG M 233 " (cutoff:3.500A) Processing helix chain 'M' and resid 260 through 271 Processing helix chain 'M' and resid 296 through 312 removed outlier: 4.052A pdb=" N VAL M 301 " --> pdb=" O GLY M 297 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN M 302 " --> pdb=" O ASP M 298 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR M 304 " --> pdb=" O GLU M 300 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N MET M 305 " --> pdb=" O VAL M 301 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN M 310 " --> pdb=" O LEU M 306 " (cutoff:3.500A) Processing helix chain 'M' and resid 335 through 338 Processing helix chain 'M' and resid 354 through 367 removed outlier: 3.694A pdb=" N ALA M 358 " --> pdb=" O GLU M 354 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN M 359 " --> pdb=" O ASP M 355 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU M 361 " --> pdb=" O ARG M 357 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG M 366 " --> pdb=" O GLN M 362 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LYS M 367 " --> pdb=" O ILE M 363 " (cutoff:3.500A) Processing helix chain 'M' and resid 376 through 381 Processing helix chain 'M' and resid 388 through 405 removed outlier: 3.753A pdb=" N THR M 395 " --> pdb=" O LEU M 391 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU M 403 " --> pdb=" O GLY M 399 " (cutoff:3.500A) Processing helix chain 'M' and resid 413 through 422 removed outlier: 3.589A pdb=" N GLY M 418 " --> pdb=" O ASP M 414 " (cutoff:3.500A) Processing helix chain 'r' and resid 31 through 43 removed outlier: 3.742A pdb=" N LEU r 35 " --> pdb=" O SER r 31 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS r 36 " --> pdb=" O ILE r 32 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N HIS r 40 " --> pdb=" O LYS r 36 " (cutoff:3.500A) Processing helix chain 'r' and resid 89 through 95 removed outlier: 3.700A pdb=" N ASP r 93 " --> pdb=" O ALA r 89 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET r 94 " --> pdb=" O LYS r 90 " (cutoff:3.500A) Processing helix chain 'r' and resid 120 through 132 removed outlier: 3.592A pdb=" N ASN r 124 " --> pdb=" O SER r 120 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER r 128 " --> pdb=" O ASN r 124 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE r 129 " --> pdb=" O THR r 125 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN r 131 " --> pdb=" O LYS r 127 " (cutoff:3.500A) Processing helix chain 'r' and resid 161 through 166 removed outlier: 3.511A pdb=" N ASN r 166 " --> pdb=" O GLY r 162 " (cutoff:3.500A) Processing helix chain 'r' and resid 185 through 187 No H-bonds generated for 'chain 'r' and resid 185 through 187' Processing helix chain 'r' and resid 207 through 216 removed outlier: 4.412A pdb=" N MET r 212 " --> pdb=" O LYS r 208 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN r 215 " --> pdb=" O LYS r 211 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N LEU r 216 " --> pdb=" O MET r 212 " (cutoff:3.500A) Processing helix chain 'r' and resid 233 through 251 removed outlier: 4.200A pdb=" N ALA r 239 " --> pdb=" O GLU r 235 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LYS r 242 " --> pdb=" O LEU r 238 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LYS r 246 " --> pdb=" O LYS r 242 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ILE r 247 " --> pdb=" O SER r 243 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN r 250 " --> pdb=" O LYS r 246 " (cutoff:3.500A) Processing helix chain 'r' and resid 253 through 255 No H-bonds generated for 'chain 'r' and resid 253 through 255' Processing helix chain 'r' and resid 276 through 304 removed outlier: 3.739A pdb=" N THR r 283 " --> pdb=" O HIS r 279 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU r 286 " --> pdb=" O GLU r 282 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL r 293 " --> pdb=" O GLU r 289 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER r 294 " --> pdb=" O ASN r 290 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA r 298 " --> pdb=" O SER r 294 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL r 303 " --> pdb=" O GLY r 299 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA r 304 " --> pdb=" O VAL r 300 " (cutoff:3.500A) Processing helix chain 'u' and resid 23 through 33 removed outlier: 3.906A pdb=" N SER u 28 " --> pdb=" O ASP u 24 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS u 29 " --> pdb=" O ASN u 25 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE u 30 " --> pdb=" O VAL u 26 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN u 31 " --> pdb=" O LYS u 27 " (cutoff:3.500A) Processing helix chain 'u' and resid 38 through 40 No H-bonds generated for 'chain 'u' and resid 38 through 40' Processing helix chain 'u' and resid 56 through 58 No H-bonds generated for 'chain 'u' and resid 56 through 58' Processing sheet with id= A, first strand: chain '1' and resid 124 through 127 removed outlier: 3.720A pdb=" N GLY 1 11 " --> pdb=" O PHE 1 8 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU 1 14 " --> pdb=" O VAL 1 176 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N VAL 1 172 " --> pdb=" O SER 1 18 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N MET 1 175 " --> pdb=" O LEU 1 186 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '1' and resid 41 through 47 removed outlier: 3.620A pdb=" N ALA 1 100 " --> pdb=" O TRP 1 42 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE 1 98 " --> pdb=" O CYS 1 44 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain '1' and resid 111 through 113 Processing sheet with id= D, first strand: chain '2' and resid 124 through 127 removed outlier: 3.525A pdb=" N GLY 2 11 " --> pdb=" O PHE 2 8 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain '2' and resid 42 through 45 removed outlier: 3.611A pdb=" N TRP 2 42 " --> pdb=" O ALA 2 101 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA 2 44 " --> pdb=" O ILE 2 99 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain '3' and resid 136 through 140 removed outlier: 5.756A pdb=" N ILE 3 11 " --> pdb=" O ASP 3 26 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ALA 3 185 " --> pdb=" O LEU 3 200 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU 3 200 " --> pdb=" O ALA 3 185 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE 3 189 " --> pdb=" O VAL 3 196 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL 3 196 " --> pdb=" O ILE 3 189 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain '3' and resid 43 through 46 removed outlier: 3.715A pdb=" N GLY 3 52 " --> pdb=" O VAL 3 108 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS 3 118 " --> pdb=" O ASN 3 113 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain '4' and resid 130 through 132 Processing sheet with id= I, first strand: chain '4' and resid 42 through 48 removed outlier: 3.973A pdb=" N GLY 4 106 " --> pdb=" O GLU 4 115 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU 4 115 " --> pdb=" O GLY 4 106 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain '4' and resid 21 through 23 removed outlier: 4.162A pdb=" N LYS 4 29 " --> pdb=" O VAL 4 21 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ARG 4 23 " --> pdb=" O VAL 4 27 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL 4 27 " --> pdb=" O ARG 4 23 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain '5' and resid 126 through 130 Processing sheet with id= L, first strand: chain '5' and resid 41 through 43 Processing sheet with id= M, first strand: chain '5' and resid 178 through 181 Processing sheet with id= N, first strand: chain '5' and resid 20 through 22 removed outlier: 6.311A pdb=" N ALA 5 22 " --> pdb=" O VAL 5 26 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N VAL 5 26 " --> pdb=" O ALA 5 22 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain '6' and resid 11 through 13 Processing sheet with id= P, first strand: chain '6' and resid 43 through 45 removed outlier: 3.579A pdb=" N PHE 6 44 " --> pdb=" O MET 6 52 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET 6 52 " --> pdb=" O PHE 6 44 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN 6 55 " --> pdb=" O HIS 6 108 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N THR 6 109 " --> pdb=" O PHE 6 125 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL 6 122 " --> pdb=" O GLU 6 134 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain '6' and resid 202 through 204 removed outlier: 3.505A pdb=" N TYR 6 217 " --> pdb=" O LEU 6 202 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain '7' and resid 11 through 15 removed outlier: 4.085A pdb=" N ILE 7 199 " --> pdb=" O THR 7 207 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR 7 207 " --> pdb=" O ILE 7 199 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain '7' and resid 49 through 52 removed outlier: 3.503A pdb=" N GLY 7 118 " --> pdb=" O PHE 7 126 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'A' and resid 168 through 170 removed outlier: 3.538A pdb=" N VAL A 52 " --> pdb=" O VAL A 45 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'A' and resid 79 through 82 Processing sheet with id= V, first strand: chain 'B' and resid 34 through 36 removed outlier: 3.601A pdb=" N THR B 162 " --> pdb=" O GLY B 36 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'B' and resid 45 through 48 removed outlier: 3.805A pdb=" N ILE B 45 " --> pdb=" O ALA B 212 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'B' and resid 134 through 136 Processing sheet with id= Y, first strand: chain 'B' and resid 65 through 68 removed outlier: 3.625A pdb=" N SER B 65 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'C' and resid 35 through 38 removed outlier: 3.592A pdb=" N ALA C 35 " --> pdb=" O VAL C 165 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'C' and resid 135 through 139 removed outlier: 3.713A pdb=" N PHE C 135 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N SER C 151 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR C 149 " --> pdb=" O TYR C 137 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY C 139 " --> pdb=" O GLN C 147 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN C 147 " --> pdb=" O GLY C 139 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'C' and resid 215 through 217 Processing sheet with id= AC, first strand: chain 'C' and resid 67 through 70 removed outlier: 6.471A pdb=" N ILE C 73 " --> pdb=" O LEU C 69 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'D' and resid 161 through 164 removed outlier: 3.515A pdb=" N VAL D 36 " --> pdb=" O VAL D 43 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'D' and resid 134 through 136 removed outlier: 3.516A pdb=" N ALA D 136 " --> pdb=" O VAL D 72 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL D 71 " --> pdb=" O ASP D 68 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASP D 68 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU D 73 " --> pdb=" O LYS D 66 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N LYS D 66 " --> pdb=" O LEU D 73 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'D' and resid 213 through 216 removed outlier: 3.714A pdb=" N VAL D 222 " --> pdb=" O VAL D 214 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'E' and resid 47 through 50 Processing sheet with id= AH, first strand: chain 'E' and resid 152 through 154 removed outlier: 3.537A pdb=" N LEU E 143 " --> pdb=" O ALA E 77 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASP E 71 " --> pdb=" O ILE E 74 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N CYS E 76 " --> pdb=" O GLU E 69 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N GLU E 69 " --> pdb=" O CYS E 76 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N MET E 78 " --> pdb=" O ILE E 67 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ILE E 67 " --> pdb=" O MET E 78 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'F' and resid 35 through 39 removed outlier: 4.223A pdb=" N SER F 212 " --> pdb=" O ALA F 48 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'F' and resid 141 through 146 removed outlier: 3.857A pdb=" N ASP F 138 " --> pdb=" O GLY F 141 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY F 136 " --> pdb=" O HIS F 143 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE F 134 " --> pdb=" O LEU F 145 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER F 73 " --> pdb=" O LEU F 133 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ILE F 135 " --> pdb=" O GLY F 71 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY F 71 " --> pdb=" O ILE F 135 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ASP F 67 " --> pdb=" O MET F 70 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU F 72 " --> pdb=" O LYS F 65 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N LYS F 65 " --> pdb=" O LEU F 72 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N LEU F 74 " --> pdb=" O ILE F 63 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ILE F 63 " --> pdb=" O LEU F 74 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'G' and resid 162 through 164 removed outlier: 3.555A pdb=" N GLY G 39 " --> pdb=" O ALA G 163 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'G' and resid 74 through 77 removed outlier: 3.544A pdb=" N GLY G 139 " --> pdb=" O GLY G 75 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY G 145 " --> pdb=" O ASP G 142 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TRP G 158 " --> pdb=" O MET G 150 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'H' and resid 100 through 104 removed outlier: 3.733A pdb=" N THR H 103 " --> pdb=" O VAL H 146 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N VAL H 146 " --> pdb=" O THR H 103 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'H' and resid 173 through 176 removed outlier: 3.805A pdb=" N LEU H 185 " --> pdb=" O GLY H 175 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'I' and resid 105 through 107 removed outlier: 3.948A pdb=" N GLY I 107 " --> pdb=" O VAL I 147 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY I 158 " --> pdb=" O LEU I 148 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'I' and resid 117 through 120 removed outlier: 3.526A pdb=" N VAL I 120 " --> pdb=" O TYR I 128 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR I 128 " --> pdb=" O VAL I 120 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'I' and resid 325 through 327 removed outlier: 6.755A pdb=" N VAL I 219 " --> pdb=" O MET I 326 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ILE I 348 " --> pdb=" O TYR I 222 " (cutoff:3.500A) No H-bonds generated for sheet with id= AQ Processing sheet with id= AR, first strand: chain 'J' and resid 112 through 116 removed outlier: 3.524A pdb=" N VAL J 84 " --> pdb=" O VAL J 96 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'J' and resid 185 through 188 removed outlier: 6.720A pdb=" N ARG J 312 " --> pdb=" O ILE J 186 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N TYR J 188 " --> pdb=" O ARG J 312 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ILE J 314 " --> pdb=" O TYR J 188 " (cutoff:3.500A) No H-bonds generated for sheet with id= AS Processing sheet with id= AT, first strand: chain 'J' and resid 209 through 213 Processing sheet with id= AU, first strand: chain 'K' and resid 95 through 97 removed outlier: 3.817A pdb=" N GLY K 97 " --> pdb=" O VAL K 137 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL K 137 " --> pdb=" O GLY K 97 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'K' and resid 117 through 120 removed outlier: 4.273A pdb=" N GLU K 101 " --> pdb=" O ILE K 109 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N SER K 111 " --> pdb=" O PHE K 99 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N PHE K 99 " --> pdb=" O SER K 111 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'K' and resid 209 through 211 Processing sheet with id= AX, first strand: chain 'K' and resid 233 through 237 removed outlier: 3.744A pdb=" N ILE K 268 " --> pdb=" O ALA K 233 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'L' and resid 104 through 107 Processing sheet with id= AZ, first strand: chain 'L' and resid 218 through 220 removed outlier: 6.596A pdb=" N ARG L 345 " --> pdb=" O LEU L 219 " (cutoff:3.500A) No H-bonds generated for sheet with id= AZ Processing sheet with id= BA, first strand: chain 'L' and resid 243 through 245 removed outlier: 6.322A pdb=" N ILE L 277 " --> pdb=" O ILE L 244 " (cutoff:3.500A) No H-bonds generated for sheet with id= BA Processing sheet with id= BB, first strand: chain 'M' and resid 78 through 80 removed outlier: 3.596A pdb=" N VAL M 146 " --> pdb=" O ALA M 80 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'M' and resid 117 through 121 removed outlier: 3.836A pdb=" N VAL M 127 " --> pdb=" O VAL M 119 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR M 121 " --> pdb=" O GLN M 125 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLN M 125 " --> pdb=" O THR M 121 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'M' and resid 220 through 222 removed outlier: 5.921A pdb=" N ILE M 347 " --> pdb=" O TYR M 221 " (cutoff:3.500A) No H-bonds generated for sheet with id= BD Processing sheet with id= BE, first strand: chain 'r' and resid 73 through 75 removed outlier: 3.922A pdb=" N GLU r 81 " --> pdb=" O SER r 74 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'r' and resid 154 through 156 removed outlier: 3.733A pdb=" N VAL r 137 " --> pdb=" O VAL r 105 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N MET r 53 " --> pdb=" O VAL r 105 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N TRP r 107 " --> pdb=" O GLY r 51 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N GLY r 51 " --> pdb=" O TRP r 107 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLU r 56 " --> pdb=" O VAL r 65 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N VAL r 65 " --> pdb=" O GLU r 56 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'u' and resid 3 through 5 Processing sheet with id= BH, first strand: chain 'u' and resid 41 through 44 1139 hydrogen bonds defined for protein. 3159 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: 14.16 Time building geometry restraints manager: 17.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 11634 1.33 - 1.45: 11424 1.45 - 1.58: 21652 1.58 - 1.71: 26 1.71 - 1.83: 275 Bond restraints: 45011 Sorted by residual: bond pdb=" C5 ATP H 501 " pdb=" N7 ATP H 501 " ideal model delta sigma weight residual 1.387 1.321 0.066 1.00e-02 1.00e+04 4.40e+01 bond pdb=" C4 ATP I 501 " pdb=" C5 ATP I 501 " ideal model delta sigma weight residual 1.388 1.452 -0.064 1.00e-02 1.00e+04 4.16e+01 bond pdb=" C4 ATP H 501 " pdb=" C5 ATP H 501 " ideal model delta sigma weight residual 1.388 1.449 -0.061 1.00e-02 1.00e+04 3.72e+01 bond pdb=" C4 ATP M 501 " pdb=" C5 ATP M 501 " ideal model delta sigma weight residual 1.388 1.448 -0.060 1.00e-02 1.00e+04 3.62e+01 bond pdb=" C5 ATP J 501 " pdb=" N7 ATP J 501 " ideal model delta sigma weight residual 1.387 1.328 0.059 1.00e-02 1.00e+04 3.52e+01 ... (remaining 45006 not shown) Histogram of bond angle deviations from ideal: 97.02 - 104.84: 719 104.84 - 112.66: 23179 112.66 - 120.48: 19203 120.48 - 128.30: 17569 128.30 - 136.12: 328 Bond angle restraints: 60998 Sorted by residual: angle pdb=" PB ATP M 501 " pdb=" O3B ATP M 501 " pdb=" PG ATP M 501 " ideal model delta sigma weight residual 139.87 112.38 27.49 1.00e+00 1.00e+00 7.56e+02 angle pdb=" PA ATP J 501 " pdb=" O3A ATP J 501 " pdb=" PB ATP J 501 " ideal model delta sigma weight residual 136.83 112.65 24.18 1.00e+00 1.00e+00 5.85e+02 angle pdb=" PB ATP H 501 " pdb=" O3B ATP H 501 " pdb=" PG ATP H 501 " ideal model delta sigma weight residual 139.87 116.41 23.46 1.00e+00 1.00e+00 5.50e+02 angle pdb=" PB ATP I 501 " pdb=" O3B ATP I 501 " pdb=" PG ATP I 501 " ideal model delta sigma weight residual 139.87 116.85 23.02 1.00e+00 1.00e+00 5.30e+02 angle pdb=" PB ATP J 501 " pdb=" O3B ATP J 501 " pdb=" PG ATP J 501 " ideal model delta sigma weight residual 139.87 117.46 22.41 1.00e+00 1.00e+00 5.02e+02 ... (remaining 60993 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.47: 26666 27.47 - 54.94: 602 54.94 - 82.41: 50 82.41 - 109.88: 2 109.88 - 137.36: 5 Dihedral angle restraints: 27325 sinusoidal: 10546 harmonic: 16779 Sorted by residual: dihedral pdb=" C5' ADP K 501 " pdb=" O5' ADP K 501 " pdb=" PA ADP K 501 " pdb=" O2A ADP K 501 " ideal model delta sinusoidal sigma weight residual -60.00 77.36 -137.36 1 2.00e+01 2.50e-03 4.17e+01 dihedral pdb=" O2A ADP L 501 " pdb=" O3A ADP L 501 " pdb=" PA ADP L 501 " pdb=" PB ADP L 501 " ideal model delta sinusoidal sigma weight residual -60.00 71.65 -131.65 1 2.00e+01 2.50e-03 4.00e+01 dihedral pdb=" O2A ADP K 501 " pdb=" O3A ADP K 501 " pdb=" PA ADP K 501 " pdb=" PB ADP K 501 " ideal model delta sinusoidal sigma weight residual -60.00 66.49 -126.49 1 2.00e+01 2.50e-03 3.83e+01 ... (remaining 27322 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 4629 0.063 - 0.127: 1916 0.127 - 0.190: 422 0.190 - 0.253: 70 0.253 - 0.317: 12 Chirality restraints: 7049 Sorted by residual: chirality pdb=" CB VAL E 200 " pdb=" CA VAL E 200 " pdb=" CG1 VAL E 200 " pdb=" CG2 VAL E 200 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" CB VAL 1 172 " pdb=" CA VAL 1 172 " pdb=" CG1 VAL 1 172 " pdb=" CG2 VAL 1 172 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CB VAL I 219 " pdb=" CA VAL I 219 " pdb=" CG1 VAL I 219 " pdb=" CG2 VAL I 219 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 7046 not shown) Planarity restraints: 7868 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN J 181 " -0.065 5.00e-02 4.00e+02 9.81e-02 1.54e+01 pdb=" N PRO J 182 " 0.170 5.00e-02 4.00e+02 pdb=" CA PRO J 182 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO J 182 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG 4 96 " 0.057 5.00e-02 4.00e+02 8.49e-02 1.15e+01 pdb=" N PRO 4 97 " -0.147 5.00e-02 4.00e+02 pdb=" CA PRO 4 97 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO 4 97 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 60 " 0.052 5.00e-02 4.00e+02 7.83e-02 9.82e+00 pdb=" N PRO G 61 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO G 61 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO G 61 " 0.043 5.00e-02 4.00e+02 ... (remaining 7865 not shown) Histogram of nonbonded interaction distances: 1.34 - 2.05: 4 2.05 - 2.76: 9535 2.76 - 3.48: 62017 3.48 - 4.19: 96568 4.19 - 4.90: 168569 Nonbonded interactions: 336693 Sorted by model distance: nonbonded pdb=" NZ LYS s 108 " pdb=" C GLY u 76 " model vdw 1.340 3.350 nonbonded pdb=" NZ LYS s 108 " pdb=" O GLY u 76 " model vdw 1.405 2.520 nonbonded pdb=" OH TYR 3 46 " pdb=" OD1 ASN 3 64 " model vdw 1.983 2.440 nonbonded pdb=" OD1 ASP G 114 " pdb=" OH TYR G 157 " model vdw 2.050 2.440 nonbonded pdb=" OG1 THR I 230 " pdb=" O3G ATP I 501 " model vdw 2.052 2.440 ... (remaining 336688 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 10.350 Check model and map are aligned: 0.670 Set scattering table: 0.410 Process input model: 109.970 Find NCS groups from input model: 2.550 Set up NCS constraints: 0.170 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 129.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 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 : 0.016 0.139 45011 Z= 1.063 Angle : 1.105 27.490 60998 Z= 0.641 Chirality : 0.070 0.317 7049 Planarity : 0.007 0.098 7868 Dihedral : 12.096 137.355 16547 Min Nonbonded Distance : 1.340 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 14.74 % Favored : 85.22 % Rotamer: Outliers : 0.07 % Allowed : 6.21 % Favored : 93.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.91 (0.08), residues: 5766 helix: -4.16 (0.07), residues: 1949 sheet: -4.23 (0.11), residues: 981 loop : -3.58 (0.10), residues: 2836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.004 TRP 7 111 HIS 0.015 0.003 HIS 2 141 PHE 0.040 0.004 PHE J 174 TYR 0.038 0.004 TYR G 160 ARG 0.018 0.002 ARG C 113 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11532 Ramachandran restraints generated. 5766 Oldfield, 0 Emsley, 5766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11532 Ramachandran restraints generated. 5766 Oldfield, 0 Emsley, 5766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1025 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1022 time to evaluate : 5.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 69 GLN cc_start: 0.7470 (mt0) cc_final: 0.6999 (mt0) REVERT: 2 71 SER cc_start: 0.8351 (m) cc_final: 0.8124 (p) REVERT: 2 179 GLU cc_start: 0.7687 (tt0) cc_final: 0.7115 (tt0) REVERT: 2 188 ARG cc_start: 0.7687 (tpt90) cc_final: 0.7481 (tpt90) REVERT: 2 200 GLN cc_start: 0.7423 (mt0) cc_final: 0.6519 (pt0) REVERT: 2 207 ARG cc_start: 0.7207 (mpt180) cc_final: 0.6876 (mmt90) REVERT: 2 214 LYS cc_start: 0.8130 (ptmt) cc_final: 0.7624 (mttp) REVERT: 3 99 ARG cc_start: 0.8872 (tpt90) cc_final: 0.8472 (tpt-90) REVERT: 3 203 ARG cc_start: 0.8345 (ptm-80) cc_final: 0.6648 (mtt180) REVERT: 4 1 MET cc_start: 0.6474 (ttp) cc_final: 0.6251 (tpt) REVERT: 4 78 GLN cc_start: 0.7792 (tm130) cc_final: 0.7500 (tp-100) REVERT: 5 24 ASN cc_start: 0.8447 (t160) cc_final: 0.7916 (t0) REVERT: 5 36 GLU cc_start: 0.6954 (mp0) cc_final: 0.6040 (tm-30) REVERT: 6 81 ASP cc_start: 0.7269 (t0) cc_final: 0.6999 (t70) REVERT: 6 159 GLN cc_start: 0.6849 (pt0) cc_final: 0.6522 (pt0) REVERT: 7 120 GLN cc_start: 0.8079 (mm110) cc_final: 0.7728 (mm-40) REVERT: A 29 GLU cc_start: 0.7620 (tt0) cc_final: 0.7020 (tt0) REVERT: A 39 ASN cc_start: 0.8374 (m-40) cc_final: 0.7772 (t0) REVERT: A 49 ASP cc_start: 0.7358 (p0) cc_final: 0.6981 (p0) REVERT: A 50 CYS cc_start: 0.7040 (m) cc_final: 0.6456 (m) REVERT: B 75 TYR cc_start: 0.8541 (p90) cc_final: 0.8011 (p90) REVERT: B 136 ILE cc_start: 0.9005 (mt) cc_final: 0.8777 (mm) REVERT: B 142 PHE cc_start: 0.8381 (m-80) cc_final: 0.7927 (m-10) REVERT: B 178 ARG cc_start: 0.7915 (mmm-85) cc_final: 0.7711 (mmt180) REVERT: B 182 GLU cc_start: 0.7718 (pm20) cc_final: 0.7340 (pm20) REVERT: C 206 LEU cc_start: 0.8797 (pt) cc_final: 0.8274 (tp) REVERT: C 212 GLU cc_start: 0.8019 (pm20) cc_final: 0.7723 (pm20) REVERT: C 238 ILE cc_start: 0.8150 (mm) cc_final: 0.7935 (mm) REVERT: E 76 CYS cc_start: 0.7778 (m) cc_final: 0.7465 (m) REVERT: E 167 TYR cc_start: 0.7987 (m-80) cc_final: 0.7748 (m-80) REVERT: E 183 LEU cc_start: 0.8560 (mp) cc_final: 0.8162 (mp) REVERT: F 27 GLU cc_start: 0.7186 (tm-30) cc_final: 0.6954 (tm-30) REVERT: F 60 GLN cc_start: 0.8428 (pt0) cc_final: 0.8173 (pt0) REVERT: F 61 LYS cc_start: 0.8518 (mppt) cc_final: 0.8314 (mmtm) REVERT: F 86 ASN cc_start: 0.8880 (m-40) cc_final: 0.8439 (m-40) REVERT: G 237 GLN cc_start: 0.7930 (tp40) cc_final: 0.7515 (mm-40) REVERT: H 105 ILE cc_start: 0.9079 (mt) cc_final: 0.8863 (tt) REVERT: H 221 LEU cc_start: 0.8950 (tt) cc_final: 0.8711 (tp) REVERT: H 235 PHE cc_start: 0.8439 (m-80) cc_final: 0.8233 (m-80) REVERT: H 442 ASP cc_start: 0.8523 (p0) cc_final: 0.8033 (p0) REVERT: I 167 MET cc_start: 0.7782 (pmm) cc_final: 0.7489 (ptp) REVERT: I 312 GLN cc_start: 0.7835 (mm-40) cc_final: 0.7510 (mm-40) REVERT: J 32 LEU cc_start: 0.8968 (mm) cc_final: 0.8675 (tp) REVERT: K 319 ASN cc_start: 0.9007 (m110) cc_final: 0.8102 (t0) REVERT: K 400 TYR cc_start: 0.3964 (m-80) cc_final: 0.3656 (m-80) REVERT: L 117 TYR cc_start: 0.8298 (m-10) cc_final: 0.7912 (m-10) REVERT: L 159 LEU cc_start: 0.7713 (pt) cc_final: 0.7261 (pp) REVERT: L 272 GLU cc_start: 0.7023 (pp20) cc_final: 0.6811 (pp20) REVERT: r 214 MET cc_start: 0.7749 (ppp) cc_final: 0.7533 (ppp) outliers start: 3 outliers final: 1 residues processed: 1024 average time/residue: 0.5631 time to fit residues: 928.0562 Evaluate side-chains 654 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 653 time to evaluate : 4.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 484 optimal weight: 30.0000 chunk 435 optimal weight: 2.9990 chunk 241 optimal weight: 0.8980 chunk 148 optimal weight: 1.9990 chunk 293 optimal weight: 2.9990 chunk 232 optimal weight: 1.9990 chunk 449 optimal weight: 4.9990 chunk 174 optimal weight: 2.9990 chunk 273 optimal weight: 0.7980 chunk 334 optimal weight: 0.9980 chunk 521 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 157 HIS 3 145 GLN 4 41 HIS 4 65 GLN 5 191 HIS 7 61 GLN 7 112 ASN 7 125 GLN 7 179 ASN ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 HIS B 190 HIS C 21 GLN C 103 ASN D 94 GLN D 178 ASN F 21 GLN F 93 ASN F 166 GLN F 210 ASN G 23 GLN G 118 GLN G 207 ASN H 54 ASN H 89 GLN H 281 GLN H 356 ASN H 359 ASN I 192 GLN ** I 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 352 ASN J 204 HIS J 269 GLN ** J 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 98 GLN K 228 ASN K 302 GLN r 126 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 45011 Z= 0.221 Angle : 0.695 10.651 60998 Z= 0.358 Chirality : 0.048 0.214 7049 Planarity : 0.005 0.064 7868 Dihedral : 8.735 121.406 6446 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 0.11 % Allowed : 3.60 % Favored : 96.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -4.50 (0.09), residues: 5766 helix: -2.87 (0.09), residues: 2025 sheet: -3.18 (0.13), residues: 961 loop : -2.94 (0.11), residues: 2780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP G 218 HIS 0.011 0.001 HIS G 204 PHE 0.020 0.002 PHE D 129 TYR 0.028 0.002 TYR A 133 ARG 0.006 0.001 ARG r 135 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11532 Ramachandran restraints generated. 5766 Oldfield, 0 Emsley, 5766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11532 Ramachandran restraints generated. 5766 Oldfield, 0 Emsley, 5766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 953 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 948 time to evaluate : 4.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 97 ILE cc_start: 0.9035 (pt) cc_final: 0.8619 (mt) REVERT: 2 12 VAL cc_start: 0.9505 (m) cc_final: 0.9227 (p) REVERT: 2 69 TYR cc_start: 0.9032 (t80) cc_final: 0.8556 (t80) REVERT: 2 71 SER cc_start: 0.8317 (m) cc_final: 0.8037 (p) REVERT: 2 112 SER cc_start: 0.8220 (t) cc_final: 0.7765 (p) REVERT: 2 120 ASP cc_start: 0.7147 (p0) cc_final: 0.6504 (p0) REVERT: 2 200 GLN cc_start: 0.7016 (mt0) cc_final: 0.6156 (pt0) REVERT: 2 214 LYS cc_start: 0.8228 (ptmt) cc_final: 0.7767 (mttp) REVERT: 3 203 ARG cc_start: 0.8474 (ptm-80) cc_final: 0.6552 (mtt180) REVERT: 4 1 MET cc_start: 0.6682 (ttp) cc_final: 0.5734 (tpt) REVERT: 4 3 ILE cc_start: 0.9114 (pt) cc_final: 0.8568 (mp) REVERT: 4 30 ASP cc_start: 0.8513 (p0) cc_final: 0.8200 (p0) REVERT: 4 99 GLN cc_start: 0.7321 (tm-30) cc_final: 0.7049 (tm-30) REVERT: 4 103 LEU cc_start: 0.9198 (mm) cc_final: 0.8936 (mp) REVERT: 5 24 ASN cc_start: 0.8668 (t0) cc_final: 0.8172 (t0) REVERT: 5 100 MET cc_start: 0.8237 (ptp) cc_final: 0.7915 (ptp) REVERT: 6 81 ASP cc_start: 0.7049 (t0) cc_final: 0.6730 (t70) REVERT: 6 159 GLN cc_start: 0.6811 (pt0) cc_final: 0.5776 (tp40) REVERT: 6 180 VAL cc_start: 0.8953 (m) cc_final: 0.8691 (t) REVERT: 7 36 PHE cc_start: 0.7658 (m-80) cc_final: 0.7149 (m-80) REVERT: 7 108 ASN cc_start: 0.7699 (p0) cc_final: 0.7169 (p0) REVERT: A 39 ASN cc_start: 0.8442 (m-40) cc_final: 0.7738 (t0) REVERT: A 49 ASP cc_start: 0.7415 (p0) cc_final: 0.7004 (p0) REVERT: A 50 CYS cc_start: 0.6932 (m) cc_final: 0.6629 (m) REVERT: A 195 ASN cc_start: 0.8406 (m-40) cc_final: 0.8141 (m110) REVERT: A 224 GLU cc_start: 0.8305 (pt0) cc_final: 0.8009 (pt0) REVERT: B 41 ASN cc_start: 0.8516 (p0) cc_final: 0.8089 (p0) REVERT: B 47 THR cc_start: 0.9003 (t) cc_final: 0.8780 (t) REVERT: B 60 THR cc_start: 0.9159 (p) cc_final: 0.8726 (t) REVERT: B 75 TYR cc_start: 0.8849 (p90) cc_final: 0.8605 (p90) REVERT: B 178 ARG cc_start: 0.8026 (mmm-85) cc_final: 0.7580 (mmt180) REVERT: B 224 TYR cc_start: 0.8322 (p90) cc_final: 0.8094 (p90) REVERT: C 195 LYS cc_start: 0.8517 (mmmt) cc_final: 0.8313 (mmmt) REVERT: C 199 LYS cc_start: 0.9205 (mtpp) cc_final: 0.8957 (mtmt) REVERT: C 206 LEU cc_start: 0.8800 (pt) cc_final: 0.8482 (tp) REVERT: C 208 TYR cc_start: 0.8177 (p90) cc_final: 0.7970 (p90) REVERT: C 212 GLU cc_start: 0.8029 (pm20) cc_final: 0.7572 (pm20) REVERT: D 47 GLU cc_start: 0.8242 (pp20) cc_final: 0.7791 (pp20) REVERT: D 86 ILE cc_start: 0.8017 (pt) cc_final: 0.7782 (pt) REVERT: E 53 ARG cc_start: 0.6895 (ttm-80) cc_final: 0.5899 (ttt-90) REVERT: E 167 TYR cc_start: 0.8146 (m-80) cc_final: 0.7765 (m-80) REVERT: E 168 ASN cc_start: 0.8343 (m110) cc_final: 0.7943 (m-40) REVERT: E 216 ASN cc_start: 0.8423 (p0) cc_final: 0.8158 (p0) REVERT: F 60 GLN cc_start: 0.8348 (pt0) cc_final: 0.8042 (pt0) REVERT: F 61 LYS cc_start: 0.8329 (mppt) cc_final: 0.8047 (mmtm) REVERT: F 70 MET cc_start: 0.8395 (ttm) cc_final: 0.8117 (ttm) REVERT: H 51 GLN cc_start: 0.8105 (pp30) cc_final: 0.7786 (pp30) REVERT: H 105 ILE cc_start: 0.8990 (mt) cc_final: 0.8738 (tt) REVERT: H 166 THR cc_start: 0.6449 (p) cc_final: 0.6209 (t) REVERT: H 330 GLN cc_start: 0.8720 (mp10) cc_final: 0.8380 (mp10) REVERT: H 348 ASN cc_start: 0.7944 (t0) cc_final: 0.7708 (t0) REVERT: H 359 ASN cc_start: 0.8967 (m-40) cc_final: 0.8565 (m110) REVERT: H 425 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7662 (mt-10) REVERT: H 442 ASP cc_start: 0.8756 (p0) cc_final: 0.8267 (p0) REVERT: I 64 ARG cc_start: 0.7288 (ptm-80) cc_final: 0.6679 (ttt180) REVERT: I 120 VAL cc_start: 0.9297 (t) cc_final: 0.8948 (m) REVERT: I 167 MET cc_start: 0.7827 (pmm) cc_final: 0.7329 (ptp) REVERT: I 293 ASP cc_start: 0.6390 (m-30) cc_final: 0.6179 (m-30) REVERT: K 149 ILE cc_start: 0.9150 (tp) cc_final: 0.8772 (tp) REVERT: K 356 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8477 (mt) REVERT: L 159 LEU cc_start: 0.7452 (pt) cc_final: 0.7227 (pp) REVERT: L 272 GLU cc_start: 0.7325 (pp20) cc_final: 0.6826 (pp20) REVERT: L 277 ILE cc_start: 0.9223 (mt) cc_final: 0.8858 (tt) REVERT: L 279 PHE cc_start: 0.8512 (t80) cc_final: 0.8227 (t80) REVERT: L 306 MET cc_start: 0.7019 (tmm) cc_final: 0.6230 (tmm) REVERT: M 187 ASP cc_start: 0.7623 (p0) cc_final: 0.7386 (p0) REVERT: M 401 ILE cc_start: 0.9110 (tt) cc_final: 0.8826 (tp) REVERT: r 50 MET cc_start: 0.8422 (ttm) cc_final: 0.8217 (ttm) REVERT: r 126 GLN cc_start: 0.8801 (tp40) cc_final: 0.8524 (tp40) outliers start: 5 outliers final: 1 residues processed: 952 average time/residue: 0.5458 time to fit residues: 848.5290 Evaluate side-chains 685 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 683 time to evaluate : 5.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 289 optimal weight: 4.9990 chunk 161 optimal weight: 2.9990 chunk 433 optimal weight: 8.9990 chunk 354 optimal weight: 4.9990 chunk 143 optimal weight: 20.0000 chunk 522 optimal weight: 8.9990 chunk 564 optimal weight: 20.0000 chunk 465 optimal weight: 2.9990 chunk 517 optimal weight: 4.9990 chunk 178 optimal weight: 0.4980 chunk 418 optimal weight: 5.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 65 GLN 4 78 GLN 4 146 HIS 6 159 GLN 7 74 ASN A 37 GLN ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 GLN E 108 ASN F 166 GLN G 207 ASN H 281 GLN H 356 ASN I 102 ASN ** I 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 ASN J 204 HIS ** J 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 238 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 45011 Z= 0.355 Angle : 0.707 9.819 60998 Z= 0.364 Chirality : 0.049 0.237 7049 Planarity : 0.005 0.059 7868 Dihedral : 8.493 120.018 6446 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 0.02 % Allowed : 4.87 % Favored : 95.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -3.98 (0.10), residues: 5766 helix: -2.40 (0.10), residues: 2049 sheet: -2.70 (0.14), residues: 1012 loop : -2.74 (0.11), residues: 2705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP G 218 HIS 0.012 0.001 HIS G 204 PHE 0.022 0.002 PHE M 432 TYR 0.031 0.002 TYR A 133 ARG 0.006 0.001 ARG 7 35 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11532 Ramachandran restraints generated. 5766 Oldfield, 0 Emsley, 5766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11532 Ramachandran restraints generated. 5766 Oldfield, 0 Emsley, 5766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 826 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 825 time to evaluate : 5.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 39 ASP cc_start: 0.8337 (p0) cc_final: 0.7663 (m-30) REVERT: 1 97 ILE cc_start: 0.9193 (pt) cc_final: 0.8843 (mt) REVERT: 1 145 ASN cc_start: 0.8502 (m-40) cc_final: 0.8298 (m-40) REVERT: 1 160 SER cc_start: 0.8220 (m) cc_final: 0.7928 (p) REVERT: 2 30 ASN cc_start: 0.8070 (t0) cc_final: 0.7746 (t0) REVERT: 2 69 TYR cc_start: 0.9144 (t80) cc_final: 0.8651 (t80) REVERT: 2 71 SER cc_start: 0.8530 (m) cc_final: 0.8295 (p) REVERT: 2 112 SER cc_start: 0.8281 (t) cc_final: 0.7793 (p) REVERT: 2 120 ASP cc_start: 0.7435 (p0) cc_final: 0.6857 (p0) REVERT: 2 200 GLN cc_start: 0.7013 (mt0) cc_final: 0.6195 (pt0) REVERT: 2 214 LYS cc_start: 0.8095 (ptmt) cc_final: 0.7757 (mttp) REVERT: 3 125 ASP cc_start: 0.7833 (p0) cc_final: 0.7578 (p0) REVERT: 4 30 ASP cc_start: 0.8425 (p0) cc_final: 0.8123 (p0) REVERT: 4 60 ILE cc_start: 0.9182 (pt) cc_final: 0.8707 (mt) REVERT: 4 99 GLN cc_start: 0.7445 (tm-30) cc_final: 0.7006 (tm-30) REVERT: 4 103 LEU cc_start: 0.9213 (mm) cc_final: 0.8948 (mp) REVERT: 4 120 ASP cc_start: 0.7696 (p0) cc_final: 0.7476 (p0) REVERT: 5 24 ASN cc_start: 0.8809 (t0) cc_final: 0.8368 (t0) REVERT: 6 81 ASP cc_start: 0.7225 (t0) cc_final: 0.6810 (t70) REVERT: 7 107 MET cc_start: 0.8552 (mmm) cc_final: 0.8186 (tpp) REVERT: 7 136 THR cc_start: 0.8956 (p) cc_final: 0.8666 (t) REVERT: A 39 ASN cc_start: 0.8304 (m-40) cc_final: 0.7661 (t0) REVERT: A 49 ASP cc_start: 0.7399 (p0) cc_final: 0.7043 (p0) REVERT: A 50 CYS cc_start: 0.7177 (m) cc_final: 0.6970 (m) REVERT: A 183 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7673 (tm-30) REVERT: A 224 GLU cc_start: 0.8244 (pt0) cc_final: 0.8030 (pt0) REVERT: A 244 ARG cc_start: 0.6610 (tpm170) cc_final: 0.6345 (tpm170) REVERT: B 60 THR cc_start: 0.9202 (p) cc_final: 0.8796 (t) REVERT: B 75 TYR cc_start: 0.8848 (p90) cc_final: 0.8492 (p90) REVERT: B 178 ARG cc_start: 0.8192 (mmm-85) cc_final: 0.7580 (mmp-170) REVERT: C 195 LYS cc_start: 0.8508 (mmmt) cc_final: 0.8307 (mmmt) REVERT: C 206 LEU cc_start: 0.8899 (pt) cc_final: 0.8588 (tp) REVERT: C 212 GLU cc_start: 0.7904 (pm20) cc_final: 0.7324 (pm20) REVERT: D 47 GLU cc_start: 0.8423 (pp20) cc_final: 0.7821 (pp20) REVERT: D 86 ILE cc_start: 0.8328 (pt) cc_final: 0.8087 (mt) REVERT: D 148 TYR cc_start: 0.9196 (m-80) cc_final: 0.8971 (m-10) REVERT: E 53 ARG cc_start: 0.7281 (ttm-80) cc_final: 0.5918 (ttt-90) REVERT: E 216 ASN cc_start: 0.8845 (p0) cc_final: 0.8428 (p0) REVERT: F 60 GLN cc_start: 0.8370 (pt0) cc_final: 0.8092 (pt0) REVERT: F 122 SER cc_start: 0.9076 (m) cc_final: 0.8621 (p) REVERT: G 26 TYR cc_start: 0.8326 (m-80) cc_final: 0.7996 (m-80) REVERT: H 51 GLN cc_start: 0.8132 (pp30) cc_final: 0.7877 (pp30) REVERT: H 98 GLN cc_start: 0.8323 (tt0) cc_final: 0.8080 (tt0) REVERT: H 105 ILE cc_start: 0.9144 (mt) cc_final: 0.8814 (tt) REVERT: H 166 THR cc_start: 0.6693 (p) cc_final: 0.6439 (t) REVERT: H 218 ILE cc_start: 0.8911 (pt) cc_final: 0.8477 (mt) REVERT: H 348 ASN cc_start: 0.7974 (t0) cc_final: 0.7667 (t0) REVERT: H 359 ASN cc_start: 0.9129 (m-40) cc_final: 0.8659 (m110) REVERT: I 64 ARG cc_start: 0.7337 (ptm-80) cc_final: 0.6804 (ttt180) REVERT: I 68 HIS cc_start: 0.7992 (m-70) cc_final: 0.7575 (m-70) REVERT: I 120 VAL cc_start: 0.9293 (t) cc_final: 0.9025 (m) REVERT: I 121 THR cc_start: 0.7859 (p) cc_final: 0.7571 (t) REVERT: I 167 MET cc_start: 0.8014 (pmm) cc_final: 0.7679 (ptp) REVERT: I 183 ASP cc_start: 0.8000 (m-30) cc_final: 0.7578 (t0) REVERT: I 208 TYR cc_start: 0.8715 (m-80) cc_final: 0.8308 (m-80) REVERT: I 312 GLN cc_start: 0.8257 (mm-40) cc_final: 0.8047 (mm-40) REVERT: J 86 VAL cc_start: 0.8812 (t) cc_final: 0.8535 (m) REVERT: J 94 TYR cc_start: 0.9118 (m-80) cc_final: 0.8867 (m-10) REVERT: J 247 MET cc_start: 0.8440 (mtp) cc_final: 0.8239 (mtp) REVERT: J 256 THR cc_start: 0.6278 (m) cc_final: 0.5890 (p) REVERT: J 270 ARG cc_start: 0.6427 (mmt90) cc_final: 0.5767 (mtt180) REVERT: J 345 LYS cc_start: 0.8263 (mttt) cc_final: 0.7842 (tppt) REVERT: K 149 ILE cc_start: 0.9175 (tp) cc_final: 0.8694 (tt) REVERT: L 82 ARG cc_start: 0.7905 (ptt180) cc_final: 0.7584 (mtm180) REVERT: L 159 LEU cc_start: 0.7608 (pt) cc_final: 0.7343 (pp) REVERT: L 195 GLU cc_start: 0.7768 (tm-30) cc_final: 0.7334 (tm-30) REVERT: L 272 GLU cc_start: 0.7490 (pp20) cc_final: 0.7211 (pp20) REVERT: L 306 MET cc_start: 0.7591 (tmm) cc_final: 0.6997 (tmm) REVERT: L 307 GLU cc_start: 0.7358 (mm-30) cc_final: 0.6729 (tp30) REVERT: M 265 ASP cc_start: 0.8055 (m-30) cc_final: 0.7614 (m-30) REVERT: M 292 ASP cc_start: 0.7754 (p0) cc_final: 0.7332 (p0) REVERT: M 397 GLU cc_start: 0.7611 (mm-30) cc_final: 0.7287 (tp30) REVERT: r 50 MET cc_start: 0.8575 (ttm) cc_final: 0.8246 (ttm) REVERT: r 130 GLU cc_start: 0.8358 (tp30) cc_final: 0.8093 (tp30) outliers start: 1 outliers final: 0 residues processed: 826 average time/residue: 0.5524 time to fit residues: 755.7808 Evaluate side-chains 648 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 648 time to evaluate : 5.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 515 optimal weight: 9.9990 chunk 392 optimal weight: 7.9990 chunk 271 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 249 optimal weight: 0.8980 chunk 350 optimal weight: 0.9980 chunk 524 optimal weight: 0.9980 chunk 554 optimal weight: 0.8980 chunk 273 optimal weight: 6.9990 chunk 496 optimal weight: 8.9990 chunk 149 optimal weight: 7.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 41 HIS 4 78 GLN 7 61 GLN 7 74 ASN ** 7 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 241 GLN C 21 GLN C 103 ASN G 207 ASN H 281 GLN I 102 ASN I 192 GLN ** I 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 ASN J 204 HIS J 240 HIS ** J 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 142 HIS M 72 ASN r 237 ASN r 291 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 45011 Z= 0.192 Angle : 0.613 10.625 60998 Z= 0.311 Chirality : 0.046 0.194 7049 Planarity : 0.004 0.051 7868 Dihedral : 7.796 114.153 6446 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 0.04 % Allowed : 3.58 % Favored : 96.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -3.40 (0.10), residues: 5766 helix: -1.91 (0.10), residues: 2054 sheet: -2.26 (0.14), residues: 1033 loop : -2.46 (0.11), residues: 2679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP G 218 HIS 0.012 0.001 HIS G 204 PHE 0.024 0.001 PHE E 138 TYR 0.031 0.001 TYR M 180 ARG 0.009 0.000 ARG A 77 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11532 Ramachandran restraints generated. 5766 Oldfield, 0 Emsley, 5766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11532 Ramachandran restraints generated. 5766 Oldfield, 0 Emsley, 5766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 848 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 846 time to evaluate : 5.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 69 TYR cc_start: 0.9108 (t80) cc_final: 0.8705 (t80) REVERT: 2 71 SER cc_start: 0.8548 (m) cc_final: 0.8332 (p) REVERT: 2 112 SER cc_start: 0.8246 (t) cc_final: 0.7838 (p) REVERT: 2 120 ASP cc_start: 0.7390 (p0) cc_final: 0.6687 (p0) REVERT: 2 200 GLN cc_start: 0.6997 (mt0) cc_final: 0.6139 (pt0) REVERT: 2 214 LYS cc_start: 0.8079 (ptmt) cc_final: 0.7784 (mttt) REVERT: 3 72 ASN cc_start: 0.8575 (m-40) cc_final: 0.7845 (t0) REVERT: 4 30 ASP cc_start: 0.8279 (p0) cc_final: 0.8033 (p0) REVERT: 4 52 ASP cc_start: 0.7593 (m-30) cc_final: 0.7115 (t0) REVERT: 4 60 ILE cc_start: 0.9186 (pt) cc_final: 0.8515 (mm) REVERT: 4 99 GLN cc_start: 0.7326 (tm-30) cc_final: 0.6841 (tm-30) REVERT: 4 103 LEU cc_start: 0.9167 (mm) cc_final: 0.8958 (mp) REVERT: 4 120 ASP cc_start: 0.7783 (p0) cc_final: 0.7543 (p0) REVERT: 4 124 THR cc_start: 0.8676 (p) cc_final: 0.8076 (p) REVERT: 5 24 ASN cc_start: 0.8971 (t0) cc_final: 0.8563 (t0) REVERT: 5 25 TRP cc_start: 0.8758 (t60) cc_final: 0.8483 (t60) REVERT: 5 36 GLU cc_start: 0.6827 (pm20) cc_final: 0.6286 (pp20) REVERT: 7 107 MET cc_start: 0.8567 (mmm) cc_final: 0.8228 (tpp) REVERT: 7 136 THR cc_start: 0.8872 (p) cc_final: 0.8585 (t) REVERT: A 39 ASN cc_start: 0.8282 (m-40) cc_final: 0.7672 (t0) REVERT: A 183 GLU cc_start: 0.7864 (tm-30) cc_final: 0.7553 (tm-30) REVERT: A 195 ASN cc_start: 0.8187 (m-40) cc_final: 0.7976 (m110) REVERT: A 224 GLU cc_start: 0.8293 (pt0) cc_final: 0.8053 (pt0) REVERT: B 60 THR cc_start: 0.9174 (p) cc_final: 0.8763 (t) REVERT: B 75 TYR cc_start: 0.8896 (p90) cc_final: 0.8452 (p90) REVERT: B 178 ARG cc_start: 0.8098 (mmm-85) cc_final: 0.7499 (mmp-170) REVERT: C 7 ASP cc_start: 0.7873 (t70) cc_final: 0.7559 (t0) REVERT: C 208 TYR cc_start: 0.8175 (p90) cc_final: 0.7851 (p90) REVERT: C 234 GLU cc_start: 0.7634 (pt0) cc_final: 0.7306 (pt0) REVERT: D 47 GLU cc_start: 0.8466 (pp20) cc_final: 0.7821 (pp20) REVERT: D 86 ILE cc_start: 0.8269 (pt) cc_final: 0.8036 (pt) REVERT: D 148 TYR cc_start: 0.9174 (m-80) cc_final: 0.8920 (m-10) REVERT: E 138 PHE cc_start: 0.7338 (p90) cc_final: 0.6872 (p90) REVERT: E 216 ASN cc_start: 0.8909 (p0) cc_final: 0.8439 (p0) REVERT: E 238 GLU cc_start: 0.7516 (pp20) cc_final: 0.7019 (pp20) REVERT: F 122 SER cc_start: 0.8989 (m) cc_final: 0.8689 (t) REVERT: G 26 TYR cc_start: 0.8318 (m-80) cc_final: 0.8043 (m-80) REVERT: G 60 VAL cc_start: 0.8691 (t) cc_final: 0.8423 (p) REVERT: G 190 ARG cc_start: 0.8559 (mmt180) cc_final: 0.8346 (mmt180) REVERT: H 51 GLN cc_start: 0.8098 (pp30) cc_final: 0.7836 (pp30) REVERT: H 98 GLN cc_start: 0.8202 (tt0) cc_final: 0.7961 (tt0) REVERT: H 105 ILE cc_start: 0.9145 (mt) cc_final: 0.8783 (tt) REVERT: H 166 THR cc_start: 0.6924 (p) cc_final: 0.6607 (t) REVERT: H 218 ILE cc_start: 0.8857 (pt) cc_final: 0.8464 (mt) REVERT: H 348 ASN cc_start: 0.8111 (t0) cc_final: 0.7775 (t0) REVERT: H 359 ASN cc_start: 0.8969 (m-40) cc_final: 0.8524 (m110) REVERT: H 442 ASP cc_start: 0.8737 (p0) cc_final: 0.8521 (p0) REVERT: I 64 ARG cc_start: 0.7239 (ptm-80) cc_final: 0.6718 (ttt180) REVERT: I 68 HIS cc_start: 0.7892 (m-70) cc_final: 0.7465 (m-70) REVERT: I 120 VAL cc_start: 0.9292 (t) cc_final: 0.8978 (m) REVERT: I 121 THR cc_start: 0.7884 (p) cc_final: 0.7672 (t) REVERT: I 167 MET cc_start: 0.7969 (pmm) cc_final: 0.7392 (ptp) REVERT: I 183 ASP cc_start: 0.7851 (m-30) cc_final: 0.7418 (t0) REVERT: I 312 GLN cc_start: 0.8394 (mm-40) cc_final: 0.8035 (mm-40) REVERT: J 32 LEU cc_start: 0.9091 (tp) cc_final: 0.8888 (pp) REVERT: J 58 ILE cc_start: 0.8803 (pt) cc_final: 0.8568 (mt) REVERT: J 86 VAL cc_start: 0.8706 (t) cc_final: 0.8475 (m) REVERT: J 239 GLU cc_start: 0.7424 (pt0) cc_final: 0.7144 (tt0) REVERT: J 247 MET cc_start: 0.8467 (mtp) cc_final: 0.8251 (mtp) REVERT: J 256 THR cc_start: 0.6412 (m) cc_final: 0.5840 (p) REVERT: J 270 ARG cc_start: 0.6407 (mmt90) cc_final: 0.5691 (mtt180) REVERT: K 149 ILE cc_start: 0.9144 (tp) cc_final: 0.8721 (tt) REVERT: L 82 ARG cc_start: 0.7868 (ptt180) cc_final: 0.7568 (mtm180) REVERT: L 122 SER cc_start: 0.7847 (m) cc_final: 0.7617 (p) REVERT: L 159 LEU cc_start: 0.7623 (pt) cc_final: 0.7358 (pp) REVERT: L 306 MET cc_start: 0.7475 (tmm) cc_final: 0.6792 (tmm) REVERT: L 307 GLU cc_start: 0.7335 (mm-30) cc_final: 0.6741 (tp30) REVERT: M 265 ASP cc_start: 0.8033 (m-30) cc_final: 0.7496 (m-30) REVERT: M 292 ASP cc_start: 0.7669 (p0) cc_final: 0.7161 (p0) REVERT: n 221 PHE cc_start: 0.8784 (p90) cc_final: 0.8580 (p90) REVERT: r 130 GLU cc_start: 0.8310 (tp30) cc_final: 0.8007 (tp30) REVERT: r 251 TYR cc_start: 0.8873 (t80) cc_final: 0.8657 (t80) REVERT: u 14 THR cc_start: 0.7953 (m) cc_final: 0.7643 (p) outliers start: 2 outliers final: 1 residues processed: 848 average time/residue: 0.5421 time to fit residues: 760.4101 Evaluate side-chains 651 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 650 time to evaluate : 4.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 462 optimal weight: 6.9990 chunk 314 optimal weight: 0.3980 chunk 8 optimal weight: 4.9990 chunk 413 optimal weight: 6.9990 chunk 228 optimal weight: 0.8980 chunk 473 optimal weight: 0.5980 chunk 383 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 283 optimal weight: 8.9990 chunk 498 optimal weight: 2.9990 chunk 140 optimal weight: 6.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 160 GLN 3 8 ASN 4 41 HIS 4 78 GLN ** 6 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 36 ASN 7 74 ASN ** 7 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 GLN D 117 GLN D 178 ASN F 60 GLN G 207 ASN H 54 ASN H 356 ASN I 102 ASN ** I 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 ASN J 204 HIS J 277 ASN ** K 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 142 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 45011 Z= 0.226 Angle : 0.611 9.158 60998 Z= 0.311 Chirality : 0.046 0.181 7049 Planarity : 0.004 0.049 7868 Dihedral : 7.586 109.395 6446 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 0.02 % Allowed : 2.76 % Favored : 97.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -3.02 (0.10), residues: 5766 helix: -1.58 (0.11), residues: 2048 sheet: -1.98 (0.15), residues: 1059 loop : -2.29 (0.12), residues: 2659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP G 218 HIS 0.008 0.001 HIS G 204 PHE 0.027 0.002 PHE 3 50 TYR 0.030 0.001 TYR M 180 ARG 0.007 0.000 ARG D 127 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11532 Ramachandran restraints generated. 5766 Oldfield, 0 Emsley, 5766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11532 Ramachandran restraints generated. 5766 Oldfield, 0 Emsley, 5766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 828 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 827 time to evaluate : 5.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 146 MET cc_start: 0.8387 (ptt) cc_final: 0.8176 (ptp) REVERT: 1 150 GLU cc_start: 0.7575 (pm20) cc_final: 0.7288 (pm20) REVERT: 2 3 ILE cc_start: 0.8578 (pt) cc_final: 0.8308 (mt) REVERT: 2 69 TYR cc_start: 0.9086 (t80) cc_final: 0.8703 (t80) REVERT: 2 71 SER cc_start: 0.8611 (m) cc_final: 0.8391 (p) REVERT: 2 112 SER cc_start: 0.8293 (t) cc_final: 0.7866 (p) REVERT: 2 200 GLN cc_start: 0.6976 (mt0) cc_final: 0.6139 (pt0) REVERT: 2 214 LYS cc_start: 0.8103 (ptmt) cc_final: 0.7786 (mttt) REVERT: 3 72 ASN cc_start: 0.8688 (m-40) cc_final: 0.8040 (t0) REVERT: 4 3 ILE cc_start: 0.9204 (pt) cc_final: 0.8718 (mp) REVERT: 4 52 ASP cc_start: 0.7536 (m-30) cc_final: 0.7094 (t0) REVERT: 4 60 ILE cc_start: 0.9204 (pt) cc_final: 0.8767 (mt) REVERT: 4 92 ILE cc_start: 0.8217 (tp) cc_final: 0.7990 (tp) REVERT: 4 99 GLN cc_start: 0.7291 (tm-30) cc_final: 0.6804 (tm-30) REVERT: 4 120 ASP cc_start: 0.7781 (p0) cc_final: 0.7519 (p0) REVERT: 5 24 ASN cc_start: 0.9043 (t0) cc_final: 0.8685 (t0) REVERT: 5 25 TRP cc_start: 0.8766 (t60) cc_final: 0.8504 (t60) REVERT: 5 36 GLU cc_start: 0.7117 (pm20) cc_final: 0.6347 (pp20) REVERT: 5 197 PHE cc_start: 0.8042 (t80) cc_final: 0.7694 (t80) REVERT: 6 81 ASP cc_start: 0.7272 (t0) cc_final: 0.6947 (t70) REVERT: 7 107 MET cc_start: 0.8587 (mmm) cc_final: 0.8106 (tpp) REVERT: 7 136 THR cc_start: 0.8903 (p) cc_final: 0.8585 (t) REVERT: A 39 ASN cc_start: 0.8283 (m-40) cc_final: 0.7975 (t0) REVERT: A 49 ASP cc_start: 0.7313 (p0) cc_final: 0.6761 (p0) REVERT: A 50 CYS cc_start: 0.7123 (m) cc_final: 0.6659 (m) REVERT: A 183 GLU cc_start: 0.7948 (tm-30) cc_final: 0.7525 (tm-30) REVERT: A 187 LYS cc_start: 0.8572 (ptpt) cc_final: 0.8295 (ptmt) REVERT: A 224 GLU cc_start: 0.8330 (pt0) cc_final: 0.8044 (pt0) REVERT: A 244 ARG cc_start: 0.6851 (tpp-160) cc_final: 0.6073 (tpm170) REVERT: B 60 THR cc_start: 0.9149 (p) cc_final: 0.8757 (t) REVERT: B 65 SER cc_start: 0.8458 (p) cc_final: 0.8238 (p) REVERT: B 75 TYR cc_start: 0.8823 (p90) cc_final: 0.8351 (p90) REVERT: B 178 ARG cc_start: 0.8188 (mmm-85) cc_final: 0.7582 (mmp-170) REVERT: B 224 TYR cc_start: 0.8378 (p90) cc_final: 0.8066 (p90) REVERT: C 7 ASP cc_start: 0.7930 (t70) cc_final: 0.7492 (t0) REVERT: C 234 GLU cc_start: 0.7674 (pt0) cc_final: 0.7393 (pt0) REVERT: D 47 GLU cc_start: 0.8411 (pp20) cc_final: 0.8111 (pp20) REVERT: D 86 ILE cc_start: 0.8334 (pt) cc_final: 0.8069 (mt) REVERT: D 148 TYR cc_start: 0.9182 (m-80) cc_final: 0.8915 (m-10) REVERT: E 140 VAL cc_start: 0.8257 (t) cc_final: 0.8052 (t) REVERT: E 238 GLU cc_start: 0.7564 (pp20) cc_final: 0.7053 (pp20) REVERT: F 122 SER cc_start: 0.8987 (m) cc_final: 0.8733 (t) REVERT: G 60 VAL cc_start: 0.8689 (t) cc_final: 0.8441 (p) REVERT: H 51 GLN cc_start: 0.8195 (pp30) cc_final: 0.7954 (pp30) REVERT: H 98 GLN cc_start: 0.8230 (tt0) cc_final: 0.7994 (tt0) REVERT: H 105 ILE cc_start: 0.9237 (mt) cc_final: 0.8849 (tt) REVERT: H 166 THR cc_start: 0.7012 (p) cc_final: 0.6702 (t) REVERT: H 178 ARG cc_start: 0.8933 (mtm110) cc_final: 0.8522 (ttp-110) REVERT: H 218 ILE cc_start: 0.8882 (pt) cc_final: 0.8506 (mt) REVERT: H 330 GLN cc_start: 0.8880 (mp10) cc_final: 0.8609 (mp10) REVERT: H 348 ASN cc_start: 0.8151 (t0) cc_final: 0.7831 (t0) REVERT: H 359 ASN cc_start: 0.8921 (m-40) cc_final: 0.8531 (m110) REVERT: I 64 ARG cc_start: 0.7279 (ptm-80) cc_final: 0.6879 (ttt180) REVERT: I 68 HIS cc_start: 0.7919 (m-70) cc_final: 0.7583 (m-70) REVERT: I 120 VAL cc_start: 0.9262 (t) cc_final: 0.8939 (m) REVERT: I 167 MET cc_start: 0.7881 (pmm) cc_final: 0.7520 (ptp) REVERT: I 303 GLN cc_start: 0.7872 (mt0) cc_final: 0.7582 (mt0) REVERT: J 58 ILE cc_start: 0.8838 (pt) cc_final: 0.8624 (mt) REVERT: J 94 TYR cc_start: 0.9073 (m-10) cc_final: 0.8867 (m-10) REVERT: J 239 GLU cc_start: 0.7523 (pt0) cc_final: 0.7254 (tt0) REVERT: J 247 MET cc_start: 0.8548 (mtp) cc_final: 0.8341 (mtp) REVERT: J 270 ARG cc_start: 0.6437 (mmt90) cc_final: 0.5836 (mtt180) REVERT: K 149 ILE cc_start: 0.9159 (tp) cc_final: 0.8766 (tt) REVERT: L 82 ARG cc_start: 0.7944 (ptt180) cc_final: 0.7607 (mtm180) REVERT: L 122 SER cc_start: 0.7914 (m) cc_final: 0.7659 (p) REVERT: L 156 MET cc_start: 0.7823 (mtp) cc_final: 0.7517 (mtp) REVERT: L 306 MET cc_start: 0.7565 (tmm) cc_final: 0.6919 (tmm) REVERT: L 346 LYS cc_start: 0.7496 (mtmm) cc_final: 0.6949 (mtmt) REVERT: M 265 ASP cc_start: 0.8087 (m-30) cc_final: 0.7639 (m-30) REVERT: M 292 ASP cc_start: 0.7688 (p0) cc_final: 0.7231 (p0) REVERT: n 221 PHE cc_start: 0.8861 (p90) cc_final: 0.8606 (p90) REVERT: r 50 MET cc_start: 0.8729 (ttm) cc_final: 0.8477 (ttm) outliers start: 1 outliers final: 0 residues processed: 828 average time/residue: 0.5469 time to fit residues: 756.5991 Evaluate side-chains 650 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 650 time to evaluate : 5.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 186 optimal weight: 0.9990 chunk 499 optimal weight: 4.9990 chunk 109 optimal weight: 0.0670 chunk 325 optimal weight: 3.9990 chunk 136 optimal weight: 0.9980 chunk 555 optimal weight: 7.9990 chunk 461 optimal weight: 6.9990 chunk 257 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 chunk 183 optimal weight: 9.9990 chunk 291 optimal weight: 10.0000 overall best weight: 2.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 8 ASN 4 41 HIS 6 36 ASN 7 61 GLN 7 74 ASN ** 7 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 GLN C 103 ASN C 156 ASN E 91 HIS I 102 ASN I 192 GLN ** I 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 ASN J 277 ASN ** K 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 142 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.4353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 45011 Z= 0.257 Angle : 0.626 10.673 60998 Z= 0.319 Chirality : 0.046 0.315 7049 Planarity : 0.004 0.064 7868 Dihedral : 7.545 106.080 6446 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 0.07 % Allowed : 2.48 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -2.83 (0.11), residues: 5766 helix: -1.38 (0.11), residues: 2051 sheet: -1.85 (0.15), residues: 1088 loop : -2.21 (0.12), residues: 2627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP G 218 HIS 0.008 0.001 HIS G 204 PHE 0.025 0.002 PHE M 432 TYR 0.025 0.001 TYR A 133 ARG 0.007 0.000 ARG 1 29 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11532 Ramachandran restraints generated. 5766 Oldfield, 0 Emsley, 5766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11532 Ramachandran restraints generated. 5766 Oldfield, 0 Emsley, 5766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 816 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 813 time to evaluate : 5.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 3 ILE cc_start: 0.8583 (pt) cc_final: 0.8320 (mt) REVERT: 2 69 TYR cc_start: 0.9077 (t80) cc_final: 0.8728 (t80) REVERT: 2 112 SER cc_start: 0.8395 (t) cc_final: 0.8046 (p) REVERT: 2 120 ASP cc_start: 0.7571 (p0) cc_final: 0.6900 (p0) REVERT: 2 200 GLN cc_start: 0.6971 (mt0) cc_final: 0.6109 (pt0) REVERT: 2 214 LYS cc_start: 0.8118 (ptmt) cc_final: 0.7755 (mttt) REVERT: 3 72 ASN cc_start: 0.8728 (m-40) cc_final: 0.8166 (t0) REVERT: 4 3 ILE cc_start: 0.9217 (pt) cc_final: 0.8706 (mp) REVERT: 4 52 ASP cc_start: 0.7547 (m-30) cc_final: 0.7061 (t0) REVERT: 4 60 ILE cc_start: 0.9268 (pt) cc_final: 0.8839 (mt) REVERT: 4 99 GLN cc_start: 0.7315 (tm-30) cc_final: 0.6795 (tm-30) REVERT: 4 120 ASP cc_start: 0.7838 (p0) cc_final: 0.7522 (p0) REVERT: 4 124 THR cc_start: 0.8638 (p) cc_final: 0.8021 (p) REVERT: 4 155 GLU cc_start: 0.8397 (pm20) cc_final: 0.7926 (pm20) REVERT: 5 19 ARG cc_start: 0.8710 (tpp-160) cc_final: 0.8259 (tpp-160) REVERT: 5 24 ASN cc_start: 0.9050 (t0) cc_final: 0.8702 (t0) REVERT: 5 25 TRP cc_start: 0.8777 (t60) cc_final: 0.8518 (t60) REVERT: 5 73 ARG cc_start: 0.7739 (ttp-170) cc_final: 0.7455 (ttp-170) REVERT: 5 197 PHE cc_start: 0.8035 (t80) cc_final: 0.7758 (t80) REVERT: 6 81 ASP cc_start: 0.7270 (t0) cc_final: 0.6944 (t70) REVERT: 6 214 LYS cc_start: 0.8001 (ptmm) cc_final: 0.7788 (ptmt) REVERT: 7 107 MET cc_start: 0.8677 (mmm) cc_final: 0.8251 (tpp) REVERT: 7 136 THR cc_start: 0.8930 (p) cc_final: 0.8606 (t) REVERT: A 39 ASN cc_start: 0.8270 (m-40) cc_final: 0.7923 (t0) REVERT: A 183 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7666 (tm-30) REVERT: A 224 GLU cc_start: 0.8313 (pt0) cc_final: 0.8047 (pt0) REVERT: A 242 GLU cc_start: 0.7204 (mp0) cc_final: 0.6840 (mp0) REVERT: B 60 THR cc_start: 0.9172 (p) cc_final: 0.8796 (t) REVERT: B 65 SER cc_start: 0.8505 (p) cc_final: 0.8279 (p) REVERT: B 75 TYR cc_start: 0.8840 (p90) cc_final: 0.8356 (p90) REVERT: B 210 GLU cc_start: 0.7792 (pt0) cc_final: 0.7535 (pt0) REVERT: C 7 ASP cc_start: 0.7980 (t70) cc_final: 0.7646 (t0) REVERT: C 39 MET cc_start: 0.8516 (ttt) cc_final: 0.8256 (ttt) REVERT: C 71 ASP cc_start: 0.7193 (t70) cc_final: 0.6875 (t70) REVERT: C 72 LYS cc_start: 0.8121 (mmtp) cc_final: 0.7702 (mmtp) REVERT: C 164 SER cc_start: 0.9192 (p) cc_final: 0.8702 (p) REVERT: C 212 GLU cc_start: 0.8256 (pt0) cc_final: 0.8056 (pt0) REVERT: C 225 VAL cc_start: 0.8849 (t) cc_final: 0.8529 (t) REVERT: D 47 GLU cc_start: 0.8430 (pp20) cc_final: 0.7999 (pp20) REVERT: D 148 TYR cc_start: 0.9191 (m-80) cc_final: 0.8915 (m-10) REVERT: F 122 SER cc_start: 0.8982 (m) cc_final: 0.8776 (t) REVERT: G 60 VAL cc_start: 0.8689 (t) cc_final: 0.8445 (p) REVERT: G 202 LEU cc_start: 0.8945 (mt) cc_final: 0.8665 (mt) REVERT: H 51 GLN cc_start: 0.8222 (pp30) cc_final: 0.7977 (pp30) REVERT: H 98 GLN cc_start: 0.8292 (tt0) cc_final: 0.8003 (tt0) REVERT: H 105 ILE cc_start: 0.9258 (mt) cc_final: 0.8836 (tt) REVERT: H 166 THR cc_start: 0.7192 (p) cc_final: 0.6861 (t) REVERT: H 178 ARG cc_start: 0.8966 (mtm110) cc_final: 0.8539 (ttp-110) REVERT: H 218 ILE cc_start: 0.8875 (pt) cc_final: 0.8532 (mt) REVERT: H 330 GLN cc_start: 0.8840 (mp10) cc_final: 0.8368 (mp10) REVERT: H 348 ASN cc_start: 0.8241 (t0) cc_final: 0.7861 (t0) REVERT: I 64 ARG cc_start: 0.7377 (ptm-80) cc_final: 0.7047 (ttt180) REVERT: I 68 HIS cc_start: 0.7924 (m-70) cc_final: 0.7624 (m-70) REVERT: I 120 VAL cc_start: 0.9290 (t) cc_final: 0.8936 (m) REVERT: I 208 TYR cc_start: 0.8426 (m-80) cc_final: 0.7699 (m-80) REVERT: I 303 GLN cc_start: 0.7937 (mt0) cc_final: 0.7671 (mt0) REVERT: J 58 ILE cc_start: 0.8859 (pt) cc_final: 0.8632 (mt) REVERT: J 270 ARG cc_start: 0.6580 (mmt90) cc_final: 0.6013 (mtt180) REVERT: K 149 ILE cc_start: 0.9153 (tp) cc_final: 0.8738 (tt) REVERT: K 221 MET cc_start: 0.8132 (ppp) cc_final: 0.7926 (ppp) REVERT: K 260 LEU cc_start: 0.9226 (pp) cc_final: 0.8724 (tt) REVERT: L 82 ARG cc_start: 0.7918 (ptt180) cc_final: 0.7655 (mtm180) REVERT: L 156 MET cc_start: 0.7926 (mtp) cc_final: 0.7623 (mtp) REVERT: L 251 ILE cc_start: 0.8251 (pt) cc_final: 0.7990 (mm) REVERT: L 306 MET cc_start: 0.7672 (tmm) cc_final: 0.7007 (tmm) REVERT: L 346 LYS cc_start: 0.7511 (mtmm) cc_final: 0.7031 (mtmt) REVERT: M 265 ASP cc_start: 0.8149 (m-30) cc_final: 0.7707 (m-30) REVERT: M 292 ASP cc_start: 0.7702 (p0) cc_final: 0.7038 (p0) REVERT: n 221 PHE cc_start: 0.8921 (p90) cc_final: 0.8611 (p90) REVERT: r 50 MET cc_start: 0.8849 (ttm) cc_final: 0.8587 (ttm) REVERT: r 282 GLU cc_start: 0.8031 (tp30) cc_final: 0.7749 (tp30) outliers start: 3 outliers final: 0 residues processed: 815 average time/residue: 0.5273 time to fit residues: 723.1368 Evaluate side-chains 645 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 645 time to evaluate : 5.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 535 optimal weight: 0.0270 chunk 62 optimal weight: 3.9990 chunk 316 optimal weight: 7.9990 chunk 405 optimal weight: 6.9990 chunk 314 optimal weight: 0.2980 chunk 467 optimal weight: 3.9990 chunk 310 optimal weight: 0.9990 chunk 553 optimal weight: 2.9990 chunk 346 optimal weight: 5.9990 chunk 337 optimal weight: 3.9990 chunk 255 optimal weight: 5.9990 overall best weight: 1.6644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 8 ASN 4 41 HIS ** 6 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 36 ASN ** 6 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 159 GLN 7 74 ASN ** 7 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 125 GLN ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 84 ASN ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 GLN C 103 ASN ** C 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 ASN H 356 ASN I 102 ASN ** I 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 ASN J 277 ASN ** K 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 142 HIS M 74 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.4560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 45011 Z= 0.210 Angle : 0.606 9.231 60998 Z= 0.307 Chirality : 0.045 0.187 7049 Planarity : 0.004 0.078 7868 Dihedral : 7.300 105.996 6446 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.07 % Allowed : 1.97 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -2.59 (0.11), residues: 5766 helix: -1.19 (0.11), residues: 2038 sheet: -1.63 (0.15), residues: 1082 loop : -2.11 (0.12), residues: 2646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP G 218 HIS 0.008 0.001 HIS G 204 PHE 0.027 0.002 PHE 7 36 TYR 0.025 0.001 TYR A 133 ARG 0.011 0.000 ARG 6 28 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11532 Ramachandran restraints generated. 5766 Oldfield, 0 Emsley, 5766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11532 Ramachandran restraints generated. 5766 Oldfield, 0 Emsley, 5766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 823 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 820 time to evaluate : 5.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 3 ILE cc_start: 0.8585 (pt) cc_final: 0.8364 (mt) REVERT: 2 30 ASN cc_start: 0.8207 (t0) cc_final: 0.7861 (t0) REVERT: 2 69 TYR cc_start: 0.9052 (t80) cc_final: 0.8764 (t80) REVERT: 2 112 SER cc_start: 0.8415 (t) cc_final: 0.7999 (p) REVERT: 2 120 ASP cc_start: 0.7603 (p0) cc_final: 0.6925 (p0) REVERT: 2 200 GLN cc_start: 0.7062 (mt0) cc_final: 0.6146 (pt0) REVERT: 2 214 LYS cc_start: 0.8133 (ptmt) cc_final: 0.7740 (mttt) REVERT: 3 59 ASP cc_start: 0.8865 (m-30) cc_final: 0.8662 (m-30) REVERT: 3 72 ASN cc_start: 0.8745 (m-40) cc_final: 0.8221 (t0) REVERT: 4 52 ASP cc_start: 0.7520 (m-30) cc_final: 0.7050 (t0) REVERT: 4 60 ILE cc_start: 0.9275 (pt) cc_final: 0.8822 (mt) REVERT: 4 99 GLN cc_start: 0.7280 (tm-30) cc_final: 0.6837 (tm-30) REVERT: 4 120 ASP cc_start: 0.7799 (p0) cc_final: 0.7398 (p0) REVERT: 4 124 THR cc_start: 0.8544 (p) cc_final: 0.7959 (p) REVERT: 4 155 GLU cc_start: 0.8350 (pm20) cc_final: 0.8007 (pm20) REVERT: 5 24 ASN cc_start: 0.9063 (t0) cc_final: 0.8762 (t0) REVERT: 5 36 GLU cc_start: 0.6796 (pm20) cc_final: 0.6086 (pp20) REVERT: 5 73 ARG cc_start: 0.7794 (ttp-170) cc_final: 0.7494 (ttp-170) REVERT: 5 197 PHE cc_start: 0.8016 (t80) cc_final: 0.7804 (t80) REVERT: 6 35 ILE cc_start: 0.8996 (mm) cc_final: 0.8762 (mm) REVERT: 6 81 ASP cc_start: 0.7320 (t0) cc_final: 0.6992 (t0) REVERT: 6 159 GLN cc_start: 0.6560 (pt0) cc_final: 0.5870 (tp40) REVERT: 6 179 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7410 (mm-30) REVERT: 6 185 ARG cc_start: 0.8076 (ptm-80) cc_final: 0.7741 (ptm-80) REVERT: 6 214 LYS cc_start: 0.8061 (ptmm) cc_final: 0.7751 (ptmt) REVERT: 7 107 MET cc_start: 0.8683 (mmm) cc_final: 0.8273 (tpp) REVERT: 7 136 THR cc_start: 0.8914 (p) cc_final: 0.8632 (t) REVERT: 7 175 GLU cc_start: 0.7155 (mm-30) cc_final: 0.6932 (mm-30) REVERT: A 39 ASN cc_start: 0.8257 (m-40) cc_final: 0.7934 (t0) REVERT: A 187 LYS cc_start: 0.8586 (ptpt) cc_final: 0.8378 (ptmt) REVERT: A 224 GLU cc_start: 0.8309 (pt0) cc_final: 0.8076 (pt0) REVERT: A 242 GLU cc_start: 0.7207 (mp0) cc_final: 0.6830 (mp0) REVERT: A 244 ARG cc_start: 0.6861 (tpp-160) cc_final: 0.6632 (tpp-160) REVERT: B 30 GLN cc_start: 0.8371 (mp10) cc_final: 0.8143 (mp10) REVERT: B 60 THR cc_start: 0.9254 (p) cc_final: 0.8839 (t) REVERT: B 75 TYR cc_start: 0.8837 (p90) cc_final: 0.8371 (p90) REVERT: B 224 TYR cc_start: 0.8332 (p90) cc_final: 0.8100 (p90) REVERT: C 7 ASP cc_start: 0.8078 (t70) cc_final: 0.7688 (t0) REVERT: C 39 MET cc_start: 0.8581 (ttt) cc_final: 0.8334 (ttt) REVERT: C 71 ASP cc_start: 0.7120 (t70) cc_final: 0.6852 (t70) REVERT: D 27 VAL cc_start: 0.8918 (t) cc_final: 0.8637 (p) REVERT: D 47 GLU cc_start: 0.8456 (pp20) cc_final: 0.7989 (pp20) REVERT: D 148 TYR cc_start: 0.9187 (m-80) cc_final: 0.8906 (m-10) REVERT: G 60 VAL cc_start: 0.8680 (t) cc_final: 0.8442 (p) REVERT: G 95 GLU cc_start: 0.7280 (pm20) cc_final: 0.7014 (pm20) REVERT: G 202 LEU cc_start: 0.8881 (mt) cc_final: 0.8664 (mt) REVERT: H 51 GLN cc_start: 0.8206 (pp30) cc_final: 0.7959 (pp30) REVERT: H 98 GLN cc_start: 0.8136 (tt0) cc_final: 0.7931 (tt0) REVERT: H 105 ILE cc_start: 0.9283 (mt) cc_final: 0.8831 (tt) REVERT: H 166 THR cc_start: 0.7149 (p) cc_final: 0.6804 (t) REVERT: H 178 ARG cc_start: 0.9019 (mtm110) cc_final: 0.8430 (ttp-110) REVERT: H 218 ILE cc_start: 0.8852 (pt) cc_final: 0.8552 (mt) REVERT: H 297 MET cc_start: 0.9054 (ptm) cc_final: 0.8832 (tmm) REVERT: H 348 ASN cc_start: 0.8298 (t0) cc_final: 0.7835 (t0) REVERT: I 64 ARG cc_start: 0.7365 (ptm-80) cc_final: 0.7048 (ttt180) REVERT: I 68 HIS cc_start: 0.7951 (m-70) cc_final: 0.7644 (m-70) REVERT: I 120 VAL cc_start: 0.9305 (t) cc_final: 0.8918 (m) REVERT: I 208 TYR cc_start: 0.8441 (m-80) cc_final: 0.7763 (m-80) REVERT: I 285 ASP cc_start: 0.7618 (p0) cc_final: 0.7320 (p0) REVERT: J 247 MET cc_start: 0.8372 (mtp) cc_final: 0.8013 (mtp) REVERT: J 270 ARG cc_start: 0.6538 (mmt90) cc_final: 0.6014 (mmt180) REVERT: J 362 CYS cc_start: 0.8840 (m) cc_final: 0.8187 (t) REVERT: K 149 ILE cc_start: 0.9146 (tp) cc_final: 0.8734 (tt) REVERT: K 260 LEU cc_start: 0.9207 (pp) cc_final: 0.8754 (tt) REVERT: K 300 LEU cc_start: 0.8792 (tp) cc_final: 0.8591 (tp) REVERT: L 82 ARG cc_start: 0.7923 (ptt180) cc_final: 0.7671 (mtm180) REVERT: L 156 MET cc_start: 0.7885 (mtp) cc_final: 0.7607 (mtp) REVERT: L 251 ILE cc_start: 0.8364 (pt) cc_final: 0.8060 (mm) REVERT: L 306 MET cc_start: 0.7697 (tmm) cc_final: 0.7023 (tmm) REVERT: L 346 LYS cc_start: 0.7543 (mtmm) cc_final: 0.7068 (mtmt) REVERT: M 265 ASP cc_start: 0.7986 (m-30) cc_final: 0.7738 (m-30) REVERT: M 292 ASP cc_start: 0.7769 (p0) cc_final: 0.7135 (p0) REVERT: n 221 PHE cc_start: 0.8951 (p90) cc_final: 0.8658 (p90) REVERT: r 282 GLU cc_start: 0.8014 (tp30) cc_final: 0.7728 (tp30) outliers start: 3 outliers final: 0 residues processed: 823 average time/residue: 0.5365 time to fit residues: 736.6362 Evaluate side-chains 660 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 660 time to evaluate : 5.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 342 optimal weight: 1.9990 chunk 220 optimal weight: 6.9990 chunk 330 optimal weight: 0.9980 chunk 166 optimal weight: 6.9990 chunk 108 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 351 optimal weight: 5.9990 chunk 376 optimal weight: 1.9990 chunk 273 optimal weight: 0.0670 chunk 51 optimal weight: 0.7980 chunk 434 optimal weight: 10.0000 overall best weight: 0.9520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 41 HIS 6 8 ASN ** 6 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 74 ASN ** 7 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 GLN C 103 ASN ** C 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 ASN I 192 GLN ** I 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 303 GLN ** I 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 ASN J 277 ASN K 72 GLN K 106 ASN K 142 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.4744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 45011 Z= 0.165 Angle : 0.590 11.424 60998 Z= 0.295 Chirality : 0.044 0.176 7049 Planarity : 0.004 0.067 7868 Dihedral : 6.929 103.746 6446 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.04 % Allowed : 1.25 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -2.36 (0.11), residues: 5766 helix: -1.03 (0.11), residues: 2042 sheet: -1.42 (0.15), residues: 1077 loop : -2.00 (0.12), residues: 2647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP G 218 HIS 0.006 0.001 HIS G 204 PHE 0.022 0.001 PHE M 432 TYR 0.025 0.001 TYR A 133 ARG 0.009 0.000 ARG J 200 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11532 Ramachandran restraints generated. 5766 Oldfield, 0 Emsley, 5766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11532 Ramachandran restraints generated. 5766 Oldfield, 0 Emsley, 5766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 832 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 830 time to evaluate : 5.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 30 ASN cc_start: 0.8238 (t0) cc_final: 0.7910 (t0) REVERT: 2 69 TYR cc_start: 0.9039 (t80) cc_final: 0.8706 (t80) REVERT: 2 112 SER cc_start: 0.8404 (t) cc_final: 0.8047 (p) REVERT: 2 120 ASP cc_start: 0.7421 (p0) cc_final: 0.6899 (p0) REVERT: 2 200 GLN cc_start: 0.7054 (mt0) cc_final: 0.6186 (pt0) REVERT: 2 214 LYS cc_start: 0.8104 (ptmt) cc_final: 0.7684 (mttt) REVERT: 3 72 ASN cc_start: 0.8632 (m-40) cc_final: 0.8209 (t0) REVERT: 4 60 ILE cc_start: 0.9206 (pt) cc_final: 0.8808 (mt) REVERT: 4 99 GLN cc_start: 0.7244 (tm-30) cc_final: 0.6843 (tm-30) REVERT: 4 120 ASP cc_start: 0.7785 (p0) cc_final: 0.7528 (p0) REVERT: 4 124 THR cc_start: 0.8541 (p) cc_final: 0.8036 (p) REVERT: 4 155 GLU cc_start: 0.8281 (pm20) cc_final: 0.7912 (pm20) REVERT: 5 24 ASN cc_start: 0.9072 (t0) cc_final: 0.8765 (t0) REVERT: 5 73 ARG cc_start: 0.7773 (ttp-170) cc_final: 0.7526 (ttp-170) REVERT: 6 81 ASP cc_start: 0.7365 (t0) cc_final: 0.7033 (t0) REVERT: 6 159 GLN cc_start: 0.7080 (pt0) cc_final: 0.6222 (tp40) REVERT: 6 174 TYR cc_start: 0.7530 (m-10) cc_final: 0.7157 (m-10) REVERT: 6 179 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7410 (mm-30) REVERT: 6 214 LYS cc_start: 0.8071 (ptmm) cc_final: 0.7743 (ptmt) REVERT: A 39 ASN cc_start: 0.8247 (m-40) cc_final: 0.7952 (t0) REVERT: A 70 SER cc_start: 0.8315 (m) cc_final: 0.7897 (m) REVERT: A 224 GLU cc_start: 0.8334 (pt0) cc_final: 0.7488 (mt-10) REVERT: A 242 GLU cc_start: 0.7228 (mp0) cc_final: 0.6906 (mp0) REVERT: B 30 GLN cc_start: 0.8348 (mp10) cc_final: 0.8144 (mp10) REVERT: B 47 THR cc_start: 0.8857 (t) cc_final: 0.8655 (t) REVERT: B 60 THR cc_start: 0.9266 (p) cc_final: 0.8817 (t) REVERT: B 75 TYR cc_start: 0.8831 (p90) cc_final: 0.8342 (p90) REVERT: B 210 GLU cc_start: 0.7465 (tp30) cc_final: 0.7214 (tp30) REVERT: C 7 ASP cc_start: 0.8067 (t70) cc_final: 0.7656 (t0) REVERT: C 39 MET cc_start: 0.8619 (ttt) cc_final: 0.8315 (ttt) REVERT: C 72 LYS cc_start: 0.8526 (mmmt) cc_final: 0.8311 (mmmt) REVERT: C 185 LYS cc_start: 0.7950 (tttt) cc_final: 0.7560 (tptt) REVERT: C 210 ARG cc_start: 0.7614 (ttm-80) cc_final: 0.7387 (ttm-80) REVERT: C 212 GLU cc_start: 0.8260 (pt0) cc_final: 0.7373 (pt0) REVERT: C 225 VAL cc_start: 0.9052 (t) cc_final: 0.8786 (t) REVERT: D 27 VAL cc_start: 0.8908 (t) cc_final: 0.8650 (p) REVERT: D 47 GLU cc_start: 0.8457 (pp20) cc_final: 0.7953 (pp20) REVERT: D 148 TYR cc_start: 0.9158 (m-80) cc_final: 0.8890 (m-10) REVERT: E 203 ILE cc_start: 0.9027 (pt) cc_final: 0.8163 (mt) REVERT: G 60 VAL cc_start: 0.8667 (t) cc_final: 0.8449 (p) REVERT: G 202 LEU cc_start: 0.8880 (mt) cc_final: 0.8666 (mt) REVERT: H 51 GLN cc_start: 0.8193 (pp30) cc_final: 0.7940 (pp30) REVERT: H 98 GLN cc_start: 0.8047 (tt0) cc_final: 0.7789 (tt0) REVERT: H 105 ILE cc_start: 0.9279 (mt) cc_final: 0.8810 (tt) REVERT: H 166 THR cc_start: 0.7069 (p) cc_final: 0.6725 (t) REVERT: H 218 ILE cc_start: 0.8773 (pt) cc_final: 0.8538 (mt) REVERT: H 348 ASN cc_start: 0.8309 (t0) cc_final: 0.7834 (t0) REVERT: I 64 ARG cc_start: 0.7341 (ptm-80) cc_final: 0.6961 (ttt180) REVERT: I 68 HIS cc_start: 0.7931 (m-70) cc_final: 0.7585 (m-70) REVERT: I 120 VAL cc_start: 0.9347 (t) cc_final: 0.8962 (m) REVERT: I 208 TYR cc_start: 0.8419 (m-80) cc_final: 0.7752 (m-80) REVERT: J 82 LYS cc_start: 0.8801 (mmmt) cc_final: 0.8502 (mmtm) REVERT: J 247 MET cc_start: 0.8530 (mtp) cc_final: 0.8275 (mtp) REVERT: J 295 ASN cc_start: 0.8892 (m-40) cc_final: 0.8676 (m-40) REVERT: J 362 CYS cc_start: 0.8837 (m) cc_final: 0.8358 (t) REVERT: K 149 ILE cc_start: 0.9166 (tp) cc_final: 0.8804 (tt) REVERT: K 260 LEU cc_start: 0.9207 (pp) cc_final: 0.8835 (tt) REVERT: L 82 ARG cc_start: 0.7902 (ptt180) cc_final: 0.7642 (mtm180) REVERT: L 156 MET cc_start: 0.7893 (mtp) cc_final: 0.7589 (mtp) REVERT: L 251 ILE cc_start: 0.8388 (pt) cc_final: 0.8042 (mt) REVERT: L 306 MET cc_start: 0.7710 (tmm) cc_final: 0.7036 (tmm) REVERT: L 346 LYS cc_start: 0.7578 (mtmm) cc_final: 0.7120 (mtmt) REVERT: M 265 ASP cc_start: 0.7999 (m-30) cc_final: 0.7657 (m-30) REVERT: M 292 ASP cc_start: 0.7747 (p0) cc_final: 0.7037 (p0) REVERT: M 305 MET cc_start: 0.8354 (ttp) cc_final: 0.8001 (ttm) REVERT: M 420 SER cc_start: 0.9096 (m) cc_final: 0.8734 (t) REVERT: n 221 PHE cc_start: 0.8913 (p90) cc_final: 0.8522 (p90) REVERT: r 282 GLU cc_start: 0.8023 (tp30) cc_final: 0.7737 (tp30) outliers start: 2 outliers final: 1 residues processed: 832 average time/residue: 0.5308 time to fit residues: 744.1879 Evaluate side-chains 662 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 661 time to evaluate : 5.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 503 optimal weight: 10.0000 chunk 530 optimal weight: 6.9990 chunk 483 optimal weight: 7.9990 chunk 515 optimal weight: 6.9990 chunk 529 optimal weight: 3.9990 chunk 310 optimal weight: 0.9990 chunk 224 optimal weight: 8.9990 chunk 404 optimal weight: 7.9990 chunk 158 optimal weight: 2.9990 chunk 465 optimal weight: 6.9990 chunk 487 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 41 HIS 5 133 GLN 6 8 ASN 7 74 ASN ** 7 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 GLN ** C 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 HIS G 33 ASN G 182 HIS I 102 ASN ** I 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 303 GLN ** I 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 277 ASN K 142 HIS M 72 ASN M 362 GLN r 237 ASN r 291 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.4864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 45011 Z= 0.378 Angle : 0.719 9.317 60998 Z= 0.366 Chirality : 0.049 0.204 7049 Planarity : 0.005 0.069 7868 Dihedral : 7.542 109.614 6446 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.86 % Favored : 92.13 % Rotamer: Outliers : 0.02 % Allowed : 1.23 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -2.52 (0.11), residues: 5766 helix: -1.13 (0.11), residues: 2038 sheet: -1.57 (0.15), residues: 1104 loop : -2.09 (0.12), residues: 2624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP n 219 HIS 0.010 0.001 HIS 1 120 PHE 0.029 0.002 PHE 7 36 TYR 0.028 0.002 TYR B 224 ARG 0.010 0.001 ARG 1 29 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11532 Ramachandran restraints generated. 5766 Oldfield, 0 Emsley, 5766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11532 Ramachandran restraints generated. 5766 Oldfield, 0 Emsley, 5766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 779 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 778 time to evaluate : 5.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 30 ASN cc_start: 0.8263 (t0) cc_final: 0.7937 (t0) REVERT: 2 112 SER cc_start: 0.8411 (t) cc_final: 0.8027 (p) REVERT: 2 120 ASP cc_start: 0.7523 (p0) cc_final: 0.6904 (p0) REVERT: 2 200 GLN cc_start: 0.7261 (mt0) cc_final: 0.6301 (pt0) REVERT: 2 214 LYS cc_start: 0.8117 (ptmt) cc_final: 0.7711 (mttp) REVERT: 3 59 ASP cc_start: 0.8972 (m-30) cc_final: 0.8760 (m-30) REVERT: 4 41 HIS cc_start: 0.8629 (m-70) cc_final: 0.8311 (m170) REVERT: 4 52 ASP cc_start: 0.7244 (m-30) cc_final: 0.6897 (t0) REVERT: 4 60 ILE cc_start: 0.9380 (pt) cc_final: 0.8923 (mm) REVERT: 4 99 GLN cc_start: 0.7292 (tm-30) cc_final: 0.6694 (tm-30) REVERT: 4 120 ASP cc_start: 0.7705 (p0) cc_final: 0.7287 (p0) REVERT: 4 155 GLU cc_start: 0.8282 (pm20) cc_final: 0.8068 (pm20) REVERT: 5 24 ASN cc_start: 0.9116 (t0) cc_final: 0.8862 (t0) REVERT: 5 73 ARG cc_start: 0.7925 (ttp-170) cc_final: 0.7640 (ttp-170) REVERT: 6 18 GLU cc_start: 0.7387 (mm-30) cc_final: 0.6175 (mm-30) REVERT: 6 174 TYR cc_start: 0.7505 (m-10) cc_final: 0.7265 (m-80) REVERT: 6 214 LYS cc_start: 0.8159 (ptmm) cc_final: 0.7848 (ptmt) REVERT: A 39 ASN cc_start: 0.8229 (m-40) cc_final: 0.7901 (t0) REVERT: A 224 GLU cc_start: 0.8328 (pt0) cc_final: 0.8073 (pt0) REVERT: A 242 GLU cc_start: 0.7133 (mp0) cc_final: 0.6641 (mp0) REVERT: A 243 GLU cc_start: 0.7595 (pt0) cc_final: 0.7226 (pt0) REVERT: A 244 ARG cc_start: 0.6996 (tpp-160) cc_final: 0.6775 (tpp-160) REVERT: B 30 GLN cc_start: 0.8353 (mp10) cc_final: 0.8070 (mp10) REVERT: B 75 TYR cc_start: 0.8843 (p90) cc_final: 0.8314 (p90) REVERT: B 178 ARG cc_start: 0.8368 (mmm-85) cc_final: 0.7750 (mmp-170) REVERT: B 210 GLU cc_start: 0.7658 (tp30) cc_final: 0.7428 (tp30) REVERT: B 224 TYR cc_start: 0.8455 (p90) cc_final: 0.8164 (p90) REVERT: C 212 GLU cc_start: 0.8187 (pt0) cc_final: 0.7310 (pt0) REVERT: D 86 ILE cc_start: 0.8470 (pt) cc_final: 0.8243 (mt) REVERT: D 148 TYR cc_start: 0.9227 (m-80) cc_final: 0.8950 (m-10) REVERT: E 140 VAL cc_start: 0.8375 (t) cc_final: 0.7919 (m) REVERT: E 203 ILE cc_start: 0.9071 (pt) cc_final: 0.8188 (mt) REVERT: G 21 ASN cc_start: 0.8864 (p0) cc_final: 0.8596 (p0) REVERT: G 60 VAL cc_start: 0.8714 (t) cc_final: 0.8433 (p) REVERT: G 95 GLU cc_start: 0.7251 (pm20) cc_final: 0.7021 (pm20) REVERT: G 150 MET cc_start: 0.8787 (tpp) cc_final: 0.8175 (ttm) REVERT: H 51 GLN cc_start: 0.8244 (pp30) cc_final: 0.7995 (pp30) REVERT: H 98 GLN cc_start: 0.8329 (tt0) cc_final: 0.8006 (tt0) REVERT: H 105 ILE cc_start: 0.9358 (mt) cc_final: 0.8856 (tt) REVERT: H 320 ASP cc_start: 0.8371 (t0) cc_final: 0.8134 (t0) REVERT: H 330 GLN cc_start: 0.8945 (mp10) cc_final: 0.8382 (mp10) REVERT: H 348 ASN cc_start: 0.8397 (t0) cc_final: 0.7998 (t0) REVERT: I 64 ARG cc_start: 0.7619 (ptm-80) cc_final: 0.7244 (ttt180) REVERT: I 68 HIS cc_start: 0.8012 (m-70) cc_final: 0.7718 (m-70) REVERT: I 74 GLU cc_start: 0.8375 (pp20) cc_final: 0.8152 (tm-30) REVERT: I 120 VAL cc_start: 0.9307 (t) cc_final: 0.8981 (m) REVERT: I 208 TYR cc_start: 0.8393 (m-80) cc_final: 0.7793 (m-80) REVERT: I 247 ILE cc_start: 0.8966 (mm) cc_final: 0.8730 (mm) REVERT: I 285 ASP cc_start: 0.7829 (p0) cc_final: 0.7476 (p0) REVERT: J 129 LYS cc_start: 0.8484 (mmmt) cc_final: 0.8253 (mmmm) REVERT: J 247 MET cc_start: 0.8443 (mtp) cc_final: 0.8056 (mtp) REVERT: J 270 ARG cc_start: 0.6632 (mmt90) cc_final: 0.6047 (mmt180) REVERT: J 295 ASN cc_start: 0.8877 (m-40) cc_final: 0.8661 (m-40) REVERT: J 362 CYS cc_start: 0.8817 (m) cc_final: 0.8330 (t) REVERT: K 149 ILE cc_start: 0.9168 (tp) cc_final: 0.8716 (tt) REVERT: K 260 LEU cc_start: 0.9305 (pp) cc_final: 0.8790 (tt) REVERT: L 156 MET cc_start: 0.8049 (mtp) cc_final: 0.7774 (mtp) REVERT: L 251 ILE cc_start: 0.8634 (pt) cc_final: 0.8214 (mt) REVERT: L 306 MET cc_start: 0.7819 (tmm) cc_final: 0.7157 (tmm) REVERT: L 346 LYS cc_start: 0.7685 (mtmm) cc_final: 0.7166 (mtmt) REVERT: L 419 VAL cc_start: 0.8591 (t) cc_final: 0.8357 (p) REVERT: M 265 ASP cc_start: 0.8071 (m-30) cc_final: 0.7812 (m-30) REVERT: M 292 ASP cc_start: 0.7773 (p0) cc_final: 0.7145 (p0) outliers start: 1 outliers final: 0 residues processed: 779 average time/residue: 0.5352 time to fit residues: 707.5679 Evaluate side-chains 634 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 634 time to evaluate : 5.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 513 optimal weight: 0.9990 chunk 338 optimal weight: 8.9990 chunk 545 optimal weight: 0.0670 chunk 332 optimal weight: 0.8980 chunk 258 optimal weight: 1.9990 chunk 378 optimal weight: 0.9990 chunk 571 optimal weight: 3.9990 chunk 526 optimal weight: 0.9990 chunk 455 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 351 optimal weight: 5.9990 overall best weight: 0.7722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 53 GLN 6 159 GLN 7 74 ASN ** 7 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 84 ASN C 21 GLN ** C 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 ASN G 182 HIS I 102 ASN I 192 GLN I 238 ASN I 303 GLN ** I 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 ASN J 277 ASN J 379 GLN K 142 HIS r 237 ASN r 291 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.5070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 45011 Z= 0.162 Angle : 0.606 10.471 60998 Z= 0.303 Chirality : 0.045 0.177 7049 Planarity : 0.004 0.086 7868 Dihedral : 6.892 101.838 6446 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 0.02 % Allowed : 0.44 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -2.24 (0.11), residues: 5766 helix: -0.93 (0.11), residues: 2037 sheet: -1.28 (0.16), residues: 1053 loop : -1.95 (0.12), residues: 2676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP 5 25 HIS 0.008 0.001 HIS F 110 PHE 0.029 0.001 PHE J 23 TYR 0.026 0.001 TYR M 180 ARG 0.011 0.000 ARG 1 29 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11532 Ramachandran restraints generated. 5766 Oldfield, 0 Emsley, 5766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11532 Ramachandran restraints generated. 5766 Oldfield, 0 Emsley, 5766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 825 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 824 time to evaluate : 5.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 30 ASN cc_start: 0.8201 (t0) cc_final: 0.7906 (t0) REVERT: 2 69 TYR cc_start: 0.9037 (t80) cc_final: 0.8786 (t80) REVERT: 2 112 SER cc_start: 0.8377 (t) cc_final: 0.8013 (p) REVERT: 2 120 ASP cc_start: 0.7512 (p0) cc_final: 0.6892 (p0) REVERT: 2 200 GLN cc_start: 0.7272 (mt0) cc_final: 0.6320 (pt0) REVERT: 2 214 LYS cc_start: 0.8078 (ptmt) cc_final: 0.7696 (mttt) REVERT: 4 52 ASP cc_start: 0.7226 (m-30) cc_final: 0.6920 (t0) REVERT: 4 60 ILE cc_start: 0.9254 (pt) cc_final: 0.8893 (mt) REVERT: 4 71 GLU cc_start: 0.8327 (mp0) cc_final: 0.8036 (mm-30) REVERT: 4 99 GLN cc_start: 0.7179 (tm-30) cc_final: 0.6703 (tm-30) REVERT: 4 120 ASP cc_start: 0.7794 (p0) cc_final: 0.7468 (p0) REVERT: 4 124 THR cc_start: 0.8576 (p) cc_final: 0.8085 (p) REVERT: 5 24 ASN cc_start: 0.9100 (t0) cc_final: 0.8845 (t0) REVERT: 5 73 ARG cc_start: 0.7835 (ttp-170) cc_final: 0.7540 (ttp-170) REVERT: 6 18 GLU cc_start: 0.7580 (mm-30) cc_final: 0.6488 (mm-30) REVERT: 6 81 ASP cc_start: 0.7395 (t0) cc_final: 0.7039 (t0) REVERT: 6 159 GLN cc_start: 0.6431 (pt0) cc_final: 0.5544 (tp40) REVERT: 6 161 GLU cc_start: 0.7288 (tm-30) cc_final: 0.7066 (tm-30) REVERT: 6 174 TYR cc_start: 0.7543 (m-10) cc_final: 0.7217 (m-10) REVERT: 6 179 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7367 (mm-30) REVERT: 6 214 LYS cc_start: 0.8147 (ptmm) cc_final: 0.7827 (ptmt) REVERT: A 39 ASN cc_start: 0.8228 (m-40) cc_final: 0.7947 (t0) REVERT: A 70 SER cc_start: 0.8360 (m) cc_final: 0.7911 (m) REVERT: A 224 GLU cc_start: 0.8257 (pt0) cc_final: 0.7467 (mt-10) REVERT: A 242 GLU cc_start: 0.7206 (mp0) cc_final: 0.6796 (mp0) REVERT: A 244 ARG cc_start: 0.6934 (tpp-160) cc_final: 0.6669 (tpp-160) REVERT: B 30 GLN cc_start: 0.8343 (mp10) cc_final: 0.8099 (mp10) REVERT: B 75 TYR cc_start: 0.8813 (p90) cc_final: 0.8341 (p90) REVERT: C 185 LYS cc_start: 0.7780 (tttt) cc_final: 0.7482 (tptt) REVERT: C 210 ARG cc_start: 0.7673 (ttm-80) cc_final: 0.7393 (ttm-80) REVERT: C 212 GLU cc_start: 0.8269 (pt0) cc_final: 0.7370 (pt0) REVERT: D 47 GLU cc_start: 0.8460 (pp20) cc_final: 0.7965 (pp20) REVERT: D 86 ILE cc_start: 0.8361 (pt) cc_final: 0.8134 (mt) REVERT: D 148 TYR cc_start: 0.9137 (m-80) cc_final: 0.8869 (m-10) REVERT: E 203 ILE cc_start: 0.9049 (pt) cc_final: 0.8192 (mt) REVERT: F 68 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7380 (mm-30) REVERT: G 60 VAL cc_start: 0.8693 (t) cc_final: 0.8449 (p) REVERT: H 51 GLN cc_start: 0.8225 (pp30) cc_final: 0.7989 (pp30) REVERT: H 98 GLN cc_start: 0.7988 (tt0) cc_final: 0.7778 (tt0) REVERT: H 105 ILE cc_start: 0.9322 (mt) cc_final: 0.8843 (tt) REVERT: H 166 THR cc_start: 0.6811 (p) cc_final: 0.6511 (t) REVERT: H 348 ASN cc_start: 0.8322 (t0) cc_final: 0.7873 (t0) REVERT: I 64 ARG cc_start: 0.7442 (ptm-80) cc_final: 0.7123 (ttt180) REVERT: I 68 HIS cc_start: 0.7921 (m-70) cc_final: 0.7605 (m-70) REVERT: I 120 VAL cc_start: 0.9309 (t) cc_final: 0.8960 (m) REVERT: I 208 TYR cc_start: 0.8392 (m-80) cc_final: 0.7766 (m-80) REVERT: I 239 GLN cc_start: 0.7716 (mp10) cc_final: 0.7478 (mp10) REVERT: J 82 LYS cc_start: 0.8848 (mmmt) cc_final: 0.8513 (mmtm) REVERT: J 247 MET cc_start: 0.8434 (mtp) cc_final: 0.8125 (mtp) REVERT: J 362 CYS cc_start: 0.8847 (m) cc_final: 0.8322 (t) REVERT: K 124 SER cc_start: 0.8790 (t) cc_final: 0.8311 (p) REVERT: K 149 ILE cc_start: 0.9143 (tp) cc_final: 0.8717 (tt) REVERT: K 260 LEU cc_start: 0.9273 (pp) cc_final: 0.8872 (tt) REVERT: K 319 ASN cc_start: 0.8940 (m-40) cc_final: 0.8135 (t0) REVERT: L 82 ARG cc_start: 0.7924 (ptt90) cc_final: 0.7417 (mtm180) REVERT: L 156 MET cc_start: 0.7994 (mtp) cc_final: 0.7697 (mtp) REVERT: L 249 SER cc_start: 0.8787 (p) cc_final: 0.8544 (p) REVERT: L 251 ILE cc_start: 0.8630 (pt) cc_final: 0.8305 (mp) REVERT: L 306 MET cc_start: 0.7869 (tmm) cc_final: 0.7265 (tmm) REVERT: L 307 GLU cc_start: 0.7464 (mm-30) cc_final: 0.7118 (tp30) REVERT: L 346 LYS cc_start: 0.7664 (mtmm) cc_final: 0.7252 (mtmt) REVERT: M 159 LEU cc_start: 0.8928 (pt) cc_final: 0.8700 (pp) REVERT: M 265 ASP cc_start: 0.8046 (m-30) cc_final: 0.7682 (m-30) REVERT: M 292 ASP cc_start: 0.7883 (p0) cc_final: 0.7155 (p0) REVERT: M 328 ASN cc_start: 0.8779 (m-40) cc_final: 0.8572 (m-40) REVERT: r 135 ARG cc_start: 0.7167 (mtm180) cc_final: 0.6896 (mtm180) outliers start: 1 outliers final: 0 residues processed: 825 average time/residue: 0.5284 time to fit residues: 736.2590 Evaluate side-chains 672 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 672 time to evaluate : 5.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 279 optimal weight: 0.6980 chunk 361 optimal weight: 7.9990 chunk 485 optimal weight: 9.9990 chunk 139 optimal weight: 6.9990 chunk 419 optimal weight: 7.9990 chunk 67 optimal weight: 0.9990 chunk 126 optimal weight: 0.7980 chunk 456 optimal weight: 0.0870 chunk 190 optimal weight: 7.9990 chunk 468 optimal weight: 0.0770 chunk 57 optimal weight: 4.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 41 HIS 7 74 ASN ** 7 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 27 GLN ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 GLN C 96 GLN G 33 ASN G 182 HIS I 238 ASN I 303 GLN ** I 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 ASN J 277 ASN K 142 HIS M 72 ASN M 362 GLN r 237 ASN r 291 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.077989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.067908 restraints weight = 114294.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.069206 restraints weight = 75660.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.069742 restraints weight = 54842.401| |-----------------------------------------------------------------------------| r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.5226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 45011 Z= 0.150 Angle : 0.586 10.361 60998 Z= 0.293 Chirality : 0.044 0.189 7049 Planarity : 0.004 0.059 7868 Dihedral : 6.443 85.080 6446 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 0.04 % Allowed : 0.35 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -2.03 (0.11), residues: 5766 helix: -0.71 (0.12), residues: 2049 sheet: -1.21 (0.16), residues: 1080 loop : -1.85 (0.12), residues: 2637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP 5 25 HIS 0.013 0.001 HIS G 204 PHE 0.021 0.001 PHE M 432 TYR 0.037 0.001 TYR B 224 ARG 0.008 0.000 ARG 1 29 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11831.18 seconds wall clock time: 214 minutes 38.48 seconds (12878.48 seconds total)