Starting phenix.real_space_refine on Sun Jul 28 07:01:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ef3_9045/07_2024/6ef3_9045.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ef3_9045/07_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_9045/07_2024/6ef3_9045.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ef3_9045/07_2024/6ef3_9045.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ef3_9045/07_2024/6ef3_9045.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ef3_9045/07_2024/6ef3_9045.cif" } 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: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 25.40, per 1000 atoms: 0.57 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: 19.23 Conformation dependent library (CDL) restraints added in 7.7 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... Secondary structure from input PDB file: 205 helices and 62 sheets defined 38.6% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.89 Creating SS restraints... Processing helix chain '1' and resid 49 through 70 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) removed outlier: 3.534A pdb=" N TYR 1 70 " --> pdb=" O TYR 1 66 " (cutoff:3.500A) Processing helix chain '1' and resid 75 through 87 removed outlier: 3.724A pdb=" N ALA 1 79 " --> pdb=" O THR 1 75 " (cutoff:3.500A) 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 134 through 140 removed outlier: 3.740A pdb=" N ASP 1 139 " --> pdb=" O TYR 1 135 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LYS 1 140 " --> pdb=" O GLY 1 136 " (cutoff:3.500A) Processing helix chain '1' and resid 147 through 165 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) removed outlier: 3.874A pdb=" N TRP 1 165 " --> pdb=" O GLN 1 161 " (cutoff:3.500A) Processing helix chain '1' and resid 189 through 195 removed outlier: 3.828A pdb=" N TYR 1 193 " --> pdb=" O TYR 1 189 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLN 1 195 " --> pdb=" O ASP 1 191 " (cutoff:3.500A) Processing helix chain '2' and resid 48 through 63 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 63 through 71 Processing helix chain '2' and resid 77 through 82 removed outlier: 3.686A pdb=" N MET 2 82 " --> pdb=" O SER 2 78 " (cutoff:3.500A) Processing helix chain '2' and resid 82 through 91 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 130 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 147 through 165 removed outlier: 3.513A pdb=" N ALA 2 151 " --> pdb=" O THR 2 147 " (cutoff:3.500A) 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 3 through 7 removed outlier: 3.673A pdb=" N SER 3 6 " --> pdb=" O ASP 3 3 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE 3 7 " --> pdb=" O PRO 3 4 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 3 through 7' Processing helix chain '3' and resid 57 through 79 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 83 through 97 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) Processing helix chain '3' and resid 147 through 152 removed outlier: 3.565A pdb=" N GLU 3 151 " --> pdb=" O PHE 3 147 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER 3 152 " --> pdb=" O GLY 3 148 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 147 through 152' Processing helix chain '3' and resid 159 through 176 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 53 through 69 removed outlier: 4.000A pdb=" N ALA 4 57 " --> pdb=" O THR 4 53 " (cutoff:3.500A) 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 76 through 92 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 136 through 140 Processing helix chain '4' and resid 153 through 162 removed outlier: 4.074A pdb=" N GLY 4 157 " --> pdb=" O THR 4 153 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LEU 4 158 " --> pdb=" O THR 4 154 " (cutoff:3.500A) Processing helix chain '4' and resid 163 through 170 removed outlier: 3.532A pdb=" N LEU 4 168 " --> pdb=" O CYS 4 164 " (cutoff:3.500A) Processing helix chain '5' and resid 48 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 66 through 71 removed outlier: 4.095A pdb=" N GLU 5 70 " --> pdb=" O HIS 5 66 " (cutoff:3.500A) Processing helix chain '5' and resid 75 through 89 removed outlier: 4.404A pdb=" N ALA 5 79 " --> pdb=" O SER 5 75 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS 5 81 " --> pdb=" O ALA 5 77 " (cutoff:3.500A) 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) Processing helix chain '5' and resid 132 through 144 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) removed outlier: 3.760A pdb=" N SER 5 142 " --> pdb=" O GLY 5 138 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN 5 143 " --> pdb=" O VAL 5 139 " (cutoff:3.500A) Processing helix chain '5' and resid 150 through 163 removed outlier: 3.742A pdb=" N LYS 5 158 " --> pdb=" O LEU 5 154 " (cutoff:3.500A) Processing helix chain '5' and resid 193 through 205 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 59 through 80 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 85 through 99 removed outlier: 3.825A pdb=" N ALA 6 89 " --> pdb=" O SER 6 85 " (cutoff:3.500A) 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 146 through 151 removed outlier: 3.565A pdb=" N LEU 6 150 " --> pdb=" O ILE 6 146 " (cutoff:3.500A) Processing helix chain '6' and resid 176 through 188 Processing helix chain '7' and resid 56 through 76 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) removed outlier: 3.563A pdb=" N TYR 7 76 " --> pdb=" O THR 7 72 " (cutoff:3.500A) Processing helix chain '7' and resid 89 through 94 removed outlier: 4.131A pdb=" N GLU 7 94 " --> pdb=" O SER 7 90 " (cutoff:3.500A) Processing helix chain '7' and resid 94 through 105 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 151 removed outlier: 3.560A pdb=" N HIS 7 149 " --> pdb=" O GLY 7 145 " (cutoff:3.500A) Processing helix chain '7' and resid 151 through 159 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 169 through 188 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 4 through 10 Processing helix chain 'A' and resid 27 through 35 removed outlier: 4.466A pdb=" N PHE A 32 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS A 33 " --> pdb=" O TYR A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 99 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 100 through 108 removed outlier: 3.579A pdb=" N PHE A 104 " --> pdb=" O GLU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 121 removed outlier: 3.651A pdb=" N MET A 121 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 126 removed outlier: 3.607A pdb=" N GLN A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 130 Processing helix chain 'A' and resid 174 through 190 removed outlier: 3.648A pdb=" N ILE A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) 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 198 through 213 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) removed outlier: 3.543A pdb=" N ALA A 213 " --> pdb=" O HIS A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 246 removed outlier: 3.875A pdb=" N VAL A 246 " --> pdb=" O GLU A 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 30 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 79 through 87 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) Processing helix chain 'B' and resid 89 through 97 removed outlier: 3.684A pdb=" N TYR B 97 " --> pdb=" O ALA B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 101 Processing helix chain 'B' and resid 107 through 116 removed outlier: 3.612A pdb=" N VAL B 111 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS B 116 " --> pdb=" O SER B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 123 removed outlier: 4.237A pdb=" N GLN B 123 " --> pdb=" O GLU B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 176 removed outlier: 3.660A pdb=" N ALA B 171 " --> pdb=" O GLY B 167 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE B 174 " --> pdb=" O ALA B 170 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLU B 176 " --> pdb=" O LYS B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 195 Processing helix chain 'B' and resid 205 through 207 No H-bonds generated for 'chain 'B' and resid 205 through 207' Processing helix chain 'B' and resid 218 through 222 Processing helix chain 'B' and resid 239 through 245 Processing helix chain 'B' and resid 246 through 250 Processing helix chain 'C' and resid 19 through 24 removed outlier: 3.964A pdb=" N GLU C 23 " --> pdb=" O LEU C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 28 Processing helix chain 'C' and resid 84 through 87 Processing helix chain 'C' and resid 88 through 103 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 107 through 119 removed outlier: 3.997A pdb=" N LEU C 111 " --> pdb=" O PRO C 107 " (cutoff:3.500A) 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 168 through 178 removed outlier: 3.678A pdb=" N LEU C 176 " --> pdb=" O ALA C 172 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET C 178 " --> pdb=" O THR C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 201 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 231 through 242 removed outlier: 3.568A pdb=" N ILE C 235 " --> pdb=" O LYS C 231 " (cutoff:3.500A) 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) removed outlier: 3.680A pdb=" N THR C 242 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 28 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) Processing helix chain 'D' and resid 78 through 101 removed outlier: 3.662A pdb=" N SER D 82 " --> pdb=" O LEU D 78 " (cutoff:3.500A) 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 105 through 114 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 167 through 179 removed outlier: 3.623A pdb=" N VAL D 171 " --> pdb=" O ASN D 167 " (cutoff:3.500A) 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) removed outlier: 3.537A pdb=" N TYR D 179 " --> pdb=" O LEU D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 200 removed outlier: 3.567A pdb=" N SER D 198 " --> pdb=" O LEU D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 239 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 21 through 31 removed outlier: 4.141A pdb=" N GLU E 25 " --> pdb=" O LEU E 21 " (cutoff:3.500A) 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) removed outlier: 3.949A pdb=" N ILE E 31 " --> pdb=" O SER E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 103 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 175 through 180 Processing helix chain 'E' and resid 193 through 198 removed outlier: 4.040A pdb=" N LEU E 198 " --> pdb=" O LYS E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 201 No H-bonds generated for 'chain 'E' and resid 199 through 201' Processing helix chain 'E' and resid 202 through 208 Processing helix chain 'E' and resid 232 through 248 removed outlier: 3.628A pdb=" N LEU E 239 " --> pdb=" O LYS E 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 26 removed outlier: 3.835A pdb=" N GLU F 23 " --> pdb=" O LEU F 19 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 32 Processing helix chain 'F' and resid 78 through 99 removed outlier: 3.805A pdb=" N VAL F 83 " --> pdb=" O PRO F 79 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N LEU F 84 " --> pdb=" O ASP F 80 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLN F 90 " --> pdb=" O ASN F 86 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER F 96 " --> pdb=" O CYS F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 110 removed outlier: 4.874A pdb=" N GLY F 109 " --> pdb=" O GLU F 106 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N HIS F 110 " --> pdb=" O ARG F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 122 removed outlier: 4.046A pdb=" N LYS F 115 " --> pdb=" O LEU F 111 " (cutoff:3.500A) 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) removed outlier: 3.775A pdb=" N SER F 122 " --> pdb=" O LYS F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 173 removed outlier: 3.509A pdb=" N LYS F 169 " --> pdb=" O SER F 165 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR F 171 " --> pdb=" O GLY F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 178 removed outlier: 4.404A pdb=" N ASP F 177 " --> pdb=" O ARG F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 198 removed outlier: 3.827A pdb=" N LEU F 189 " --> pdb=" O ASN F 185 " (cutoff:3.500A) 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) Processing helix chain 'F' and resid 199 through 201 No H-bonds generated for 'chain 'F' and resid 199 through 201' Processing helix chain 'F' and resid 230 through 234 Processing helix chain 'G' and resid 23 through 32 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 81 through 104 removed outlier: 3.502A pdb=" N GLY G 85 " --> pdb=" O LEU G 81 " (cutoff:3.500A) 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 109 through 114 Processing helix chain 'G' and resid 119 through 124 removed outlier: 3.733A pdb=" N HIS G 123 " --> pdb=" O TYR G 119 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR G 124 " --> pdb=" O VAL G 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 119 through 124' Processing helix chain 'G' and resid 168 through 183 removed outlier: 3.562A pdb=" N ALA G 172 " --> pdb=" O GLY G 168 " (cutoff:3.500A) 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 191 through 204 removed outlier: 4.094A pdb=" N ILE G 199 " --> pdb=" O GLN G 195 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 207 No H-bonds generated for 'chain 'G' and resid 205 through 207' Processing helix chain 'G' and resid 220 through 225 Processing helix chain 'G' and resid 233 through 247 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 45 through 65 removed outlier: 3.720A pdb=" N LEU H 49 " --> pdb=" O TYR H 45 " (cutoff:3.500A) 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 84 through 91 removed outlier: 4.423A pdb=" N ARG H 88 " --> pdb=" O ILE H 84 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU H 91 " --> pdb=" O ASP H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 192 through 197 removed outlier: 3.973A pdb=" N THR H 196 " --> pdb=" O ASP H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 214 through 226 removed outlier: 3.860A pdb=" N ILE H 218 " --> pdb=" O CYS H 214 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU H 219 " --> pdb=" O LYS H 215 " (cutoff:3.500A) 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 226 through 231 Processing helix chain 'H' and resid 231 through 239 removed outlier: 4.183A pdb=" N PHE H 235 " --> pdb=" O SER H 231 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR H 237 " --> pdb=" O GLU H 233 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY H 239 " --> pdb=" O PHE H 235 " (cutoff:3.500A) Processing helix chain 'H' and resid 257 through 266 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) removed outlier: 3.601A pdb=" N ARG H 266 " --> pdb=" O ALA H 262 " (cutoff:3.500A) Processing helix chain 'H' and resid 275 through 279 removed outlier: 3.582A pdb=" N LEU H 279 " --> pdb=" O GLY H 276 " (cutoff:3.500A) Processing helix chain 'H' and resid 286 through 301 removed outlier: 3.775A pdb=" N ALA H 298 " --> pdb=" O LEU H 294 " (cutoff:3.500A) Processing helix chain 'H' and resid 326 through 341 removed outlier: 3.552A pdb=" N GLN H 330 " --> pdb=" O ASP H 326 " (cutoff:3.500A) 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 362 through 367 removed outlier: 3.717A pdb=" N ARG H 367 " --> pdb=" O ALA H 364 " (cutoff:3.500A) Processing helix chain 'H' and resid 381 through 393 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 403 through 411 removed outlier: 4.082A pdb=" N ILE H 407 " --> pdb=" O ARG H 403 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ARG H 409 " --> pdb=" O GLU H 405 " (cutoff:3.500A) Processing helix chain 'H' and resid 415 through 432 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 440 through 451 removed outlier: 3.612A pdb=" N LEU H 444 " --> pdb=" O GLU H 440 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LYS H 449 " --> pdb=" O LYS H 445 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 59 removed outlier: 4.401A pdb=" N LYS I 58 " --> pdb=" O CYS I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 79 removed outlier: 3.892A pdb=" N ARG I 64 " --> pdb=" O LEU I 60 " (cutoff:3.500A) 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 86 through 91 removed outlier: 3.514A pdb=" N GLU I 90 " --> pdb=" O GLU I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 100 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 165 through 172 removed outlier: 3.823A pdb=" N SER I 169 " --> pdb=" O ASP I 165 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS I 172 " --> pdb=" O VAL I 168 " (cutoff:3.500A) Processing helix chain 'I' and resid 191 through 199 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 210 Processing helix chain 'I' and resid 228 through 237 removed outlier: 3.626A pdb=" N VAL I 236 " --> pdb=" O LEU I 232 " (cutoff:3.500A) Processing helix chain 'I' and resid 248 through 253 removed outlier: 3.600A pdb=" N ILE I 253 " --> pdb=" O SER I 250 " (cutoff:3.500A) Processing helix chain 'I' and resid 259 through 274 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 283 through 287 Processing helix chain 'I' and resid 298 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 354 through 366 removed outlier: 3.824A pdb=" N LYS I 358 " --> pdb=" O ASP I 354 " (cutoff:3.500A) 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 376 through 380 removed outlier: 3.562A pdb=" N THR I 379 " --> pdb=" O ASN I 376 " (cutoff:3.500A) Processing helix chain 'I' and resid 389 through 405 removed outlier: 3.826A pdb=" N GLN I 393 " --> pdb=" O GLY I 389 " (cutoff:3.500A) 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) Processing helix chain 'I' and resid 412 through 426 removed outlier: 3.703A pdb=" N PHE I 416 " --> pdb=" O THR I 412 " (cutoff:3.500A) 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 25 through 66 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) removed outlier: 3.974A pdb=" N GLN J 66 " --> pdb=" O LEU J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 154 through 164 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 165 through 170 Processing helix chain 'J' and resid 171 through 178 removed outlier: 4.051A pdb=" N GLU J 175 " --> pdb=" O PRO J 171 " (cutoff:3.500A) Processing helix chain 'J' and resid 194 through 203 removed outlier: 3.664A pdb=" N LEU J 198 " --> pdb=" O GLY J 194 " (cutoff:3.500A) 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) Processing helix chain 'J' and resid 204 through 206 No H-bonds generated for 'chain 'J' and resid 204 through 206' Processing helix chain 'J' and resid 226 through 239 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) removed outlier: 3.523A pdb=" N GLU J 239 " --> pdb=" O VAL J 235 " (cutoff:3.500A) Processing helix chain 'J' and resid 265 through 278 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 278 through 285 Processing helix chain 'J' and resid 320 through 332 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 342 through 350 removed outlier: 3.705A pdb=" N VAL J 346 " --> pdb=" O ASN J 342 " (cutoff:3.500A) 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 356 through 373 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 384 Processing helix chain 'J' and resid 385 through 390 Processing helix chain 'J' and resid 390 through 398 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) removed outlier: 3.830A pdb=" N ILE J 398 " --> pdb=" O GLN J 394 " (cutoff:3.500A) Processing helix chain 'K' and resid 49 through 83 removed outlier: 3.664A pdb=" N LYS K 53 " --> pdb=" O PHE K 49 " (cutoff:3.500A) 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 84 through 90 removed outlier: 3.753A pdb=" N ILE K 89 " --> pdb=" O GLU K 85 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN K 90 " --> pdb=" O VAL K 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 177 through 188 removed outlier: 3.708A pdb=" N ILE K 184 " --> pdb=" O GLN K 180 " (cutoff:3.500A) Processing helix chain 'K' and resid 189 through 194 removed outlier: 3.587A pdb=" N VAL K 193 " --> pdb=" O GLU K 189 " (cutoff:3.500A) Processing helix chain 'K' and resid 195 through 202 removed outlier: 3.880A pdb=" N ILE K 201 " --> pdb=" O LEU K 197 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLY K 202 " --> pdb=" O TYR K 198 " (cutoff:3.500A) Processing helix chain 'K' and resid 218 through 231 Processing helix chain 'K' and resid 238 through 243 removed outlier: 4.015A pdb=" N PHE K 242 " --> pdb=" O ASN K 238 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N VAL K 243 " --> pdb=" O GLY K 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 238 through 243' Processing helix chain 'K' and resid 250 through 262 removed outlier: 4.113A pdb=" N PHE K 258 " --> pdb=" O VAL K 254 " (cutoff:3.500A) Processing helix chain 'K' and resid 287 through 305 removed outlier: 3.721A pdb=" N GLU K 291 " --> pdb=" O GLY K 287 " (cutoff:3.500A) 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 345 through 360 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 381 through 391 removed outlier: 3.721A pdb=" N GLU K 389 " --> pdb=" O ALA K 385 " (cutoff:3.500A) Processing helix chain 'K' and resid 392 through 397 removed outlier: 3.557A pdb=" N ARG K 396 " --> pdb=" O LEU K 392 " (cutoff:3.500A) Processing helix chain 'K' and resid 404 through 412 removed outlier: 3.835A pdb=" N GLU K 408 " --> pdb=" O GLN K 404 " (cutoff:3.500A) 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) removed outlier: 3.988A pdb=" N ALA K 412 " --> pdb=" O GLU K 408 " (cutoff:3.500A) Processing helix chain 'L' and resid 71 through 99 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) removed outlier: 3.804A pdb=" N GLN L 99 " --> pdb=" O ILE L 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 172 through 176 Processing helix chain 'L' and resid 187 through 198 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 198 through 203 removed outlier: 3.703A pdb=" N ASN L 203 " --> pdb=" O LEU L 199 " (cutoff:3.500A) Processing helix chain 'L' and resid 206 through 211 removed outlier: 3.505A pdb=" N GLY L 211 " --> pdb=" O PHE L 207 " (cutoff:3.500A) Processing helix chain 'L' and resid 228 through 239 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 249 through 254 Processing helix chain 'L' and resid 259 through 273 removed outlier: 3.687A pdb=" N ILE L 263 " --> pdb=" O SER L 259 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA L 270 " --> pdb=" O MET L 266 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS L 273 " --> pdb=" O TYR L 269 " (cutoff:3.500A) Processing helix chain 'L' and resid 282 through 286 removed outlier: 3.597A pdb=" N ILE L 286 " --> pdb=" O VAL L 283 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 314 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) Processing helix chain 'L' and resid 329 through 333 Processing helix chain 'L' and resid 355 through 365 removed outlier: 4.316A pdb=" N ILE L 363 " --> pdb=" O GLU L 359 " (cutoff:3.500A) Processing helix chain 'L' and resid 366 through 368 No H-bonds generated for 'chain 'L' and resid 366 through 368' Processing helix chain 'L' and resid 374 through 381 removed outlier: 4.522A pdb=" N ALA L 378 " --> pdb=" O PHE L 374 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS L 381 " --> pdb=" O GLU L 377 " (cutoff:3.500A) Processing helix chain 'L' and resid 390 through 403 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) removed outlier: 3.724A pdb=" N ILE L 403 " --> pdb=" O GLY L 399 " (cutoff:3.500A) Processing helix chain 'L' and resid 411 through 417 removed outlier: 4.056A pdb=" N LEU L 415 " --> pdb=" O ASN L 411 " (cutoff:3.500A) Processing helix chain 'L' and resid 417 through 426 removed outlier: 4.078A pdb=" N LYS L 421 " --> pdb=" O LYS L 417 " (cutoff:3.500A) 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) Processing helix chain 'M' and resid 38 through 45 removed outlier: 3.546A pdb=" N ARG M 42 " --> pdb=" O ASP M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 72 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 136 through 140 removed outlier: 3.527A pdb=" N LEU M 140 " --> pdb=" O PRO M 137 " (cutoff:3.500A) Processing helix chain 'M' and resid 164 through 169 Processing helix chain 'M' and resid 186 through 195 removed outlier: 3.576A pdb=" N GLU M 195 " --> pdb=" O GLU M 191 " (cutoff:3.500A) Processing helix chain 'M' and resid 197 through 203 Processing helix chain 'M' and resid 204 through 209 Processing helix chain 'M' and resid 228 through 239 removed outlier: 3.543A pdb=" N ALA M 232 " --> pdb=" O LYS M 228 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA M 237 " --> pdb=" O ARG M 233 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR M 239 " --> pdb=" O CYS M 235 " (cutoff:3.500A) Processing helix chain 'M' and resid 259 through 272 Processing helix chain 'M' and resid 295 through 313 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 334 through 339 Processing helix chain 'M' and resid 353 through 365 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) Processing helix chain 'M' and resid 366 through 368 No H-bonds generated for 'chain 'M' and resid 366 through 368' Processing helix chain 'M' and resid 375 through 382 removed outlier: 3.668A pdb=" N LEU M 379 " --> pdb=" O ASN M 375 " (cutoff:3.500A) Processing helix chain 'M' and resid 387 through 406 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 412 through 423 removed outlier: 3.589A pdb=" N GLY M 418 " --> pdb=" O ASP M 414 " (cutoff:3.500A) Processing helix chain 'r' and resid 30 through 44 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) removed outlier: 4.113A pdb=" N GLY r 44 " --> pdb=" O HIS r 40 " (cutoff:3.500A) Processing helix chain 'r' and resid 88 through 96 removed outlier: 3.715A pdb=" N MET r 92 " --> pdb=" O GLN r 88 " (cutoff:3.500A) 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 119 through 133 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 160 through 167 removed outlier: 3.511A pdb=" N ASN r 166 " --> pdb=" O GLY r 162 " (cutoff:3.500A) Processing helix chain 'r' and resid 184 through 188 Processing helix chain 'r' and resid 206 through 214 removed outlier: 4.412A pdb=" N MET r 212 " --> pdb=" O LYS r 208 " (cutoff:3.500A) Processing helix chain 'r' and resid 215 through 217 No H-bonds generated for 'chain 'r' and resid 215 through 217' Processing helix chain 'r' and resid 232 through 252 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 256 Processing helix chain 'r' and resid 275 through 303 removed outlier: 3.703A pdb=" N HIS r 279 " --> pdb=" O ASP r 275 " (cutoff:3.500A) 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) Processing helix chain 'u' and resid 22 through 34 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 37 through 39 No H-bonds generated for 'chain 'u' and resid 37 through 39' Processing helix chain 'u' and resid 55 through 59 Processing sheet with id=AA1, 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=AA2, 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) removed outlier: 4.063A pdb=" N TYR 1 111 " --> pdb=" O VAL 1 99 " (cutoff:3.500A) Processing sheet with id=AA3, 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) removed outlier: 6.434A pdb=" N VAL 2 173 " --> pdb=" O ASN 2 189 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '2' and resid 34 through 35 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=AA5, first strand: chain '2' and resid 215 through 218 removed outlier: 4.478A pdb=" N VAL 3 195 " --> pdb=" O VAL 2 218 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL 3 196 " --> pdb=" O ILE 3 189 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE 3 189 " --> pdb=" O VAL 3 196 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU 3 200 " --> pdb=" O ALA 3 185 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ALA 3 185 " --> pdb=" O LEU 3 200 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N ILE 3 11 " --> pdb=" O ASP 3 26 " (cutoff:3.500A) Processing sheet with id=AA6, 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=AA7, first strand: chain '4' and resid 130 through 132 Processing sheet with id=AA8, first strand: chain '4' and resid 22 through 23 removed outlier: 4.142A pdb=" N SER 4 26 " --> pdb=" O ARG 4 23 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '4' and resid 35 through 39 removed outlier: 3.657A pdb=" N MET 4 44 " --> pdb=" O ARG 4 36 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU 4 38 " --> pdb=" O THR 4 42 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N THR 4 42 " --> pdb=" O LEU 4 38 " (cutoff:3.500A) 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=AB1, first strand: chain '5' and resid 126 through 130 removed outlier: 6.341A pdb=" N VAL 5 175 " --> pdb=" O ASN 5 190 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ASN 5 190 " --> pdb=" O VAL 5 175 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LEU 5 177 " --> pdb=" O HIS 5 188 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '5' and resid 20 through 22 removed outlier: 6.807A pdb=" N ALA 5 20 " --> pdb=" O ALA 5 27 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA 5 22 " --> pdb=" O TRP 5 25 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '5' and resid 34 through 38 removed outlier: 3.984A pdb=" N GLY 5 43 " --> pdb=" O ILE 5 35 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ILE 5 37 " --> pdb=" O LEU 5 41 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N LEU 5 41 " --> pdb=" O ILE 5 37 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR 5 44 " --> pdb=" O MET 5 100 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N MET 5 100 " --> pdb=" O THR 5 44 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '6' and resid 136 through 140 removed outlier: 3.968A pdb=" N ARG 6 137 " --> pdb=" O GLY 6 14 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU 6 203 " --> pdb=" O GLY 6 25 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR 6 217 " --> pdb=" O LEU 6 202 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '6' and resid 29 through 30 removed outlier: 6.619A pdb=" N ASN 6 29 " --> pdb=" O ASN 6 36 " (cutoff:3.500A) Processing sheet with id=AB6, 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: 3.592A pdb=" N VAL 6 122 " --> pdb=" O GLU 6 134 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain '6' and resid 207 through 208 Processing sheet with id=AB8, 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=AB9, first strand: chain '7' and resid 28 through 29 Processing sheet with id=AC1, 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) removed outlier: 3.596A pdb=" N TYR 7 129 " --> pdb=" O TYR 7 137 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR 7 137 " --> pdb=" O TYR 7 129 " (cutoff:3.500A) Processing sheet with id=AC2, 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=AC3, first strand: chain 'A' and resid 72 through 73 removed outlier: 3.510A pdb=" N MET A 81 " --> pdb=" O PHE A 73 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 161 through 164 removed outlier: 3.601A pdb=" N THR B 162 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE B 45 " --> pdb=" O ALA B 212 " (cutoff:3.500A) Processing sheet with id=AC5, 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=AC6, 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=AC7, first strand: chain 'C' and resid 45 through 46 removed outlier: 3.592A pdb=" N ALA C 35 " --> pdb=" O VAL C 165 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 66 through 70 removed outlier: 6.471A pdb=" N ILE C 73 " --> pdb=" O LEU C 69 " (cutoff:3.500A) Processing sheet with id=AC9, 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=AD1, first strand: chain 'C' and resid 215 through 217 Processing sheet with id=AD2, first strand: chain 'D' and resid 161 through 163 removed outlier: 3.515A pdb=" N VAL D 36 " --> pdb=" O VAL D 43 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL D 222 " --> pdb=" O VAL D 214 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 65 through 68 removed outlier: 3.552A pdb=" N ILE D 67 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL D 71 " --> pdb=" O ILE D 67 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA D 136 " --> pdb=" O VAL D 72 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 148 through 151 removed outlier: 3.683A pdb=" N SER D 157 " --> pdb=" O GLN D 149 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU D 151 " --> pdb=" O ILE D 155 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE D 155 " --> pdb=" O GLU D 151 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 169 through 172 removed outlier: 3.689A pdb=" N GLN E 218 " --> pdb=" O VAL E 50 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 67 through 71 removed outlier: 5.939A pdb=" N GLU E 69 " --> pdb=" O CYS E 76 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N CYS E 76 " --> pdb=" O GLU E 69 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASP E 71 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 142 through 143 removed outlier: 3.657A pdb=" N ALA E 158 " --> pdb=" O LEU E 142 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 160 through 161 Processing sheet with id=AD9, first strand: chain 'F' and resid 63 through 67 removed outlier: 6.365A pdb=" N ILE F 63 " --> pdb=" O LEU F 74 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N LEU F 74 " --> pdb=" O ILE F 63 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N LYS F 65 " --> pdb=" O LEU F 72 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU F 72 " --> pdb=" O LYS F 65 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ASP F 67 " --> pdb=" O MET F 70 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY F 71 " --> pdb=" O ILE F 135 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ILE F 135 " --> pdb=" O GLY F 71 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER F 73 " --> pdb=" O LEU F 133 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE F 134 " --> pdb=" O LEU F 145 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY F 136 " --> pdb=" O HIS F 143 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASP F 138 " --> pdb=" O GLY F 141 " (cutoff:3.500A) Processing sheet with id=AE1, 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=AE2, first strand: chain 'G' and resid 68 through 69 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=AE3, 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=AE4, first strand: chain 'H' and resid 155 through 156 removed outlier: 3.516A pdb=" N TYR M 77 " --> pdb=" O VAL H 156 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL M 146 " --> pdb=" O ALA M 80 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASP M 157 " --> pdb=" O GLY M 147 " (cutoff:3.500A) Processing sheet with id=AE5, 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=AE6, first strand: chain 'H' and resid 248 through 249 Processing sheet with id=AE7, first strand: chain 'H' and resid 304 through 305 removed outlier: 6.923A pdb=" N CYS H 304 " --> pdb=" O LYS H 350 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, 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: 6.777A pdb=" N LEU I 148 " --> pdb=" O VAL I 157 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 112 through 113 removed outlier: 3.565A pdb=" N HIS I 117 " --> pdb=" O ILE I 113 " (cutoff:3.500A) 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=AF1, first strand: chain 'I' and resid 325 through 327 removed outlier: 6.856A pdb=" N ILE I 220 " --> pdb=" O ILE I 348 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N PHE I 350 " --> pdb=" O ILE I 220 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N TYR I 222 " --> pdb=" O PHE I 350 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 93 through 96 removed outlier: 3.524A pdb=" N VAL J 84 " --> pdb=" O VAL J 96 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N LEU J 85 " --> pdb=" O ILE J 76 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE J 76 " --> pdb=" O LEU J 85 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 185 through 188 Processing sheet with id=AF4, first strand: chain 'J' and resid 209 through 213 removed outlier: 7.872A pdb=" N ILE J 291 " --> pdb=" O SER J 243 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N ILE J 245 " --> pdb=" O ILE J 291 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N ALA J 293 " --> pdb=" O ILE J 245 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N MET J 247 " --> pdb=" O ALA J 293 " (cutoff:3.500A) Processing sheet with id=AF5, 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) removed outlier: 3.768A pdb=" N ASP K 148 " --> pdb=" O ALA K 138 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 99 through 104 removed outlier: 6.050A pdb=" N PHE K 99 " --> pdb=" O SER K 111 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N SER K 111 " --> pdb=" O PHE K 99 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLU K 101 " --> pdb=" O ILE K 109 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N THR K 107 " --> pdb=" O ILE K 103 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 209 through 211 Processing sheet with id=AF8, first strand: chain 'K' and resid 233 through 237 removed outlier: 6.528A pdb=" N ALA K 233 " --> pdb=" O ILE K 268 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N PHE K 270 " --> pdb=" O ALA K 233 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ILE K 235 " --> pdb=" O PHE K 270 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'L' and resid 111 through 113 removed outlier: 6.107A pdb=" N GLU L 111 " --> pdb=" O ILE L 118 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ILE L 118 " --> pdb=" O GLU L 111 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL L 129 " --> pdb=" O TYR L 117 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N ILE L 155 " --> pdb=" O ILE L 128 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N GLY L 130 " --> pdb=" O ILE L 155 " (cutoff:3.500A) removed outlier: 9.235A pdb=" N ARG L 157 " --> pdb=" O GLY L 130 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N THR L 147 " --> pdb=" O MET L 156 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'L' and resid 170 through 171 removed outlier: 3.849A pdb=" N PHE L 243 " --> pdb=" O THR L 171 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 326 through 327 removed outlier: 8.917A pdb=" N THR L 327 " --> pdb=" O VAL L 218 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU L 220 " --> pdb=" O THR L 327 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'M' and resid 117 through 120 removed outlier: 3.836A pdb=" N VAL M 127 " --> pdb=" O VAL M 119 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'M' and resid 220 through 221 Processing sheet with id=AG5, first strand: chain 'r' and resid 64 through 70 removed outlier: 3.845A pdb=" N ASN r 64 " --> pdb=" O GLU r 56 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU r 56 " --> pdb=" O ASN r 64 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LEU r 54 " --> pdb=" O VAL r 66 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N VAL r 68 " --> pdb=" O LEU r 52 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU r 52 " --> pdb=" O VAL r 68 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLY r 51 " --> pdb=" O TYR r 108 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY r 106 " --> pdb=" O MET r 53 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N GLY r 55 " --> pdb=" O VAL r 104 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N VAL r 104 " --> pdb=" O GLY r 55 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL r 137 " --> pdb=" O VAL r 105 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL r 141 " --> pdb=" O HIS r 109 " (cutoff:3.500A) Processing sheet with id=AG6, 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=AG7, first strand: chain 'u' and resid 3 through 5 Processing sheet with id=AG8, first strand: chain 'u' and resid 48 through 49 1444 hydrogen bonds defined for protein. 3972 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: 23.10 Time building geometry restraints manager: 19.18 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: 9472 2.76 - 3.48: 61690 3.48 - 4.19: 95994 4.19 - 4.90: 168329 Nonbonded interactions: 335489 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 335484 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: 2.370 Check model and map are aligned: 0.320 Set scattering table: 0.420 Process input model: 125.820 Find NCS groups from input model: 3.440 Set up NCS constraints: 0.300 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: 0.030 Load rotamer database and sin/cos tables:3.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 138.450 ------------------------------------------------------------------------------- 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= 1.051 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 : 5.276 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: 0.5839 time to fit residues: 961.4440 Evaluate side-chains 654 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 653 time to evaluate : 9.142 ------------------------------------------------------------------------------- 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: 3.9990 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: 3.9990 chunk 174 optimal weight: 1.9990 chunk 273 optimal weight: 0.9980 chunk 334 optimal weight: 0.9980 chunk 521 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 4 78 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 E 91 HIS F 21 GLN F 166 GLN F 210 ASN G 23 GLN G 207 ASN G 228 HIS H 54 ASN H 89 GLN H 217 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 M 238 GLN r 126 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 45011 Z= 0.223 Angle : 0.712 10.354 60998 Z= 0.367 Chirality : 0.048 0.207 7049 Planarity : 0.005 0.063 7868 Dihedral : 8.746 121.258 6446 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 0.13 % Allowed : 3.84 % Favored : 96.03 % 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: -4.48 (0.09), residues: 5766 helix: -2.79 (0.09), residues: 2090 sheet: -3.07 (0.13), residues: 980 loop : -3.00 (0.11), residues: 2696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP G 218 HIS 0.010 0.001 HIS G 204 PHE 0.019 0.002 PHE M 432 TYR 0.029 0.001 TYR A 133 ARG 0.008 0.001 ARG G 91 *********************** 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 961 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 955 time to evaluate : 4.955 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 97 ILE cc_start: 0.8850 (pt) cc_final: 0.8599 (mt) REVERT: 2 12 VAL cc_start: 0.9506 (m) cc_final: 0.9234 (p) REVERT: 2 69 TYR cc_start: 0.9026 (t80) cc_final: 0.8475 (t80) REVERT: 2 71 SER cc_start: 0.8421 (m) cc_final: 0.8162 (p) REVERT: 2 112 SER cc_start: 0.8214 (t) cc_final: 0.7763 (p) REVERT: 2 120 ASP cc_start: 0.7160 (p0) cc_final: 0.6471 (p0) REVERT: 2 200 GLN cc_start: 0.7021 (mt0) cc_final: 0.6160 (pt0) REVERT: 2 214 LYS cc_start: 0.8234 (ptmt) cc_final: 0.7778 (mttp) REVERT: 3 203 ARG cc_start: 0.8476 (ptm-80) cc_final: 0.6546 (mtt180) REVERT: 4 1 MET cc_start: 0.6663 (ttp) cc_final: 0.5698 (tpt) REVERT: 4 3 ILE cc_start: 0.9112 (pt) cc_final: 0.8585 (mp) REVERT: 4 30 ASP cc_start: 0.8462 (p0) cc_final: 0.8210 (p0) REVERT: 4 99 GLN cc_start: 0.7329 (tm-30) cc_final: 0.7051 (tm-30) REVERT: 5 24 ASN cc_start: 0.8661 (t0) cc_final: 0.8220 (t0) REVERT: 5 100 MET cc_start: 0.8243 (ptp) cc_final: 0.7897 (ptp) REVERT: 6 81 ASP cc_start: 0.7066 (t0) cc_final: 0.6675 (t70) REVERT: 6 159 GLN cc_start: 0.6823 (pt0) cc_final: 0.5773 (tp40) REVERT: 6 180 VAL cc_start: 0.8999 (m) cc_final: 0.8753 (t) REVERT: 7 108 ASN cc_start: 0.7683 (p0) cc_final: 0.7169 (p0) REVERT: A 39 ASN cc_start: 0.8440 (m-40) cc_final: 0.7728 (t0) REVERT: A 49 ASP cc_start: 0.7426 (p0) cc_final: 0.7025 (p0) REVERT: A 50 CYS cc_start: 0.6939 (m) cc_final: 0.6655 (m) REVERT: A 183 GLU cc_start: 0.7797 (tm-30) cc_final: 0.7559 (tm-30) REVERT: A 195 ASN cc_start: 0.8359 (m-40) cc_final: 0.8080 (m110) REVERT: A 224 GLU cc_start: 0.8289 (pt0) cc_final: 0.8020 (pt0) REVERT: B 41 ASN cc_start: 0.8535 (p0) cc_final: 0.8157 (p0) REVERT: B 60 THR cc_start: 0.9156 (p) cc_final: 0.8715 (t) REVERT: B 75 TYR cc_start: 0.8803 (p90) cc_final: 0.8551 (p90) REVERT: B 178 ARG cc_start: 0.8038 (mmm-85) cc_final: 0.7552 (mpt180) REVERT: B 224 TYR cc_start: 0.8332 (p90) cc_final: 0.8110 (p90) REVERT: C 199 LYS cc_start: 0.9234 (mtpp) cc_final: 0.8996 (mtmt) REVERT: C 206 LEU cc_start: 0.8755 (pt) cc_final: 0.8536 (tp) REVERT: C 208 TYR cc_start: 0.8173 (p90) cc_final: 0.7952 (p90) REVERT: C 212 GLU cc_start: 0.8022 (pm20) cc_final: 0.7560 (pm20) REVERT: D 86 ILE cc_start: 0.8056 (pt) cc_final: 0.7817 (pt) REVERT: E 53 ARG cc_start: 0.6941 (ttm-80) cc_final: 0.5905 (ttt-90) REVERT: E 166 ARG cc_start: 0.8265 (ttt-90) cc_final: 0.8031 (ttt-90) REVERT: E 167 TYR cc_start: 0.8223 (m-80) cc_final: 0.7828 (m-80) REVERT: E 168 ASN cc_start: 0.8376 (m110) cc_final: 0.7908 (m-40) REVERT: E 208 MET cc_start: 0.7735 (ptm) cc_final: 0.7358 (ptm) REVERT: E 216 ASN cc_start: 0.8381 (p0) cc_final: 0.7936 (p0) REVERT: F 27 GLU cc_start: 0.7251 (tm-30) cc_final: 0.7037 (tm-30) REVERT: F 60 GLN cc_start: 0.8348 (pt0) cc_final: 0.8054 (pt0) REVERT: F 61 LYS cc_start: 0.8371 (mppt) cc_final: 0.8084 (mmtm) REVERT: F 111 LEU cc_start: 0.7996 (mt) cc_final: 0.7790 (mt) REVERT: G 235 LEU cc_start: 0.7220 (tp) cc_final: 0.6895 (tp) REVERT: H 51 GLN cc_start: 0.8109 (pp30) cc_final: 0.7804 (pp30) REVERT: H 105 ILE cc_start: 0.8987 (mt) cc_final: 0.8734 (tt) REVERT: H 166 THR cc_start: 0.6440 (p) cc_final: 0.6199 (t) REVERT: H 218 ILE cc_start: 0.8860 (pt) cc_final: 0.8404 (mt) REVERT: H 330 GLN cc_start: 0.8767 (mp10) cc_final: 0.8405 (mp10) REVERT: H 348 ASN cc_start: 0.7794 (t0) cc_final: 0.7574 (t0) REVERT: H 359 ASN cc_start: 0.8980 (m-40) cc_final: 0.8572 (m110) REVERT: H 425 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7584 (mt-10) REVERT: H 442 ASP cc_start: 0.8766 (p0) cc_final: 0.8211 (p0) REVERT: I 64 ARG cc_start: 0.7299 (ptm-80) cc_final: 0.6702 (ttt180) REVERT: I 120 VAL cc_start: 0.9292 (t) cc_final: 0.8942 (m) REVERT: I 167 MET cc_start: 0.7767 (pmm) cc_final: 0.7286 (ptp) REVERT: I 293 ASP cc_start: 0.6329 (m-30) cc_final: 0.6121 (m-30) REVERT: J 239 GLU cc_start: 0.7425 (pt0) cc_final: 0.7213 (pt0) REVERT: K 149 ILE cc_start: 0.9175 (tp) cc_final: 0.8871 (tp) REVERT: L 159 LEU cc_start: 0.7397 (pt) cc_final: 0.7118 (pp) REVERT: L 272 GLU cc_start: 0.7507 (pp20) cc_final: 0.7122 (pp20) REVERT: L 277 ILE cc_start: 0.9095 (mt) cc_final: 0.8592 (tt) REVERT: L 306 MET cc_start: 0.7043 (tmm) cc_final: 0.6495 (tmm) REVERT: M 77 TYR cc_start: 0.8455 (p90) cc_final: 0.8226 (p90) REVERT: M 187 ASP cc_start: 0.7648 (p0) cc_final: 0.7393 (p0) REVERT: M 401 ILE cc_start: 0.9099 (tt) cc_final: 0.8868 (tp) REVERT: r 126 GLN cc_start: 0.8842 (tp40) cc_final: 0.8548 (tp40) outliers start: 6 outliers final: 0 residues processed: 960 average time/residue: 0.5547 time to fit residues: 871.6983 Evaluate side-chains 681 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 681 time to evaluate : 4.933 ------------------------------------------------------------------------------- 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: 0.8980 chunk 161 optimal weight: 4.9990 chunk 433 optimal weight: 9.9990 chunk 354 optimal weight: 5.9990 chunk 143 optimal weight: 20.0000 chunk 522 optimal weight: 9.9990 chunk 564 optimal weight: 20.0000 chunk 465 optimal weight: 7.9990 chunk 517 optimal weight: 10.0000 chunk 178 optimal weight: 0.9980 chunk 418 optimal weight: 8.9990 overall best weight: 4.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 65 GLN 4 146 HIS ** 6 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 GLN ** D 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 152 ASN F 166 GLN G 118 GLN G 237 GLN H 281 GLN H 356 ASN ** I 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 123 HIS 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 72 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 45011 Z= 0.451 Angle : 0.791 10.728 60998 Z= 0.408 Chirality : 0.051 0.248 7049 Planarity : 0.005 0.055 7868 Dihedral : 8.728 121.574 6446 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 0.07 % Allowed : 6.03 % Favored : 93.90 % 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: -4.01 (0.10), residues: 5766 helix: -2.33 (0.10), residues: 2129 sheet: -2.60 (0.14), residues: 1041 loop : -2.88 (0.11), residues: 2596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP G 218 HIS 0.013 0.002 HIS G 204 PHE 0.038 0.003 PHE E 138 TYR 0.034 0.002 TYR A 133 ARG 0.008 0.001 ARG C 129 *********************** 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 832 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 829 time to evaluate : 4.557 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 97 ILE cc_start: 0.9055 (pt) cc_final: 0.8799 (mt) REVERT: 1 160 SER cc_start: 0.8412 (m) cc_final: 0.8181 (p) REVERT: 2 30 ASN cc_start: 0.7982 (t0) cc_final: 0.7703 (t0) REVERT: 2 69 TYR cc_start: 0.9119 (t80) cc_final: 0.8631 (t80) REVERT: 2 71 SER cc_start: 0.8641 (m) cc_final: 0.8391 (p) REVERT: 2 112 SER cc_start: 0.8303 (t) cc_final: 0.7892 (p) REVERT: 2 120 ASP cc_start: 0.7478 (p0) cc_final: 0.6789 (p0) REVERT: 2 200 GLN cc_start: 0.7033 (mt0) cc_final: 0.6204 (pt0) REVERT: 2 214 LYS cc_start: 0.8110 (ptmt) cc_final: 0.7734 (mttt) REVERT: 3 61 THR cc_start: 0.9090 (m) cc_final: 0.8819 (m) REVERT: 3 125 ASP cc_start: 0.8004 (p0) cc_final: 0.7753 (p0) REVERT: 4 30 ASP cc_start: 0.8472 (p0) cc_final: 0.8226 (p0) REVERT: 4 52 ASP cc_start: 0.7663 (m-30) cc_final: 0.7125 (t0) REVERT: 4 99 GLN cc_start: 0.7349 (tm-30) cc_final: 0.6869 (tm-30) REVERT: 4 103 LEU cc_start: 0.9142 (mm) cc_final: 0.8834 (mp) REVERT: 4 120 ASP cc_start: 0.7677 (p0) cc_final: 0.7384 (p0) REVERT: 4 167 GLU cc_start: 0.8656 (pm20) cc_final: 0.8323 (pm20) REVERT: 5 24 ASN cc_start: 0.8875 (t0) cc_final: 0.8526 (t0) REVERT: 5 63 CYS cc_start: 0.8872 (m) cc_final: 0.8609 (m) REVERT: 5 197 PHE cc_start: 0.7881 (t80) cc_final: 0.7447 (t80) REVERT: 6 81 ASP cc_start: 0.7296 (t0) cc_final: 0.6860 (t70) REVERT: 6 159 GLN cc_start: 0.7017 (pt0) cc_final: 0.5791 (tp40) REVERT: A 39 ASN cc_start: 0.8313 (m-40) cc_final: 0.7681 (t0) REVERT: A 96 ARG cc_start: 0.7758 (tpt90) cc_final: 0.7487 (tpt170) REVERT: A 183 GLU cc_start: 0.8053 (tm-30) cc_final: 0.7741 (tm-30) REVERT: B 60 THR cc_start: 0.9217 (p) cc_final: 0.8813 (t) REVERT: B 75 TYR cc_start: 0.8740 (p90) cc_final: 0.8297 (p90) REVERT: B 178 ARG cc_start: 0.8303 (mmm-85) cc_final: 0.7672 (mmp-170) REVERT: C 122 TYR cc_start: 0.8264 (m-10) cc_final: 0.8040 (m-10) REVERT: C 206 LEU cc_start: 0.8909 (pt) cc_final: 0.8641 (tp) REVERT: D 47 GLU cc_start: 0.8408 (pp20) cc_final: 0.7749 (pp20) REVERT: D 148 TYR cc_start: 0.9230 (m-80) cc_final: 0.8989 (m-10) REVERT: E 140 VAL cc_start: 0.8274 (t) cc_final: 0.7819 (t) REVERT: F 60 GLN cc_start: 0.8408 (pt0) cc_final: 0.8137 (pt0) REVERT: F 122 SER cc_start: 0.9106 (m) cc_final: 0.8636 (p) REVERT: F 195 GLU cc_start: 0.8604 (tm-30) cc_final: 0.8402 (tm-30) REVERT: G 26 TYR cc_start: 0.8424 (m-80) cc_final: 0.8211 (m-80) REVERT: H 51 GLN cc_start: 0.8142 (pp30) cc_final: 0.7894 (pp30) REVERT: H 98 GLN cc_start: 0.8441 (tt0) cc_final: 0.8184 (tt0) REVERT: H 105 ILE cc_start: 0.9205 (mt) cc_final: 0.8858 (tt) REVERT: H 218 ILE cc_start: 0.8876 (pt) cc_final: 0.8457 (mt) REVERT: H 348 ASN cc_start: 0.8090 (t0) cc_final: 0.7801 (t0) REVERT: H 359 ASN cc_start: 0.9121 (m-40) cc_final: 0.8607 (m110) REVERT: I 64 ARG cc_start: 0.7470 (ptm-80) cc_final: 0.6933 (ttt180) REVERT: I 68 HIS cc_start: 0.8021 (m-70) cc_final: 0.7671 (m-70) REVERT: I 120 VAL cc_start: 0.9293 (t) cc_final: 0.9024 (m) REVERT: I 121 THR cc_start: 0.7984 (p) cc_final: 0.7688 (t) REVERT: I 167 MET cc_start: 0.7997 (pmm) cc_final: 0.7628 (ptp) REVERT: I 183 ASP cc_start: 0.8123 (m-30) cc_final: 0.7637 (t0) REVERT: I 312 GLN cc_start: 0.8368 (mm-40) cc_final: 0.8145 (mm-40) REVERT: J 28 GLN cc_start: 0.8817 (tm-30) cc_final: 0.8421 (tm-30) REVERT: J 86 VAL cc_start: 0.8900 (t) cc_final: 0.8648 (m) REVERT: J 94 TYR cc_start: 0.9204 (m-80) cc_final: 0.8973 (m-10) REVERT: J 270 ARG cc_start: 0.6730 (mmt90) cc_final: 0.6221 (mtt180) REVERT: J 345 LYS cc_start: 0.8214 (mttt) cc_final: 0.7835 (tppt) REVERT: K 149 ILE cc_start: 0.9177 (tp) cc_final: 0.8728 (tt) REVERT: L 82 ARG cc_start: 0.7930 (ptt180) cc_final: 0.7589 (mtm180) REVERT: L 159 LEU cc_start: 0.7747 (pt) cc_final: 0.7447 (pp) REVERT: L 195 GLU cc_start: 0.7796 (tm-30) cc_final: 0.7557 (tm-30) REVERT: L 272 GLU cc_start: 0.7479 (pp20) cc_final: 0.7091 (tp30) REVERT: L 306 MET cc_start: 0.7442 (tmm) cc_final: 0.7221 (tmm) REVERT: L 307 GLU cc_start: 0.7684 (tp30) cc_final: 0.7439 (tp30) REVERT: M 265 ASP cc_start: 0.8128 (m-30) cc_final: 0.7682 (m-30) REVERT: M 292 ASP cc_start: 0.7770 (p0) cc_final: 0.7341 (p0) REVERT: r 130 GLU cc_start: 0.8398 (tp30) cc_final: 0.8180 (tp30) outliers start: 3 outliers final: 2 residues processed: 832 average time/residue: 0.5471 time to fit residues: 753.3002 Evaluate side-chains 670 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 668 time to evaluate : 4.991 ------------------------------------------------------------------------------- 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: 1.9990 chunk 57 optimal weight: 7.9990 chunk 249 optimal weight: 0.9980 chunk 350 optimal weight: 3.9990 chunk 524 optimal weight: 0.5980 chunk 554 optimal weight: 4.9990 chunk 273 optimal weight: 3.9990 chunk 496 optimal weight: 20.0000 chunk 149 optimal weight: 7.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 8 ASN ** 6 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 159 GLN 7 74 ASN ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 GLN C 103 ASN D 178 ASN G 21 ASN H 54 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 311 GLN r 237 ASN r 291 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 45011 Z= 0.267 Angle : 0.666 9.962 60998 Z= 0.341 Chirality : 0.047 0.244 7049 Planarity : 0.004 0.054 7868 Dihedral : 8.228 116.577 6446 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 0.04 % Allowed : 4.32 % Favored : 95.63 % 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: -3.41 (0.10), residues: 5766 helix: -1.84 (0.10), residues: 2104 sheet: -2.16 (0.15), residues: 1035 loop : -2.59 (0.12), residues: 2627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 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 M 180 ARG 0.010 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 836 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 834 time to evaluate : 5.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 146 MET cc_start: 0.8710 (ptt) cc_final: 0.8499 (ptp) REVERT: 1 160 SER cc_start: 0.8458 (m) cc_final: 0.8209 (p) REVERT: 2 35 HIS cc_start: 0.7641 (m-70) cc_final: 0.7319 (m-70) REVERT: 2 69 TYR cc_start: 0.9086 (t80) cc_final: 0.8657 (t80) REVERT: 2 71 SER cc_start: 0.8687 (m) cc_final: 0.8452 (p) REVERT: 2 112 SER cc_start: 0.8265 (t) cc_final: 0.7885 (p) REVERT: 2 120 ASP cc_start: 0.7358 (p0) cc_final: 0.6695 (p0) REVERT: 2 200 GLN cc_start: 0.7061 (mt0) cc_final: 0.6199 (pt0) REVERT: 2 214 LYS cc_start: 0.8006 (ptmt) cc_final: 0.7674 (mttt) REVERT: 3 61 THR cc_start: 0.9065 (m) cc_final: 0.8845 (m) REVERT: 3 125 ASP cc_start: 0.7933 (p0) cc_final: 0.7715 (p0) REVERT: 4 3 ILE cc_start: 0.9104 (pt) cc_final: 0.8638 (mp) REVERT: 4 30 ASP cc_start: 0.8407 (p0) cc_final: 0.8192 (p0) REVERT: 4 52 ASP cc_start: 0.7668 (m-30) cc_final: 0.7157 (t0) REVERT: 4 99 GLN cc_start: 0.7381 (tm-30) cc_final: 0.6906 (tm-30) REVERT: 4 103 LEU cc_start: 0.9165 (mm) cc_final: 0.8885 (mp) REVERT: 4 120 ASP cc_start: 0.7756 (p0) cc_final: 0.7500 (p0) REVERT: 4 124 THR cc_start: 0.8707 (p) cc_final: 0.8106 (p) REVERT: 4 169 GLU cc_start: 0.7869 (pt0) cc_final: 0.7434 (pt0) REVERT: 5 19 ARG cc_start: 0.8665 (tpp-160) cc_final: 0.8413 (tpp-160) REVERT: 5 24 ASN cc_start: 0.8988 (t0) cc_final: 0.8645 (t0) REVERT: 5 145 LYS cc_start: 0.8641 (pttp) cc_final: 0.7911 (pttp) REVERT: 5 197 PHE cc_start: 0.7908 (t80) cc_final: 0.7494 (t80) REVERT: 6 81 ASP cc_start: 0.7323 (t0) cc_final: 0.6874 (t70) REVERT: 7 136 THR cc_start: 0.8866 (p) cc_final: 0.8553 (t) REVERT: A 39 ASN cc_start: 0.8304 (m-40) cc_final: 0.7654 (t0) REVERT: A 49 ASP cc_start: 0.7297 (p0) cc_final: 0.6896 (p0) REVERT: A 50 CYS cc_start: 0.7232 (m) cc_final: 0.6915 (m) REVERT: A 96 ARG cc_start: 0.7696 (tpt90) cc_final: 0.7371 (tpt170) REVERT: A 183 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7721 (tm-30) REVERT: A 243 GLU cc_start: 0.7650 (pt0) cc_final: 0.7439 (pt0) REVERT: B 60 THR cc_start: 0.9209 (p) cc_final: 0.8809 (t) REVERT: B 75 TYR cc_start: 0.8851 (p90) cc_final: 0.8503 (p90) REVERT: B 118 MET cc_start: 0.8675 (ttm) cc_final: 0.8428 (ttm) REVERT: B 176 GLU cc_start: 0.7991 (pm20) cc_final: 0.7653 (pm20) REVERT: B 178 ARG cc_start: 0.8231 (mmm-85) cc_final: 0.7607 (mmp-170) REVERT: C 72 LYS cc_start: 0.8594 (mmmt) cc_final: 0.8257 (mmtp) REVERT: C 122 TYR cc_start: 0.8215 (m-10) cc_final: 0.7913 (m-10) REVERT: C 212 GLU cc_start: 0.8474 (pt0) cc_final: 0.8042 (pt0) REVERT: C 234 GLU cc_start: 0.7709 (pt0) cc_final: 0.7376 (pt0) REVERT: D 43 VAL cc_start: 0.9027 (m) cc_final: 0.8785 (t) REVERT: D 47 GLU cc_start: 0.8425 (pp20) cc_final: 0.8063 (pp20) REVERT: D 148 TYR cc_start: 0.9200 (m-80) cc_final: 0.8919 (m-10) REVERT: F 60 GLN cc_start: 0.8303 (pt0) cc_final: 0.8080 (pt0) REVERT: F 122 SER cc_start: 0.9006 (m) cc_final: 0.8645 (t) REVERT: G 26 TYR cc_start: 0.8440 (m-80) cc_final: 0.8197 (m-80) REVERT: G 60 VAL cc_start: 0.8748 (t) cc_final: 0.8433 (p) REVERT: G 202 LEU cc_start: 0.8996 (mt) cc_final: 0.8748 (mt) REVERT: H 51 GLN cc_start: 0.8212 (pp30) cc_final: 0.7951 (pp30) REVERT: H 98 GLN cc_start: 0.8345 (tt0) cc_final: 0.8078 (tt0) REVERT: H 105 ILE cc_start: 0.9187 (mt) cc_final: 0.8822 (tt) REVERT: H 166 THR cc_start: 0.6929 (p) cc_final: 0.6611 (t) REVERT: H 348 ASN cc_start: 0.8119 (t0) cc_final: 0.7800 (t0) REVERT: H 359 ASN cc_start: 0.8957 (m-40) cc_final: 0.8679 (m110) REVERT: I 64 ARG cc_start: 0.7348 (ptm-80) cc_final: 0.6847 (ttt180) REVERT: I 68 HIS cc_start: 0.7960 (m-70) cc_final: 0.7599 (m-70) REVERT: I 120 VAL cc_start: 0.9293 (t) cc_final: 0.9010 (m) REVERT: I 121 THR cc_start: 0.8051 (p) cc_final: 0.7678 (t) REVERT: I 167 MET cc_start: 0.7770 (pmm) cc_final: 0.7540 (ptp) REVERT: I 183 ASP cc_start: 0.8020 (m-30) cc_final: 0.7390 (t0) REVERT: I 312 GLN cc_start: 0.8425 (mm-40) cc_final: 0.8069 (mm-40) REVERT: J 86 VAL cc_start: 0.8781 (t) cc_final: 0.8534 (m) REVERT: J 94 TYR cc_start: 0.9138 (m-80) cc_final: 0.8931 (m-10) REVERT: J 239 GLU cc_start: 0.7443 (pt0) cc_final: 0.7192 (tt0) REVERT: J 247 MET cc_start: 0.8410 (mtp) cc_final: 0.8206 (mtp) REVERT: J 256 THR cc_start: 0.6474 (m) cc_final: 0.6065 (p) REVERT: J 270 ARG cc_start: 0.6645 (mmt90) cc_final: 0.6114 (mmt180) REVERT: J 345 LYS cc_start: 0.8250 (mttt) cc_final: 0.7875 (tppt) REVERT: K 149 ILE cc_start: 0.9140 (tp) cc_final: 0.8743 (tt) REVERT: K 221 MET cc_start: 0.7987 (ppp) cc_final: 0.7764 (ppp) REVERT: L 82 ARG cc_start: 0.7900 (ptt180) cc_final: 0.7533 (mtm180) REVERT: L 156 MET cc_start: 0.7776 (mtp) cc_final: 0.7559 (mtp) REVERT: L 159 LEU cc_start: 0.7770 (pt) cc_final: 0.7503 (pp) REVERT: L 195 GLU cc_start: 0.7805 (tm-30) cc_final: 0.7569 (tm-30) REVERT: L 221 TYR cc_start: 0.7935 (p90) cc_final: 0.6083 (p90) REVERT: L 272 GLU cc_start: 0.7479 (pp20) cc_final: 0.7206 (tp30) REVERT: L 306 MET cc_start: 0.7415 (tmm) cc_final: 0.7166 (tmm) REVERT: L 307 GLU cc_start: 0.7596 (tp30) cc_final: 0.7275 (tp30) REVERT: M 265 ASP cc_start: 0.8154 (m-30) cc_final: 0.7591 (m-30) REVERT: M 292 ASP cc_start: 0.7600 (p0) cc_final: 0.7146 (p0) REVERT: r 251 TYR cc_start: 0.8920 (t80) cc_final: 0.8681 (t80) outliers start: 2 outliers final: 1 residues processed: 836 average time/residue: 0.5430 time to fit residues: 750.0179 Evaluate side-chains 661 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 660 time to evaluate : 5.946 ------------------------------------------------------------------------------- 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: 20.0000 chunk 314 optimal weight: 0.3980 chunk 8 optimal weight: 5.9990 chunk 413 optimal weight: 5.9990 chunk 228 optimal weight: 0.0570 chunk 473 optimal weight: 0.9980 chunk 383 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 283 optimal weight: 6.9990 chunk 498 optimal weight: 8.9990 chunk 140 optimal weight: 0.5980 overall best weight: 1.2100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 74 ASN 7 120 GLN ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 21 ASN G 182 HIS H 281 GLN H 356 ASN I 238 ASN I 303 GLN ** I 410 GLN ** 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: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.4305 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= 0.188 Angle : 0.614 8.523 60998 Z= 0.313 Chirality : 0.045 0.173 7049 Planarity : 0.004 0.051 7868 Dihedral : 7.732 110.761 6446 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 0.04 % Allowed : 3.05 % Favored : 96.91 % 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: -2.95 (0.10), residues: 5766 helix: -1.41 (0.11), residues: 2111 sheet: -1.84 (0.15), residues: 1033 loop : -2.40 (0.12), residues: 2622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP G 218 HIS 0.010 0.001 HIS G 204 PHE 0.025 0.002 PHE 3 50 TYR 0.025 0.001 TYR A 133 ARG 0.009 0.000 ARG r 135 *********************** 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 857 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 855 time to evaluate : 5.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 160 SER cc_start: 0.8491 (m) cc_final: 0.8159 (p) REVERT: 2 26 VAL cc_start: 0.8767 (p) cc_final: 0.8565 (t) REVERT: 2 35 HIS cc_start: 0.7697 (m-70) cc_final: 0.7441 (m-70) REVERT: 2 69 TYR cc_start: 0.9014 (t80) cc_final: 0.8694 (t80) REVERT: 2 71 SER cc_start: 0.8694 (m) cc_final: 0.8421 (p) REVERT: 2 112 SER cc_start: 0.8282 (t) cc_final: 0.7913 (p) REVERT: 2 120 ASP cc_start: 0.7317 (p0) cc_final: 0.6666 (p0) REVERT: 2 200 GLN cc_start: 0.6990 (mt0) cc_final: 0.6162 (pt0) REVERT: 2 214 LYS cc_start: 0.8024 (ptmt) cc_final: 0.7670 (mttt) REVERT: 3 61 THR cc_start: 0.9076 (m) cc_final: 0.8834 (m) REVERT: 4 30 ASP cc_start: 0.8330 (p0) cc_final: 0.8125 (p0) REVERT: 4 52 ASP cc_start: 0.7488 (m-30) cc_final: 0.7057 (t0) REVERT: 4 60 ILE cc_start: 0.9223 (pt) cc_final: 0.8487 (mm) REVERT: 4 99 GLN cc_start: 0.7305 (tm-30) cc_final: 0.6877 (tm-30) REVERT: 4 103 LEU cc_start: 0.9129 (mm) cc_final: 0.8912 (mp) REVERT: 4 120 ASP cc_start: 0.7810 (p0) cc_final: 0.7555 (p0) REVERT: 5 24 ASN cc_start: 0.9037 (t0) cc_final: 0.8683 (t0) REVERT: 5 73 ARG cc_start: 0.7720 (ttp-170) cc_final: 0.7450 (ttp-170) REVERT: 5 197 PHE cc_start: 0.8068 (t80) cc_final: 0.7735 (t80) REVERT: 6 81 ASP cc_start: 0.7369 (t0) cc_final: 0.6953 (t70) REVERT: 6 174 TYR cc_start: 0.7412 (m-80) cc_final: 0.7037 (m-80) REVERT: 7 136 THR cc_start: 0.8863 (p) cc_final: 0.8592 (t) REVERT: A 39 ASN cc_start: 0.8317 (m-40) cc_final: 0.7954 (t0) REVERT: A 49 ASP cc_start: 0.7284 (p0) cc_final: 0.6928 (p0) REVERT: A 50 CYS cc_start: 0.7037 (m) cc_final: 0.6797 (m) REVERT: A 183 GLU cc_start: 0.8025 (tm-30) cc_final: 0.7555 (tm-30) REVERT: A 243 GLU cc_start: 0.7687 (pt0) cc_final: 0.7464 (pt0) REVERT: B 60 THR cc_start: 0.9235 (p) cc_final: 0.8784 (t) REVERT: B 75 TYR cc_start: 0.8827 (p90) cc_final: 0.8403 (p90) REVERT: B 178 ARG cc_start: 0.8149 (mmm-85) cc_final: 0.7522 (mmp-170) REVERT: B 224 TYR cc_start: 0.8333 (p90) cc_final: 0.8091 (p90) REVERT: C 7 ASP cc_start: 0.7929 (t70) cc_final: 0.7596 (t0) REVERT: C 122 TYR cc_start: 0.8133 (m-10) cc_final: 0.7833 (m-10) REVERT: D 27 VAL cc_start: 0.8933 (t) cc_final: 0.8608 (p) REVERT: D 47 GLU cc_start: 0.8309 (pp20) cc_final: 0.7991 (pp20) REVERT: D 148 TYR cc_start: 0.9151 (m-80) cc_final: 0.8840 (m-10) REVERT: D 203 VAL cc_start: 0.7772 (t) cc_final: 0.7516 (t) REVERT: E 53 ARG cc_start: 0.7685 (ttm110) cc_final: 0.6039 (ttt-90) REVERT: E 182 GLU cc_start: 0.7288 (tm-30) cc_final: 0.7072 (tm-30) REVERT: F 122 SER cc_start: 0.8989 (m) cc_final: 0.8731 (t) REVERT: G 9 ASP cc_start: 0.7695 (m-30) cc_final: 0.7412 (m-30) REVERT: G 26 TYR cc_start: 0.8421 (m-80) cc_final: 0.7898 (m-80) REVERT: G 60 VAL cc_start: 0.8693 (t) cc_final: 0.8440 (p) REVERT: H 51 GLN cc_start: 0.8176 (pp30) cc_final: 0.7900 (pp30) REVERT: H 98 GLN cc_start: 0.8226 (tt0) cc_final: 0.7947 (tt0) REVERT: H 105 ILE cc_start: 0.9229 (mt) cc_final: 0.8816 (tt) REVERT: H 166 THR cc_start: 0.6863 (p) cc_final: 0.6533 (t) REVERT: H 218 ILE cc_start: 0.8809 (pt) cc_final: 0.8446 (mt) REVERT: H 348 ASN cc_start: 0.8198 (t0) cc_final: 0.7761 (t0) REVERT: H 359 ASN cc_start: 0.8936 (m-40) cc_final: 0.8514 (m110) REVERT: I 64 ARG cc_start: 0.7328 (ptm-80) cc_final: 0.6930 (ttt180) REVERT: I 68 HIS cc_start: 0.7963 (m-70) cc_final: 0.7616 (m-70) REVERT: I 120 VAL cc_start: 0.9265 (t) cc_final: 0.8971 (m) REVERT: I 121 THR cc_start: 0.7902 (p) cc_final: 0.7583 (t) REVERT: I 167 MET cc_start: 0.7855 (pmm) cc_final: 0.7562 (ptp) REVERT: I 312 GLN cc_start: 0.8552 (mm-40) cc_final: 0.8141 (mm-40) REVERT: J 247 MET cc_start: 0.8299 (mtp) cc_final: 0.8066 (mtp) REVERT: J 270 ARG cc_start: 0.6623 (mmt90) cc_final: 0.6125 (mmt180) REVERT: J 362 CYS cc_start: 0.8861 (m) cc_final: 0.8285 (t) REVERT: K 149 ILE cc_start: 0.9118 (tp) cc_final: 0.8816 (tt) REVERT: K 221 MET cc_start: 0.7984 (ppp) cc_final: 0.7716 (ppp) REVERT: K 260 LEU cc_start: 0.9267 (pp) cc_final: 0.8832 (tt) REVERT: L 82 ARG cc_start: 0.7850 (ptt180) cc_final: 0.7536 (mtm180) REVERT: L 156 MET cc_start: 0.7804 (mtp) cc_final: 0.7543 (mtp) REVERT: L 159 LEU cc_start: 0.7585 (pt) cc_final: 0.7362 (pp) REVERT: L 306 MET cc_start: 0.7425 (tmm) cc_final: 0.6961 (tmm) REVERT: L 307 GLU cc_start: 0.7731 (tp30) cc_final: 0.7233 (tp30) REVERT: M 265 ASP cc_start: 0.8137 (m-30) cc_final: 0.7583 (m-30) REVERT: M 292 ASP cc_start: 0.7623 (p0) cc_final: 0.6942 (p0) REVERT: n 221 PHE cc_start: 0.8862 (p90) cc_final: 0.8662 (p90) REVERT: r 130 GLU cc_start: 0.8328 (tp30) cc_final: 0.8109 (tp30) outliers start: 2 outliers final: 1 residues processed: 857 average time/residue: 0.5474 time to fit residues: 778.5183 Evaluate side-chains 669 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 668 time to evaluate : 5.294 ------------------------------------------------------------------------------- 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: 8.9990 chunk 499 optimal weight: 0.8980 chunk 109 optimal weight: 9.9990 chunk 325 optimal weight: 0.9990 chunk 136 optimal weight: 4.9990 chunk 555 optimal weight: 7.9990 chunk 461 optimal weight: 10.0000 chunk 257 optimal weight: 8.9990 chunk 46 optimal weight: 5.9990 chunk 183 optimal weight: 10.0000 chunk 291 optimal weight: 8.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 133 GLN ** 6 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 74 ASN ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 HIS G 204 HIS H 89 GLN I 192 GLN ** I 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 239 GLN ** 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 128 ASN J 277 ASN ** K 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 74 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.4566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 45011 Z= 0.429 Angle : 0.768 9.606 60998 Z= 0.394 Chirality : 0.051 0.206 7049 Planarity : 0.005 0.054 7868 Dihedral : 8.287 114.909 6446 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % 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: -3.01 (0.10), residues: 5766 helix: -1.52 (0.11), residues: 2116 sheet: -1.84 (0.15), residues: 1085 loop : -2.40 (0.12), residues: 2565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP G 218 HIS 0.014 0.002 HIS 1 120 PHE 0.062 0.003 PHE E 138 TYR 0.026 0.002 TYR B 224 ARG 0.008 0.001 ARG C 129 *********************** 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 786 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 786 time to evaluate : 4.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 145 ASN cc_start: 0.8564 (m110) cc_final: 0.8352 (m-40) REVERT: 1 160 SER cc_start: 0.8544 (m) cc_final: 0.8269 (p) REVERT: 2 35 HIS cc_start: 0.7826 (m-70) cc_final: 0.7533 (m-70) REVERT: 2 112 SER cc_start: 0.8327 (t) cc_final: 0.7939 (p) REVERT: 2 120 ASP cc_start: 0.7383 (p0) cc_final: 0.6765 (p0) REVERT: 2 200 GLN cc_start: 0.7100 (mt0) cc_final: 0.6255 (pt0) REVERT: 2 214 LYS cc_start: 0.8126 (ptmt) cc_final: 0.7752 (mttt) REVERT: 3 59 ASP cc_start: 0.8963 (m-30) cc_final: 0.8738 (m-30) REVERT: 3 79 GLU cc_start: 0.7842 (mp0) cc_final: 0.7358 (mm-30) REVERT: 4 3 ILE cc_start: 0.9243 (pt) cc_final: 0.8761 (mp) REVERT: 4 30 ASP cc_start: 0.8477 (p0) cc_final: 0.8254 (p0) REVERT: 4 52 ASP cc_start: 0.7521 (m-30) cc_final: 0.6994 (t0) REVERT: 4 60 ILE cc_start: 0.9304 (pt) cc_final: 0.9000 (mt) REVERT: 4 99 GLN cc_start: 0.7298 (tm-30) cc_final: 0.6744 (tm-30) REVERT: 4 120 ASP cc_start: 0.7713 (p0) cc_final: 0.7306 (p0) REVERT: 4 124 THR cc_start: 0.8575 (p) cc_final: 0.8004 (p) REVERT: 5 24 ASN cc_start: 0.9053 (t0) cc_final: 0.8781 (t0) REVERT: 5 25 TRP cc_start: 0.8966 (t60) cc_final: 0.8740 (t60) REVERT: 5 73 ARG cc_start: 0.7913 (ttp-170) cc_final: 0.7587 (ttp-170) REVERT: 5 197 PHE cc_start: 0.7907 (t80) cc_final: 0.7622 (t80) REVERT: 6 81 ASP cc_start: 0.7349 (t0) cc_final: 0.6930 (t70) REVERT: 6 174 TYR cc_start: 0.7283 (m-80) cc_final: 0.6990 (m-80) REVERT: 6 200 ASP cc_start: 0.6524 (t0) cc_final: 0.6236 (t0) REVERT: 7 35 ARG cc_start: 0.7675 (ttm-80) cc_final: 0.7209 (ttm-80) REVERT: 7 120 GLN cc_start: 0.8286 (mm110) cc_final: 0.7844 (mm-40) REVERT: 7 136 THR cc_start: 0.8917 (p) cc_final: 0.8627 (t) REVERT: A 39 ASN cc_start: 0.8249 (m-40) cc_final: 0.7843 (t0) REVERT: A 96 ARG cc_start: 0.7728 (tpt90) cc_final: 0.7302 (tpt170) REVERT: A 243 GLU cc_start: 0.7671 (pt0) cc_final: 0.7232 (pt0) REVERT: B 60 THR cc_start: 0.9271 (p) cc_final: 0.8820 (t) REVERT: B 75 TYR cc_start: 0.8752 (p90) cc_final: 0.8307 (p90) REVERT: B 176 GLU cc_start: 0.8310 (pm20) cc_final: 0.8055 (pm20) REVERT: B 178 ARG cc_start: 0.8389 (mmm-85) cc_final: 0.7721 (mmp-170) REVERT: B 210 GLU cc_start: 0.7714 (tp30) cc_final: 0.7395 (tp30) REVERT: C 7 ASP cc_start: 0.8160 (t70) cc_final: 0.7947 (t0) REVERT: D 47 GLU cc_start: 0.8350 (pp20) cc_final: 0.7877 (pp20) REVERT: D 148 TYR cc_start: 0.9204 (m-80) cc_final: 0.8914 (m-10) REVERT: E 132 ARG cc_start: 0.7220 (ttm170) cc_final: 0.6770 (ttp-170) REVERT: E 138 PHE cc_start: 0.7971 (p90) cc_final: 0.7474 (p90) REVERT: E 182 GLU cc_start: 0.7622 (tm-30) cc_final: 0.7267 (tm-30) REVERT: E 203 ILE cc_start: 0.8880 (pt) cc_final: 0.8162 (mt) REVERT: F 122 SER cc_start: 0.8971 (m) cc_final: 0.8760 (t) REVERT: G 60 VAL cc_start: 0.8789 (t) cc_final: 0.8479 (p) REVERT: H 51 GLN cc_start: 0.8250 (pp30) cc_final: 0.8013 (pp30) REVERT: H 98 GLN cc_start: 0.8495 (tt0) cc_final: 0.8137 (tt0) REVERT: H 105 ILE cc_start: 0.9309 (mt) cc_final: 0.8877 (tt) REVERT: H 320 ASP cc_start: 0.8193 (t0) cc_final: 0.7975 (t0) REVERT: H 348 ASN cc_start: 0.8312 (t0) cc_final: 0.8020 (t0) REVERT: I 64 ARG cc_start: 0.7671 (ptm-80) cc_final: 0.7196 (ttt180) REVERT: I 68 HIS cc_start: 0.8023 (m-70) cc_final: 0.7690 (m-70) REVERT: I 120 VAL cc_start: 0.9253 (t) cc_final: 0.8946 (m) REVERT: I 167 MET cc_start: 0.8098 (pmm) cc_final: 0.7741 (ptp) REVERT: I 283 GLU cc_start: 0.7749 (mp0) cc_final: 0.7486 (mp0) REVERT: I 312 GLN cc_start: 0.8608 (mm-40) cc_final: 0.8311 (mm-40) REVERT: J 247 MET cc_start: 0.8440 (mtp) cc_final: 0.8170 (mtp) REVERT: J 270 ARG cc_start: 0.6800 (mmt90) cc_final: 0.6384 (mmt180) REVERT: J 362 CYS cc_start: 0.8921 (m) cc_final: 0.8383 (t) REVERT: K 149 ILE cc_start: 0.9126 (tp) cc_final: 0.8723 (tt) REVERT: K 221 MET cc_start: 0.8127 (ppp) cc_final: 0.7865 (ppp) REVERT: K 260 LEU cc_start: 0.9334 (pp) cc_final: 0.8784 (tt) REVERT: L 82 ARG cc_start: 0.7842 (ptt180) cc_final: 0.7624 (mtm180) REVERT: L 195 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7403 (tm-30) REVERT: L 251 ILE cc_start: 0.8497 (pt) cc_final: 0.8141 (mt) REVERT: L 306 MET cc_start: 0.7626 (tmm) cc_final: 0.7336 (tmm) REVERT: L 307 GLU cc_start: 0.8060 (tp30) cc_final: 0.7707 (tp30) REVERT: M 265 ASP cc_start: 0.8092 (m-30) cc_final: 0.7768 (m-30) REVERT: M 292 ASP cc_start: 0.7777 (p0) cc_final: 0.7140 (p0) REVERT: M 305 MET cc_start: 0.8446 (ttp) cc_final: 0.8211 (ttm) REVERT: r 130 GLU cc_start: 0.8312 (tp30) cc_final: 0.8026 (tp30) outliers start: 0 outliers final: 0 residues processed: 786 average time/residue: 0.5478 time to fit residues: 719.7425 Evaluate side-chains 643 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 643 time to evaluate : 5.674 ------------------------------------------------------------------------------- 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: 7.9990 chunk 62 optimal weight: 2.9990 chunk 316 optimal weight: 2.9990 chunk 405 optimal weight: 5.9990 chunk 314 optimal weight: 0.7980 chunk 467 optimal weight: 1.9990 chunk 310 optimal weight: 1.9990 chunk 553 optimal weight: 0.9980 chunk 346 optimal weight: 0.7980 chunk 337 optimal weight: 0.9980 chunk 255 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 74 ASN ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 ASN ** C 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 182 HIS H 54 ASN H 89 GLN H 281 GLN H 356 ASN I 238 ASN ** I 239 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** K 142 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.4799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 45011 Z= 0.187 Angle : 0.618 8.649 60998 Z= 0.315 Chirality : 0.045 0.219 7049 Planarity : 0.004 0.086 7868 Dihedral : 7.611 108.634 6446 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 0.04 % Allowed : 1.58 % Favored : 98.38 % 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: -2.55 (0.11), residues: 5766 helix: -1.09 (0.11), residues: 2103 sheet: -1.57 (0.15), residues: 1068 loop : -2.18 (0.12), residues: 2595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP G 218 HIS 0.009 0.001 HIS 1 120 PHE 0.021 0.002 PHE M 432 TYR 0.024 0.001 TYR M 180 ARG 0.008 0.000 ARG J 200 *********************** 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 831 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 829 time to evaluate : 4.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 160 SER cc_start: 0.8514 (m) cc_final: 0.8222 (p) REVERT: 2 35 HIS cc_start: 0.7732 (m-70) cc_final: 0.7483 (m-70) REVERT: 2 69 TYR cc_start: 0.9044 (t80) cc_final: 0.8820 (t80) REVERT: 2 112 SER cc_start: 0.8294 (t) cc_final: 0.7900 (p) REVERT: 2 200 GLN cc_start: 0.7082 (mt0) cc_final: 0.6222 (pt0) REVERT: 2 214 LYS cc_start: 0.8067 (ptmt) cc_final: 0.7698 (mttt) REVERT: 3 79 GLU cc_start: 0.7784 (mp0) cc_final: 0.7253 (mm-30) REVERT: 4 30 ASP cc_start: 0.8314 (p0) cc_final: 0.8065 (p0) REVERT: 4 31 SER cc_start: 0.8940 (m) cc_final: 0.8381 (t) REVERT: 4 52 ASP cc_start: 0.7416 (m-30) cc_final: 0.7038 (t0) REVERT: 4 60 ILE cc_start: 0.9125 (pt) cc_final: 0.8898 (mt) REVERT: 4 86 GLN cc_start: 0.8530 (tm-30) cc_final: 0.8017 (tp-100) REVERT: 4 99 GLN cc_start: 0.7241 (tm-30) cc_final: 0.6774 (tm-30) REVERT: 4 120 ASP cc_start: 0.7851 (p0) cc_final: 0.7395 (p0) REVERT: 4 124 THR cc_start: 0.8632 (p) cc_final: 0.8053 (p) REVERT: 4 155 GLU cc_start: 0.8409 (pm20) cc_final: 0.8067 (pm20) REVERT: 5 24 ASN cc_start: 0.9033 (t0) cc_final: 0.8753 (t0) REVERT: 5 25 TRP cc_start: 0.8903 (t60) cc_final: 0.8680 (t60) REVERT: 5 73 ARG cc_start: 0.7823 (ttp-170) cc_final: 0.7511 (ttp-170) REVERT: 5 197 PHE cc_start: 0.7976 (t80) cc_final: 0.7756 (t80) REVERT: 6 81 ASP cc_start: 0.7368 (t0) cc_final: 0.6966 (t70) REVERT: 6 200 ASP cc_start: 0.6471 (t0) cc_final: 0.6218 (t0) REVERT: 7 35 ARG cc_start: 0.7790 (ttm-80) cc_final: 0.7294 (ttm-80) REVERT: 7 120 GLN cc_start: 0.8187 (mm110) cc_final: 0.7804 (mm-40) REVERT: 7 186 TYR cc_start: 0.6375 (t80) cc_final: 0.6035 (t80) REVERT: A 39 ASN cc_start: 0.8285 (m-40) cc_final: 0.7920 (t0) REVERT: A 242 GLU cc_start: 0.6959 (mp0) cc_final: 0.6648 (mp0) REVERT: B 60 THR cc_start: 0.9227 (p) cc_final: 0.8808 (t) REVERT: B 75 TYR cc_start: 0.8773 (p90) cc_final: 0.8317 (p90) REVERT: B 176 GLU cc_start: 0.8004 (pm20) cc_final: 0.7775 (pm20) REVERT: B 178 ARG cc_start: 0.8227 (mmm-85) cc_final: 0.7542 (mmp-170) REVERT: B 210 GLU cc_start: 0.7576 (tp30) cc_final: 0.7366 (tp30) REVERT: C 7 ASP cc_start: 0.8135 (t70) cc_final: 0.7788 (t0) REVERT: C 122 TYR cc_start: 0.8142 (m-10) cc_final: 0.7841 (m-10) REVERT: C 212 GLU cc_start: 0.8335 (pt0) cc_final: 0.7515 (pt0) REVERT: D 47 GLU cc_start: 0.8397 (pp20) cc_final: 0.7879 (pp20) REVERT: D 148 TYR cc_start: 0.9107 (m-80) cc_final: 0.8620 (m-10) REVERT: E 76 CYS cc_start: 0.8765 (t) cc_final: 0.8555 (t) REVERT: E 238 GLU cc_start: 0.7559 (pp20) cc_final: 0.7145 (pp20) REVERT: G 26 TYR cc_start: 0.8437 (m-80) cc_final: 0.8061 (m-80) REVERT: G 60 VAL cc_start: 0.8718 (t) cc_final: 0.8473 (p) REVERT: H 51 GLN cc_start: 0.8183 (pp30) cc_final: 0.7931 (pp30) REVERT: H 98 GLN cc_start: 0.8204 (tt0) cc_final: 0.7928 (tt0) REVERT: H 105 ILE cc_start: 0.9309 (mt) cc_final: 0.8840 (tt) REVERT: H 166 THR cc_start: 0.6885 (p) cc_final: 0.6583 (t) REVERT: H 320 ASP cc_start: 0.8186 (t0) cc_final: 0.7942 (t0) REVERT: H 348 ASN cc_start: 0.8354 (t0) cc_final: 0.7959 (t0) REVERT: I 64 ARG cc_start: 0.7464 (ptm-80) cc_final: 0.7104 (ttt180) REVERT: I 68 HIS cc_start: 0.7916 (m-70) cc_final: 0.7630 (m-70) REVERT: I 120 VAL cc_start: 0.9270 (t) cc_final: 0.8977 (m) REVERT: I 285 ASP cc_start: 0.7981 (p0) cc_final: 0.7391 (p0) REVERT: I 312 GLN cc_start: 0.8596 (mm-40) cc_final: 0.8165 (mm-40) REVERT: I 371 LEU cc_start: 0.8145 (pp) cc_final: 0.7841 (pp) REVERT: J 25 GLN cc_start: 0.7936 (mm110) cc_final: 0.7555 (mm110) REVERT: J 82 LYS cc_start: 0.8606 (mmtp) cc_final: 0.8379 (mmmt) REVERT: J 247 MET cc_start: 0.8336 (mtp) cc_final: 0.8083 (mtp) REVERT: J 270 ARG cc_start: 0.6709 (mmt90) cc_final: 0.6257 (mtt180) REVERT: J 362 CYS cc_start: 0.8912 (m) cc_final: 0.8255 (t) REVERT: K 149 ILE cc_start: 0.9102 (tp) cc_final: 0.8787 (tt) REVERT: K 221 MET cc_start: 0.8004 (ppp) cc_final: 0.7653 (ppp) REVERT: K 260 LEU cc_start: 0.9303 (pp) cc_final: 0.8807 (tt) REVERT: K 319 ASN cc_start: 0.8941 (m-40) cc_final: 0.8173 (t0) REVERT: L 82 ARG cc_start: 0.7915 (ptt180) cc_final: 0.7674 (mtm180) REVERT: L 251 ILE cc_start: 0.8452 (pt) cc_final: 0.8125 (mt) REVERT: L 306 MET cc_start: 0.7554 (tmm) cc_final: 0.7122 (tmm) REVERT: L 307 GLU cc_start: 0.7916 (tp30) cc_final: 0.7442 (tp30) REVERT: M 159 LEU cc_start: 0.9000 (pt) cc_final: 0.8795 (pp) REVERT: M 265 ASP cc_start: 0.8072 (m-30) cc_final: 0.7631 (m-30) REVERT: M 292 ASP cc_start: 0.7748 (p0) cc_final: 0.7027 (p0) REVERT: M 305 MET cc_start: 0.8377 (ttp) cc_final: 0.8171 (ttm) REVERT: M 306 LEU cc_start: 0.9312 (mp) cc_final: 0.9099 (mm) REVERT: r 130 GLU cc_start: 0.8260 (tp30) cc_final: 0.8028 (tp30) outliers start: 2 outliers final: 1 residues processed: 830 average time/residue: 0.5384 time to fit residues: 745.4565 Evaluate side-chains 663 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 662 time to evaluate : 5.571 ------------------------------------------------------------------------------- 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: 5.9990 chunk 330 optimal weight: 0.9980 chunk 166 optimal weight: 10.0000 chunk 108 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 351 optimal weight: 0.1980 chunk 376 optimal weight: 2.9990 chunk 273 optimal weight: 0.4980 chunk 51 optimal weight: 4.9990 chunk 434 optimal weight: 8.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 133 GLN 6 159 GLN 7 74 ASN A 27 GLN ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 241 GLN C 103 ASN D 235 GLN H 54 ASN H 281 GLN H 356 ASN I 192 GLN I 238 ASN I 303 GLN I 312 GLN ** I 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 ASN J 277 ASN K 72 GLN K 142 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.4970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 45011 Z= 0.185 Angle : 0.614 12.051 60998 Z= 0.309 Chirality : 0.045 0.193 7049 Planarity : 0.004 0.070 7868 Dihedral : 7.232 107.780 6446 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 0.02 % Allowed : 1.36 % Favored : 98.62 % 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: -2.35 (0.11), residues: 5766 helix: -0.89 (0.11), residues: 2130 sheet: -1.45 (0.15), residues: 1081 loop : -2.12 (0.12), residues: 2555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP G 218 HIS 0.006 0.001 HIS 1 120 PHE 0.025 0.002 PHE 3 50 TYR 0.036 0.001 TYR B 224 ARG 0.006 0.000 ARG A 14 *********************** 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 808 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 807 time to evaluate : 5.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 160 SER cc_start: 0.8548 (m) cc_final: 0.8300 (p) REVERT: 2 35 HIS cc_start: 0.7755 (m-70) cc_final: 0.7553 (m-70) REVERT: 2 69 TYR cc_start: 0.9037 (t80) cc_final: 0.8812 (t80) REVERT: 2 112 SER cc_start: 0.8415 (t) cc_final: 0.8158 (p) REVERT: 2 120 ASP cc_start: 0.7483 (p0) cc_final: 0.6884 (p0) REVERT: 2 200 GLN cc_start: 0.7075 (mt0) cc_final: 0.6200 (pt0) REVERT: 2 214 LYS cc_start: 0.8136 (ptmt) cc_final: 0.7733 (mttt) REVERT: 3 79 GLU cc_start: 0.7807 (mp0) cc_final: 0.7229 (mm-30) REVERT: 4 30 ASP cc_start: 0.8317 (p0) cc_final: 0.8029 (p0) REVERT: 4 31 SER cc_start: 0.8932 (m) cc_final: 0.8377 (t) REVERT: 4 52 ASP cc_start: 0.7377 (m-30) cc_final: 0.7004 (t0) REVERT: 4 60 ILE cc_start: 0.9122 (pt) cc_final: 0.8700 (mm) REVERT: 4 86 GLN cc_start: 0.8489 (tm-30) cc_final: 0.7997 (tp-100) REVERT: 4 99 GLN cc_start: 0.7213 (tm-30) cc_final: 0.6697 (tm-30) REVERT: 4 103 LEU cc_start: 0.9326 (mm) cc_final: 0.8978 (mp) REVERT: 4 120 ASP cc_start: 0.7843 (p0) cc_final: 0.7385 (p0) REVERT: 4 124 THR cc_start: 0.8604 (p) cc_final: 0.8020 (p) REVERT: 4 155 GLU cc_start: 0.8379 (pm20) cc_final: 0.7983 (pm20) REVERT: 5 24 ASN cc_start: 0.9051 (t0) cc_final: 0.8758 (t0) REVERT: 5 73 ARG cc_start: 0.7803 (ttp-170) cc_final: 0.7481 (ttp-170) REVERT: 6 81 ASP cc_start: 0.7360 (t0) cc_final: 0.6942 (t0) REVERT: 6 159 GLN cc_start: 0.6526 (pt0) cc_final: 0.5861 (tp40) REVERT: 7 120 GLN cc_start: 0.8135 (mm110) cc_final: 0.7786 (mm-40) REVERT: A 39 ASN cc_start: 0.8272 (m-40) cc_final: 0.7922 (t0) REVERT: A 243 GLU cc_start: 0.7757 (pt0) cc_final: 0.7348 (pt0) REVERT: B 60 THR cc_start: 0.9196 (p) cc_final: 0.8772 (t) REVERT: B 75 TYR cc_start: 0.8784 (p90) cc_final: 0.8362 (p90) REVERT: B 176 GLU cc_start: 0.8022 (pm20) cc_final: 0.7691 (pm20) REVERT: B 178 ARG cc_start: 0.8209 (mmm-85) cc_final: 0.7536 (mmp-170) REVERT: C 7 ASP cc_start: 0.8157 (t70) cc_final: 0.7751 (t0) REVERT: C 122 TYR cc_start: 0.8117 (m-10) cc_final: 0.7850 (m-10) REVERT: C 164 SER cc_start: 0.9179 (p) cc_final: 0.8952 (p) REVERT: C 212 GLU cc_start: 0.8326 (pt0) cc_final: 0.7483 (pt0) REVERT: D 47 GLU cc_start: 0.8408 (pp20) cc_final: 0.7887 (pp20) REVERT: D 148 TYR cc_start: 0.9086 (m-80) cc_final: 0.8767 (m-10) REVERT: E 182 GLU cc_start: 0.7503 (tm-30) cc_final: 0.7220 (tm-30) REVERT: G 26 TYR cc_start: 0.8310 (m-80) cc_final: 0.7883 (m-80) REVERT: G 60 VAL cc_start: 0.8695 (t) cc_final: 0.8449 (p) REVERT: G 78 TYR cc_start: 0.7668 (m-10) cc_final: 0.7260 (m-10) REVERT: G 95 GLU cc_start: 0.7219 (pm20) cc_final: 0.6897 (pm20) REVERT: H 51 GLN cc_start: 0.8209 (pp30) cc_final: 0.7995 (pp30) REVERT: H 98 GLN cc_start: 0.8158 (tt0) cc_final: 0.7907 (tt0) REVERT: H 105 ILE cc_start: 0.9295 (mt) cc_final: 0.8834 (tt) REVERT: H 166 THR cc_start: 0.6890 (p) cc_final: 0.6563 (t) REVERT: H 178 ARG cc_start: 0.8399 (ttm110) cc_final: 0.8169 (ttp-110) REVERT: H 320 ASP cc_start: 0.8209 (t0) cc_final: 0.7981 (t0) REVERT: H 348 ASN cc_start: 0.8342 (t0) cc_final: 0.7903 (t0) REVERT: I 64 ARG cc_start: 0.7479 (ptm-80) cc_final: 0.7166 (ttt180) REVERT: I 68 HIS cc_start: 0.7923 (m-70) cc_final: 0.7650 (m-70) REVERT: I 120 VAL cc_start: 0.9304 (t) cc_final: 0.9003 (m) REVERT: I 121 THR cc_start: 0.7993 (p) cc_final: 0.7566 (t) REVERT: I 125 MET cc_start: 0.7583 (pmm) cc_final: 0.7278 (pmm) REVERT: I 285 ASP cc_start: 0.7956 (p0) cc_final: 0.7367 (p0) REVERT: J 82 LYS cc_start: 0.8552 (mmtp) cc_final: 0.8271 (mmmt) REVERT: J 165 GLU cc_start: 0.8307 (mm-30) cc_final: 0.7749 (tp30) REVERT: J 247 MET cc_start: 0.8280 (mtp) cc_final: 0.7894 (mtp) REVERT: J 270 ARG cc_start: 0.6584 (mmt90) cc_final: 0.6272 (mmt180) REVERT: J 362 CYS cc_start: 0.8879 (m) cc_final: 0.8396 (t) REVERT: K 149 ILE cc_start: 0.9083 (tp) cc_final: 0.8819 (tp) REVERT: K 212 TYR cc_start: 0.8948 (p90) cc_final: 0.8742 (p90) REVERT: K 221 MET cc_start: 0.8115 (ppp) cc_final: 0.7773 (ppp) REVERT: K 260 LEU cc_start: 0.9351 (pp) cc_final: 0.8879 (tt) REVERT: K 319 ASN cc_start: 0.8916 (m-40) cc_final: 0.8209 (t0) REVERT: L 82 ARG cc_start: 0.7910 (ptt180) cc_final: 0.7661 (mtm180) REVERT: L 251 ILE cc_start: 0.8541 (pt) cc_final: 0.8202 (mt) REVERT: L 306 MET cc_start: 0.7509 (tmm) cc_final: 0.7080 (tmm) REVERT: L 307 GLU cc_start: 0.7855 (tp30) cc_final: 0.7397 (tp30) REVERT: M 265 ASP cc_start: 0.8039 (m-30) cc_final: 0.7549 (m-30) REVERT: M 292 ASP cc_start: 0.7780 (p0) cc_final: 0.7065 (p0) REVERT: M 397 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7456 (mm-30) REVERT: M 401 ILE cc_start: 0.9137 (tt) cc_final: 0.8922 (tp) REVERT: r 282 GLU cc_start: 0.8067 (tp30) cc_final: 0.7819 (tp30) outliers start: 1 outliers final: 0 residues processed: 808 average time/residue: 0.5295 time to fit residues: 715.2107 Evaluate side-chains 652 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 652 time to evaluate : 5.075 ------------------------------------------------------------------------------- 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: 8.9990 chunk 483 optimal weight: 0.0060 chunk 515 optimal weight: 9.9990 chunk 529 optimal weight: 6.9990 chunk 310 optimal weight: 0.9980 chunk 224 optimal weight: 4.9990 chunk 404 optimal weight: 5.9990 chunk 158 optimal weight: 3.9990 chunk 465 optimal weight: 0.9990 chunk 487 optimal weight: 0.8980 overall best weight: 1.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 41 HIS ** 4 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 74 ASN ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 235 GLN G 182 HIS I 238 ASN ** I 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 ASN J 240 HIS J 277 ASN K 142 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.5087 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= 0.200 Angle : 0.613 10.386 60998 Z= 0.309 Chirality : 0.045 0.170 7049 Planarity : 0.004 0.066 7868 Dihedral : 7.050 108.263 6446 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 0.02 % Allowed : 1.01 % Favored : 98.97 % 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: -2.17 (0.11), residues: 5766 helix: -0.76 (0.11), residues: 2123 sheet: -1.30 (0.15), residues: 1080 loop : -2.03 (0.12), residues: 2563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP G 218 HIS 0.013 0.001 HIS J 240 PHE 0.023 0.001 PHE 3 50 TYR 0.021 0.001 TYR M 180 ARG 0.005 0.000 ARG I 291 *********************** 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 825 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 824 time to evaluate : 4.986 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: 1 160 SER cc_start: 0.8534 (m) cc_final: 0.8253 (p) REVERT: 2 69 TYR cc_start: 0.9035 (t80) cc_final: 0.8814 (t80) REVERT: 2 112 SER cc_start: 0.8410 (t) cc_final: 0.8146 (p) REVERT: 2 120 ASP cc_start: 0.7398 (p0) cc_final: 0.6895 (p0) REVERT: 2 200 GLN cc_start: 0.7229 (mt0) cc_final: 0.6294 (pt0) REVERT: 2 214 LYS cc_start: 0.8130 (ptmt) cc_final: 0.7769 (mttt) REVERT: 3 79 GLU cc_start: 0.7848 (mp0) cc_final: 0.7223 (mm-30) REVERT: 3 151 GLU cc_start: 0.8149 (tp30) cc_final: 0.7586 (tm-30) REVERT: 3 180 LEU cc_start: 0.8228 (mp) cc_final: 0.7960 (mp) REVERT: 4 30 ASP cc_start: 0.8301 (p0) cc_final: 0.8030 (p0) REVERT: 4 31 SER cc_start: 0.8908 (m) cc_final: 0.8412 (t) REVERT: 4 52 ASP cc_start: 0.7401 (m-30) cc_final: 0.7064 (t0) REVERT: 4 60 ILE cc_start: 0.9202 (pt) cc_final: 0.8706 (mm) REVERT: 4 86 GLN cc_start: 0.8610 (tm-30) cc_final: 0.8066 (tp-100) REVERT: 4 99 GLN cc_start: 0.7221 (tm-30) cc_final: 0.6677 (tm-30) REVERT: 4 103 LEU cc_start: 0.9308 (mm) cc_final: 0.8991 (mp) REVERT: 4 120 ASP cc_start: 0.7820 (p0) cc_final: 0.7329 (p0) REVERT: 4 155 GLU cc_start: 0.8268 (pm20) cc_final: 0.7944 (pm20) REVERT: 5 24 ASN cc_start: 0.9045 (t0) cc_final: 0.8735 (t0) REVERT: 5 73 ARG cc_start: 0.7763 (ttp-170) cc_final: 0.7497 (ttp-170) REVERT: 6 81 ASP cc_start: 0.7385 (t0) cc_final: 0.6922 (t0) REVERT: 7 120 GLN cc_start: 0.8142 (mm110) cc_final: 0.7817 (mm-40) REVERT: A 39 ASN cc_start: 0.8245 (m-40) cc_final: 0.7897 (t0) REVERT: A 243 GLU cc_start: 0.7823 (pt0) cc_final: 0.7394 (pt0) REVERT: B 75 TYR cc_start: 0.8716 (p90) cc_final: 0.8257 (p90) REVERT: B 176 GLU cc_start: 0.8086 (pm20) cc_final: 0.7806 (pm20) REVERT: B 178 ARG cc_start: 0.8212 (mmm-85) cc_final: 0.7534 (mmp-170) REVERT: C 7 ASP cc_start: 0.8159 (t70) cc_final: 0.7734 (t0) REVERT: C 122 TYR cc_start: 0.8088 (m-10) cc_final: 0.7803 (m-10) REVERT: C 212 GLU cc_start: 0.8304 (pt0) cc_final: 0.7477 (pt0) REVERT: D 148 TYR cc_start: 0.9086 (m-80) cc_final: 0.8830 (m-10) REVERT: E 182 GLU cc_start: 0.7414 (tm-30) cc_final: 0.7174 (tm-30) REVERT: E 238 GLU cc_start: 0.7578 (pp20) cc_final: 0.7047 (pp20) REVERT: F 68 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7503 (mm-30) REVERT: G 26 TYR cc_start: 0.8330 (m-80) cc_final: 0.7922 (m-80) REVERT: G 60 VAL cc_start: 0.8678 (t) cc_final: 0.8466 (p) REVERT: G 78 TYR cc_start: 0.7704 (m-10) cc_final: 0.7215 (m-10) REVERT: H 51 GLN cc_start: 0.8181 (pp30) cc_final: 0.7969 (pp30) REVERT: H 98 GLN cc_start: 0.8156 (tt0) cc_final: 0.7938 (tt0) REVERT: H 105 ILE cc_start: 0.9297 (mt) cc_final: 0.8811 (tt) REVERT: H 166 THR cc_start: 0.6873 (p) cc_final: 0.6542 (t) REVERT: H 320 ASP cc_start: 0.8226 (t0) cc_final: 0.7968 (t0) REVERT: H 348 ASN cc_start: 0.8385 (t0) cc_final: 0.7955 (t0) REVERT: H 442 ASP cc_start: 0.8585 (p0) cc_final: 0.8222 (p0) REVERT: I 64 ARG cc_start: 0.7481 (ptm-80) cc_final: 0.7187 (ttt180) REVERT: I 68 HIS cc_start: 0.7926 (m-70) cc_final: 0.7631 (m-70) REVERT: I 120 VAL cc_start: 0.9308 (t) cc_final: 0.9025 (m) REVERT: I 121 THR cc_start: 0.8028 (p) cc_final: 0.7760 (t) REVERT: I 285 ASP cc_start: 0.7936 (p0) cc_final: 0.7342 (p0) REVERT: I 312 GLN cc_start: 0.8837 (mm110) cc_final: 0.8512 (mm-40) REVERT: J 82 LYS cc_start: 0.8561 (mmtp) cc_final: 0.8269 (mmmt) REVERT: J 247 MET cc_start: 0.8313 (mtp) cc_final: 0.7909 (mtp) REVERT: J 270 ARG cc_start: 0.6588 (mmt90) cc_final: 0.6310 (mmt180) REVERT: J 362 CYS cc_start: 0.8845 (m) cc_final: 0.8391 (t) REVERT: K 149 ILE cc_start: 0.9098 (tp) cc_final: 0.8823 (tp) REVERT: K 212 TYR cc_start: 0.8946 (p90) cc_final: 0.8738 (p90) REVERT: K 221 MET cc_start: 0.8126 (ppp) cc_final: 0.7780 (ppp) REVERT: K 260 LEU cc_start: 0.9347 (pp) cc_final: 0.8902 (tt) REVERT: K 319 ASN cc_start: 0.8906 (m-40) cc_final: 0.8181 (t0) REVERT: L 82 ARG cc_start: 0.8002 (ptt180) cc_final: 0.7640 (mtm180) REVERT: L 251 ILE cc_start: 0.8546 (pt) cc_final: 0.8217 (mt) REVERT: L 306 MET cc_start: 0.7548 (tmm) cc_final: 0.7104 (tmm) REVERT: L 307 GLU cc_start: 0.7837 (tp30) cc_final: 0.7390 (tp30) REVERT: M 265 ASP cc_start: 0.8073 (m-30) cc_final: 0.7582 (m-30) REVERT: M 292 ASP cc_start: 0.7854 (p0) cc_final: 0.7195 (p0) REVERT: M 305 MET cc_start: 0.8356 (ttp) cc_final: 0.8020 (ttm) REVERT: M 401 ILE cc_start: 0.9132 (tt) cc_final: 0.8916 (tp) REVERT: r 282 GLU cc_start: 0.8073 (tp30) cc_final: 0.7820 (tp30) outliers start: 1 outliers final: 1 residues processed: 824 average time/residue: 0.5277 time to fit residues: 735.3804 Evaluate side-chains 645 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 644 time to evaluate : 5.511 ------------------------------------------------------------------------------- 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: 0.0570 chunk 338 optimal weight: 0.7980 chunk 545 optimal weight: 5.9990 chunk 332 optimal weight: 4.9990 chunk 258 optimal weight: 1.9990 chunk 378 optimal weight: 1.9990 chunk 571 optimal weight: 0.2980 chunk 526 optimal weight: 0.9980 chunk 455 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 chunk 351 optimal weight: 0.8980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 41 HIS ** 4 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 133 GLN 7 74 ASN A 41 ASN A 56 GLN A 84 ASN ** C 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 235 GLN G 21 ASN G 182 HIS I 238 ASN ** I 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 ASN J 277 ASN K 142 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.5267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 45011 Z= 0.156 Angle : 0.600 10.690 60998 Z= 0.301 Chirality : 0.044 0.204 7049 Planarity : 0.004 0.082 7868 Dihedral : 6.661 104.766 6446 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 0.04 % Allowed : 0.50 % Favored : 99.45 % 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: -1.95 (0.11), residues: 5766 helix: -0.55 (0.11), residues: 2127 sheet: -1.19 (0.15), residues: 1090 loop : -1.92 (0.12), residues: 2549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP 5 25 HIS 0.005 0.001 HIS A 209 PHE 0.024 0.001 PHE J 23 TYR 0.035 0.001 TYR B 224 ARG 0.012 0.000 ARG A 77 ********************** 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 839 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 837 time to evaluate : 5.405 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: 1 150 GLU cc_start: 0.7529 (pm20) cc_final: 0.7103 (pm20) REVERT: 1 160 SER cc_start: 0.8529 (m) cc_final: 0.8212 (p) REVERT: 2 22 GLN cc_start: 0.8668 (pt0) cc_final: 0.8389 (pt0) REVERT: 2 69 TYR cc_start: 0.8985 (t80) cc_final: 0.8729 (t80) REVERT: 2 112 SER cc_start: 0.8442 (t) cc_final: 0.8140 (p) REVERT: 2 120 ASP cc_start: 0.7617 (p0) cc_final: 0.6976 (p0) REVERT: 2 200 GLN cc_start: 0.7266 (mt0) cc_final: 0.6302 (pt0) REVERT: 2 214 LYS cc_start: 0.8124 (ptmt) cc_final: 0.7737 (mttt) REVERT: 3 79 GLU cc_start: 0.7797 (mp0) cc_final: 0.7170 (mm-30) REVERT: 4 30 ASP cc_start: 0.8298 (p0) cc_final: 0.8039 (p0) REVERT: 4 31 SER cc_start: 0.8869 (m) cc_final: 0.8349 (t) REVERT: 4 52 ASP cc_start: 0.7385 (m-30) cc_final: 0.7090 (t0) REVERT: 4 60 ILE cc_start: 0.9058 (pt) cc_final: 0.8653 (mm) REVERT: 4 86 GLN cc_start: 0.8466 (tm-30) cc_final: 0.8030 (tp40) REVERT: 4 99 GLN cc_start: 0.7198 (tm-30) cc_final: 0.6533 (tm-30) REVERT: 4 103 LEU cc_start: 0.9293 (mm) cc_final: 0.9021 (mp) REVERT: 4 120 ASP cc_start: 0.7848 (p0) cc_final: 0.7416 (p0) REVERT: 4 124 THR cc_start: 0.8633 (p) cc_final: 0.8123 (p) REVERT: 4 155 GLU cc_start: 0.8242 (pm20) cc_final: 0.7955 (pm20) REVERT: 4 169 GLU cc_start: 0.7877 (pt0) cc_final: 0.7657 (pt0) REVERT: 5 24 ASN cc_start: 0.9047 (t0) cc_final: 0.8743 (t0) REVERT: 5 25 TRP cc_start: 0.8800 (t60) cc_final: 0.8237 (t60) REVERT: 5 45 MET cc_start: 0.7900 (tmm) cc_final: 0.7657 (tmm) REVERT: 5 73 ARG cc_start: 0.7789 (ttp-170) cc_final: 0.7534 (ttp-170) REVERT: 5 111 THR cc_start: 0.8231 (m) cc_final: 0.7640 (p) REVERT: 6 35 ILE cc_start: 0.8932 (mm) cc_final: 0.8631 (mm) REVERT: 6 81 ASP cc_start: 0.7349 (t0) cc_final: 0.6896 (t0) REVERT: 6 159 GLN cc_start: 0.6904 (pt0) cc_final: 0.6187 (tp40) REVERT: 7 120 GLN cc_start: 0.8066 (mm110) cc_final: 0.7715 (mm-40) REVERT: A 39 ASN cc_start: 0.8325 (m-40) cc_final: 0.8042 (t0) REVERT: A 243 GLU cc_start: 0.7810 (pt0) cc_final: 0.7395 (pt0) REVERT: B 75 TYR cc_start: 0.8674 (p90) cc_final: 0.8197 (p90) REVERT: B 176 GLU cc_start: 0.8058 (pm20) cc_final: 0.7770 (pm20) REVERT: B 178 ARG cc_start: 0.8160 (mmm-85) cc_final: 0.7490 (mmp-170) REVERT: C 7 ASP cc_start: 0.8178 (t70) cc_final: 0.7738 (t0) REVERT: C 39 MET cc_start: 0.8407 (ttt) cc_final: 0.8202 (ttt) REVERT: C 104 GLU cc_start: 0.7903 (pt0) cc_final: 0.7572 (mt-10) REVERT: C 122 TYR cc_start: 0.7963 (m-10) cc_final: 0.7700 (m-10) REVERT: C 212 GLU cc_start: 0.8285 (pt0) cc_final: 0.7419 (pt0) REVERT: C 234 GLU cc_start: 0.7515 (pt0) cc_final: 0.7137 (pt0) REVERT: D 148 TYR cc_start: 0.8999 (m-80) cc_final: 0.8748 (m-10) REVERT: E 88 MET cc_start: 0.6972 (mtt) cc_final: 0.6628 (mtt) REVERT: F 68 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7504 (mm-30) REVERT: G 26 TYR cc_start: 0.8380 (m-80) cc_final: 0.7803 (m-80) REVERT: G 60 VAL cc_start: 0.8659 (t) cc_final: 0.8457 (p) REVERT: G 78 TYR cc_start: 0.7667 (m-10) cc_final: 0.7212 (m-10) REVERT: H 51 GLN cc_start: 0.8162 (pp30) cc_final: 0.7962 (pp30) REVERT: H 98 GLN cc_start: 0.7977 (tt0) cc_final: 0.7720 (tt0) REVERT: H 105 ILE cc_start: 0.9260 (mt) cc_final: 0.8835 (tt) REVERT: H 166 THR cc_start: 0.6744 (p) cc_final: 0.6420 (t) REVERT: H 348 ASN cc_start: 0.8356 (t0) cc_final: 0.7930 (t0) REVERT: H 442 ASP cc_start: 0.8617 (p0) cc_final: 0.8275 (p0) REVERT: I 64 ARG cc_start: 0.7434 (ptm-80) cc_final: 0.7151 (ttt180) REVERT: I 120 VAL cc_start: 0.9248 (t) cc_final: 0.8963 (m) REVERT: I 121 THR cc_start: 0.7915 (p) cc_final: 0.7661 (t) REVERT: I 285 ASP cc_start: 0.7887 (p0) cc_final: 0.7272 (p0) REVERT: I 312 GLN cc_start: 0.8672 (mm110) cc_final: 0.8414 (mm-40) REVERT: J 79 VAL cc_start: 0.8377 (t) cc_final: 0.8097 (t) REVERT: J 82 LYS cc_start: 0.8520 (mmtp) cc_final: 0.8277 (mmmt) REVERT: J 247 MET cc_start: 0.8249 (mtp) cc_final: 0.7983 (mtm) REVERT: J 270 ARG cc_start: 0.6480 (mmt90) cc_final: 0.6237 (mmt180) REVERT: J 297 LEU cc_start: 0.9300 (pt) cc_final: 0.9068 (pp) REVERT: J 362 CYS cc_start: 0.8824 (m) cc_final: 0.8381 (t) REVERT: K 124 SER cc_start: 0.8682 (t) cc_final: 0.8202 (p) REVERT: K 149 ILE cc_start: 0.9047 (tp) cc_final: 0.8768 (tp) REVERT: K 212 TYR cc_start: 0.8963 (p90) cc_final: 0.8727 (p90) REVERT: K 221 MET cc_start: 0.8157 (ppp) cc_final: 0.7801 (ppp) REVERT: K 260 LEU cc_start: 0.9298 (pp) cc_final: 0.8961 (tt) REVERT: K 319 ASN cc_start: 0.8912 (m-40) cc_final: 0.8153 (t0) REVERT: L 251 ILE cc_start: 0.8511 (pt) cc_final: 0.8185 (mt) REVERT: L 306 MET cc_start: 0.7450 (tmm) cc_final: 0.7025 (tmm) REVERT: L 307 GLU cc_start: 0.7785 (tp30) cc_final: 0.7373 (tp30) REVERT: L 346 LYS cc_start: 0.6965 (mttp) cc_final: 0.6716 (mtmm) REVERT: M 159 LEU cc_start: 0.8977 (pt) cc_final: 0.8772 (pp) REVERT: M 265 ASP cc_start: 0.8065 (m-30) cc_final: 0.7557 (m-30) REVERT: M 292 ASP cc_start: 0.7825 (p0) cc_final: 0.7146 (p0) REVERT: M 401 ILE cc_start: 0.9126 (tt) cc_final: 0.8925 (tp) REVERT: r 282 GLU cc_start: 0.8094 (tp30) cc_final: 0.7834 (tp30) outliers start: 2 outliers final: 0 residues processed: 838 average time/residue: 0.5411 time to fit residues: 764.8480 Evaluate side-chains 687 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 687 time to evaluate : 5.153 ------------------------------------------------------------------------------- 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: 10.0000 chunk 361 optimal weight: 4.9990 chunk 485 optimal weight: 10.0000 chunk 139 optimal weight: 0.0000 chunk 419 optimal weight: 0.8980 chunk 67 optimal weight: 5.9990 chunk 126 optimal weight: 10.0000 chunk 456 optimal weight: 0.7980 chunk 190 optimal weight: 6.9990 chunk 468 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 41 HIS ** 4 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 74 ASN ** C 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 GLN D 235 GLN G 182 HIS I 192 GLN I 238 ASN I 410 GLN J 277 ASN K 142 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.075943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.065105 restraints weight = 115475.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.066343 restraints weight = 72027.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.067190 restraints weight = 51286.343| |-----------------------------------------------------------------------------| r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.5293 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= 0.222 Angle : 0.623 9.912 60998 Z= 0.315 Chirality : 0.045 0.183 7049 Planarity : 0.004 0.079 7868 Dihedral : 6.734 100.630 6446 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 0.02 % Allowed : 0.46 % Favored : 99.52 % 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: -1.93 (0.11), residues: 5766 helix: -0.54 (0.12), residues: 2130 sheet: -1.18 (0.15), residues: 1083 loop : -1.91 (0.12), residues: 2553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP G 218 HIS 0.005 0.001 HIS I 68 PHE 0.022 0.002 PHE M 432 TYR 0.022 0.001 TYR A 133 ARG 0.012 0.000 ARG A 77 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11913.88 seconds wall clock time: 214 minutes 6.43 seconds (12846.43 seconds total)