Starting phenix.real_space_refine (version: dev) on Tue May 17 21:04:23 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ef3_9045/05_2022/6ef3_9045_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ef3_9045/05_2022/6ef3_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_9045/05_2022/6ef3_9045.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ef3_9045/05_2022/6ef3_9045.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ef3_9045/05_2022/6ef3_9045_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ef3_9045/05_2022/6ef3_9045_updated.pdb" } resolution = 4.17 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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: 0.33s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/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: {'PTRANS': 16, 'TRANS': 366, 'PCIS': 1} 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: {'PTRANS': 14, 'TRANS': 367, 'PCIS': 1} 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: {'PTRANS': 15, 'TRANS': 352, 'PCIS': 2} 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: {'PTRANS': 16, 'TRANS': 342, 'PCIS': 1} 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: {'PTRANS': 14, 'TRANS': 355, 'PCIS': 1} 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: {'PTRANS': 4, 'TRANS': 274, 'PCIS': 1} 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: 24.20, per 1000 atoms: 0.55 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: 17.50 Conformation dependent library (CDL) restraints added in 6.9 seconds 11532 Ramachandran restraints generated. 5766 Oldfield, 0 Emsley, 5766 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10778 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 200 helices and 60 sheets defined 32.9% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.71 Creating SS restraints... Processing helix chain '1' and resid 50 through 69 removed outlier: 4.026A pdb=" N ALA 1 54 " --> pdb=" O ALA 1 50 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N TYR 1 61 " --> pdb=" O ASP 1 57 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER 1 68 " --> pdb=" O GLU 1 64 " (cutoff:3.500A) Processing helix chain '1' and resid 76 through 86 removed outlier: 3.524A pdb=" N SER 1 80 " --> pdb=" O GLU 1 76 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N GLU 1 84 " --> pdb=" O SER 1 80 " (cutoff:3.500A) Processing helix chain '1' and resid 135 through 139 removed outlier: 3.740A pdb=" N ASP 1 139 " --> pdb=" O TYR 1 135 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 135 through 139' Processing helix chain '1' and resid 148 through 164 removed outlier: 4.071A pdb=" N ASP 1 153 " --> pdb=" O GLU 1 149 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE 1 154 " --> pdb=" O GLU 1 150 " (cutoff:3.500A) Processing helix chain '1' and resid 190 through 194 Processing helix chain '2' and resid 49 through 62 removed outlier: 4.131A pdb=" N VAL 2 55 " --> pdb=" O ASP 2 51 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER 2 61 " --> pdb=" O GLN 2 57 " (cutoff:3.500A) Processing helix chain '2' and resid 64 through 70 Processing helix chain '2' and resid 77 through 81 removed outlier: 3.986A pdb=" N GLN 2 81 " --> pdb=" O SER 2 78 " (cutoff:3.500A) Processing helix chain '2' and resid 83 through 90 removed outlier: 3.586A pdb=" N PHE 2 88 " --> pdb=" O LYS 2 84 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS 2 89 " --> pdb=" O GLN 2 85 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TYR 2 90 " --> pdb=" O HIS 2 86 " (cutoff:3.500A) Processing helix chain '2' and resid 131 through 140 removed outlier: 3.525A pdb=" N MET 2 135 " --> pdb=" O SER 2 131 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU 2 138 " --> pdb=" O ALA 2 134 " (cutoff:3.500A) Processing helix chain '2' and resid 148 through 164 removed outlier: 4.278A pdb=" N LYS 2 153 " --> pdb=" O GLU 2 149 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE 2 159 " --> pdb=" O ALA 2 155 " (cutoff:3.500A) Processing helix chain '3' and resid 4 through 6 No H-bonds generated for 'chain '3' and resid 4 through 6' Processing helix chain '3' and resid 58 through 78 removed outlier: 4.038A pdb=" N LEU 3 63 " --> pdb=" O ASP 3 59 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU 3 65 " --> pdb=" O THR 3 61 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N MET 3 66 " --> pdb=" O THR 3 62 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS 3 70 " --> pdb=" O MET 3 66 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASN 3 72 " --> pdb=" O ARG 3 68 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LEU 3 73 " --> pdb=" O TYR 3 69 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU 3 76 " --> pdb=" O ASN 3 72 " (cutoff:3.500A) Processing helix chain '3' and resid 84 through 98 removed outlier: 4.283A pdb=" N GLN 3 89 " --> pdb=" O GLU 3 85 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER 3 92 " --> pdb=" O THR 3 88 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU 3 97 " --> pdb=" O SER 3 93 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N ARG 3 98 " --> pdb=" O SER 3 94 " (cutoff:3.500A) Processing helix chain '3' and resid 148 through 153 removed outlier: 3.597A pdb=" N SER 3 152 " --> pdb=" O GLY 3 148 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N LEU 3 153 " --> pdb=" O MET 3 149 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 148 through 153' Processing helix chain '3' and resid 160 through 175 removed outlier: 4.224A pdb=" N THR 3 166 " --> pdb=" O ASP 3 162 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN 3 169 " --> pdb=" O GLU 3 165 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA 3 174 " --> pdb=" O ALA 3 170 " (cutoff:3.500A) Processing helix chain '4' and resid 54 through 68 removed outlier: 3.666A pdb=" N GLU 4 58 " --> pdb=" O VAL 4 54 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR 4 59 " --> pdb=" O GLN 4 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU 4 66 " --> pdb=" O ALA 4 62 " (cutoff:3.500A) Processing helix chain '4' and resid 77 through 91 removed outlier: 3.507A pdb=" N SER 4 82 " --> pdb=" O GLN 4 78 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG 4 85 " --> pdb=" O SER 4 81 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLN 4 86 " --> pdb=" O SER 4 82 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU 4 87 " --> pdb=" O PHE 4 83 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU 4 88 " --> pdb=" O VAL 4 84 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS 4 90 " --> pdb=" O GLN 4 86 " (cutoff:3.500A) Processing helix chain '4' and resid 137 through 139 No H-bonds generated for 'chain '4' and resid 137 through 139' Processing helix chain '4' and resid 154 through 161 removed outlier: 4.341A pdb=" N LEU 4 158 " --> pdb=" O THR 4 154 " (cutoff:3.500A) Processing helix chain '4' and resid 164 through 169 removed outlier: 3.532A pdb=" N LEU 4 168 " --> pdb=" O CYS 4 164 " (cutoff:3.500A) Processing helix chain '5' and resid 49 through 65 removed outlier: 4.757A pdb=" N TRP 5 55 " --> pdb=" O ASP 5 51 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR 5 57 " --> pdb=" O GLN 5 53 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER 5 61 " --> pdb=" O THR 5 57 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN 5 62 " --> pdb=" O TRP 5 58 " (cutoff:3.500A) Processing helix chain '5' and resid 67 through 70 No H-bonds generated for 'chain '5' and resid 67 through 70' Processing helix chain '5' and resid 79 through 90 removed outlier: 3.536A pdb=" N LEU 5 83 " --> pdb=" O ALA 5 79 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER 5 84 " --> pdb=" O SER 5 80 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLN 5 89 " --> pdb=" O ASN 5 85 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N TYR 5 90 " --> pdb=" O LEU 5 86 " (cutoff:3.500A) Processing helix chain '5' and resid 133 through 141 removed outlier: 3.724A pdb=" N GLY 5 138 " --> pdb=" O THR 5 134 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N VAL 5 139 " --> pdb=" O PHE 5 135 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU 5 140 " --> pdb=" O ALA 5 136 " (cutoff:3.500A) Processing helix chain '5' and resid 151 through 165 removed outlier: 3.742A pdb=" N LYS 5 158 " --> pdb=" O LEU 5 154 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ALA 5 164 " --> pdb=" O SER 5 160 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ALA 5 165 " --> pdb=" O ILE 5 161 " (cutoff:3.500A) Processing helix chain '5' and resid 193 through 204 removed outlier: 4.560A pdb=" N TRP 5 198 " --> pdb=" O GLY 5 194 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LYS 5 199 " --> pdb=" O GLU 5 195 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU 5 202 " --> pdb=" O TRP 5 198 " (cutoff:3.500A) Processing helix chain '6' and resid 60 through 79 removed outlier: 4.598A pdb=" N VAL 6 65 " --> pdb=" O GLY 6 61 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN 6 70 " --> pdb=" O LYS 6 66 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LYS 6 73 " --> pdb=" O LYS 6 69 " (cutoff:3.500A) Processing helix chain '6' and resid 86 through 98 removed outlier: 3.874A pdb=" N ARG 6 91 " --> pdb=" O ASN 6 87 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE 6 93 " --> pdb=" O ALA 6 89 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN 6 94 " --> pdb=" O ALA 6 90 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N HIS 6 95 " --> pdb=" O ARG 6 91 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU 6 97 " --> pdb=" O ILE 6 93 " (cutoff:3.500A) Processing helix chain '6' and resid 147 through 150 No H-bonds generated for 'chain '6' and resid 147 through 150' Processing helix chain '6' and resid 177 through 187 Processing helix chain '7' and resid 57 through 75 removed outlier: 3.851A pdb=" N HIS 7 62 " --> pdb=" O SER 7 58 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU 7 66 " --> pdb=" O HIS 7 62 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS 7 68 " --> pdb=" O GLU 7 64 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASP 7 69 " --> pdb=" O ARG 7 65 " (cutoff:3.500A) Processing helix chain '7' and resid 89 through 93 removed outlier: 3.993A pdb=" N PHE 7 93 " --> pdb=" O SER 7 90 " (cutoff:3.500A) Processing helix chain '7' and resid 95 through 104 removed outlier: 4.664A pdb=" N MET 7 100 " --> pdb=" O LEU 7 96 " (cutoff:3.500A) Processing helix chain '7' and resid 145 through 150 removed outlier: 3.722A pdb=" N MET 7 150 " --> pdb=" O GLY 7 147 " (cutoff:3.500A) Processing helix chain '7' and resid 152 through 158 removed outlier: 3.542A pdb=" N LYS 7 157 " --> pdb=" O PRO 7 153 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL 7 158 " --> pdb=" O LEU 7 154 " (cutoff:3.500A) Processing helix chain '7' and resid 162 through 165 removed outlier: 4.000A pdb=" N ILE 7 165 " --> pdb=" O GLU 7 162 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 162 through 165' Processing helix chain '7' and resid 170 through 187 removed outlier: 3.613A pdb=" N ALA 7 176 " --> pdb=" O VAL 7 172 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE 7 177 " --> pdb=" O ALA 7 173 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ASN 7 179 " --> pdb=" O GLU 7 175 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL 7 183 " --> pdb=" O ASN 7 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 5 through 9 Processing helix chain 'A' and resid 27 through 34 removed outlier: 3.975A pdb=" N PHE A 32 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N LYS A 33 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ALA A 34 " --> pdb=" O TYR A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 98 removed outlier: 3.549A pdb=" N ASN A 92 " --> pdb=" O PRO A 88 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ALA A 93 " --> pdb=" O ASP A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 107 Processing helix chain 'A' and resid 114 through 120 Processing helix chain 'A' and resid 122 through 125 No H-bonds generated for 'chain 'A' and resid 122 through 125' Processing helix chain 'A' and resid 127 through 129 No H-bonds generated for 'chain 'A' and resid 127 through 129' Processing helix chain 'A' and resid 175 through 189 removed outlier: 5.231A pdb=" N HIS A 185 " --> pdb=" O ASN A 181 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER A 189 " --> pdb=" O HIS A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 212 removed outlier: 3.684A pdb=" N VAL A 203 " --> pdb=" O TRP A 199 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU A 204 " --> pdb=" O GLU A 200 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE A 205 " --> pdb=" O LYS A 201 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR A 208 " --> pdb=" O GLU A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 245 No H-bonds generated for 'chain 'A' and resid 242 through 245' Processing helix chain 'B' and resid 21 through 29 removed outlier: 3.985A pdb=" N THR B 26 " --> pdb=" O ASP B 22 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS B 29 " --> pdb=" O LEU B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 88 removed outlier: 4.407A pdb=" N LEU B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASP B 87 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS B 88 " --> pdb=" O VAL B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 96 Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 108 through 115 Processing helix chain 'B' and resid 120 through 122 No H-bonds generated for 'chain 'B' and resid 120 through 122' Processing helix chain 'B' and resid 168 through 175 removed outlier: 3.535A pdb=" N PHE B 174 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 194 No H-bonds generated for 'chain 'B' and resid 191 through 194' Processing helix chain 'B' and resid 206 through 208 No H-bonds generated for 'chain 'B' and resid 206 through 208' Processing helix chain 'B' and resid 219 through 221 No H-bonds generated for 'chain 'B' and resid 219 through 221' Processing helix chain 'B' and resid 240 through 244 Processing helix chain 'C' and resid 20 through 23 No H-bonds generated for 'chain 'C' and resid 20 through 23' Processing helix chain 'C' and resid 25 through 27 No H-bonds generated for 'chain 'C' and resid 25 through 27' Processing helix chain 'C' and resid 85 through 102 removed outlier: 3.903A pdb=" N THR C 90 " --> pdb=" O ILE C 86 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA C 91 " --> pdb=" O LEU C 87 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASN C 97 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N THR C 101 " --> pdb=" O ASN C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 120 removed outlier: 3.588A pdb=" N ARG C 113 " --> pdb=" O GLU C 109 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS C 119 " --> pdb=" O LEU C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 177 removed outlier: 3.678A pdb=" N LEU C 176 " --> pdb=" O ALA C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 200 removed outlier: 3.745A pdb=" N GLU C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU C 192 " --> pdb=" O ASP C 188 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LYS C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 241 removed outlier: 3.712A pdb=" N LYS C 236 " --> pdb=" O PRO C 232 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASP C 237 " --> pdb=" O GLN C 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 29 removed outlier: 3.674A pdb=" N LEU D 24 " --> pdb=" O VAL D 20 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU D 25 " --> pdb=" O GLU D 21 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA D 26 " --> pdb=" O TYR D 22 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS D 28 " --> pdb=" O LEU D 24 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG D 29 " --> pdb=" O GLU D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 100 removed outlier: 4.739A pdb=" N ILE D 84 " --> pdb=" O ALA D 80 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU D 85 " --> pdb=" O ASP D 81 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N VAL D 91 " --> pdb=" O GLU D 87 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG D 97 " --> pdb=" O ALA D 93 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU D 98 " --> pdb=" O GLN D 94 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N THR D 99 " --> pdb=" O SER D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 113 removed outlier: 3.746A pdb=" N ARG D 111 " --> pdb=" O GLU D 107 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TYR D 112 " --> pdb=" O TYR D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 118 No H-bonds generated for 'chain 'D' and resid 115 through 118' Processing helix chain 'D' and resid 168 through 178 removed outlier: 5.084A pdb=" N GLU D 173 " --> pdb=" O LYS D 169 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE D 174 " --> pdb=" O THR D 170 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN D 178 " --> pdb=" O PHE D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 199 removed outlier: 3.567A pdb=" N SER D 198 " --> pdb=" O LEU D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 240 removed outlier: 3.954A pdb=" N GLN D 231 " --> pdb=" O GLU D 227 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TYR D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN D 235 " --> pdb=" O GLN D 231 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ILE D 236 " --> pdb=" O TYR D 232 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU D 237 " --> pdb=" O VAL D 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 30 removed outlier: 3.810A pdb=" N SER E 27 " --> pdb=" O GLN E 23 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU E 29 " --> pdb=" O GLU E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 86 No H-bonds generated for 'chain 'E' and resid 83 through 86' Processing helix chain 'E' and resid 89 through 102 removed outlier: 4.426A pdb=" N THR E 94 " --> pdb=" O GLU E 90 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA E 96 " --> pdb=" O ALA E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 117 Processing helix chain 'E' and resid 120 through 122 No H-bonds generated for 'chain 'E' and resid 120 through 122' Processing helix chain 'E' and resid 176 through 179 No H-bonds generated for 'chain 'E' and resid 176 through 179' Processing helix chain 'E' and resid 194 through 197 No H-bonds generated for 'chain 'E' and resid 194 through 197' Processing helix chain 'E' and resid 203 through 207 Processing helix chain 'E' and resid 233 through 247 removed outlier: 3.628A pdb=" N LEU E 239 " --> pdb=" O LYS E 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 25 Processing helix chain 'F' and resid 28 through 31 Processing helix chain 'F' and resid 78 through 98 removed outlier: 4.064A pdb=" N ARG F 82 " --> pdb=" O PRO F 79 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N VAL F 83 " --> pdb=" O ASP F 80 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER F 85 " --> pdb=" O ARG F 82 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ARG F 89 " --> pdb=" O ASN F 86 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN F 91 " --> pdb=" O LEU F 88 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N CYS F 92 " --> pdb=" O ARG F 89 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N SER F 95 " --> pdb=" O CYS F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 107 No H-bonds generated for 'chain 'F' and resid 105 through 107' Processing helix chain 'F' and resid 112 through 121 removed outlier: 3.854A pdb=" N GLN F 117 " --> pdb=" O CYS F 113 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN F 119 " --> pdb=" O LYS F 115 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N THR F 120 " --> pdb=" O ALA F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 172 removed outlier: 3.699A pdb=" N TYR F 171 " --> pdb=" O GLY F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 177 No H-bonds generated for 'chain 'F' and resid 175 through 177' Processing helix chain 'F' and resid 186 through 200 removed outlier: 4.227A pdb=" N LYS F 191 " --> pdb=" O ASP F 187 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY F 193 " --> pdb=" O LEU F 189 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU F 195 " --> pdb=" O LYS F 191 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER F 198 " --> pdb=" O VAL F 194 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN F 199 " --> pdb=" O GLU F 195 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N SER F 200 " --> pdb=" O ALA F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 231 through 233 No H-bonds generated for 'chain 'F' and resid 231 through 233' Processing helix chain 'G' and resid 22 through 31 removed outlier: 4.922A pdb=" N LYS G 29 " --> pdb=" O GLU G 25 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA G 30 " --> pdb=" O TYR G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 103 removed outlier: 3.533A pdb=" N ARG G 91 " --> pdb=" O HIS G 87 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N GLU G 94 " --> pdb=" O ASN G 90 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA G 96 " --> pdb=" O GLY G 92 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ALA G 97 " --> pdb=" O ARG G 93 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N LEU G 102 " --> pdb=" O SER G 98 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR G 103 " --> pdb=" O PHE G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 113 No H-bonds generated for 'chain 'G' and resid 110 through 113' Processing helix chain 'G' and resid 120 through 123 No H-bonds generated for 'chain 'G' and resid 120 through 123' Processing helix chain 'G' and resid 169 through 182 removed outlier: 4.360A pdb=" N ALA G 174 " --> pdb=" O GLN G 170 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU G 175 " --> pdb=" O SER G 171 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLU G 177 " --> pdb=" O LYS G 173 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU G 179 " --> pdb=" O GLU G 175 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL G 180 " --> pdb=" O LEU G 176 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP G 181 " --> pdb=" O GLU G 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 192 through 206 removed outlier: 4.094A pdb=" N ILE G 199 " --> pdb=" O GLN G 195 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N GLU G 205 " --> pdb=" O TYR G 201 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ASP G 206 " --> pdb=" O LEU G 202 " (cutoff:3.500A) Processing helix chain 'G' and resid 221 through 224 No H-bonds generated for 'chain 'G' and resid 221 through 224' Processing helix chain 'G' and resid 234 through 246 removed outlier: 3.694A pdb=" N LYS G 245 " --> pdb=" O ASP G 241 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU G 246 " --> pdb=" O PHE G 242 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 64 removed outlier: 3.520A pdb=" N LYS H 50 " --> pdb=" O ALA H 46 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLN H 51 " --> pdb=" O ALA H 47 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASN H 54 " --> pdb=" O LYS H 50 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU H 56 " --> pdb=" O THR H 52 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LYS H 57 " --> pdb=" O GLU H 53 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ASP H 58 " --> pdb=" O ASN H 54 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS H 64 " --> pdb=" O GLU H 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 88 No H-bonds generated for 'chain 'H' and resid 85 through 88' Processing helix chain 'H' and resid 193 through 196 No H-bonds generated for 'chain 'H' and resid 193 through 196' Processing helix chain 'H' and resid 217 through 225 removed outlier: 3.526A pdb=" N GLU H 223 " --> pdb=" O GLU H 219 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL H 224 " --> pdb=" O LYS H 220 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 230 No H-bonds generated for 'chain 'H' and resid 227 through 230' Processing helix chain 'H' and resid 232 through 238 removed outlier: 4.016A pdb=" N THR H 237 " --> pdb=" O GLU H 233 " (cutoff:3.500A) Processing helix chain 'H' and resid 258 through 265 removed outlier: 3.506A pdb=" N VAL H 263 " --> pdb=" O CYS H 259 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA H 264 " --> pdb=" O ALA H 260 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASN H 265 " --> pdb=" O ARG H 261 " (cutoff:3.500A) Processing helix chain 'H' and resid 276 through 278 No H-bonds generated for 'chain 'H' and resid 276 through 278' Processing helix chain 'H' and resid 287 through 300 removed outlier: 3.775A pdb=" N ALA H 298 " --> pdb=" O LEU H 294 " (cutoff:3.500A) Processing helix chain 'H' and resid 327 through 340 removed outlier: 3.624A pdb=" N ARG H 331 " --> pdb=" O ASN H 327 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU H 335 " --> pdb=" O ARG H 331 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU H 336 " --> pdb=" O THR H 332 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN H 339 " --> pdb=" O GLU H 335 " (cutoff:3.500A) Processing helix chain 'H' and resid 363 through 366 Processing helix chain 'H' and resid 382 through 392 removed outlier: 3.710A pdb=" N ASN H 387 " --> pdb=" O GLU H 383 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE H 388 " --> pdb=" O GLY H 384 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE H 389 " --> pdb=" O ARG H 385 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE H 391 " --> pdb=" O ASN H 387 " (cutoff:3.500A) Processing helix chain 'H' and resid 404 through 410 removed outlier: 4.008A pdb=" N ARG H 409 " --> pdb=" O GLU H 405 " (cutoff:3.500A) Processing helix chain 'H' and resid 416 through 431 removed outlier: 3.974A pdb=" N VAL H 422 " --> pdb=" O GLU H 418 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY H 427 " --> pdb=" O CYS H 423 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA H 430 " --> pdb=" O ALA H 426 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE H 431 " --> pdb=" O GLY H 427 " (cutoff:3.500A) Processing helix chain 'H' and resid 441 through 450 removed outlier: 3.979A pdb=" N LYS H 449 " --> pdb=" O LYS H 445 " (cutoff:3.500A) Processing helix chain 'I' and resid 56 through 59 Processing helix chain 'I' and resid 61 through 78 removed outlier: 4.211A pdb=" N ILE I 65 " --> pdb=" O ARG I 61 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS I 66 " --> pdb=" O MET I 62 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE I 75 " --> pdb=" O LEU I 71 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL I 76 " --> pdb=" O GLU I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 92 through 99 removed outlier: 4.485A pdb=" N GLU I 97 " --> pdb=" O LYS I 93 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLU I 98 " --> pdb=" O LYS I 94 " (cutoff:3.500A) Processing helix chain 'I' and resid 166 through 171 Processing helix chain 'I' and resid 190 through 198 removed outlier: 3.986A pdb=" N ILE I 194 " --> pdb=" O GLN I 190 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N SER I 197 " --> pdb=" O GLU I 193 " (cutoff:3.500A) Processing helix chain 'I' and resid 205 through 209 Processing helix chain 'I' and resid 229 through 238 removed outlier: 3.626A pdb=" N VAL I 236 " --> pdb=" O LEU I 232 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASN I 238 " --> pdb=" O LYS I 234 " (cutoff:3.500A) Processing helix chain 'I' and resid 249 through 252 Processing helix chain 'I' and resid 260 through 273 removed outlier: 3.766A pdb=" N ARG I 265 " --> pdb=" O PRO I 261 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE I 268 " --> pdb=" O CYS I 264 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS I 269 " --> pdb=" O ARG I 265 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLY I 272 " --> pdb=" O PHE I 268 " (cutoff:3.500A) Processing helix chain 'I' and resid 284 through 286 No H-bonds generated for 'chain 'I' and resid 284 through 286' Processing helix chain 'I' and resid 299 through 313 removed outlier: 3.680A pdb=" N THR I 305 " --> pdb=" O GLU I 301 " (cutoff:3.500A) Processing helix chain 'I' and resid 355 through 365 removed outlier: 3.587A pdb=" N LYS I 359 " --> pdb=" O LEU I 355 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LYS I 360 " --> pdb=" O SER I 356 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLY I 363 " --> pdb=" O LYS I 359 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ILE I 364 " --> pdb=" O LYS I 360 " (cutoff:3.500A) Processing helix chain 'I' and resid 377 through 379 No H-bonds generated for 'chain 'I' and resid 377 through 379' Processing helix chain 'I' and resid 390 through 406 removed outlier: 3.710A pdb=" N ALA I 394 " --> pdb=" O ALA I 390 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET I 395 " --> pdb=" O ASP I 391 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY I 400 " --> pdb=" O CYS I 396 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA I 403 " --> pdb=" O ALA I 399 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU I 404 " --> pdb=" O GLY I 400 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU I 406 " --> pdb=" O LEU I 402 " (cutoff:3.500A) Processing helix chain 'I' and resid 413 through 426 removed outlier: 3.676A pdb=" N ALA I 419 " --> pdb=" O ASP I 415 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ARG I 422 " --> pdb=" O GLN I 418 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASN I 426 " --> pdb=" O ARG I 422 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 65 removed outlier: 3.896A pdb=" N LEU J 32 " --> pdb=" O GLN J 28 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG J 35 " --> pdb=" O GLU J 31 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ASN J 40 " --> pdb=" O SER J 36 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL J 41 " --> pdb=" O LYS J 37 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LYS J 54 " --> pdb=" O ALA J 50 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL J 55 " --> pdb=" O LEU J 51 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE J 58 " --> pdb=" O LYS J 54 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG J 63 " --> pdb=" O LYS J 59 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU J 64 " --> pdb=" O ASP J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 155 through 163 removed outlier: 3.598A pdb=" N GLU J 159 " --> pdb=" O LYS J 155 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE J 160 " --> pdb=" O GLN J 156 " (cutoff:3.500A) Processing helix chain 'J' and resid 166 through 169 No H-bonds generated for 'chain 'J' and resid 166 through 169' Processing helix chain 'J' and resid 171 through 177 Processing helix chain 'J' and resid 195 through 205 removed outlier: 3.728A pdb=" N ALA J 199 " --> pdb=" O LYS J 195 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG J 200 " --> pdb=" O THR J 196 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA J 203 " --> pdb=" O ALA J 199 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N HIS J 204 " --> pdb=" O ARG J 200 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N HIS J 205 " --> pdb=" O ALA J 201 " (cutoff:3.500A) Processing helix chain 'J' and resid 227 through 238 removed outlier: 3.879A pdb=" N ARG J 231 " --> pdb=" O SER J 227 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL J 235 " --> pdb=" O ARG J 231 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N MET J 236 " --> pdb=" O GLU J 232 " (cutoff:3.500A) Processing helix chain 'J' and resid 266 through 277 removed outlier: 4.029A pdb=" N THR J 271 " --> pdb=" O GLU J 267 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N MET J 272 " --> pdb=" O VAL J 268 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU J 273 " --> pdb=" O GLN J 269 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU J 274 " --> pdb=" O ARG J 270 " (cutoff:3.500A) Processing helix chain 'J' and resid 279 through 284 Processing helix chain 'J' and resid 321 through 331 removed outlier: 4.553A pdb=" N GLU J 326 " --> pdb=" O ALA J 322 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ILE J 327 " --> pdb=" O ALA J 323 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N HIS J 331 " --> pdb=" O ILE J 327 " (cutoff:3.500A) Processing helix chain 'J' and resid 343 through 349 removed outlier: 3.933A pdb=" N ALA J 347 " --> pdb=" O LEU J 343 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLU J 348 " --> pdb=" O ARG J 344 " (cutoff:3.500A) Processing helix chain 'J' and resid 357 through 372 removed outlier: 3.504A pdb=" N THR J 363 " --> pdb=" O LYS J 359 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLY J 366 " --> pdb=" O CYS J 362 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR J 368 " --> pdb=" O GLU J 364 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA J 369 " --> pdb=" O ALA J 365 " (cutoff:3.500A) Processing helix chain 'J' and resid 379 through 383 Processing helix chain 'J' and resid 385 through 389 removed outlier: 3.770A pdb=" N VAL J 389 " --> pdb=" O VAL J 386 " (cutoff:3.500A) Processing helix chain 'J' and resid 391 through 397 removed outlier: 3.605A pdb=" N THR J 396 " --> pdb=" O LYS J 392 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALA J 397 " --> pdb=" O ASN J 393 " (cutoff:3.500A) Processing helix chain 'K' and resid 50 through 83 removed outlier: 3.530A pdb=" N LYS K 56 " --> pdb=" O LYS K 52 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR K 58 " --> pdb=" O LEU K 54 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU K 63 " --> pdb=" O GLU K 59 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN K 64 " --> pdb=" O LEU K 60 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP K 66 " --> pdb=" O THR K 62 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TYR K 67 " --> pdb=" O LEU K 63 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS K 69 " --> pdb=" O GLU K 65 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN K 72 " --> pdb=" O ILE K 68 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ARG K 77 " --> pdb=" O ARG K 73 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLU K 78 " --> pdb=" O HIS K 74 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU K 79 " --> pdb=" O LEU K 75 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS K 80 " --> pdb=" O LYS K 76 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG K 81 " --> pdb=" O ARG K 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 89 removed outlier: 3.753A pdb=" N ILE K 89 " --> pdb=" O GLU K 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 85 through 89' Processing helix chain 'K' and resid 178 through 187 removed outlier: 3.708A pdb=" N ILE K 184 " --> pdb=" O GLN K 180 " (cutoff:3.500A) Processing helix chain 'K' and resid 190 through 193 No H-bonds generated for 'chain 'K' and resid 190 through 193' Processing helix chain 'K' and resid 196 through 201 removed outlier: 3.880A pdb=" N ILE K 201 " --> pdb=" O LEU K 197 " (cutoff:3.500A) Processing helix chain 'K' and resid 219 through 230 Processing helix chain 'K' and resid 239 through 242 No H-bonds generated for 'chain 'K' and resid 239 through 242' Processing helix chain 'K' and resid 251 through 261 removed outlier: 4.113A pdb=" N PHE K 258 " --> pdb=" O VAL K 254 " (cutoff:3.500A) Processing helix chain 'K' and resid 288 through 304 removed outlier: 3.688A pdb=" N VAL K 292 " --> pdb=" O SER K 288 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN K 293 " --> pdb=" O ASP K 289 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU K 298 " --> pdb=" O ARG K 294 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N MET K 303 " --> pdb=" O LEU K 299 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP K 304 " --> pdb=" O LEU K 300 " (cutoff:3.500A) Processing helix chain 'K' and resid 346 through 359 removed outlier: 4.055A pdb=" N ILE K 352 " --> pdb=" O GLU K 348 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N PHE K 353 " --> pdb=" O ARG K 349 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLY K 354 " --> pdb=" O ARG K 350 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N THR K 355 " --> pdb=" O LEU K 351 " (cutoff:3.500A) Processing helix chain 'K' and resid 369 through 372 No H-bonds generated for 'chain 'K' and resid 369 through 372' Processing helix chain 'K' and resid 382 through 390 removed outlier: 3.721A pdb=" N GLU K 389 " --> pdb=" O ALA K 385 " (cutoff:3.500A) Processing helix chain 'K' and resid 393 through 396 No H-bonds generated for 'chain 'K' and resid 393 through 396' Processing helix chain 'K' and resid 405 through 411 removed outlier: 4.157A pdb=" N GLU K 409 " --> pdb=" O SER K 405 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA K 410 " --> pdb=" O ASP K 406 " (cutoff:3.500A) Processing helix chain 'L' and resid 72 through 98 removed outlier: 4.748A pdb=" N ARG L 77 " --> pdb=" O GLN L 73 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG L 78 " --> pdb=" O LEU L 74 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLN L 79 " --> pdb=" O LYS L 75 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU L 87 " --> pdb=" O ASP L 83 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS L 90 " --> pdb=" O LYS L 86 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE L 95 " --> pdb=" O THR L 91 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS L 96 " --> pdb=" O GLU L 92 " (cutoff:3.500A) Processing helix chain 'L' and resid 173 through 175 No H-bonds generated for 'chain 'L' and resid 173 through 175' Processing helix chain 'L' and resid 188 through 197 removed outlier: 3.701A pdb=" N ARG L 194 " --> pdb=" O ILE L 190 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU L 195 " --> pdb=" O ARG L 191 " (cutoff:3.500A) Processing helix chain 'L' and resid 199 through 202 No H-bonds generated for 'chain 'L' and resid 199 through 202' Processing helix chain 'L' and resid 207 through 210 No H-bonds generated for 'chain 'L' and resid 207 through 210' Processing helix chain 'L' and resid 229 through 238 removed outlier: 3.801A pdb=" N ALA L 236 " --> pdb=" O ALA L 232 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA L 237 " --> pdb=" O LYS L 233 " (cutoff:3.500A) Processing helix chain 'L' and resid 250 through 253 No H-bonds generated for 'chain 'L' and resid 250 through 253' Processing helix chain 'L' and resid 260 through 272 removed outlier: 3.632A pdb=" N ALA L 270 " --> pdb=" O MET L 266 " (cutoff:3.500A) Processing helix chain 'L' and resid 283 through 285 No H-bonds generated for 'chain 'L' and resid 283 through 285' Processing helix chain 'L' and resid 299 through 315 removed outlier: 4.601A pdb=" N LEU L 305 " --> pdb=" O ILE L 301 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU L 308 " --> pdb=" O THR L 304 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE L 315 " --> pdb=" O GLN L 311 " (cutoff:3.500A) Processing helix chain 'L' and resid 330 through 332 No H-bonds generated for 'chain 'L' and resid 330 through 332' Processing helix chain 'L' and resid 356 through 367 removed outlier: 4.316A pdb=" N ILE L 363 " --> pdb=" O GLU L 359 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ALA L 366 " --> pdb=" O LYS L 362 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS L 367 " --> pdb=" O ILE L 363 " (cutoff:3.500A) Processing helix chain 'L' and resid 375 through 380 Processing helix chain 'L' and resid 391 through 402 removed outlier: 3.752A pdb=" N THR L 396 " --> pdb=" O ARG L 392 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N PHE L 401 " --> pdb=" O GLU L 397 " (cutoff:3.500A) Processing helix chain 'L' and resid 412 through 416 Processing helix chain 'L' and resid 418 through 427 removed outlier: 3.700A pdb=" N VAL L 422 " --> pdb=" O ALA L 418 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N GLU L 424 " --> pdb=" O ARG L 420 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LYS L 427 " --> pdb=" O ALA L 423 " (cutoff:3.500A) Processing helix chain 'M' and resid 38 through 44 removed outlier: 3.546A pdb=" N ARG M 42 " --> pdb=" O ASP M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 46 through 71 removed outlier: 3.737A pdb=" N HIS M 53 " --> pdb=" O GLN M 49 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE M 62 " --> pdb=" O MET M 58 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS M 63 " --> pdb=" O LEU M 59 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYS M 70 " --> pdb=" O LYS M 66 " (cutoff:3.500A) Processing helix chain 'M' and resid 137 through 139 No H-bonds generated for 'chain 'M' and resid 137 through 139' Processing helix chain 'M' and resid 165 through 170 removed outlier: 5.298A pdb=" N MET M 170 " --> pdb=" O ARG M 166 " (cutoff:3.500A) Processing helix chain 'M' and resid 187 through 196 removed outlier: 3.576A pdb=" N GLU M 195 " --> pdb=" O GLU M 191 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA M 196 " --> pdb=" O GLU M 192 " (cutoff:3.500A) Processing helix chain 'M' and resid 198 through 202 Processing helix chain 'M' and resid 204 through 208 Processing helix chain 'M' and resid 229 through 238 removed outlier: 3.948A pdb=" N ALA M 237 " --> pdb=" O ARG M 233 " (cutoff:3.500A) Processing helix chain 'M' and resid 260 through 271 Processing helix chain 'M' and resid 296 through 312 removed outlier: 4.052A pdb=" N VAL M 301 " --> pdb=" O GLY M 297 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN M 302 " --> pdb=" O ASP M 298 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR M 304 " --> pdb=" O GLU M 300 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N MET M 305 " --> pdb=" O VAL M 301 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN M 310 " --> pdb=" O LEU M 306 " (cutoff:3.500A) Processing helix chain 'M' and resid 335 through 338 Processing helix chain 'M' and resid 354 through 367 removed outlier: 3.694A pdb=" N ALA M 358 " --> pdb=" O GLU M 354 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN M 359 " --> pdb=" O ASP M 355 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU M 361 " --> pdb=" O ARG M 357 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG M 366 " --> pdb=" O GLN M 362 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LYS M 367 " --> pdb=" O ILE M 363 " (cutoff:3.500A) Processing helix chain 'M' and resid 376 through 381 Processing helix chain 'M' and resid 388 through 405 removed outlier: 3.753A pdb=" N THR M 395 " --> pdb=" O LEU M 391 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU M 403 " --> pdb=" O GLY M 399 " (cutoff:3.500A) Processing helix chain 'M' and resid 413 through 422 removed outlier: 3.589A pdb=" N GLY M 418 " --> pdb=" O ASP M 414 " (cutoff:3.500A) Processing helix chain 'r' and resid 31 through 43 removed outlier: 3.742A pdb=" N LEU r 35 " --> pdb=" O SER r 31 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS r 36 " --> pdb=" O ILE r 32 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N HIS r 40 " --> pdb=" O LYS r 36 " (cutoff:3.500A) Processing helix chain 'r' and resid 89 through 95 removed outlier: 3.700A pdb=" N ASP r 93 " --> pdb=" O ALA r 89 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET r 94 " --> pdb=" O LYS r 90 " (cutoff:3.500A) Processing helix chain 'r' and resid 120 through 132 removed outlier: 3.592A pdb=" N ASN r 124 " --> pdb=" O SER r 120 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER r 128 " --> pdb=" O ASN r 124 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE r 129 " --> pdb=" O THR r 125 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN r 131 " --> pdb=" O LYS r 127 " (cutoff:3.500A) Processing helix chain 'r' and resid 161 through 166 removed outlier: 3.511A pdb=" N ASN r 166 " --> pdb=" O GLY r 162 " (cutoff:3.500A) Processing helix chain 'r' and resid 185 through 187 No H-bonds generated for 'chain 'r' and resid 185 through 187' Processing helix chain 'r' and resid 207 through 216 removed outlier: 4.412A pdb=" N MET r 212 " --> pdb=" O LYS r 208 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN r 215 " --> pdb=" O LYS r 211 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N LEU r 216 " --> pdb=" O MET r 212 " (cutoff:3.500A) Processing helix chain 'r' and resid 233 through 251 removed outlier: 4.200A pdb=" N ALA r 239 " --> pdb=" O GLU r 235 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LYS r 242 " --> pdb=" O LEU r 238 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LYS r 246 " --> pdb=" O LYS r 242 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ILE r 247 " --> pdb=" O SER r 243 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN r 250 " --> pdb=" O LYS r 246 " (cutoff:3.500A) Processing helix chain 'r' and resid 253 through 255 No H-bonds generated for 'chain 'r' and resid 253 through 255' Processing helix chain 'r' and resid 276 through 304 removed outlier: 3.739A pdb=" N THR r 283 " --> pdb=" O HIS r 279 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU r 286 " --> pdb=" O GLU r 282 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL r 293 " --> pdb=" O GLU r 289 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER r 294 " --> pdb=" O ASN r 290 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA r 298 " --> pdb=" O SER r 294 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL r 303 " --> pdb=" O GLY r 299 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA r 304 " --> pdb=" O VAL r 300 " (cutoff:3.500A) Processing helix chain 'u' and resid 23 through 33 removed outlier: 3.906A pdb=" N SER u 28 " --> pdb=" O ASP u 24 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS u 29 " --> pdb=" O ASN u 25 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE u 30 " --> pdb=" O VAL u 26 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN u 31 " --> pdb=" O LYS u 27 " (cutoff:3.500A) Processing helix chain 'u' and resid 38 through 40 No H-bonds generated for 'chain 'u' and resid 38 through 40' Processing helix chain 'u' and resid 56 through 58 No H-bonds generated for 'chain 'u' and resid 56 through 58' Processing sheet with id= A, first strand: chain '1' and resid 124 through 127 removed outlier: 3.720A pdb=" N GLY 1 11 " --> pdb=" O PHE 1 8 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU 1 14 " --> pdb=" O VAL 1 176 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N VAL 1 172 " --> pdb=" O SER 1 18 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N MET 1 175 " --> pdb=" O LEU 1 186 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '1' and resid 41 through 47 removed outlier: 3.620A pdb=" N ALA 1 100 " --> pdb=" O TRP 1 42 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE 1 98 " --> pdb=" O CYS 1 44 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain '1' and resid 111 through 113 Processing sheet with id= D, first strand: chain '2' and resid 124 through 127 removed outlier: 3.525A pdb=" N GLY 2 11 " --> pdb=" O PHE 2 8 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain '2' and resid 42 through 45 removed outlier: 3.611A pdb=" N TRP 2 42 " --> pdb=" O ALA 2 101 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA 2 44 " --> pdb=" O ILE 2 99 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain '3' and resid 136 through 140 removed outlier: 5.756A pdb=" N ILE 3 11 " --> pdb=" O ASP 3 26 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ALA 3 185 " --> pdb=" O LEU 3 200 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU 3 200 " --> pdb=" O ALA 3 185 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE 3 189 " --> pdb=" O VAL 3 196 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL 3 196 " --> pdb=" O ILE 3 189 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain '3' and resid 43 through 46 removed outlier: 3.715A pdb=" N GLY 3 52 " --> pdb=" O VAL 3 108 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS 3 118 " --> pdb=" O ASN 3 113 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain '4' and resid 130 through 132 Processing sheet with id= I, first strand: chain '4' and resid 42 through 48 removed outlier: 3.973A pdb=" N GLY 4 106 " --> pdb=" O GLU 4 115 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU 4 115 " --> pdb=" O GLY 4 106 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain '4' and resid 21 through 23 removed outlier: 4.162A pdb=" N LYS 4 29 " --> pdb=" O VAL 4 21 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ARG 4 23 " --> pdb=" O VAL 4 27 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL 4 27 " --> pdb=" O ARG 4 23 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain '5' and resid 126 through 130 Processing sheet with id= L, first strand: chain '5' and resid 41 through 43 Processing sheet with id= M, first strand: chain '5' and resid 178 through 181 Processing sheet with id= N, first strand: chain '5' and resid 20 through 22 removed outlier: 6.311A pdb=" N ALA 5 22 " --> pdb=" O VAL 5 26 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N VAL 5 26 " --> pdb=" O ALA 5 22 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain '6' and resid 11 through 13 Processing sheet with id= P, first strand: chain '6' and resid 43 through 45 removed outlier: 3.579A pdb=" N PHE 6 44 " --> pdb=" O MET 6 52 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET 6 52 " --> pdb=" O PHE 6 44 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN 6 55 " --> pdb=" O HIS 6 108 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N THR 6 109 " --> pdb=" O PHE 6 125 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL 6 122 " --> pdb=" O GLU 6 134 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain '6' and resid 202 through 204 removed outlier: 3.505A pdb=" N TYR 6 217 " --> pdb=" O LEU 6 202 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain '7' and resid 11 through 15 removed outlier: 4.085A pdb=" N ILE 7 199 " --> pdb=" O THR 7 207 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR 7 207 " --> pdb=" O ILE 7 199 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain '7' and resid 49 through 52 removed outlier: 3.503A pdb=" N GLY 7 118 " --> pdb=" O PHE 7 126 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'A' and resid 168 through 170 removed outlier: 3.538A pdb=" N VAL A 52 " --> pdb=" O VAL A 45 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'A' and resid 79 through 82 Processing sheet with id= V, first strand: chain 'B' and resid 34 through 36 removed outlier: 3.601A pdb=" N THR B 162 " --> pdb=" O GLY B 36 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'B' and resid 45 through 48 removed outlier: 3.805A pdb=" N ILE B 45 " --> pdb=" O ALA B 212 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'B' and resid 134 through 136 Processing sheet with id= Y, first strand: chain 'B' and resid 65 through 68 removed outlier: 3.625A pdb=" N SER B 65 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'C' and resid 35 through 38 removed outlier: 3.592A pdb=" N ALA C 35 " --> pdb=" O VAL C 165 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'C' and resid 135 through 139 removed outlier: 3.713A pdb=" N PHE C 135 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N SER C 151 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR C 149 " --> pdb=" O TYR C 137 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY C 139 " --> pdb=" O GLN C 147 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN C 147 " --> pdb=" O GLY C 139 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'C' and resid 215 through 217 Processing sheet with id= AC, first strand: chain 'C' and resid 67 through 70 removed outlier: 6.471A pdb=" N ILE C 73 " --> pdb=" O LEU C 69 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'D' and resid 161 through 164 removed outlier: 3.515A pdb=" N VAL D 36 " --> pdb=" O VAL D 43 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'D' and resid 134 through 136 removed outlier: 3.516A pdb=" N ALA D 136 " --> pdb=" O VAL D 72 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL D 71 " --> pdb=" O ASP D 68 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASP D 68 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU D 73 " --> pdb=" O LYS D 66 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N LYS D 66 " --> pdb=" O LEU D 73 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'D' and resid 213 through 216 removed outlier: 3.714A pdb=" N VAL D 222 " --> pdb=" O VAL D 214 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'E' and resid 47 through 50 Processing sheet with id= AH, first strand: chain 'E' and resid 152 through 154 removed outlier: 3.537A pdb=" N LEU E 143 " --> pdb=" O ALA E 77 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASP E 71 " --> pdb=" O ILE E 74 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N CYS E 76 " --> pdb=" O GLU E 69 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N GLU E 69 " --> pdb=" O CYS E 76 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N MET E 78 " --> pdb=" O ILE E 67 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ILE E 67 " --> pdb=" O MET E 78 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'F' and resid 35 through 39 removed outlier: 4.223A pdb=" N SER F 212 " --> pdb=" O ALA F 48 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'F' and resid 141 through 146 removed outlier: 3.857A pdb=" N ASP F 138 " --> pdb=" O GLY F 141 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY F 136 " --> pdb=" O HIS F 143 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE F 134 " --> pdb=" O LEU F 145 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER F 73 " --> pdb=" O LEU F 133 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ILE F 135 " --> pdb=" O GLY F 71 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY F 71 " --> pdb=" O ILE F 135 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ASP F 67 " --> pdb=" O MET F 70 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU F 72 " --> pdb=" O LYS F 65 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N LYS F 65 " --> pdb=" O LEU F 72 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N LEU F 74 " --> pdb=" O ILE F 63 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ILE F 63 " --> pdb=" O LEU F 74 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'G' and resid 162 through 164 removed outlier: 3.555A pdb=" N GLY G 39 " --> pdb=" O ALA G 163 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'G' and resid 74 through 77 removed outlier: 3.544A pdb=" N GLY G 139 " --> pdb=" O GLY G 75 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY G 145 " --> pdb=" O ASP G 142 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TRP G 158 " --> pdb=" O MET G 150 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'H' and resid 100 through 104 removed outlier: 3.733A pdb=" N THR H 103 " --> pdb=" O VAL H 146 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N VAL H 146 " --> pdb=" O THR H 103 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'H' and resid 173 through 176 removed outlier: 3.805A pdb=" N LEU H 185 " --> pdb=" O GLY H 175 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'I' and resid 105 through 107 removed outlier: 3.948A pdb=" N GLY I 107 " --> pdb=" O VAL I 147 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY I 158 " --> pdb=" O LEU I 148 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'I' and resid 117 through 120 removed outlier: 3.526A pdb=" N VAL I 120 " --> pdb=" O TYR I 128 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR I 128 " --> pdb=" O VAL I 120 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'I' and resid 325 through 327 removed outlier: 6.755A pdb=" N VAL I 219 " --> pdb=" O MET I 326 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ILE I 348 " --> pdb=" O TYR I 222 " (cutoff:3.500A) No H-bonds generated for sheet with id= AQ Processing sheet with id= AR, first strand: chain 'J' and resid 112 through 116 removed outlier: 3.524A pdb=" N VAL J 84 " --> pdb=" O VAL J 96 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'J' and resid 185 through 188 removed outlier: 6.720A pdb=" N ARG J 312 " --> pdb=" O ILE J 186 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N TYR J 188 " --> pdb=" O ARG J 312 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ILE J 314 " --> pdb=" O TYR J 188 " (cutoff:3.500A) No H-bonds generated for sheet with id= AS Processing sheet with id= AT, first strand: chain 'J' and resid 209 through 213 Processing sheet with id= AU, first strand: chain 'K' and resid 95 through 97 removed outlier: 3.817A pdb=" N GLY K 97 " --> pdb=" O VAL K 137 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL K 137 " --> pdb=" O GLY K 97 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'K' and resid 117 through 120 removed outlier: 4.273A pdb=" N GLU K 101 " --> pdb=" O ILE K 109 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N SER K 111 " --> pdb=" O PHE K 99 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N PHE K 99 " --> pdb=" O SER K 111 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'K' and resid 209 through 211 Processing sheet with id= AX, first strand: chain 'K' and resid 233 through 237 removed outlier: 3.744A pdb=" N ILE K 268 " --> pdb=" O ALA K 233 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'L' and resid 104 through 107 Processing sheet with id= AZ, first strand: chain 'L' and resid 218 through 220 removed outlier: 6.596A pdb=" N ARG L 345 " --> pdb=" O LEU L 219 " (cutoff:3.500A) No H-bonds generated for sheet with id= AZ Processing sheet with id= BA, first strand: chain 'L' and resid 243 through 245 removed outlier: 6.322A pdb=" N ILE L 277 " --> pdb=" O ILE L 244 " (cutoff:3.500A) No H-bonds generated for sheet with id= BA Processing sheet with id= BB, first strand: chain 'M' and resid 78 through 80 removed outlier: 3.596A pdb=" N VAL M 146 " --> pdb=" O ALA M 80 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'M' and resid 117 through 121 removed outlier: 3.836A pdb=" N VAL M 127 " --> pdb=" O VAL M 119 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR M 121 " --> pdb=" O GLN M 125 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLN M 125 " --> pdb=" O THR M 121 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'M' and resid 220 through 222 removed outlier: 5.921A pdb=" N ILE M 347 " --> pdb=" O TYR M 221 " (cutoff:3.500A) No H-bonds generated for sheet with id= BD Processing sheet with id= BE, first strand: chain 'r' and resid 73 through 75 removed outlier: 3.922A pdb=" N GLU r 81 " --> pdb=" O SER r 74 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'r' and resid 154 through 156 removed outlier: 3.733A pdb=" N VAL r 137 " --> pdb=" O VAL r 105 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N MET r 53 " --> pdb=" O VAL r 105 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N TRP r 107 " --> pdb=" O GLY r 51 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N GLY r 51 " --> pdb=" O TRP r 107 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLU r 56 " --> pdb=" O VAL r 65 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N VAL r 65 " --> pdb=" O GLU r 56 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'u' and resid 3 through 5 Processing sheet with id= BH, first strand: chain 'u' and resid 41 through 44 1139 hydrogen bonds defined for protein. 3159 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 14.45 Time building geometry restraints manager: 18.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 11634 1.33 - 1.45: 11424 1.45 - 1.58: 21652 1.58 - 1.71: 26 1.71 - 1.83: 275 Bond restraints: 45011 Sorted by residual: bond pdb=" C5 ATP H 501 " pdb=" N7 ATP H 501 " ideal model delta sigma weight residual 1.387 1.321 0.066 1.00e-02 1.00e+04 4.40e+01 bond pdb=" C4 ATP I 501 " pdb=" C5 ATP I 501 " ideal model delta sigma weight residual 1.388 1.452 -0.064 1.00e-02 1.00e+04 4.16e+01 bond pdb=" C4 ATP H 501 " pdb=" C5 ATP H 501 " ideal model delta sigma weight residual 1.388 1.449 -0.061 1.00e-02 1.00e+04 3.72e+01 bond pdb=" C4 ATP M 501 " pdb=" C5 ATP M 501 " ideal model delta sigma weight residual 1.388 1.448 -0.060 1.00e-02 1.00e+04 3.62e+01 bond pdb=" C5 ATP J 501 " pdb=" N7 ATP J 501 " ideal model delta sigma weight residual 1.387 1.328 0.059 1.00e-02 1.00e+04 3.52e+01 ... (remaining 45006 not shown) Histogram of bond angle deviations from ideal: 97.02 - 104.84: 719 104.84 - 112.66: 23179 112.66 - 120.48: 19203 120.48 - 128.30: 17569 128.30 - 136.12: 328 Bond angle restraints: 60998 Sorted by residual: angle pdb=" PB ATP M 501 " pdb=" O3B ATP M 501 " pdb=" PG ATP M 501 " ideal model delta sigma weight residual 139.87 112.38 27.49 1.00e+00 1.00e+00 7.56e+02 angle pdb=" PA ATP J 501 " pdb=" O3A ATP J 501 " pdb=" PB ATP J 501 " ideal model delta sigma weight residual 136.83 112.65 24.18 1.00e+00 1.00e+00 5.85e+02 angle pdb=" PB ATP H 501 " pdb=" O3B ATP H 501 " pdb=" PG ATP H 501 " ideal model delta sigma weight residual 139.87 116.41 23.46 1.00e+00 1.00e+00 5.50e+02 angle pdb=" PB ATP I 501 " pdb=" O3B ATP I 501 " pdb=" PG ATP I 501 " ideal model delta sigma weight residual 139.87 116.85 23.02 1.00e+00 1.00e+00 5.30e+02 angle pdb=" PB ATP J 501 " pdb=" O3B ATP J 501 " pdb=" PG ATP J 501 " ideal model delta sigma weight residual 139.87 117.46 22.41 1.00e+00 1.00e+00 5.02e+02 ... (remaining 60993 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.47: 26599 27.47 - 54.94: 552 54.94 - 82.41: 44 82.41 - 109.88: 1 109.88 - 137.36: 5 Dihedral angle restraints: 27201 sinusoidal: 10422 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 27198 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 4629 0.063 - 0.127: 1916 0.127 - 0.190: 422 0.190 - 0.253: 70 0.253 - 0.317: 12 Chirality restraints: 7049 Sorted by residual: chirality pdb=" CB VAL E 200 " pdb=" CA VAL E 200 " pdb=" CG1 VAL E 200 " pdb=" CG2 VAL E 200 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" CB VAL 1 172 " pdb=" CA VAL 1 172 " pdb=" CG1 VAL 1 172 " pdb=" CG2 VAL 1 172 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CB VAL I 219 " pdb=" CA VAL I 219 " pdb=" CG1 VAL I 219 " pdb=" CG2 VAL I 219 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 7046 not shown) Planarity restraints: 7868 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN J 181 " -0.065 5.00e-02 4.00e+02 9.81e-02 1.54e+01 pdb=" N PRO J 182 " 0.170 5.00e-02 4.00e+02 pdb=" CA PRO J 182 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO J 182 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG 4 96 " 0.057 5.00e-02 4.00e+02 8.49e-02 1.15e+01 pdb=" N PRO 4 97 " -0.147 5.00e-02 4.00e+02 pdb=" CA PRO 4 97 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO 4 97 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 60 " 0.052 5.00e-02 4.00e+02 7.83e-02 9.82e+00 pdb=" N PRO G 61 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO G 61 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO G 61 " 0.043 5.00e-02 4.00e+02 ... (remaining 7865 not shown) Histogram of nonbonded interaction distances: 1.34 - 2.05: 4 2.05 - 2.76: 9535 2.76 - 3.48: 62017 3.48 - 4.19: 96568 4.19 - 4.90: 168569 Nonbonded interactions: 336693 Sorted by model distance: nonbonded pdb=" NZ LYS s 108 " pdb=" C GLY u 76 " model vdw 1.340 3.350 nonbonded pdb=" NZ LYS s 108 " pdb=" O GLY u 76 " model vdw 1.405 2.520 nonbonded pdb=" OH TYR 3 46 " pdb=" OD1 ASN 3 64 " model vdw 1.983 2.440 nonbonded pdb=" OD1 ASP G 114 " pdb=" OH TYR G 157 " model vdw 2.050 2.440 nonbonded pdb=" OG1 THR I 230 " pdb=" O3G ATP I 501 " model vdw 2.052 2.440 ... (remaining 336688 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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. 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: 2.160 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: 0.030 Extract box with map and model: 11.980 Check model and map are aligned: 0.700 Convert atoms to be neutral: 0.420 Process input model: 104.870 Find NCS groups from input model: 2.270 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 125.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.016 0.139 45011 Z= 1.063 Angle : 1.105 27.490 60998 Z= 0.641 Chirality : 0.070 0.317 7049 Planarity : 0.007 0.098 7868 Dihedral : 11.793 137.355 16423 Min Nonbonded Distance : 1.340 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 14.74 % Favored : 85.22 % Rotamer Outliers : 0.07 % 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 *********************** 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 : 5.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 1024 average time/residue: 0.5709 time to fit residues: 946.5998 Evaluate side-chains 639 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 638 time to evaluate : 5.301 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3796 time to fit residues: 7.9556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 484 optimal weight: 30.0000 chunk 435 optimal weight: 2.9990 chunk 241 optimal weight: 0.7980 chunk 148 optimal weight: 1.9990 chunk 293 optimal weight: 2.9990 chunk 232 optimal weight: 1.9990 chunk 449 optimal weight: 4.9990 chunk 174 optimal weight: 0.9980 chunk 273 optimal weight: 0.7980 chunk 334 optimal weight: 0.9980 chunk 521 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 69 GLN ** 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 24 ASN 5 191 HIS 7 61 GLN 7 112 ASN 7 125 GLN 7 179 ASN ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 HIS B 190 HIS C 21 GLN C 103 ASN D 94 GLN D 178 ASN F 21 GLN F 86 ASN ** F 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 166 GLN F 210 ASN G 23 GLN G 118 GLN G 207 ASN G 228 HIS H 54 ASN H 89 GLN H 281 GLN H 356 ASN H 359 ASN I 192 GLN ** I 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 352 ASN J 204 HIS J 269 GLN ** J 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 98 GLN K 228 ASN K 302 GLN r 126 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2557 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= 0.207 Angle : 0.689 9.921 60998 Z= 0.354 Chirality : 0.048 0.261 7049 Planarity : 0.005 0.059 7868 Dihedral : 7.478 121.261 6322 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer Outliers : 0.15 % 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: -2.86 (0.09), residues: 2025 sheet: -3.13 (0.14), residues: 959 loop : -2.94 (0.11), residues: 2782 *********************** 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 952 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 945 time to evaluate : 5.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 950 average time/residue: 0.5454 time to fit residues: 850.6869 Evaluate side-chains 653 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 652 time to evaluate : 4.922 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3442 time to fit residues: 7.2554 ------------------------------------------------------------------------------- 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: 0.7980 chunk 161 optimal weight: 2.9990 chunk 433 optimal weight: 10.0000 chunk 354 optimal weight: 2.9990 chunk 143 optimal weight: 9.9990 chunk 522 optimal weight: 8.9990 chunk 564 optimal weight: 20.0000 chunk 465 optimal weight: 3.9990 chunk 517 optimal weight: 6.9990 chunk 178 optimal weight: 3.9990 chunk 418 optimal weight: 2.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 65 GLN 4 78 GLN 4 146 HIS ** 6 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 159 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 21 GLN D 178 ASN D 230 ASN E 91 HIS F 86 ASN G 207 ASN H 54 ASN H 217 GLN H 356 ASN H 359 ASN ** I 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 312 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 72 ASN M 238 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.063 45011 Z= 0.313 Angle : 0.702 10.942 60998 Z= 0.359 Chirality : 0.048 0.260 7049 Planarity : 0.005 0.071 7868 Dihedral : 7.099 119.802 6322 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer Outliers : 0.09 % 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: -3.81 (0.10), residues: 5766 helix: -2.23 (0.10), residues: 2047 sheet: -2.57 (0.14), residues: 1044 loop : -2.68 (0.11), residues: 2675 *********************** 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 839 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 835 time to evaluate : 4.822 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 outliers start: 4 outliers final: 2 residues processed: 838 average time/residue: 0.5406 time to fit residues: 750.0494 Evaluate side-chains 621 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 619 time to evaluate : 5.260 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3771 time to fit residues: 8.4804 ------------------------------------------------------------------------------- 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: 10.0000 chunk 392 optimal weight: 7.9990 chunk 271 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 chunk 249 optimal weight: 0.9980 chunk 350 optimal weight: 1.9990 chunk 524 optimal weight: 8.9990 chunk 554 optimal weight: 0.6980 chunk 273 optimal weight: 4.9990 chunk 496 optimal weight: 10.0000 chunk 149 optimal weight: 6.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 8 ASN 4 41 HIS 5 29 GLN ** 6 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 61 GLN 7 74 ASN ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 GLN D 117 GLN ** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 86 ASN H 281 GLN H 359 ASN ** I 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 ASN J 204 HIS J 240 HIS ** J 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 237 ASN r 291 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.071 45011 Z= 0.266 Angle : 0.653 13.991 60998 Z= 0.333 Chirality : 0.047 0.278 7049 Planarity : 0.004 0.049 7868 Dihedral : 6.722 115.826 6322 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer Outliers : 0.09 % 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: -3.33 (0.10), residues: 5766 helix: -1.81 (0.11), residues: 2058 sheet: -2.12 (0.14), residues: 1035 loop : -2.49 (0.11), residues: 2673 *********************** 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 819 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 815 time to evaluate : 5.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 818 average time/residue: 0.5397 time to fit residues: 737.6921 Evaluate side-chains 622 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 620 time to evaluate : 5.107 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3790 time to fit residues: 8.5098 ------------------------------------------------------------------------------- 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: 6.9990 chunk 8 optimal weight: 0.9990 chunk 413 optimal weight: 0.0040 chunk 228 optimal weight: 0.8980 chunk 473 optimal weight: 4.9990 chunk 383 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 283 optimal weight: 7.9990 chunk 498 optimal weight: 5.9990 chunk 140 optimal weight: 8.9990 overall best weight: 2.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 29 GLN ** 6 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 74 ASN ** 7 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 241 GLN C 21 GLN C 103 ASN C 156 ASN ** D 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 216 ASN G 33 ASN H 54 ASN H 356 ASN H 359 ASN ** I 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 303 GLN ** I 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.151 45011 Z= 0.291 Angle : 0.662 19.524 60998 Z= 0.337 Chirality : 0.047 0.278 7049 Planarity : 0.004 0.049 7868 Dihedral : 6.614 111.425 6322 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer Outliers : 0.13 % 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: -3.07 (0.10), residues: 5766 helix: -1.60 (0.11), residues: 2058 sheet: -2.00 (0.15), residues: 1066 loop : -2.32 (0.12), residues: 2642 *********************** 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 827 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 821 time to evaluate : 5.214 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 outliers start: 6 outliers final: 1 residues processed: 825 average time/residue: 0.5431 time to fit residues: 750.8619 Evaluate side-chains 634 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 633 time to evaluate : 5.704 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4364 time to fit residues: 8.6880 ------------------------------------------------------------------------------- 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: 2.9990 chunk 499 optimal weight: 0.8980 chunk 109 optimal weight: 0.6980 chunk 325 optimal weight: 4.9990 chunk 136 optimal weight: 4.9990 chunk 555 optimal weight: 6.9990 chunk 461 optimal weight: 10.0000 chunk 257 optimal weight: 7.9990 chunk 46 optimal weight: 5.9990 chunk 183 optimal weight: 8.9990 chunk 291 optimal weight: 7.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 74 ASN ** 7 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 84 ASN ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 GLN C 103 ASN C 156 ASN ** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 ASN H 54 ASN ** I 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 303 GLN ** I 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 ASN J 277 ASN ** K 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 142 HIS M 72 ASN r 237 ASN r 291 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.4580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.112 45011 Z= 0.317 Angle : 0.678 17.672 60998 Z= 0.346 Chirality : 0.048 0.226 7049 Planarity : 0.004 0.066 7868 Dihedral : 6.633 111.070 6322 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer Outliers : 0.07 % 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: -2.85 (0.11), residues: 5766 helix: -1.40 (0.11), residues: 2051 sheet: -1.80 (0.15), residues: 1067 loop : -2.26 (0.12), residues: 2648 *********************** 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 793 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 790 time to evaluate : 5.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 792 average time/residue: 0.5517 time to fit residues: 729.6942 Evaluate side-chains 618 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 618 time to evaluate : 4.976 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.8110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 535 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 316 optimal weight: 0.8980 chunk 405 optimal weight: 5.9990 chunk 314 optimal weight: 4.9990 chunk 467 optimal weight: 1.9990 chunk 310 optimal weight: 0.9980 chunk 553 optimal weight: 9.9990 chunk 346 optimal weight: 4.9990 chunk 337 optimal weight: 3.9990 chunk 255 optimal weight: 6.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 74 ASN ** 7 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 GLN C 103 ASN G 33 ASN H 356 ASN I 238 ASN I 303 GLN ** I 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 28 GLN J 128 ASN J 277 ASN ** K 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 142 HIS M 74 GLN M 311 GLN r 237 ASN r 291 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.225 45011 Z= 0.227 Angle : 0.638 20.468 60998 Z= 0.325 Chirality : 0.046 0.189 7049 Planarity : 0.004 0.079 7868 Dihedral : 6.360 109.360 6322 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer Outliers : 0.09 % 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: -2.63 (0.11), residues: 5766 helix: -1.25 (0.11), residues: 2055 sheet: -1.63 (0.15), residues: 1080 loop : -2.11 (0.12), residues: 2631 *********************** 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 799 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 795 time to evaluate : 5.411 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 outliers start: 4 outliers final: 0 residues processed: 798 average time/residue: 0.5818 time to fit residues: 783.7408 Evaluate side-chains 626 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 626 time to evaluate : 5.447 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.3653 ------------------------------------------------------------------------------- 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: 0.9980 chunk 220 optimal weight: 10.0000 chunk 330 optimal weight: 5.9990 chunk 166 optimal weight: 8.9990 chunk 108 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 351 optimal weight: 0.9990 chunk 376 optimal weight: 2.9990 chunk 273 optimal weight: 4.9990 chunk 51 optimal weight: 0.0870 chunk 434 optimal weight: 6.9990 overall best weight: 2.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 74 ASN ** 7 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 27 GLN ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 84 ASN ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 GLN C 103 ASN ** C 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 ASN H 356 ASN I 238 ASN I 303 GLN ** I 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 ASN J 277 ASN ** K 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 142 HIS M 72 ASN r 237 ASN r 291 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.4895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.508 45011 Z= 0.273 Angle : 0.698 54.832 60998 Z= 0.347 Chirality : 0.046 0.189 7049 Planarity : 0.004 0.071 7868 Dihedral : 6.221 110.101 6322 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer Outliers : 0.09 % 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: -2.50 (0.11), residues: 5766 helix: -1.13 (0.11), residues: 2047 sheet: -1.52 (0.15), residues: 1084 loop : -2.07 (0.12), residues: 2635 *********************** 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 784 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 780 time to evaluate : 5.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 784 average time/residue: 0.5462 time to fit residues: 719.3417 Evaluate side-chains 633 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 633 time to evaluate : 5.427 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.3384 ------------------------------------------------------------------------------- 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: 7.9990 chunk 530 optimal weight: 6.9990 chunk 483 optimal weight: 3.9990 chunk 515 optimal weight: 7.9990 chunk 529 optimal weight: 0.7980 chunk 310 optimal weight: 0.8980 chunk 224 optimal weight: 6.9990 chunk 404 optimal weight: 6.9990 chunk 158 optimal weight: 5.9990 chunk 465 optimal weight: 2.9990 chunk 487 optimal weight: 6.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 112 ASN ** 5 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 133 GLN ** 6 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 74 ASN 7 120 GLN ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 GLN C 103 ASN ** C 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 HIS G 33 ASN H 54 ASN ** I 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 303 GLN ** I 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 ASN J 269 GLN J 277 ASN ** K 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 142 HIS M 72 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.4992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.509 45011 Z= 0.344 Angle : 0.735 53.098 60998 Z= 0.367 Chirality : 0.048 0.215 7049 Planarity : 0.005 0.142 7868 Dihedral : 6.314 112.634 6322 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.11), residues: 5766 helix: -1.13 (0.11), residues: 2049 sheet: -1.55 (0.15), residues: 1099 loop : -2.10 (0.12), residues: 2618 *********************** 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 764 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 761 time to evaluate : 5.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 764 average time/residue: 0.5405 time to fit residues: 694.4042 Evaluate side-chains 617 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 616 time to evaluate : 5.170 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3749 time to fit residues: 7.7302 ------------------------------------------------------------------------------- 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: 1.9990 chunk 338 optimal weight: 0.9980 chunk 545 optimal weight: 0.1980 chunk 332 optimal weight: 0.8980 chunk 258 optimal weight: 1.9990 chunk 378 optimal weight: 9.9990 chunk 571 optimal weight: 0.9980 chunk 526 optimal weight: 0.9980 chunk 455 optimal weight: 10.0000 chunk 47 optimal weight: 0.6980 chunk 351 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 8 ASN ** 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 21 GLN ** C 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 ASN H 54 ASN I 238 ASN I 303 GLN ** I 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 ASN J 277 ASN K 72 GLN K 142 HIS M 72 ASN r 237 ASN r 291 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.5120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.467 45011 Z= 0.212 Angle : 0.672 44.226 60998 Z= 0.335 Chirality : 0.045 0.209 7049 Planarity : 0.004 0.139 7868 Dihedral : 5.963 108.004 6322 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer Outliers : 0.04 % 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: -2.29 (0.11), residues: 5766 helix: -0.98 (0.11), residues: 2047 sheet: -1.32 (0.16), residues: 1069 loop : -1.97 (0.12), residues: 2650 ********************** 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 791 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 789 time to evaluate : 5.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 791 average time/residue: 0.5678 time to fit residues: 759.4953 Evaluate side-chains 627 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 627 time to evaluate : 5.374 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.0264 ------------------------------------------------------------------------------- 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: 8.9990 chunk 361 optimal weight: 7.9990 chunk 485 optimal weight: 6.9990 chunk 139 optimal weight: 0.0040 chunk 419 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 126 optimal weight: 9.9990 chunk 456 optimal weight: 10.0000 chunk 190 optimal weight: 5.9990 chunk 468 optimal weight: 7.9990 chunk 57 optimal weight: 6.9990 overall best weight: 4.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 41 HIS ** 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** C 21 GLN C 103 ASN ** C 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 216 ASN G 33 ASN H 89 GLN H 265 ASN ** I 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 277 ASN M 72 ASN M 362 GLN r 237 ASN r 291 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.072260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.062229 restraints weight = 118089.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.063025 restraints weight = 84148.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.063222 restraints weight = 66330.462| |-----------------------------------------------------------------------------| r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.5176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.490 45011 Z= 0.450 Angle : 0.797 35.336 60998 Z= 0.406 Chirality : 0.051 0.289 7049 Planarity : 0.005 0.094 7868 Dihedral : 6.490 110.103 6322 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.86 % Favored : 91.12 % Rotamer Outliers : 0.09 % 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: -1.19 (0.11), residues: 2055 sheet: -1.54 (0.15), residues: 1113 loop : -2.09 (0.12), residues: 2598 =============================================================================== Job complete usr+sys time: 11333.58 seconds wall clock time: 204 minutes 43.92 seconds (12283.92 seconds total)