Starting phenix.real_space_refine on Tue Sep 15 19:22:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ef3_9045/09_2026/6ef3_9045.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ef3_9045/09_2026/6ef3_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6ef3_9045/09_2026/6ef3_9045.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ef3_9045/09_2026/6ef3_9045.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ef3_9045/09_2026/6ef3_9045.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ef3_9045/09_2026/6ef3_9045.map" model { file = "/net/cci-nas-00/data/ceres_data/6ef3_9045/09_2026/6ef3_9045.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ef3_9045/09_2026/6ef3_9045.cif" } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 164 5.16 5 C 27951 2.51 5 N 7654 2.21 5 O 8486 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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: {'ASP:plan': 2, 'GLN:plan1': 1} 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: {'ASP:plan': 1, 'ARG: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: {'ARG:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 2, 'ASN:plan1': 1} 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: {'ARG:plan': 5, 'GLU:plan': 4, 'HIS:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 55 Chain: "I" Number of atoms: 2871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2871 Classifications: {'peptide': 384} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 366} Unresolved non-hydrogen bonds: 145 Unresolved non-hydrogen angles: 175 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 1, 'PHE:plan': 1, 'GLU:plan': 12, 'GLN:plan1': 2, 'ASP:plan': 7, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 91 Chain: "J" Number of atoms: 2918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2918 Classifications: {'peptide': 383} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 367} Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 52 Chain: "K" Number of atoms: 2761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2761 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 352} Chain breaks: 1 Unresolved non-hydrogen bonds: 186 Unresolved non-hydrogen angles: 230 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 3, 'GLU:plan': 6, 'ASP:plan': 10, 'GLN:plan1': 3, 'ARG:plan': 5, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 122 Chain: "L" Number of atoms: 2525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2525 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 342} Unresolved non-hydrogen bonds: 321 Unresolved non-hydrogen angles: 396 Unresolved non-hydrogen dihedrals: 259 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ARG:plan': 9, 'TYR:plan': 1, 'ASP:plan': 12, 'GLN:plan1': 4, 'GLU:plan': 19, 'ASN:plan1': 3, 'PHE:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 218 Chain: "M" Number of atoms: 2717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2717 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 355} Chain breaks: 1 Unresolved non-hydrogen bonds: 187 Unresolved non-hydrogen angles: 219 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 7, 'GLU:plan': 10, 'ASP:plan': 11, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 112 Chain: "n" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 14} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "r" Number of atoms: 2088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2088 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 274} Chain breaks: 1 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 4, 'ASN:plan1': 1, 'TYR:plan': 2, 'GLU:plan': 4, '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: {'HIS:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 1, 'GLN:plan1': 1, 'TYR: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: {'GLU:plan': 5, 'ASP:plan': 6, 'ASN:plan1': 1, 'GLN:plan1': 2, 'ARG:plan': 3} 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: 8.61, per 1000 atoms: 0.19 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 - 3.00 Amino acid : True - 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.41 Conformation dependent library (CDL) restraints added in 1.8 seconds 11532 Ramachandran restraints generated. 5766 Oldfield, 0 Emsley, 5766 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10778 Finding SS restraints... Secondary structure from input PDB file: 205 helices and 62 sheets defined 38.6% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain '1' and resid 49 through 70 removed outlier: 4.026A pdb=" N ALA 1 54 " --> pdb=" O ALA 1 50 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N TYR 1 61 " --> pdb=" O ASP 1 57 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER 1 68 " --> pdb=" O GLU 1 64 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR 1 70 " --> pdb=" O TYR 1 66 " (cutoff:3.500A) Processing helix chain '1' and resid 75 through 87 removed outlier: 3.724A pdb=" N ALA 1 79 " --> pdb=" O THR 1 75 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER 1 80 " --> pdb=" O GLU 1 76 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N GLU 1 84 " --> pdb=" O SER 1 80 " (cutoff:3.500A) Processing helix chain '1' and resid 134 through 140 removed outlier: 3.740A pdb=" N ASP 1 139 " --> pdb=" O TYR 1 135 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LYS 1 140 " --> pdb=" O GLY 1 136 " (cutoff:3.500A) Processing helix chain '1' and resid 147 through 165 removed outlier: 4.071A pdb=" N ASP 1 153 " --> pdb=" O GLU 1 149 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE 1 154 " --> pdb=" O GLU 1 150 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TRP 1 165 " --> pdb=" O GLN 1 161 " (cutoff:3.500A) Processing helix chain '1' and resid 189 through 195 removed outlier: 3.828A pdb=" N TYR 1 193 " --> pdb=" O TYR 1 189 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLN 1 195 " --> pdb=" O ASP 1 191 " (cutoff:3.500A) Processing helix chain '2' and resid 48 through 63 removed outlier: 4.131A pdb=" N VAL 2 55 " --> pdb=" O ASP 2 51 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER 2 61 " --> pdb=" O GLN 2 57 " (cutoff:3.500A) Processing helix chain '2' and resid 63 through 71 Processing helix chain '2' and resid 77 through 82 removed outlier: 3.686A pdb=" N MET 2 82 " --> pdb=" O SER 2 78 " (cutoff:3.500A) Processing helix chain '2' and resid 82 through 91 removed outlier: 3.586A pdb=" N PHE 2 88 " --> pdb=" O LYS 2 84 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS 2 89 " --> pdb=" O GLN 2 85 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TYR 2 90 " --> pdb=" O HIS 2 86 " (cutoff:3.500A) Processing helix chain '2' and resid 130 through 140 removed outlier: 3.525A pdb=" N MET 2 135 " --> pdb=" O SER 2 131 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU 2 138 " --> pdb=" O ALA 2 134 " (cutoff:3.500A) Processing helix chain '2' and resid 147 through 165 removed outlier: 3.513A pdb=" N ALA 2 151 " --> pdb=" O THR 2 147 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LYS 2 153 " --> pdb=" O GLU 2 149 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE 2 159 " --> pdb=" O ALA 2 155 " (cutoff:3.500A) Processing helix chain '3' and resid 3 through 7 removed outlier: 3.673A pdb=" N SER 3 6 " --> pdb=" O ASP 3 3 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE 3 7 " --> pdb=" O PRO 3 4 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 3 through 7' Processing helix chain '3' and resid 57 through 79 removed outlier: 4.038A pdb=" N LEU 3 63 " --> pdb=" O ASP 3 59 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU 3 65 " --> pdb=" O THR 3 61 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N MET 3 66 " --> pdb=" O THR 3 62 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS 3 70 " --> pdb=" O MET 3 66 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASN 3 72 " --> pdb=" O ARG 3 68 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LEU 3 73 " --> pdb=" O TYR 3 69 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU 3 76 " --> pdb=" O ASN 3 72 " (cutoff:3.500A) Processing helix chain '3' and resid 83 through 97 removed outlier: 4.283A pdb=" N GLN 3 89 " --> pdb=" O GLU 3 85 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER 3 92 " --> pdb=" O THR 3 88 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU 3 97 " --> pdb=" O SER 3 93 " (cutoff:3.500A) Processing helix chain '3' and resid 147 through 152 removed outlier: 3.565A pdb=" N GLU 3 151 " --> pdb=" O PHE 3 147 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER 3 152 " --> pdb=" O GLY 3 148 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 147 through 152' Processing helix chain '3' and resid 159 through 176 removed outlier: 4.224A pdb=" N THR 3 166 " --> pdb=" O ASP 3 162 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN 3 169 " --> pdb=" O GLU 3 165 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA 3 174 " --> pdb=" O ALA 3 170 " (cutoff:3.500A) Processing helix chain '4' and resid 53 through 69 removed outlier: 4.000A pdb=" N ALA 4 57 " --> pdb=" O THR 4 53 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU 4 58 " --> pdb=" O VAL 4 54 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR 4 59 " --> pdb=" O GLN 4 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU 4 66 " --> pdb=" O ALA 4 62 " (cutoff:3.500A) Processing helix chain '4' and resid 76 through 92 removed outlier: 3.507A pdb=" N SER 4 82 " --> pdb=" O GLN 4 78 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG 4 85 " --> pdb=" O SER 4 81 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLN 4 86 " --> pdb=" O SER 4 82 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU 4 87 " --> pdb=" O PHE 4 83 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU 4 88 " --> pdb=" O VAL 4 84 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS 4 90 " --> pdb=" O GLN 4 86 " (cutoff:3.500A) Processing helix chain '4' and resid 136 through 140 Processing helix chain '4' and resid 153 through 162 removed outlier: 4.074A pdb=" N GLY 4 157 " --> pdb=" O THR 4 153 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LEU 4 158 " --> pdb=" O THR 4 154 " (cutoff:3.500A) Processing helix chain '4' and resid 163 through 170 removed outlier: 3.532A pdb=" N LEU 4 168 " --> pdb=" O CYS 4 164 " (cutoff:3.500A) Processing helix chain '5' and resid 48 through 65 removed outlier: 4.757A pdb=" N TRP 5 55 " --> pdb=" O ASP 5 51 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR 5 57 " --> pdb=" O GLN 5 53 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER 5 61 " --> pdb=" O THR 5 57 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN 5 62 " --> pdb=" O TRP 5 58 " (cutoff:3.500A) Processing helix chain '5' and resid 66 through 71 removed outlier: 4.095A pdb=" N GLU 5 70 " --> pdb=" O HIS 5 66 " (cutoff:3.500A) Processing helix chain '5' and resid 75 through 89 removed outlier: 4.404A pdb=" N ALA 5 79 " --> pdb=" O SER 5 75 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS 5 81 " --> pdb=" O ALA 5 77 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU 5 83 " --> pdb=" O ALA 5 79 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER 5 84 " --> pdb=" O SER 5 80 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLN 5 89 " --> pdb=" O ASN 5 85 " (cutoff:3.500A) Processing helix chain '5' and resid 132 through 144 removed outlier: 3.724A pdb=" N GLY 5 138 " --> pdb=" O THR 5 134 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N VAL 5 139 " --> pdb=" O PHE 5 135 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU 5 140 " --> pdb=" O ALA 5 136 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER 5 142 " --> pdb=" O GLY 5 138 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN 5 143 " --> pdb=" O VAL 5 139 " (cutoff:3.500A) Processing helix chain '5' and resid 150 through 163 removed outlier: 3.742A pdb=" N LYS 5 158 " --> pdb=" O LEU 5 154 " (cutoff:3.500A) Processing helix chain '5' and resid 193 through 205 removed outlier: 4.560A pdb=" N TRP 5 198 " --> pdb=" O GLY 5 194 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LYS 5 199 " --> pdb=" O GLU 5 195 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU 5 202 " --> pdb=" O TRP 5 198 " (cutoff:3.500A) Processing helix chain '6' and resid 59 through 80 removed outlier: 4.598A pdb=" N VAL 6 65 " --> pdb=" O GLY 6 61 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN 6 70 " --> pdb=" O LYS 6 66 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LYS 6 73 " --> pdb=" O LYS 6 69 " (cutoff:3.500A) Processing helix chain '6' and resid 85 through 99 removed outlier: 3.825A pdb=" N ALA 6 89 " --> pdb=" O SER 6 85 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG 6 91 " --> pdb=" O ASN 6 87 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE 6 93 " --> pdb=" O ALA 6 89 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN 6 94 " --> pdb=" O ALA 6 90 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N HIS 6 95 " --> pdb=" O ARG 6 91 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU 6 97 " --> pdb=" O ILE 6 93 " (cutoff:3.500A) Processing helix chain '6' and resid 146 through 151 removed outlier: 3.565A pdb=" N LEU 6 150 " --> pdb=" O ILE 6 146 " (cutoff:3.500A) Processing helix chain '6' and resid 176 through 188 Processing helix chain '7' and resid 56 through 76 removed outlier: 3.851A pdb=" N HIS 7 62 " --> pdb=" O SER 7 58 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU 7 66 " --> pdb=" O HIS 7 62 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS 7 68 " --> pdb=" O GLU 7 64 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASP 7 69 " --> pdb=" O ARG 7 65 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR 7 76 " --> pdb=" O THR 7 72 " (cutoff:3.500A) Processing helix chain '7' and resid 89 through 94 removed outlier: 4.131A pdb=" N GLU 7 94 " --> pdb=" O SER 7 90 " (cutoff:3.500A) Processing helix chain '7' and resid 94 through 105 removed outlier: 4.664A pdb=" N MET 7 100 " --> pdb=" O LEU 7 96 " (cutoff:3.500A) Processing helix chain '7' and resid 145 through 151 removed outlier: 3.560A pdb=" N HIS 7 149 " --> pdb=" O GLY 7 145 " (cutoff:3.500A) Processing helix chain '7' and resid 151 through 159 removed outlier: 3.542A pdb=" N LYS 7 157 " --> pdb=" O PRO 7 153 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL 7 158 " --> pdb=" O LEU 7 154 " (cutoff:3.500A) Processing helix chain '7' and resid 169 through 188 removed outlier: 3.613A pdb=" N ALA 7 176 " --> pdb=" O VAL 7 172 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE 7 177 " --> pdb=" O ALA 7 173 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ASN 7 179 " --> pdb=" O GLU 7 175 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL 7 183 " --> pdb=" O ASN 7 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 4 through 10 Processing helix chain 'A' and resid 27 through 35 removed outlier: 4.466A pdb=" N PHE A 32 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS A 33 " --> pdb=" O TYR A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 99 removed outlier: 3.549A pdb=" N ASN A 92 " --> pdb=" O PRO A 88 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ALA A 93 " --> pdb=" O ASP A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 108 removed outlier: 3.579A pdb=" N PHE A 104 " --> pdb=" O GLU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 121 removed outlier: 3.651A pdb=" N MET A 121 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 126 removed outlier: 3.607A pdb=" N GLN A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 130 Processing helix chain 'A' and resid 174 through 190 removed outlier: 3.648A pdb=" N ILE A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N HIS A 185 " --> pdb=" O ASN A 181 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER A 189 " --> pdb=" O HIS A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 213 removed outlier: 3.684A pdb=" N VAL A 203 " --> pdb=" O TRP A 199 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU A 204 " --> pdb=" O GLU A 200 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE A 205 " --> pdb=" O LYS A 201 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR A 208 " --> pdb=" O GLU A 204 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA A 213 " --> pdb=" O HIS A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 246 removed outlier: 3.875A pdb=" N VAL A 246 " --> pdb=" O GLU A 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 30 removed outlier: 3.985A pdb=" N THR B 26 " --> pdb=" O ASP B 22 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS B 29 " --> pdb=" O LEU B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 87 removed outlier: 4.407A pdb=" N LEU B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASP B 87 " --> pdb=" O ARG B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 97 removed outlier: 3.684A pdb=" N TYR B 97 " --> pdb=" O ALA B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 101 Processing helix chain 'B' and resid 107 through 116 removed outlier: 3.612A pdb=" N VAL B 111 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS B 116 " --> pdb=" O SER B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 123 removed outlier: 4.237A pdb=" N GLN B 123 " --> pdb=" O GLU B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 176 removed outlier: 3.660A pdb=" N ALA B 171 " --> pdb=" O GLY B 167 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE B 174 " --> pdb=" O ALA B 170 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLU B 176 " --> pdb=" O LYS B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 195 Processing helix chain 'B' and resid 205 through 207 No H-bonds generated for 'chain 'B' and resid 205 through 207' Processing helix chain 'B' and resid 218 through 222 Processing helix chain 'B' and resid 239 through 245 Processing helix chain 'B' and resid 246 through 250 Processing helix chain 'C' and resid 19 through 24 removed outlier: 3.964A pdb=" N GLU C 23 " --> pdb=" O LEU C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 28 Processing helix chain 'C' and resid 84 through 87 Processing helix chain 'C' and resid 88 through 103 removed outlier: 3.706A pdb=" N ASN C 97 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N THR C 101 " --> pdb=" O ASN C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 119 removed outlier: 3.997A pdb=" N LEU C 111 " --> pdb=" O PRO C 107 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG C 113 " --> pdb=" O GLU C 109 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS C 119 " --> pdb=" O LEU C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 178 removed outlier: 3.678A pdb=" N LEU C 176 " --> pdb=" O ALA C 172 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET C 178 " --> pdb=" O THR C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 201 removed outlier: 3.745A pdb=" N GLU C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU C 192 " --> pdb=" O ASP C 188 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LYS C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 242 removed outlier: 3.568A pdb=" N ILE C 235 " --> pdb=" O LYS C 231 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS C 236 " --> pdb=" O PRO C 232 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASP C 237 " --> pdb=" O GLN C 233 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR C 242 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 28 removed outlier: 3.674A pdb=" N LEU D 24 " --> pdb=" O VAL D 20 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU D 25 " --> pdb=" O GLU D 21 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA D 26 " --> pdb=" O TYR D 22 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS D 28 " --> pdb=" O LEU D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 101 removed outlier: 3.662A pdb=" N SER D 82 " --> pdb=" O LEU D 78 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ILE D 84 " --> pdb=" O ALA D 80 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU D 85 " --> pdb=" O ASP D 81 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N VAL D 91 " --> pdb=" O GLU D 87 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG D 97 " --> pdb=" O ALA D 93 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU D 98 " --> pdb=" O GLN D 94 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N THR D 99 " --> pdb=" O SER D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 114 removed outlier: 3.746A pdb=" N ARG D 111 " --> pdb=" O GLU D 107 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TYR D 112 " --> pdb=" O TYR D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 179 removed outlier: 3.623A pdb=" N VAL D 171 " --> pdb=" O ASN D 167 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N GLU D 173 " --> pdb=" O LYS D 169 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE D 174 " --> pdb=" O THR D 170 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN D 178 " --> pdb=" O PHE D 174 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR D 179 " --> pdb=" O LEU D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 200 removed outlier: 3.567A pdb=" N SER D 198 " --> pdb=" O LEU D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 239 removed outlier: 3.954A pdb=" N GLN D 231 " --> pdb=" O GLU D 227 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TYR D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN D 235 " --> pdb=" O GLN D 231 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ILE D 236 " --> pdb=" O TYR D 232 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU D 237 " --> pdb=" O VAL D 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 31 removed outlier: 4.141A pdb=" N GLU E 25 " --> pdb=" O LEU E 21 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER E 27 " --> pdb=" O GLN E 23 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU E 29 " --> pdb=" O GLU E 25 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE E 31 " --> pdb=" O SER E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 103 removed outlier: 4.426A pdb=" N THR E 94 " --> pdb=" O GLU E 90 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA E 96 " --> pdb=" O ALA E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 117 Processing helix chain 'E' and resid 175 through 180 Processing helix chain 'E' and resid 193 through 198 removed outlier: 4.040A pdb=" N LEU E 198 " --> pdb=" O LYS E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 201 No H-bonds generated for 'chain 'E' and resid 199 through 201' Processing helix chain 'E' and resid 202 through 208 Processing helix chain 'E' and resid 232 through 248 removed outlier: 3.628A pdb=" N LEU E 239 " --> pdb=" O LYS E 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 26 removed outlier: 3.835A pdb=" N GLU F 23 " --> pdb=" O LEU F 19 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 32 Processing helix chain 'F' and resid 78 through 99 removed outlier: 3.805A pdb=" N VAL F 83 " --> pdb=" O PRO F 79 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N LEU F 84 " --> pdb=" O ASP F 80 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLN F 90 " --> pdb=" O ASN F 86 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER F 96 " --> pdb=" O CYS F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 110 removed outlier: 4.874A pdb=" N GLY F 109 " --> pdb=" O GLU F 106 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N HIS F 110 " --> pdb=" O ARG F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 122 removed outlier: 4.046A pdb=" N LYS F 115 " --> pdb=" O LEU F 111 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN F 117 " --> pdb=" O CYS F 113 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN F 119 " --> pdb=" O LYS F 115 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N THR F 120 " --> pdb=" O ALA F 116 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER F 122 " --> pdb=" O LYS F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 173 removed outlier: 3.509A pdb=" N LYS F 169 " --> pdb=" O SER F 165 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR F 171 " --> pdb=" O GLY F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 178 removed outlier: 4.404A pdb=" N ASP F 177 " --> pdb=" O ARG F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 198 removed outlier: 3.827A pdb=" N LEU F 189 " --> pdb=" O ASN F 185 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LYS F 191 " --> pdb=" O ASP F 187 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY F 193 " --> pdb=" O LEU F 189 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU F 195 " --> pdb=" O LYS F 191 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER F 198 " --> pdb=" O VAL F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 201 No H-bonds generated for 'chain 'F' and resid 199 through 201' Processing helix chain 'F' and resid 230 through 234 Processing helix chain 'G' and resid 23 through 32 removed outlier: 4.922A pdb=" N LYS G 29 " --> pdb=" O GLU G 25 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA G 30 " --> pdb=" O TYR G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 104 removed outlier: 3.502A pdb=" N GLY G 85 " --> pdb=" O LEU G 81 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG G 91 " --> pdb=" O HIS G 87 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N GLU G 94 " --> pdb=" O ASN G 90 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA G 96 " --> pdb=" O GLY G 92 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ALA G 97 " --> pdb=" O ARG G 93 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N LEU G 102 " --> pdb=" O SER G 98 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR G 103 " --> pdb=" O PHE G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 114 Processing helix chain 'G' and resid 119 through 124 removed outlier: 3.733A pdb=" N HIS G 123 " --> pdb=" O TYR G 119 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR G 124 " --> pdb=" O VAL G 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 119 through 124' Processing helix chain 'G' and resid 168 through 183 removed outlier: 3.562A pdb=" N ALA G 172 " --> pdb=" O GLY G 168 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ALA G 174 " --> pdb=" O GLN G 170 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU G 175 " --> pdb=" O SER G 171 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLU G 177 " --> pdb=" O LYS G 173 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU G 179 " --> pdb=" O GLU G 175 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL G 180 " --> pdb=" O LEU G 176 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP G 181 " --> pdb=" O GLU G 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 204 removed outlier: 4.094A pdb=" N ILE G 199 " --> pdb=" O GLN G 195 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 207 No H-bonds generated for 'chain 'G' and resid 205 through 207' Processing helix chain 'G' and resid 220 through 225 Processing helix chain 'G' and resid 233 through 247 removed outlier: 3.694A pdb=" N LYS G 245 " --> pdb=" O ASP G 241 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU G 246 " --> pdb=" O PHE G 242 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 65 removed outlier: 3.720A pdb=" N LEU H 49 " --> pdb=" O TYR H 45 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS H 50 " --> pdb=" O ALA H 46 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLN H 51 " --> pdb=" O ALA H 47 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASN H 54 " --> pdb=" O LYS H 50 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU H 56 " --> pdb=" O THR H 52 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LYS H 57 " --> pdb=" O GLU H 53 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ASP H 58 " --> pdb=" O ASN H 54 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS H 64 " --> pdb=" O GLU H 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 84 through 91 removed outlier: 4.423A pdb=" N ARG H 88 " --> pdb=" O ILE H 84 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU H 91 " --> pdb=" O ASP H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 192 through 197 removed outlier: 3.973A pdb=" N THR H 196 " --> pdb=" O ASP H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 214 through 226 removed outlier: 3.860A pdb=" N ILE H 218 " --> pdb=" O CYS H 214 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU H 219 " --> pdb=" O LYS H 215 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU H 223 " --> pdb=" O GLU H 219 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL H 224 " --> pdb=" O LYS H 220 " (cutoff:3.500A) Processing helix chain 'H' and resid 226 through 231 Processing helix chain 'H' and resid 231 through 239 removed outlier: 4.183A pdb=" N PHE H 235 " --> pdb=" O SER H 231 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR H 237 " --> pdb=" O GLU H 233 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY H 239 " --> pdb=" O PHE H 235 " (cutoff:3.500A) Processing helix chain 'H' and resid 257 through 266 removed outlier: 3.506A pdb=" N VAL H 263 " --> pdb=" O CYS H 259 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA H 264 " --> pdb=" O ALA H 260 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASN H 265 " --> pdb=" O ARG H 261 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG H 266 " --> pdb=" O ALA H 262 " (cutoff:3.500A) Processing helix chain 'H' and resid 275 through 279 removed outlier: 3.582A pdb=" N LEU H 279 " --> pdb=" O GLY H 276 " (cutoff:3.500A) Processing helix chain 'H' and resid 286 through 301 removed outlier: 3.775A pdb=" N ALA H 298 " --> pdb=" O LEU H 294 " (cutoff:3.500A) Processing helix chain 'H' and resid 326 through 341 removed outlier: 3.552A pdb=" N GLN H 330 " --> pdb=" O ASP H 326 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG H 331 " --> pdb=" O ASN H 327 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU H 335 " --> pdb=" O ARG H 331 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU H 336 " --> pdb=" O THR H 332 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN H 339 " --> pdb=" O GLU H 335 " (cutoff:3.500A) Processing helix chain 'H' and resid 362 through 367 removed outlier: 3.717A pdb=" N ARG H 367 " --> pdb=" O ALA H 364 " (cutoff:3.500A) Processing helix chain 'H' and resid 381 through 393 removed outlier: 3.710A pdb=" N ASN H 387 " --> pdb=" O GLU H 383 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE H 388 " --> pdb=" O GLY H 384 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE H 389 " --> pdb=" O ARG H 385 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE H 391 " --> pdb=" O ASN H 387 " (cutoff:3.500A) Processing helix chain 'H' and resid 403 through 411 removed outlier: 4.082A pdb=" N ILE H 407 " --> pdb=" O ARG H 403 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ARG H 409 " --> pdb=" O GLU H 405 " (cutoff:3.500A) Processing helix chain 'H' and resid 415 through 432 removed outlier: 3.974A pdb=" N VAL H 422 " --> pdb=" O GLU H 418 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY H 427 " --> pdb=" O CYS H 423 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA H 430 " --> pdb=" O ALA H 426 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE H 431 " --> pdb=" O GLY H 427 " (cutoff:3.500A) Processing helix chain 'H' and resid 440 through 451 removed outlier: 3.612A pdb=" N LEU H 444 " --> pdb=" O GLU H 440 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LYS H 449 " --> pdb=" O LYS H 445 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 59 removed outlier: 4.401A pdb=" N LYS I 58 " --> pdb=" O CYS I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 79 removed outlier: 3.892A pdb=" N ARG I 64 " --> pdb=" O LEU I 60 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ILE I 65 " --> pdb=" O ARG I 61 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS I 66 " --> pdb=" O MET I 62 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE I 75 " --> pdb=" O LEU I 71 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL I 76 " --> pdb=" O GLU I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 91 removed outlier: 3.514A pdb=" N GLU I 90 " --> pdb=" O GLU I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 100 removed outlier: 4.485A pdb=" N GLU I 97 " --> pdb=" O LYS I 93 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLU I 98 " --> pdb=" O LYS I 94 " (cutoff:3.500A) Processing helix chain 'I' and resid 165 through 172 removed outlier: 3.823A pdb=" N SER I 169 " --> pdb=" O ASP I 165 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS I 172 " --> pdb=" O VAL I 168 " (cutoff:3.500A) Processing helix chain 'I' and resid 191 through 199 removed outlier: 4.859A pdb=" N SER I 197 " --> pdb=" O GLU I 193 " (cutoff:3.500A) Processing helix chain 'I' and resid 205 through 210 Processing helix chain 'I' and resid 228 through 237 removed outlier: 3.626A pdb=" N VAL I 236 " --> pdb=" O LEU I 232 " (cutoff:3.500A) Processing helix chain 'I' and resid 248 through 253 removed outlier: 3.600A pdb=" N ILE I 253 " --> pdb=" O SER I 250 " (cutoff:3.500A) Processing helix chain 'I' and resid 259 through 274 removed outlier: 3.766A pdb=" N ARG I 265 " --> pdb=" O PRO I 261 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE I 268 " --> pdb=" O CYS I 264 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS I 269 " --> pdb=" O ARG I 265 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLY I 272 " --> pdb=" O PHE I 268 " (cutoff:3.500A) Processing helix chain 'I' and resid 283 through 287 Processing helix chain 'I' and resid 298 through 313 removed outlier: 3.680A pdb=" N THR I 305 " --> pdb=" O GLU I 301 " (cutoff:3.500A) Processing helix chain 'I' and resid 354 through 366 removed outlier: 3.824A pdb=" N LYS I 358 " --> pdb=" O ASP I 354 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS I 359 " --> pdb=" O LEU I 355 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LYS I 360 " --> pdb=" O SER I 356 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLY I 363 " --> pdb=" O LYS I 359 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ILE I 364 " --> pdb=" O LYS I 360 " (cutoff:3.500A) Processing helix chain 'I' and resid 376 through 380 removed outlier: 3.562A pdb=" N THR I 379 " --> pdb=" O ASN I 376 " (cutoff:3.500A) Processing helix chain 'I' and resid 389 through 405 removed outlier: 3.826A pdb=" N GLN I 393 " --> pdb=" O GLY I 389 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA I 394 " --> pdb=" O ALA I 390 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET I 395 " --> pdb=" O ASP I 391 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY I 400 " --> pdb=" O CYS I 396 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA I 403 " --> pdb=" O ALA I 399 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU I 404 " --> pdb=" O GLY I 400 " (cutoff:3.500A) Processing helix chain 'I' and resid 412 through 426 removed outlier: 3.703A pdb=" N PHE I 416 " --> pdb=" O THR I 412 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA I 419 " --> pdb=" O ASP I 415 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ARG I 422 " --> pdb=" O GLN I 418 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASN I 426 " --> pdb=" O ARG I 422 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 66 removed outlier: 3.896A pdb=" N LEU J 32 " --> pdb=" O GLN J 28 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG J 35 " --> pdb=" O GLU J 31 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ASN J 40 " --> pdb=" O SER J 36 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL J 41 " --> pdb=" O LYS J 37 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LYS J 54 " --> pdb=" O ALA J 50 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL J 55 " --> pdb=" O LEU J 51 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE J 58 " --> pdb=" O LYS J 54 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG J 63 " --> pdb=" O LYS J 59 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU J 64 " --> pdb=" O ASP J 60 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLN J 66 " --> pdb=" O LEU J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 154 through 164 removed outlier: 3.598A pdb=" N GLU J 159 " --> pdb=" O LYS J 155 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE J 160 " --> pdb=" O GLN J 156 " (cutoff:3.500A) Processing helix chain 'J' and resid 165 through 170 Processing helix chain 'J' and resid 171 through 178 removed outlier: 4.051A pdb=" N GLU J 175 " --> pdb=" O PRO J 171 " (cutoff:3.500A) Processing helix chain 'J' and resid 194 through 203 removed outlier: 3.664A pdb=" N LEU J 198 " --> pdb=" O GLY J 194 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA J 199 " --> pdb=" O LYS J 195 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG J 200 " --> pdb=" O THR J 196 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA J 203 " --> pdb=" O ALA J 199 " (cutoff:3.500A) Processing helix chain 'J' and resid 204 through 206 No H-bonds generated for 'chain 'J' and resid 204 through 206' Processing helix chain 'J' and resid 226 through 239 removed outlier: 3.879A pdb=" N ARG J 231 " --> pdb=" O SER J 227 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL J 235 " --> pdb=" O ARG J 231 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N MET J 236 " --> pdb=" O GLU J 232 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU J 239 " --> pdb=" O VAL J 235 " (cutoff:3.500A) Processing helix chain 'J' and resid 265 through 278 removed outlier: 4.029A pdb=" N THR J 271 " --> pdb=" O GLU J 267 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N MET J 272 " --> pdb=" O VAL J 268 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU J 273 " --> pdb=" O GLN J 269 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU J 274 " --> pdb=" O ARG J 270 " (cutoff:3.500A) Processing helix chain 'J' and resid 278 through 285 Processing helix chain 'J' and resid 320 through 332 removed outlier: 4.553A pdb=" N GLU J 326 " --> pdb=" O ALA J 322 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ILE J 327 " --> pdb=" O ALA J 323 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N HIS J 331 " --> pdb=" O ILE J 327 " (cutoff:3.500A) Processing helix chain 'J' and resid 342 through 350 removed outlier: 3.705A pdb=" N VAL J 346 " --> pdb=" O ASN J 342 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA J 347 " --> pdb=" O LEU J 343 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLU J 348 " --> pdb=" O ARG J 344 " (cutoff:3.500A) Processing helix chain 'J' and resid 356 through 373 removed outlier: 3.504A pdb=" N THR J 363 " --> pdb=" O LYS J 359 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLY J 366 " --> pdb=" O CYS J 362 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR J 368 " --> pdb=" O GLU J 364 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA J 369 " --> pdb=" O ALA J 365 " (cutoff:3.500A) Processing helix chain 'J' and resid 379 through 384 Processing helix chain 'J' and resid 385 through 390 Processing helix chain 'J' and resid 390 through 398 removed outlier: 3.605A pdb=" N THR J 396 " --> pdb=" O LYS J 392 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALA J 397 " --> pdb=" O ASN J 393 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE J 398 " --> pdb=" O GLN J 394 " (cutoff:3.500A) Processing helix chain 'K' and resid 49 through 83 removed outlier: 3.664A pdb=" N LYS K 53 " --> pdb=" O PHE K 49 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS K 56 " --> pdb=" O LYS K 52 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR K 58 " --> pdb=" O LEU K 54 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU K 63 " --> pdb=" O GLU K 59 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN K 64 " --> pdb=" O LEU K 60 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP K 66 " --> pdb=" O THR K 62 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TYR K 67 " --> pdb=" O LEU K 63 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS K 69 " --> pdb=" O GLU K 65 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN K 72 " --> pdb=" O ILE K 68 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ARG K 77 " --> pdb=" O ARG K 73 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLU K 78 " --> pdb=" O HIS K 74 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU K 79 " --> pdb=" O LEU K 75 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS K 80 " --> pdb=" O LYS K 76 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG K 81 " --> pdb=" O ARG K 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 84 through 90 removed outlier: 3.753A pdb=" N ILE K 89 " --> pdb=" O GLU K 85 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN K 90 " --> pdb=" O VAL K 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 177 through 188 removed outlier: 3.708A pdb=" N ILE K 184 " --> pdb=" O GLN K 180 " (cutoff:3.500A) Processing helix chain 'K' and resid 189 through 194 removed outlier: 3.587A pdb=" N VAL K 193 " --> pdb=" O GLU K 189 " (cutoff:3.500A) Processing helix chain 'K' and resid 195 through 202 removed outlier: 3.880A pdb=" N ILE K 201 " --> pdb=" O LEU K 197 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLY K 202 " --> pdb=" O TYR K 198 " (cutoff:3.500A) Processing helix chain 'K' and resid 218 through 231 Processing helix chain 'K' and resid 238 through 243 removed outlier: 4.015A pdb=" N PHE K 242 " --> pdb=" O ASN K 238 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N VAL K 243 " --> pdb=" O GLY K 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 238 through 243' Processing helix chain 'K' and resid 250 through 262 removed outlier: 4.113A pdb=" N PHE K 258 " --> pdb=" O VAL K 254 " (cutoff:3.500A) Processing helix chain 'K' and resid 287 through 305 removed outlier: 3.721A pdb=" N GLU K 291 " --> pdb=" O GLY K 287 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL K 292 " --> pdb=" O SER K 288 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN K 293 " --> pdb=" O ASP K 289 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU K 298 " --> pdb=" O ARG K 294 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N MET K 303 " --> pdb=" O LEU K 299 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP K 304 " --> pdb=" O LEU K 300 " (cutoff:3.500A) Processing helix chain 'K' and resid 345 through 360 removed outlier: 4.055A pdb=" N ILE K 352 " --> pdb=" O GLU K 348 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N PHE K 353 " --> pdb=" O ARG K 349 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLY K 354 " --> pdb=" O ARG K 350 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N THR K 355 " --> pdb=" O LEU K 351 " (cutoff:3.500A) Processing helix chain 'K' and resid 381 through 391 removed outlier: 3.721A pdb=" N GLU K 389 " --> pdb=" O ALA K 385 " (cutoff:3.500A) Processing helix chain 'K' and resid 392 through 397 removed outlier: 3.557A pdb=" N ARG K 396 " --> pdb=" O LEU K 392 " (cutoff:3.500A) Processing helix chain 'K' and resid 404 through 412 removed outlier: 3.835A pdb=" N GLU K 408 " --> pdb=" O GLN K 404 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLU K 409 " --> pdb=" O SER K 405 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA K 410 " --> pdb=" O ASP K 406 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA K 412 " --> pdb=" O GLU K 408 " (cutoff:3.500A) Processing helix chain 'L' and resid 71 through 99 removed outlier: 4.748A pdb=" N ARG L 77 " --> pdb=" O GLN L 73 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG L 78 " --> pdb=" O LEU L 74 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLN L 79 " --> pdb=" O LYS L 75 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU L 87 " --> pdb=" O ASP L 83 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS L 90 " --> pdb=" O LYS L 86 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE L 95 " --> pdb=" O THR L 91 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS L 96 " --> pdb=" O GLU L 92 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLN L 99 " --> pdb=" O ILE L 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 172 through 176 Processing helix chain 'L' and resid 187 through 198 removed outlier: 3.701A pdb=" N ARG L 194 " --> pdb=" O ILE L 190 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU L 195 " --> pdb=" O ARG L 191 " (cutoff:3.500A) Processing helix chain 'L' and resid 198 through 203 removed outlier: 3.703A pdb=" N ASN L 203 " --> pdb=" O LEU L 199 " (cutoff:3.500A) Processing helix chain 'L' and resid 206 through 211 removed outlier: 3.505A pdb=" N GLY L 211 " --> pdb=" O PHE L 207 " (cutoff:3.500A) Processing helix chain 'L' and resid 228 through 239 removed outlier: 3.801A pdb=" N ALA L 236 " --> pdb=" O ALA L 232 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA L 237 " --> pdb=" O LYS L 233 " (cutoff:3.500A) Processing helix chain 'L' and resid 249 through 254 Processing helix chain 'L' and resid 259 through 273 removed outlier: 3.687A pdb=" N ILE L 263 " --> pdb=" O SER L 259 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA L 270 " --> pdb=" O MET L 266 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS L 273 " --> pdb=" O TYR L 269 " (cutoff:3.500A) Processing helix chain 'L' and resid 282 through 286 removed outlier: 3.597A pdb=" N ILE L 286 " --> pdb=" O VAL L 283 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 314 removed outlier: 4.601A pdb=" N LEU L 305 " --> pdb=" O ILE L 301 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU L 308 " --> pdb=" O THR L 304 " (cutoff:3.500A) Processing helix chain 'L' and resid 329 through 333 Processing helix chain 'L' and resid 355 through 365 removed outlier: 4.316A pdb=" N ILE L 363 " --> pdb=" O GLU L 359 " (cutoff:3.500A) Processing helix chain 'L' and resid 366 through 368 No H-bonds generated for 'chain 'L' and resid 366 through 368' Processing helix chain 'L' and resid 374 through 381 removed outlier: 4.522A pdb=" N ALA L 378 " --> pdb=" O PHE L 374 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS L 381 " --> pdb=" O GLU L 377 " (cutoff:3.500A) Processing helix chain 'L' and resid 390 through 403 removed outlier: 3.752A pdb=" N THR L 396 " --> pdb=" O ARG L 392 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N PHE L 401 " --> pdb=" O GLU L 397 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE L 403 " --> pdb=" O GLY L 399 " (cutoff:3.500A) Processing helix chain 'L' and resid 411 through 417 removed outlier: 4.056A pdb=" N LEU L 415 " --> pdb=" O ASN L 411 " (cutoff:3.500A) Processing helix chain 'L' and resid 417 through 426 removed outlier: 4.078A pdb=" N LYS L 421 " --> pdb=" O LYS L 417 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL L 422 " --> pdb=" O ALA L 418 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N GLU L 424 " --> pdb=" O ARG L 420 " (cutoff:3.500A) Processing helix chain 'M' and resid 38 through 45 removed outlier: 3.546A pdb=" N ARG M 42 " --> pdb=" O ASP M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 72 removed outlier: 3.737A pdb=" N HIS M 53 " --> pdb=" O GLN M 49 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE M 62 " --> pdb=" O MET M 58 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS M 63 " --> pdb=" O LEU M 59 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYS M 70 " --> pdb=" O LYS M 66 " (cutoff:3.500A) Processing helix chain 'M' and resid 136 through 140 removed outlier: 3.527A pdb=" N LEU M 140 " --> pdb=" O PRO M 137 " (cutoff:3.500A) Processing helix chain 'M' and resid 164 through 169 Processing helix chain 'M' and resid 186 through 195 removed outlier: 3.576A pdb=" N GLU M 195 " --> pdb=" O GLU M 191 " (cutoff:3.500A) Processing helix chain 'M' and resid 197 through 203 Processing helix chain 'M' and resid 204 through 209 Processing helix chain 'M' and resid 228 through 239 removed outlier: 3.543A pdb=" N ALA M 232 " --> pdb=" O LYS M 228 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA M 237 " --> pdb=" O ARG M 233 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR M 239 " --> pdb=" O CYS M 235 " (cutoff:3.500A) Processing helix chain 'M' and resid 259 through 272 Processing helix chain 'M' and resid 295 through 313 removed outlier: 4.052A pdb=" N VAL M 301 " --> pdb=" O GLY M 297 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN M 302 " --> pdb=" O ASP M 298 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR M 304 " --> pdb=" O GLU M 300 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N MET M 305 " --> pdb=" O VAL M 301 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN M 310 " --> pdb=" O LEU M 306 " (cutoff:3.500A) Processing helix chain 'M' and resid 334 through 339 Processing helix chain 'M' and resid 353 through 365 removed outlier: 3.694A pdb=" N ALA M 358 " --> pdb=" O GLU M 354 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN M 359 " --> pdb=" O ASP M 355 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU M 361 " --> pdb=" O ARG M 357 " (cutoff:3.500A) Processing helix chain 'M' and resid 366 through 368 No H-bonds generated for 'chain 'M' and resid 366 through 368' Processing helix chain 'M' and resid 375 through 382 removed outlier: 3.668A pdb=" N LEU M 379 " --> pdb=" O ASN M 375 " (cutoff:3.500A) Processing helix chain 'M' and resid 387 through 406 removed outlier: 3.753A pdb=" N THR M 395 " --> pdb=" O LEU M 391 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU M 403 " --> pdb=" O GLY M 399 " (cutoff:3.500A) Processing helix chain 'M' and resid 412 through 423 removed outlier: 3.589A pdb=" N GLY M 418 " --> pdb=" O ASP M 414 " (cutoff:3.500A) Processing helix chain 'r' and resid 30 through 44 removed outlier: 3.742A pdb=" N LEU r 35 " --> pdb=" O SER r 31 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS r 36 " --> pdb=" O ILE r 32 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N HIS r 40 " --> pdb=" O LYS r 36 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLY r 44 " --> pdb=" O HIS r 40 " (cutoff:3.500A) Processing helix chain 'r' and resid 88 through 96 removed outlier: 3.715A pdb=" N MET r 92 " --> pdb=" O GLN r 88 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP r 93 " --> pdb=" O ALA r 89 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET r 94 " --> pdb=" O LYS r 90 " (cutoff:3.500A) Processing helix chain 'r' and resid 119 through 133 removed outlier: 3.592A pdb=" N ASN r 124 " --> pdb=" O SER r 120 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER r 128 " --> pdb=" O ASN r 124 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE r 129 " --> pdb=" O THR r 125 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN r 131 " --> pdb=" O LYS r 127 " (cutoff:3.500A) Processing helix chain 'r' and resid 160 through 167 removed outlier: 3.511A pdb=" N ASN r 166 " --> pdb=" O GLY r 162 " (cutoff:3.500A) Processing helix chain 'r' and resid 184 through 188 Processing helix chain 'r' and resid 206 through 214 removed outlier: 4.412A pdb=" N MET r 212 " --> pdb=" O LYS r 208 " (cutoff:3.500A) Processing helix chain 'r' and resid 215 through 217 No H-bonds generated for 'chain 'r' and resid 215 through 217' Processing helix chain 'r' and resid 232 through 252 removed outlier: 4.200A pdb=" N ALA r 239 " --> pdb=" O GLU r 235 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LYS r 242 " --> pdb=" O LEU r 238 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LYS r 246 " --> pdb=" O LYS r 242 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ILE r 247 " --> pdb=" O SER r 243 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN r 250 " --> pdb=" O LYS r 246 " (cutoff:3.500A) Processing helix chain 'r' and resid 253 through 256 Processing helix chain 'r' and resid 275 through 303 removed outlier: 3.703A pdb=" N HIS r 279 " --> pdb=" O ASP r 275 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR r 283 " --> pdb=" O HIS r 279 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU r 286 " --> pdb=" O GLU r 282 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL r 293 " --> pdb=" O GLU r 289 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER r 294 " --> pdb=" O ASN r 290 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA r 298 " --> pdb=" O SER r 294 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL r 303 " --> pdb=" O GLY r 299 " (cutoff:3.500A) Processing helix chain 'u' and resid 22 through 34 removed outlier: 3.906A pdb=" N SER u 28 " --> pdb=" O ASP u 24 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS u 29 " --> pdb=" O ASN u 25 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE u 30 " --> pdb=" O VAL u 26 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN u 31 " --> pdb=" O LYS u 27 " (cutoff:3.500A) Processing helix chain 'u' and resid 37 through 39 No H-bonds generated for 'chain 'u' and resid 37 through 39' Processing helix chain 'u' and resid 55 through 59 Processing sheet with id=AA1, first strand: chain '1' and resid 124 through 127 removed outlier: 3.720A pdb=" N GLY 1 11 " --> pdb=" O PHE 1 8 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU 1 14 " --> pdb=" O VAL 1 176 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N VAL 1 172 " --> pdb=" O SER 1 18 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N MET 1 175 " --> pdb=" O LEU 1 186 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '1' and resid 41 through 47 removed outlier: 3.620A pdb=" N ALA 1 100 " --> pdb=" O TRP 1 42 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE 1 98 " --> pdb=" O CYS 1 44 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N TYR 1 111 " --> pdb=" O VAL 1 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '2' and resid 124 through 127 removed outlier: 3.525A pdb=" N GLY 2 11 " --> pdb=" O PHE 2 8 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL 2 173 " --> pdb=" O ASN 2 189 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '2' and resid 34 through 35 removed outlier: 3.611A pdb=" N TRP 2 42 " --> pdb=" O ALA 2 101 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA 2 44 " --> pdb=" O ILE 2 99 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '2' and resid 215 through 218 removed outlier: 4.478A pdb=" N VAL 3 195 " --> pdb=" O VAL 2 218 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL 3 196 " --> pdb=" O ILE 3 189 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE 3 189 " --> pdb=" O VAL 3 196 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU 3 200 " --> pdb=" O ALA 3 185 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ALA 3 185 " --> pdb=" O LEU 3 200 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N ILE 3 11 " --> pdb=" O ASP 3 26 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '3' and resid 43 through 46 removed outlier: 3.715A pdb=" N GLY 3 52 " --> pdb=" O VAL 3 108 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS 3 118 " --> pdb=" O ASN 3 113 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '4' and resid 130 through 132 Processing sheet with id=AA8, first strand: chain '4' and resid 22 through 23 removed outlier: 4.142A pdb=" N SER 4 26 " --> pdb=" O ARG 4 23 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '4' and resid 35 through 39 removed outlier: 3.657A pdb=" N MET 4 44 " --> pdb=" O ARG 4 36 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU 4 38 " --> pdb=" O THR 4 42 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N THR 4 42 " --> pdb=" O LEU 4 38 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY 4 106 " --> pdb=" O GLU 4 115 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU 4 115 " --> pdb=" O GLY 4 106 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '5' and resid 126 through 130 removed outlier: 6.341A pdb=" N VAL 5 175 " --> pdb=" O ASN 5 190 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ASN 5 190 " --> pdb=" O VAL 5 175 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LEU 5 177 " --> pdb=" O HIS 5 188 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '5' and resid 20 through 22 removed outlier: 6.807A pdb=" N ALA 5 20 " --> pdb=" O ALA 5 27 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA 5 22 " --> pdb=" O TRP 5 25 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '5' and resid 34 through 38 removed outlier: 3.984A pdb=" N GLY 5 43 " --> pdb=" O ILE 5 35 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ILE 5 37 " --> pdb=" O LEU 5 41 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N LEU 5 41 " --> pdb=" O ILE 5 37 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR 5 44 " --> pdb=" O MET 5 100 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N MET 5 100 " --> pdb=" O THR 5 44 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '6' and resid 136 through 140 removed outlier: 3.968A pdb=" N ARG 6 137 " --> pdb=" O GLY 6 14 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU 6 203 " --> pdb=" O GLY 6 25 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR 6 217 " --> pdb=" O LEU 6 202 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '6' and resid 29 through 30 removed outlier: 6.619A pdb=" N ASN 6 29 " --> pdb=" O ASN 6 36 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain '6' and resid 43 through 45 removed outlier: 3.579A pdb=" N PHE 6 44 " --> pdb=" O MET 6 52 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET 6 52 " --> pdb=" O PHE 6 44 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN 6 55 " --> pdb=" O HIS 6 108 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL 6 122 " --> pdb=" O GLU 6 134 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain '6' and resid 207 through 208 Processing sheet with id=AB8, first strand: chain '7' and resid 11 through 15 removed outlier: 4.085A pdb=" N ILE 7 199 " --> pdb=" O THR 7 207 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR 7 207 " --> pdb=" O ILE 7 199 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain '7' and resid 28 through 29 Processing sheet with id=AC1, first strand: chain '7' and resid 49 through 52 removed outlier: 3.503A pdb=" N GLY 7 118 " --> pdb=" O PHE 7 126 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR 7 129 " --> pdb=" O TYR 7 137 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR 7 137 " --> pdb=" O TYR 7 129 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 168 through 170 removed outlier: 3.538A pdb=" N VAL A 52 " --> pdb=" O VAL A 45 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 72 through 73 removed outlier: 3.510A pdb=" N MET A 81 " --> pdb=" O PHE A 73 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 161 through 164 removed outlier: 3.601A pdb=" N THR B 162 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE B 45 " --> pdb=" O ALA B 212 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 65 through 68 removed outlier: 3.625A pdb=" N SER B 65 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 65 through 68 removed outlier: 3.625A pdb=" N SER B 65 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 45 through 46 removed outlier: 3.592A pdb=" N ALA C 35 " --> pdb=" O VAL C 165 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 66 through 70 removed outlier: 6.471A pdb=" N ILE C 73 " --> pdb=" O LEU C 69 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 135 through 139 removed outlier: 3.713A pdb=" N PHE C 135 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N SER C 151 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR C 149 " --> pdb=" O TYR C 137 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY C 139 " --> pdb=" O GLN C 147 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN C 147 " --> pdb=" O GLY C 139 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 215 through 217 Processing sheet with id=AD2, first strand: chain 'D' and resid 161 through 163 removed outlier: 3.515A pdb=" N VAL D 36 " --> pdb=" O VAL D 43 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL D 222 " --> pdb=" O VAL D 214 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 65 through 68 removed outlier: 3.552A pdb=" N ILE D 67 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL D 71 " --> pdb=" O ILE D 67 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA D 136 " --> pdb=" O VAL D 72 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 148 through 151 removed outlier: 3.683A pdb=" N SER D 157 " --> pdb=" O GLN D 149 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU D 151 " --> pdb=" O ILE D 155 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE D 155 " --> pdb=" O GLU D 151 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 169 through 172 removed outlier: 3.689A pdb=" N GLN E 218 " --> pdb=" O VAL E 50 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 67 through 71 removed outlier: 5.939A pdb=" N GLU E 69 " --> pdb=" O CYS E 76 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N CYS E 76 " --> pdb=" O GLU E 69 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASP E 71 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 142 through 143 removed outlier: 3.657A pdb=" N ALA E 158 " --> pdb=" O LEU E 142 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 160 through 161 Processing sheet with id=AD9, first strand: chain 'F' and resid 63 through 67 removed outlier: 6.365A pdb=" N ILE F 63 " --> pdb=" O LEU F 74 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N LEU F 74 " --> pdb=" O ILE F 63 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N LYS F 65 " --> pdb=" O LEU F 72 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU F 72 " --> pdb=" O LYS F 65 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ASP F 67 " --> pdb=" O MET F 70 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY F 71 " --> pdb=" O ILE F 135 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ILE F 135 " --> pdb=" O GLY F 71 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER F 73 " --> pdb=" O LEU F 133 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE F 134 " --> pdb=" O LEU F 145 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY F 136 " --> pdb=" O HIS F 143 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASP F 138 " --> pdb=" O GLY F 141 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 162 through 164 removed outlier: 3.555A pdb=" N GLY G 39 " --> pdb=" O ALA G 163 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 68 through 69 removed outlier: 3.544A pdb=" N GLY G 139 " --> pdb=" O GLY G 75 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY G 145 " --> pdb=" O ASP G 142 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TRP G 158 " --> pdb=" O MET G 150 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 100 through 104 removed outlier: 3.733A pdb=" N THR H 103 " --> pdb=" O VAL H 146 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N VAL H 146 " --> pdb=" O THR H 103 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 155 through 156 removed outlier: 3.516A pdb=" N TYR M 77 " --> pdb=" O VAL H 156 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL M 146 " --> pdb=" O ALA M 80 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASP M 157 " --> pdb=" O GLY M 147 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 173 through 176 removed outlier: 3.805A pdb=" N LEU H 185 " --> pdb=" O GLY H 175 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 248 through 249 Processing sheet with id=AE7, first strand: chain 'H' and resid 304 through 305 removed outlier: 6.923A pdb=" N CYS H 304 " --> pdb=" O LYS H 350 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'I' and resid 105 through 107 removed outlier: 3.948A pdb=" N GLY I 107 " --> pdb=" O VAL I 147 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LEU I 148 " --> pdb=" O VAL I 157 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 112 through 113 removed outlier: 3.565A pdb=" N HIS I 117 " --> pdb=" O ILE I 113 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL I 120 " --> pdb=" O TYR I 128 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR I 128 " --> pdb=" O VAL I 120 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 325 through 327 removed outlier: 6.856A pdb=" N ILE I 220 " --> pdb=" O ILE I 348 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N PHE I 350 " --> pdb=" O ILE I 220 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N TYR I 222 " --> pdb=" O PHE I 350 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 93 through 96 removed outlier: 3.524A pdb=" N VAL J 84 " --> pdb=" O VAL J 96 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N LEU J 85 " --> pdb=" O ILE J 76 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE J 76 " --> pdb=" O LEU J 85 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 185 through 188 Processing sheet with id=AF4, first strand: chain 'J' and resid 209 through 213 removed outlier: 7.872A pdb=" N ILE J 291 " --> pdb=" O SER J 243 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N ILE J 245 " --> pdb=" O ILE J 291 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N ALA J 293 " --> pdb=" O ILE J 245 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N MET J 247 " --> pdb=" O ALA J 293 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 95 through 97 removed outlier: 3.817A pdb=" N GLY K 97 " --> pdb=" O VAL K 137 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL K 137 " --> pdb=" O GLY K 97 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP K 148 " --> pdb=" O ALA K 138 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 99 through 104 removed outlier: 6.050A pdb=" N PHE K 99 " --> pdb=" O SER K 111 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N SER K 111 " --> pdb=" O PHE K 99 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLU K 101 " --> pdb=" O ILE K 109 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N THR K 107 " --> pdb=" O ILE K 103 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 209 through 211 Processing sheet with id=AF8, first strand: chain 'K' and resid 233 through 237 removed outlier: 6.528A pdb=" N ALA K 233 " --> pdb=" O ILE K 268 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N PHE K 270 " --> pdb=" O ALA K 233 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ILE K 235 " --> pdb=" O PHE K 270 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'L' and resid 111 through 113 removed outlier: 6.107A pdb=" N GLU L 111 " --> pdb=" O ILE L 118 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ILE L 118 " --> pdb=" O GLU L 111 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL L 129 " --> pdb=" O TYR L 117 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N ILE L 155 " --> pdb=" O ILE L 128 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N GLY L 130 " --> pdb=" O ILE L 155 " (cutoff:3.500A) removed outlier: 9.235A pdb=" N ARG L 157 " --> pdb=" O GLY L 130 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N THR L 147 " --> pdb=" O MET L 156 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'L' and resid 170 through 171 removed outlier: 3.849A pdb=" N PHE L 243 " --> pdb=" O THR L 171 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 326 through 327 removed outlier: 8.917A pdb=" N THR L 327 " --> pdb=" O VAL L 218 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU L 220 " --> pdb=" O THR L 327 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'M' and resid 117 through 120 removed outlier: 3.836A pdb=" N VAL M 127 " --> pdb=" O VAL M 119 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'M' and resid 220 through 221 Processing sheet with id=AG5, first strand: chain 'r' and resid 64 through 70 removed outlier: 3.845A pdb=" N ASN r 64 " --> pdb=" O GLU r 56 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU r 56 " --> pdb=" O ASN r 64 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LEU r 54 " --> pdb=" O VAL r 66 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N VAL r 68 " --> pdb=" O LEU r 52 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU r 52 " --> pdb=" O VAL r 68 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLY r 51 " --> pdb=" O TYR r 108 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY r 106 " --> pdb=" O MET r 53 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N GLY r 55 " --> pdb=" O VAL r 104 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N VAL r 104 " --> pdb=" O GLY r 55 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL r 137 " --> pdb=" O VAL r 105 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL r 141 " --> pdb=" O HIS r 109 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'r' and resid 73 through 75 removed outlier: 3.922A pdb=" N GLU r 81 " --> pdb=" O SER r 74 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'u' and resid 3 through 5 Processing sheet with id=AG8, first strand: chain 'u' and resid 48 through 49 1444 hydrogen bonds defined for protein. 3972 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.46 Time building geometry restraints manager: 4.56 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: 0.00 - 5.50: 60826 5.50 - 11.00: 164 11.00 - 16.49: 0 16.49 - 21.99: 3 21.99 - 27.49: 5 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: 1.98 - 2.57: 473 2.57 - 3.15: 40861 3.15 - 3.73: 62116 3.73 - 4.32: 88454 4.32 - 4.90: 143581 Nonbonded interactions: 335485 Sorted by model distance: nonbonded pdb=" OH TYR 3 46 " pdb=" OD1 ASN 3 64 " model vdw 1.983 3.040 nonbonded pdb=" OD1 ASP G 114 " pdb=" OH TYR G 157 " model vdw 2.050 3.040 nonbonded pdb=" OG1 THR I 230 " pdb=" O3G ATP I 501 " model vdw 2.052 3.040 nonbonded pdb=" OH TYR 6 75 " pdb=" OE2 GLU E 105 " model vdw 2.055 3.040 nonbonded pdb=" OG SER E 16 " pdb=" O ARG E 20 " model vdw 2.133 3.040 ... (remaining 335480 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.370 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: 0.020 Extract box with map and model: 0.740 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 37.090 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.550 ------------------------------------------------------------------------------- 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 45012 Z= 0.661 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 : 1.983 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 14.74 % Favored : 85.22 % Rotamer: Outliers : 0.07 % Allowed : 6.21 % Favored : 93.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.91 (0.08), residues: 5766 helix: -4.16 (0.07), residues: 1949 sheet: -4.23 (0.11), residues: 981 loop : -3.58 (0.10), residues: 2836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.002 ARG C 113 TYR 0.038 0.004 TYR G 160 PHE 0.040 0.004 PHE J 174 TRP 0.041 0.004 TRP 7 111 HIS 0.015 0.003 HIS 2 141 Details of bonding type rmsd/Z covalent geometry : bond 0.01605 / 0.66 (45011) covalent geometry : angle 1.10500 / 0.64 (60998) hydrogen bonds : bond 0.31139 / 20.91 ( 1440) hydrogen bonds : angle 11.51556 / 8.05 ( 3972) Misc. bond : bond 0.09002 / 4.74 ( 1) *********************** 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 to be fit. rotamer outliers: 3 poor density : 1022 time to evaluate : 1.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 69 GLN cc_start: 0.7470 (mt0) cc_final: 0.7001 (mt0) REVERT: 2 71 SER cc_start: 0.8351 (m) cc_final: 0.8120 (p) REVERT: 2 179 GLU cc_start: 0.7687 (tt0) cc_final: 0.7115 (tt0) REVERT: 2 188 ARG cc_start: 0.7687 (tpt90) cc_final: 0.7481 (tpt90) REVERT: 2 200 GLN cc_start: 0.7423 (mt0) cc_final: 0.6523 (pt0) REVERT: 2 207 ARG cc_start: 0.7207 (mpt180) cc_final: 0.6872 (mmt90) REVERT: 2 214 LYS cc_start: 0.8130 (ptmt) cc_final: 0.7627 (mttp) REVERT: 3 99 ARG cc_start: 0.8872 (tpt90) cc_final: 0.8605 (tpt-90) REVERT: 3 203 ARG cc_start: 0.8345 (ptm-80) cc_final: 0.6653 (mtt180) REVERT: 4 1 MET cc_start: 0.6474 (ttp) cc_final: 0.6250 (tpt) REVERT: 4 78 GLN cc_start: 0.7792 (tm130) cc_final: 0.7475 (tp-100) REVERT: 5 24 ASN cc_start: 0.8447 (t160) cc_final: 0.7915 (t0) REVERT: 5 36 GLU cc_start: 0.6954 (mp0) cc_final: 0.6041 (tm-30) REVERT: 6 81 ASP cc_start: 0.7269 (t0) cc_final: 0.6998 (t70) REVERT: 6 159 GLN cc_start: 0.6849 (pt0) cc_final: 0.5913 (tp40) REVERT: 6 161 GLU cc_start: 0.7220 (tm-30) cc_final: 0.6973 (tm-30) REVERT: 6 162 PRO cc_start: 0.7490 (Cg_exo) cc_final: 0.7271 (Cg_endo) REVERT: 7 120 GLN cc_start: 0.8079 (mm110) cc_final: 0.7730 (mm-40) REVERT: A 29 GLU cc_start: 0.7620 (tt0) cc_final: 0.7021 (tt0) REVERT: A 39 ASN cc_start: 0.8374 (m-40) cc_final: 0.7774 (t0) REVERT: A 49 ASP cc_start: 0.7358 (p0) cc_final: 0.6979 (p0) REVERT: A 50 CYS cc_start: 0.7040 (m) cc_final: 0.6458 (m) REVERT: B 75 TYR cc_start: 0.8541 (p90) cc_final: 0.8011 (p90) REVERT: B 136 ILE cc_start: 0.9005 (mt) cc_final: 0.8778 (mm) REVERT: B 178 ARG cc_start: 0.7915 (mmm-85) cc_final: 0.7709 (mmt180) REVERT: B 182 GLU cc_start: 0.7718 (pm20) cc_final: 0.7348 (pm20) REVERT: C 206 LEU cc_start: 0.8797 (pt) cc_final: 0.8266 (tp) REVERT: C 212 GLU cc_start: 0.8019 (pm20) cc_final: 0.7725 (pm20) REVERT: C 238 ILE cc_start: 0.8150 (mm) cc_final: 0.7873 (mm) REVERT: E 76 CYS cc_start: 0.7778 (m) cc_final: 0.7466 (m) REVERT: E 167 TYR cc_start: 0.7987 (m-80) cc_final: 0.7750 (m-80) REVERT: E 183 LEU cc_start: 0.8560 (mp) cc_final: 0.8163 (mp) REVERT: F 27 GLU cc_start: 0.7186 (tm-30) cc_final: 0.6954 (tm-30) REVERT: F 60 GLN cc_start: 0.8428 (pt0) cc_final: 0.8174 (pt0) REVERT: F 61 LYS cc_start: 0.8518 (mppt) cc_final: 0.8313 (mmtm) REVERT: F 86 ASN cc_start: 0.8880 (m-40) cc_final: 0.8439 (m-40) REVERT: G 237 GLN cc_start: 0.7930 (tp40) cc_final: 0.7514 (mm-40) REVERT: H 105 ILE cc_start: 0.9079 (mt) cc_final: 0.8862 (tt) REVERT: H 221 LEU cc_start: 0.8950 (tt) cc_final: 0.8709 (tp) REVERT: H 235 PHE cc_start: 0.8439 (m-80) cc_final: 0.8233 (m-80) REVERT: H 442 ASP cc_start: 0.8523 (p0) cc_final: 0.8033 (p0) REVERT: I 167 MET cc_start: 0.7782 (pmm) cc_final: 0.7489 (ptp) REVERT: I 312 GLN cc_start: 0.7834 (mm-40) cc_final: 0.7509 (mm-40) REVERT: J 32 LEU cc_start: 0.8968 (mm) cc_final: 0.8675 (tp) REVERT: K 319 ASN cc_start: 0.9007 (m110) cc_final: 0.8102 (t0) REVERT: K 400 TYR cc_start: 0.3964 (m-80) cc_final: 0.3657 (m-80) REVERT: L 117 TYR cc_start: 0.8298 (m-10) cc_final: 0.7911 (m-10) REVERT: L 159 LEU cc_start: 0.7713 (pt) cc_final: 0.7264 (pp) REVERT: L 272 GLU cc_start: 0.7023 (pp20) cc_final: 0.6812 (pp20) REVERT: L 279 PHE cc_start: 0.8403 (t80) cc_final: 0.8199 (t80) REVERT: r 214 MET cc_start: 0.7749 (ppp) cc_final: 0.7530 (ppp) outliers start: 3 outliers final: 1 residues processed: 1024 average time/residue: 0.2535 time to fit residues: 423.0413 Evaluate side-chains 653 residues out of total 4951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 652 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 394 optimal weight: 0.7980 chunk 430 optimal weight: 0.7980 chunk 41 optimal weight: 7.9990 chunk 265 optimal weight: 2.9990 chunk 523 optimal weight: 6.9990 chunk 497 optimal weight: 0.0070 chunk 414 optimal weight: 1.9990 chunk 310 optimal weight: 0.8980 chunk 488 optimal weight: 3.9990 chunk 366 optimal weight: 4.9990 chunk 223 optimal weight: 0.8980 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 145 ASN 3 145 GLN 4 41 HIS 4 78 GLN 5 191 HIS 7 61 GLN 7 112 ASN 7 125 GLN 7 179 ASN A 37 GLN ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 HIS B 190 HIS C 21 GLN C 103 ASN F 21 GLN ** 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 217 GLN H 281 GLN H 356 ASN H 359 ASN I 192 GLN I 238 ASN I 352 ASN J 204 HIS J 269 GLN ** J 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 98 GLN K 228 ASN r 126 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.084915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.075392 restraints weight = 112658.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.076569 restraints weight = 71021.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.077369 restraints weight = 50906.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.077922 restraints weight = 40166.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.078236 restraints weight = 33918.014| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 45012 Z= 0.141 Angle : 0.710 10.443 60998 Z= 0.368 Chirality : 0.048 0.219 7049 Planarity : 0.005 0.073 7868 Dihedral : 7.560 120.676 6322 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 0.09 % Allowed : 3.38 % Favored : 96.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.46 (0.09), residues: 5766 helix: -2.77 (0.09), residues: 2090 sheet: -3.10 (0.13), residues: 977 loop : -2.97 (0.11), residues: 2699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 91 TYR 0.031 0.002 TYR A 133 PHE 0.020 0.002 PHE M 432 TRP 0.024 0.002 TRP C 160 HIS 0.010 0.001 HIS G 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (45011) covalent geometry : angle 0.71012 / 0.37 (60998) hydrogen bonds : bond 0.05187 / 3.49 ( 1440) hydrogen bonds : angle 6.50581 / 4.53 ( 3972) Misc. bond : bond 0.00000 / 0.00 ( 1) *********************** 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 978 residues out of total 4951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 974 time to evaluate : 1.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 97 ILE cc_start: 0.8818 (pt) cc_final: 0.8579 (mt) REVERT: 2 12 VAL cc_start: 0.9532 (m) cc_final: 0.9330 (p) REVERT: 2 69 TYR cc_start: 0.8890 (t80) cc_final: 0.8344 (t80) REVERT: 2 71 SER cc_start: 0.8193 (m) cc_final: 0.7964 (p) REVERT: 2 112 SER cc_start: 0.8499 (t) cc_final: 0.8078 (p) REVERT: 2 120 ASP cc_start: 0.7097 (p0) cc_final: 0.6516 (p0) REVERT: 2 200 GLN cc_start: 0.6875 (mt0) cc_final: 0.6175 (pt0) REVERT: 2 214 LYS cc_start: 0.8144 (ptmt) cc_final: 0.7813 (mttp) REVERT: 3 199 TYR cc_start: 0.8365 (m-10) cc_final: 0.8149 (m-10) REVERT: 3 203 ARG cc_start: 0.8334 (ptm-80) cc_final: 0.6578 (mtt180) REVERT: 4 1 MET cc_start: 0.6427 (ttp) cc_final: 0.5481 (tpt) REVERT: 4 3 ILE cc_start: 0.9031 (pt) cc_final: 0.8469 (mp) REVERT: 4 30 ASP cc_start: 0.8329 (p0) cc_final: 0.8093 (p0) REVERT: 4 99 GLN cc_start: 0.7192 (tm-30) cc_final: 0.6962 (tm-30) REVERT: 4 120 ASP cc_start: 0.7605 (p0) cc_final: 0.7352 (p0) REVERT: 5 24 ASN cc_start: 0.8571 (t0) cc_final: 0.8079 (t0) REVERT: 5 36 GLU cc_start: 0.6703 (mp0) cc_final: 0.6412 (pp20) REVERT: 6 81 ASP cc_start: 0.6841 (t0) cc_final: 0.6458 (t70) REVERT: 6 159 GLN cc_start: 0.6531 (pt0) cc_final: 0.5638 (tp40) REVERT: 7 108 ASN cc_start: 0.7679 (p0) cc_final: 0.7158 (p0) REVERT: A 39 ASN cc_start: 0.8368 (m-40) cc_final: 0.7769 (t0) REVERT: A 128 TYR cc_start: 0.7642 (m-80) cc_final: 0.7277 (m-80) REVERT: A 195 ASN cc_start: 0.8207 (m-40) cc_final: 0.7937 (m110) REVERT: A 222 ASP cc_start: 0.7250 (p0) cc_final: 0.6987 (p0) REVERT: A 224 GLU cc_start: 0.8334 (pt0) cc_final: 0.7993 (pt0) REVERT: B 41 ASN cc_start: 0.8511 (p0) cc_final: 0.8092 (p0) REVERT: B 47 THR cc_start: 0.8871 (t) cc_final: 0.8639 (t) REVERT: B 60 THR cc_start: 0.8900 (p) cc_final: 0.8446 (t) REVERT: B 75 TYR cc_start: 0.8773 (p90) cc_final: 0.8498 (p90) REVERT: B 177 LYS cc_start: 0.6839 (mmpt) cc_final: 0.6424 (tptt) REVERT: C 206 LEU cc_start: 0.8635 (pt) cc_final: 0.8285 (tp) REVERT: C 212 GLU cc_start: 0.7991 (pm20) cc_final: 0.7633 (pm20) REVERT: D 47 GLU cc_start: 0.8253 (pp20) cc_final: 0.7995 (pp20) REVERT: D 86 ILE cc_start: 0.8084 (pt) cc_final: 0.7855 (pt) REVERT: E 35 SER cc_start: 0.8344 (m) cc_final: 0.8142 (m) REVERT: E 53 ARG cc_start: 0.6611 (ttm-80) cc_final: 0.5830 (ttt-90) REVERT: E 166 ARG cc_start: 0.8232 (ttt-90) cc_final: 0.8003 (ttt-90) REVERT: E 167 TYR cc_start: 0.8108 (m-80) cc_final: 0.7757 (m-80) REVERT: E 168 ASN cc_start: 0.8128 (m110) cc_final: 0.7784 (m-40) REVERT: E 203 ILE cc_start: 0.8284 (pt) cc_final: 0.7923 (pt) REVERT: E 216 ASN cc_start: 0.8592 (p0) cc_final: 0.8015 (p0) REVERT: F 60 GLN cc_start: 0.8273 (pt0) cc_final: 0.7968 (pt0) REVERT: F 61 LYS cc_start: 0.8371 (mppt) cc_final: 0.8135 (mmtm) REVERT: F 111 LEU cc_start: 0.7812 (mt) cc_final: 0.7563 (mt) REVERT: G 235 LEU cc_start: 0.7132 (tp) cc_final: 0.6826 (tp) REVERT: H 51 GLN cc_start: 0.7758 (pp30) cc_final: 0.7467 (pp30) REVERT: H 330 GLN cc_start: 0.8617 (mp10) cc_final: 0.8233 (mp10) REVERT: H 425 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7256 (mt-10) REVERT: H 442 ASP cc_start: 0.8718 (p0) cc_final: 0.7950 (p0) REVERT: I 64 ARG cc_start: 0.7029 (ptm-80) cc_final: 0.6542 (ttt180) REVERT: I 120 VAL cc_start: 0.9350 (t) cc_final: 0.8997 (m) REVERT: I 167 MET cc_start: 0.7309 (pmm) cc_final: 0.6814 (ptp) REVERT: I 312 GLN cc_start: 0.7764 (mm-40) cc_final: 0.7528 (mm-40) REVERT: K 124 SER cc_start: 0.8745 (t) cc_final: 0.8468 (p) REVERT: K 149 ILE cc_start: 0.9159 (tp) cc_final: 0.8907 (tp) REVERT: L 159 LEU cc_start: 0.7431 (pt) cc_final: 0.7135 (pp) REVERT: L 272 GLU cc_start: 0.7297 (pp20) cc_final: 0.6831 (pp20) REVERT: L 277 ILE cc_start: 0.9064 (mt) cc_final: 0.8563 (tt) REVERT: L 306 MET cc_start: 0.6862 (tmm) cc_final: 0.6616 (tmm) REVERT: M 187 ASP cc_start: 0.7392 (p0) cc_final: 0.7182 (p0) REVERT: M 292 ASP cc_start: 0.7310 (p0) cc_final: 0.7001 (p0) REVERT: M 401 ILE cc_start: 0.8991 (tt) cc_final: 0.8750 (tp) REVERT: n 221 PHE cc_start: 0.8525 (p90) cc_final: 0.8317 (p90) REVERT: r 126 GLN cc_start: 0.8694 (tp40) cc_final: 0.8435 (tp40) REVERT: r 282 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7444 (mt-10) outliers start: 4 outliers final: 0 residues processed: 977 average time/residue: 0.2478 time to fit residues: 399.6793 Evaluate side-chains 683 residues out of total 4951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 683 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 560 optimal weight: 1.9990 chunk 498 optimal weight: 8.9990 chunk 139 optimal weight: 0.6980 chunk 420 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 202 optimal weight: 4.9990 chunk 328 optimal weight: 2.9990 chunk 288 optimal weight: 0.0270 chunk 305 optimal weight: 10.0000 chunk 51 optimal weight: 0.0370 overall best weight: 1.1520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 120 HIS 4 146 HIS 7 74 ASN A 37 GLN ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 GLN D 235 GLN E 91 HIS E 108 ASN F 60 GLN G 207 ASN G 237 GLN H 356 ASN I 238 ASN ** J 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 ASN ** J 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 228 ASN K 302 GLN M 72 ASN M 238 GLN r 237 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.082577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.073120 restraints weight = 112589.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.074093 restraints weight = 70140.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.074341 restraints weight = 55759.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.074899 restraints weight = 46448.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.074921 restraints weight = 43106.550| |-----------------------------------------------------------------------------| r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 45012 Z= 0.131 Angle : 0.638 10.338 60998 Z= 0.328 Chirality : 0.046 0.258 7049 Planarity : 0.004 0.051 7868 Dihedral : 6.782 119.225 6322 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 0.04 % Allowed : 4.21 % Favored : 95.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.61 (0.10), residues: 5766 helix: -2.00 (0.10), residues: 2101 sheet: -2.50 (0.14), residues: 1019 loop : -2.59 (0.11), residues: 2646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 396 TYR 0.033 0.001 TYR B 224 PHE 0.024 0.002 PHE 7 36 TRP 0.020 0.002 TRP G 218 HIS 0.010 0.001 HIS G 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (45011) covalent geometry : angle 0.63806 / 0.33 (60998) hydrogen bonds : bond 0.03962 / 2.66 ( 1440) hydrogen bonds : angle 5.54888 / 3.87 ( 3972) Misc. bond : bond 0.00011 / 0.01 ( 1) *********************** 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 891 residues out of total 4951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 889 time to evaluate : 1.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 97 ILE cc_start: 0.8979 (pt) cc_final: 0.8722 (mt) REVERT: 1 160 SER cc_start: 0.8096 (m) cc_final: 0.7860 (p) REVERT: 2 30 ASN cc_start: 0.8127 (t0) cc_final: 0.7699 (t0) REVERT: 2 71 SER cc_start: 0.8342 (m) cc_final: 0.8031 (p) REVERT: 2 112 SER cc_start: 0.8510 (t) cc_final: 0.8121 (p) REVERT: 2 120 ASP cc_start: 0.7256 (p0) cc_final: 0.6661 (p0) REVERT: 2 152 ILE cc_start: 0.9090 (OUTLIER) cc_final: 0.8822 (mt) REVERT: 2 200 GLN cc_start: 0.6825 (mt0) cc_final: 0.6090 (pt0) REVERT: 2 214 LYS cc_start: 0.8118 (ptmt) cc_final: 0.7844 (mttp) REVERT: 3 98 ARG cc_start: 0.7841 (mtp-110) cc_final: 0.7368 (mtp85) REVERT: 3 125 ASP cc_start: 0.7956 (p0) cc_final: 0.7704 (p0) REVERT: 3 180 LEU cc_start: 0.7967 (mp) cc_final: 0.7738 (mp) REVERT: 3 203 ARG cc_start: 0.8426 (ptm-80) cc_final: 0.8215 (ptm-80) REVERT: 4 1 MET cc_start: 0.6567 (ttp) cc_final: 0.5365 (tpt) REVERT: 4 3 ILE cc_start: 0.9011 (pt) cc_final: 0.8533 (mp) REVERT: 4 99 GLN cc_start: 0.7370 (tm-30) cc_final: 0.7052 (tm-30) REVERT: 4 103 LEU cc_start: 0.9259 (mm) cc_final: 0.9057 (mp) REVERT: 4 124 THR cc_start: 0.8899 (p) cc_final: 0.8190 (p) REVERT: 5 24 ASN cc_start: 0.8638 (t0) cc_final: 0.8189 (t0) REVERT: 5 25 TRP cc_start: 0.8616 (t60) cc_final: 0.8378 (t60) REVERT: 5 63 CYS cc_start: 0.8661 (m) cc_final: 0.8374 (m) REVERT: 5 111 THR cc_start: 0.8036 (m) cc_final: 0.7629 (p) REVERT: 5 133 GLN cc_start: 0.8115 (pt0) cc_final: 0.7914 (pt0) REVERT: 6 28 ARG cc_start: 0.7904 (ttm170) cc_final: 0.7682 (ttm110) REVERT: 6 81 ASP cc_start: 0.6906 (t0) cc_final: 0.6543 (t70) REVERT: 6 159 GLN cc_start: 0.6591 (pt0) cc_final: 0.5703 (tp40) REVERT: 6 161 GLU cc_start: 0.7418 (tm-30) cc_final: 0.7183 (tm-30) REVERT: 6 185 ARG cc_start: 0.7911 (ptm-80) cc_final: 0.7397 (ttp-110) REVERT: 6 200 ASP cc_start: 0.5983 (t0) cc_final: 0.5718 (t0) REVERT: 7 107 MET cc_start: 0.8309 (mmm) cc_final: 0.8048 (tpp) REVERT: 7 108 ASN cc_start: 0.7838 (p0) cc_final: 0.7376 (p0) REVERT: 7 136 THR cc_start: 0.8876 (p) cc_final: 0.8565 (t) REVERT: A 39 ASN cc_start: 0.8353 (m-40) cc_final: 0.7769 (t0) REVERT: A 195 ASN cc_start: 0.7903 (m-40) cc_final: 0.7567 (m110) REVERT: A 222 ASP cc_start: 0.7370 (p0) cc_final: 0.7073 (p0) REVERT: A 224 GLU cc_start: 0.8287 (pt0) cc_final: 0.8043 (pt0) REVERT: B 41 ASN cc_start: 0.8423 (p0) cc_final: 0.8082 (p0) REVERT: B 60 THR cc_start: 0.8919 (p) cc_final: 0.8480 (t) REVERT: B 75 TYR cc_start: 0.8811 (p90) cc_final: 0.8417 (p90) REVERT: C 72 LYS cc_start: 0.8599 (mmmt) cc_final: 0.8376 (mmmt) REVERT: C 195 LYS cc_start: 0.8177 (mmmt) cc_final: 0.7807 (mmmt) REVERT: C 199 LYS cc_start: 0.8930 (mtmt) cc_final: 0.8540 (mtmm) REVERT: C 206 LEU cc_start: 0.8682 (pt) cc_final: 0.8386 (tp) REVERT: E 35 SER cc_start: 0.8346 (m) cc_final: 0.8124 (m) REVERT: E 53 ARG cc_start: 0.6929 (ttm-80) cc_final: 0.5950 (ttt-90) REVERT: F 60 GLN cc_start: 0.8402 (pt0) cc_final: 0.8129 (pt0) REVERT: F 61 LYS cc_start: 0.8483 (mppt) cc_final: 0.8234 (mmtm) REVERT: G 150 MET cc_start: 0.8744 (tpp) cc_final: 0.8400 (ttm) REVERT: H 51 GLN cc_start: 0.7805 (pp30) cc_final: 0.7549 (pp30) REVERT: H 181 TYR cc_start: 0.8422 (m-80) cc_final: 0.8219 (m-80) REVERT: H 359 ASN cc_start: 0.8814 (m-40) cc_final: 0.8392 (m110) REVERT: H 442 ASP cc_start: 0.8739 (p0) cc_final: 0.8177 (p0) REVERT: I 64 ARG cc_start: 0.7139 (ptm-80) cc_final: 0.6611 (ttt180) REVERT: I 68 HIS cc_start: 0.7787 (m-70) cc_final: 0.7550 (m-70) REVERT: I 120 VAL cc_start: 0.9311 (t) cc_final: 0.8999 (m) REVERT: I 167 MET cc_start: 0.7346 (pmm) cc_final: 0.6904 (ptp) REVERT: I 183 ASP cc_start: 0.7545 (m-30) cc_final: 0.6964 (t0) REVERT: I 371 LEU cc_start: 0.7974 (pp) cc_final: 0.7736 (pp) REVERT: J 58 ILE cc_start: 0.8925 (pt) cc_final: 0.8529 (mt) REVERT: J 86 VAL cc_start: 0.8821 (t) cc_final: 0.8475 (m) REVERT: J 345 LYS cc_start: 0.7988 (mttt) cc_final: 0.7692 (tppt) REVERT: J 389 VAL cc_start: 0.8158 (m) cc_final: 0.7942 (t) REVERT: K 124 SER cc_start: 0.8776 (t) cc_final: 0.8435 (p) REVERT: K 149 ILE cc_start: 0.9155 (tp) cc_final: 0.8803 (tt) REVERT: L 159 LEU cc_start: 0.7458 (pt) cc_final: 0.7160 (pp) REVERT: L 188 GLU cc_start: 0.8336 (pp20) cc_final: 0.8049 (pp20) REVERT: L 306 MET cc_start: 0.7434 (tmm) cc_final: 0.6770 (tmm) REVERT: L 307 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7015 (tp30) REVERT: M 265 ASP cc_start: 0.7593 (m-30) cc_final: 0.7181 (m-30) REVERT: M 292 ASP cc_start: 0.7476 (p0) cc_final: 0.7138 (p0) outliers start: 2 outliers final: 0 residues processed: 890 average time/residue: 0.2442 time to fit residues: 361.9361 Evaluate side-chains 683 residues out of total 4951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 682 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 31 optimal weight: 0.1980 chunk 245 optimal weight: 0.9980 chunk 220 optimal weight: 1.9990 chunk 175 optimal weight: 0.9980 chunk 341 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 506 optimal weight: 0.0050 chunk 416 optimal weight: 1.9990 chunk 557 optimal weight: 0.7980 chunk 288 optimal weight: 4.9990 chunk 498 optimal weight: 8.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 120 HIS 2 160 GLN 6 36 ASN 6 159 GLN 7 74 ASN 7 112 ASN ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 241 GLN D 235 GLN F 60 GLN G 182 HIS G 207 ASN H 281 GLN I 238 ASN I 303 GLN ** I 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 376 ASN ** J 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 ASN J 204 HIS ** J 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.083547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.073961 restraints weight = 112616.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.074871 restraints weight = 70685.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.075187 restraints weight = 56896.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.075924 restraints weight = 46371.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.075906 restraints weight = 40001.568| |-----------------------------------------------------------------------------| r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 45012 Z= 0.108 Angle : 0.597 10.980 60998 Z= 0.304 Chirality : 0.045 0.300 7049 Planarity : 0.004 0.051 7868 Dihedral : 6.331 116.951 6322 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.07 % Allowed : 3.27 % Favored : 96.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.09 (0.10), residues: 5766 helix: -1.56 (0.10), residues: 2105 sheet: -2.13 (0.14), residues: 1037 loop : -2.35 (0.12), residues: 2624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 77 TYR 0.032 0.001 TYR 5 137 PHE 0.023 0.001 PHE M 432 TRP 0.017 0.001 TRP G 218 HIS 0.011 0.001 HIS G 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (45011) covalent geometry : angle 0.59742 / 0.30 (60998) hydrogen bonds : bond 0.03372 / 2.27 ( 1440) hydrogen bonds : angle 5.15182 / 3.59 ( 3972) Misc. bond : bond 0.00013 / 0.01 ( 1) *********************** 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 895 residues out of total 4951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 892 time to evaluate : 1.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 19 ARG cc_start: 0.8529 (ttm170) cc_final: 0.7059 (ttm-80) REVERT: 1 160 SER cc_start: 0.8146 (m) cc_final: 0.7834 (p) REVERT: 2 30 ASN cc_start: 0.7860 (t0) cc_final: 0.7566 (t0) REVERT: 2 70 THR cc_start: 0.8511 (m) cc_final: 0.8112 (p) REVERT: 2 112 SER cc_start: 0.8505 (t) cc_final: 0.8116 (p) REVERT: 2 120 ASP cc_start: 0.7271 (p0) cc_final: 0.6693 (p0) REVERT: 2 200 GLN cc_start: 0.6811 (mt0) cc_final: 0.6115 (pt0) REVERT: 2 214 LYS cc_start: 0.8076 (ptmt) cc_final: 0.7840 (mttp) REVERT: 3 16 THR cc_start: 0.8065 (m) cc_final: 0.7520 (m) REVERT: 3 98 ARG cc_start: 0.7821 (mtp-110) cc_final: 0.7355 (mtp85) REVERT: 3 125 ASP cc_start: 0.7922 (p0) cc_final: 0.7667 (p0) REVERT: 3 154 TYR cc_start: 0.7591 (t80) cc_final: 0.6914 (t80) REVERT: 3 180 LEU cc_start: 0.7954 (mp) cc_final: 0.7737 (mp) REVERT: 3 203 ARG cc_start: 0.8403 (ptm-80) cc_final: 0.6392 (mtt-85) REVERT: 4 3 ILE cc_start: 0.9086 (pt) cc_final: 0.8487 (mp) REVERT: 4 99 GLN cc_start: 0.7259 (tm-30) cc_final: 0.6915 (tm-30) REVERT: 4 120 ASP cc_start: 0.7890 (p0) cc_final: 0.7658 (p0) REVERT: 4 124 THR cc_start: 0.8803 (p) cc_final: 0.8205 (p) REVERT: 5 24 ASN cc_start: 0.8711 (t0) cc_final: 0.8277 (t0) REVERT: 5 63 CYS cc_start: 0.8690 (m) cc_final: 0.8467 (m) REVERT: 5 111 THR cc_start: 0.7854 (m) cc_final: 0.7414 (p) REVERT: 6 159 GLN cc_start: 0.6614 (pt0) cc_final: 0.5670 (tp40) REVERT: 6 161 GLU cc_start: 0.7420 (tm-30) cc_final: 0.6998 (tm-30) REVERT: 7 108 ASN cc_start: 0.7665 (p0) cc_final: 0.7411 (p0) REVERT: 7 136 THR cc_start: 0.8879 (p) cc_final: 0.8626 (t) REVERT: 7 169 THR cc_start: 0.8537 (t) cc_final: 0.8273 (m) REVERT: A 39 ASN cc_start: 0.8249 (m-40) cc_final: 0.7759 (t0) REVERT: A 134 MET cc_start: 0.7716 (ptp) cc_final: 0.7394 (ptp) REVERT: A 195 ASN cc_start: 0.7713 (m-40) cc_final: 0.7366 (m110) REVERT: A 222 ASP cc_start: 0.7566 (p0) cc_final: 0.7294 (p0) REVERT: A 224 GLU cc_start: 0.8318 (pt0) cc_final: 0.8103 (pt0) REVERT: B 41 ASN cc_start: 0.8441 (p0) cc_final: 0.7917 (p0) REVERT: B 60 THR cc_start: 0.8928 (p) cc_final: 0.8466 (t) REVERT: B 75 TYR cc_start: 0.8850 (p90) cc_final: 0.8390 (p90) REVERT: B 118 MET cc_start: 0.8782 (ttm) cc_final: 0.8300 (mtt) REVERT: B 210 GLU cc_start: 0.7536 (tp30) cc_final: 0.7266 (tp30) REVERT: B 224 TYR cc_start: 0.8164 (p90) cc_final: 0.7924 (p90) REVERT: C 7 ASP cc_start: 0.7484 (t70) cc_final: 0.7126 (t0) REVERT: C 199 LYS cc_start: 0.8892 (mtmt) cc_final: 0.8585 (mtmm) REVERT: D 43 VAL cc_start: 0.9118 (p) cc_final: 0.8746 (t) REVERT: D 47 GLU cc_start: 0.8411 (pp20) cc_final: 0.7927 (pp20) REVERT: E 35 SER cc_start: 0.8314 (m) cc_final: 0.8111 (m) REVERT: E 53 ARG cc_start: 0.7011 (ttm-80) cc_final: 0.5995 (ttt-90) REVERT: E 182 GLU cc_start: 0.7075 (pp20) cc_final: 0.6872 (pp20) REVERT: F 60 GLN cc_start: 0.8375 (pt0) cc_final: 0.8119 (pt0) REVERT: F 61 LYS cc_start: 0.8442 (mppt) cc_final: 0.8237 (mmtm) REVERT: F 117 GLN cc_start: 0.8360 (tm-30) cc_final: 0.7792 (tm-30) REVERT: F 122 SER cc_start: 0.8975 (m) cc_final: 0.8605 (p) REVERT: G 26 TYR cc_start: 0.8140 (m-80) cc_final: 0.7920 (m-80) REVERT: G 60 VAL cc_start: 0.8627 (t) cc_final: 0.8314 (p) REVERT: H 51 GLN cc_start: 0.7760 (pp30) cc_final: 0.7484 (pp30) REVERT: H 98 GLN cc_start: 0.7996 (tt0) cc_final: 0.7777 (tt0) REVERT: H 359 ASN cc_start: 0.8703 (m-40) cc_final: 0.8394 (m110) REVERT: H 442 ASP cc_start: 0.8751 (p0) cc_final: 0.8216 (p0) REVERT: I 64 ARG cc_start: 0.7021 (ptm-80) cc_final: 0.6481 (ttt180) REVERT: I 68 HIS cc_start: 0.7773 (m-70) cc_final: 0.7499 (m-70) REVERT: I 120 VAL cc_start: 0.9332 (t) cc_final: 0.9055 (m) REVERT: I 167 MET cc_start: 0.7390 (pmm) cc_final: 0.6811 (ptp) REVERT: I 349 LEU cc_start: 0.8899 (tp) cc_final: 0.8678 (tp) REVERT: I 371 LEU cc_start: 0.7936 (pp) cc_final: 0.7604 (pp) REVERT: J 58 ILE cc_start: 0.8977 (pt) cc_final: 0.8652 (mt) REVERT: J 86 VAL cc_start: 0.8796 (t) cc_final: 0.8495 (m) REVERT: J 247 MET cc_start: 0.8047 (mtp) cc_final: 0.7678 (mtm) REVERT: J 345 LYS cc_start: 0.8116 (mttt) cc_final: 0.7796 (tppt) REVERT: K 124 SER cc_start: 0.8725 (t) cc_final: 0.8376 (p) REVERT: K 149 ILE cc_start: 0.9117 (tp) cc_final: 0.8878 (mm) REVERT: L 159 LEU cc_start: 0.7424 (pt) cc_final: 0.7120 (pp) REVERT: L 255 TYR cc_start: 0.8547 (m-80) cc_final: 0.8123 (m-80) REVERT: L 306 MET cc_start: 0.7449 (tmm) cc_final: 0.6745 (tmm) REVERT: L 307 GLU cc_start: 0.7562 (mm-30) cc_final: 0.7264 (tp30) REVERT: M 265 ASP cc_start: 0.7566 (m-30) cc_final: 0.7196 (m-30) REVERT: M 292 ASP cc_start: 0.7465 (p0) cc_final: 0.7141 (p0) outliers start: 3 outliers final: 1 residues processed: 894 average time/residue: 0.2392 time to fit residues: 359.3857 Evaluate side-chains 707 residues out of total 4951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 706 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 200 optimal weight: 0.0050 chunk 304 optimal weight: 6.9990 chunk 54 optimal weight: 10.0000 chunk 240 optimal weight: 4.9990 chunk 439 optimal weight: 6.9990 chunk 560 optimal weight: 8.9990 chunk 225 optimal weight: 4.9990 chunk 533 optimal weight: 2.9990 chunk 501 optimal weight: 2.9990 chunk 564 optimal weight: 20.0000 chunk 346 optimal weight: 0.0770 overall best weight: 2.2158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 4 41 HIS 6 36 ASN ** 6 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 61 GLN 7 74 ASN 7 112 ASN ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 HIS D 117 GLN D 235 GLN G 207 ASN H 281 GLN ** 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 240 HIS ** K 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 131 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.078740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.068555 restraints weight = 114155.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.069861 restraints weight = 74970.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.070358 restraints weight = 53896.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.071012 restraints weight = 44698.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.071243 restraints weight = 37888.206| |-----------------------------------------------------------------------------| r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.4094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 45012 Z= 0.170 Angle : 0.644 8.442 60998 Z= 0.330 Chirality : 0.047 0.320 7049 Planarity : 0.004 0.060 7868 Dihedral : 6.380 118.685 6322 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.80 (0.11), residues: 5766 helix: -1.31 (0.11), residues: 2108 sheet: -1.89 (0.15), residues: 1061 loop : -2.22 (0.12), residues: 2597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 127 TYR 0.036 0.002 TYR M 180 PHE 0.024 0.002 PHE E 138 TRP 0.021 0.002 TRP 1 165 HIS 0.009 0.001 HIS G 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 (45011) covalent geometry : angle 0.64385 / 0.33 (60998) hydrogen bonds : bond 0.03573 / 2.40 ( 1440) hydrogen bonds : angle 5.18957 / 3.61 ( 3972) Misc. bond : bond 0.00009 / 0.00 ( 1) *********************** 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 824 residues out of total 4951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 824 time to evaluate : 1.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 44 CYS cc_start: 0.9096 (m) cc_final: 0.8775 (m) REVERT: 1 160 SER cc_start: 0.8324 (m) cc_final: 0.8074 (p) REVERT: 2 3 ILE cc_start: 0.8584 (pt) cc_final: 0.8357 (mt) REVERT: 2 30 ASN cc_start: 0.8014 (t0) cc_final: 0.7708 (t0) REVERT: 2 112 SER cc_start: 0.8442 (t) cc_final: 0.8016 (p) REVERT: 2 120 ASP cc_start: 0.7391 (p0) cc_final: 0.6851 (p0) REVERT: 2 200 GLN cc_start: 0.6869 (mt0) cc_final: 0.6143 (pt0) REVERT: 2 214 LYS cc_start: 0.8116 (ptmt) cc_final: 0.7780 (mttp) REVERT: 3 61 THR cc_start: 0.9069 (m) cc_final: 0.8833 (m) REVERT: 4 3 ILE cc_start: 0.9077 (pt) cc_final: 0.8556 (mp) REVERT: 4 58 GLU cc_start: 0.8306 (mp0) cc_final: 0.8089 (mp0) REVERT: 4 60 ILE cc_start: 0.9169 (pt) cc_final: 0.8615 (mm) REVERT: 4 99 GLN cc_start: 0.7413 (tm-30) cc_final: 0.7009 (tm-30) REVERT: 4 120 ASP cc_start: 0.7924 (p0) cc_final: 0.7541 (p0) REVERT: 4 124 THR cc_start: 0.8717 (p) cc_final: 0.8020 (p) REVERT: 4 167 GLU cc_start: 0.8652 (pm20) cc_final: 0.8148 (pm20) REVERT: 5 19 ARG cc_start: 0.8511 (tpp-160) cc_final: 0.8109 (tpp-160) REVERT: 5 24 ASN cc_start: 0.8851 (t0) cc_final: 0.8434 (t0) REVERT: 5 25 TRP cc_start: 0.8673 (t60) cc_final: 0.8466 (t60) REVERT: 5 111 THR cc_start: 0.7945 (m) cc_final: 0.7529 (p) REVERT: 6 81 ASP cc_start: 0.7151 (t0) cc_final: 0.6767 (t70) REVERT: 6 159 GLN cc_start: 0.6794 (pt0) cc_final: 0.6097 (tp40) REVERT: 7 169 THR cc_start: 0.8605 (t) cc_final: 0.8319 (m) REVERT: A 39 ASN cc_start: 0.8244 (m-40) cc_final: 0.7753 (t0) REVERT: A 103 GLU cc_start: 0.7978 (tt0) cc_final: 0.7734 (tt0) REVERT: A 195 ASN cc_start: 0.7745 (m-40) cc_final: 0.7372 (m110) REVERT: A 224 GLU cc_start: 0.8413 (pt0) cc_final: 0.8088 (pt0) REVERT: A 242 GLU cc_start: 0.7076 (mp0) cc_final: 0.6741 (mp0) REVERT: B 60 THR cc_start: 0.9074 (p) cc_final: 0.8640 (t) REVERT: B 75 TYR cc_start: 0.8811 (p90) cc_final: 0.8342 (p90) REVERT: B 118 MET cc_start: 0.8758 (ttm) cc_final: 0.8341 (mtt) REVERT: B 177 LYS cc_start: 0.6825 (mmpt) cc_final: 0.6358 (tptp) REVERT: B 210 GLU cc_start: 0.7603 (tp30) cc_final: 0.7387 (tp30) REVERT: C 7 ASP cc_start: 0.7854 (t70) cc_final: 0.7370 (t0) REVERT: C 39 MET cc_start: 0.8409 (ttt) cc_final: 0.8129 (ttt) REVERT: C 72 LYS cc_start: 0.8548 (mmmt) cc_final: 0.8237 (mmtp) REVERT: D 43 VAL cc_start: 0.9180 (p) cc_final: 0.8918 (t) REVERT: D 47 GLU cc_start: 0.8500 (pp20) cc_final: 0.8031 (pp20) REVERT: D 86 ILE cc_start: 0.8602 (pt) cc_final: 0.8111 (mt) REVERT: D 148 TYR cc_start: 0.9102 (m-80) cc_final: 0.8768 (m-10) REVERT: D 203 VAL cc_start: 0.7671 (t) cc_final: 0.7454 (t) REVERT: E 203 ILE cc_start: 0.8618 (pt) cc_final: 0.8384 (pt) REVERT: E 238 GLU cc_start: 0.7463 (pp20) cc_final: 0.6975 (pp20) REVERT: F 60 GLN cc_start: 0.8277 (pt0) cc_final: 0.8074 (pt0) REVERT: F 117 GLN cc_start: 0.8600 (tm-30) cc_final: 0.7947 (tm-30) REVERT: F 122 SER cc_start: 0.8912 (m) cc_final: 0.8678 (t) REVERT: G 60 VAL cc_start: 0.8680 (t) cc_final: 0.8425 (p) REVERT: G 202 LEU cc_start: 0.8959 (mt) cc_final: 0.8630 (mt) REVERT: H 51 GLN cc_start: 0.7974 (pp30) cc_final: 0.7703 (pp30) REVERT: H 98 GLN cc_start: 0.8240 (tt0) cc_final: 0.7983 (tt0) REVERT: H 218 ILE cc_start: 0.8812 (pt) cc_final: 0.8517 (mt) REVERT: H 297 MET cc_start: 0.8777 (ptm) cc_final: 0.8540 (ptm) REVERT: H 359 ASN cc_start: 0.8810 (m-40) cc_final: 0.8458 (m110) REVERT: H 442 ASP cc_start: 0.8755 (p0) cc_final: 0.8466 (p0) REVERT: I 64 ARG cc_start: 0.7272 (ptm-80) cc_final: 0.6876 (ttt180) REVERT: I 68 HIS cc_start: 0.7936 (m-70) cc_final: 0.7652 (m-70) REVERT: I 120 VAL cc_start: 0.9335 (t) cc_final: 0.9058 (m) REVERT: I 167 MET cc_start: 0.7686 (pmm) cc_final: 0.7265 (ptp) REVERT: I 208 TYR cc_start: 0.8558 (m-80) cc_final: 0.8215 (m-10) REVERT: J 58 ILE cc_start: 0.9023 (pt) cc_final: 0.8702 (mt) REVERT: J 86 VAL cc_start: 0.8883 (t) cc_final: 0.8618 (m) REVERT: J 94 TYR cc_start: 0.9116 (m-10) cc_final: 0.8817 (m-10) REVERT: J 247 MET cc_start: 0.8483 (mtp) cc_final: 0.8191 (mtp) REVERT: J 256 THR cc_start: 0.6569 (m) cc_final: 0.5982 (p) REVERT: J 270 ARG cc_start: 0.5912 (mmt90) cc_final: 0.5694 (mtt180) REVERT: J 295 ASN cc_start: 0.8995 (m-40) cc_final: 0.8728 (m-40) REVERT: J 345 LYS cc_start: 0.8420 (mttt) cc_final: 0.7935 (tppt) REVERT: K 124 SER cc_start: 0.8901 (t) cc_final: 0.8532 (p) REVERT: K 149 ILE cc_start: 0.9116 (tp) cc_final: 0.8747 (tt) REVERT: L 159 LEU cc_start: 0.7897 (pt) cc_final: 0.7688 (pp) REVERT: L 306 MET cc_start: 0.7535 (tmm) cc_final: 0.6906 (tmm) REVERT: L 307 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7332 (tp30) REVERT: M 265 ASP cc_start: 0.7840 (m-30) cc_final: 0.7464 (m-30) REVERT: M 292 ASP cc_start: 0.7498 (p0) cc_final: 0.6916 (p0) outliers start: 0 outliers final: 0 residues processed: 824 average time/residue: 0.2330 time to fit residues: 324.2447 Evaluate side-chains 684 residues out of total 4951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 684 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 434 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 529 optimal weight: 0.9990 chunk 488 optimal weight: 0.0470 chunk 358 optimal weight: 3.9990 chunk 138 optimal weight: 0.9980 chunk 545 optimal weight: 0.9990 chunk 456 optimal weight: 0.0980 chunk 479 optimal weight: 6.9990 chunk 432 optimal weight: 7.9990 chunk 152 optimal weight: 1.9990 overall best weight: 0.6282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 157 HIS 3 8 ASN 6 36 ASN ** 6 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 159 GLN 7 74 ASN 7 112 ASN 7 120 GLN ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 235 GLN G 182 HIS H 281 GLN I 238 ASN I 303 GLN ** I 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 ASN J 204 HIS J 277 ASN K 72 GLN K 142 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.081033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.071253 restraints weight = 113336.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.072001 restraints weight = 72746.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.072347 restraints weight = 59087.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.072647 restraints weight = 50991.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.072745 restraints weight = 48189.061| |-----------------------------------------------------------------------------| r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 45012 Z= 0.107 Angle : 0.585 9.365 60998 Z= 0.296 Chirality : 0.045 0.303 7049 Planarity : 0.004 0.056 7868 Dihedral : 6.012 114.251 6322 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 0.02 % Allowed : 2.13 % Favored : 97.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.43 (0.11), residues: 5766 helix: -1.01 (0.11), residues: 2112 sheet: -1.56 (0.15), residues: 1064 loop : -2.06 (0.12), residues: 2590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 77 TYR 0.032 0.001 TYR B 224 PHE 0.032 0.001 PHE I 75 TRP 0.025 0.001 TRP G 218 HIS 0.008 0.001 HIS G 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (45011) covalent geometry : angle 0.58476 / 0.30 (60998) hydrogen bonds : bond 0.03137 / 2.10 ( 1440) hydrogen bonds : angle 4.86749 / 3.39 ( 3972) Misc. bond : bond 0.00002 / 0.00 ( 1) *********************** 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 869 residues out of total 4951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 868 time to evaluate : 1.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 44 CYS cc_start: 0.8981 (m) cc_final: 0.8723 (m) REVERT: 1 145 ASN cc_start: 0.8427 (m-40) cc_final: 0.8199 (m-40) REVERT: 1 160 SER cc_start: 0.8376 (m) cc_final: 0.8125 (p) REVERT: 2 30 ASN cc_start: 0.8113 (t0) cc_final: 0.7797 (t0) REVERT: 2 200 GLN cc_start: 0.6900 (mt0) cc_final: 0.6108 (pt0) REVERT: 2 214 LYS cc_start: 0.8122 (ptmt) cc_final: 0.7806 (mttt) REVERT: 3 98 ARG cc_start: 0.7706 (mtp-110) cc_final: 0.7268 (mtp85) REVERT: 3 125 ASP cc_start: 0.7917 (p0) cc_final: 0.7639 (p0) REVERT: 4 3 ILE cc_start: 0.9128 (pt) cc_final: 0.8588 (mp) REVERT: 4 58 GLU cc_start: 0.8241 (mp0) cc_final: 0.7973 (mp0) REVERT: 4 60 ILE cc_start: 0.9277 (pt) cc_final: 0.8399 (mm) REVERT: 4 99 GLN cc_start: 0.7286 (tm-30) cc_final: 0.6958 (tm-30) REVERT: 4 120 ASP cc_start: 0.7897 (p0) cc_final: 0.7531 (p0) REVERT: 4 124 THR cc_start: 0.8634 (p) cc_final: 0.8032 (p) REVERT: 5 19 ARG cc_start: 0.8485 (tpp-160) cc_final: 0.8178 (tpp-160) REVERT: 5 24 ASN cc_start: 0.8931 (t0) cc_final: 0.8489 (t0) REVERT: 5 111 THR cc_start: 0.7969 (m) cc_final: 0.7526 (p) REVERT: 6 81 ASP cc_start: 0.7086 (t0) cc_final: 0.6734 (t70) REVERT: 6 159 GLN cc_start: 0.6978 (pt0) cc_final: 0.6167 (tp40) REVERT: 6 179 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7579 (mm-30) REVERT: 7 169 THR cc_start: 0.8586 (t) cc_final: 0.8318 (m) REVERT: A 39 ASN cc_start: 0.8222 (m-40) cc_final: 0.7733 (t0) REVERT: A 242 GLU cc_start: 0.7184 (mp0) cc_final: 0.6806 (mp0) REVERT: B 75 TYR cc_start: 0.8823 (p90) cc_final: 0.8380 (p90) REVERT: C 7 ASP cc_start: 0.7780 (t70) cc_final: 0.7238 (t0) REVERT: C 39 MET cc_start: 0.8499 (ttt) cc_final: 0.8152 (ttt) REVERT: C 72 LYS cc_start: 0.8493 (mmmt) cc_final: 0.8172 (mmtp) REVERT: D 27 VAL cc_start: 0.9003 (t) cc_final: 0.8707 (p) REVERT: D 43 VAL cc_start: 0.9167 (p) cc_final: 0.8903 (t) REVERT: D 148 TYR cc_start: 0.9023 (m-80) cc_final: 0.8699 (m-10) REVERT: E 182 GLU cc_start: 0.7710 (pp20) cc_final: 0.6988 (pp20) REVERT: E 238 GLU cc_start: 0.7474 (pp20) cc_final: 0.6942 (pp20) REVERT: F 51 ARG cc_start: 0.7745 (ttp-110) cc_final: 0.7086 (mtm-85) REVERT: F 60 GLN cc_start: 0.8049 (pt0) cc_final: 0.7706 (pt0) REVERT: G 26 TYR cc_start: 0.8371 (m-80) cc_final: 0.8101 (m-80) REVERT: G 60 VAL cc_start: 0.8660 (t) cc_final: 0.8428 (p) REVERT: G 202 LEU cc_start: 0.9018 (mt) cc_final: 0.8725 (mt) REVERT: H 51 GLN cc_start: 0.7990 (pp30) cc_final: 0.7714 (pp30) REVERT: H 98 GLN cc_start: 0.8039 (tt0) cc_final: 0.7824 (tt0) REVERT: H 218 ILE cc_start: 0.8822 (pt) cc_final: 0.8451 (mt) REVERT: H 297 MET cc_start: 0.8784 (ptm) cc_final: 0.8564 (ptm) REVERT: H 359 ASN cc_start: 0.8788 (m-40) cc_final: 0.8450 (m110) REVERT: H 442 ASP cc_start: 0.8765 (p0) cc_final: 0.8451 (p0) REVERT: I 64 ARG cc_start: 0.7194 (ptm-80) cc_final: 0.6843 (ttt180) REVERT: I 68 HIS cc_start: 0.7877 (m-70) cc_final: 0.7558 (m-70) REVERT: I 120 VAL cc_start: 0.9312 (t) cc_final: 0.8959 (m) REVERT: I 167 MET cc_start: 0.7656 (pmm) cc_final: 0.7404 (ptp) REVERT: I 208 TYR cc_start: 0.8443 (m-80) cc_final: 0.8108 (m-10) REVERT: J 86 VAL cc_start: 0.8798 (t) cc_final: 0.8583 (m) REVERT: J 94 TYR cc_start: 0.9123 (m-10) cc_final: 0.8766 (m-10) REVERT: J 247 MET cc_start: 0.8390 (mtp) cc_final: 0.8004 (mtp) REVERT: J 256 THR cc_start: 0.6335 (m) cc_final: 0.5697 (p) REVERT: J 270 ARG cc_start: 0.5936 (mmt90) cc_final: 0.5551 (mtt180) REVERT: J 295 ASN cc_start: 0.8921 (m-40) cc_final: 0.8693 (m-40) REVERT: K 124 SER cc_start: 0.8748 (t) cc_final: 0.8219 (p) REVERT: K 149 ILE cc_start: 0.9064 (tp) cc_final: 0.8673 (tt) REVERT: K 260 LEU cc_start: 0.9180 (pp) cc_final: 0.8730 (tt) REVERT: L 156 MET cc_start: 0.7855 (mtp) cc_final: 0.7604 (mtp) REVERT: L 159 LEU cc_start: 0.7731 (pt) cc_final: 0.7485 (pp) REVERT: L 188 GLU cc_start: 0.8322 (pp20) cc_final: 0.8050 (pp20) REVERT: L 255 TYR cc_start: 0.8660 (m-80) cc_final: 0.8238 (m-80) REVERT: L 306 MET cc_start: 0.7674 (tmm) cc_final: 0.6973 (tmm) REVERT: L 307 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7343 (tp30) REVERT: M 265 ASP cc_start: 0.7776 (m-30) cc_final: 0.7359 (m-30) REVERT: M 292 ASP cc_start: 0.7500 (p0) cc_final: 0.6814 (p0) REVERT: M 397 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7348 (mm-30) outliers start: 1 outliers final: 1 residues processed: 869 average time/residue: 0.2386 time to fit residues: 347.4683 Evaluate side-chains 696 residues out of total 4951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 695 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 22 optimal weight: 6.9990 chunk 457 optimal weight: 5.9990 chunk 512 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 190 optimal weight: 0.9980 chunk 83 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 chunk 550 optimal weight: 9.9990 chunk 230 optimal weight: 4.9990 chunk 402 optimal weight: 5.9990 chunk 569 optimal weight: 2.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 6 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 36 ASN 7 74 ASN 7 112 ASN A 27 GLN ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 19 GLN D 235 GLN G 33 ASN G 182 HIS G 204 HIS I 102 ASN ** I 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 303 GLN ** I 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 ASN J 204 HIS K 142 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.074432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.063570 restraints weight = 116588.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.064818 restraints weight = 72750.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.065662 restraints weight = 51783.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.066230 restraints weight = 40852.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.066614 restraints weight = 34641.720| |-----------------------------------------------------------------------------| r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.4556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 45012 Z= 0.257 Angle : 0.737 9.619 60998 Z= 0.378 Chirality : 0.050 0.276 7049 Planarity : 0.005 0.068 7868 Dihedral : 6.494 121.655 6322 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.58 % Favored : 92.40 % Rotamer: Outliers : 0.02 % Allowed : 2.52 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.51 (0.11), residues: 5766 helix: -1.13 (0.11), residues: 2105 sheet: -1.54 (0.15), residues: 1072 loop : -2.09 (0.12), residues: 2589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 210 TYR 0.034 0.002 TYR M 180 PHE 0.041 0.003 PHE 7 36 TRP 0.033 0.002 TRP G 218 HIS 0.016 0.001 HIS 1 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00607 / 0.26 (45011) covalent geometry : angle 0.73690 / 0.38 (60998) hydrogen bonds : bond 0.04005 / 2.70 ( 1440) hydrogen bonds : angle 5.36534 / 3.74 ( 3972) Misc. bond : bond 0.00010 / 0.01 ( 1) *********************** 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 798 residues out of total 4951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 797 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 32 ASP cc_start: 0.8069 (t0) cc_final: 0.7859 (t0) REVERT: 1 145 ASN cc_start: 0.8542 (m-40) cc_final: 0.8248 (m-40) REVERT: 1 160 SER cc_start: 0.8544 (m) cc_final: 0.8292 (p) REVERT: 2 30 ASN cc_start: 0.8164 (t0) cc_final: 0.7789 (t0) REVERT: 2 200 GLN cc_start: 0.6829 (mt0) cc_final: 0.6155 (pt0) REVERT: 2 214 LYS cc_start: 0.8195 (ptmt) cc_final: 0.7839 (mttp) REVERT: 3 98 ARG cc_start: 0.7611 (mtp-110) cc_final: 0.7315 (mtp85) REVERT: 4 52 ASP cc_start: 0.7964 (m-30) cc_final: 0.7574 (t0) REVERT: 4 60 ILE cc_start: 0.9425 (pt) cc_final: 0.8921 (mt) REVERT: 4 71 GLU cc_start: 0.8096 (mp0) cc_final: 0.7780 (mp0) REVERT: 4 99 GLN cc_start: 0.7340 (tm-30) cc_final: 0.6880 (tm-30) REVERT: 4 120 ASP cc_start: 0.7835 (p0) cc_final: 0.7452 (p0) REVERT: 4 124 THR cc_start: 0.8506 (p) cc_final: 0.7830 (p) REVERT: 5 24 ASN cc_start: 0.9058 (t0) cc_final: 0.8709 (t0) REVERT: 5 25 TRP cc_start: 0.8695 (t60) cc_final: 0.8451 (t60) REVERT: 5 145 LYS cc_start: 0.8747 (pttp) cc_final: 0.7956 (pttp) REVERT: 5 146 TRP cc_start: 0.8335 (t-100) cc_final: 0.7335 (t60) REVERT: 5 197 PHE cc_start: 0.8043 (t80) cc_final: 0.7765 (t80) REVERT: 6 81 ASP cc_start: 0.7217 (t0) cc_final: 0.6820 (t70) REVERT: 7 120 GLN cc_start: 0.8330 (mm110) cc_final: 0.7908 (mm-40) REVERT: A 39 ASN cc_start: 0.8243 (m-40) cc_final: 0.7723 (t0) REVERT: A 242 GLU cc_start: 0.7181 (mp0) cc_final: 0.6671 (mp0) REVERT: B 75 TYR cc_start: 0.8785 (p90) cc_final: 0.8339 (p90) REVERT: B 178 ARG cc_start: 0.7852 (mmm-85) cc_final: 0.7481 (mmp-170) REVERT: C 7 ASP cc_start: 0.7899 (t70) cc_final: 0.7493 (t0) REVERT: C 164 SER cc_start: 0.9128 (p) cc_final: 0.8859 (p) REVERT: C 195 LYS cc_start: 0.8308 (mmmt) cc_final: 0.8016 (mmmt) REVERT: D 43 VAL cc_start: 0.9161 (p) cc_final: 0.8929 (t) REVERT: D 86 ILE cc_start: 0.8614 (pt) cc_final: 0.8259 (mt) REVERT: D 148 TYR cc_start: 0.9172 (m-80) cc_final: 0.8951 (m-10) REVERT: E 76 CYS cc_start: 0.8871 (t) cc_final: 0.8632 (t) REVERT: E 132 ARG cc_start: 0.7117 (ttm170) cc_final: 0.6835 (ttp-170) REVERT: E 133 LEU cc_start: 0.8216 (tp) cc_final: 0.7741 (tp) REVERT: E 182 GLU cc_start: 0.7906 (pp20) cc_final: 0.7446 (pp20) REVERT: E 238 GLU cc_start: 0.7589 (pp20) cc_final: 0.7093 (pp20) REVERT: F 60 GLN cc_start: 0.8004 (pt0) cc_final: 0.7751 (pt0) REVERT: G 60 VAL cc_start: 0.8715 (t) cc_final: 0.8417 (p) REVERT: G 202 LEU cc_start: 0.9017 (mt) cc_final: 0.8777 (mt) REVERT: H 51 GLN cc_start: 0.8119 (pp30) cc_final: 0.7848 (pp30) REVERT: H 98 GLN cc_start: 0.8360 (tt0) cc_final: 0.8116 (tt0) REVERT: H 330 GLN cc_start: 0.8943 (mp10) cc_final: 0.8693 (mp10) REVERT: H 359 ASN cc_start: 0.8930 (m-40) cc_final: 0.8665 (m110) REVERT: H 372 ASP cc_start: 0.8037 (m-30) cc_final: 0.7557 (t0) REVERT: I 64 ARG cc_start: 0.7479 (ptm-80) cc_final: 0.7001 (ttt180) REVERT: I 68 HIS cc_start: 0.7996 (m-70) cc_final: 0.7698 (m-70) REVERT: I 120 VAL cc_start: 0.9373 (t) cc_final: 0.9091 (m) REVERT: I 121 THR cc_start: 0.8094 (p) cc_final: 0.7760 (t) REVERT: I 167 MET cc_start: 0.7648 (pmm) cc_final: 0.7407 (ptp) REVERT: I 208 TYR cc_start: 0.8476 (m-80) cc_final: 0.8128 (m-80) REVERT: I 285 ASP cc_start: 0.7728 (p0) cc_final: 0.7447 (p0) REVERT: J 86 VAL cc_start: 0.8933 (t) cc_final: 0.8700 (m) REVERT: J 247 MET cc_start: 0.8435 (mtp) cc_final: 0.8171 (mtp) REVERT: J 256 THR cc_start: 0.6507 (m) cc_final: 0.6109 (p) REVERT: J 270 ARG cc_start: 0.6450 (mmt90) cc_final: 0.6041 (mmt180) REVERT: J 345 LYS cc_start: 0.8450 (mttt) cc_final: 0.7965 (tppt) REVERT: J 362 CYS cc_start: 0.8878 (m) cc_final: 0.8339 (t) REVERT: K 149 ILE cc_start: 0.9065 (tp) cc_final: 0.8612 (tt) REVERT: K 260 LEU cc_start: 0.9298 (pp) cc_final: 0.8864 (tt) REVERT: L 156 MET cc_start: 0.7975 (mtp) cc_final: 0.7773 (mtp) REVERT: L 188 GLU cc_start: 0.8416 (pp20) cc_final: 0.8111 (pp20) REVERT: L 306 MET cc_start: 0.7786 (tmm) cc_final: 0.7109 (tmm) REVERT: L 307 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7439 (tp30) REVERT: M 265 ASP cc_start: 0.7851 (m-30) cc_final: 0.7647 (m-30) REVERT: M 292 ASP cc_start: 0.7448 (p0) cc_final: 0.6913 (p0) REVERT: M 328 ASN cc_start: 0.8949 (m-40) cc_final: 0.8708 (m-40) outliers start: 1 outliers final: 0 residues processed: 798 average time/residue: 0.2382 time to fit residues: 320.6512 Evaluate side-chains 660 residues out of total 4951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 660 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 175 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 371 optimal weight: 0.9990 chunk 290 optimal weight: 0.9980 chunk 554 optimal weight: 0.0980 chunk 376 optimal weight: 1.9990 chunk 273 optimal weight: 1.9990 chunk 313 optimal weight: 5.9990 chunk 134 optimal weight: 1.9990 chunk 379 optimal weight: 3.9990 chunk 247 optimal weight: 0.9980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 5 53 GLN 5 133 GLN 6 36 ASN ** 6 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 159 GLN 7 74 ASN ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 181 ASN C 21 GLN C 103 ASN C 156 ASN D 19 GLN D 117 GLN G 33 ASN H 356 ASN I 238 ASN I 303 GLN ** I 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 ASN J 277 ASN K 142 HIS M 311 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.077771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.067504 restraints weight = 114807.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.068742 restraints weight = 77147.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.069387 restraints weight = 56316.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.070023 restraints weight = 45467.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.070229 restraints weight = 38133.118| |-----------------------------------------------------------------------------| r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.4796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 45012 Z= 0.120 Angle : 0.620 9.002 60998 Z= 0.313 Chirality : 0.045 0.213 7049 Planarity : 0.004 0.086 7868 Dihedral : 6.079 115.388 6322 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 0.09 % Allowed : 1.16 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.19 (0.11), residues: 5766 helix: -0.86 (0.11), residues: 2116 sheet: -1.38 (0.15), residues: 1075 loop : -1.91 (0.12), residues: 2575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 210 TYR 0.019 0.001 TYR M 180 PHE 0.024 0.002 PHE M 432 TRP 0.029 0.001 TRP G 218 HIS 0.009 0.001 HIS 1 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (45011) covalent geometry : angle 0.62017 / 0.31 (60998) hydrogen bonds : bond 0.03338 / 2.25 ( 1440) hydrogen bonds : angle 4.99525 / 3.47 ( 3972) Misc. bond : bond 0.00004 / 0.00 ( 1) *********************** 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 813 residues out of total 4951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 809 time to evaluate : 1.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 29 ARG cc_start: 0.8438 (ptt90) cc_final: 0.8019 (ptt-90) REVERT: 1 32 ASP cc_start: 0.7841 (t0) cc_final: 0.7634 (t0) REVERT: 1 160 SER cc_start: 0.8585 (m) cc_final: 0.8320 (p) REVERT: 2 30 ASN cc_start: 0.7985 (t0) cc_final: 0.7736 (t0) REVERT: 2 120 ASP cc_start: 0.7523 (p0) cc_final: 0.7215 (p0) REVERT: 2 200 GLN cc_start: 0.6818 (mt0) cc_final: 0.6133 (pt0) REVERT: 2 214 LYS cc_start: 0.8139 (ptmt) cc_final: 0.7838 (mttt) REVERT: 3 72 ASN cc_start: 0.8599 (m-40) cc_final: 0.7979 (t0) REVERT: 3 98 ARG cc_start: 0.7598 (mtp-110) cc_final: 0.7187 (mtp85) REVERT: 4 31 SER cc_start: 0.8767 (m) cc_final: 0.8226 (t) REVERT: 4 60 ILE cc_start: 0.9362 (pt) cc_final: 0.8713 (mt) REVERT: 4 92 ILE cc_start: 0.8630 (tp) cc_final: 0.8356 (tp) REVERT: 4 99 GLN cc_start: 0.7261 (tm-30) cc_final: 0.6884 (tm-30) REVERT: 4 120 ASP cc_start: 0.7907 (p0) cc_final: 0.7504 (p0) REVERT: 4 124 THR cc_start: 0.8549 (p) cc_final: 0.7916 (p) REVERT: 4 162 LYS cc_start: 0.6365 (tptp) cc_final: 0.5825 (tptp) REVERT: 5 19 ARG cc_start: 0.8765 (tpp-160) cc_final: 0.8512 (tpp-160) REVERT: 5 24 ASN cc_start: 0.9093 (t0) cc_final: 0.8719 (t0) REVERT: 5 25 TRP cc_start: 0.8734 (t60) cc_final: 0.8530 (t60) REVERT: 5 111 THR cc_start: 0.8148 (m) cc_final: 0.7558 (p) REVERT: 5 146 TRP cc_start: 0.8373 (t-100) cc_final: 0.7266 (t60) REVERT: 5 197 PHE cc_start: 0.8038 (t80) cc_final: 0.7796 (t80) REVERT: 6 81 ASP cc_start: 0.7137 (t0) cc_final: 0.6797 (t70) REVERT: A 39 ASN cc_start: 0.8191 (m-40) cc_final: 0.7793 (t0) REVERT: A 242 GLU cc_start: 0.7208 (mp0) cc_final: 0.6745 (mp0) REVERT: A 244 ARG cc_start: 0.6905 (tpp-160) cc_final: 0.6660 (tpp-160) REVERT: B 75 TYR cc_start: 0.8769 (p90) cc_final: 0.8304 (p90) REVERT: C 7 ASP cc_start: 0.7924 (t70) cc_final: 0.7477 (t0) REVERT: C 39 MET cc_start: 0.8393 (ttt) cc_final: 0.8132 (ttt) REVERT: C 212 GLU cc_start: 0.8385 (pt0) cc_final: 0.8165 (pt0) REVERT: D 43 VAL cc_start: 0.9108 (p) cc_final: 0.8907 (t) REVERT: D 47 GLU cc_start: 0.8436 (pp20) cc_final: 0.8066 (pp20) REVERT: D 148 TYR cc_start: 0.9105 (m-80) cc_final: 0.8631 (m-10) REVERT: E 133 LEU cc_start: 0.8206 (tp) cc_final: 0.7938 (tp) REVERT: E 138 PHE cc_start: 0.7675 (p90) cc_final: 0.6776 (p90) REVERT: E 182 GLU cc_start: 0.7820 (pp20) cc_final: 0.7477 (pp20) REVERT: E 238 GLU cc_start: 0.7453 (pp20) cc_final: 0.7035 (pp20) REVERT: F 60 GLN cc_start: 0.7834 (pt0) cc_final: 0.7627 (pt0) REVERT: G 60 VAL cc_start: 0.8687 (t) cc_final: 0.8435 (p) REVERT: H 51 GLN cc_start: 0.8031 (pp30) cc_final: 0.7775 (pp30) REVERT: H 98 GLN cc_start: 0.8196 (tt0) cc_final: 0.7932 (tt0) REVERT: H 359 ASN cc_start: 0.8832 (m-40) cc_final: 0.8631 (m110) REVERT: I 64 ARG cc_start: 0.7335 (ptm-80) cc_final: 0.6989 (ttt180) REVERT: I 68 HIS cc_start: 0.7924 (m-70) cc_final: 0.7646 (m-70) REVERT: I 120 VAL cc_start: 0.9340 (t) cc_final: 0.9007 (m) REVERT: I 208 TYR cc_start: 0.8384 (m-80) cc_final: 0.8158 (m-80) REVERT: I 285 ASP cc_start: 0.7630 (p0) cc_final: 0.6910 (p0) REVERT: J 86 VAL cc_start: 0.8860 (t) cc_final: 0.8646 (m) REVERT: J 247 MET cc_start: 0.8416 (mtp) cc_final: 0.8052 (mtp) REVERT: J 256 THR cc_start: 0.6379 (m) cc_final: 0.6155 (p) REVERT: J 270 ARG cc_start: 0.6256 (mmt90) cc_final: 0.5962 (mtt180) REVERT: K 149 ILE cc_start: 0.9104 (tp) cc_final: 0.8759 (tt) REVERT: K 260 LEU cc_start: 0.9258 (pp) cc_final: 0.8773 (tt) REVERT: L 156 MET cc_start: 0.7895 (mtp) cc_final: 0.7692 (mtp) REVERT: L 188 GLU cc_start: 0.8428 (pp20) cc_final: 0.8157 (pp20) REVERT: L 306 MET cc_start: 0.7775 (tmm) cc_final: 0.7114 (tmm) REVERT: L 307 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7406 (tp30) REVERT: M 265 ASP cc_start: 0.7718 (m-30) cc_final: 0.7496 (m-30) REVERT: M 292 ASP cc_start: 0.7506 (p0) cc_final: 0.6940 (p0) REVERT: M 328 ASN cc_start: 0.8803 (m-40) cc_final: 0.8572 (m-40) REVERT: M 397 GLU cc_start: 0.7527 (mm-30) cc_final: 0.7318 (mm-30) outliers start: 4 outliers final: 0 residues processed: 812 average time/residue: 0.2337 time to fit residues: 320.2094 Evaluate side-chains 662 residues out of total 4951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 662 time to evaluate : 1.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 419 optimal weight: 9.9990 chunk 201 optimal weight: 4.9990 chunk 523 optimal weight: 10.0000 chunk 448 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 391 optimal weight: 2.9990 chunk 557 optimal weight: 0.8980 chunk 256 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 309 optimal weight: 0.7980 chunk 365 optimal weight: 6.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 36 ASN 7 74 ASN 7 120 GLN ** A 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 181 ASN C 103 ASN G 33 ASN I 102 ASN ** I 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 303 GLN I 393 GLN ** I 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 ASN J 277 ASN K 142 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.076894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.065983 restraints weight = 115146.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.067258 restraints weight = 71548.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.068118 restraints weight = 50856.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.068702 restraints weight = 40106.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.069093 restraints weight = 33972.580| |-----------------------------------------------------------------------------| r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.4900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 45012 Z= 0.143 Angle : 0.635 11.675 60998 Z= 0.320 Chirality : 0.046 0.217 7049 Planarity : 0.004 0.075 7868 Dihedral : 5.990 114.718 6322 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 0.07 % Allowed : 0.66 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.11), residues: 5766 helix: -0.76 (0.11), residues: 2123 sheet: -1.31 (0.15), residues: 1086 loop : -1.86 (0.12), residues: 2557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 210 TYR 0.033 0.001 TYR B 224 PHE 0.025 0.002 PHE 7 36 TRP 0.024 0.002 TRP G 218 HIS 0.010 0.001 HIS 1 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.14 (45011) covalent geometry : angle 0.63459 / 0.32 (60998) hydrogen bonds : bond 0.03382 / 2.29 ( 1440) hydrogen bonds : angle 4.98493 / 3.47 ( 3972) Misc. bond : bond 0.00008 / 0.00 ( 1) *********************** 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 796 residues out of total 4951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 793 time to evaluate : 1.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 160 SER cc_start: 0.8559 (m) cc_final: 0.8286 (p) REVERT: 2 30 ASN cc_start: 0.8075 (t0) cc_final: 0.7684 (t0) REVERT: 2 120 ASP cc_start: 0.7481 (p0) cc_final: 0.7225 (p0) REVERT: 2 200 GLN cc_start: 0.7028 (mt0) cc_final: 0.6218 (pt0) REVERT: 2 214 LYS cc_start: 0.8192 (ptmt) cc_final: 0.7834 (mttt) REVERT: 3 98 ARG cc_start: 0.7612 (mtp-110) cc_final: 0.7203 (mtp85) REVERT: 4 31 SER cc_start: 0.8811 (m) cc_final: 0.8303 (t) REVERT: 4 52 ASP cc_start: 0.7847 (m-30) cc_final: 0.7532 (t0) REVERT: 4 60 ILE cc_start: 0.9386 (pt) cc_final: 0.8742 (mt) REVERT: 4 99 GLN cc_start: 0.7263 (tm-30) cc_final: 0.6840 (tm-30) REVERT: 4 120 ASP cc_start: 0.7885 (p0) cc_final: 0.7462 (p0) REVERT: 4 162 LYS cc_start: 0.6405 (tptp) cc_final: 0.5828 (tptp) REVERT: 5 24 ASN cc_start: 0.9108 (t0) cc_final: 0.8755 (t0) REVERT: 5 25 TRP cc_start: 0.8719 (t60) cc_final: 0.8496 (t60) REVERT: 5 111 THR cc_start: 0.8122 (m) cc_final: 0.7578 (p) REVERT: 5 146 TRP cc_start: 0.8367 (t-100) cc_final: 0.7269 (t60) REVERT: 6 81 ASP cc_start: 0.7260 (t0) cc_final: 0.6865 (t70) REVERT: 6 107 VAL cc_start: 0.8832 (t) cc_final: 0.8543 (m) REVERT: 6 179 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7582 (mm-30) REVERT: A 242 GLU cc_start: 0.7252 (mp0) cc_final: 0.6725 (mp0) REVERT: A 244 ARG cc_start: 0.7037 (tpp-160) cc_final: 0.6787 (tpp-160) REVERT: B 75 TYR cc_start: 0.8791 (p90) cc_final: 0.8287 (p90) REVERT: C 7 ASP cc_start: 0.7951 (t70) cc_final: 0.7518 (t0) REVERT: C 39 MET cc_start: 0.8471 (ttt) cc_final: 0.8186 (ttt) REVERT: D 43 VAL cc_start: 0.9144 (p) cc_final: 0.8915 (t) REVERT: D 148 TYR cc_start: 0.9105 (m-80) cc_final: 0.8785 (m-10) REVERT: E 138 PHE cc_start: 0.7568 (p90) cc_final: 0.7357 (p90) REVERT: E 182 GLU cc_start: 0.7949 (pp20) cc_final: 0.7591 (pp20) REVERT: E 238 GLU cc_start: 0.7600 (pp20) cc_final: 0.6995 (pp20) REVERT: G 60 VAL cc_start: 0.8708 (t) cc_final: 0.8431 (p) REVERT: H 51 GLN cc_start: 0.8068 (pp30) cc_final: 0.7823 (pp30) REVERT: H 98 GLN cc_start: 0.8233 (tt0) cc_final: 0.7982 (tt0) REVERT: H 359 ASN cc_start: 0.8886 (m-40) cc_final: 0.8659 (m110) REVERT: H 372 ASP cc_start: 0.7923 (m-30) cc_final: 0.7494 (t0) REVERT: I 64 ARG cc_start: 0.7420 (ptm-80) cc_final: 0.7008 (ttt180) REVERT: I 68 HIS cc_start: 0.7951 (m-70) cc_final: 0.7653 (m-70) REVERT: I 120 VAL cc_start: 0.9359 (t) cc_final: 0.9080 (m) REVERT: I 121 THR cc_start: 0.8022 (p) cc_final: 0.7684 (t) REVERT: I 147 VAL cc_start: 0.9544 (m) cc_final: 0.9261 (p) REVERT: I 285 ASP cc_start: 0.7649 (p0) cc_final: 0.7045 (p0) REVERT: J 86 VAL cc_start: 0.8911 (t) cc_final: 0.8676 (m) REVERT: J 247 MET cc_start: 0.8447 (mtp) cc_final: 0.8054 (mtp) REVERT: J 270 ARG cc_start: 0.6220 (mmt90) cc_final: 0.5908 (mtt180) REVERT: J 362 CYS cc_start: 0.8941 (m) cc_final: 0.8300 (t) REVERT: K 124 SER cc_start: 0.9082 (t) cc_final: 0.8634 (p) REVERT: K 149 ILE cc_start: 0.9104 (tp) cc_final: 0.8753 (tt) REVERT: K 260 LEU cc_start: 0.9274 (pp) cc_final: 0.8812 (tt) REVERT: L 188 GLU cc_start: 0.8451 (pp20) cc_final: 0.8149 (pp20) REVERT: L 306 MET cc_start: 0.7820 (tmm) cc_final: 0.7180 (tmm) REVERT: L 307 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7456 (tp30) REVERT: M 265 ASP cc_start: 0.7824 (m-30) cc_final: 0.7577 (m-30) REVERT: M 292 ASP cc_start: 0.7519 (p0) cc_final: 0.6914 (p0) REVERT: M 328 ASN cc_start: 0.8853 (m-40) cc_final: 0.8627 (m-40) REVERT: r 135 ARG cc_start: 0.7270 (mtm180) cc_final: 0.6886 (mtm180) outliers start: 3 outliers final: 0 residues processed: 796 average time/residue: 0.2317 time to fit residues: 314.3433 Evaluate side-chains 641 residues out of total 4951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 641 time to evaluate : 1.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 390 optimal weight: 10.0000 chunk 409 optimal weight: 0.6980 chunk 137 optimal weight: 8.9990 chunk 524 optimal weight: 0.4980 chunk 362 optimal weight: 0.0170 chunk 172 optimal weight: 0.5980 chunk 334 optimal weight: 0.6980 chunk 354 optimal weight: 0.9990 chunk 311 optimal weight: 1.9990 chunk 143 optimal weight: 9.9990 chunk 79 optimal weight: 10.0000 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 5 133 GLN ** 6 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 74 ASN 7 125 GLN A 41 ASN A 56 GLN A 181 ASN D 117 GLN D 235 GLN H 356 ASN I 238 ASN I 303 GLN I 393 GLN ** I 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 ASN J 269 GLN J 277 ASN K 142 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.079295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.068543 restraints weight = 114224.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.069844 restraints weight = 70598.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.070723 restraints weight = 49961.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.071348 restraints weight = 39004.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.071757 restraints weight = 32668.075| |-----------------------------------------------------------------------------| r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.5116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 45012 Z= 0.107 Angle : 0.608 11.945 60998 Z= 0.305 Chirality : 0.045 0.203 7049 Planarity : 0.004 0.088 7868 Dihedral : 5.693 107.702 6322 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.04 % Allowed : 0.46 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.11), residues: 5766 helix: -0.55 (0.12), residues: 2113 sheet: -1.21 (0.15), residues: 1099 loop : -1.76 (0.12), residues: 2554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 210 TYR 0.022 0.001 TYR K 58 PHE 0.023 0.001 PHE M 432 TRP 0.025 0.001 TRP G 218 HIS 0.006 0.001 HIS 1 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (45011) covalent geometry : angle 0.60804 / 0.30 (60998) hydrogen bonds : bond 0.03085 / 2.08 ( 1440) hydrogen bonds : angle 4.76913 / 3.31 ( 3972) Misc. bond : bond 0.00003 / 0.00 ( 1) ********************** 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 831 residues out of total 4951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 829 time to evaluate : 1.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 160 SER cc_start: 0.8535 (m) cc_final: 0.8265 (p) REVERT: 2 30 ASN cc_start: 0.8004 (t0) cc_final: 0.7670 (t0) REVERT: 2 120 ASP cc_start: 0.7545 (p0) cc_final: 0.7326 (p0) REVERT: 2 200 GLN cc_start: 0.7001 (mt0) cc_final: 0.6152 (pt0) REVERT: 2 214 LYS cc_start: 0.8179 (ptmt) cc_final: 0.7832 (mttp) REVERT: 3 72 ASN cc_start: 0.8436 (m-40) cc_final: 0.8089 (t0) REVERT: 3 98 ARG cc_start: 0.7655 (mtp-110) cc_final: 0.7267 (mtp85) REVERT: 4 31 SER cc_start: 0.8776 (m) cc_final: 0.8281 (t) REVERT: 4 60 ILE cc_start: 0.9284 (pt) cc_final: 0.8512 (mm) REVERT: 4 99 GLN cc_start: 0.7145 (tm-30) cc_final: 0.6687 (tm-30) REVERT: 4 120 ASP cc_start: 0.7883 (p0) cc_final: 0.7578 (p0) REVERT: 4 124 THR cc_start: 0.8503 (p) cc_final: 0.8056 (p) REVERT: 4 162 LYS cc_start: 0.6483 (tptp) cc_final: 0.5888 (tptt) REVERT: 5 24 ASN cc_start: 0.9099 (t0) cc_final: 0.8741 (t0) REVERT: 5 111 THR cc_start: 0.8081 (m) cc_final: 0.7570 (p) REVERT: 5 146 TRP cc_start: 0.8308 (t-100) cc_final: 0.7231 (t60) REVERT: 6 81 ASP cc_start: 0.7317 (t0) cc_final: 0.6909 (t0) REVERT: 6 107 VAL cc_start: 0.8744 (t) cc_final: 0.8518 (m) REVERT: 6 179 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7507 (mm-30) REVERT: 7 171 GLN cc_start: 0.8648 (mm-40) cc_final: 0.8118 (mm-40) REVERT: A 242 GLU cc_start: 0.7243 (mp0) cc_final: 0.6772 (mp0) REVERT: A 244 ARG cc_start: 0.7017 (tpp-160) cc_final: 0.6803 (tpp-160) REVERT: B 75 TYR cc_start: 0.8735 (p90) cc_final: 0.8241 (p90) REVERT: C 7 ASP cc_start: 0.8057 (t70) cc_final: 0.7531 (t0) REVERT: C 39 MET cc_start: 0.8432 (ttt) cc_final: 0.8170 (ttt) REVERT: C 71 ASP cc_start: 0.7144 (t70) cc_final: 0.6893 (t70) REVERT: C 104 GLU cc_start: 0.7839 (pt0) cc_final: 0.7449 (mt-10) REVERT: C 210 ARG cc_start: 0.7947 (ttm110) cc_final: 0.7507 (ttm110) REVERT: D 43 VAL cc_start: 0.9104 (p) cc_final: 0.8882 (t) REVERT: D 148 TYR cc_start: 0.9023 (m-80) cc_final: 0.8780 (m-10) REVERT: E 133 LEU cc_start: 0.8142 (tp) cc_final: 0.7923 (tp) REVERT: E 182 GLU cc_start: 0.7903 (pp20) cc_final: 0.7664 (pp20) REVERT: E 238 GLU cc_start: 0.7561 (pp20) cc_final: 0.6937 (pp20) REVERT: F 60 GLN cc_start: 0.7752 (pt0) cc_final: 0.7495 (pt0) REVERT: F 68 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7272 (mm-30) REVERT: G 26 TYR cc_start: 0.8504 (m-80) cc_final: 0.8211 (m-80) REVERT: G 60 VAL cc_start: 0.8686 (t) cc_final: 0.8443 (p) REVERT: G 95 GLU cc_start: 0.7333 (pm20) cc_final: 0.7023 (pm20) REVERT: H 51 GLN cc_start: 0.7999 (pp30) cc_final: 0.7739 (pp30) REVERT: H 219 GLU cc_start: 0.8253 (tm-30) cc_final: 0.7708 (tm-30) REVERT: H 359 ASN cc_start: 0.8834 (m-40) cc_final: 0.8517 (m110) REVERT: I 64 ARG cc_start: 0.7328 (ptm-80) cc_final: 0.7042 (ttt180) REVERT: I 68 HIS cc_start: 0.7864 (m-70) cc_final: 0.7610 (m-70) REVERT: I 120 VAL cc_start: 0.9320 (t) cc_final: 0.9030 (m) REVERT: I 147 VAL cc_start: 0.9475 (m) cc_final: 0.9098 (p) REVERT: I 285 ASP cc_start: 0.7845 (p0) cc_final: 0.7468 (p0) REVERT: I 306 MET cc_start: 0.7778 (ttp) cc_final: 0.7578 (ttt) REVERT: J 25 GLN cc_start: 0.7787 (mm110) cc_final: 0.7452 (mm110) REVERT: J 32 LEU cc_start: 0.9035 (pp) cc_final: 0.8833 (tp) REVERT: J 86 VAL cc_start: 0.8837 (t) cc_final: 0.8629 (m) REVERT: J 129 LYS cc_start: 0.8230 (mmmt) cc_final: 0.7485 (mtmt) REVERT: J 165 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7605 (tp30) REVERT: J 247 MET cc_start: 0.8392 (mtp) cc_final: 0.7909 (mtp) REVERT: J 362 CYS cc_start: 0.8934 (m) cc_final: 0.8318 (t) REVERT: K 124 SER cc_start: 0.9012 (t) cc_final: 0.8544 (p) REVERT: K 149 ILE cc_start: 0.9060 (tp) cc_final: 0.8723 (tt) REVERT: K 260 LEU cc_start: 0.9291 (pp) cc_final: 0.8964 (tt) REVERT: L 109 MET cc_start: 0.7954 (mmm) cc_final: 0.7569 (mmp) REVERT: L 306 MET cc_start: 0.7761 (tmm) cc_final: 0.7106 (tmm) REVERT: L 307 GLU cc_start: 0.7624 (mm-30) cc_final: 0.7376 (tp30) REVERT: M 180 TYR cc_start: 0.8641 (m-80) cc_final: 0.8425 (m-80) REVERT: M 265 ASP cc_start: 0.7758 (m-30) cc_final: 0.7472 (m-30) REVERT: M 292 ASP cc_start: 0.7580 (p0) cc_final: 0.7003 (p0) REVERT: M 397 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7409 (mm-30) REVERT: r 135 ARG cc_start: 0.7293 (mtm180) cc_final: 0.6941 (mtm180) outliers start: 2 outliers final: 0 residues processed: 829 average time/residue: 0.2271 time to fit residues: 321.5549 Evaluate side-chains 665 residues out of total 4951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 665 time to evaluate : 1.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 48 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 540 optimal weight: 0.4980 chunk 26 optimal weight: 0.4980 chunk 448 optimal weight: 5.9990 chunk 315 optimal weight: 10.0000 chunk 179 optimal weight: 0.2980 chunk 462 optimal weight: 20.0000 chunk 219 optimal weight: 9.9990 chunk 483 optimal weight: 5.9990 chunk 230 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 6 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 74 ASN A 41 ASN A 181 ASN A 209 HIS D 235 GLN G 182 HIS I 238 ASN I 303 GLN I 393 GLN ** I 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 ASN J 277 ASN J 379 GLN K 142 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.078380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.067527 restraints weight = 115019.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.068819 restraints weight = 71031.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.069720 restraints weight = 50241.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.070316 restraints weight = 39330.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.070726 restraints weight = 33177.214| |-----------------------------------------------------------------------------| r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.5200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 45012 Z= 0.116 Angle : 0.613 10.885 60998 Z= 0.307 Chirality : 0.045 0.200 7049 Planarity : 0.004 0.078 7868 Dihedral : 5.599 104.544 6322 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 0.04 % Allowed : 0.46 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.11), residues: 5766 helix: -0.48 (0.11), residues: 2127 sheet: -1.16 (0.15), residues: 1095 loop : -1.73 (0.12), residues: 2544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 210 TYR 0.032 0.001 TYR B 224 PHE 0.023 0.001 PHE M 432 TRP 0.026 0.001 TRP 5 25 HIS 0.004 0.001 HIS G 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (45011) covalent geometry : angle 0.61271 / 0.31 (60998) hydrogen bonds : bond 0.03092 / 2.09 ( 1440) hydrogen bonds : angle 4.78587 / 3.32 ( 3972) Misc. bond : bond 0.00003 / 0.00 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7822.08 seconds wall clock time: 135 minutes 49.62 seconds (8149.62 seconds total)