Starting phenix.real_space_refine on Fri Nov 21 03:41:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ef3_9045/11_2025/6ef3_9045.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ef3_9045/11_2025/6ef3_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 { model { file = "/net/cci-nas-00/data/ceres_data/6ef3_9045/11_2025/6ef3_9045.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ef3_9045/11_2025/6ef3_9045.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ef3_9045/11_2025/6ef3_9045.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ef3_9045/11_2025/6ef3_9045.map" } 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): 0.06s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/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: 10.59, per 1000 atoms: 0.24 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: 4.27 Conformation dependent library (CDL) restraints added in 2.1 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: 1.76 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: 11.68 Time building geometry restraints manager: 5.47 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: 26666 27.47 - 54.94: 602 54.94 - 82.41: 50 82.41 - 109.88: 2 109.88 - 137.36: 5 Dihedral angle restraints: 27325 sinusoidal: 10546 harmonic: 16779 Sorted by residual: dihedral pdb=" C5' ADP K 501 " pdb=" O5' ADP K 501 " pdb=" PA ADP K 501 " pdb=" O2A ADP K 501 " ideal model delta sinusoidal sigma weight residual -60.00 77.36 -137.36 1 2.00e+01 2.50e-03 4.17e+01 dihedral pdb=" O2A ADP L 501 " pdb=" O3A ADP L 501 " pdb=" PA ADP L 501 " pdb=" PB ADP L 501 " ideal model delta sinusoidal sigma weight residual -60.00 71.65 -131.65 1 2.00e+01 2.50e-03 4.00e+01 dihedral pdb=" O2A ADP K 501 " pdb=" O3A ADP K 501 " pdb=" PA ADP K 501 " pdb=" PB ADP K 501 " ideal model delta sinusoidal sigma weight residual -60.00 66.49 -126.49 1 2.00e+01 2.50e-03 3.83e+01 ... (remaining 27322 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 4629 0.063 - 0.127: 1916 0.127 - 0.190: 422 0.190 - 0.253: 70 0.253 - 0.317: 12 Chirality restraints: 7049 Sorted by residual: chirality pdb=" CB VAL E 200 " pdb=" CA VAL E 200 " pdb=" CG1 VAL E 200 " pdb=" CG2 VAL E 200 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" CB VAL 1 172 " pdb=" CA VAL 1 172 " pdb=" CG1 VAL 1 172 " pdb=" CG2 VAL 1 172 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CB VAL I 219 " pdb=" CA VAL I 219 " pdb=" CG1 VAL I 219 " pdb=" CG2 VAL I 219 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 7046 not shown) Planarity restraints: 7868 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN J 181 " -0.065 5.00e-02 4.00e+02 9.81e-02 1.54e+01 pdb=" N PRO J 182 " 0.170 5.00e-02 4.00e+02 pdb=" CA PRO J 182 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO J 182 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG 4 96 " 0.057 5.00e-02 4.00e+02 8.49e-02 1.15e+01 pdb=" N PRO 4 97 " -0.147 5.00e-02 4.00e+02 pdb=" CA PRO 4 97 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO 4 97 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 60 " 0.052 5.00e-02 4.00e+02 7.83e-02 9.82e+00 pdb=" N PRO G 61 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO G 61 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO G 61 " 0.043 5.00e-02 4.00e+02 ... (remaining 7865 not shown) Histogram of nonbonded interaction distances: 1.98 - 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: 3.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.690 Check model and map are aligned: 0.140 Set scattering table: 0.140 Process input model: 45.090 Find NCS groups from input model: 0.640 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.139 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 : 12.096 137.355 16547 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 covalent geometry : bond 0.01605 (45011) covalent geometry : angle 1.10500 (60998) hydrogen bonds : bond 0.31139 ( 1440) hydrogen bonds : angle 11.51556 ( 3972) Misc. bond : bond 0.09002 ( 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 : 1.880 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: 0.7835 (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: 0.2918 time to fit residues: 482.3998 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 : 1.772 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3203 r_free = 0.3203 target = 0.084904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.075667 restraints weight = 112671.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.076701 restraints weight = 70634.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.076866 restraints weight = 54934.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.077299 restraints weight = 46376.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.077379 restraints weight = 41781.028| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 45012 Z= 0.144 Angle : 0.708 10.610 60998 Z= 0.367 Chirality : 0.048 0.220 7049 Planarity : 0.005 0.077 7868 Dihedral : 8.755 121.061 6446 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 0.11 % Allowed : 3.33 % Favored : 96.56 % 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: -4.47 (0.09), residues: 5766 helix: -2.76 (0.09), residues: 2101 sheet: -3.11 (0.13), residues: 986 loop : -2.99 (0.11), residues: 2679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG r 42 TYR 0.030 0.001 TYR A 133 PHE 0.020 0.002 PHE M 432 TRP 0.023 0.002 TRP C 160 HIS 0.010 0.001 HIS G 204 Details of bonding type rmsd covalent geometry : bond 0.00300 (45011) covalent geometry : angle 0.70816 (60998) hydrogen bonds : bond 0.05118 ( 1440) hydrogen bonds : angle 6.49985 ( 3972) Misc. bond : bond 0.00011 ( 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 976 residues out of total 4951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 971 time to evaluate : 1.865 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: 0.8813 (pt) cc_final: 0.8574 (mt) REVERT: 2 12 VAL cc_start: 0.9534 (m) cc_final: 0.9330 (p) REVERT: 2 69 TYR cc_start: 0.8893 (t80) cc_final: 0.8348 (t80) REVERT: 2 71 SER cc_start: 0.8184 (m) cc_final: 0.7949 (p) REVERT: 2 112 SER cc_start: 0.8500 (t) cc_final: 0.8079 (p) REVERT: 2 120 ASP cc_start: 0.7104 (p0) cc_final: 0.6523 (p0) REVERT: 2 200 GLN cc_start: 0.6942 (mt0) cc_final: 0.6161 (pt0) REVERT: 2 214 LYS cc_start: 0.8152 (ptmt) cc_final: 0.7795 (mttp) REVERT: 3 199 TYR cc_start: 0.8364 (m-10) cc_final: 0.8158 (m-10) REVERT: 3 203 ARG cc_start: 0.8383 (ptm-80) cc_final: 0.6585 (mtt180) REVERT: 4 1 MET cc_start: 0.6541 (ttp) cc_final: 0.5498 (tpt) REVERT: 4 3 ILE cc_start: 0.9055 (pt) cc_final: 0.8479 (mp) REVERT: 4 30 ASP cc_start: 0.8364 (p0) cc_final: 0.8127 (p0) REVERT: 4 99 GLN cc_start: 0.7198 (tm-30) cc_final: 0.6977 (tm-30) REVERT: 4 120 ASP cc_start: 0.7626 (p0) cc_final: 0.7366 (p0) REVERT: 5 24 ASN cc_start: 0.8612 (t0) cc_final: 0.8136 (t0) REVERT: 5 36 GLU cc_start: 0.6700 (mp0) cc_final: 0.6421 (pp20) REVERT: 6 81 ASP cc_start: 0.6827 (t0) cc_final: 0.6420 (t70) REVERT: 6 159 GLN cc_start: 0.6576 (pt0) cc_final: 0.5666 (tp40) REVERT: 7 108 ASN cc_start: 0.7676 (p0) cc_final: 0.7149 (p0) REVERT: A 39 ASN cc_start: 0.8370 (m-40) cc_final: 0.7767 (t0) REVERT: A 128 TYR cc_start: 0.7627 (m-80) cc_final: 0.7252 (m-80) REVERT: A 195 ASN cc_start: 0.8284 (m-40) cc_final: 0.8006 (m110) REVERT: A 222 ASP cc_start: 0.7228 (p0) cc_final: 0.6964 (p0) REVERT: A 224 GLU cc_start: 0.8315 (pt0) cc_final: 0.7996 (pt0) REVERT: B 41 ASN cc_start: 0.8517 (p0) cc_final: 0.8098 (p0) REVERT: B 47 THR cc_start: 0.8865 (t) cc_final: 0.8636 (t) REVERT: B 60 THR cc_start: 0.8911 (p) cc_final: 0.8457 (t) REVERT: B 75 TYR cc_start: 0.8795 (p90) cc_final: 0.8519 (p90) REVERT: B 177 LYS cc_start: 0.6854 (mmpt) cc_final: 0.6428 (tptt) REVERT: C 206 LEU cc_start: 0.8630 (pt) cc_final: 0.8297 (tp) REVERT: C 212 GLU cc_start: 0.7990 (pm20) cc_final: 0.7625 (pm20) REVERT: D 47 GLU cc_start: 0.8258 (pp20) cc_final: 0.7953 (pp20) REVERT: D 82 SER cc_start: 0.8673 (m) cc_final: 0.8446 (p) REVERT: E 53 ARG cc_start: 0.6621 (ttm-80) cc_final: 0.5839 (ttt-90) REVERT: E 167 TYR cc_start: 0.8122 (m-80) cc_final: 0.7788 (m-80) REVERT: E 168 ASN cc_start: 0.8142 (m110) cc_final: 0.7872 (m-40) REVERT: E 203 ILE cc_start: 0.8290 (pt) cc_final: 0.7913 (pt) REVERT: E 216 ASN cc_start: 0.8597 (p0) cc_final: 0.8031 (p0) REVERT: E 238 GLU cc_start: 0.7648 (pp20) cc_final: 0.7040 (pp20) REVERT: F 60 GLN cc_start: 0.8273 (pt0) cc_final: 0.7974 (pt0) REVERT: F 61 LYS cc_start: 0.8369 (mppt) cc_final: 0.8150 (mmtm) REVERT: F 111 LEU cc_start: 0.7815 (mt) cc_final: 0.7565 (mt) REVERT: G 235 LEU cc_start: 0.7223 (tp) cc_final: 0.6902 (tp) REVERT: H 51 GLN cc_start: 0.7793 (pp30) cc_final: 0.7555 (pp30) REVERT: H 330 GLN cc_start: 0.8661 (mp10) cc_final: 0.8279 (mp10) REVERT: H 425 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7249 (mt-10) REVERT: H 442 ASP cc_start: 0.8722 (p0) cc_final: 0.7954 (p0) REVERT: I 64 ARG cc_start: 0.7044 (ptm-80) cc_final: 0.6681 (ttt180) REVERT: I 120 VAL cc_start: 0.9346 (t) cc_final: 0.8989 (m) REVERT: I 167 MET cc_start: 0.7318 (pmm) cc_final: 0.6821 (ptp) REVERT: I 312 GLN cc_start: 0.7766 (mm-40) cc_final: 0.7371 (mm-40) REVERT: K 124 SER cc_start: 0.8773 (t) cc_final: 0.8480 (p) REVERT: K 149 ILE cc_start: 0.9160 (tp) cc_final: 0.8904 (tp) REVERT: L 159 LEU cc_start: 0.7453 (pt) cc_final: 0.7164 (pp) REVERT: L 272 GLU cc_start: 0.7303 (pp20) cc_final: 0.6837 (pp20) REVERT: L 306 MET cc_start: 0.6964 (tmm) cc_final: 0.6697 (tmm) REVERT: M 187 ASP cc_start: 0.7411 (p0) cc_final: 0.7202 (p0) REVERT: M 292 ASP cc_start: 0.7394 (p0) cc_final: 0.7072 (p0) REVERT: M 401 ILE cc_start: 0.8989 (tt) cc_final: 0.8745 (tp) REVERT: r 282 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7468 (mt-10) outliers start: 5 outliers final: 1 residues processed: 975 average time/residue: 0.2736 time to fit residues: 438.8299 Evaluate side-chains 679 residues out of total 4951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 678 time to evaluate : 1.794 ------------------------------------------------------------------------------- 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: 0.0060 chunk 498 optimal weight: 8.9990 chunk 139 optimal weight: 0.0470 chunk 420 optimal weight: 10.0000 chunk 2 optimal weight: 0.0770 chunk 28 optimal weight: 8.9990 chunk 202 optimal weight: 4.9990 chunk 328 optimal weight: 2.9990 chunk 288 optimal weight: 0.0010 chunk 305 optimal weight: 9.9990 chunk 51 optimal weight: 0.0670 overall best weight: 0.0396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 120 HIS 1 157 HIS 4 78 GLN 4 146 HIS 7 62 HIS 7 74 ASN A 37 GLN ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 GLN E 91 HIS E 108 ASN F 60 GLN G 182 HIS 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 M 72 ASN M 238 GLN r 237 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.086705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.077485 restraints weight = 111420.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.078563 restraints weight = 68911.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.078936 restraints weight = 53043.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.079395 restraints weight = 42699.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.079519 restraints weight = 37415.294| |-----------------------------------------------------------------------------| r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 45012 Z= 0.115 Angle : 0.625 10.774 60998 Z= 0.320 Chirality : 0.045 0.316 7049 Planarity : 0.004 0.054 7868 Dihedral : 7.873 118.033 6446 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.04 % Allowed : 3.80 % Favored : 96.16 % 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: -3.59 (0.10), residues: 5766 helix: -1.98 (0.10), residues: 2108 sheet: -2.49 (0.14), residues: 988 loop : -2.60 (0.11), residues: 2670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 396 TYR 0.030 0.001 TYR B 224 PHE 0.021 0.001 PHE 7 36 TRP 0.019 0.002 TRP G 218 HIS 0.009 0.001 HIS G 204 Details of bonding type rmsd covalent geometry : bond 0.00241 (45011) covalent geometry : angle 0.62452 (60998) hydrogen bonds : bond 0.03817 ( 1440) hydrogen bonds : angle 5.45215 ( 3972) Misc. bond : bond 0.00019 ( 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 942 residues out of total 4951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 940 time to evaluate : 1.836 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: 0.8911 (pt) cc_final: 0.8701 (mt) REVERT: 1 160 SER cc_start: 0.7980 (m) cc_final: 0.7697 (p) REVERT: 2 30 ASN cc_start: 0.8123 (t0) cc_final: 0.7694 (t0) REVERT: 2 71 SER cc_start: 0.8256 (m) cc_final: 0.7972 (p) REVERT: 2 112 SER cc_start: 0.8536 (t) cc_final: 0.8216 (p) REVERT: 2 120 ASP cc_start: 0.7257 (p0) cc_final: 0.6649 (p0) REVERT: 2 152 ILE cc_start: 0.9057 (OUTLIER) cc_final: 0.8802 (mt) REVERT: 2 200 GLN cc_start: 0.6805 (mt0) cc_final: 0.6112 (pt0) REVERT: 2 214 LYS cc_start: 0.8084 (ptmt) cc_final: 0.7838 (mttp) REVERT: 3 125 ASP cc_start: 0.7784 (p0) cc_final: 0.7505 (p0) REVERT: 3 163 LEU cc_start: 0.6955 (tp) cc_final: 0.6695 (tp) REVERT: 3 180 LEU cc_start: 0.7939 (mp) cc_final: 0.7693 (mp) REVERT: 4 1 MET cc_start: 0.6490 (ttp) cc_final: 0.5347 (tpt) REVERT: 4 3 ILE cc_start: 0.8765 (pt) cc_final: 0.8381 (mp) REVERT: 4 99 GLN cc_start: 0.7293 (tm-30) cc_final: 0.6996 (tm-30) REVERT: 4 124 THR cc_start: 0.8935 (p) cc_final: 0.8210 (p) REVERT: 5 63 CYS cc_start: 0.8622 (m) cc_final: 0.8411 (m) REVERT: 5 111 THR cc_start: 0.7933 (m) cc_final: 0.7610 (p) REVERT: 6 159 GLN cc_start: 0.6457 (pt0) cc_final: 0.5631 (tp40) REVERT: 6 185 ARG cc_start: 0.7850 (ptm-80) cc_final: 0.7526 (ttp-110) REVERT: 6 200 ASP cc_start: 0.5845 (t0) cc_final: 0.5572 (t0) REVERT: 7 108 ASN cc_start: 0.7678 (p0) cc_final: 0.7212 (p0) REVERT: 7 136 THR cc_start: 0.8802 (p) cc_final: 0.8549 (t) REVERT: A 39 ASN cc_start: 0.8405 (m-40) cc_final: 0.7778 (t0) REVERT: A 195 ASN cc_start: 0.7790 (m-40) cc_final: 0.7533 (m110) REVERT: A 224 GLU cc_start: 0.8261 (pt0) cc_final: 0.7988 (pt0) REVERT: B 41 ASN cc_start: 0.8319 (p0) cc_final: 0.8031 (p0) REVERT: B 60 THR cc_start: 0.8848 (p) cc_final: 0.8351 (t) REVERT: B 75 TYR cc_start: 0.8779 (p90) cc_final: 0.8367 (p90) REVERT: B 143 ASN cc_start: 0.7161 (p0) cc_final: 0.6927 (p0) REVERT: B 224 TYR cc_start: 0.8188 (p90) cc_final: 0.7813 (p90) REVERT: C 7 ASP cc_start: 0.7451 (t70) cc_final: 0.6924 (t70) REVERT: C 72 LYS cc_start: 0.8587 (mmmt) cc_final: 0.8113 (mmtp) REVERT: C 195 LYS cc_start: 0.8184 (mmmt) cc_final: 0.7841 (mmmt) REVERT: C 199 LYS cc_start: 0.8923 (mtmt) cc_final: 0.8592 (mtmm) REVERT: D 211 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7445 (tt0) REVERT: D 233 VAL cc_start: 0.8902 (t) cc_final: 0.8692 (p) REVERT: E 53 ARG cc_start: 0.6763 (ttm-80) cc_final: 0.5981 (ttt-90) REVERT: E 166 ARG cc_start: 0.8153 (ttt-90) cc_final: 0.7895 (ttt-90) REVERT: E 167 TYR cc_start: 0.8133 (m-80) cc_final: 0.7854 (m-80) REVERT: E 168 ASN cc_start: 0.8215 (m110) cc_final: 0.7765 (m-40) REVERT: E 216 ASN cc_start: 0.8634 (p0) cc_final: 0.8337 (p0) REVERT: F 60 GLN cc_start: 0.8367 (pt0) cc_final: 0.7991 (pt0) REVERT: F 61 LYS cc_start: 0.8430 (mppt) cc_final: 0.8214 (mmtm) REVERT: H 51 GLN cc_start: 0.7738 (pp30) cc_final: 0.7416 (pp30) REVERT: H 442 ASP cc_start: 0.8653 (p0) cc_final: 0.7763 (m-30) REVERT: I 64 ARG cc_start: 0.6969 (ptm-80) cc_final: 0.6389 (ttt180) REVERT: I 68 HIS cc_start: 0.7765 (m-70) cc_final: 0.7531 (m-70) REVERT: I 120 VAL cc_start: 0.9282 (t) cc_final: 0.8976 (m) REVERT: I 167 MET cc_start: 0.7252 (pmm) cc_final: 0.6896 (ptp) REVERT: I 312 GLN cc_start: 0.7841 (mm-40) cc_final: 0.7361 (mm-40) REVERT: I 349 LEU cc_start: 0.8829 (tp) cc_final: 0.8618 (tp) REVERT: I 371 LEU cc_start: 0.7919 (pp) cc_final: 0.7696 (pp) REVERT: J 58 ILE cc_start: 0.8854 (pt) cc_final: 0.8476 (mt) REVERT: J 247 MET cc_start: 0.8074 (mtp) cc_final: 0.7596 (mtm) REVERT: J 345 LYS cc_start: 0.8019 (mttt) cc_final: 0.7726 (tppt) REVERT: K 124 SER cc_start: 0.8629 (t) cc_final: 0.8289 (p) REVERT: K 135 MET cc_start: 0.7709 (mmm) cc_final: 0.7444 (ttm) REVERT: K 319 ASN cc_start: 0.9111 (m-40) cc_final: 0.7820 (t0) REVERT: L 159 LEU cc_start: 0.7288 (pt) cc_final: 0.7055 (pp) REVERT: L 306 MET cc_start: 0.7330 (tmm) cc_final: 0.6698 (tmm) REVERT: L 307 GLU cc_start: 0.7490 (mm-30) cc_final: 0.6972 (tp30) REVERT: L 346 LYS cc_start: 0.7549 (mttp) cc_final: 0.7060 (mtmm) REVERT: M 265 ASP cc_start: 0.7446 (m-30) cc_final: 0.7189 (m-30) REVERT: M 292 ASP cc_start: 0.7409 (p0) cc_final: 0.7059 (p0) REVERT: M 333 LEU cc_start: 0.8436 (pt) cc_final: 0.8235 (pt) outliers start: 2 outliers final: 0 residues processed: 941 average time/residue: 0.2656 time to fit residues: 413.8906 Evaluate side-chains 700 residues out of total 4951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 699 time to evaluate : 1.856 ------------------------------------------------------------------------------- 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: 0.7980 chunk 245 optimal weight: 1.9990 chunk 220 optimal weight: 7.9990 chunk 175 optimal weight: 0.7980 chunk 341 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 506 optimal weight: 10.0000 chunk 416 optimal weight: 0.8980 chunk 557 optimal weight: 5.9990 chunk 288 optimal weight: 0.8980 chunk 498 optimal weight: 10.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 160 GLN 5 190 ASN 7 74 ASN 7 112 ASN A 37 GLN ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 241 GLN F 31 GLN F 86 ASN G 207 ASN H 281 GLN I 238 ASN I 376 ASN ** J 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 ASN ** J 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 302 GLN r 131 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.084685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.074810 restraints weight = 112107.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.076146 restraints weight = 72925.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.076844 restraints weight = 51401.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.077547 restraints weight = 40925.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.077798 restraints weight = 33575.541| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 45012 Z= 0.115 Angle : 0.599 8.500 60998 Z= 0.306 Chirality : 0.045 0.303 7049 Planarity : 0.004 0.051 7868 Dihedral : 7.458 116.882 6446 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.07 % Allowed : 3.16 % Favored : 96.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.06 (0.10), residues: 5766 helix: -1.53 (0.10), residues: 2104 sheet: -2.13 (0.15), residues: 1026 loop : -2.32 (0.12), residues: 2636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 210 TYR 0.030 0.001 TYR 5 137 PHE 0.024 0.001 PHE M 432 TRP 0.019 0.001 TRP G 218 HIS 0.010 0.001 HIS G 204 Details of bonding type rmsd covalent geometry : bond 0.00259 (45011) covalent geometry : angle 0.59916 (60998) hydrogen bonds : bond 0.03351 ( 1440) hydrogen bonds : angle 5.12204 ( 3972) Misc. bond : bond 0.00007 ( 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 877 residues out of total 4951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 874 time to evaluate : 1.825 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: 0.8005 (m) cc_final: 0.7723 (p) REVERT: 2 30 ASN cc_start: 0.7931 (t0) cc_final: 0.7550 (t0) REVERT: 2 112 SER cc_start: 0.8591 (t) cc_final: 0.8219 (p) REVERT: 2 120 ASP cc_start: 0.7189 (p0) cc_final: 0.6704 (p0) REVERT: 2 200 GLN cc_start: 0.6649 (mt0) cc_final: 0.5970 (pt0) REVERT: 2 214 LYS cc_start: 0.8075 (ptmt) cc_final: 0.7856 (mttp) REVERT: 3 98 ARG cc_start: 0.7773 (mtp-110) cc_final: 0.7374 (mtp85) REVERT: 3 125 ASP cc_start: 0.7909 (p0) cc_final: 0.7526 (p0) REVERT: 3 203 ARG cc_start: 0.6398 (tmt170) cc_final: 0.5775 (mtt-85) REVERT: 4 1 MET cc_start: 0.6554 (ttp) cc_final: 0.5180 (tpt) REVERT: 4 3 ILE cc_start: 0.8923 (pt) cc_final: 0.8394 (mp) REVERT: 4 99 GLN cc_start: 0.7294 (tm-30) cc_final: 0.6957 (tm-30) REVERT: 4 120 ASP cc_start: 0.7916 (p0) cc_final: 0.7675 (p0) REVERT: 4 124 THR cc_start: 0.8800 (p) cc_final: 0.8201 (p) REVERT: 5 63 CYS cc_start: 0.8715 (m) cc_final: 0.8489 (m) REVERT: 5 111 THR cc_start: 0.7792 (m) cc_final: 0.7398 (p) REVERT: 6 159 GLN cc_start: 0.6484 (pt0) cc_final: 0.5588 (tp40) REVERT: 6 185 ARG cc_start: 0.7881 (ptm-80) cc_final: 0.7422 (ttp-110) REVERT: 6 200 ASP cc_start: 0.6127 (t0) cc_final: 0.5903 (t0) REVERT: 7 82 ASP cc_start: 0.7968 (m-30) cc_final: 0.7131 (t0) REVERT: 7 136 THR cc_start: 0.8827 (p) cc_final: 0.8556 (t) REVERT: 7 169 THR cc_start: 0.8438 (t) cc_final: 0.8182 (m) REVERT: A 39 ASN cc_start: 0.8334 (m-40) cc_final: 0.7765 (t0) REVERT: A 195 ASN cc_start: 0.7600 (m-40) cc_final: 0.7329 (m110) REVERT: A 224 GLU cc_start: 0.8313 (pt0) cc_final: 0.7911 (pt0) REVERT: B 41 ASN cc_start: 0.8483 (p0) cc_final: 0.7955 (p0) REVERT: B 60 THR cc_start: 0.8843 (p) cc_final: 0.8376 (t) REVERT: B 75 TYR cc_start: 0.8843 (p90) cc_final: 0.8355 (p90) REVERT: B 143 ASN cc_start: 0.7247 (p0) cc_final: 0.7016 (p0) REVERT: B 210 GLU cc_start: 0.7541 (tp30) cc_final: 0.7237 (tp30) REVERT: B 224 TYR cc_start: 0.8205 (p90) cc_final: 0.7664 (p90) REVERT: C 7 ASP cc_start: 0.7459 (t70) cc_final: 0.7068 (t0) REVERT: C 39 MET cc_start: 0.8292 (ttt) cc_final: 0.7990 (ttt) REVERT: C 199 LYS cc_start: 0.8861 (mtmt) cc_final: 0.8563 (mtmm) REVERT: D 47 GLU cc_start: 0.8351 (pp20) cc_final: 0.7980 (pp20) REVERT: D 203 VAL cc_start: 0.7277 (t) cc_final: 0.7045 (t) REVERT: E 35 SER cc_start: 0.8295 (m) cc_final: 0.8084 (m) REVERT: E 53 ARG cc_start: 0.6995 (ttm-80) cc_final: 0.6012 (ttt-90) REVERT: E 89 ILE cc_start: 0.7948 (pt) cc_final: 0.7547 (mt) REVERT: E 167 TYR cc_start: 0.8132 (m-80) cc_final: 0.7879 (m-80) REVERT: E 182 GLU cc_start: 0.7232 (pp20) cc_final: 0.6803 (pp20) REVERT: F 60 GLN cc_start: 0.8324 (pt0) cc_final: 0.8083 (pt0) REVERT: F 61 LYS cc_start: 0.8491 (mppt) cc_final: 0.8196 (mmtm) REVERT: F 122 SER cc_start: 0.9066 (m) cc_final: 0.8662 (p) REVERT: H 359 ASN cc_start: 0.8647 (m-40) cc_final: 0.8360 (m110) REVERT: H 442 ASP cc_start: 0.8675 (p0) cc_final: 0.8009 (p0) REVERT: I 64 ARG cc_start: 0.7023 (ptm-80) cc_final: 0.6436 (ttt180) REVERT: I 68 HIS cc_start: 0.7739 (m-70) cc_final: 0.7480 (m-70) REVERT: I 120 VAL cc_start: 0.9287 (t) cc_final: 0.9023 (m) REVERT: I 167 MET cc_start: 0.7324 (pmm) cc_final: 0.6689 (ptp) REVERT: I 312 GLN cc_start: 0.7923 (mm-40) cc_final: 0.7455 (tp40) REVERT: I 349 LEU cc_start: 0.8892 (tp) cc_final: 0.8671 (tp) REVERT: J 58 ILE cc_start: 0.8946 (pt) cc_final: 0.8624 (mt) REVERT: J 86 VAL cc_start: 0.8772 (t) cc_final: 0.8448 (m) REVERT: J 247 MET cc_start: 0.8064 (mtp) cc_final: 0.7705 (mtm) REVERT: K 149 ILE cc_start: 0.9098 (tp) cc_final: 0.8805 (mm) REVERT: K 319 ASN cc_start: 0.8992 (m-40) cc_final: 0.7756 (t0) REVERT: L 159 LEU cc_start: 0.7434 (pt) cc_final: 0.7147 (pp) REVERT: L 255 TYR cc_start: 0.8506 (m-80) cc_final: 0.8103 (m-80) REVERT: L 306 MET cc_start: 0.7295 (tmm) cc_final: 0.6614 (tmm) REVERT: L 307 GLU cc_start: 0.7480 (mm-30) cc_final: 0.7129 (tp30) REVERT: M 265 ASP cc_start: 0.7556 (m-30) cc_final: 0.7172 (m-30) REVERT: M 292 ASP cc_start: 0.7405 (p0) cc_final: 0.7093 (p0) REVERT: M 333 LEU cc_start: 0.8555 (pt) cc_final: 0.8346 (pt) REVERT: M 397 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6975 (tp30) outliers start: 3 outliers final: 1 residues processed: 876 average time/residue: 0.2606 time to fit residues: 382.3698 Evaluate side-chains 690 residues out of total 4951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 689 time to evaluate : 1.905 ------------------------------------------------------------------------------- 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: 1.9990 chunk 304 optimal weight: 4.9990 chunk 54 optimal weight: 9.9990 chunk 240 optimal weight: 3.9990 chunk 439 optimal weight: 6.9990 chunk 560 optimal weight: 8.9990 chunk 225 optimal weight: 1.9990 chunk 533 optimal weight: 6.9990 chunk 501 optimal weight: 1.9990 chunk 564 optimal weight: 30.0000 chunk 346 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 41 HIS 6 159 GLN 7 61 GLN 7 74 ASN ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 HIS ** C 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 GLN G 207 ASN H 281 GLN I 150 HIS ** 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 240 HIS J 277 ASN ** K 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 106 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.078083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.067937 restraints weight = 114299.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.068557 restraints weight = 85635.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.068987 restraints weight = 68566.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.069221 restraints weight = 58941.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.069308 restraints weight = 52198.269| |-----------------------------------------------------------------------------| r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 45012 Z= 0.193 Angle : 0.677 9.133 60998 Z= 0.348 Chirality : 0.048 0.318 7049 Planarity : 0.005 0.057 7868 Dihedral : 7.605 119.502 6446 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 0.02 % Allowed : 3.38 % Favored : 96.60 % 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: -2.84 (0.10), residues: 5766 helix: -1.38 (0.11), residues: 2106 sheet: -1.86 (0.15), residues: 1050 loop : -2.24 (0.12), residues: 2610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 77 TYR 0.036 0.002 TYR M 180 PHE 0.029 0.002 PHE J 23 TRP 0.027 0.002 TRP G 218 HIS 0.010 0.001 HIS G 204 Details of bonding type rmsd covalent geometry : bond 0.00451 (45011) covalent geometry : angle 0.67671 (60998) hydrogen bonds : bond 0.03792 ( 1440) hydrogen bonds : angle 5.26802 ( 3972) Misc. bond : bond 0.00021 ( 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 826 residues out of total 4951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 825 time to evaluate : 1.805 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: 1 145 ASN cc_start: 0.8481 (m-40) cc_final: 0.8206 (m-40) REVERT: 1 160 SER cc_start: 0.8312 (m) cc_final: 0.8053 (p) REVERT: 1 185 ARG cc_start: 0.7846 (tpp80) cc_final: 0.7612 (tpp80) REVERT: 2 30 ASN cc_start: 0.7949 (t0) cc_final: 0.7600 (t0) REVERT: 2 112 SER cc_start: 0.8555 (t) cc_final: 0.8140 (p) REVERT: 2 120 ASP cc_start: 0.7353 (p0) cc_final: 0.6786 (p0) REVERT: 2 200 GLN cc_start: 0.6913 (mt0) cc_final: 0.6167 (pt0) REVERT: 2 214 LYS cc_start: 0.8112 (ptmt) cc_final: 0.7783 (mttp) REVERT: 3 61 THR cc_start: 0.9085 (m) cc_final: 0.8842 (m) REVERT: 3 98 ARG cc_start: 0.7718 (mtp-110) cc_final: 0.7483 (mtp-110) REVERT: 3 203 ARG cc_start: 0.7039 (tmt170) cc_final: 0.5918 (mtt180) REVERT: 4 3 ILE cc_start: 0.9035 (pt) cc_final: 0.8513 (mp) REVERT: 4 60 ILE cc_start: 0.9341 (pt) cc_final: 0.8765 (mt) REVERT: 4 99 GLN cc_start: 0.7390 (tm-30) cc_final: 0.6968 (tm-30) REVERT: 4 120 ASP cc_start: 0.7917 (p0) cc_final: 0.7546 (p0) REVERT: 4 124 THR cc_start: 0.8715 (p) cc_final: 0.8008 (p) REVERT: 4 167 GLU cc_start: 0.8751 (pm20) cc_final: 0.8136 (pm20) REVERT: 4 193 ASP cc_start: 0.7821 (p0) cc_final: 0.7589 (p0) REVERT: 5 19 ARG cc_start: 0.8492 (tpp-160) cc_final: 0.8040 (tpp-160) REVERT: 5 24 ASN cc_start: 0.8738 (t0) cc_final: 0.8372 (t0) REVERT: 5 111 THR cc_start: 0.7971 (m) cc_final: 0.7514 (p) REVERT: 5 146 TRP cc_start: 0.8245 (t-100) cc_final: 0.7313 (t60) REVERT: 6 81 ASP cc_start: 0.7130 (t0) cc_final: 0.6752 (t70) REVERT: 6 150 LEU cc_start: 0.8647 (mt) cc_final: 0.8440 (mt) REVERT: 6 200 ASP cc_start: 0.6346 (t0) cc_final: 0.6080 (t0) REVERT: 7 82 ASP cc_start: 0.7889 (m-30) cc_final: 0.7439 (t0) REVERT: 7 107 MET cc_start: 0.8507 (mmm) cc_final: 0.8208 (tpp) REVERT: 7 169 THR cc_start: 0.8688 (t) cc_final: 0.8421 (m) REVERT: A 39 ASN cc_start: 0.8254 (m-40) cc_final: 0.7727 (t0) REVERT: A 49 ASP cc_start: 0.7165 (p0) cc_final: 0.6719 (p0) REVERT: A 50 CYS cc_start: 0.7177 (m) cc_final: 0.6909 (m) REVERT: A 195 ASN cc_start: 0.7834 (m-40) cc_final: 0.7599 (m110) REVERT: A 224 GLU cc_start: 0.8376 (pt0) cc_final: 0.8070 (pt0) REVERT: A 242 GLU cc_start: 0.7122 (mp0) cc_final: 0.6719 (mp0) REVERT: B 60 THR cc_start: 0.9072 (p) cc_final: 0.8646 (t) REVERT: B 75 TYR cc_start: 0.8850 (p90) cc_final: 0.8414 (p90) REVERT: B 118 MET cc_start: 0.8735 (ttm) cc_final: 0.8389 (mtt) REVERT: B 210 GLU cc_start: 0.7652 (tp30) cc_final: 0.7401 (tp30) REVERT: C 7 ASP cc_start: 0.7830 (t70) cc_final: 0.7346 (t0) REVERT: C 39 MET cc_start: 0.8532 (ttt) cc_final: 0.8275 (ttt) REVERT: C 212 GLU cc_start: 0.8389 (pt0) cc_final: 0.8135 (pt0) REVERT: D 43 VAL cc_start: 0.9159 (p) cc_final: 0.8931 (t) REVERT: D 86 ILE cc_start: 0.8641 (pt) cc_final: 0.8182 (mt) REVERT: D 148 TYR cc_start: 0.9096 (m-80) cc_final: 0.8856 (m-10) REVERT: E 182 GLU cc_start: 0.7530 (pp20) cc_final: 0.7253 (pp20) REVERT: E 203 ILE cc_start: 0.8670 (pt) cc_final: 0.8414 (pt) REVERT: F 60 GLN cc_start: 0.8256 (pt0) cc_final: 0.7903 (pt0) REVERT: F 122 SER cc_start: 0.8969 (m) cc_final: 0.8737 (t) REVERT: G 43 ASN cc_start: 0.8265 (p0) cc_final: 0.8030 (p0) REVERT: G 60 VAL cc_start: 0.8642 (t) cc_final: 0.8354 (p) REVERT: H 51 GLN cc_start: 0.7995 (pp30) cc_final: 0.7770 (pp30) REVERT: H 98 GLN cc_start: 0.8266 (tt0) cc_final: 0.7977 (tt0) REVERT: H 218 ILE cc_start: 0.8834 (pt) cc_final: 0.8498 (mt) REVERT: H 359 ASN cc_start: 0.8822 (m-40) cc_final: 0.8475 (m110) REVERT: H 442 ASP cc_start: 0.8646 (p0) cc_final: 0.8379 (p0) REVERT: I 64 ARG cc_start: 0.7240 (ptm-80) cc_final: 0.6740 (ttt180) REVERT: I 68 HIS cc_start: 0.7923 (m-70) cc_final: 0.7613 (m-70) REVERT: I 120 VAL cc_start: 0.9289 (t) cc_final: 0.9076 (m) REVERT: I 121 THR cc_start: 0.8026 (p) cc_final: 0.7750 (t) REVERT: I 167 MET cc_start: 0.7665 (pmm) cc_final: 0.7175 (ptp) REVERT: I 208 TYR cc_start: 0.8529 (m-80) cc_final: 0.8076 (m-80) REVERT: I 312 GLN cc_start: 0.8243 (mm-40) cc_final: 0.7987 (mm-40) REVERT: J 58 ILE cc_start: 0.9054 (pt) cc_final: 0.8672 (mt) REVERT: J 86 VAL cc_start: 0.8893 (t) cc_final: 0.8635 (m) REVERT: J 239 GLU cc_start: 0.7184 (pt0) cc_final: 0.6936 (tt0) REVERT: J 256 THR cc_start: 0.6588 (m) cc_final: 0.5984 (p) REVERT: J 270 ARG cc_start: 0.6088 (mmt90) cc_final: 0.5850 (mtt180) REVERT: J 295 ASN cc_start: 0.8978 (m-40) cc_final: 0.8739 (m-40) REVERT: J 362 CYS cc_start: 0.8881 (m) cc_final: 0.8260 (t) REVERT: K 124 SER cc_start: 0.8860 (t) cc_final: 0.8484 (p) REVERT: K 149 ILE cc_start: 0.9055 (tp) cc_final: 0.8660 (tt) REVERT: L 306 MET cc_start: 0.7531 (tmm) cc_final: 0.6870 (tmm) REVERT: L 307 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7345 (tp30) REVERT: M 265 ASP cc_start: 0.7817 (m-30) cc_final: 0.7462 (m-30) REVERT: M 292 ASP cc_start: 0.7577 (p0) cc_final: 0.7309 (p0) REVERT: n 219 TRP cc_start: 0.7750 (m-10) cc_final: 0.7513 (m-10) outliers start: 1 outliers final: 0 residues processed: 825 average time/residue: 0.2654 time to fit residues: 365.8881 Evaluate side-chains 668 residues out of total 4951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 668 time to evaluate : 1.798 ------------------------------------------------------------------------------- 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: 8.9990 chunk 73 optimal weight: 0.9990 chunk 529 optimal weight: 0.9980 chunk 488 optimal weight: 0.4980 chunk 358 optimal weight: 0.9990 chunk 138 optimal weight: 9.9990 chunk 545 optimal weight: 10.0000 chunk 456 optimal weight: 0.0870 chunk 479 optimal weight: 1.9990 chunk 432 optimal weight: 0.8980 chunk 152 optimal weight: 5.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 8 ASN 4 41 HIS 5 53 GLN 5 190 ASN 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** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** J 331 HIS ** K 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 142 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.080539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.069786 restraints weight = 113286.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.071096 restraints weight = 69336.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.071999 restraints weight = 48914.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.072599 restraints weight = 38159.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.073011 restraints weight = 32097.552| |-----------------------------------------------------------------------------| r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.4456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 45012 Z= 0.108 Angle : 0.593 11.311 60998 Z= 0.301 Chirality : 0.045 0.241 7049 Planarity : 0.004 0.055 7868 Dihedral : 7.091 114.729 6446 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 0.02 % Allowed : 1.78 % Favored : 98.20 % 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: -2.44 (0.11), residues: 5766 helix: -1.02 (0.11), residues: 2107 sheet: -1.63 (0.15), residues: 1065 loop : -2.03 (0.12), residues: 2594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 77 TYR 0.028 0.001 TYR 5 137 PHE 0.028 0.001 PHE 3 50 TRP 0.022 0.001 TRP G 218 HIS 0.009 0.001 HIS G 204 Details of bonding type rmsd covalent geometry : bond 0.00245 (45011) covalent geometry : angle 0.59338 (60998) hydrogen bonds : bond 0.03191 ( 1440) hydrogen bonds : angle 4.86861 ( 3972) Misc. bond : bond 0.00004 ( 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 847 residues out of total 4951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 846 time to evaluate : 1.816 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: 1 107 LYS cc_start: 0.7777 (mmtt) cc_final: 0.7566 (mmtm) REVERT: 1 109 GLU cc_start: 0.7123 (mt-10) cc_final: 0.6900 (mt-10) REVERT: 1 145 ASN cc_start: 0.8375 (m-40) cc_final: 0.8128 (m-40) REVERT: 1 160 SER cc_start: 0.8296 (m) cc_final: 0.8052 (p) REVERT: 2 30 ASN cc_start: 0.7970 (t0) cc_final: 0.7587 (t0) REVERT: 2 112 SER cc_start: 0.8467 (t) cc_final: 0.8088 (p) REVERT: 2 120 ASP cc_start: 0.7394 (p0) cc_final: 0.6713 (p0) REVERT: 2 200 GLN cc_start: 0.6852 (mt0) cc_final: 0.6117 (pt0) REVERT: 2 214 LYS cc_start: 0.8139 (ptmt) cc_final: 0.7832 (mttt) REVERT: 3 15 MET cc_start: 0.7695 (ttm) cc_final: 0.6312 (ttm) REVERT: 3 61 THR cc_start: 0.9060 (m) cc_final: 0.8858 (m) REVERT: 3 98 ARG cc_start: 0.7764 (mtp-110) cc_final: 0.7464 (mtp85) REVERT: 3 154 TYR cc_start: 0.7807 (t80) cc_final: 0.7265 (t80) REVERT: 3 203 ARG cc_start: 0.7026 (tmt170) cc_final: 0.5887 (mtt180) REVERT: 4 3 ILE cc_start: 0.9071 (pt) cc_final: 0.8520 (mp) REVERT: 4 60 ILE cc_start: 0.9235 (pt) cc_final: 0.8596 (mt) REVERT: 4 71 GLU cc_start: 0.7962 (mp0) cc_final: 0.7703 (mp0) REVERT: 4 99 GLN cc_start: 0.7328 (tm-30) cc_final: 0.6987 (tm-30) REVERT: 4 120 ASP cc_start: 0.7880 (p0) cc_final: 0.7533 (p0) REVERT: 4 124 THR cc_start: 0.8613 (p) cc_final: 0.7995 (p) REVERT: 5 19 ARG cc_start: 0.8495 (tpp-160) cc_final: 0.8219 (tpp-160) REVERT: 5 24 ASN cc_start: 0.8797 (t0) cc_final: 0.8374 (t0) REVERT: 5 111 THR cc_start: 0.7914 (m) cc_final: 0.7479 (p) REVERT: 5 146 TRP cc_start: 0.8196 (t-100) cc_final: 0.7282 (t60) REVERT: 6 81 ASP cc_start: 0.7164 (t0) cc_final: 0.6790 (t70) REVERT: 6 159 GLN cc_start: 0.6754 (pt0) cc_final: 0.6085 (tp40) REVERT: 6 200 ASP cc_start: 0.6388 (t0) cc_final: 0.6101 (t0) REVERT: 7 82 ASP cc_start: 0.7891 (m-30) cc_final: 0.7439 (t0) REVERT: 7 107 MET cc_start: 0.8528 (mmm) cc_final: 0.8213 (tpp) REVERT: 7 169 THR cc_start: 0.8642 (t) cc_final: 0.8440 (m) REVERT: A 39 ASN cc_start: 0.8247 (m-40) cc_final: 0.7778 (t0) REVERT: A 242 GLU cc_start: 0.7191 (mp0) cc_final: 0.6869 (mp0) REVERT: A 244 ARG cc_start: 0.6600 (tpp-160) cc_final: 0.5837 (tpp-160) REVERT: B 60 THR cc_start: 0.9028 (p) cc_final: 0.8639 (t) REVERT: B 75 TYR cc_start: 0.8805 (p90) cc_final: 0.8342 (p90) REVERT: C 7 ASP cc_start: 0.7847 (t70) cc_final: 0.7320 (t0) REVERT: C 39 MET cc_start: 0.8509 (ttt) cc_final: 0.8206 (ttt) REVERT: C 199 LYS cc_start: 0.8906 (mtmt) cc_final: 0.8601 (mtmm) REVERT: C 210 ARG cc_start: 0.7947 (ttm110) cc_final: 0.7639 (ttm-80) REVERT: C 212 GLU cc_start: 0.8361 (pt0) cc_final: 0.8137 (pt0) REVERT: D 27 VAL cc_start: 0.8988 (t) cc_final: 0.8665 (p) REVERT: D 43 VAL cc_start: 0.9142 (p) cc_final: 0.8903 (t) REVERT: D 148 TYR cc_start: 0.9050 (m-80) cc_final: 0.8780 (m-10) REVERT: E 182 GLU cc_start: 0.7800 (pp20) cc_final: 0.7021 (pp20) REVERT: F 60 GLN cc_start: 0.8135 (pt0) cc_final: 0.7756 (pt0) REVERT: G 43 ASN cc_start: 0.8236 (p0) cc_final: 0.8031 (p0) REVERT: G 202 LEU cc_start: 0.9030 (mt) cc_final: 0.8727 (mt) REVERT: H 51 GLN cc_start: 0.7936 (pp30) cc_final: 0.7727 (pp30) REVERT: H 297 MET cc_start: 0.8828 (ptm) cc_final: 0.8616 (ptm) REVERT: H 359 ASN cc_start: 0.8807 (m-40) cc_final: 0.8453 (m110) REVERT: H 442 ASP cc_start: 0.8693 (p0) cc_final: 0.8377 (p0) REVERT: I 64 ARG cc_start: 0.7263 (ptm-80) cc_final: 0.6832 (ttt180) REVERT: I 68 HIS cc_start: 0.7895 (m-70) cc_final: 0.7598 (m-70) REVERT: I 120 VAL cc_start: 0.9295 (t) cc_final: 0.9075 (m) REVERT: I 121 THR cc_start: 0.7783 (p) cc_final: 0.7395 (t) REVERT: I 167 MET cc_start: 0.7517 (pmm) cc_final: 0.7295 (ptp) REVERT: I 208 TYR cc_start: 0.8455 (m-80) cc_final: 0.8108 (m-10) REVERT: I 312 GLN cc_start: 0.8314 (mm-40) cc_final: 0.8011 (mm-40) REVERT: J 86 VAL cc_start: 0.8778 (t) cc_final: 0.8559 (m) REVERT: J 239 GLU cc_start: 0.7294 (pt0) cc_final: 0.7094 (tt0) REVERT: J 247 MET cc_start: 0.8079 (mtp) cc_final: 0.7709 (mtm) REVERT: J 256 THR cc_start: 0.6478 (m) cc_final: 0.5882 (p) REVERT: J 270 ARG cc_start: 0.6133 (mmt90) cc_final: 0.5656 (mtt180) REVERT: J 295 ASN cc_start: 0.8950 (m-40) cc_final: 0.8736 (m-40) REVERT: J 362 CYS cc_start: 0.8853 (m) cc_final: 0.8297 (t) REVERT: K 124 SER cc_start: 0.8743 (t) cc_final: 0.8345 (p) REVERT: K 149 ILE cc_start: 0.9065 (tp) cc_final: 0.8743 (tt) REVERT: K 260 LEU cc_start: 0.9177 (pp) cc_final: 0.8747 (tt) REVERT: L 221 TYR cc_start: 0.7992 (p90) cc_final: 0.7000 (p90) REVERT: L 255 TYR cc_start: 0.8678 (m-80) cc_final: 0.8282 (m-80) REVERT: L 306 MET cc_start: 0.7564 (tmm) cc_final: 0.6834 (tmm) REVERT: L 307 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7289 (tp30) REVERT: M 265 ASP cc_start: 0.7676 (m-30) cc_final: 0.7406 (m-30) REVERT: M 292 ASP cc_start: 0.7400 (p0) cc_final: 0.6754 (p0) outliers start: 1 outliers final: 1 residues processed: 847 average time/residue: 0.2639 time to fit residues: 371.7782 Evaluate side-chains 673 residues out of total 4951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 672 time to evaluate : 1.833 ------------------------------------------------------------------------------- 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: 10.0000 chunk 457 optimal weight: 5.9990 chunk 512 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 190 optimal weight: 3.9990 chunk 83 optimal weight: 9.9990 chunk 119 optimal weight: 1.9990 chunk 550 optimal weight: 8.9990 chunk 230 optimal weight: 2.9990 chunk 402 optimal weight: 5.9990 chunk 569 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 160 GLN 5 133 GLN 6 8 ASN ** 6 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 74 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 F 166 GLN G 182 HIS G 204 HIS ** I 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 303 GLN I 312 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 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 142 HIS ** K 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.074563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.063769 restraints weight = 116522.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.065277 restraints weight = 73495.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.065701 restraints weight = 51757.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.066529 restraints weight = 40959.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.066540 restraints weight = 34041.989| |-----------------------------------------------------------------------------| r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.4618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 45012 Z= 0.244 Angle : 0.730 8.828 60998 Z= 0.374 Chirality : 0.050 0.272 7049 Planarity : 0.005 0.063 7868 Dihedral : 7.617 122.047 6446 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.35 % Favored : 92.63 % Rotamer: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % 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: -2.46 (0.11), residues: 5766 helix: -1.08 (0.11), residues: 2084 sheet: -1.54 (0.15), residues: 1087 loop : -2.05 (0.12), residues: 2595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 91 TYR 0.024 0.002 TYR M 180 PHE 0.028 0.002 PHE 3 50 TRP 0.037 0.003 TRP G 218 HIS 0.009 0.001 HIS G 204 Details of bonding type rmsd covalent geometry : bond 0.00582 (45011) covalent geometry : angle 0.72986 (60998) hydrogen bonds : bond 0.03951 ( 1440) hydrogen bonds : angle 5.33254 ( 3972) Misc. bond : bond 0.00020 ( 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 778 residues out of total 4951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 778 time to evaluate : 1.910 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 14 LEU cc_start: 0.8554 (mt) cc_final: 0.8338 (mp) REVERT: 1 160 SER cc_start: 0.8626 (m) cc_final: 0.8343 (p) REVERT: 2 30 ASN cc_start: 0.8080 (t0) cc_final: 0.7763 (t0) REVERT: 2 112 SER cc_start: 0.8477 (t) cc_final: 0.8146 (p) REVERT: 2 120 ASP cc_start: 0.7447 (p0) cc_final: 0.6798 (p0) REVERT: 2 200 GLN cc_start: 0.6875 (mt0) cc_final: 0.6179 (pt0) REVERT: 2 214 LYS cc_start: 0.8192 (ptmt) cc_final: 0.7819 (mttp) REVERT: 3 203 ARG cc_start: 0.7065 (tmt170) cc_final: 0.5881 (mtt180) REVERT: 4 52 ASP cc_start: 0.7908 (m-30) cc_final: 0.7569 (t0) REVERT: 4 60 ILE cc_start: 0.9455 (pt) cc_final: 0.8859 (mt) REVERT: 4 99 GLN cc_start: 0.7351 (tm-30) cc_final: 0.6904 (tm-30) REVERT: 4 120 ASP cc_start: 0.7848 (p0) cc_final: 0.7462 (p0) REVERT: 4 124 THR cc_start: 0.8484 (p) cc_final: 0.7802 (p) REVERT: 5 24 ASN cc_start: 0.8916 (t0) cc_final: 0.8596 (t0) REVERT: 5 73 ARG cc_start: 0.7688 (ttp-170) cc_final: 0.7483 (ttp-170) REVERT: 5 146 TRP cc_start: 0.8413 (t-100) cc_final: 0.7274 (t60) REVERT: 5 197 PHE cc_start: 0.8092 (t80) cc_final: 0.7848 (t80) REVERT: 6 81 ASP cc_start: 0.7267 (t0) cc_final: 0.6893 (t70) REVERT: 6 200 ASP cc_start: 0.6590 (t0) cc_final: 0.6292 (t0) REVERT: 7 107 MET cc_start: 0.8728 (mmm) cc_final: 0.8486 (tpp) REVERT: 7 120 GLN cc_start: 0.8375 (mm110) cc_final: 0.7970 (mm-40) REVERT: A 39 ASN cc_start: 0.8243 (m-40) cc_final: 0.7692 (t0) REVERT: A 242 GLU cc_start: 0.7191 (mp0) cc_final: 0.6671 (mp0) REVERT: B 75 TYR cc_start: 0.8794 (p90) cc_final: 0.8298 (p90) REVERT: B 178 ARG cc_start: 0.7929 (mmm-85) cc_final: 0.7407 (mmp-170) REVERT: C 7 ASP cc_start: 0.7893 (t70) cc_final: 0.7459 (t0) REVERT: C 39 MET cc_start: 0.8499 (ttt) cc_final: 0.8284 (ttt) REVERT: C 51 LYS cc_start: 0.7247 (mmmm) cc_final: 0.6983 (ptmt) REVERT: C 164 SER cc_start: 0.9109 (p) cc_final: 0.8820 (p) REVERT: D 43 VAL cc_start: 0.9155 (p) cc_final: 0.8938 (t) REVERT: D 86 ILE cc_start: 0.8643 (pt) cc_final: 0.8289 (mt) REVERT: D 148 TYR cc_start: 0.9168 (m-80) cc_final: 0.8871 (m-10) REVERT: E 182 GLU cc_start: 0.7896 (pp20) cc_final: 0.7424 (pp20) REVERT: F 60 GLN cc_start: 0.8011 (pt0) cc_final: 0.7781 (pt0) REVERT: G 202 LEU cc_start: 0.9042 (mt) cc_final: 0.8785 (mt) REVERT: H 51 GLN cc_start: 0.8037 (pp30) cc_final: 0.7811 (pp30) REVERT: H 98 GLN cc_start: 0.8328 (tt0) cc_final: 0.8041 (tt0) REVERT: H 218 ILE cc_start: 0.8714 (pt) cc_final: 0.8439 (mt) REVERT: H 330 GLN cc_start: 0.8997 (mp10) cc_final: 0.8790 (mp10) REVERT: H 359 ASN cc_start: 0.8929 (m-40) cc_final: 0.8618 (m110) REVERT: I 64 ARG cc_start: 0.7446 (ptm-80) cc_final: 0.6953 (ttt180) REVERT: I 68 HIS cc_start: 0.8036 (m-70) cc_final: 0.7739 (m-70) REVERT: I 120 VAL cc_start: 0.9317 (t) cc_final: 0.9051 (m) REVERT: I 121 THR cc_start: 0.8187 (p) cc_final: 0.7823 (t) REVERT: I 167 MET cc_start: 0.7657 (pmm) cc_final: 0.7334 (ptp) REVERT: I 208 TYR cc_start: 0.8455 (m-80) cc_final: 0.7977 (m-80) REVERT: I 283 GLU cc_start: 0.7589 (mp0) cc_final: 0.7351 (mp0) REVERT: I 285 ASP cc_start: 0.7709 (p0) cc_final: 0.7214 (p0) REVERT: J 86 VAL cc_start: 0.8907 (t) cc_final: 0.8700 (m) REVERT: J 94 TYR cc_start: 0.9114 (m-10) cc_final: 0.8902 (m-10) REVERT: J 256 THR cc_start: 0.6688 (m) cc_final: 0.6269 (p) REVERT: J 270 ARG cc_start: 0.6432 (mmt90) cc_final: 0.5999 (mmt180) REVERT: J 295 ASN cc_start: 0.8982 (m-40) cc_final: 0.8703 (m-40) REVERT: J 362 CYS cc_start: 0.8833 (m) cc_final: 0.8341 (t) REVERT: K 124 SER cc_start: 0.9103 (t) cc_final: 0.8681 (p) REVERT: K 149 ILE cc_start: 0.9086 (tp) cc_final: 0.8749 (tt) REVERT: K 260 LEU cc_start: 0.9266 (pp) cc_final: 0.8855 (tt) REVERT: L 306 MET cc_start: 0.7781 (tmm) cc_final: 0.7305 (tmm) REVERT: M 292 ASP cc_start: 0.7477 (p0) cc_final: 0.6888 (p0) outliers start: 0 outliers final: 0 residues processed: 778 average time/residue: 0.2663 time to fit residues: 344.5498 Evaluate side-chains 644 residues out of total 4951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 644 time to evaluate : 1.653 ------------------------------------------------------------------------------- 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: 0.9980 chunk 5 optimal weight: 0.9990 chunk 371 optimal weight: 2.9990 chunk 290 optimal weight: 3.9990 chunk 554 optimal weight: 0.0870 chunk 376 optimal weight: 1.9990 chunk 273 optimal weight: 2.9990 chunk 313 optimal weight: 0.0470 chunk 134 optimal weight: 7.9990 chunk 379 optimal weight: 5.9990 chunk 247 optimal weight: 0.8980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 8 ASN 6 159 GLN 7 74 ASN A 41 ASN A 56 GLN A 181 ASN A 209 HIS C 21 GLN C 103 ASN ** C 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 19 GLN D 117 GLN H 356 ASN I 102 ASN I 238 ASN I 303 GLN ** I 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 ASN J 277 ASN ** K 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 142 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.078585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.067765 restraints weight = 114008.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.069046 restraints weight = 74649.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.069625 restraints weight = 55148.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.070736 restraints weight = 41505.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.070622 restraints weight = 32917.772| |-----------------------------------------------------------------------------| r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.4883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 45012 Z= 0.111 Angle : 0.611 11.937 60998 Z= 0.308 Chirality : 0.045 0.202 7049 Planarity : 0.004 0.090 7868 Dihedral : 7.009 113.286 6446 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.07 % Allowed : 0.83 % Favored : 99.10 % 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: -2.13 (0.11), residues: 5766 helix: -0.77 (0.11), residues: 2093 sheet: -1.32 (0.15), residues: 1085 loop : -1.91 (0.12), residues: 2588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG J 312 TYR 0.023 0.001 TYR M 180 PHE 0.025 0.001 PHE E 138 TRP 0.024 0.002 TRP G 218 HIS 0.005 0.001 HIS J 170 Details of bonding type rmsd covalent geometry : bond 0.00250 (45011) covalent geometry : angle 0.61115 (60998) hydrogen bonds : bond 0.03216 ( 1440) hydrogen bonds : angle 4.87181 ( 3972) Misc. bond : bond 0.00004 ( 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 832 residues out of total 4951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 829 time to evaluate : 1.895 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 29 ARG cc_start: 0.8047 (ptt90) cc_final: 0.7769 (ptt-90) REVERT: 1 107 LYS cc_start: 0.7824 (mmtt) cc_final: 0.7525 (mmtm) REVERT: 1 109 GLU cc_start: 0.7162 (mt-10) cc_final: 0.6853 (mt-10) REVERT: 1 145 ASN cc_start: 0.8364 (m-40) cc_final: 0.8156 (m-40) REVERT: 1 160 SER cc_start: 0.8596 (m) cc_final: 0.8326 (p) REVERT: 2 30 ASN cc_start: 0.8130 (t0) cc_final: 0.7759 (t0) REVERT: 2 112 SER cc_start: 0.8404 (t) cc_final: 0.8113 (p) REVERT: 2 120 ASP cc_start: 0.7383 (p0) cc_final: 0.6639 (p0) REVERT: 2 200 GLN cc_start: 0.6875 (mt0) cc_final: 0.6044 (pt0) REVERT: 2 214 LYS cc_start: 0.8130 (ptmt) cc_final: 0.7778 (mttt) REVERT: 3 72 ASN cc_start: 0.8597 (m-40) cc_final: 0.8002 (t0) REVERT: 3 147 PHE cc_start: 0.6035 (t80) cc_final: 0.5790 (t80) REVERT: 3 203 ARG cc_start: 0.6930 (tmt170) cc_final: 0.5579 (mtt-85) REVERT: 4 60 ILE cc_start: 0.9333 (pt) cc_final: 0.8692 (mt) REVERT: 4 92 ILE cc_start: 0.8605 (tp) cc_final: 0.8389 (tp) REVERT: 4 99 GLN cc_start: 0.7288 (tm-30) cc_final: 0.6898 (tm-30) REVERT: 4 120 ASP cc_start: 0.7912 (p0) cc_final: 0.7535 (p0) REVERT: 4 124 THR cc_start: 0.8507 (p) cc_final: 0.7960 (p) REVERT: 4 162 LYS cc_start: 0.6369 (tptp) cc_final: 0.5669 (tptp) REVERT: 5 19 ARG cc_start: 0.8693 (tpp-160) cc_final: 0.8410 (tpp-160) REVERT: 5 24 ASN cc_start: 0.8983 (t0) cc_final: 0.8616 (t0) REVERT: 5 111 THR cc_start: 0.8065 (m) cc_final: 0.7493 (p) REVERT: 5 146 TRP cc_start: 0.8413 (t-100) cc_final: 0.7201 (t60) REVERT: 5 197 PHE cc_start: 0.8117 (t80) cc_final: 0.7863 (t80) REVERT: 6 81 ASP cc_start: 0.7194 (t0) cc_final: 0.6832 (t70) REVERT: 6 159 GLN cc_start: 0.6221 (pt0) cc_final: 0.5569 (tp40) REVERT: 6 200 ASP cc_start: 0.6569 (t0) cc_final: 0.6316 (t0) REVERT: 7 107 MET cc_start: 0.8662 (mmm) cc_final: 0.8396 (tpp) REVERT: A 242 GLU cc_start: 0.7206 (mp0) cc_final: 0.6713 (mp0) REVERT: A 244 ARG cc_start: 0.7036 (tpp-160) cc_final: 0.6824 (tpp-160) REVERT: B 75 TYR cc_start: 0.8815 (p90) cc_final: 0.8319 (p90) REVERT: C 7 ASP cc_start: 0.7996 (t70) cc_final: 0.7440 (t0) REVERT: C 39 MET cc_start: 0.8546 (ttt) cc_final: 0.8289 (ttt) REVERT: C 185 LYS cc_start: 0.7824 (tptt) cc_final: 0.7265 (tttt) REVERT: C 199 LYS cc_start: 0.8887 (mtmt) cc_final: 0.8653 (mtmm) REVERT: D 43 VAL cc_start: 0.9116 (p) cc_final: 0.8884 (t) REVERT: D 148 TYR cc_start: 0.9086 (m-80) cc_final: 0.8787 (m-10) REVERT: E 182 GLU cc_start: 0.7866 (pp20) cc_final: 0.7554 (pp20) REVERT: G 60 VAL cc_start: 0.8657 (t) cc_final: 0.8401 (p) REVERT: G 190 ARG cc_start: 0.8707 (mmt180) cc_final: 0.8398 (mmm-85) REVERT: H 51 GLN cc_start: 0.8022 (pp30) cc_final: 0.7783 (pp30) REVERT: H 98 GLN cc_start: 0.8155 (tt0) cc_final: 0.7853 (tt0) REVERT: H 359 ASN cc_start: 0.8855 (m-40) cc_final: 0.8606 (m110) REVERT: I 64 ARG cc_start: 0.7289 (ptm-80) cc_final: 0.6901 (ttt180) REVERT: I 68 HIS cc_start: 0.7922 (m-70) cc_final: 0.7633 (m-70) REVERT: I 120 VAL cc_start: 0.9354 (t) cc_final: 0.9106 (m) REVERT: I 121 THR cc_start: 0.7881 (p) cc_final: 0.7526 (t) REVERT: I 285 ASP cc_start: 0.7646 (p0) cc_final: 0.6930 (p0) REVERT: J 94 TYR cc_start: 0.9076 (m-10) cc_final: 0.8835 (m-10) REVERT: J 270 ARG cc_start: 0.6251 (mmt90) cc_final: 0.5840 (mtt180) REVERT: J 295 ASN cc_start: 0.8923 (m-40) cc_final: 0.8707 (m-40) REVERT: J 403 LEU cc_start: 0.7027 (mt) cc_final: 0.6706 (mt) REVERT: K 124 SER cc_start: 0.8893 (t) cc_final: 0.8458 (p) REVERT: K 149 ILE cc_start: 0.9055 (tp) cc_final: 0.8706 (tt) REVERT: K 212 TYR cc_start: 0.8933 (p90) cc_final: 0.8726 (p90) REVERT: K 260 LEU cc_start: 0.9219 (pp) cc_final: 0.8815 (tt) REVERT: L 188 GLU cc_start: 0.8373 (pp20) cc_final: 0.8150 (pp20) REVERT: L 255 TYR cc_start: 0.8711 (m-80) cc_final: 0.8286 (m-80) REVERT: L 306 MET cc_start: 0.7613 (tmm) cc_final: 0.7094 (tmm) REVERT: M 261 LYS cc_start: 0.8057 (tmtt) cc_final: 0.7184 (tmtt) REVERT: M 265 ASP cc_start: 0.7632 (m-30) cc_final: 0.6813 (m-30) REVERT: M 292 ASP cc_start: 0.7433 (p0) cc_final: 0.6711 (p0) REVERT: r 135 ARG cc_start: 0.7259 (mtm180) cc_final: 0.6933 (mtm180) outliers start: 3 outliers final: 0 residues processed: 831 average time/residue: 0.2610 time to fit residues: 364.1799 Evaluate side-chains 673 residues out of total 4951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 673 time to evaluate : 1.848 ------------------------------------------------------------------------------- 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: 10.0000 chunk 201 optimal weight: 4.9990 chunk 523 optimal weight: 9.9990 chunk 448 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 391 optimal weight: 6.9990 chunk 557 optimal weight: 0.8980 chunk 256 optimal weight: 0.0470 chunk 39 optimal weight: 1.9990 chunk 309 optimal weight: 9.9990 chunk 365 optimal weight: 5.9990 overall best weight: 2.7884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 53 GLN 5 133 GLN ** 6 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 74 ASN 7 120 GLN ** A 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 41 ASN A 181 ASN D 19 GLN G 182 HIS ** I 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 303 GLN ** I 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 277 ASN ** K 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 142 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.074975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.064259 restraints weight = 115988.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.065823 restraints weight = 71063.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.066299 restraints weight = 49746.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.067093 restraints weight = 38894.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.067050 restraints weight = 32865.587| |-----------------------------------------------------------------------------| r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.4956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 45012 Z= 0.200 Angle : 0.689 10.209 60998 Z= 0.352 Chirality : 0.048 0.242 7049 Planarity : 0.005 0.083 7868 Dihedral : 7.233 116.728 6446 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.95 % Favored : 93.03 % Rotamer: Outliers : 0.07 % Allowed : 1.03 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.15 (0.11), residues: 5766 helix: -0.80 (0.11), residues: 2100 sheet: -1.33 (0.15), residues: 1085 loop : -1.91 (0.12), residues: 2581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 210 TYR 0.024 0.002 TYR M 180 PHE 0.024 0.002 PHE C 13 TRP 0.034 0.002 TRP G 218 HIS 0.006 0.001 HIS G 73 Details of bonding type rmsd covalent geometry : bond 0.00477 (45011) covalent geometry : angle 0.68930 (60998) hydrogen bonds : bond 0.03675 ( 1440) hydrogen bonds : angle 5.10431 ( 3972) Misc. bond : bond 0.00024 ( 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 789 residues out of total 4951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 786 time to evaluate : 1.844 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: 1 107 LYS cc_start: 0.7912 (mmtt) cc_final: 0.7654 (mmtm) REVERT: 1 109 GLU cc_start: 0.7197 (mt-10) cc_final: 0.6959 (mt-10) REVERT: 1 160 SER cc_start: 0.8564 (m) cc_final: 0.8303 (p) REVERT: 2 30 ASN cc_start: 0.8172 (t0) cc_final: 0.7792 (t0) REVERT: 2 112 SER cc_start: 0.8426 (t) cc_final: 0.8103 (p) REVERT: 2 120 ASP cc_start: 0.7341 (p0) cc_final: 0.6824 (p0) REVERT: 2 200 GLN cc_start: 0.7112 (mt0) cc_final: 0.6287 (pt0) REVERT: 2 214 LYS cc_start: 0.8216 (ptmt) cc_final: 0.7804 (mttp) REVERT: 3 79 GLU cc_start: 0.7639 (mp0) cc_final: 0.7013 (mm-30) REVERT: 3 203 ARG cc_start: 0.6695 (tmt170) cc_final: 0.5611 (mmt90) REVERT: 4 52 ASP cc_start: 0.7818 (m-30) cc_final: 0.7444 (t0) REVERT: 4 60 ILE cc_start: 0.9459 (pt) cc_final: 0.8814 (mt) REVERT: 4 99 GLN cc_start: 0.7210 (tm-30) cc_final: 0.6723 (tm-30) REVERT: 4 120 ASP cc_start: 0.7849 (p0) cc_final: 0.7446 (p0) REVERT: 4 162 LYS cc_start: 0.6564 (tptp) cc_final: 0.6117 (tptp) REVERT: 5 19 ARG cc_start: 0.8830 (tpp-160) cc_final: 0.8532 (tpt170) REVERT: 5 24 ASN cc_start: 0.9000 (t0) cc_final: 0.8683 (t0) REVERT: 5 146 TRP cc_start: 0.8435 (t-100) cc_final: 0.7255 (t60) REVERT: 6 81 ASP cc_start: 0.7240 (t0) cc_final: 0.6858 (t70) REVERT: 6 159 GLN cc_start: 0.6904 (pt0) cc_final: 0.6415 (tp40) REVERT: 6 174 TYR cc_start: 0.7374 (m-80) cc_final: 0.6516 (m-80) REVERT: 6 200 ASP cc_start: 0.6282 (t0) cc_final: 0.5959 (t0) REVERT: 7 107 MET cc_start: 0.8748 (mmm) cc_final: 0.8474 (tpp) REVERT: A 242 GLU cc_start: 0.7279 (mp0) cc_final: 0.6698 (mp0) REVERT: A 244 ARG cc_start: 0.7173 (tpp-160) cc_final: 0.6935 (tpp-160) REVERT: B 75 TYR cc_start: 0.8779 (p90) cc_final: 0.8327 (p90) REVERT: B 178 ARG cc_start: 0.7847 (mmm-85) cc_final: 0.7396 (mmp-170) REVERT: B 183 LEU cc_start: 0.8620 (tp) cc_final: 0.8409 (tp) REVERT: C 7 ASP cc_start: 0.7990 (t70) cc_final: 0.7551 (t0) REVERT: C 39 MET cc_start: 0.8487 (ttt) cc_final: 0.8283 (ttt) REVERT: D 43 VAL cc_start: 0.9153 (p) cc_final: 0.8928 (t) REVERT: D 86 ILE cc_start: 0.8575 (pt) cc_final: 0.8273 (mt) REVERT: D 148 TYR cc_start: 0.9153 (m-80) cc_final: 0.8904 (m-10) REVERT: E 132 ARG cc_start: 0.7165 (ttm170) cc_final: 0.6800 (mtp-110) REVERT: E 133 LEU cc_start: 0.8238 (tp) cc_final: 0.7870 (tp) REVERT: E 182 GLU cc_start: 0.7991 (pp20) cc_final: 0.7640 (pp20) REVERT: F 60 GLN cc_start: 0.7914 (pt0) cc_final: 0.7625 (pt0) REVERT: H 51 GLN cc_start: 0.8044 (pp30) cc_final: 0.7822 (pp30) REVERT: H 98 GLN cc_start: 0.8272 (tt0) cc_final: 0.7999 (tt0) REVERT: H 218 ILE cc_start: 0.8712 (pt) cc_final: 0.8471 (mt) REVERT: H 359 ASN cc_start: 0.8902 (m-40) cc_final: 0.8657 (m110) REVERT: I 64 ARG cc_start: 0.7465 (ptm-80) cc_final: 0.7045 (ttt180) REVERT: I 68 HIS cc_start: 0.7969 (m-70) cc_final: 0.7661 (m-70) REVERT: I 120 VAL cc_start: 0.9284 (t) cc_final: 0.9027 (m) REVERT: I 121 THR cc_start: 0.8221 (p) cc_final: 0.7823 (t) REVERT: I 147 VAL cc_start: 0.9567 (m) cc_final: 0.9281 (p) REVERT: I 208 TYR cc_start: 0.8308 (m-80) cc_final: 0.7939 (m-80) REVERT: I 285 ASP cc_start: 0.7742 (p0) cc_final: 0.7285 (p0) REVERT: J 25 GLN cc_start: 0.7801 (mm110) cc_final: 0.7402 (mm-40) REVERT: J 247 MET cc_start: 0.8359 (mtm) cc_final: 0.8131 (mtp) REVERT: J 295 ASN cc_start: 0.9002 (m-40) cc_final: 0.8747 (m-40) REVERT: J 330 ILE cc_start: 0.8682 (tp) cc_final: 0.8111 (tp) REVERT: J 362 CYS cc_start: 0.8863 (m) cc_final: 0.8357 (t) REVERT: K 124 SER cc_start: 0.9046 (t) cc_final: 0.8630 (p) REVERT: K 149 ILE cc_start: 0.9059 (tp) cc_final: 0.8699 (tt) REVERT: K 221 MET cc_start: 0.8183 (ppp) cc_final: 0.7975 (ppp) REVERT: K 260 LEU cc_start: 0.9336 (pp) cc_final: 0.8811 (tt) REVERT: L 306 MET cc_start: 0.7825 (tmm) cc_final: 0.7309 (tmm) REVERT: L 307 GLU cc_start: 0.7821 (tp30) cc_final: 0.7549 (tp30) REVERT: M 292 ASP cc_start: 0.7477 (p0) cc_final: 0.6855 (p0) REVERT: M 305 MET cc_start: 0.8244 (ttp) cc_final: 0.8008 (ttm) REVERT: r 135 ARG cc_start: 0.7266 (mtm180) cc_final: 0.6919 (mtm180) outliers start: 3 outliers final: 0 residues processed: 787 average time/residue: 0.2624 time to fit residues: 347.2500 Evaluate side-chains 636 residues out of total 4951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 636 time to evaluate : 1.882 ------------------------------------------------------------------------------- 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: 3.9990 chunk 409 optimal weight: 6.9990 chunk 137 optimal weight: 0.5980 chunk 524 optimal weight: 9.9990 chunk 362 optimal weight: 0.0980 chunk 172 optimal weight: 0.0040 chunk 334 optimal weight: 0.7980 chunk 354 optimal weight: 3.9990 chunk 311 optimal weight: 0.4980 chunk 143 optimal weight: 9.9990 chunk 79 optimal weight: 4.9990 overall best weight: 0.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 74 ASN A 41 ASN A 181 ASN C 103 ASN D 19 GLN D 117 GLN G 182 HIS H 356 ASN I 238 ASN I 303 GLN ** I 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 426 ASN J 128 ASN J 277 ASN K 72 GLN K 142 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.079090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.068946 restraints weight = 114177.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.070075 restraints weight = 82462.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.070689 restraints weight = 58814.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.070925 restraints weight = 45236.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.070995 restraints weight = 43323.075| |-----------------------------------------------------------------------------| r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.5198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 45012 Z= 0.110 Angle : 0.611 11.006 60998 Z= 0.308 Chirality : 0.045 0.205 7049 Planarity : 0.004 0.075 7868 Dihedral : 6.734 106.781 6446 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.07 % Allowed : 0.35 % Favored : 99.58 % 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: -1.86 (0.11), residues: 5766 helix: -0.54 (0.12), residues: 2105 sheet: -1.22 (0.15), residues: 1095 loop : -1.75 (0.12), residues: 2566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG 3 98 TYR 0.030 0.001 TYR B 224 PHE 0.021 0.001 PHE A 104 TRP 0.021 0.002 TRP 5 25 HIS 0.004 0.001 HIS J 170 Details of bonding type rmsd covalent geometry : bond 0.00241 (45011) covalent geometry : angle 0.61126 (60998) hydrogen bonds : bond 0.03110 ( 1440) hydrogen bonds : angle 4.73775 ( 3972) Misc. bond : bond 0.00006 ( 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 853 residues out of total 4951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 850 time to evaluate : 1.783 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: 1 145 ASN cc_start: 0.8311 (m-40) cc_final: 0.8105 (m-40) REVERT: 1 160 SER cc_start: 0.8544 (m) cc_final: 0.8262 (p) REVERT: 2 30 ASN cc_start: 0.8082 (t0) cc_final: 0.7505 (t0) REVERT: 2 112 SER cc_start: 0.8409 (t) cc_final: 0.8146 (p) REVERT: 2 120 ASP cc_start: 0.7350 (p0) cc_final: 0.6664 (p0) REVERT: 2 200 GLN cc_start: 0.6991 (mt0) cc_final: 0.6147 (pt0) REVERT: 2 214 LYS cc_start: 0.8190 (ptmt) cc_final: 0.7821 (mttp) REVERT: 3 72 ASN cc_start: 0.8408 (m-40) cc_final: 0.8149 (t0) REVERT: 3 79 GLU cc_start: 0.7558 (mp0) cc_final: 0.7083 (mm-30) REVERT: 3 203 ARG cc_start: 0.6890 (tmt170) cc_final: 0.5439 (mtt-85) REVERT: 4 31 SER cc_start: 0.8764 (m) cc_final: 0.8202 (t) REVERT: 4 60 ILE cc_start: 0.9333 (pt) cc_final: 0.8674 (mt) REVERT: 4 71 GLU cc_start: 0.7881 (mp0) cc_final: 0.7640 (mp0) REVERT: 4 99 GLN cc_start: 0.7119 (tm-30) cc_final: 0.6735 (tm-30) REVERT: 4 120 ASP cc_start: 0.7883 (p0) cc_final: 0.7546 (p0) REVERT: 4 124 THR cc_start: 0.8581 (p) cc_final: 0.8075 (p) REVERT: 4 162 LYS cc_start: 0.6442 (tptp) cc_final: 0.6112 (tptp) REVERT: 4 169 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8204 (mt-10) REVERT: 5 24 ASN cc_start: 0.8998 (t0) cc_final: 0.8677 (t0) REVERT: 5 111 THR cc_start: 0.8057 (m) cc_final: 0.7577 (p) REVERT: 6 81 ASP cc_start: 0.7169 (t0) cc_final: 0.6839 (t0) REVERT: 6 107 VAL cc_start: 0.8758 (t) cc_final: 0.8510 (m) REVERT: 6 159 GLN cc_start: 0.6883 (pt0) cc_final: 0.6103 (tp40) REVERT: 6 161 GLU cc_start: 0.7333 (tm-30) cc_final: 0.7081 (tm-30) REVERT: 6 200 ASP cc_start: 0.6216 (t0) cc_final: 0.5938 (t0) REVERT: 7 107 MET cc_start: 0.8630 (mmm) cc_final: 0.8377 (tpp) REVERT: 7 174 GLU cc_start: 0.7824 (pt0) cc_final: 0.6752 (pt0) REVERT: A 182 LEU cc_start: 0.8727 (pp) cc_final: 0.8214 (mt) REVERT: A 242 GLU cc_start: 0.7300 (mp0) cc_final: 0.6782 (mp0) REVERT: A 244 ARG cc_start: 0.7161 (tpp-160) cc_final: 0.6921 (tpp-160) REVERT: B 75 TYR cc_start: 0.8730 (p90) cc_final: 0.8215 (p90) REVERT: C 7 ASP cc_start: 0.8012 (t70) cc_final: 0.7549 (t0) REVERT: C 39 MET cc_start: 0.8509 (ttt) cc_final: 0.8268 (ttt) REVERT: C 185 LYS cc_start: 0.7851 (tptt) cc_final: 0.7236 (tttt) REVERT: C 188 ASP cc_start: 0.7827 (m-30) cc_final: 0.7529 (m-30) REVERT: C 200 THR cc_start: 0.8373 (t) cc_final: 0.8172 (t) REVERT: C 210 ARG cc_start: 0.7787 (ttm110) cc_final: 0.7244 (ttm110) REVERT: D 43 VAL cc_start: 0.9117 (p) cc_final: 0.8894 (t) REVERT: D 148 TYR cc_start: 0.9032 (m-80) cc_final: 0.8770 (m-10) REVERT: E 76 CYS cc_start: 0.8885 (t) cc_final: 0.8648 (t) REVERT: E 133 LEU cc_start: 0.8263 (tp) cc_final: 0.8057 (tp) REVERT: E 182 GLU cc_start: 0.7911 (pp20) cc_final: 0.7678 (pp20) REVERT: F 60 GLN cc_start: 0.7789 (pt0) cc_final: 0.7505 (pt0) REVERT: G 43 ASN cc_start: 0.8227 (p0) cc_final: 0.7979 (p0) REVERT: H 51 GLN cc_start: 0.8015 (pp30) cc_final: 0.7786 (pp30) REVERT: H 359 ASN cc_start: 0.8863 (m-40) cc_final: 0.8632 (m110) REVERT: I 64 ARG cc_start: 0.7317 (ptm-80) cc_final: 0.6878 (ttt180) REVERT: I 68 HIS cc_start: 0.7937 (m-70) cc_final: 0.7618 (m-70) REVERT: I 120 VAL cc_start: 0.9306 (t) cc_final: 0.9088 (m) REVERT: I 121 THR cc_start: 0.7859 (p) cc_final: 0.7603 (t) REVERT: I 147 VAL cc_start: 0.9493 (m) cc_final: 0.9106 (p) REVERT: I 285 ASP cc_start: 0.7731 (p0) cc_final: 0.7331 (p0) REVERT: I 371 LEU cc_start: 0.7796 (pp) cc_final: 0.7503 (pp) REVERT: J 25 GLN cc_start: 0.7861 (mm110) cc_final: 0.7539 (mm110) REVERT: J 129 LYS cc_start: 0.7743 (tppt) cc_final: 0.7418 (ttpp) REVERT: J 165 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7842 (tp30) REVERT: J 247 MET cc_start: 0.8252 (mtm) cc_final: 0.8049 (mtp) REVERT: J 295 ASN cc_start: 0.8980 (m-40) cc_final: 0.8740 (m-40) REVERT: J 297 LEU cc_start: 0.9342 (pt) cc_final: 0.9074 (pp) REVERT: J 329 ARG cc_start: 0.8040 (tmm160) cc_final: 0.7823 (ttp80) REVERT: J 330 ILE cc_start: 0.8573 (tp) cc_final: 0.8324 (tp) REVERT: J 362 CYS cc_start: 0.8870 (m) cc_final: 0.8392 (t) REVERT: K 124 SER cc_start: 0.8894 (t) cc_final: 0.8501 (p) REVERT: K 149 ILE cc_start: 0.9070 (tp) cc_final: 0.8727 (tt) REVERT: K 260 LEU cc_start: 0.9260 (pp) cc_final: 0.8917 (tt) REVERT: L 255 TYR cc_start: 0.8602 (m-80) cc_final: 0.8207 (m-80) REVERT: L 306 MET cc_start: 0.7562 (tmm) cc_final: 0.7053 (tmm) REVERT: L 307 GLU cc_start: 0.7635 (tp30) cc_final: 0.7347 (tp30) REVERT: M 180 TYR cc_start: 0.8711 (m-80) cc_final: 0.8482 (m-80) REVERT: M 261 LYS cc_start: 0.8063 (tmtt) cc_final: 0.7208 (tmtt) REVERT: M 265 ASP cc_start: 0.7626 (m-30) cc_final: 0.6623 (m-30) REVERT: M 292 ASP cc_start: 0.7575 (p0) cc_final: 0.6975 (p0) REVERT: r 135 ARG cc_start: 0.7211 (mtm180) cc_final: 0.6900 (mtm180) outliers start: 3 outliers final: 0 residues processed: 851 average time/residue: 0.2582 time to fit residues: 370.5501 Evaluate side-chains 682 residues out of total 4951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 682 time to evaluate : 1.972 ------------------------------------------------------------------------------- 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: 5.9990 chunk 10 optimal weight: 0.0060 chunk 540 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 chunk 448 optimal weight: 1.9990 chunk 315 optimal weight: 6.9990 chunk 179 optimal weight: 0.9980 chunk 462 optimal weight: 20.0000 chunk 219 optimal weight: 10.0000 chunk 483 optimal weight: 7.9990 chunk 230 optimal weight: 0.9980 overall best weight: 0.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 62 HIS 2 160 GLN 5 53 GLN 5 133 GLN 7 74 ASN A 37 GLN A 41 ASN A 181 ASN C 156 ASN C 168 ASN I 238 ASN I 303 GLN I 393 GLN ** I 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 277 ASN J 379 GLN K 142 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.078190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.067424 restraints weight = 114755.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.068946 restraints weight = 72689.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.069921 restraints weight = 48588.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.070218 restraints weight = 36203.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.070345 restraints weight = 32184.303| |-----------------------------------------------------------------------------| r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.5302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 45012 Z= 0.115 Angle : 0.612 11.051 60998 Z= 0.309 Chirality : 0.045 0.197 7049 Planarity : 0.004 0.069 7868 Dihedral : 6.627 104.309 6446 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.09 % Allowed : 0.35 % Favored : 99.56 % 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: -1.77 (0.11), residues: 5766 helix: -0.45 (0.12), residues: 2108 sheet: -1.15 (0.15), residues: 1099 loop : -1.73 (0.12), residues: 2559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 200 TYR 0.027 0.001 TYR B 224 PHE 0.022 0.001 PHE E 138 TRP 0.022 0.001 TRP 5 25 HIS 0.019 0.001 HIS J 240 Details of bonding type rmsd covalent geometry : bond 0.00269 (45011) covalent geometry : angle 0.61196 (60998) hydrogen bonds : bond 0.03090 ( 1440) hydrogen bonds : angle 4.73130 ( 3972) Misc. bond : bond 0.00003 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8283.01 seconds wall clock time: 143 minutes 37.73 seconds (8617.73 seconds total)