Starting phenix.real_space_refine on Sun Jun 22 17:43:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pbd_17585/06_2025/8pbd_17585.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pbd_17585/06_2025/8pbd_17585.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pbd_17585/06_2025/8pbd_17585.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pbd_17585/06_2025/8pbd_17585.map" model { file = "/net/cci-nas-00/data/ceres_data/8pbd_17585/06_2025/8pbd_17585.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pbd_17585/06_2025/8pbd_17585.cif" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.072 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: 6 Type Number sf(0) Gaussians Ca 20 9.91 5 P 84 5.49 5 S 139 5.16 5 C 16254 2.51 5 N 4665 2.21 5 O 5204 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 26366 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 Chain: "K" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 121 Classifications: {'peptide': 16} Link IDs: {'PTRANS': 3, 'TRANS': 12} Chain: "T" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 585 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "U" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 522 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' CA': 3, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, L, M, N, O, P, Q, R, S Time building chain proxies: 9.51, per 1000 atoms: 0.36 Number of scatterers: 26366 At special positions: 0 Unit cell: (123.88, 121.272, 220.376, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 20 19.99 S 139 16.00 P 84 15.00 O 5204 8.00 N 4665 7.00 C 16254 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=0, symmetry=0 Time building additional restraints: 7.04 Conformation dependent library (CDL) restraints added in 3.3 seconds 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5968 Finding SS restraints... Secondary structure from input PDB file: 170 helices and 30 sheets defined 51.4% alpha, 16.3% beta 20 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 10.18 Creating SS restraints... Processing helix chain 'A' and resid 24 through 32 removed outlier: 3.796A pdb=" N GLN A 30 " --> pdb=" O ARG A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 43 Processing helix chain 'A' and resid 48 through 54 Processing helix chain 'A' and resid 56 through 62 removed outlier: 3.688A pdb=" N LEU A 60 " --> pdb=" O PRO A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 82 removed outlier: 3.789A pdb=" N LEU A 81 " --> pdb=" O GLU A 77 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A 82 " --> pdb=" O ALA A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 98 removed outlier: 3.775A pdb=" N GLU A 98 " --> pdb=" O GLN A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 114 removed outlier: 3.589A pdb=" N LEU A 112 " --> pdb=" O GLU A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 144 Processing helix chain 'A' and resid 145 through 146 No H-bonds generated for 'chain 'A' and resid 145 through 146' Processing helix chain 'A' and resid 147 through 151 Processing helix chain 'A' and resid 167 through 179 removed outlier: 3.789A pdb=" N LEU A 171 " --> pdb=" O ARG A 167 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL A 174 " --> pdb=" O ARG A 170 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 186 Processing helix chain 'A' and resid 196 through 214 removed outlier: 3.935A pdb=" N LEU A 204 " --> pdb=" O GLN A 200 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR A 205 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA A 209 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU A 213 " --> pdb=" O ALA A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 232 removed outlier: 3.817A pdb=" N TYR A 232 " --> pdb=" O TYR A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 236 No H-bonds generated for 'chain 'A' and resid 234 through 236' Processing helix chain 'A' and resid 237 through 259 Processing helix chain 'A' and resid 288 through 296 removed outlier: 3.740A pdb=" N ILE A 292 " --> pdb=" O GLY A 288 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA A 295 " --> pdb=" O ILE A 291 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER A 296 " --> pdb=" O ILE A 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 32 removed outlier: 3.795A pdb=" N GLN B 30 " --> pdb=" O ARG B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 43 Processing helix chain 'B' and resid 48 through 54 Processing helix chain 'B' and resid 56 through 62 removed outlier: 3.688A pdb=" N LEU B 60 " --> pdb=" O PRO B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 82 removed outlier: 3.789A pdb=" N LEU B 81 " --> pdb=" O GLU B 77 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL B 82 " --> pdb=" O ALA B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 98 removed outlier: 3.775A pdb=" N GLU B 98 " --> pdb=" O GLN B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 114 removed outlier: 3.590A pdb=" N LEU B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 144 Processing helix chain 'B' and resid 145 through 146 No H-bonds generated for 'chain 'B' and resid 145 through 146' Processing helix chain 'B' and resid 147 through 151 Processing helix chain 'B' and resid 167 through 179 removed outlier: 3.789A pdb=" N LEU B 171 " --> pdb=" O ARG B 167 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL B 174 " --> pdb=" O ARG B 170 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG B 177 " --> pdb=" O ALA B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 186 Processing helix chain 'B' and resid 196 through 214 removed outlier: 3.935A pdb=" N LEU B 204 " --> pdb=" O GLN B 200 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR B 205 " --> pdb=" O THR B 201 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA B 209 " --> pdb=" O TYR B 205 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU B 213 " --> pdb=" O ALA B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 232 removed outlier: 3.816A pdb=" N TYR B 232 " --> pdb=" O TYR B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 236 No H-bonds generated for 'chain 'B' and resid 234 through 236' Processing helix chain 'B' and resid 237 through 259 Processing helix chain 'B' and resid 288 through 296 removed outlier: 3.740A pdb=" N ILE B 292 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA B 295 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER B 296 " --> pdb=" O ILE B 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 32 removed outlier: 3.796A pdb=" N GLN C 30 " --> pdb=" O ARG C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 43 Processing helix chain 'C' and resid 48 through 54 Processing helix chain 'C' and resid 56 through 62 removed outlier: 3.688A pdb=" N LEU C 60 " --> pdb=" O PRO C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 82 removed outlier: 3.789A pdb=" N LEU C 81 " --> pdb=" O GLU C 77 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL C 82 " --> pdb=" O ALA C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 98 removed outlier: 3.776A pdb=" N GLU C 98 " --> pdb=" O GLN C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 114 removed outlier: 3.590A pdb=" N LEU C 112 " --> pdb=" O GLU C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 144 Processing helix chain 'C' and resid 145 through 146 No H-bonds generated for 'chain 'C' and resid 145 through 146' Processing helix chain 'C' and resid 147 through 151 Processing helix chain 'C' and resid 167 through 179 removed outlier: 3.789A pdb=" N LEU C 171 " --> pdb=" O ARG C 167 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL C 174 " --> pdb=" O ARG C 170 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG C 177 " --> pdb=" O ALA C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 186 Processing helix chain 'C' and resid 196 through 214 removed outlier: 3.935A pdb=" N LEU C 204 " --> pdb=" O GLN C 200 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR C 205 " --> pdb=" O THR C 201 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA C 209 " --> pdb=" O TYR C 205 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL C 212 " --> pdb=" O SER C 208 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 232 removed outlier: 3.817A pdb=" N TYR C 232 " --> pdb=" O TYR C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 236 No H-bonds generated for 'chain 'C' and resid 234 through 236' Processing helix chain 'C' and resid 237 through 259 Processing helix chain 'C' and resid 288 through 296 removed outlier: 3.740A pdb=" N ILE C 292 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA C 295 " --> pdb=" O ILE C 291 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER C 296 " --> pdb=" O ILE C 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 32 removed outlier: 3.795A pdb=" N GLN D 30 " --> pdb=" O ARG D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 43 Processing helix chain 'D' and resid 48 through 54 Processing helix chain 'D' and resid 56 through 62 removed outlier: 3.688A pdb=" N LEU D 60 " --> pdb=" O PRO D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 82 removed outlier: 3.789A pdb=" N LEU D 81 " --> pdb=" O GLU D 77 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL D 82 " --> pdb=" O ALA D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 98 removed outlier: 3.776A pdb=" N GLU D 98 " --> pdb=" O GLN D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 114 removed outlier: 3.590A pdb=" N LEU D 112 " --> pdb=" O GLU D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 144 Processing helix chain 'D' and resid 145 through 146 No H-bonds generated for 'chain 'D' and resid 145 through 146' Processing helix chain 'D' and resid 147 through 151 Processing helix chain 'D' and resid 167 through 179 removed outlier: 3.790A pdb=" N LEU D 171 " --> pdb=" O ARG D 167 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL D 174 " --> pdb=" O ARG D 170 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG D 177 " --> pdb=" O ALA D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 186 Processing helix chain 'D' and resid 196 through 214 removed outlier: 3.935A pdb=" N LEU D 204 " --> pdb=" O GLN D 200 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR D 205 " --> pdb=" O THR D 201 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA D 209 " --> pdb=" O TYR D 205 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL D 212 " --> pdb=" O SER D 208 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU D 213 " --> pdb=" O ALA D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 232 removed outlier: 3.818A pdb=" N TYR D 232 " --> pdb=" O TYR D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 236 No H-bonds generated for 'chain 'D' and resid 234 through 236' Processing helix chain 'D' and resid 237 through 259 Processing helix chain 'D' and resid 288 through 296 removed outlier: 3.740A pdb=" N ILE D 292 " --> pdb=" O GLY D 288 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA D 295 " --> pdb=" O ILE D 291 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER D 296 " --> pdb=" O ILE D 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 32 removed outlier: 3.796A pdb=" N GLN E 30 " --> pdb=" O ARG E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 34 through 43 Processing helix chain 'E' and resid 48 through 54 Processing helix chain 'E' and resid 56 through 62 removed outlier: 3.688A pdb=" N LEU E 60 " --> pdb=" O PRO E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 82 removed outlier: 3.788A pdb=" N LEU E 81 " --> pdb=" O GLU E 77 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL E 82 " --> pdb=" O ALA E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 98 removed outlier: 3.775A pdb=" N GLU E 98 " --> pdb=" O GLN E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 114 removed outlier: 3.589A pdb=" N LEU E 112 " --> pdb=" O GLU E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 144 Processing helix chain 'E' and resid 145 through 146 No H-bonds generated for 'chain 'E' and resid 145 through 146' Processing helix chain 'E' and resid 147 through 151 Processing helix chain 'E' and resid 167 through 179 removed outlier: 3.789A pdb=" N LEU E 171 " --> pdb=" O ARG E 167 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL E 174 " --> pdb=" O ARG E 170 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG E 177 " --> pdb=" O ALA E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 186 Processing helix chain 'E' and resid 196 through 214 removed outlier: 3.935A pdb=" N LEU E 204 " --> pdb=" O GLN E 200 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR E 205 " --> pdb=" O THR E 201 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA E 209 " --> pdb=" O TYR E 205 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL E 212 " --> pdb=" O SER E 208 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU E 213 " --> pdb=" O ALA E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 232 removed outlier: 3.816A pdb=" N TYR E 232 " --> pdb=" O TYR E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 236 No H-bonds generated for 'chain 'E' and resid 234 through 236' Processing helix chain 'E' and resid 237 through 259 Processing helix chain 'E' and resid 288 through 296 removed outlier: 3.740A pdb=" N ILE E 292 " --> pdb=" O GLY E 288 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA E 295 " --> pdb=" O ILE E 291 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER E 296 " --> pdb=" O ILE E 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 32 removed outlier: 3.795A pdb=" N GLN F 30 " --> pdb=" O ARG F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 34 through 43 Processing helix chain 'F' and resid 48 through 54 Processing helix chain 'F' and resid 56 through 62 removed outlier: 3.688A pdb=" N LEU F 60 " --> pdb=" O PRO F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 82 removed outlier: 3.789A pdb=" N LEU F 81 " --> pdb=" O GLU F 77 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL F 82 " --> pdb=" O ALA F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 98 removed outlier: 3.777A pdb=" N GLU F 98 " --> pdb=" O GLN F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 114 removed outlier: 3.589A pdb=" N LEU F 112 " --> pdb=" O GLU F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 144 Processing helix chain 'F' and resid 145 through 146 No H-bonds generated for 'chain 'F' and resid 145 through 146' Processing helix chain 'F' and resid 147 through 151 Processing helix chain 'F' and resid 167 through 179 removed outlier: 3.789A pdb=" N LEU F 171 " --> pdb=" O ARG F 167 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL F 174 " --> pdb=" O ARG F 170 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG F 177 " --> pdb=" O ALA F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 186 Processing helix chain 'F' and resid 196 through 214 removed outlier: 3.936A pdb=" N LEU F 204 " --> pdb=" O GLN F 200 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR F 205 " --> pdb=" O THR F 201 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA F 209 " --> pdb=" O TYR F 205 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL F 212 " --> pdb=" O SER F 208 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU F 213 " --> pdb=" O ALA F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 232 removed outlier: 3.817A pdb=" N TYR F 232 " --> pdb=" O TYR F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 236 No H-bonds generated for 'chain 'F' and resid 234 through 236' Processing helix chain 'F' and resid 237 through 259 Processing helix chain 'F' and resid 288 through 296 removed outlier: 3.740A pdb=" N ILE F 292 " --> pdb=" O GLY F 288 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA F 295 " --> pdb=" O ILE F 291 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER F 296 " --> pdb=" O ILE F 292 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 32 removed outlier: 3.795A pdb=" N GLN G 30 " --> pdb=" O ARG G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 43 Processing helix chain 'G' and resid 48 through 54 Processing helix chain 'G' and resid 56 through 62 removed outlier: 3.688A pdb=" N LEU G 60 " --> pdb=" O PRO G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 82 removed outlier: 3.789A pdb=" N LEU G 81 " --> pdb=" O GLU G 77 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL G 82 " --> pdb=" O ALA G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 98 removed outlier: 3.775A pdb=" N GLU G 98 " --> pdb=" O GLN G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 114 removed outlier: 3.590A pdb=" N LEU G 112 " --> pdb=" O GLU G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 144 Processing helix chain 'G' and resid 145 through 146 No H-bonds generated for 'chain 'G' and resid 145 through 146' Processing helix chain 'G' and resid 147 through 151 Processing helix chain 'G' and resid 167 through 179 removed outlier: 3.790A pdb=" N LEU G 171 " --> pdb=" O ARG G 167 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL G 174 " --> pdb=" O ARG G 170 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG G 177 " --> pdb=" O ALA G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 186 Processing helix chain 'G' and resid 196 through 214 removed outlier: 3.936A pdb=" N LEU G 204 " --> pdb=" O GLN G 200 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR G 205 " --> pdb=" O THR G 201 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA G 209 " --> pdb=" O TYR G 205 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL G 212 " --> pdb=" O SER G 208 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU G 213 " --> pdb=" O ALA G 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 232 removed outlier: 3.817A pdb=" N TYR G 232 " --> pdb=" O TYR G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 236 No H-bonds generated for 'chain 'G' and resid 234 through 236' Processing helix chain 'G' and resid 237 through 259 Processing helix chain 'G' and resid 288 through 296 removed outlier: 3.740A pdb=" N ILE G 292 " --> pdb=" O GLY G 288 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA G 295 " --> pdb=" O ILE G 291 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER G 296 " --> pdb=" O ILE G 292 " (cutoff:3.500A) Processing helix chain 'H' and resid 24 through 32 removed outlier: 3.796A pdb=" N GLN H 30 " --> pdb=" O ARG H 27 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 43 Processing helix chain 'H' and resid 48 through 54 Processing helix chain 'H' and resid 56 through 62 removed outlier: 3.688A pdb=" N LEU H 60 " --> pdb=" O PRO H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 82 removed outlier: 3.789A pdb=" N LEU H 81 " --> pdb=" O GLU H 77 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL H 82 " --> pdb=" O ALA H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 89 through 98 removed outlier: 3.775A pdb=" N GLU H 98 " --> pdb=" O GLN H 94 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 114 removed outlier: 3.590A pdb=" N LEU H 112 " --> pdb=" O GLU H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 144 Processing helix chain 'H' and resid 145 through 146 No H-bonds generated for 'chain 'H' and resid 145 through 146' Processing helix chain 'H' and resid 147 through 151 Processing helix chain 'H' and resid 167 through 179 removed outlier: 3.789A pdb=" N LEU H 171 " --> pdb=" O ARG H 167 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL H 174 " --> pdb=" O ARG H 170 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG H 177 " --> pdb=" O ALA H 173 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 186 Processing helix chain 'H' and resid 196 through 214 removed outlier: 3.935A pdb=" N LEU H 204 " --> pdb=" O GLN H 200 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR H 205 " --> pdb=" O THR H 201 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA H 209 " --> pdb=" O TYR H 205 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL H 212 " --> pdb=" O SER H 208 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU H 213 " --> pdb=" O ALA H 209 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 232 removed outlier: 3.817A pdb=" N TYR H 232 " --> pdb=" O TYR H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 234 through 236 No H-bonds generated for 'chain 'H' and resid 234 through 236' Processing helix chain 'H' and resid 237 through 259 Processing helix chain 'H' and resid 288 through 296 removed outlier: 3.740A pdb=" N ILE H 292 " --> pdb=" O GLY H 288 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA H 295 " --> pdb=" O ILE H 291 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER H 296 " --> pdb=" O ILE H 292 " (cutoff:3.500A) Processing helix chain 'I' and resid 24 through 32 removed outlier: 3.796A pdb=" N GLN I 30 " --> pdb=" O ARG I 27 " (cutoff:3.500A) Processing helix chain 'I' and resid 34 through 43 Processing helix chain 'I' and resid 48 through 54 Processing helix chain 'I' and resid 56 through 62 removed outlier: 3.688A pdb=" N LEU I 60 " --> pdb=" O PRO I 56 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 82 removed outlier: 3.789A pdb=" N LEU I 81 " --> pdb=" O GLU I 77 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL I 82 " --> pdb=" O ALA I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 89 through 98 removed outlier: 3.776A pdb=" N GLU I 98 " --> pdb=" O GLN I 94 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 114 removed outlier: 3.590A pdb=" N LEU I 112 " --> pdb=" O GLU I 108 " (cutoff:3.500A) Processing helix chain 'I' and resid 132 through 144 Processing helix chain 'I' and resid 145 through 146 No H-bonds generated for 'chain 'I' and resid 145 through 146' Processing helix chain 'I' and resid 147 through 151 Processing helix chain 'I' and resid 167 through 179 removed outlier: 3.789A pdb=" N LEU I 171 " --> pdb=" O ARG I 167 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL I 174 " --> pdb=" O ARG I 170 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG I 177 " --> pdb=" O ALA I 173 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 186 Processing helix chain 'I' and resid 196 through 214 removed outlier: 3.935A pdb=" N LEU I 204 " --> pdb=" O GLN I 200 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR I 205 " --> pdb=" O THR I 201 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA I 209 " --> pdb=" O TYR I 205 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL I 212 " --> pdb=" O SER I 208 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU I 213 " --> pdb=" O ALA I 209 " (cutoff:3.500A) Processing helix chain 'I' and resid 227 through 232 removed outlier: 3.817A pdb=" N TYR I 232 " --> pdb=" O TYR I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 234 through 236 No H-bonds generated for 'chain 'I' and resid 234 through 236' Processing helix chain 'I' and resid 237 through 259 Processing helix chain 'I' and resid 288 through 296 removed outlier: 3.739A pdb=" N ILE I 292 " --> pdb=" O GLY I 288 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA I 295 " --> pdb=" O ILE I 291 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER I 296 " --> pdb=" O ILE I 292 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 32 removed outlier: 3.797A pdb=" N GLN J 30 " --> pdb=" O ARG J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 34 through 43 Processing helix chain 'J' and resid 48 through 54 Processing helix chain 'J' and resid 56 through 62 removed outlier: 3.688A pdb=" N LEU J 60 " --> pdb=" O PRO J 56 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 82 removed outlier: 3.789A pdb=" N LEU J 81 " --> pdb=" O GLU J 77 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL J 82 " --> pdb=" O ALA J 78 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 98 removed outlier: 3.775A pdb=" N GLU J 98 " --> pdb=" O GLN J 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 106 through 114 removed outlier: 3.589A pdb=" N LEU J 112 " --> pdb=" O GLU J 108 " (cutoff:3.500A) Processing helix chain 'J' and resid 132 through 144 Processing helix chain 'J' and resid 145 through 146 No H-bonds generated for 'chain 'J' and resid 145 through 146' Processing helix chain 'J' and resid 147 through 151 Processing helix chain 'J' and resid 167 through 179 removed outlier: 3.789A pdb=" N LEU J 171 " --> pdb=" O ARG J 167 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL J 174 " --> pdb=" O ARG J 170 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG J 177 " --> pdb=" O ALA J 173 " (cutoff:3.500A) Processing helix chain 'J' and resid 181 through 186 Processing helix chain 'J' and resid 196 through 214 removed outlier: 3.935A pdb=" N LEU J 204 " --> pdb=" O GLN J 200 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR J 205 " --> pdb=" O THR J 201 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA J 209 " --> pdb=" O TYR J 205 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL J 212 " --> pdb=" O SER J 208 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU J 213 " --> pdb=" O ALA J 209 " (cutoff:3.500A) Processing helix chain 'J' and resid 227 through 232 removed outlier: 3.817A pdb=" N TYR J 232 " --> pdb=" O TYR J 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 234 through 236 No H-bonds generated for 'chain 'J' and resid 234 through 236' Processing helix chain 'J' and resid 237 through 259 Processing helix chain 'J' and resid 288 through 296 removed outlier: 3.740A pdb=" N ILE J 292 " --> pdb=" O GLY J 288 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA J 295 " --> pdb=" O ILE J 291 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER J 296 " --> pdb=" O ILE J 292 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 88 removed outlier: 6.902A pdb=" N ALA B 157 " --> pdb=" O ALA B 190 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N ALA B 192 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N TYR B 159 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LYS B 156 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N ILE B 220 " --> pdb=" O LYS B 156 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N MET B 158 " --> pdb=" O ILE B 220 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASP B 222 " --> pdb=" O MET B 158 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE B 160 " --> pdb=" O ASP B 222 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N VAL B 264 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU B 219 " --> pdb=" O VAL B 264 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N THR B 266 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N VAL B 221 " --> pdb=" O THR B 266 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY B 127 " --> pdb=" O ASN B 267 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TYR B 301 " --> pdb=" O ILE B 314 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ILE B 314 " --> pdb=" O TYR B 301 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ARG B 303 " --> pdb=" O CYS B 312 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N CYS B 312 " --> pdb=" O ARG B 303 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 102 Processing sheet with id=AA3, first strand: chain 'A' and resid 189 through 193 removed outlier: 6.901A pdb=" N ALA A 157 " --> pdb=" O ALA A 190 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N ALA A 192 " --> pdb=" O ALA A 157 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N TYR A 159 " --> pdb=" O ALA A 192 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LYS A 156 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N ILE A 220 " --> pdb=" O LYS A 156 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N MET A 158 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASP A 222 " --> pdb=" O MET A 158 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE A 160 " --> pdb=" O ASP A 222 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N VAL A 264 " --> pdb=" O ALA A 217 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU A 219 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N THR A 266 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N VAL A 221 " --> pdb=" O THR A 266 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY A 127 " --> pdb=" O ASN A 267 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TYR A 301 " --> pdb=" O ILE A 314 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ILE A 314 " --> pdb=" O TYR A 301 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ARG A 303 " --> pdb=" O CYS A 312 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N CYS A 312 " --> pdb=" O ARG A 303 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 269 through 271 Processing sheet with id=AA5, first strand: chain 'B' and resid 87 through 88 removed outlier: 6.901A pdb=" N ALA C 157 " --> pdb=" O ALA C 190 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N ALA C 192 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N TYR C 159 " --> pdb=" O ALA C 192 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LYS C 156 " --> pdb=" O LEU C 218 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N ILE C 220 " --> pdb=" O LYS C 156 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N MET C 158 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASP C 222 " --> pdb=" O MET C 158 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE C 160 " --> pdb=" O ASP C 222 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N VAL C 264 " --> pdb=" O ALA C 217 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU C 219 " --> pdb=" O VAL C 264 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N THR C 266 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N VAL C 221 " --> pdb=" O THR C 266 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY C 127 " --> pdb=" O ASN C 267 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TYR C 301 " --> pdb=" O ILE C 314 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ILE C 314 " --> pdb=" O TYR C 301 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ARG C 303 " --> pdb=" O CYS C 312 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N CYS C 312 " --> pdb=" O ARG C 303 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 101 through 102 Processing sheet with id=AA7, first strand: chain 'B' and resid 269 through 271 Processing sheet with id=AA8, first strand: chain 'C' and resid 87 through 88 removed outlier: 6.900A pdb=" N ALA D 157 " --> pdb=" O ALA D 190 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N ALA D 192 " --> pdb=" O ALA D 157 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N TYR D 159 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LYS D 156 " --> pdb=" O LEU D 218 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N ILE D 220 " --> pdb=" O LYS D 156 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N MET D 158 " --> pdb=" O ILE D 220 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASP D 222 " --> pdb=" O MET D 158 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE D 160 " --> pdb=" O ASP D 222 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N VAL D 264 " --> pdb=" O ALA D 217 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU D 219 " --> pdb=" O VAL D 264 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N THR D 266 " --> pdb=" O LEU D 219 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N VAL D 221 " --> pdb=" O THR D 266 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY D 127 " --> pdb=" O ASN D 267 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TYR D 301 " --> pdb=" O ILE D 314 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ILE D 314 " --> pdb=" O TYR D 301 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ARG D 303 " --> pdb=" O CYS D 312 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N CYS D 312 " --> pdb=" O ARG D 303 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 101 through 102 Processing sheet with id=AB1, first strand: chain 'C' and resid 269 through 271 Processing sheet with id=AB2, first strand: chain 'D' and resid 87 through 88 removed outlier: 6.901A pdb=" N ALA E 157 " --> pdb=" O ALA E 190 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N ALA E 192 " --> pdb=" O ALA E 157 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N TYR E 159 " --> pdb=" O ALA E 192 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LYS E 156 " --> pdb=" O LEU E 218 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N ILE E 220 " --> pdb=" O LYS E 156 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N MET E 158 " --> pdb=" O ILE E 220 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASP E 222 " --> pdb=" O MET E 158 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE E 160 " --> pdb=" O ASP E 222 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N VAL E 264 " --> pdb=" O ALA E 217 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU E 219 " --> pdb=" O VAL E 264 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N THR E 266 " --> pdb=" O LEU E 219 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N VAL E 221 " --> pdb=" O THR E 266 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY E 127 " --> pdb=" O ASN E 267 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TYR E 301 " --> pdb=" O ILE E 314 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ILE E 314 " --> pdb=" O TYR E 301 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ARG E 303 " --> pdb=" O CYS E 312 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N CYS E 312 " --> pdb=" O ARG E 303 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 101 through 102 Processing sheet with id=AB4, first strand: chain 'D' and resid 269 through 271 Processing sheet with id=AB5, first strand: chain 'E' and resid 87 through 88 removed outlier: 6.901A pdb=" N ALA F 157 " --> pdb=" O ALA F 190 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N ALA F 192 " --> pdb=" O ALA F 157 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N TYR F 159 " --> pdb=" O ALA F 192 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LYS F 156 " --> pdb=" O LEU F 218 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N ILE F 220 " --> pdb=" O LYS F 156 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N MET F 158 " --> pdb=" O ILE F 220 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASP F 222 " --> pdb=" O MET F 158 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE F 160 " --> pdb=" O ASP F 222 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N VAL F 264 " --> pdb=" O ALA F 217 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU F 219 " --> pdb=" O VAL F 264 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N THR F 266 " --> pdb=" O LEU F 219 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N VAL F 221 " --> pdb=" O THR F 266 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY F 127 " --> pdb=" O ASN F 267 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TYR F 301 " --> pdb=" O ILE F 314 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ILE F 314 " --> pdb=" O TYR F 301 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ARG F 303 " --> pdb=" O CYS F 312 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N CYS F 312 " --> pdb=" O ARG F 303 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 101 through 102 Processing sheet with id=AB7, first strand: chain 'E' and resid 269 through 271 Processing sheet with id=AB8, first strand: chain 'F' and resid 87 through 88 removed outlier: 6.902A pdb=" N ALA G 157 " --> pdb=" O ALA G 190 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N ALA G 192 " --> pdb=" O ALA G 157 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N TYR G 159 " --> pdb=" O ALA G 192 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LYS G 156 " --> pdb=" O LEU G 218 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N ILE G 220 " --> pdb=" O LYS G 156 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N MET G 158 " --> pdb=" O ILE G 220 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASP G 222 " --> pdb=" O MET G 158 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE G 160 " --> pdb=" O ASP G 222 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N VAL G 264 " --> pdb=" O ALA G 217 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU G 219 " --> pdb=" O VAL G 264 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N THR G 266 " --> pdb=" O LEU G 219 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N VAL G 221 " --> pdb=" O THR G 266 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY G 127 " --> pdb=" O ASN G 267 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TYR G 301 " --> pdb=" O ILE G 314 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ILE G 314 " --> pdb=" O TYR G 301 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ARG G 303 " --> pdb=" O CYS G 312 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N CYS G 312 " --> pdb=" O ARG G 303 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 101 through 102 Processing sheet with id=AC1, first strand: chain 'F' and resid 269 through 271 Processing sheet with id=AC2, first strand: chain 'G' and resid 87 through 88 removed outlier: 6.902A pdb=" N ALA H 157 " --> pdb=" O ALA H 190 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N ALA H 192 " --> pdb=" O ALA H 157 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N TYR H 159 " --> pdb=" O ALA H 192 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LYS H 156 " --> pdb=" O LEU H 218 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N ILE H 220 " --> pdb=" O LYS H 156 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N MET H 158 " --> pdb=" O ILE H 220 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASP H 222 " --> pdb=" O MET H 158 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE H 160 " --> pdb=" O ASP H 222 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N VAL H 264 " --> pdb=" O ALA H 217 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU H 219 " --> pdb=" O VAL H 264 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N THR H 266 " --> pdb=" O LEU H 219 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N VAL H 221 " --> pdb=" O THR H 266 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY H 127 " --> pdb=" O ASN H 267 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TYR H 301 " --> pdb=" O ILE H 314 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ILE H 314 " --> pdb=" O TYR H 301 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ARG H 303 " --> pdb=" O CYS H 312 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N CYS H 312 " --> pdb=" O ARG H 303 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 101 through 102 Processing sheet with id=AC4, first strand: chain 'G' and resid 269 through 271 Processing sheet with id=AC5, first strand: chain 'H' and resid 87 through 88 removed outlier: 6.901A pdb=" N ALA I 157 " --> pdb=" O ALA I 190 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N ALA I 192 " --> pdb=" O ALA I 157 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N TYR I 159 " --> pdb=" O ALA I 192 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LYS I 156 " --> pdb=" O LEU I 218 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N ILE I 220 " --> pdb=" O LYS I 156 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N MET I 158 " --> pdb=" O ILE I 220 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASP I 222 " --> pdb=" O MET I 158 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE I 160 " --> pdb=" O ASP I 222 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N VAL I 264 " --> pdb=" O ALA I 217 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU I 219 " --> pdb=" O VAL I 264 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N THR I 266 " --> pdb=" O LEU I 219 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N VAL I 221 " --> pdb=" O THR I 266 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY I 127 " --> pdb=" O ASN I 267 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TYR I 301 " --> pdb=" O ILE I 314 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ILE I 314 " --> pdb=" O TYR I 301 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ARG I 303 " --> pdb=" O CYS I 312 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N CYS I 312 " --> pdb=" O ARG I 303 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 101 through 102 Processing sheet with id=AC7, first strand: chain 'H' and resid 269 through 271 Processing sheet with id=AC8, first strand: chain 'I' and resid 87 through 88 removed outlier: 6.901A pdb=" N ALA J 157 " --> pdb=" O ALA J 190 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N ALA J 192 " --> pdb=" O ALA J 157 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N TYR J 159 " --> pdb=" O ALA J 192 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LYS J 156 " --> pdb=" O LEU J 218 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N ILE J 220 " --> pdb=" O LYS J 156 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N MET J 158 " --> pdb=" O ILE J 220 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ASP J 222 " --> pdb=" O MET J 158 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE J 160 " --> pdb=" O ASP J 222 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N VAL J 264 " --> pdb=" O ALA J 217 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU J 219 " --> pdb=" O VAL J 264 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N THR J 266 " --> pdb=" O LEU J 219 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N VAL J 221 " --> pdb=" O THR J 266 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY J 127 " --> pdb=" O ASN J 267 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N TYR J 301 " --> pdb=" O ILE J 314 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ILE J 314 " --> pdb=" O TYR J 301 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ARG J 303 " --> pdb=" O CYS J 312 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N CYS J 312 " --> pdb=" O ARG J 303 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 101 through 102 Processing sheet with id=AD1, first strand: chain 'I' and resid 269 through 271 Processing sheet with id=AD2, first strand: chain 'J' and resid 101 through 102 Processing sheet with id=AD3, first strand: chain 'J' and resid 269 through 271 1109 hydrogen bonds defined for protein. 3000 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 50 hydrogen bonds 100 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 10.14 Time building geometry restraints manager: 8.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6155 1.33 - 1.45: 5382 1.45 - 1.57: 14983 1.57 - 1.69: 136 1.69 - 1.81: 219 Bond restraints: 26875 Sorted by residual: bond pdb=" CA TYR G 232 " pdb=" CB TYR G 232 " ideal model delta sigma weight residual 1.528 1.502 0.026 1.51e-02 4.39e+03 3.04e+00 bond pdb=" CA TYR F 232 " pdb=" CB TYR F 232 " ideal model delta sigma weight residual 1.528 1.502 0.026 1.51e-02 4.39e+03 3.00e+00 bond pdb=" CA TYR H 232 " pdb=" CB TYR H 232 " ideal model delta sigma weight residual 1.528 1.503 0.026 1.51e-02 4.39e+03 2.93e+00 bond pdb=" CA TYR D 232 " pdb=" CB TYR D 232 " ideal model delta sigma weight residual 1.528 1.503 0.026 1.51e-02 4.39e+03 2.92e+00 bond pdb=" CA TYR B 232 " pdb=" CB TYR B 232 " ideal model delta sigma weight residual 1.528 1.503 0.026 1.51e-02 4.39e+03 2.89e+00 ... (remaining 26870 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 35357 1.21 - 2.41: 972 2.41 - 3.62: 181 3.62 - 4.82: 30 4.82 - 6.03: 10 Bond angle restraints: 36550 Sorted by residual: angle pdb=" C PHE A 129 " pdb=" N ARG A 130 " pdb=" CA ARG A 130 " ideal model delta sigma weight residual 121.54 127.57 -6.03 1.91e+00 2.74e-01 9.97e+00 angle pdb=" C PHE J 129 " pdb=" N ARG J 130 " pdb=" CA ARG J 130 " ideal model delta sigma weight residual 121.54 127.57 -6.03 1.91e+00 2.74e-01 9.97e+00 angle pdb=" C PHE C 129 " pdb=" N ARG C 130 " pdb=" CA ARG C 130 " ideal model delta sigma weight residual 121.54 127.56 -6.02 1.91e+00 2.74e-01 9.95e+00 angle pdb=" C PHE I 129 " pdb=" N ARG I 130 " pdb=" CA ARG I 130 " ideal model delta sigma weight residual 121.54 127.53 -5.99 1.91e+00 2.74e-01 9.84e+00 angle pdb=" C PHE D 129 " pdb=" N ARG D 130 " pdb=" CA ARG D 130 " ideal model delta sigma weight residual 121.54 127.52 -5.98 1.91e+00 2.74e-01 9.81e+00 ... (remaining 36545 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.81: 15674 30.81 - 61.62: 665 61.62 - 92.43: 41 92.43 - 123.24: 0 123.24 - 154.05: 1 Dihedral angle restraints: 16381 sinusoidal: 7088 harmonic: 9293 Sorted by residual: dihedral pdb=" C4' DT U 1 " pdb=" C3' DT U 1 " pdb=" O3' DT U 1 " pdb=" P DC U 2 " ideal model delta sinusoidal sigma weight residual 220.00 65.95 154.05 1 3.50e+01 8.16e-04 1.49e+01 dihedral pdb=" CA ASP H 316 " pdb=" CB ASP H 316 " pdb=" CG ASP H 316 " pdb=" OD1 ASP H 316 " ideal model delta sinusoidal sigma weight residual -30.00 -83.00 53.00 1 2.00e+01 2.50e-03 9.56e+00 dihedral pdb=" CA ASP A 316 " pdb=" CB ASP A 316 " pdb=" CG ASP A 316 " pdb=" OD1 ASP A 316 " ideal model delta sinusoidal sigma weight residual -30.00 -82.98 52.98 1 2.00e+01 2.50e-03 9.55e+00 ... (remaining 16378 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2289 0.028 - 0.057: 1210 0.057 - 0.085: 413 0.085 - 0.113: 214 0.113 - 0.141: 13 Chirality restraints: 4139 Sorted by residual: chirality pdb=" C3' DG T 2 " pdb=" C4' DG T 2 " pdb=" O3' DG T 2 " pdb=" C2' DG T 2 " both_signs ideal model delta sigma weight residual False -2.66 -2.52 -0.14 2.00e-01 2.50e+01 5.01e-01 chirality pdb=" CA VAL L3290 " pdb=" N VAL L3290 " pdb=" C VAL L3290 " pdb=" CB VAL L3290 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.75e-01 chirality pdb=" CA VAL M3290 " pdb=" N VAL M3290 " pdb=" C VAL M3290 " pdb=" CB VAL M3290 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.73e-01 ... (remaining 4136 not shown) Planarity restraints: 4521 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA T 18 " 0.015 2.00e-02 2.50e+03 6.92e-03 1.32e+00 pdb=" N9 DA T 18 " -0.016 2.00e-02 2.50e+03 pdb=" C8 DA T 18 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DA T 18 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DA T 18 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DA T 18 " 0.002 2.00e-02 2.50e+03 pdb=" N6 DA T 18 " 0.004 2.00e-02 2.50e+03 pdb=" N1 DA T 18 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA T 18 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DA T 18 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DA T 18 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA T 15 " 0.014 2.00e-02 2.50e+03 6.32e-03 1.10e+00 pdb=" N9 DA T 15 " -0.014 2.00e-02 2.50e+03 pdb=" C8 DA T 15 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DA T 15 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DA T 15 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DA T 15 " 0.001 2.00e-02 2.50e+03 pdb=" N6 DA T 15 " 0.005 2.00e-02 2.50e+03 pdb=" N1 DA T 15 " -0.000 2.00e-02 2.50e+03 pdb=" C2 DA T 15 " -0.000 2.00e-02 2.50e+03 pdb=" N3 DA T 15 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DA T 15 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG E 167 " -0.017 5.00e-02 4.00e+02 2.51e-02 1.01e+00 pdb=" N PRO E 168 " 0.043 5.00e-02 4.00e+02 pdb=" CA PRO E 168 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO E 168 " -0.014 5.00e-02 4.00e+02 ... (remaining 4518 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 932 2.70 - 3.25: 26667 3.25 - 3.80: 41632 3.80 - 4.35: 59171 4.35 - 4.90: 95745 Nonbonded interactions: 224147 Sorted by model distance: nonbonded pdb=" OG1 THR G 134 " pdb="CA CA G 401 " model vdw 2.152 2.510 nonbonded pdb=" OG1 THR I 134 " pdb="CA CA I 401 " model vdw 2.152 2.510 nonbonded pdb=" OG1 THR H 134 " pdb="CA CA H 401 " model vdw 2.152 2.510 nonbonded pdb=" OG1 THR D 134 " pdb="CA CA D 401 " model vdw 2.152 2.510 nonbonded pdb=" OG1 THR C 134 " pdb="CA CA C 401 " model vdw 2.152 2.510 ... (remaining 224142 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 21 through 339 or resid 401 through 402)) selection = (chain 'B' and (resid 21 through 339 or resid 400 through 401)) selection = (chain 'C' and (resid 21 through 339 or resid 400 through 401)) selection = (chain 'D' and (resid 21 through 339 or resid 400 through 401)) selection = (chain 'E' and (resid 21 through 339 or resid 400 through 401)) selection = (chain 'F' and (resid 21 through 339 or resid 400 through 401)) selection = (chain 'G' and (resid 21 through 339 or resid 400 through 401)) selection = (chain 'H' and (resid 21 through 339 or resid 400 through 401)) selection = (chain 'I' and (resid 21 through 339 or resid 400 through 401)) selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } 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 individual isotropic 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: 0.520 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: 1.150 Check model and map are aligned: 0.210 Set scattering table: 0.280 Process input model: 62.210 Find NCS groups from input model: 1.840 Set up NCS constraints: 0.130 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:13.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 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 : 0.007 0.041 26875 Z= 0.327 Angle : 0.522 6.030 36550 Z= 0.283 Chirality : 0.041 0.141 4139 Planarity : 0.003 0.025 4521 Dihedral : 15.391 154.054 10413 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.23 % Favored : 93.46 % Rotamer: Outliers : 1.92 % Allowed : 6.14 % Favored : 91.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.28 (0.11), residues: 3196 helix: -2.99 (0.09), residues: 1360 sheet: -2.18 (0.23), residues: 480 loop : -2.77 (0.12), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS C 294 PHE 0.009 0.001 PHE G 126 TYR 0.009 0.001 TYR B 301 ARG 0.004 0.001 ARG I 229 Details of bonding type rmsd hydrogen bonds : bond 0.25628 ( 1159) hydrogen bonds : angle 9.18582 ( 3100) covalent geometry : bond 0.00738 (26875) covalent geometry : angle 0.52157 (36550) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 924 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 874 time to evaluate : 3.056 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 LYS cc_start: 0.7490 (mtpp) cc_final: 0.6507 (mtpt) REVERT: A 68 GLU cc_start: 0.7149 (mt-10) cc_final: 0.6575 (tm-30) REVERT: A 94 GLN cc_start: 0.8543 (mm-40) cc_final: 0.8224 (mt0) REVERT: A 176 GLU cc_start: 0.7254 (mm-30) cc_final: 0.6973 (mm-30) REVERT: A 202 GLN cc_start: 0.8343 (mm-40) cc_final: 0.8085 (tt0) REVERT: A 247 ARG cc_start: 0.8231 (mtp-110) cc_final: 0.7992 (mmm-85) REVERT: A 303 ARG cc_start: 0.7845 (mtp180) cc_final: 0.7607 (mtm180) REVERT: A 329 ILE cc_start: 0.8060 (mt) cc_final: 0.7774 (mt) REVERT: B 26 SER cc_start: 0.7862 (p) cc_final: 0.7366 (p) REVERT: B 33 ILE cc_start: 0.8471 (mm) cc_final: 0.8228 (mm) REVERT: B 42 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7296 (mt-10) REVERT: B 43 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7352 (pp20) REVERT: B 94 GLN cc_start: 0.8369 (mm-40) cc_final: 0.8078 (mm-40) REVERT: B 95 ARG cc_start: 0.8061 (ttp80) cc_final: 0.7741 (ttt-90) REVERT: B 206 GLN cc_start: 0.8094 (mt0) cc_final: 0.7863 (mt0) REVERT: B 232 TYR cc_start: 0.9070 (m-80) cc_final: 0.8851 (m-80) REVERT: C 82 VAL cc_start: 0.9006 (OUTLIER) cc_final: 0.8796 (p) REVERT: C 94 GLN cc_start: 0.8010 (mm-40) cc_final: 0.7421 (tp40) REVERT: C 95 ARG cc_start: 0.8339 (ttp80) cc_final: 0.7782 (ttp-170) REVERT: C 107 LYS cc_start: 0.8249 (mmtm) cc_final: 0.7905 (ptpp) REVERT: C 154 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7230 (mt-10) REVERT: C 202 GLN cc_start: 0.8214 (mm-40) cc_final: 0.7717 (mt0) REVERT: C 216 TYR cc_start: 0.8968 (m-80) cc_final: 0.8728 (m-80) REVERT: C 232 TYR cc_start: 0.9196 (m-80) cc_final: 0.8853 (m-80) REVERT: C 251 MET cc_start: 0.8319 (ttm) cc_final: 0.8069 (tpt) REVERT: D 34 ASN cc_start: 0.6981 (OUTLIER) cc_final: 0.6510 (t0) REVERT: D 37 ASP cc_start: 0.6792 (m-30) cc_final: 0.6461 (m-30) REVERT: D 57 LYS cc_start: 0.8277 (tttp) cc_final: 0.8071 (ttpt) REVERT: D 68 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7624 (tp30) REVERT: D 94 GLN cc_start: 0.7989 (mm-40) cc_final: 0.7377 (tm-30) REVERT: D 107 LYS cc_start: 0.8382 (mmtm) cc_final: 0.8164 (mtmt) REVERT: D 181 SER cc_start: 0.8642 (t) cc_final: 0.8438 (t) REVERT: D 330 ASN cc_start: 0.9052 (m-40) cc_final: 0.8818 (m110) REVERT: E 34 ASN cc_start: 0.7170 (OUTLIER) cc_final: 0.6862 (t160) REVERT: E 81 LEU cc_start: 0.8800 (mt) cc_final: 0.8511 (mt) REVERT: E 107 LYS cc_start: 0.8218 (mmtm) cc_final: 0.7751 (ttmt) REVERT: E 196 ASN cc_start: 0.8771 (p0) cc_final: 0.8427 (p0) REVERT: E 202 GLN cc_start: 0.8224 (mm-40) cc_final: 0.7673 (mt0) REVERT: E 211 MET cc_start: 0.9097 (mtt) cc_final: 0.8816 (mtt) REVERT: E 243 MET cc_start: 0.9050 (mtm) cc_final: 0.8715 (mtt) REVERT: E 251 MET cc_start: 0.8280 (ttm) cc_final: 0.8079 (ttm) REVERT: E 272 GLN cc_start: 0.8518 (pt0) cc_final: 0.8250 (mt0) REVERT: E 296 SER cc_start: 0.8815 (p) cc_final: 0.8537 (m) REVERT: F 26 SER cc_start: 0.9037 (p) cc_final: 0.8799 (m) REVERT: F 39 LYS cc_start: 0.7952 (mttt) cc_final: 0.7403 (mtpp) REVERT: F 68 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8158 (mp0) REVERT: F 95 ARG cc_start: 0.8440 (ttp80) cc_final: 0.8073 (ttp-110) REVERT: F 158 MET cc_start: 0.9055 (ttm) cc_final: 0.8816 (ttp) REVERT: F 202 GLN cc_start: 0.8594 (mm-40) cc_final: 0.8028 (mt0) REVERT: F 206 GLN cc_start: 0.8854 (mt0) cc_final: 0.8503 (mt0) REVERT: F 253 LEU cc_start: 0.8913 (tp) cc_final: 0.8673 (tp) REVERT: G 39 LYS cc_start: 0.8363 (mttt) cc_final: 0.7928 (mtpp) REVERT: G 107 LYS cc_start: 0.7294 (mmtm) cc_final: 0.7081 (ttmm) REVERT: G 187 ASP cc_start: 0.8754 (m-30) cc_final: 0.8523 (m-30) REVERT: G 202 GLN cc_start: 0.8542 (mm-40) cc_final: 0.8186 (mt0) REVERT: G 285 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8542 (ptmt) REVERT: G 308 GLU cc_start: 0.8295 (pm20) cc_final: 0.8087 (pm20) REVERT: H 27 ARG cc_start: 0.8046 (mtp-110) cc_final: 0.7366 (tmt170) REVERT: H 39 LYS cc_start: 0.8642 (mttt) cc_final: 0.8285 (mtpm) REVERT: H 94 GLN cc_start: 0.8632 (mm-40) cc_final: 0.8390 (tp40) REVERT: H 125 MET cc_start: 0.8665 (mtp) cc_final: 0.8388 (mtm) REVERT: H 158 MET cc_start: 0.8720 (ttm) cc_final: 0.8329 (ttm) REVERT: H 187 ASP cc_start: 0.8631 (m-30) cc_final: 0.8408 (m-30) REVERT: H 254 ARG cc_start: 0.8386 (ttt-90) cc_final: 0.8103 (tmm-80) REVERT: I 27 ARG cc_start: 0.8444 (mtp-110) cc_final: 0.8224 (mtp-110) REVERT: I 33 ILE cc_start: 0.8221 (mm) cc_final: 0.7936 (mm) REVERT: I 39 LYS cc_start: 0.8739 (mttt) cc_final: 0.8394 (mmmm) REVERT: I 40 LYS cc_start: 0.8562 (mtpp) cc_final: 0.8065 (mtmm) REVERT: I 50 GLU cc_start: 0.8810 (mp0) cc_final: 0.8574 (mp0) REVERT: I 94 GLN cc_start: 0.8826 (mm-40) cc_final: 0.8549 (tp40) REVERT: I 125 MET cc_start: 0.8812 (mtp) cc_final: 0.8498 (mtp) REVERT: I 223 SER cc_start: 0.9124 (t) cc_final: 0.8903 (t) REVERT: I 247 ARG cc_start: 0.8240 (mtp-110) cc_final: 0.8033 (mtp85) REVERT: I 285 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8684 (ptpt) REVERT: I 322 GLU cc_start: 0.7731 (tt0) cc_final: 0.7496 (tt0) REVERT: J 38 VAL cc_start: 0.8027 (t) cc_final: 0.7799 (m) REVERT: J 39 LYS cc_start: 0.8539 (mttt) cc_final: 0.7774 (mmmt) REVERT: J 40 LYS cc_start: 0.8232 (mtpp) cc_final: 0.7632 (mtpt) REVERT: J 50 GLU cc_start: 0.8500 (mp0) cc_final: 0.8120 (mp0) REVERT: J 73 LYS cc_start: 0.6797 (mttt) cc_final: 0.6358 (tptt) REVERT: J 101 GLN cc_start: 0.8832 (mt0) cc_final: 0.8478 (mt0) REVERT: J 112 LEU cc_start: 0.8659 (tp) cc_final: 0.8446 (tp) REVERT: J 184 ASP cc_start: 0.7989 (m-30) cc_final: 0.7787 (m-30) REVERT: J 231 ASP cc_start: 0.8638 (m-30) cc_final: 0.8397 (m-30) REVERT: J 249 LEU cc_start: 0.9057 (mt) cc_final: 0.8793 (mp) REVERT: J 308 GLU cc_start: 0.7778 (pm20) cc_final: 0.7514 (mt-10) REVERT: J 332 ASP cc_start: 0.8251 (p0) cc_final: 0.8019 (p0) outliers start: 50 outliers final: 5 residues processed: 900 average time/residue: 1.6294 time to fit residues: 1663.1258 Evaluate side-chains 623 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 613 time to evaluate : 2.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain D residue 34 ASN Chi-restraints excluded: chain E residue 34 ASN Chi-restraints excluded: chain G residue 285 LYS Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 149 ASP Chi-restraints excluded: chain I residue 285 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 272 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 135 optimal weight: 0.5980 chunk 83 optimal weight: 3.9990 chunk 165 optimal weight: 0.7980 chunk 130 optimal weight: 5.9990 chunk 253 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 188 optimal weight: 0.8980 chunk 293 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN A 244 HIS A 330 ASN B 145 GLN B 202 GLN B 244 HIS C 23 GLN C 30 GLN C 145 GLN C 244 HIS D 30 GLN D 135 GLN D 202 GLN D 244 HIS D 330 ASN ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 244 HIS F 244 HIS G 242 GLN ** H 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 34 ASN J 135 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.146245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.111964 restraints weight = 31989.661| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.98 r_work: 0.3139 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 26875 Z= 0.139 Angle : 0.508 6.578 36550 Z= 0.271 Chirality : 0.040 0.155 4139 Planarity : 0.004 0.035 4521 Dihedral : 14.047 148.169 4476 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.34 % Allowed : 17.53 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.13), residues: 3196 helix: -0.74 (0.12), residues: 1400 sheet: -1.37 (0.23), residues: 490 loop : -2.04 (0.14), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 244 PHE 0.011 0.001 PHE I 126 TYR 0.008 0.001 TYR I 301 ARG 0.008 0.001 ARG F 215 Details of bonding type rmsd hydrogen bonds : bond 0.04100 ( 1159) hydrogen bonds : angle 4.93965 ( 3100) covalent geometry : bond 0.00301 (26875) covalent geometry : angle 0.50815 (36550) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 822 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 735 time to evaluate : 3.249 Fit side-chains revert: symmetry clash REVERT: A 33 ILE cc_start: 0.7613 (mm) cc_final: 0.7245 (mp) REVERT: A 37 ASP cc_start: 0.7137 (m-30) cc_final: 0.6879 (m-30) REVERT: A 40 LYS cc_start: 0.6862 (mtpp) cc_final: 0.6140 (mtpt) REVERT: A 42 GLU cc_start: 0.6637 (pt0) cc_final: 0.6426 (pt0) REVERT: A 68 GLU cc_start: 0.6665 (mt-10) cc_final: 0.6035 (tm-30) REVERT: A 77 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7267 (mp0) REVERT: A 84 MET cc_start: 0.8865 (mtp) cc_final: 0.8653 (mtp) REVERT: A 107 LYS cc_start: 0.7137 (mmtm) cc_final: 0.6682 (mttm) REVERT: A 130 ARG cc_start: 0.7210 (OUTLIER) cc_final: 0.5603 (ptp90) REVERT: A 145 GLN cc_start: 0.8469 (mt0) cc_final: 0.8172 (mt0) REVERT: A 186 LEU cc_start: 0.8359 (mm) cc_final: 0.8145 (mm) REVERT: A 202 GLN cc_start: 0.8252 (mm-40) cc_final: 0.7883 (tt0) REVERT: A 210 MET cc_start: 0.7968 (mtp) cc_final: 0.7391 (mtp) REVERT: A 247 ARG cc_start: 0.7280 (mtp-110) cc_final: 0.6803 (mmm-85) REVERT: A 254 ARG cc_start: 0.7512 (ttp80) cc_final: 0.7147 (tmt90) REVERT: A 303 ARG cc_start: 0.7420 (mtp180) cc_final: 0.6738 (mtm180) REVERT: A 308 GLU cc_start: 0.7160 (pt0) cc_final: 0.6754 (tt0) REVERT: A 329 ILE cc_start: 0.8626 (mt) cc_final: 0.8189 (mt) REVERT: B 30 GLN cc_start: 0.6782 (mp10) cc_final: 0.6484 (mp10) REVERT: B 42 GLU cc_start: 0.7434 (mt-10) cc_final: 0.6950 (mt-10) REVERT: B 43 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7232 (mt-10) REVERT: B 59 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7680 (tt0) REVERT: B 95 ARG cc_start: 0.7846 (ttp80) cc_final: 0.7276 (ttt-90) REVERT: B 107 LYS cc_start: 0.7736 (mmtm) cc_final: 0.6866 (ptpt) REVERT: B 206 GLN cc_start: 0.7536 (mt0) cc_final: 0.7046 (mt0) REVERT: B 306 ARG cc_start: 0.7563 (tpp80) cc_final: 0.6935 (ptm-80) REVERT: B 324 GLU cc_start: 0.8304 (mt-10) cc_final: 0.8077 (mt-10) REVERT: B 332 ASP cc_start: 0.8815 (p0) cc_final: 0.8575 (p0) REVERT: B 334 VAL cc_start: 0.8995 (t) cc_final: 0.8794 (p) REVERT: C 80 LYS cc_start: 0.7937 (mtmm) cc_final: 0.7552 (ttpp) REVERT: C 82 VAL cc_start: 0.8902 (OUTLIER) cc_final: 0.8645 (p) REVERT: C 94 GLN cc_start: 0.7769 (mm-40) cc_final: 0.6987 (tp40) REVERT: C 95 ARG cc_start: 0.8193 (ttp80) cc_final: 0.7766 (ttm170) REVERT: C 107 LYS cc_start: 0.7871 (mmtm) cc_final: 0.7118 (ptpp) REVERT: C 154 GLU cc_start: 0.7751 (mt-10) cc_final: 0.6955 (mt-10) REVERT: C 181 SER cc_start: 0.8644 (t) cc_final: 0.8186 (p) REVERT: C 202 GLN cc_start: 0.7972 (mm-40) cc_final: 0.7426 (mt0) REVERT: C 216 TYR cc_start: 0.8983 (m-80) cc_final: 0.8620 (m-80) REVERT: C 222 ASP cc_start: 0.8783 (OUTLIER) cc_final: 0.8476 (t70) REVERT: C 251 MET cc_start: 0.8152 (ttm) cc_final: 0.7655 (mtt) REVERT: C 308 GLU cc_start: 0.8560 (pm20) cc_final: 0.8062 (pm20) REVERT: D 27 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.7422 (mtp180) REVERT: D 37 ASP cc_start: 0.7107 (m-30) cc_final: 0.6750 (m-30) REVERT: D 57 LYS cc_start: 0.7892 (tttp) cc_final: 0.7658 (ttpt) REVERT: D 68 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7701 (tp30) REVERT: D 94 GLN cc_start: 0.7610 (mm-40) cc_final: 0.6870 (tm-30) REVERT: D 107 LYS cc_start: 0.8311 (mmtm) cc_final: 0.7950 (mtmt) REVERT: D 181 SER cc_start: 0.9025 (t) cc_final: 0.8494 (p) REVERT: D 187 ASP cc_start: 0.8965 (OUTLIER) cc_final: 0.8551 (t70) REVERT: D 334 VAL cc_start: 0.9191 (t) cc_final: 0.8886 (p) REVERT: E 68 GLU cc_start: 0.7833 (mp0) cc_final: 0.7331 (tp30) REVERT: E 98 GLU cc_start: 0.8434 (tp30) cc_final: 0.8181 (mm-30) REVERT: E 107 LYS cc_start: 0.8018 (mmtm) cc_final: 0.7568 (mtmt) REVERT: E 176 GLU cc_start: 0.8510 (mm-30) cc_final: 0.7993 (tt0) REVERT: E 202 GLN cc_start: 0.7916 (mm-40) cc_final: 0.7668 (mt0) REVERT: E 211 MET cc_start: 0.9094 (mtt) cc_final: 0.8804 (mtt) REVERT: F 39 LYS cc_start: 0.7375 (mttt) cc_final: 0.6597 (mtmt) REVERT: F 43 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7360 (mp0) REVERT: F 68 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7663 (mp0) REVERT: F 95 ARG cc_start: 0.8212 (ttp80) cc_final: 0.7894 (ttp-110) REVERT: F 187 ASP cc_start: 0.8745 (m-30) cc_final: 0.8512 (m-30) REVERT: F 202 GLN cc_start: 0.8112 (mm-40) cc_final: 0.7712 (mt0) REVERT: G 39 LYS cc_start: 0.7771 (mttt) cc_final: 0.7447 (mtpp) REVERT: G 94 GLN cc_start: 0.7815 (OUTLIER) cc_final: 0.7520 (tp-100) REVERT: G 98 GLU cc_start: 0.8244 (mm-30) cc_final: 0.8011 (mm-30) REVERT: G 107 LYS cc_start: 0.7115 (mmtm) cc_final: 0.6588 (ttmm) REVERT: G 176 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7875 (mm-30) REVERT: G 187 ASP cc_start: 0.8781 (m-30) cc_final: 0.8454 (m-30) REVERT: G 202 GLN cc_start: 0.8031 (mm-40) cc_final: 0.7749 (mt0) REVERT: G 247 ARG cc_start: 0.8193 (mtp-110) cc_final: 0.7841 (mtp85) REVERT: G 300 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8140 (mt) REVERT: G 308 GLU cc_start: 0.8316 (pm20) cc_final: 0.7977 (pm20) REVERT: H 27 ARG cc_start: 0.7729 (mtp-110) cc_final: 0.7287 (tmt170) REVERT: H 39 LYS cc_start: 0.7721 (mttt) cc_final: 0.7426 (mtpm) REVERT: H 66 ILE cc_start: 0.8376 (mm) cc_final: 0.8076 (mp) REVERT: H 94 GLN cc_start: 0.8492 (mm-40) cc_final: 0.8224 (tp40) REVERT: H 96 ARG cc_start: 0.7816 (ttt90) cc_final: 0.7558 (ttt180) REVERT: H 187 ASP cc_start: 0.8562 (m-30) cc_final: 0.8340 (m-30) REVERT: H 205 TYR cc_start: 0.8644 (m-80) cc_final: 0.8371 (m-10) REVERT: H 210 MET cc_start: 0.8729 (mtp) cc_final: 0.8464 (mtm) REVERT: H 247 ARG cc_start: 0.7958 (mtp-110) cc_final: 0.7380 (mmm160) REVERT: H 254 ARG cc_start: 0.8092 (ttt-90) cc_final: 0.7827 (tmm-80) REVERT: H 258 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7942 (mt-10) REVERT: I 27 ARG cc_start: 0.8156 (mtp-110) cc_final: 0.7871 (mtp-110) REVERT: I 39 LYS cc_start: 0.8165 (mttt) cc_final: 0.7812 (mmmm) REVERT: I 40 LYS cc_start: 0.7695 (mtpp) cc_final: 0.7233 (mtmm) REVERT: I 50 GLU cc_start: 0.8641 (mp0) cc_final: 0.7767 (mp0) REVERT: I 90 THR cc_start: 0.8269 (OUTLIER) cc_final: 0.8042 (p) REVERT: I 110 ASP cc_start: 0.8637 (m-30) cc_final: 0.8340 (m-30) REVERT: I 154 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7815 (mt-10) REVERT: I 176 GLU cc_start: 0.7338 (mm-30) cc_final: 0.7030 (tm-30) REVERT: I 215 ARG cc_start: 0.7979 (tmm160) cc_final: 0.7760 (tmm160) REVERT: I 223 SER cc_start: 0.9344 (t) cc_final: 0.9130 (t) REVERT: I 247 ARG cc_start: 0.7861 (mtp-110) cc_final: 0.7422 (mtp85) REVERT: I 322 GLU cc_start: 0.8150 (tt0) cc_final: 0.7817 (tt0) REVERT: J 39 LYS cc_start: 0.7158 (mttt) cc_final: 0.6260 (mmmt) REVERT: J 40 LYS cc_start: 0.7011 (mtpp) cc_final: 0.6556 (mtpt) REVERT: J 42 GLU cc_start: 0.7078 (mt-10) cc_final: 0.6723 (tp30) REVERT: J 50 GLU cc_start: 0.7912 (mp0) cc_final: 0.7298 (mp0) REVERT: J 68 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7116 (tm-30) REVERT: J 73 LYS cc_start: 0.6827 (mttt) cc_final: 0.5970 (tptt) REVERT: J 77 GLU cc_start: 0.7178 (mp0) cc_final: 0.5990 (mp0) REVERT: J 95 ARG cc_start: 0.8075 (ttp-170) cc_final: 0.7677 (ttm110) REVERT: J 110 ASP cc_start: 0.8091 (m-30) cc_final: 0.7880 (m-30) REVERT: J 124 GLU cc_start: 0.9098 (tt0) cc_final: 0.8803 (tt0) REVERT: J 154 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7458 (mm-30) REVERT: J 183 SER cc_start: 0.8482 (m) cc_final: 0.8245 (m) REVERT: J 184 ASP cc_start: 0.8470 (m-30) cc_final: 0.8132 (m-30) REVERT: J 231 ASP cc_start: 0.8539 (m-30) cc_final: 0.8329 (m-30) REVERT: J 243 MET cc_start: 0.8712 (mtm) cc_final: 0.8506 (mtp) REVERT: J 247 ARG cc_start: 0.7377 (mtp-110) cc_final: 0.6697 (ttm-80) REVERT: J 258 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7134 (tp30) REVERT: J 308 GLU cc_start: 0.7861 (pm20) cc_final: 0.7056 (mt-10) REVERT: J 332 ASP cc_start: 0.8196 (p0) cc_final: 0.7837 (p0) outliers start: 87 outliers final: 29 residues processed: 778 average time/residue: 1.5439 time to fit residues: 1370.5851 Evaluate side-chains 680 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 642 time to evaluate : 2.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain B residue 31 CYS Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 272 GLN Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 272 GLN Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain F residue 97 SER Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 272 GLN Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 94 GLN Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain G residue 272 GLN Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 308 GLU Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 183 SER Chi-restraints excluded: chain I residue 201 THR Chi-restraints excluded: chain J residue 100 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 66.9243 > 50: distance: 49 - 54: 14.186 distance: 54 - 55: 19.374 distance: 54 - 109: 26.863 distance: 55 - 56: 42.390 distance: 55 - 58: 9.472 distance: 56 - 57: 27.174 distance: 56 - 61: 15.491 distance: 57 - 106: 48.201 distance: 58 - 59: 30.321 distance: 58 - 60: 47.702 distance: 61 - 62: 30.921 distance: 62 - 63: 7.810 distance: 62 - 65: 36.974 distance: 63 - 64: 42.193 distance: 63 - 66: 22.212 distance: 66 - 67: 10.683 distance: 67 - 68: 26.137 distance: 67 - 70: 6.301 distance: 68 - 69: 43.884 distance: 68 - 75: 18.041 distance: 70 - 71: 10.213 distance: 71 - 72: 5.491 distance: 72 - 73: 5.906 distance: 72 - 74: 10.344 distance: 75 - 76: 5.601 distance: 76 - 77: 12.586 distance: 76 - 79: 9.556 distance: 77 - 78: 16.478 distance: 77 - 82: 12.096 distance: 79 - 80: 8.683 distance: 79 - 81: 4.666 distance: 82 - 83: 5.498 distance: 84 - 85: 11.928 distance: 86 - 87: 9.843 distance: 87 - 88: 6.519 distance: 87 - 89: 7.624 distance: 90 - 91: 14.335 distance: 90 - 96: 23.761 distance: 91 - 92: 46.503 distance: 91 - 94: 26.163 distance: 92 - 93: 37.701 distance: 92 - 97: 19.154 distance: 94 - 95: 14.998 distance: 95 - 96: 13.112 distance: 97 - 98: 29.474 distance: 98 - 99: 17.111 distance: 98 - 101: 34.483 distance: 99 - 100: 41.054 distance: 99 - 106: 4.975 distance: 101 - 102: 45.877 distance: 102 - 103: 14.425 distance: 103 - 104: 14.230 distance: 104 - 105: 6.934 distance: 107 - 108: 30.813 distance: 107 - 110: 36.406 distance: 108 - 109: 23.673 distance: 108 - 115: 18.921 distance: 110 - 111: 36.344 distance: 111 - 112: 22.135 distance: 112 - 113: 9.156 distance: 113 - 114: 17.943 distance: 115 - 116: 23.762 distance: 115 - 121: 8.707 distance: 116 - 117: 25.990 distance: 116 - 119: 16.755 distance: 117 - 118: 54.269 distance: 117 - 122: 35.051 distance: 119 - 120: 31.460 distance: 120 - 121: 39.022 distance: 122 - 123: 42.422 distance: 123 - 124: 11.877 distance: 123 - 126: 11.930 distance: 124 - 125: 24.331 distance: 124 - 130: 20.488 distance: 126 - 127: 16.882 distance: 126 - 128: 20.264 distance: 127 - 129: 31.049