Starting phenix.real_space_refine on Fri Mar 15 19:11:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vde_43147/03_2024/8vde_43147.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vde_43147/03_2024/8vde_43147.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vde_43147/03_2024/8vde_43147.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vde_43147/03_2024/8vde_43147.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vde_43147/03_2024/8vde_43147.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vde_43147/03_2024/8vde_43147.pdb" } resolution = 3.4 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= 0.026 sd= 0.161 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: 4 Type Number sf(0) Gaussians S 247 5.16 5 C 44211 2.51 5 N 11699 2.21 5 O 14020 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B1 PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B1 PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q1 TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q1 ASP 208": "OD1" <-> "OD2" Residue "Q2 TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q2 PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 70177 Number of models: 1 Model: "" Number of chains: 27 Chain: "B1" Number of atoms: 2377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2377 Classifications: {'peptide': 298} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 284} Chain: "B2" Number of atoms: 2377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2377 Classifications: {'peptide': 298} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 284} Chain: "B3" Number of atoms: 2377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2377 Classifications: {'peptide': 298} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 284} Chain: "B4" Number of atoms: 2377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2377 Classifications: {'peptide': 298} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 284} Chain: "B5" Number of atoms: 2377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2377 Classifications: {'peptide': 298} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 284} Chain: "C1" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 276 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "C2" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 276 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "C3" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 276 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "C4" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 276 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "C5" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 276 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "D1" Number of atoms: 2101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2101 Classifications: {'peptide': 264} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 251} Chain breaks: 1 Chain: "D2" Number of atoms: 2101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2101 Classifications: {'peptide': 264} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 251} Chain breaks: 1 Chain: "D3" Number of atoms: 2101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2101 Classifications: {'peptide': 264} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 251} Chain breaks: 1 Chain: "D4" Number of atoms: 2101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2101 Classifications: {'peptide': 264} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 251} Chain breaks: 1 Chain: "D5" Number of atoms: 2101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2101 Classifications: {'peptide': 264} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 251} Chain breaks: 1 Chain: "P1" Number of atoms: 3941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3941 Classifications: {'peptide': 481} Link IDs: {'PTRANS': 10, 'TRANS': 470} Chain: "P2" Number of atoms: 3819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3819 Classifications: {'peptide': 466} Link IDs: {'PTRANS': 10, 'TRANS': 455} Chain: "P3" Number of atoms: 3941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3941 Classifications: {'peptide': 481} Link IDs: {'PTRANS': 10, 'TRANS': 470} Chain: "P4" Number of atoms: 3819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3819 Classifications: {'peptide': 466} Link IDs: {'PTRANS': 10, 'TRANS': 455} Chain: "P5" Number of atoms: 3819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3819 Classifications: {'peptide': 466} Link IDs: {'PTRANS': 10, 'TRANS': 455} Chain: "P6" Number of atoms: 3941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3941 Classifications: {'peptide': 481} Link IDs: {'PTRANS': 10, 'TRANS': 470} Chain: "P7" Number of atoms: 3819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3819 Classifications: {'peptide': 466} Link IDs: {'PTRANS': 10, 'TRANS': 455} Chain: "P8" Number of atoms: 3941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3941 Classifications: {'peptide': 481} Link IDs: {'PTRANS': 10, 'TRANS': 470} Chain: "P9" Number of atoms: 3819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3819 Classifications: {'peptide': 466} Link IDs: {'PTRANS': 10, 'TRANS': 455} Chain: "Q1" Number of atoms: 3910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3910 Classifications: {'peptide': 477} Link IDs: {'PTRANS': 10, 'TRANS': 466} Chain breaks: 1 Chain: "Q2" Number of atoms: 3819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3819 Classifications: {'peptide': 466} Link IDs: {'PTRANS': 10, 'TRANS': 455} Chain: "Q3" Number of atoms: 3819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3819 Classifications: {'peptide': 466} Link IDs: {'PTRANS': 10, 'TRANS': 455} Time building chain proxies: 25.80, per 1000 atoms: 0.37 Number of scatterers: 70177 At special positions: 0 Unit cell: (234.08, 236.74, 143.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 247 16.00 O 14020 8.00 N 11699 7.00 C 44211 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 20.32 Conformation dependent library (CDL) restraints added in 9.3 seconds 17154 Ramachandran restraints generated. 8577 Oldfield, 0 Emsley, 8577 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16406 Finding SS restraints... Secondary structure from input PDB file: 295 helices and 106 sheets defined 40.6% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.03 Creating SS restraints... Processing helix chain 'B1' and resid 55 through 61 Processing helix chain 'B1' and resid 116 through 122 Processing helix chain 'B1' and resid 125 through 147 Proline residue: B1 132 - end of helix Processing helix chain 'B1' and resid 158 through 167 Processing helix chain 'B1' and resid 175 through 188 removed outlier: 4.029A pdb=" N LEUB1 186 " --> pdb=" O LEUB1 182 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLUB1 187 " --> pdb=" O GLUB1 183 " (cutoff:3.500A) Processing helix chain 'B1' and resid 202 through 207 Processing helix chain 'B1' and resid 283 through 287 Processing helix chain 'B1' and resid 303 through 305 No H-bonds generated for 'chain 'B1' and resid 303 through 305' Processing helix chain 'B2' and resid 55 through 61 Processing helix chain 'B2' and resid 116 through 122 Processing helix chain 'B2' and resid 125 through 147 removed outlier: 3.562A pdb=" N GLUB2 129 " --> pdb=" O GLNB2 125 " (cutoff:3.500A) Proline residue: B2 132 - end of helix Processing helix chain 'B2' and resid 158 through 167 Processing helix chain 'B2' and resid 175 through 188 removed outlier: 4.045A pdb=" N LEUB2 186 " --> pdb=" O LEUB2 182 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLUB2 187 " --> pdb=" O GLUB2 183 " (cutoff:3.500A) Processing helix chain 'B2' and resid 202 through 207 Processing helix chain 'B3' and resid 55 through 61 Processing helix chain 'B3' and resid 116 through 122 Processing helix chain 'B3' and resid 125 through 147 removed outlier: 4.623A pdb=" N LYSB3 131 " --> pdb=" O PHEB3 127 " (cutoff:3.500A) Proline residue: B3 132 - end of helix Processing helix chain 'B3' and resid 158 through 167 Processing helix chain 'B3' and resid 175 through 188 removed outlier: 3.970A pdb=" N LEUB3 186 " --> pdb=" O LEUB3 182 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLUB3 187 " --> pdb=" O GLUB3 183 " (cutoff:3.500A) Processing helix chain 'B3' and resid 202 through 207 Processing helix chain 'B4' and resid 55 through 61 Processing helix chain 'B4' and resid 116 through 122 Processing helix chain 'B4' and resid 125 through 147 Proline residue: B4 132 - end of helix Processing helix chain 'B4' and resid 158 through 167 Processing helix chain 'B4' and resid 175 through 188 removed outlier: 4.017A pdb=" N LEUB4 186 " --> pdb=" O LEUB4 182 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLUB4 187 " --> pdb=" O GLUB4 183 " (cutoff:3.500A) Processing helix chain 'B4' and resid 202 through 208 removed outlier: 3.715A pdb=" N LYSB4 208 " --> pdb=" O SERB4 204 " (cutoff:3.500A) Processing helix chain 'B4' and resid 303 through 305 No H-bonds generated for 'chain 'B4' and resid 303 through 305' Processing helix chain 'B5' and resid 55 through 61 Processing helix chain 'B5' and resid 117 through 122 Processing helix chain 'B5' and resid 125 through 147 removed outlier: 3.523A pdb=" N LYSB5 131 " --> pdb=" O PHEB5 127 " (cutoff:3.500A) Proline residue: B5 132 - end of helix Processing helix chain 'B5' and resid 158 through 167 Processing helix chain 'B5' and resid 175 through 188 removed outlier: 3.983A pdb=" N LEUB5 186 " --> pdb=" O LEUB5 182 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLUB5 187 " --> pdb=" O GLUB5 183 " (cutoff:3.500A) Processing helix chain 'B5' and resid 202 through 207 Processing helix chain 'B5' and resid 283 through 287 Processing helix chain 'B5' and resid 303 through 305 No H-bonds generated for 'chain 'B5' and resid 303 through 305' Processing helix chain 'D1' and resid 55 through 61 Processing helix chain 'D1' and resid 116 through 121 Processing helix chain 'D1' and resid 125 through 147 removed outlier: 3.655A pdb=" N LYSD1 131 " --> pdb=" O PHED1 127 " (cutoff:3.500A) Proline residue: D1 132 - end of helix Processing helix chain 'D1' and resid 158 through 167 Processing helix chain 'D1' and resid 175 through 188 removed outlier: 3.851A pdb=" N LEUD1 186 " --> pdb=" O LEUD1 182 " (cutoff:3.500A) Processing helix chain 'D1' and resid 202 through 207 Processing helix chain 'D2' and resid 55 through 61 Processing helix chain 'D2' and resid 116 through 122 Processing helix chain 'D2' and resid 125 through 149 removed outlier: 3.702A pdb=" N LYSD2 131 " --> pdb=" O PHED2 127 " (cutoff:3.500A) Proline residue: D2 132 - end of helix Processing helix chain 'D2' and resid 158 through 167 Processing helix chain 'D2' and resid 175 through 188 removed outlier: 3.778A pdb=" N LEUD2 186 " --> pdb=" O LEUD2 182 " (cutoff:3.500A) Processing helix chain 'D2' and resid 202 through 207 Processing helix chain 'D3' and resid 55 through 61 Processing helix chain 'D3' and resid 116 through 121 Processing helix chain 'D3' and resid 125 through 130 Processing helix chain 'D3' and resid 130 through 147 Processing helix chain 'D3' and resid 158 through 167 Processing helix chain 'D3' and resid 175 through 188 removed outlier: 3.777A pdb=" N LEUD3 186 " --> pdb=" O LEUD3 182 " (cutoff:3.500A) Processing helix chain 'D3' and resid 202 through 207 Processing helix chain 'D4' and resid 55 through 61 Processing helix chain 'D4' and resid 116 through 121 Processing helix chain 'D4' and resid 125 through 149 removed outlier: 3.516A pdb=" N LYSD4 131 " --> pdb=" O PHED4 127 " (cutoff:3.500A) Proline residue: D4 132 - end of helix Processing helix chain 'D4' and resid 158 through 167 Processing helix chain 'D4' and resid 175 through 188 removed outlier: 3.825A pdb=" N LEUD4 186 " --> pdb=" O LEUD4 182 " (cutoff:3.500A) Processing helix chain 'D4' and resid 202 through 207 Processing helix chain 'D5' and resid 55 through 61 Processing helix chain 'D5' and resid 116 through 121 Processing helix chain 'D5' and resid 125 through 149 Proline residue: D5 132 - end of helix Processing helix chain 'D5' and resid 158 through 167 Processing helix chain 'D5' and resid 175 through 188 removed outlier: 3.883A pdb=" N LEUD5 186 " --> pdb=" O LEUD5 182 " (cutoff:3.500A) Processing helix chain 'D5' and resid 202 through 207 Processing helix chain 'P1' and resid 5 through 10 Processing helix chain 'P1' and resid 23 through 27 removed outlier: 4.386A pdb=" N ASNP1 26 " --> pdb=" O ASPP1 23 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VALP1 27 " --> pdb=" O GLUP1 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'P1' and resid 23 through 27' Processing helix chain 'P1' and resid 34 through 40 Processing helix chain 'P1' and resid 42 through 69 removed outlier: 4.474A pdb=" N ARGP1 57 " --> pdb=" O METP1 53 " (cutoff:3.500A) Proline residue: P1 58 - end of helix Processing helix chain 'P1' and resid 71 through 76 removed outlier: 3.618A pdb=" N VALP1 75 " --> pdb=" O THRP1 71 " (cutoff:3.500A) Processing helix chain 'P1' and resid 77 through 80 Processing helix chain 'P1' and resid 93 through 108 Processing helix chain 'P1' and resid 117 through 132 Processing helix chain 'P1' and resid 132 through 147 removed outlier: 3.563A pdb=" N SERP1 145 " --> pdb=" O GLYP1 141 " (cutoff:3.500A) Processing helix chain 'P1' and resid 261 through 282 removed outlier: 3.627A pdb=" N LEUP1 282 " --> pdb=" O TYRP1 278 " (cutoff:3.500A) Processing helix chain 'P1' and resid 299 through 305 removed outlier: 4.147A pdb=" N LYSP1 304 " --> pdb=" O ARGP1 301 " (cutoff:3.500A) Processing helix chain 'P1' and resid 338 through 357 Processing helix chain 'P1' and resid 361 through 365 removed outlier: 3.805A pdb=" N ASPP1 365 " --> pdb=" O METP1 362 " (cutoff:3.500A) Processing helix chain 'P1' and resid 371 through 380 removed outlier: 4.289A pdb=" N ALAP1 375 " --> pdb=" O GLNP1 371 " (cutoff:3.500A) Processing helix chain 'P1' and resid 380 through 412 removed outlier: 3.847A pdb=" N ARGP1 386 " --> pdb=" O GLYP1 382 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THRP1 389 " --> pdb=" O GLNP1 385 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARGP1 400 " --> pdb=" O LYSP1 396 " (cutoff:3.500A) Processing helix chain 'P1' and resid 435 through 445 Processing helix chain 'P1' and resid 451 through 459 removed outlier: 3.841A pdb=" N PHEP1 459 " --> pdb=" O LEUP1 455 " (cutoff:3.500A) Processing helix chain 'P1' and resid 466 through 479 removed outlier: 3.773A pdb=" N LYSP1 470 " --> pdb=" O GLUP1 466 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASPP1 475 " --> pdb=" O LYSP1 471 " (cutoff:3.500A) Processing helix chain 'P2' and resid 17 through 21 Processing helix chain 'P2' and resid 34 through 40 Processing helix chain 'P2' and resid 42 through 55 Processing helix chain 'P2' and resid 55 through 68 removed outlier: 3.890A pdb=" N ARGP2 59 " --> pdb=" O TYRP2 55 " (cutoff:3.500A) Processing helix chain 'P2' and resid 71 through 76 removed outlier: 3.769A pdb=" N VALP2 75 " --> pdb=" O THRP2 71 " (cutoff:3.500A) Processing helix chain 'P2' and resid 77 through 80 Processing helix chain 'P2' and resid 93 through 108 Processing helix chain 'P2' and resid 117 through 132 Processing helix chain 'P2' and resid 132 through 148 Processing helix chain 'P2' and resid 168 through 170 No H-bonds generated for 'chain 'P2' and resid 168 through 170' Processing helix chain 'P2' and resid 223 through 225 No H-bonds generated for 'chain 'P2' and resid 223 through 225' Processing helix chain 'P2' and resid 258 through 260 No H-bonds generated for 'chain 'P2' and resid 258 through 260' Processing helix chain 'P2' and resid 261 through 282 removed outlier: 3.554A pdb=" N LEUP2 282 " --> pdb=" O TYRP2 278 " (cutoff:3.500A) Processing helix chain 'P2' and resid 298 through 305 removed outlier: 4.202A pdb=" N LYSP2 304 " --> pdb=" O ARGP2 301 " (cutoff:3.500A) Processing helix chain 'P2' and resid 338 through 357 Processing helix chain 'P2' and resid 361 through 365 removed outlier: 3.928A pdb=" N ASPP2 365 " --> pdb=" O METP2 362 " (cutoff:3.500A) Processing helix chain 'P2' and resid 371 through 380 removed outlier: 3.724A pdb=" N LYSP2 377 " --> pdb=" O GLYP2 373 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N TYRP2 378 " --> pdb=" O GLUP2 374 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYSP2 379 " --> pdb=" O ALAP2 375 " (cutoff:3.500A) Processing helix chain 'P2' and resid 380 through 412 removed outlier: 3.929A pdb=" N ARGP2 386 " --> pdb=" O GLYP2 382 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THRP2 389 " --> pdb=" O GLNP2 385 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARGP2 400 " --> pdb=" O LYSP2 396 " (cutoff:3.500A) Processing helix chain 'P2' and resid 435 through 445 Processing helix chain 'P2' and resid 451 through 459 removed outlier: 3.802A pdb=" N PHEP2 459 " --> pdb=" O LEUP2 455 " (cutoff:3.500A) Processing helix chain 'P2' and resid 466 through 479 removed outlier: 3.853A pdb=" N LYSP2 470 " --> pdb=" O GLUP2 466 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASPP2 475 " --> pdb=" O LYSP2 471 " (cutoff:3.500A) Processing helix chain 'P3' and resid 2 through 6 removed outlier: 3.532A pdb=" N GLUP3 6 " --> pdb=" O LYSP3 3 " (cutoff:3.500A) Processing helix chain 'P3' and resid 34 through 40 Processing helix chain 'P3' and resid 42 through 55 Processing helix chain 'P3' and resid 55 through 68 removed outlier: 3.809A pdb=" N ARGP3 59 " --> pdb=" O TYRP3 55 " (cutoff:3.500A) Processing helix chain 'P3' and resid 71 through 76 removed outlier: 3.608A pdb=" N VALP3 75 " --> pdb=" O THRP3 71 " (cutoff:3.500A) Processing helix chain 'P3' and resid 77 through 80 Processing helix chain 'P3' and resid 93 through 108 Processing helix chain 'P3' and resid 117 through 132 Processing helix chain 'P3' and resid 132 through 147 Processing helix chain 'P3' and resid 168 through 170 No H-bonds generated for 'chain 'P3' and resid 168 through 170' Processing helix chain 'P3' and resid 258 through 260 No H-bonds generated for 'chain 'P3' and resid 258 through 260' Processing helix chain 'P3' and resid 261 through 282 Processing helix chain 'P3' and resid 298 through 305 removed outlier: 4.308A pdb=" N LYSP3 304 " --> pdb=" O ARGP3 301 " (cutoff:3.500A) Processing helix chain 'P3' and resid 338 through 356 Processing helix chain 'P3' and resid 361 through 365 removed outlier: 3.957A pdb=" N ASPP3 365 " --> pdb=" O METP3 362 " (cutoff:3.500A) Processing helix chain 'P3' and resid 371 through 380 removed outlier: 3.717A pdb=" N LYSP3 377 " --> pdb=" O GLYP3 373 " (cutoff:3.500A) Processing helix chain 'P3' and resid 380 through 412 removed outlier: 3.750A pdb=" N ARGP3 386 " --> pdb=" O GLYP3 382 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N THRP3 389 " --> pdb=" O GLNP3 385 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARGP3 400 " --> pdb=" O LYSP3 396 " (cutoff:3.500A) Processing helix chain 'P3' and resid 435 through 445 Processing helix chain 'P3' and resid 446 through 448 No H-bonds generated for 'chain 'P3' and resid 446 through 448' Processing helix chain 'P3' and resid 451 through 459 removed outlier: 3.830A pdb=" N PHEP3 459 " --> pdb=" O LEUP3 455 " (cutoff:3.500A) Processing helix chain 'P3' and resid 466 through 479 removed outlier: 3.753A pdb=" N LYSP3 470 " --> pdb=" O GLUP3 466 " (cutoff:3.500A) Processing helix chain 'P4' and resid 17 through 21 Processing helix chain 'P4' and resid 34 through 40 Processing helix chain 'P4' and resid 42 through 68 removed outlier: 4.471A pdb=" N ARGP4 57 " --> pdb=" O METP4 53 " (cutoff:3.500A) Proline residue: P4 58 - end of helix Processing helix chain 'P4' and resid 71 through 76 removed outlier: 3.609A pdb=" N VALP4 75 " --> pdb=" O THRP4 71 " (cutoff:3.500A) Processing helix chain 'P4' and resid 77 through 80 Processing helix chain 'P4' and resid 93 through 108 Processing helix chain 'P4' and resid 117 through 132 Processing helix chain 'P4' and resid 132 through 148 Processing helix chain 'P4' and resid 168 through 170 No H-bonds generated for 'chain 'P4' and resid 168 through 170' Processing helix chain 'P4' and resid 261 through 282 removed outlier: 3.606A pdb=" N LEUP4 282 " --> pdb=" O TYRP4 278 " (cutoff:3.500A) Processing helix chain 'P4' and resid 298 through 305 removed outlier: 4.222A pdb=" N LYSP4 304 " --> pdb=" O ARGP4 301 " (cutoff:3.500A) Processing helix chain 'P4' and resid 338 through 356 Processing helix chain 'P4' and resid 361 through 365 removed outlier: 3.969A pdb=" N ASPP4 365 " --> pdb=" O METP4 362 " (cutoff:3.500A) Processing helix chain 'P4' and resid 371 through 380 Processing helix chain 'P4' and resid 380 through 412 removed outlier: 3.840A pdb=" N ARGP4 386 " --> pdb=" O GLYP4 382 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THRP4 389 " --> pdb=" O GLNP4 385 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARGP4 400 " --> pdb=" O LYSP4 396 " (cutoff:3.500A) Processing helix chain 'P4' and resid 435 through 445 Processing helix chain 'P4' and resid 451 through 459 removed outlier: 3.828A pdb=" N PHEP4 459 " --> pdb=" O LEUP4 455 " (cutoff:3.500A) Processing helix chain 'P4' and resid 466 through 479 removed outlier: 3.803A pdb=" N LYSP4 470 " --> pdb=" O GLUP4 466 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASPP4 475 " --> pdb=" O LYSP4 471 " (cutoff:3.500A) Processing helix chain 'P5' and resid 17 through 21 Processing helix chain 'P5' and resid 34 through 40 Processing helix chain 'P5' and resid 42 through 69 removed outlier: 4.375A pdb=" N ARGP5 57 " --> pdb=" O METP5 53 " (cutoff:3.500A) Proline residue: P5 58 - end of helix Processing helix chain 'P5' and resid 71 through 76 removed outlier: 3.596A pdb=" N VALP5 75 " --> pdb=" O THRP5 71 " (cutoff:3.500A) Processing helix chain 'P5' and resid 77 through 80 Processing helix chain 'P5' and resid 93 through 108 Processing helix chain 'P5' and resid 117 through 132 Processing helix chain 'P5' and resid 132 through 147 Processing helix chain 'P5' and resid 168 through 170 No H-bonds generated for 'chain 'P5' and resid 168 through 170' Processing helix chain 'P5' and resid 258 through 260 No H-bonds generated for 'chain 'P5' and resid 258 through 260' Processing helix chain 'P5' and resid 261 through 282 Processing helix chain 'P5' and resid 298 through 305 removed outlier: 4.205A pdb=" N LYSP5 304 " --> pdb=" O ARGP5 301 " (cutoff:3.500A) Processing helix chain 'P5' and resid 338 through 356 Processing helix chain 'P5' and resid 361 through 365 removed outlier: 3.923A pdb=" N ASPP5 365 " --> pdb=" O METP5 362 " (cutoff:3.500A) Processing helix chain 'P5' and resid 371 through 380 removed outlier: 3.515A pdb=" N METP5 376 " --> pdb=" O SERP5 372 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYSP5 379 " --> pdb=" O ALAP5 375 " (cutoff:3.500A) Processing helix chain 'P5' and resid 380 through 412 removed outlier: 3.823A pdb=" N ARGP5 386 " --> pdb=" O GLYP5 382 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THRP5 389 " --> pdb=" O GLNP5 385 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARGP5 400 " --> pdb=" O LYSP5 396 " (cutoff:3.500A) Processing helix chain 'P5' and resid 435 through 445 Processing helix chain 'P5' and resid 451 through 459 removed outlier: 3.782A pdb=" N PHEP5 459 " --> pdb=" O LEUP5 455 " (cutoff:3.500A) Processing helix chain 'P5' and resid 466 through 479 removed outlier: 3.752A pdb=" N LYSP5 470 " --> pdb=" O GLUP5 466 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASPP5 475 " --> pdb=" O LYSP5 471 " (cutoff:3.500A) Processing helix chain 'P6' and resid 2 through 6 Processing helix chain 'P6' and resid 34 through 40 Processing helix chain 'P6' and resid 42 through 56 Processing helix chain 'P6' and resid 56 through 68 removed outlier: 3.645A pdb=" N VALP6 62 " --> pdb=" O PROP6 58 " (cutoff:3.500A) Processing helix chain 'P6' and resid 71 through 76 removed outlier: 3.688A pdb=" N VALP6 75 " --> pdb=" O THRP6 71 " (cutoff:3.500A) Processing helix chain 'P6' and resid 77 through 80 Processing helix chain 'P6' and resid 93 through 108 Processing helix chain 'P6' and resid 117 through 132 Processing helix chain 'P6' and resid 132 through 148 Processing helix chain 'P6' and resid 261 through 282 removed outlier: 3.604A pdb=" N LEUP6 282 " --> pdb=" O TYRP6 278 " (cutoff:3.500A) Processing helix chain 'P6' and resid 298 through 306 removed outlier: 3.551A pdb=" N ARGP6 301 " --> pdb=" O VALP6 298 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LYSP6 304 " --> pdb=" O ARGP6 301 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALAP6 306 " --> pdb=" O GLNP6 303 " (cutoff:3.500A) Processing helix chain 'P6' and resid 338 through 358 Processing helix chain 'P6' and resid 361 through 365 removed outlier: 3.915A pdb=" N ASPP6 365 " --> pdb=" O METP6 362 " (cutoff:3.500A) Processing helix chain 'P6' and resid 371 through 380 removed outlier: 3.744A pdb=" N ALAP6 375 " --> pdb=" O GLNP6 371 " (cutoff:3.500A) Processing helix chain 'P6' and resid 380 through 412 removed outlier: 3.884A pdb=" N ARGP6 386 " --> pdb=" O GLYP6 382 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THRP6 389 " --> pdb=" O GLNP6 385 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARGP6 400 " --> pdb=" O LYSP6 396 " (cutoff:3.500A) Processing helix chain 'P6' and resid 435 through 445 Processing helix chain 'P6' and resid 451 through 459 removed outlier: 3.767A pdb=" N PHEP6 459 " --> pdb=" O LEUP6 455 " (cutoff:3.500A) Processing helix chain 'P6' and resid 466 through 479 removed outlier: 3.860A pdb=" N LYSP6 470 " --> pdb=" O GLUP6 466 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASPP6 475 " --> pdb=" O LYSP6 471 " (cutoff:3.500A) Processing helix chain 'P7' and resid 17 through 21 Processing helix chain 'P7' and resid 34 through 40 Processing helix chain 'P7' and resid 42 through 68 removed outlier: 4.351A pdb=" N ARGP7 57 " --> pdb=" O METP7 53 " (cutoff:3.500A) Proline residue: P7 58 - end of helix Processing helix chain 'P7' and resid 71 through 76 removed outlier: 3.637A pdb=" N VALP7 75 " --> pdb=" O THRP7 71 " (cutoff:3.500A) Processing helix chain 'P7' and resid 93 through 108 Processing helix chain 'P7' and resid 117 through 132 Processing helix chain 'P7' and resid 132 through 148 Processing helix chain 'P7' and resid 168 through 170 No H-bonds generated for 'chain 'P7' and resid 168 through 170' Processing helix chain 'P7' and resid 223 through 225 No H-bonds generated for 'chain 'P7' and resid 223 through 225' Processing helix chain 'P7' and resid 258 through 260 No H-bonds generated for 'chain 'P7' and resid 258 through 260' Processing helix chain 'P7' and resid 261 through 282 removed outlier: 3.529A pdb=" N LEUP7 282 " --> pdb=" O TYRP7 278 " (cutoff:3.500A) Processing helix chain 'P7' and resid 299 through 305 removed outlier: 4.227A pdb=" N LYSP7 304 " --> pdb=" O ARGP7 301 " (cutoff:3.500A) Processing helix chain 'P7' and resid 338 through 357 removed outlier: 3.623A pdb=" N THRP7 357 " --> pdb=" O ILEP7 353 " (cutoff:3.500A) Processing helix chain 'P7' and resid 361 through 365 removed outlier: 3.974A pdb=" N ASPP7 365 " --> pdb=" O METP7 362 " (cutoff:3.500A) Processing helix chain 'P7' and resid 371 through 380 removed outlier: 3.746A pdb=" N ALAP7 375 " --> pdb=" O GLNP7 371 " (cutoff:3.500A) Processing helix chain 'P7' and resid 380 through 412 removed outlier: 3.855A pdb=" N ARGP7 386 " --> pdb=" O GLYP7 382 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THRP7 389 " --> pdb=" O GLNP7 385 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARGP7 400 " --> pdb=" O LYSP7 396 " (cutoff:3.500A) Processing helix chain 'P7' and resid 435 through 445 Processing helix chain 'P7' and resid 451 through 458 removed outlier: 3.528A pdb=" N LEUP7 458 " --> pdb=" O THRP7 454 " (cutoff:3.500A) Processing helix chain 'P7' and resid 466 through 479 removed outlier: 3.892A pdb=" N LYSP7 470 " --> pdb=" O GLUP7 466 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASPP7 475 " --> pdb=" O LYSP7 471 " (cutoff:3.500A) Processing helix chain 'P8' and resid 2 through 6 Processing helix chain 'P8' and resid 34 through 40 Processing helix chain 'P8' and resid 42 through 68 removed outlier: 4.460A pdb=" N ARGP8 57 " --> pdb=" O METP8 53 " (cutoff:3.500A) Proline residue: P8 58 - end of helix Processing helix chain 'P8' and resid 71 through 77 removed outlier: 3.719A pdb=" N VALP8 75 " --> pdb=" O THRP8 71 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEUP8 77 " --> pdb=" O ASNP8 73 " (cutoff:3.500A) Processing helix chain 'P8' and resid 78 through 80 No H-bonds generated for 'chain 'P8' and resid 78 through 80' Processing helix chain 'P8' and resid 93 through 108 Processing helix chain 'P8' and resid 117 through 132 Processing helix chain 'P8' and resid 132 through 148 Processing helix chain 'P8' and resid 168 through 170 No H-bonds generated for 'chain 'P8' and resid 168 through 170' Processing helix chain 'P8' and resid 258 through 260 No H-bonds generated for 'chain 'P8' and resid 258 through 260' Processing helix chain 'P8' and resid 261 through 282 removed outlier: 3.585A pdb=" N LEUP8 282 " --> pdb=" O TYRP8 278 " (cutoff:3.500A) Processing helix chain 'P8' and resid 298 through 305 removed outlier: 4.179A pdb=" N LYSP8 304 " --> pdb=" O ARGP8 301 " (cutoff:3.500A) Processing helix chain 'P8' and resid 338 through 356 Processing helix chain 'P8' and resid 361 through 365 removed outlier: 3.912A pdb=" N ASPP8 365 " --> pdb=" O METP8 362 " (cutoff:3.500A) Processing helix chain 'P8' and resid 371 through 380 removed outlier: 3.730A pdb=" N TYRP8 378 " --> pdb=" O GLUP8 374 " (cutoff:3.500A) Processing helix chain 'P8' and resid 380 through 412 removed outlier: 3.831A pdb=" N ARGP8 386 " --> pdb=" O GLYP8 382 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THRP8 389 " --> pdb=" O GLNP8 385 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ARGP8 400 " --> pdb=" O LYSP8 396 " (cutoff:3.500A) Processing helix chain 'P8' and resid 435 through 445 Processing helix chain 'P8' and resid 451 through 459 removed outlier: 3.847A pdb=" N PHEP8 459 " --> pdb=" O LEUP8 455 " (cutoff:3.500A) Processing helix chain 'P8' and resid 466 through 479 removed outlier: 3.735A pdb=" N LYSP8 470 " --> pdb=" O GLUP8 466 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASPP8 475 " --> pdb=" O LYSP8 471 " (cutoff:3.500A) Processing helix chain 'P9' and resid 17 through 21 Processing helix chain 'P9' and resid 34 through 41 removed outlier: 3.510A pdb=" N ASNP9 41 " --> pdb=" O ASPP9 37 " (cutoff:3.500A) Processing helix chain 'P9' and resid 42 through 55 Processing helix chain 'P9' and resid 55 through 68 removed outlier: 3.879A pdb=" N ARGP9 59 " --> pdb=" O TYRP9 55 " (cutoff:3.500A) Processing helix chain 'P9' and resid 71 through 76 removed outlier: 3.574A pdb=" N VALP9 75 " --> pdb=" O THRP9 71 " (cutoff:3.500A) Processing helix chain 'P9' and resid 77 through 80 Processing helix chain 'P9' and resid 93 through 108 Processing helix chain 'P9' and resid 117 through 132 Processing helix chain 'P9' and resid 132 through 148 Processing helix chain 'P9' and resid 168 through 170 No H-bonds generated for 'chain 'P9' and resid 168 through 170' Processing helix chain 'P9' and resid 258 through 260 No H-bonds generated for 'chain 'P9' and resid 258 through 260' Processing helix chain 'P9' and resid 261 through 282 removed outlier: 3.572A pdb=" N LEUP9 282 " --> pdb=" O TYRP9 278 " (cutoff:3.500A) Processing helix chain 'P9' and resid 299 through 305 removed outlier: 4.089A pdb=" N LYSP9 304 " --> pdb=" O ARGP9 301 " (cutoff:3.500A) Processing helix chain 'P9' and resid 338 through 357 removed outlier: 3.580A pdb=" N THRP9 357 " --> pdb=" O ILEP9 353 " (cutoff:3.500A) Processing helix chain 'P9' and resid 361 through 365 removed outlier: 3.810A pdb=" N ASPP9 365 " --> pdb=" O METP9 362 " (cutoff:3.500A) Processing helix chain 'P9' and resid 371 through 380 removed outlier: 3.864A pdb=" N ALAP9 375 " --> pdb=" O GLNP9 371 " (cutoff:3.500A) Processing helix chain 'P9' and resid 380 through 412 removed outlier: 3.718A pdb=" N ARGP9 386 " --> pdb=" O GLYP9 382 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THRP9 389 " --> pdb=" O GLNP9 385 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARGP9 400 " --> pdb=" O LYSP9 396 " (cutoff:3.500A) Processing helix chain 'P9' and resid 435 through 445 Processing helix chain 'P9' and resid 451 through 459 removed outlier: 3.896A pdb=" N PHEP9 459 " --> pdb=" O LEUP9 455 " (cutoff:3.500A) Processing helix chain 'P9' and resid 466 through 479 removed outlier: 3.711A pdb=" N LYSP9 470 " --> pdb=" O GLUP9 466 " (cutoff:3.500A) Processing helix chain 'Q1' and resid 2 through 6 Processing helix chain 'Q1' and resid 17 through 21 Processing helix chain 'Q1' and resid 34 through 41 removed outlier: 3.581A pdb=" N ASNQ1 41 " --> pdb=" O ASPQ1 37 " (cutoff:3.500A) Processing helix chain 'Q1' and resid 42 through 68 removed outlier: 4.448A pdb=" N ARGQ1 57 " --> pdb=" O METQ1 53 " (cutoff:3.500A) Proline residue: Q1 58 - end of helix Processing helix chain 'Q1' and resid 71 through 76 removed outlier: 3.654A pdb=" N VALQ1 75 " --> pdb=" O THRQ1 71 " (cutoff:3.500A) Processing helix chain 'Q1' and resid 77 through 80 Processing helix chain 'Q1' and resid 93 through 108 Processing helix chain 'Q1' and resid 117 through 132 Processing helix chain 'Q1' and resid 132 through 147 Processing helix chain 'Q1' and resid 261 through 282 removed outlier: 3.554A pdb=" N LEUQ1 282 " --> pdb=" O TYRQ1 278 " (cutoff:3.500A) Processing helix chain 'Q1' and resid 298 through 305 removed outlier: 3.539A pdb=" N ARGQ1 301 " --> pdb=" O VALQ1 298 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LYSQ1 304 " --> pdb=" O ARGQ1 301 " (cutoff:3.500A) Processing helix chain 'Q1' and resid 338 through 357 removed outlier: 3.555A pdb=" N THRQ1 357 " --> pdb=" O ILEQ1 353 " (cutoff:3.500A) Processing helix chain 'Q1' and resid 361 through 365 removed outlier: 3.880A pdb=" N ASPQ1 365 " --> pdb=" O METQ1 362 " (cutoff:3.500A) Processing helix chain 'Q1' and resid 371 through 380 Processing helix chain 'Q1' and resid 380 through 412 removed outlier: 3.972A pdb=" N ARGQ1 386 " --> pdb=" O GLYQ1 382 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THRQ1 389 " --> pdb=" O GLNQ1 385 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARGQ1 400 " --> pdb=" O LYSQ1 396 " (cutoff:3.500A) Processing helix chain 'Q1' and resid 435 through 445 Processing helix chain 'Q1' and resid 451 through 459 removed outlier: 3.817A pdb=" N PHEQ1 459 " --> pdb=" O LEUQ1 455 " (cutoff:3.500A) Processing helix chain 'Q1' and resid 466 through 479 removed outlier: 3.755A pdb=" N LYSQ1 470 " --> pdb=" O GLUQ1 466 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASPQ1 475 " --> pdb=" O LYSQ1 471 " (cutoff:3.500A) Processing helix chain 'Q2' and resid 17 through 21 Processing helix chain 'Q2' and resid 34 through 40 Processing helix chain 'Q2' and resid 42 through 68 removed outlier: 4.449A pdb=" N ARGQ2 57 " --> pdb=" O METQ2 53 " (cutoff:3.500A) Proline residue: Q2 58 - end of helix Processing helix chain 'Q2' and resid 71 through 76 removed outlier: 3.582A pdb=" N VALQ2 75 " --> pdb=" O THRQ2 71 " (cutoff:3.500A) Processing helix chain 'Q2' and resid 77 through 80 Processing helix chain 'Q2' and resid 93 through 108 Processing helix chain 'Q2' and resid 117 through 132 Processing helix chain 'Q2' and resid 132 through 147 Processing helix chain 'Q2' and resid 168 through 170 No H-bonds generated for 'chain 'Q2' and resid 168 through 170' Processing helix chain 'Q2' and resid 258 through 260 No H-bonds generated for 'chain 'Q2' and resid 258 through 260' Processing helix chain 'Q2' and resid 261 through 282 removed outlier: 3.582A pdb=" N LEUQ2 282 " --> pdb=" O TYRQ2 278 " (cutoff:3.500A) Processing helix chain 'Q2' and resid 299 through 305 removed outlier: 4.112A pdb=" N LYSQ2 304 " --> pdb=" O ARGQ2 301 " (cutoff:3.500A) Processing helix chain 'Q2' and resid 338 through 356 Processing helix chain 'Q2' and resid 361 through 365 removed outlier: 3.974A pdb=" N ASPQ2 365 " --> pdb=" O METQ2 362 " (cutoff:3.500A) Processing helix chain 'Q2' and resid 373 through 380 Processing helix chain 'Q2' and resid 380 through 412 removed outlier: 3.906A pdb=" N ARGQ2 386 " --> pdb=" O GLYQ2 382 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THRQ2 389 " --> pdb=" O GLNQ2 385 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLYQ2 392 " --> pdb=" O LYSQ2 388 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARGQ2 400 " --> pdb=" O LYSQ2 396 " (cutoff:3.500A) Processing helix chain 'Q2' and resid 435 through 445 Processing helix chain 'Q2' and resid 451 through 459 removed outlier: 3.965A pdb=" N PHEQ2 459 " --> pdb=" O LEUQ2 455 " (cutoff:3.500A) Processing helix chain 'Q2' and resid 466 through 479 removed outlier: 3.773A pdb=" N LYSQ2 470 " --> pdb=" O GLUQ2 466 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASPQ2 475 " --> pdb=" O LYSQ2 471 " (cutoff:3.500A) Processing helix chain 'Q3' and resid 17 through 21 Processing helix chain 'Q3' and resid 34 through 40 Processing helix chain 'Q3' and resid 42 through 68 removed outlier: 4.394A pdb=" N ARGQ3 57 " --> pdb=" O METQ3 53 " (cutoff:3.500A) Proline residue: Q3 58 - end of helix Processing helix chain 'Q3' and resid 71 through 76 removed outlier: 3.676A pdb=" N VALQ3 75 " --> pdb=" O THRQ3 71 " (cutoff:3.500A) Processing helix chain 'Q3' and resid 77 through 80 Processing helix chain 'Q3' and resid 93 through 108 Processing helix chain 'Q3' and resid 117 through 132 Processing helix chain 'Q3' and resid 132 through 147 Processing helix chain 'Q3' and resid 168 through 170 No H-bonds generated for 'chain 'Q3' and resid 168 through 170' Processing helix chain 'Q3' and resid 258 through 260 No H-bonds generated for 'chain 'Q3' and resid 258 through 260' Processing helix chain 'Q3' and resid 261 through 282 removed outlier: 3.598A pdb=" N LEUQ3 282 " --> pdb=" O TYRQ3 278 " (cutoff:3.500A) Processing helix chain 'Q3' and resid 299 through 305 removed outlier: 4.081A pdb=" N LYSQ3 304 " --> pdb=" O ARGQ3 301 " (cutoff:3.500A) Processing helix chain 'Q3' and resid 338 through 356 Processing helix chain 'Q3' and resid 361 through 365 removed outlier: 3.905A pdb=" N ASPQ3 365 " --> pdb=" O METQ3 362 " (cutoff:3.500A) Processing helix chain 'Q3' and resid 371 through 380 removed outlier: 4.358A pdb=" N ALAQ3 375 " --> pdb=" O GLNQ3 371 " (cutoff:3.500A) Processing helix chain 'Q3' and resid 380 through 412 removed outlier: 3.834A pdb=" N ARGQ3 386 " --> pdb=" O GLYQ3 382 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THRQ3 389 " --> pdb=" O GLNQ3 385 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARGQ3 400 " --> pdb=" O LYSQ3 396 " (cutoff:3.500A) Processing helix chain 'Q3' and resid 435 through 445 Processing helix chain 'Q3' and resid 451 through 459 removed outlier: 3.927A pdb=" N PHEQ3 459 " --> pdb=" O LEUQ3 455 " (cutoff:3.500A) Processing helix chain 'Q3' and resid 466 through 479 removed outlier: 3.915A pdb=" N LYSQ3 470 " --> pdb=" O GLUQ3 466 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASPQ3 475 " --> pdb=" O LYSQ3 471 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B1' and resid 24 through 25 Processing sheet with id=AA2, first strand: chain 'B1' and resid 62 through 63 removed outlier: 6.685A pdb=" N HISB1 296 " --> pdb=" O PROB1 257 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N LEUB1 259 " --> pdb=" O THRB1 294 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N THRB1 294 " --> pdb=" O LEUB1 259 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N GLUB1 261 " --> pdb=" O ARGB1 292 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ARGB1 292 " --> pdb=" O GLUB1 261 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LYSB1 263 " --> pdb=" O ALAB1 290 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ALAB1 290 " --> pdb=" O LYSB1 263 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ASPB1 265 " --> pdb=" O METB1 288 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N METB1 288 " --> pdb=" O ASPB1 265 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEUB1 299 " --> pdb=" O ARGB1 104 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ARGB1 104 " --> pdb=" O LEUB1 299 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ILEB1 301 " --> pdb=" O THRB1 102 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N THRB1 102 " --> pdb=" O ILEB1 301 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N THRB1 97 " --> pdb=" O ALAB1 77 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B1' and resid 62 through 63 removed outlier: 6.685A pdb=" N HISB1 296 " --> pdb=" O PROB1 257 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N LEUB1 259 " --> pdb=" O THRB1 294 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N THRB1 294 " --> pdb=" O LEUB1 259 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N GLUB1 261 " --> pdb=" O ARGB1 292 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ARGB1 292 " --> pdb=" O GLUB1 261 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LYSB1 263 " --> pdb=" O ALAB1 290 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ALAB1 290 " --> pdb=" O LYSB1 263 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ASPB1 265 " --> pdb=" O METB1 288 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N METB1 288 " --> pdb=" O ASPB1 265 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEUB1 299 " --> pdb=" O ARGB1 104 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ARGB1 104 " --> pdb=" O LEUB1 299 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ILEB1 301 " --> pdb=" O THRB1 102 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N THRB1 102 " --> pdb=" O ILEB1 301 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LYSB1 107 " --> pdb=" O VALC1 85 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B1' and resid 83 through 85 removed outlier: 4.304A pdb=" N LYSD1 107 " --> pdb=" O VALB1 85 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N METD1 288 " --> pdb=" O ASPD1 265 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ASPD1 265 " --> pdb=" O METD1 288 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ALAD1 290 " --> pdb=" O LYSD1 263 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LYSD1 263 " --> pdb=" O ALAD1 290 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ARGD1 292 " --> pdb=" O GLUD1 261 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLUD1 261 " --> pdb=" O ARGD1 292 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N THRD1 294 " --> pdb=" O LEUD1 259 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N LEUD1 259 " --> pdb=" O THRD1 294 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N HISD1 296 " --> pdb=" O PROD1 257 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B1' and resid 169 through 171 removed outlier: 6.225A pdb=" N ILEB1 170 " --> pdb=" O VALB1 311 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SERB1 225 " --> pdb=" O ASPB1 220 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B2' and resid 24 through 25 removed outlier: 3.675A pdb=" N VALB2 281 " --> pdb=" O LEUB2 270 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B2' and resid 62 through 63 removed outlier: 6.471A pdb=" N HISB2 296 " --> pdb=" O PROB2 257 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N LEUB2 259 " --> pdb=" O THRB2 294 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N THRB2 294 " --> pdb=" O LEUB2 259 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLUB2 261 " --> pdb=" O ARGB2 292 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ARGB2 292 " --> pdb=" O GLUB2 261 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LYSB2 263 " --> pdb=" O ALAB2 290 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ALAB2 290 " --> pdb=" O LYSB2 263 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ASPB2 265 " --> pdb=" O METB2 288 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N METB2 288 " --> pdb=" O ASPB2 265 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LEUB2 299 " --> pdb=" O ARGB2 104 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N ARGB2 104 " --> pdb=" O LEUB2 299 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ILEB2 301 " --> pdb=" O THRB2 102 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N THRB2 102 " --> pdb=" O ILEB2 301 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N THRB2 97 " --> pdb=" O ALAB2 77 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B2' and resid 62 through 63 removed outlier: 6.471A pdb=" N HISB2 296 " --> pdb=" O PROB2 257 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N LEUB2 259 " --> pdb=" O THRB2 294 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N THRB2 294 " --> pdb=" O LEUB2 259 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLUB2 261 " --> pdb=" O ARGB2 292 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ARGB2 292 " --> pdb=" O GLUB2 261 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LYSB2 263 " --> pdb=" O ALAB2 290 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ALAB2 290 " --> pdb=" O LYSB2 263 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ASPB2 265 " --> pdb=" O METB2 288 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N METB2 288 " --> pdb=" O ASPB2 265 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LEUB2 299 " --> pdb=" O ARGB2 104 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N ARGB2 104 " --> pdb=" O LEUB2 299 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ILEB2 301 " --> pdb=" O THRB2 102 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N THRB2 102 " --> pdb=" O ILEB2 301 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B2' and resid 83 through 85 removed outlier: 3.959A pdb=" N LYSD2 107 " --> pdb=" O VALB2 85 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N METD2 288 " --> pdb=" O ASPD2 265 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ASPD2 265 " --> pdb=" O METD2 288 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ALAD2 290 " --> pdb=" O LYSD2 263 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LYSD2 263 " --> pdb=" O ALAD2 290 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ARGD2 292 " --> pdb=" O GLUD2 261 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLUD2 261 " --> pdb=" O ARGD2 292 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N THRD2 294 " --> pdb=" O LEUD2 259 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N LEUD2 259 " --> pdb=" O THRD2 294 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N HISD2 296 " --> pdb=" O PROD2 257 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B2' and resid 169 through 171 removed outlier: 3.585A pdb=" N SERB2 225 " --> pdb=" O ASPB2 220 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B3' and resid 24 through 25 Processing sheet with id=AB3, first strand: chain 'B3' and resid 62 through 63 removed outlier: 7.759A pdb=" N GLYB3 255 " --> pdb=" O HISB3 300 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N HISB3 300 " --> pdb=" O GLYB3 255 " (cutoff:3.500A) removed outlier: 9.170A pdb=" N ALAB3 298 " --> pdb=" O PROB3 257 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N LEUB3 259 " --> pdb=" O HISB3 296 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N HISB3 296 " --> pdb=" O LEUB3 259 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEUB3 299 " --> pdb=" O ARGB3 104 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ARGB3 104 " --> pdb=" O LEUB3 299 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ILEB3 301 " --> pdb=" O THRB3 102 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N THRB3 102 " --> pdb=" O ILEB3 301 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N THRB3 97 " --> pdb=" O ALAB3 77 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B3' and resid 62 through 63 removed outlier: 7.759A pdb=" N GLYB3 255 " --> pdb=" O HISB3 300 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N HISB3 300 " --> pdb=" O GLYB3 255 " (cutoff:3.500A) removed outlier: 9.170A pdb=" N ALAB3 298 " --> pdb=" O PROB3 257 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N LEUB3 259 " --> pdb=" O HISB3 296 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N HISB3 296 " --> pdb=" O LEUB3 259 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEUB3 299 " --> pdb=" O ARGB3 104 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ARGB3 104 " --> pdb=" O LEUB3 299 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ILEB3 301 " --> pdb=" O THRB3 102 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N THRB3 102 " --> pdb=" O ILEB3 301 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LYSB3 107 " --> pdb=" O VALC3 85 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B3' and resid 83 through 85 removed outlier: 4.227A pdb=" N LYSD3 107 " --> pdb=" O VALB3 85 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N METD3 288 " --> pdb=" O ASPD3 265 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ASPD3 265 " --> pdb=" O METD3 288 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ALAD3 290 " --> pdb=" O LYSD3 263 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LYSD3 263 " --> pdb=" O ALAD3 290 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ARGD3 292 " --> pdb=" O GLUD3 261 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLUD3 261 " --> pdb=" O ARGD3 292 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N THRD3 294 " --> pdb=" O LEUD3 259 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEUD3 259 " --> pdb=" O THRD3 294 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N HISD3 296 " --> pdb=" O PROD3 257 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B3' and resid 169 through 171 removed outlier: 6.195A pdb=" N ILEB3 170 " --> pdb=" O VALB3 311 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N PHEB3 196 " --> pdb=" O VALB3 232 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N LEUB3 234 " --> pdb=" O PHEB3 196 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N SERB3 198 " --> pdb=" O LEUB3 234 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SERB3 225 " --> pdb=" O ASPB3 220 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B4' and resid 24 through 25 Processing sheet with id=AB8, first strand: chain 'B4' and resid 62 through 63 removed outlier: 7.723A pdb=" N GLYB4 255 " --> pdb=" O HISB4 300 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N HISB4 300 " --> pdb=" O GLYB4 255 " (cutoff:3.500A) removed outlier: 9.077A pdb=" N ALAB4 298 " --> pdb=" O PROB4 257 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N LEUB4 259 " --> pdb=" O HISB4 296 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N HISB4 296 " --> pdb=" O LEUB4 259 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEUB4 299 " --> pdb=" O ARGB4 104 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ARGB4 104 " --> pdb=" O LEUB4 299 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ILEB4 301 " --> pdb=" O THRB4 102 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N THRB4 102 " --> pdb=" O ILEB4 301 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N THRB4 97 " --> pdb=" O ALAB4 77 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B4' and resid 62 through 63 removed outlier: 7.723A pdb=" N GLYB4 255 " --> pdb=" O HISB4 300 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N HISB4 300 " --> pdb=" O GLYB4 255 " (cutoff:3.500A) removed outlier: 9.077A pdb=" N ALAB4 298 " --> pdb=" O PROB4 257 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N LEUB4 259 " --> pdb=" O HISB4 296 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N HISB4 296 " --> pdb=" O LEUB4 259 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEUB4 299 " --> pdb=" O ARGB4 104 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ARGB4 104 " --> pdb=" O LEUB4 299 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ILEB4 301 " --> pdb=" O THRB4 102 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N THRB4 102 " --> pdb=" O ILEB4 301 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LYSB4 107 " --> pdb=" O VALC4 85 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B4' and resid 83 through 85 removed outlier: 3.691A pdb=" N LYSD4 107 " --> pdb=" O VALB4 85 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N METD4 288 " --> pdb=" O ASPD4 265 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ASPD4 265 " --> pdb=" O METD4 288 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ALAD4 290 " --> pdb=" O LYSD4 263 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LYSD4 263 " --> pdb=" O ALAD4 290 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ARGD4 292 " --> pdb=" O GLUD4 261 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLUD4 261 " --> pdb=" O ARGD4 292 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N THRD4 294 " --> pdb=" O LEUD4 259 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N LEUD4 259 " --> pdb=" O THRD4 294 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N HISD4 296 " --> pdb=" O PROD4 257 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B4' and resid 169 through 171 removed outlier: 6.197A pdb=" N ILEB4 170 " --> pdb=" O VALB4 311 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N PHEB4 196 " --> pdb=" O VALB4 232 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N LEUB4 234 " --> pdb=" O PHEB4 196 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N SERB4 198 " --> pdb=" O LEUB4 234 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SERB4 225 " --> pdb=" O ASPB4 220 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B5' and resid 24 through 25 removed outlier: 3.605A pdb=" N VALB5 281 " --> pdb=" O LEUB5 270 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B5' and resid 62 through 63 removed outlier: 7.783A pdb=" N GLYB5 255 " --> pdb=" O HISB5 300 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N HISB5 300 " --> pdb=" O GLYB5 255 " (cutoff:3.500A) removed outlier: 9.157A pdb=" N ALAB5 298 " --> pdb=" O PROB5 257 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N LEUB5 259 " --> pdb=" O HISB5 296 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N HISB5 296 " --> pdb=" O LEUB5 259 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEUB5 299 " --> pdb=" O ARGB5 104 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ARGB5 104 " --> pdb=" O LEUB5 299 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ILEB5 301 " --> pdb=" O THRB5 102 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N THRB5 102 " --> pdb=" O ILEB5 301 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N THRB5 97 " --> pdb=" O ALAB5 77 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B5' and resid 62 through 63 removed outlier: 7.783A pdb=" N GLYB5 255 " --> pdb=" O HISB5 300 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N HISB5 300 " --> pdb=" O GLYB5 255 " (cutoff:3.500A) removed outlier: 9.157A pdb=" N ALAB5 298 " --> pdb=" O PROB5 257 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N LEUB5 259 " --> pdb=" O HISB5 296 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N HISB5 296 " --> pdb=" O LEUB5 259 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEUB5 299 " --> pdb=" O ARGB5 104 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ARGB5 104 " --> pdb=" O LEUB5 299 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ILEB5 301 " --> pdb=" O THRB5 102 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N THRB5 102 " --> pdb=" O ILEB5 301 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LYSB5 107 " --> pdb=" O VALC5 85 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B5' and resid 83 through 85 removed outlier: 3.899A pdb=" N LYSD5 107 " --> pdb=" O VALB5 85 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B5' and resid 83 through 85 removed outlier: 3.899A pdb=" N LYSD5 107 " --> pdb=" O VALB5 85 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B5' and resid 169 through 171 removed outlier: 3.680A pdb=" N SERB5 225 " --> pdb=" O ASPB5 220 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C1' and resid 71 through 78 removed outlier: 6.180A pdb=" N THRC1 97 " --> pdb=" O ALAC1 77 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C2' and resid 71 through 78 removed outlier: 6.042A pdb=" N THRC2 97 " --> pdb=" O ALAC2 77 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C3' and resid 71 through 78 removed outlier: 6.250A pdb=" N THRC3 97 " --> pdb=" O ALAC3 77 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C4' and resid 71 through 78 removed outlier: 6.380A pdb=" N THRC4 97 " --> pdb=" O ALAC4 77 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C5' and resid 71 through 78 removed outlier: 6.263A pdb=" N THRC5 97 " --> pdb=" O ALAC5 77 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D1' and resid 169 through 171 removed outlier: 6.445A pdb=" N PHED1 196 " --> pdb=" O VALD1 232 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D1' and resid 210 through 211 removed outlier: 3.532A pdb=" N GLUD1 216 " --> pdb=" O ASPD1 211 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D1' and resid 269 through 274 removed outlier: 3.785A pdb=" N VALD1 281 " --> pdb=" O LEUD1 270 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D2' and resid 24 through 25 removed outlier: 3.855A pdb=" N VALD2 281 " --> pdb=" O LEUD2 270 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D2' and resid 169 through 171 removed outlier: 6.067A pdb=" N ILED2 170 " --> pdb=" O VALD2 311 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N PHED2 196 " --> pdb=" O VALD2 232 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D2' and resid 210 through 211 removed outlier: 3.637A pdb=" N GLUD2 216 " --> pdb=" O ASPD2 211 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D3' and resid 24 through 25 removed outlier: 3.618A pdb=" N VALD3 281 " --> pdb=" O LEUD3 270 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D3' and resid 169 through 171 removed outlier: 6.383A pdb=" N PHED3 196 " --> pdb=" O VALD3 232 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D3' and resid 210 through 211 removed outlier: 3.568A pdb=" N GLUD3 216 " --> pdb=" O ASPD3 211 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D4' and resid 24 through 25 removed outlier: 6.765A pdb=" N VALD4 273 " --> pdb=" O VALD4 281 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D4' and resid 169 through 171 removed outlier: 6.023A pdb=" N ILED4 170 " --> pdb=" O VALD4 311 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N PHED4 196 " --> pdb=" O VALD4 232 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D4' and resid 210 through 211 removed outlier: 3.573A pdb=" N GLUD4 216 " --> pdb=" O ASPD4 211 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D5' and resid 24 through 25 removed outlier: 3.759A pdb=" N VALD5 281 " --> pdb=" O LEUD5 270 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D5' and resid 169 through 171 removed outlier: 6.066A pdb=" N ILED5 170 " --> pdb=" O VALD5 311 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N PHED5 196 " --> pdb=" O VALD5 232 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N LEUD5 234 " --> pdb=" O PHED5 196 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N SERD5 198 " --> pdb=" O LEUD5 234 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D5' and resid 210 through 211 removed outlier: 3.551A pdb=" N GLUD5 216 " --> pdb=" O ASPD5 211 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'P1' and resid 30 through 31 removed outlier: 5.736A pdb=" N ASPP1 177 " --> pdb=" O SERP1 184 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N SERP1 184 " --> pdb=" O ASPP1 177 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N SERP1 234 " --> pdb=" O ARGP1 217 " (cutoff:3.500A) removed outlier: 8.989A pdb=" N LEUP1 219 " --> pdb=" O GLUP1 232 " (cutoff:3.500A) removed outlier: 9.311A pdb=" N GLUP1 232 " --> pdb=" O LEUP1 219 " (cutoff:3.500A) removed outlier: 11.160A pdb=" N ASNP1 221 " --> pdb=" O PROP1 230 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'P1' and resid 112 through 114 Processing sheet with id=AF4, first strand: chain 'P1' and resid 162 through 167 removed outlier: 4.163A pdb=" N TYRP1 151 " --> pdb=" O SERP1 167 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'P1' and resid 329 through 334 removed outlier: 3.833A pdb=" N ASPP1 329 " --> pdb=" O LYSP1 290 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'P1' and resid 308 through 311 Processing sheet with id=AF7, first strand: chain 'P1' and resid 315 through 317 Processing sheet with id=AF8, first strand: chain 'P2' and resid 29 through 31 removed outlier: 4.515A pdb=" N TYRP2 29 " --> pdb=" O ILEP2 174 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N ASPP2 177 " --> pdb=" O SERP2 184 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N SERP2 184 " --> pdb=" O ASPP2 177 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N SERP2 234 " --> pdb=" O ARGP2 217 " (cutoff:3.500A) removed outlier: 9.090A pdb=" N LEUP2 219 " --> pdb=" O GLUP2 232 " (cutoff:3.500A) removed outlier: 9.512A pdb=" N GLUP2 232 " --> pdb=" O LEUP2 219 " (cutoff:3.500A) removed outlier: 11.359A pdb=" N ASNP2 221 " --> pdb=" O PROP2 230 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'P2' and resid 112 through 114 Processing sheet with id=AG1, first strand: chain 'P2' and resid 162 through 167 removed outlier: 4.043A pdb=" N TYRP2 151 " --> pdb=" O SERP2 167 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'P2' and resid 308 through 311 removed outlier: 6.287A pdb=" N LEUP2 309 " --> pdb=" O ILEP3 289 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASPP3 329 " --> pdb=" O LYSP3 290 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'P2' and resid 315 through 317 Processing sheet with id=AG4, first strand: chain 'P3' and resid 30 through 31 removed outlier: 5.730A pdb=" N ASPP3 177 " --> pdb=" O SERP3 184 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N SERP3 184 " --> pdb=" O ASPP3 177 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N VALP3 204 " --> pdb=" O THRP3 193 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N SERP3 234 " --> pdb=" O ARGP3 217 " (cutoff:3.500A) removed outlier: 9.183A pdb=" N LEUP3 219 " --> pdb=" O GLUP3 232 " (cutoff:3.500A) removed outlier: 9.559A pdb=" N GLUP3 232 " --> pdb=" O LEUP3 219 " (cutoff:3.500A) removed outlier: 11.312A pdb=" N ASNP3 221 " --> pdb=" O PROP3 230 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'P3' and resid 112 through 114 Processing sheet with id=AG6, first strand: chain 'P3' and resid 162 through 167 removed outlier: 4.250A pdb=" N TYRP3 151 " --> pdb=" O SERP3 167 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'P3' and resid 308 through 310 removed outlier: 6.338A pdb=" N LEUP3 309 " --> pdb=" O ILEP4 289 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASPP4 329 " --> pdb=" O LYSP4 290 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'P3' and resid 315 through 317 Processing sheet with id=AG9, first strand: chain 'P4' and resid 29 through 31 removed outlier: 6.758A pdb=" N TYRP4 29 " --> pdb=" O TYRP4 176 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ASPP4 177 " --> pdb=" O SERP4 184 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N SERP4 184 " --> pdb=" O ASPP4 177 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N SERP4 234 " --> pdb=" O ARGP4 217 " (cutoff:3.500A) removed outlier: 8.965A pdb=" N LEUP4 219 " --> pdb=" O GLUP4 232 " (cutoff:3.500A) removed outlier: 9.438A pdb=" N GLUP4 232 " --> pdb=" O LEUP4 219 " (cutoff:3.500A) removed outlier: 11.324A pdb=" N ASNP4 221 " --> pdb=" O PROP4 230 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'P4' and resid 112 through 114 Processing sheet with id=AH2, first strand: chain 'P4' and resid 162 through 167 removed outlier: 4.047A pdb=" N TYRP4 151 " --> pdb=" O SERP4 167 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'P4' and resid 308 through 310 removed outlier: 6.433A pdb=" N LEUP4 309 " --> pdb=" O ILEP5 289 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASPP5 329 " --> pdb=" O LYSP5 290 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'P4' and resid 315 through 317 Processing sheet with id=AH5, first strand: chain 'P5' and resid 29 through 31 removed outlier: 6.851A pdb=" N TYRP5 29 " --> pdb=" O TYRP5 176 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N ASPP5 177 " --> pdb=" O SERP5 184 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N SERP5 184 " --> pdb=" O ASPP5 177 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N SERP5 234 " --> pdb=" O ARGP5 217 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N LEUP5 219 " --> pdb=" O GLUP5 232 " (cutoff:3.500A) removed outlier: 9.275A pdb=" N GLUP5 232 " --> pdb=" O LEUP5 219 " (cutoff:3.500A) removed outlier: 10.934A pdb=" N ASNP5 221 " --> pdb=" O PROP5 230 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'P5' and resid 112 through 114 Processing sheet with id=AH7, first strand: chain 'P5' and resid 162 through 167 removed outlier: 4.073A pdb=" N TYRP5 151 " --> pdb=" O SERP5 167 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'P5' and resid 308 through 310 removed outlier: 6.313A pdb=" N LEUP5 309 " --> pdb=" O ILEP6 289 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASPP6 329 " --> pdb=" O LYSP6 290 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'P5' and resid 315 through 317 Processing sheet with id=AI1, first strand: chain 'P6' and resid 30 through 31 removed outlier: 5.854A pdb=" N ASPP6 177 " --> pdb=" O SERP6 184 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N SERP6 184 " --> pdb=" O ASPP6 177 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N SERP6 234 " --> pdb=" O ARGP6 217 " (cutoff:3.500A) removed outlier: 9.117A pdb=" N LEUP6 219 " --> pdb=" O GLUP6 232 " (cutoff:3.500A) removed outlier: 9.327A pdb=" N GLUP6 232 " --> pdb=" O LEUP6 219 " (cutoff:3.500A) removed outlier: 11.255A pdb=" N ASNP6 221 " --> pdb=" O PROP6 230 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'P6' and resid 112 through 114 Processing sheet with id=AI3, first strand: chain 'P6' and resid 162 through 167 removed outlier: 4.080A pdb=" N TYRP6 151 " --> pdb=" O SERP6 167 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'P6' and resid 308 through 310 removed outlier: 6.368A pdb=" N LEUP6 309 " --> pdb=" O ILEP7 289 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASPP7 329 " --> pdb=" O LYSP7 290 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'P6' and resid 315 through 317 Processing sheet with id=AI6, first strand: chain 'P7' and resid 29 through 31 removed outlier: 4.445A pdb=" N TYRP7 29 " --> pdb=" O ILEP7 174 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ASPP7 177 " --> pdb=" O SERP7 184 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N SERP7 184 " --> pdb=" O ASPP7 177 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLYP7 214 " --> pdb=" O THRP7 211 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N SERP7 234 " --> pdb=" O ARGP7 217 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N LEUP7 219 " --> pdb=" O GLUP7 232 " (cutoff:3.500A) removed outlier: 9.319A pdb=" N GLUP7 232 " --> pdb=" O LEUP7 219 " (cutoff:3.500A) removed outlier: 11.280A pdb=" N ASNP7 221 " --> pdb=" O PROP7 230 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'P7' and resid 112 through 114 Processing sheet with id=AI8, first strand: chain 'P7' and resid 162 through 167 removed outlier: 4.085A pdb=" N TYRP7 151 " --> pdb=" O SERP7 167 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'P7' and resid 308 through 310 removed outlier: 6.371A pdb=" N LEUP7 309 " --> pdb=" O ILEP8 289 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASPP8 329 " --> pdb=" O LYSP8 290 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'P7' and resid 315 through 317 Processing sheet with id=AJ2, first strand: chain 'P8' and resid 30 through 31 removed outlier: 5.765A pdb=" N ASPP8 177 " --> pdb=" O SERP8 184 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N SERP8 184 " --> pdb=" O ASPP8 177 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N SERP8 234 " --> pdb=" O ARGP8 217 " (cutoff:3.500A) removed outlier: 9.032A pdb=" N LEUP8 219 " --> pdb=" O GLUP8 232 " (cutoff:3.500A) removed outlier: 9.230A pdb=" N GLUP8 232 " --> pdb=" O LEUP8 219 " (cutoff:3.500A) removed outlier: 11.487A pdb=" N ASNP8 221 " --> pdb=" O PROP8 230 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'P8' and resid 112 through 114 Processing sheet with id=AJ4, first strand: chain 'P8' and resid 162 through 167 removed outlier: 3.983A pdb=" N TYRP8 151 " --> pdb=" O SERP8 167 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'P8' and resid 308 through 310 removed outlier: 6.377A pdb=" N LEUP8 309 " --> pdb=" O ILEP9 289 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASPP9 329 " --> pdb=" O LYSP9 290 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'P8' and resid 315 through 317 Processing sheet with id=AJ7, first strand: chain 'P9' and resid 30 through 31 removed outlier: 5.714A pdb=" N ASPP9 177 " --> pdb=" O SERP9 184 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N SERP9 184 " --> pdb=" O ASPP9 177 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N SERP9 234 " --> pdb=" O ARGP9 217 " (cutoff:3.500A) removed outlier: 9.101A pdb=" N LEUP9 219 " --> pdb=" O GLUP9 232 " (cutoff:3.500A) removed outlier: 9.470A pdb=" N GLUP9 232 " --> pdb=" O LEUP9 219 " (cutoff:3.500A) removed outlier: 11.416A pdb=" N ASNP9 221 " --> pdb=" O PROP9 230 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'P9' and resid 112 through 114 Processing sheet with id=AJ9, first strand: chain 'P9' and resid 162 through 167 removed outlier: 4.062A pdb=" N TYRP9 151 " --> pdb=" O SERP9 167 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'P9' and resid 308 through 310 removed outlier: 6.356A pdb=" N LEUP9 309 " --> pdb=" O ILEQ1 289 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASPQ1 329 " --> pdb=" O LYSQ1 290 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'P9' and resid 315 through 317 Processing sheet with id=AK3, first strand: chain 'Q1' and resid 30 through 31 removed outlier: 6.591A pdb=" N PHEQ1 173 " --> pdb=" O GLYQ1 187 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N GLYQ1 187 " --> pdb=" O PHEQ1 173 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILEQ1 175 " --> pdb=" O ILEQ1 185 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N SERQ1 234 " --> pdb=" O ARGQ1 217 " (cutoff:3.500A) removed outlier: 8.794A pdb=" N LEUQ1 219 " --> pdb=" O GLUQ1 232 " (cutoff:3.500A) removed outlier: 9.263A pdb=" N GLUQ1 232 " --> pdb=" O LEUQ1 219 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'Q1' and resid 112 through 114 Processing sheet with id=AK5, first strand: chain 'Q1' and resid 162 through 167 removed outlier: 4.115A pdb=" N TYRQ1 151 " --> pdb=" O SERQ1 167 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'Q1' and resid 308 through 311 removed outlier: 6.306A pdb=" N LEUQ1 309 " --> pdb=" O ILEQ2 289 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASPQ2 329 " --> pdb=" O LYSQ2 290 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'Q1' and resid 315 through 317 Processing sheet with id=AK8, first strand: chain 'Q2' and resid 30 through 31 removed outlier: 5.736A pdb=" N ASPQ2 177 " --> pdb=" O SERQ2 184 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N SERQ2 184 " --> pdb=" O ASPQ2 177 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N VALQ2 215 " --> pdb=" O ASNQ2 233 " (cutoff:3.500A) removed outlier: 9.113A pdb=" N ASNQ2 233 " --> pdb=" O VALQ2 215 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ARGQ2 217 " --> pdb=" O ARGQ2 231 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARGQ2 231 " --> pdb=" O ARGQ2 217 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'Q2' and resid 112 through 114 Processing sheet with id=AL1, first strand: chain 'Q2' and resid 162 through 167 removed outlier: 4.064A pdb=" N TYRQ2 151 " --> pdb=" O SERQ2 167 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'Q2' and resid 308 through 311 removed outlier: 6.380A pdb=" N LEUQ2 309 " --> pdb=" O ILEQ3 289 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'Q2' and resid 315 through 317 Processing sheet with id=AL4, first strand: chain 'Q3' and resid 30 through 31 removed outlier: 5.803A pdb=" N ASPQ3 177 " --> pdb=" O SERQ3 184 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N SERQ3 184 " --> pdb=" O ASPQ3 177 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N SERQ3 234 " --> pdb=" O ARGQ3 217 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N LEUQ3 219 " --> pdb=" O GLUQ3 232 " (cutoff:3.500A) removed outlier: 9.574A pdb=" N GLUQ3 232 " --> pdb=" O LEUQ3 219 " (cutoff:3.500A) removed outlier: 10.991A pdb=" N ASNQ3 221 " --> pdb=" O PROQ3 230 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'Q3' and resid 112 through 114 Processing sheet with id=AL6, first strand: chain 'Q3' and resid 162 through 167 removed outlier: 4.031A pdb=" N TYRQ3 151 " --> pdb=" O SERQ3 167 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'Q3' and resid 315 through 317 3172 hydrogen bonds defined for protein. 9000 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: 26.50 Time building geometry restraints manager: 22.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 22996 1.34 - 1.45: 9610 1.45 - 1.57: 38313 1.57 - 1.69: 0 1.69 - 1.81: 494 Bond restraints: 71413 Sorted by residual: bond pdb=" N SERB2 16 " pdb=" CA SERB2 16 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.90e-02 2.77e+03 3.63e+00 bond pdb=" N SERB1 16 " pdb=" CA SERB1 16 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.19e+00 bond pdb=" N GLUC1 70 " pdb=" CA GLUC1 70 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.12e+00 bond pdb=" N SERD1 16 " pdb=" CA SERD1 16 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.12e+00 bond pdb=" N GLUC2 70 " pdb=" CA GLUC2 70 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.07e+00 ... (remaining 71408 not shown) Histogram of bond angle deviations from ideal: 97.22 - 104.59: 947 104.59 - 111.96: 32139 111.96 - 119.33: 27796 119.33 - 126.70: 34984 126.70 - 134.07: 455 Bond angle restraints: 96321 Sorted by residual: angle pdb=" N HISQ3 92 " pdb=" CA HISQ3 92 " pdb=" C HISQ3 92 " ideal model delta sigma weight residual 113.50 118.89 -5.39 1.23e+00 6.61e-01 1.92e+01 angle pdb=" N HISP7 92 " pdb=" CA HISP7 92 " pdb=" C HISP7 92 " ideal model delta sigma weight residual 113.23 118.31 -5.08 1.24e+00 6.50e-01 1.68e+01 angle pdb=" N HISP5 92 " pdb=" CA HISP5 92 " pdb=" C HISP5 92 " ideal model delta sigma weight residual 113.50 118.53 -5.03 1.23e+00 6.61e-01 1.67e+01 angle pdb=" N HISP4 92 " pdb=" CA HISP4 92 " pdb=" C HISP4 92 " ideal model delta sigma weight residual 113.38 118.03 -4.65 1.23e+00 6.61e-01 1.43e+01 angle pdb=" N HISP8 92 " pdb=" CA HISP8 92 " pdb=" C HISP8 92 " ideal model delta sigma weight residual 113.28 117.80 -4.52 1.22e+00 6.72e-01 1.37e+01 ... (remaining 96316 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 40207 17.84 - 35.68: 2660 35.68 - 53.51: 526 53.51 - 71.35: 158 71.35 - 89.19: 77 Dihedral angle restraints: 43628 sinusoidal: 18160 harmonic: 25468 Sorted by residual: dihedral pdb=" CA ILEP6 196 " pdb=" C ILEP6 196 " pdb=" N ASPP6 197 " pdb=" CA ASPP6 197 " ideal model delta harmonic sigma weight residual -180.00 -150.35 -29.65 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA THRP6 11 " pdb=" C THRP6 11 " pdb=" N ASPP6 12 " pdb=" CA ASPP6 12 " ideal model delta harmonic sigma weight residual -180.00 -150.93 -29.07 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA ASPP8 12 " pdb=" C ASPP8 12 " pdb=" N LEUP8 13 " pdb=" CA LEUP8 13 " ideal model delta harmonic sigma weight residual -180.00 -151.56 -28.44 0 5.00e+00 4.00e-02 3.24e+01 ... (remaining 43625 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 7172 0.047 - 0.095: 2642 0.095 - 0.142: 614 0.142 - 0.190: 90 0.190 - 0.237: 7 Chirality restraints: 10525 Sorted by residual: chirality pdb=" CA HISQ3 92 " pdb=" N HISQ3 92 " pdb=" C HISQ3 92 " pdb=" CB HISQ3 92 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA HISP5 92 " pdb=" N HISP5 92 " pdb=" C HISP5 92 " pdb=" CB HISP5 92 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA ILEP1 175 " pdb=" N ILEP1 175 " pdb=" C ILEP1 175 " pdb=" CB ILEP1 175 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 10522 not shown) Planarity restraints: 12635 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYSP2 290 " 0.019 2.00e-02 2.50e+03 3.82e-02 1.46e+01 pdb=" C LYSP2 290 " -0.066 2.00e-02 2.50e+03 pdb=" O LYSP2 290 " 0.025 2.00e-02 2.50e+03 pdb=" N GLYP2 291 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLYP3 141 " 0.019 2.00e-02 2.50e+03 3.78e-02 1.43e+01 pdb=" C GLYP3 141 " -0.065 2.00e-02 2.50e+03 pdb=" O GLYP3 141 " 0.024 2.00e-02 2.50e+03 pdb=" N LEUP3 142 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HISQ1 52 " 0.018 2.00e-02 2.50e+03 3.64e-02 1.32e+01 pdb=" C HISQ1 52 " -0.063 2.00e-02 2.50e+03 pdb=" O HISQ1 52 " 0.023 2.00e-02 2.50e+03 pdb=" N METQ1 53 " 0.021 2.00e-02 2.50e+03 ... (remaining 12632 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 13048 2.77 - 3.30: 68543 3.30 - 3.83: 110233 3.83 - 4.37: 136189 4.37 - 4.90: 234647 Nonbonded interactions: 562660 Sorted by model distance: nonbonded pdb=" ND2 ASNP1 283 " pdb=" O ALAQ3 306 " model vdw 2.235 2.520 nonbonded pdb=" OH TYRP4 105 " pdb=" OE1 GLUP4 384 " model vdw 2.269 2.440 nonbonded pdb=" OG SERP4 145 " pdb=" OD2 ASPP4 257 " model vdw 2.291 2.440 nonbonded pdb=" ND1 HISQ1 92 " pdb=" OD1 ASPQ1 269 " model vdw 2.310 2.520 nonbonded pdb=" OD1 ASNP3 224 " pdb=" N LEUP3 226 " model vdw 2.312 2.520 ... (remaining 562655 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'B1' and (resid 16 through 69 or resid 104 through 313)) selection = (chain 'B2' and (resid 16 through 69 or resid 104 through 313)) selection = (chain 'B3' and (resid 16 through 69 or resid 104 through 313)) selection = (chain 'B4' and (resid 16 through 69 or resid 104 through 313)) selection = (chain 'B5' and (resid 16 through 69 or resid 104 through 313)) selection = chain 'D1' selection = chain 'D2' selection = chain 'D3' selection = chain 'D4' selection = chain 'D5' } ncs_group { reference = chain 'C1' selection = chain 'C2' selection = chain 'C3' selection = chain 'C4' selection = chain 'C5' } ncs_group { reference = (chain 'P1' and resid 16 through 481) selection = chain 'P2' selection = (chain 'P3' and resid 16 through 481) selection = chain 'P4' selection = chain 'P5' selection = (chain 'P6' and resid 16 through 481) selection = chain 'P7' selection = (chain 'P8' and resid 16 through 481) selection = chain 'P9' selection = (chain 'Q1' and resid 16 through 481) selection = chain 'Q2' selection = chain 'Q3' } 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: 0.510 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: 0.070 Extract box with map and model: 5.800 Check model and map are aligned: 0.800 Set scattering table: 0.540 Process input model: 137.150 Find NCS groups from input model: 4.060 Set up NCS constraints: 0.270 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:2.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 151.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 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 : 0.006 0.042 71413 Z= 0.372 Angle : 0.856 6.761 96321 Z= 0.512 Chirality : 0.050 0.237 10525 Planarity : 0.010 0.130 12635 Dihedral : 13.484 89.191 27222 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.36 % Favored : 96.63 % Rotamer: Outliers : 0.09 % Allowed : 2.92 % Favored : 96.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.08), residues: 8577 helix: -1.46 (0.08), residues: 3173 sheet: 0.09 (0.12), residues: 1799 loop : -0.85 (0.09), residues: 3605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.005 TRPC2 84 HIS 0.015 0.003 HISQ2 238 PHE 0.050 0.004 PHEP9 173 TYR 0.046 0.006 TYRP8 66 ARG 0.023 0.004 ARGP2 163 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17154 Ramachandran restraints generated. 8577 Oldfield, 0 Emsley, 8577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17154 Ramachandran restraints generated. 8577 Oldfield, 0 Emsley, 8577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2398 residues out of total 7775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 2391 time to evaluate : 6.245 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B1 177 ASP cc_start: 0.6283 (t0) cc_final: 0.6074 (t70) REVERT: B1 194 ASN cc_start: 0.7901 (t0) cc_final: 0.7700 (t0) REVERT: B2 18 ASN cc_start: 0.5909 (t0) cc_final: 0.4371 (p0) REVERT: B2 54 ASN cc_start: 0.7318 (m-40) cc_final: 0.7013 (m110) REVERT: B2 89 GLN cc_start: 0.7544 (mm-40) cc_final: 0.7217 (mm-40) REVERT: B2 133 MET cc_start: 0.8685 (mtp) cc_final: 0.8142 (mtt) REVERT: B2 250 ASP cc_start: 0.7790 (m-30) cc_final: 0.7310 (p0) REVERT: B3 34 LYS cc_start: 0.8170 (mttt) cc_final: 0.7771 (mmmt) REVERT: B3 63 TYR cc_start: 0.7763 (t80) cc_final: 0.7534 (t80) REVERT: B3 240 LYS cc_start: 0.8472 (mmtm) cc_final: 0.8041 (tptp) REVERT: B3 279 THR cc_start: 0.8660 (m) cc_final: 0.8380 (p) REVERT: B4 25 ASN cc_start: 0.8466 (t0) cc_final: 0.7487 (p0) REVERT: B4 45 THR cc_start: 0.8107 (m) cc_final: 0.7847 (m) REVERT: B4 123 TYR cc_start: 0.7836 (t80) cc_final: 0.7106 (t80) REVERT: B4 130 MET cc_start: 0.7120 (mmp) cc_final: 0.6895 (mmp) REVERT: B5 49 GLN cc_start: 0.4736 (mm-40) cc_final: 0.4305 (tp40) REVERT: B5 162 SER cc_start: 0.9217 (m) cc_final: 0.8821 (t) REVERT: B5 215 LYS cc_start: 0.7933 (mttt) cc_final: 0.7330 (tttt) REVERT: C1 79 LYS cc_start: 0.8492 (mmtp) cc_final: 0.7180 (mtpt) REVERT: C1 93 THR cc_start: 0.7452 (p) cc_final: 0.7206 (p) REVERT: C2 83 TYR cc_start: 0.8057 (m-80) cc_final: 0.7761 (m-10) REVERT: C3 83 TYR cc_start: 0.6726 (m-80) cc_final: 0.6348 (m-80) REVERT: C5 71 LYS cc_start: 0.8211 (tptm) cc_final: 0.7808 (tppt) REVERT: C5 103 MET cc_start: 0.3050 (ttp) cc_final: 0.1617 (mtm) REVERT: D1 25 ASN cc_start: 0.7897 (t0) cc_final: 0.7606 (p0) REVERT: D1 58 MET cc_start: 0.7491 (mtt) cc_final: 0.7099 (mtt) REVERT: D2 40 MET cc_start: 0.1599 (mpp) cc_final: -0.1181 (tpp) REVERT: D3 231 VAL cc_start: 0.8758 (t) cc_final: 0.8461 (t) REVERT: D3 288 MET cc_start: 0.7571 (ttm) cc_final: 0.6838 (ttm) REVERT: D4 30 MET cc_start: 0.6071 (mmm) cc_final: 0.5778 (mmm) REVERT: D4 226 LEU cc_start: 0.7918 (tp) cc_final: 0.7475 (tt) REVERT: D5 30 MET cc_start: 0.6636 (mmm) cc_final: 0.6011 (mmp) REVERT: D5 40 MET cc_start: 0.0621 (mpp) cc_final: 0.0295 (mmp) REVERT: D5 64 GLU cc_start: 0.6259 (tp30) cc_final: 0.5965 (pt0) REVERT: D5 246 THR cc_start: 0.7264 (t) cc_final: 0.6767 (m) REVERT: P1 41 ASN cc_start: 0.8944 (m-40) cc_final: 0.8683 (m-40) REVERT: P1 89 ARG cc_start: 0.8633 (ptt180) cc_final: 0.8421 (mtm110) REVERT: P1 136 HIS cc_start: 0.8910 (t70) cc_final: 0.8532 (t-90) REVERT: P1 194 LYS cc_start: 0.8570 (ptmt) cc_final: 0.8364 (ptmm) REVERT: P1 302 LYS cc_start: 0.8698 (mtmt) cc_final: 0.8298 (pptt) REVERT: P1 438 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7900 (mt-10) REVERT: P1 441 LYS cc_start: 0.9034 (tmmt) cc_final: 0.8701 (ttpp) REVERT: P1 445 ASP cc_start: 0.8787 (m-30) cc_final: 0.8565 (m-30) REVERT: P1 468 GLU cc_start: 0.8940 (tp30) cc_final: 0.8295 (tp30) REVERT: P1 470 LYS cc_start: 0.9398 (mmmm) cc_final: 0.9045 (ptmt) REVERT: P1 471 LYS cc_start: 0.9165 (tttt) cc_final: 0.8814 (ttmt) REVERT: P2 40 GLN cc_start: 0.8711 (mt0) cc_final: 0.8427 (mt0) REVERT: P2 68 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8205 (mt-10) REVERT: P2 70 LYS cc_start: 0.8936 (mtpt) cc_final: 0.8651 (mtmm) REVERT: P2 115 ASP cc_start: 0.7774 (t0) cc_final: 0.7509 (t70) REVERT: P2 132 ASP cc_start: 0.8207 (t0) cc_final: 0.7740 (t0) REVERT: P2 170 MET cc_start: 0.9393 (mtm) cc_final: 0.9124 (mtt) REVERT: P2 227 LYS cc_start: 0.8955 (tppt) cc_final: 0.8576 (mttt) REVERT: P2 239 SER cc_start: 0.9387 (m) cc_final: 0.9116 (t) REVERT: P2 367 PHE cc_start: 0.5938 (t80) cc_final: 0.5327 (t80) REVERT: P2 439 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8336 (mt-10) REVERT: P2 467 LEU cc_start: 0.9353 (tp) cc_final: 0.8694 (tp) REVERT: P3 72 LYS cc_start: 0.8956 (ttpt) cc_final: 0.8724 (ttpp) REVERT: P3 121 LEU cc_start: 0.9239 (tp) cc_final: 0.8836 (mt) REVERT: P3 129 ASP cc_start: 0.8706 (t0) cc_final: 0.8441 (p0) REVERT: P3 293 LEU cc_start: 0.9071 (mt) cc_final: 0.8857 (tp) REVERT: P3 425 ARG cc_start: 0.8018 (mtm-85) cc_final: 0.7781 (mtt-85) REVERT: P3 438 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7998 (mm-30) REVERT: P3 456 MET cc_start: 0.8971 (mtt) cc_final: 0.8705 (mtt) REVERT: P3 468 GLU cc_start: 0.7893 (tp30) cc_final: 0.7048 (tp30) REVERT: P3 472 ILE cc_start: 0.8202 (mt) cc_final: 0.7911 (mp) REVERT: P3 476 GLU cc_start: 0.8394 (tt0) cc_final: 0.8046 (pt0) REVERT: P4 24 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8278 (mm-30) REVERT: P4 61 LYS cc_start: 0.8530 (tttt) cc_final: 0.8271 (tmtt) REVERT: P4 125 GLU cc_start: 0.8628 (tt0) cc_final: 0.8012 (tm-30) REVERT: P4 152 GLU cc_start: 0.8250 (pt0) cc_final: 0.7980 (pp20) REVERT: P4 215 VAL cc_start: 0.9255 (t) cc_final: 0.9049 (t) REVERT: P4 243 MET cc_start: 0.8891 (tmm) cc_final: 0.8653 (tmm) REVERT: P4 274 ASP cc_start: 0.9124 (t0) cc_final: 0.8795 (t0) REVERT: P4 279 MET cc_start: 0.8584 (mmm) cc_final: 0.8343 (mmm) REVERT: P4 376 MET cc_start: 0.9196 (mmm) cc_final: 0.8051 (mmp) REVERT: P4 416 ASP cc_start: 0.7749 (m-30) cc_final: 0.7367 (p0) REVERT: P4 428 TYR cc_start: 0.8744 (m-80) cc_final: 0.8401 (m-80) REVERT: P4 435 SER cc_start: 0.8265 (t) cc_final: 0.7897 (p) REVERT: P4 468 GLU cc_start: 0.8178 (tp30) cc_final: 0.7914 (tp30) REVERT: P4 471 LYS cc_start: 0.8872 (tttt) cc_final: 0.8120 (tttm) REVERT: P4 473 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8256 (mm-30) REVERT: P5 26 ASN cc_start: 0.8872 (t0) cc_final: 0.8377 (t0) REVERT: P5 37 ASP cc_start: 0.8357 (m-30) cc_final: 0.8144 (m-30) REVERT: P5 94 TYR cc_start: 0.8988 (m-80) cc_final: 0.8643 (m-80) REVERT: P5 115 ASP cc_start: 0.6688 (t0) cc_final: 0.6309 (t0) REVERT: P5 122 GLU cc_start: 0.8801 (pt0) cc_final: 0.8577 (pp20) REVERT: P5 132 ASP cc_start: 0.8447 (t0) cc_final: 0.7866 (t0) REVERT: P5 434 LYS cc_start: 0.8173 (mttt) cc_final: 0.7915 (mtpt) REVERT: P5 441 LYS cc_start: 0.8829 (tmmt) cc_final: 0.8585 (tppp) REVERT: P6 93 ASP cc_start: 0.8442 (t0) cc_final: 0.8190 (t0) REVERT: P6 149 LYS cc_start: 0.9301 (pttt) cc_final: 0.9082 (pttp) REVERT: P6 159 ASP cc_start: 0.8697 (m-30) cc_final: 0.7399 (m-30) REVERT: P6 161 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8264 (pt0) REVERT: P6 208 ASP cc_start: 0.8314 (m-30) cc_final: 0.7675 (p0) REVERT: P6 249 SER cc_start: 0.9382 (m) cc_final: 0.9064 (t) REVERT: P6 302 LYS cc_start: 0.8596 (mtmt) cc_final: 0.8220 (pttm) REVERT: P6 327 SER cc_start: 0.9206 (m) cc_final: 0.8778 (p) REVERT: P6 343 GLU cc_start: 0.8780 (mm-30) cc_final: 0.8289 (mm-30) REVERT: P6 347 ASP cc_start: 0.8806 (m-30) cc_final: 0.8479 (m-30) REVERT: P6 396 LYS cc_start: 0.9313 (ttmm) cc_final: 0.8845 (tppt) REVERT: P6 451 SER cc_start: 0.8324 (t) cc_final: 0.7549 (p) REVERT: P7 70 LYS cc_start: 0.9002 (mtpt) cc_final: 0.8795 (mtpp) REVERT: P7 112 GLN cc_start: 0.8302 (mt0) cc_final: 0.8083 (mt0) REVERT: P7 279 MET cc_start: 0.8888 (mmm) cc_final: 0.8636 (mmm) REVERT: P7 318 ASP cc_start: 0.8130 (t0) cc_final: 0.7724 (t0) REVERT: P7 320 GLU cc_start: 0.8104 (pt0) cc_final: 0.7896 (pt0) REVERT: P7 422 ASN cc_start: 0.8896 (m110) cc_final: 0.8473 (m110) REVERT: P7 467 LEU cc_start: 0.9039 (tp) cc_final: 0.8466 (mt) REVERT: P8 24 GLU cc_start: 0.9107 (mm-30) cc_final: 0.8827 (mm-30) REVERT: P8 76 GLU cc_start: 0.8070 (tp30) cc_final: 0.7529 (tp30) REVERT: P8 81 LYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7682 (mtpt) REVERT: P8 115 ASP cc_start: 0.7795 (t0) cc_final: 0.7528 (t70) REVERT: P8 121 LEU cc_start: 0.9044 (tp) cc_final: 0.8822 (mt) REVERT: P8 164 LEU cc_start: 0.9361 (tp) cc_final: 0.9137 (tp) REVERT: P8 236 GLU cc_start: 0.8324 (tt0) cc_final: 0.8088 (tt0) REVERT: P8 303 GLN cc_start: 0.9282 (tm130) cc_final: 0.9026 (tm-30) REVERT: P8 376 MET cc_start: 0.9125 (mmm) cc_final: 0.8887 (mmm) REVERT: P8 411 ASN cc_start: 0.8540 (m-40) cc_final: 0.8310 (m110) REVERT: P8 438 GLU cc_start: 0.8379 (mt-10) cc_final: 0.8057 (mt-10) REVERT: P8 467 LEU cc_start: 0.9115 (tp) cc_final: 0.8851 (tt) REVERT: P8 474 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8375 (mm-30) REVERT: P9 26 ASN cc_start: 0.8533 (t0) cc_final: 0.8092 (t0) REVERT: P9 132 ASP cc_start: 0.8709 (t0) cc_final: 0.8507 (t70) REVERT: P9 164 LEU cc_start: 0.9178 (tp) cc_final: 0.8782 (tp) REVERT: P9 170 MET cc_start: 0.9077 (mtm) cc_final: 0.8825 (mtm) REVERT: P9 215 VAL cc_start: 0.9126 (t) cc_final: 0.8925 (p) REVERT: P9 227 LYS cc_start: 0.8656 (tppt) cc_final: 0.8062 (tmtt) REVERT: P9 322 ARG cc_start: 0.8015 (mtp85) cc_final: 0.7799 (mmm160) REVERT: P9 343 GLU cc_start: 0.8806 (mm-30) cc_final: 0.8433 (mm-30) REVERT: P9 361 ASN cc_start: 0.8600 (t0) cc_final: 0.8368 (t0) REVERT: P9 376 MET cc_start: 0.9463 (mmm) cc_final: 0.9263 (mmp) REVERT: Q1 32 ASP cc_start: 0.8064 (m-30) cc_final: 0.7709 (m-30) REVERT: Q1 50 GLU cc_start: 0.8811 (tt0) cc_final: 0.8409 (tm-30) REVERT: Q1 53 MET cc_start: 0.9282 (mtt) cc_final: 0.9035 (mtp) REVERT: Q1 115 ASP cc_start: 0.7762 (t0) cc_final: 0.7026 (t70) REVERT: Q1 132 ASP cc_start: 0.8000 (t0) cc_final: 0.7711 (t0) REVERT: Q1 178 ASN cc_start: 0.8904 (t0) cc_final: 0.8695 (t0) REVERT: Q1 196 ILE cc_start: 0.8497 (pt) cc_final: 0.8077 (pt) REVERT: Q1 201 GLU cc_start: 0.2819 (OUTLIER) cc_final: 0.2248 (tm-30) REVERT: Q1 336 GLN cc_start: 0.9164 (tt0) cc_final: 0.8923 (tt0) REVERT: Q1 358 ASN cc_start: 0.9208 (m-40) cc_final: 0.8892 (m110) REVERT: Q1 376 MET cc_start: 0.9062 (mmm) cc_final: 0.8649 (mmp) REVERT: Q2 22 ASN cc_start: 0.8995 (t0) cc_final: 0.8676 (t0) REVERT: Q2 47 LYS cc_start: 0.8997 (mttt) cc_final: 0.8772 (ttmm) REVERT: Q2 61 LYS cc_start: 0.8560 (tttt) cc_final: 0.8295 (tptm) REVERT: Q2 120 VAL cc_start: 0.9019 (t) cc_final: 0.8815 (p) REVERT: Q2 153 LEU cc_start: 0.9204 (tp) cc_final: 0.8986 (tt) REVERT: Q2 163 ARG cc_start: 0.9190 (mmm160) cc_final: 0.8859 (mmm160) REVERT: Q2 170 MET cc_start: 0.8976 (mtm) cc_final: 0.8516 (mtm) REVERT: Q2 279 MET cc_start: 0.9146 (mmm) cc_final: 0.8757 (mmm) REVERT: Q2 327 SER cc_start: 0.9074 (m) cc_final: 0.8844 (p) REVERT: Q2 359 THR cc_start: 0.9317 (m) cc_final: 0.9116 (p) REVERT: Q3 61 LYS cc_start: 0.8464 (tttt) cc_final: 0.8144 (ttpt) REVERT: Q3 74 LEU cc_start: 0.8967 (mt) cc_final: 0.8747 (mt) REVERT: Q3 76 GLU cc_start: 0.8201 (tt0) cc_final: 0.7871 (tp30) REVERT: Q3 96 SER cc_start: 0.9008 (t) cc_final: 0.8750 (t) REVERT: Q3 221 ASN cc_start: 0.8347 (p0) cc_final: 0.8045 (p0) REVERT: Q3 296 ASP cc_start: 0.8206 (t0) cc_final: 0.8001 (t70) REVERT: Q3 363 LYS cc_start: 0.9160 (tttm) cc_final: 0.8951 (ttpt) REVERT: Q3 411 ASN cc_start: 0.9202 (m-40) cc_final: 0.8974 (m110) REVERT: Q3 474 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8410 (tp30) outliers start: 7 outliers final: 2 residues processed: 2397 average time/residue: 0.7380 time to fit residues: 2944.9453 Evaluate side-chains 1328 residues out of total 7775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1324 time to evaluate : 6.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P7 residue 146 ILE Chi-restraints excluded: chain P7 residue 372 SER Chi-restraints excluded: chain P8 residue 81 LYS Chi-restraints excluded: chain Q1 residue 201 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 851 random chunks: chunk 718 optimal weight: 8.9990 chunk 645 optimal weight: 1.9990 chunk 357 optimal weight: 5.9990 chunk 220 optimal weight: 9.9990 chunk 435 optimal weight: 6.9990 chunk 344 optimal weight: 10.0000 chunk 667 optimal weight: 4.9990 chunk 258 optimal weight: 40.0000 chunk 405 optimal weight: 4.9990 chunk 496 optimal weight: 4.9990 chunk 772 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1 17 ASN ** B1 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1 28 ASN B1 41 ASN B1 100 ASN B1 178 ASN B1 300 HIS ** B2 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2 258 GLN B3 22 GLN B3 120 ASN B3 149 ASN ** B3 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3 296 HIS B3 300 HIS B4 18 ASN ** B4 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4 149 ASN B4 161 GLN ** B4 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4 300 HIS B5 120 ASN B5 275 ASN B5 300 HIS C4 100 ASN D1 258 GLN D1 282 ASN D2 28 ASN D2 32 HIS D2 238 ASN ** D2 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 275 ASN ** D3 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3 282 ASN D4 152 ASN D4 258 GLN P1 178 ASN P1 233 ASN P1 354 HIS P1 452 GLN P2 26 ASN P2 56 GLN P2 354 HIS P3 40 GLN P3 114 GLN P3 463 GLN P4 26 ASN P4 73 ASN P4 128 ASN P4 354 HIS P5 26 ASN P5 41 ASN P5 88 ASN P5 114 GLN P5 358 ASN P6 73 ASN P6 336 GLN P6 452 GLN P7 26 ASN P8 157 ASN P9 26 ASN P9 41 ASN P9 183 ASN ** P9 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P9 354 HIS P9 358 ASN Q1 26 ASN Q1 88 ASN ** Q1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q1 354 HIS Q1 429 ASN Q2 40 GLN Q2 73 ASN Q2 354 HIS Q3 26 ASN ** Q3 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q3 354 HIS Total number of N/Q/H flips: 67 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 71413 Z= 0.281 Angle : 0.611 8.412 96321 Z= 0.331 Chirality : 0.044 0.251 10525 Planarity : 0.004 0.045 12635 Dihedral : 5.054 34.171 9470 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.92 % Favored : 98.06 % Rotamer: Outliers : 2.05 % Allowed : 10.57 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.09), residues: 8577 helix: 0.85 (0.09), residues: 3148 sheet: 0.48 (0.12), residues: 1806 loop : -0.35 (0.10), residues: 3623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRPC3 76 HIS 0.005 0.001 HISP5 136 PHE 0.027 0.002 PHEP5 173 TYR 0.026 0.002 TYRD1 262 ARG 0.009 0.001 ARGP1 301 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17154 Ramachandran restraints generated. 8577 Oldfield, 0 Emsley, 8577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17154 Ramachandran restraints generated. 8577 Oldfield, 0 Emsley, 8577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1619 residues out of total 7775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 1460 time to evaluate : 6.341 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B1 208 LYS cc_start: 0.6342 (pttt) cc_final: 0.6133 (mttt) REVERT: B2 18 ASN cc_start: 0.6848 (t0) cc_final: 0.4762 (p0) REVERT: B2 30 MET cc_start: 0.7264 (mmm) cc_final: 0.6947 (mpp) REVERT: B2 123 TYR cc_start: 0.7670 (t80) cc_final: 0.7041 (t80) REVERT: B2 243 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7561 (mm-30) REVERT: B2 309 LYS cc_start: 0.7927 (tttt) cc_final: 0.7595 (tttm) REVERT: B3 34 LYS cc_start: 0.8298 (mttt) cc_final: 0.7710 (mmmt) REVERT: B3 149 ASN cc_start: 0.8064 (t160) cc_final: 0.7726 (t0) REVERT: B3 240 LYS cc_start: 0.8647 (mmtm) cc_final: 0.8166 (tptp) REVERT: B3 279 THR cc_start: 0.8647 (m) cc_final: 0.8398 (p) REVERT: B4 45 THR cc_start: 0.7928 (m) cc_final: 0.7694 (m) REVERT: B4 123 TYR cc_start: 0.7350 (t80) cc_final: 0.7014 (t80) REVERT: B4 179 ILE cc_start: 0.9041 (mt) cc_final: 0.8754 (mm) REVERT: B4 266 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7309 (mt-10) REVERT: B5 130 MET cc_start: 0.7871 (mmm) cc_final: 0.7640 (mmm) REVERT: B5 133 MET cc_start: 0.7474 (mtt) cc_final: 0.7255 (mtp) REVERT: B5 162 SER cc_start: 0.9103 (m) cc_final: 0.8700 (t) REVERT: B5 215 LYS cc_start: 0.7836 (mttt) cc_final: 0.7386 (tttt) REVERT: B5 279 THR cc_start: 0.8751 (m) cc_final: 0.8397 (p) REVERT: C1 73 PHE cc_start: 0.6621 (m-80) cc_final: 0.6353 (m-10) REVERT: C1 79 LYS cc_start: 0.8342 (mmtp) cc_final: 0.7154 (mtmt) REVERT: C4 94 SER cc_start: 0.8565 (t) cc_final: 0.8291 (t) REVERT: C5 90 LYS cc_start: 0.7906 (mmtp) cc_final: 0.7700 (mmtp) REVERT: D1 191 LEU cc_start: 0.6572 (mm) cc_final: 0.6148 (tp) REVERT: D1 262 TYR cc_start: 0.8594 (m-80) cc_final: 0.8181 (m-80) REVERT: D2 31 MET cc_start: 0.7120 (mtp) cc_final: 0.6478 (ttm) REVERT: D2 40 MET cc_start: 0.1253 (mpp) cc_final: -0.1315 (tpp) REVERT: D2 58 MET cc_start: 0.9013 (mtp) cc_final: 0.8721 (mtm) REVERT: D2 309 LYS cc_start: 0.8028 (tttt) cc_final: 0.7776 (tttp) REVERT: D3 25 ASN cc_start: 0.8730 (t0) cc_final: 0.8216 (m-40) REVERT: D3 30 MET cc_start: 0.5546 (mmm) cc_final: 0.5277 (mmm) REVERT: D3 104 ARG cc_start: 0.5812 (tmt-80) cc_final: 0.4141 (mpt180) REVERT: D3 176 GLN cc_start: 0.8160 (pp30) cc_final: 0.7836 (pp30) REVERT: D3 252 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7542 (tt) REVERT: D3 266 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.6937 (tm-30) REVERT: D4 30 MET cc_start: 0.7122 (mmm) cc_final: 0.6166 (mmm) REVERT: D5 30 MET cc_start: 0.6496 (mmm) cc_final: 0.6264 (mmp) REVERT: D5 40 MET cc_start: 0.1054 (mpp) cc_final: 0.0755 (mmp) REVERT: D5 52 MET cc_start: 0.7750 (mmt) cc_final: 0.7540 (mmp) REVERT: P1 96 SER cc_start: 0.9166 (t) cc_final: 0.8903 (p) REVERT: P1 136 HIS cc_start: 0.8796 (t70) cc_final: 0.8362 (t-90) REVERT: P1 301 ARG cc_start: 0.8068 (mmp80) cc_final: 0.7385 (ttm-80) REVERT: P1 302 LYS cc_start: 0.8595 (mtmt) cc_final: 0.7868 (pptt) REVERT: P1 303 GLN cc_start: 0.9017 (tm130) cc_final: 0.8794 (tm-30) REVERT: P1 383 LEU cc_start: 0.9373 (tp) cc_final: 0.9110 (tp) REVERT: P1 438 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7839 (mt-10) REVERT: P1 441 LYS cc_start: 0.8955 (tmmt) cc_final: 0.8688 (ttpp) REVERT: P1 468 GLU cc_start: 0.8797 (tp30) cc_final: 0.8306 (tp30) REVERT: P1 470 LYS cc_start: 0.9337 (mmmm) cc_final: 0.9060 (mmmt) REVERT: P1 471 LYS cc_start: 0.9124 (tttt) cc_final: 0.8787 (ttmt) REVERT: P2 50 GLU cc_start: 0.8711 (tt0) cc_final: 0.8336 (tp30) REVERT: P2 68 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8268 (mt-10) REVERT: P2 70 LYS cc_start: 0.9079 (mtpt) cc_final: 0.8607 (mtmm) REVERT: P2 93 ASP cc_start: 0.8417 (t0) cc_final: 0.8094 (t70) REVERT: P2 132 ASP cc_start: 0.8314 (t0) cc_final: 0.7593 (t0) REVERT: P2 217 ARG cc_start: 0.8718 (mtm-85) cc_final: 0.8350 (mtt90) REVERT: P2 227 LYS cc_start: 0.8988 (tppt) cc_final: 0.8620 (mttt) REVERT: P2 239 SER cc_start: 0.9302 (m) cc_final: 0.9035 (t) REVERT: P2 302 LYS cc_start: 0.8926 (mtmt) cc_final: 0.8715 (mtmm) REVERT: P2 329 ASP cc_start: 0.8501 (OUTLIER) cc_final: 0.8239 (m-30) REVERT: P2 376 MET cc_start: 0.9066 (mmm) cc_final: 0.8820 (mmm) REVERT: P2 377 LYS cc_start: 0.8757 (mtmt) cc_final: 0.8452 (mtmm) REVERT: P2 425 ARG cc_start: 0.8308 (mtm-85) cc_final: 0.8098 (mtm180) REVERT: P2 439 GLU cc_start: 0.8462 (mt-10) cc_final: 0.8150 (mt-10) REVERT: P2 441 LYS cc_start: 0.9037 (tmmt) cc_final: 0.8765 (tttm) REVERT: P2 473 GLU cc_start: 0.8987 (mm-30) cc_final: 0.8488 (mm-30) REVERT: P3 1 MET cc_start: 0.8204 (ptp) cc_final: 0.7929 (ptp) REVERT: P3 24 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8569 (mm-30) REVERT: P3 121 LEU cc_start: 0.9107 (tp) cc_final: 0.8840 (mt) REVERT: P3 129 ASP cc_start: 0.8539 (t0) cc_final: 0.8280 (t0) REVERT: P3 144 LEU cc_start: 0.9521 (mt) cc_final: 0.9237 (mt) REVERT: P3 152 GLU cc_start: 0.8406 (pp20) cc_final: 0.8185 (pp20) REVERT: P3 159 ASP cc_start: 0.8660 (t0) cc_final: 0.8460 (t0) REVERT: P3 200 ASP cc_start: 0.7993 (OUTLIER) cc_final: 0.7756 (p0) REVERT: P3 425 ARG cc_start: 0.8187 (mtm-85) cc_final: 0.7871 (mtt-85) REVERT: P3 456 MET cc_start: 0.8973 (mtt) cc_final: 0.8538 (mtt) REVERT: P3 468 GLU cc_start: 0.7945 (tp30) cc_final: 0.6960 (tp30) REVERT: P3 472 ILE cc_start: 0.8242 (mt) cc_final: 0.7436 (mt) REVERT: P3 476 GLU cc_start: 0.8512 (tt0) cc_final: 0.8252 (pt0) REVERT: P4 61 LYS cc_start: 0.8425 (tttt) cc_final: 0.8021 (tmtt) REVERT: P4 89 ARG cc_start: 0.8772 (ptt180) cc_final: 0.8562 (mtm180) REVERT: P4 112 GLN cc_start: 0.7871 (mp10) cc_final: 0.7394 (mp10) REVERT: P4 125 GLU cc_start: 0.8562 (tt0) cc_final: 0.7921 (tm-30) REVERT: P4 243 MET cc_start: 0.8784 (tmm) cc_final: 0.8582 (tmm) REVERT: P4 274 ASP cc_start: 0.9247 (t0) cc_final: 0.8834 (t0) REVERT: P4 279 MET cc_start: 0.8755 (mmm) cc_final: 0.8352 (mmm) REVERT: P4 428 TYR cc_start: 0.8724 (m-80) cc_final: 0.8453 (m-80) REVERT: P4 435 SER cc_start: 0.8692 (t) cc_final: 0.8209 (p) REVERT: P4 471 LYS cc_start: 0.8480 (tttt) cc_final: 0.8056 (tttm) REVERT: P4 476 GLU cc_start: 0.7834 (pt0) cc_final: 0.7582 (pt0) REVERT: P5 26 ASN cc_start: 0.8613 (t0) cc_final: 0.7967 (t0) REVERT: P5 122 GLU cc_start: 0.8749 (pt0) cc_final: 0.8508 (pp20) REVERT: P5 132 ASP cc_start: 0.8595 (t0) cc_final: 0.7997 (t0) REVERT: P5 170 MET cc_start: 0.9308 (mtm) cc_final: 0.8994 (mtt) REVERT: P6 31 TYR cc_start: 0.9214 (t80) cc_final: 0.8589 (t80) REVERT: P6 85 MET cc_start: 0.5222 (pmm) cc_final: 0.3848 (pmm) REVERT: P6 93 ASP cc_start: 0.8445 (t0) cc_final: 0.8128 (t0) REVERT: P6 103 ASN cc_start: 0.9317 (t0) cc_final: 0.8789 (t0) REVERT: P6 124 ILE cc_start: 0.9436 (mm) cc_final: 0.9208 (tt) REVERT: P6 149 LYS cc_start: 0.9224 (pttt) cc_final: 0.8963 (pttp) REVERT: P6 154 MET cc_start: 0.8679 (ttm) cc_final: 0.8407 (ttm) REVERT: P6 161 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8131 (pt0) REVERT: P6 192 ARG cc_start: 0.7053 (ttt-90) cc_final: 0.6846 (ttt-90) REVERT: P6 208 ASP cc_start: 0.8308 (m-30) cc_final: 0.7759 (p0) REVERT: P6 222 ARG cc_start: 0.7920 (ttt180) cc_final: 0.7706 (ttt-90) REVERT: P6 249 SER cc_start: 0.9487 (m) cc_final: 0.9096 (t) REVERT: P6 302 LYS cc_start: 0.8759 (mtmt) cc_final: 0.8441 (pttt) REVERT: P6 327 SER cc_start: 0.9129 (m) cc_final: 0.8692 (p) REVERT: P6 343 GLU cc_start: 0.8919 (mm-30) cc_final: 0.8204 (mm-30) REVERT: P6 347 ASP cc_start: 0.8796 (m-30) cc_final: 0.8210 (m-30) REVERT: P6 378 TYR cc_start: 0.8614 (t80) cc_final: 0.8299 (t80) REVERT: P6 396 LYS cc_start: 0.9334 (ttmm) cc_final: 0.8735 (tppt) REVERT: P6 451 SER cc_start: 0.7967 (t) cc_final: 0.7428 (p) REVERT: P7 24 GLU cc_start: 0.8352 (mm-30) cc_final: 0.8141 (mm-30) REVERT: P7 44 GLU cc_start: 0.8394 (mm-30) cc_final: 0.8082 (mp0) REVERT: P7 70 LYS cc_start: 0.9129 (mtpt) cc_final: 0.8898 (mtpp) REVERT: P7 146 ILE cc_start: 0.9015 (pt) cc_final: 0.8691 (pt) REVERT: P7 279 MET cc_start: 0.8805 (mmm) cc_final: 0.8505 (mmm) REVERT: P7 286 MET cc_start: 0.9063 (mtm) cc_final: 0.8761 (mtp) REVERT: P7 318 ASP cc_start: 0.8184 (t0) cc_final: 0.7782 (t0) REVERT: P8 24 GLU cc_start: 0.9112 (mm-30) cc_final: 0.8858 (mm-30) REVERT: P8 76 GLU cc_start: 0.7940 (tp30) cc_final: 0.7530 (tp30) REVERT: P8 177 ASP cc_start: 0.8441 (t0) cc_final: 0.8121 (t0) REVERT: P8 236 GLU cc_start: 0.7956 (tt0) cc_final: 0.7701 (tt0) REVERT: P8 340 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.8446 (mt0) REVERT: P8 411 ASN cc_start: 0.8268 (m-40) cc_final: 0.7872 (m110) REVERT: P8 438 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8052 (mt-10) REVERT: P8 456 MET cc_start: 0.9435 (mtt) cc_final: 0.9189 (mtt) REVERT: P9 26 ASN cc_start: 0.8306 (t0) cc_final: 0.7755 (t0) REVERT: P9 227 LYS cc_start: 0.8913 (tppt) cc_final: 0.8635 (mmmt) REVERT: P9 274 ASP cc_start: 0.8787 (t70) cc_final: 0.8415 (t0) REVERT: P9 322 ARG cc_start: 0.8369 (mtp85) cc_final: 0.8057 (mtt180) REVERT: P9 343 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8547 (mm-30) REVERT: P9 376 MET cc_start: 0.9281 (mmm) cc_final: 0.9032 (mmp) REVERT: P9 463 GLN cc_start: 0.8236 (tp40) cc_final: 0.7551 (tp-100) REVERT: Q1 50 GLU cc_start: 0.8902 (tt0) cc_final: 0.8288 (tm-30) REVERT: Q1 54 ASP cc_start: 0.9123 (t0) cc_final: 0.8721 (t0) REVERT: Q1 82 GLU cc_start: 0.5814 (pm20) cc_final: 0.5152 (pm20) REVERT: Q1 161 GLU cc_start: 0.8287 (pm20) cc_final: 0.8032 (pm20) REVERT: Q1 185 ILE cc_start: 0.9232 (mm) cc_final: 0.8955 (mp) REVERT: Q1 257 ASP cc_start: 0.8185 (m-30) cc_final: 0.7974 (m-30) REVERT: Q1 296 ASP cc_start: 0.8041 (t0) cc_final: 0.7770 (t70) REVERT: Q1 358 ASN cc_start: 0.9231 (m-40) cc_final: 0.8730 (m110) REVERT: Q1 367 PHE cc_start: 0.5801 (t80) cc_final: 0.5262 (t80) REVERT: Q1 472 ILE cc_start: 0.8728 (mt) cc_final: 0.8462 (mt) REVERT: Q1 476 GLU cc_start: 0.9069 (tp30) cc_final: 0.8839 (pp20) REVERT: Q2 22 ASN cc_start: 0.9082 (t0) cc_final: 0.8721 (t0) REVERT: Q2 26 ASN cc_start: 0.8515 (t0) cc_final: 0.8310 (t0) REVERT: Q2 61 LYS cc_start: 0.8595 (tttt) cc_final: 0.8272 (tptp) REVERT: Q2 161 GLU cc_start: 0.7529 (pm20) cc_final: 0.7180 (pm20) REVERT: Q2 279 MET cc_start: 0.9261 (mmm) cc_final: 0.9005 (mmm) REVERT: Q2 327 SER cc_start: 0.8974 (m) cc_final: 0.8745 (p) REVERT: Q2 359 THR cc_start: 0.9338 (m) cc_final: 0.8874 (p) REVERT: Q2 425 ARG cc_start: 0.8274 (mtm-85) cc_final: 0.7565 (mtm-85) REVERT: Q2 457 SER cc_start: 0.9183 (OUTLIER) cc_final: 0.8885 (p) REVERT: Q2 468 GLU cc_start: 0.8475 (tp30) cc_final: 0.7458 (mm-30) REVERT: Q3 61 LYS cc_start: 0.8531 (tttt) cc_final: 0.8162 (ttpt) REVERT: Q3 76 GLU cc_start: 0.8215 (tt0) cc_final: 0.7875 (tp30) REVERT: Q3 83 GLU cc_start: 0.7451 (pt0) cc_final: 0.7237 (pm20) REVERT: Q3 192 ARG cc_start: 0.8512 (mtp85) cc_final: 0.8270 (mtp85) REVERT: Q3 221 ASN cc_start: 0.8142 (p0) cc_final: 0.7835 (p0) REVERT: Q3 296 ASP cc_start: 0.8160 (t0) cc_final: 0.7960 (t70) REVERT: Q3 340 GLN cc_start: 0.8358 (mm-40) cc_final: 0.8128 (mt0) REVERT: Q3 358 ASN cc_start: 0.9221 (m-40) cc_final: 0.8971 (m-40) REVERT: Q3 363 LYS cc_start: 0.9102 (tttm) cc_final: 0.8776 (tttt) REVERT: Q3 408 ILE cc_start: 0.8843 (tp) cc_final: 0.8492 (tp) REVERT: Q3 411 ASN cc_start: 0.8959 (m-40) cc_final: 0.8759 (m110) REVERT: Q3 474 GLU cc_start: 0.8765 (mm-30) cc_final: 0.8522 (mt-10) outliers start: 159 outliers final: 97 residues processed: 1559 average time/residue: 0.7147 time to fit residues: 1884.5111 Evaluate side-chains 1287 residues out of total 7775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 1184 time to evaluate : 6.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B1 residue 162 SER Chi-restraints excluded: chain B1 residue 169 VAL Chi-restraints excluded: chain B1 residue 222 ASN Chi-restraints excluded: chain B2 residue 47 ILE Chi-restraints excluded: chain B2 residue 93 THR Chi-restraints excluded: chain B2 residue 119 LEU Chi-restraints excluded: chain B2 residue 234 LEU Chi-restraints excluded: chain B3 residue 27 ASP Chi-restraints excluded: chain B3 residue 182 LEU Chi-restraints excluded: chain B3 residue 245 ILE Chi-restraints excluded: chain B3 residue 272 THR Chi-restraints excluded: chain B4 residue 29 VAL Chi-restraints excluded: chain B4 residue 60 LEU Chi-restraints excluded: chain B4 residue 124 SER Chi-restraints excluded: chain B4 residue 149 ASN Chi-restraints excluded: chain B4 residue 169 VAL Chi-restraints excluded: chain B4 residue 232 VAL Chi-restraints excluded: chain B5 residue 44 THR Chi-restraints excluded: chain B5 residue 47 ILE Chi-restraints excluded: chain B5 residue 51 VAL Chi-restraints excluded: chain B5 residue 205 LEU Chi-restraints excluded: chain B5 residue 223 SER Chi-restraints excluded: chain B5 residue 234 LEU Chi-restraints excluded: chain B5 residue 264 ILE Chi-restraints excluded: chain C1 residue 74 THR Chi-restraints excluded: chain C4 residue 73 PHE Chi-restraints excluded: chain C5 residue 94 SER Chi-restraints excluded: chain C5 residue 99 VAL Chi-restraints excluded: chain D2 residue 111 ILE Chi-restraints excluded: chain D3 residue 177 ASP Chi-restraints excluded: chain D3 residue 198 SER Chi-restraints excluded: chain D3 residue 252 LEU Chi-restraints excluded: chain D3 residue 266 GLU Chi-restraints excluded: chain D4 residue 57 ILE Chi-restraints excluded: chain D4 residue 175 THR Chi-restraints excluded: chain D4 residue 177 ASP Chi-restraints excluded: chain D4 residue 205 LEU Chi-restraints excluded: chain D4 residue 231 VAL Chi-restraints excluded: chain D4 residue 259 LEU Chi-restraints excluded: chain D5 residue 299 LEU Chi-restraints excluded: chain P1 residue 2 LEU Chi-restraints excluded: chain P1 residue 18 ASN Chi-restraints excluded: chain P1 residue 99 SER Chi-restraints excluded: chain P1 residue 119 ASP Chi-restraints excluded: chain P1 residue 206 THR Chi-restraints excluded: chain P1 residue 211 THR Chi-restraints excluded: chain P1 residue 415 ILE Chi-restraints excluded: chain P1 residue 416 ASP Chi-restraints excluded: chain P1 residue 450 ILE Chi-restraints excluded: chain P2 residue 229 THR Chi-restraints excluded: chain P2 residue 298 VAL Chi-restraints excluded: chain P2 residue 327 SER Chi-restraints excluded: chain P2 residue 329 ASP Chi-restraints excluded: chain P3 residue 23 ASP Chi-restraints excluded: chain P3 residue 135 SER Chi-restraints excluded: chain P3 residue 170 MET Chi-restraints excluded: chain P3 residue 191 LEU Chi-restraints excluded: chain P3 residue 200 ASP Chi-restraints excluded: chain P3 residue 208 ASP Chi-restraints excluded: chain P3 residue 229 THR Chi-restraints excluded: chain P3 residue 295 LEU Chi-restraints excluded: chain P3 residue 296 ASP Chi-restraints excluded: chain P4 residue 77 LEU Chi-restraints excluded: chain P4 residue 154 MET Chi-restraints excluded: chain P4 residue 206 THR Chi-restraints excluded: chain P5 residue 42 VAL Chi-restraints excluded: chain P5 residue 135 SER Chi-restraints excluded: chain P5 residue 469 VAL Chi-restraints excluded: chain P6 residue 193 THR Chi-restraints excluded: chain P7 residue 71 THR Chi-restraints excluded: chain P7 residue 116 ASP Chi-restraints excluded: chain P7 residue 143 ASP Chi-restraints excluded: chain P7 residue 188 VAL Chi-restraints excluded: chain P7 residue 211 THR Chi-restraints excluded: chain P7 residue 407 THR Chi-restraints excluded: chain P8 residue 152 GLU Chi-restraints excluded: chain P8 residue 188 VAL Chi-restraints excluded: chain P8 residue 208 ASP Chi-restraints excluded: chain P8 residue 340 GLN Chi-restraints excluded: chain P9 residue 18 ASN Chi-restraints excluded: chain P9 residue 50 GLU Chi-restraints excluded: chain P9 residue 96 SER Chi-restraints excluded: chain P9 residue 119 ASP Chi-restraints excluded: chain P9 residue 152 GLU Chi-restraints excluded: chain P9 residue 206 THR Chi-restraints excluded: chain P9 residue 409 LEU Chi-restraints excluded: chain Q1 residue 45 VAL Chi-restraints excluded: chain Q1 residue 204 VAL Chi-restraints excluded: chain Q1 residue 215 VAL Chi-restraints excluded: chain Q1 residue 229 THR Chi-restraints excluded: chain Q1 residue 284 ASP Chi-restraints excluded: chain Q1 residue 298 VAL Chi-restraints excluded: chain Q1 residue 362 MET Chi-restraints excluded: chain Q2 residue 119 ASP Chi-restraints excluded: chain Q2 residue 155 ILE Chi-restraints excluded: chain Q2 residue 298 VAL Chi-restraints excluded: chain Q2 residue 406 GLU Chi-restraints excluded: chain Q2 residue 457 SER Chi-restraints excluded: chain Q3 residue 211 THR Chi-restraints excluded: chain Q3 residue 220 THR Chi-restraints excluded: chain Q3 residue 298 VAL Chi-restraints excluded: chain Q3 residue 317 VAL Chi-restraints excluded: chain Q3 residue 324 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 851 random chunks: chunk 429 optimal weight: 0.9990 chunk 239 optimal weight: 20.0000 chunk 643 optimal weight: 10.0000 chunk 526 optimal weight: 10.0000 chunk 213 optimal weight: 7.9990 chunk 774 optimal weight: 10.0000 chunk 836 optimal weight: 7.9990 chunk 689 optimal weight: 10.0000 chunk 767 optimal weight: 8.9990 chunk 263 optimal weight: 20.0000 chunk 621 optimal weight: 0.0980 overall best weight: 5.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1 100 ASN B2 22 GLN ** B2 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2 167 ASN B2 258 GLN B2 269 GLN B3 161 GLN B4 22 GLN B4 161 GLN B4 275 ASN B4 286 GLN C2 89 GLN C4 100 ASN D1 32 HIS D1 201 GLN D1 275 ASN D1 286 GLN D2 258 GLN ** D2 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4 28 ASN P1 178 ASN P1 452 GLN P2 26 ASN P3 40 GLN P3 354 HIS P3 463 GLN P5 88 ASN P5 112 GLN ** P5 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P6 336 GLN P6 358 ASN ** P7 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P8 16 ASN P9 16 ASN P9 43 ASN ** P9 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q2 73 ASN Q3 16 ASN ** Q3 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q3 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 71413 Z= 0.302 Angle : 0.576 9.317 96321 Z= 0.309 Chirality : 0.043 0.175 10525 Planarity : 0.004 0.046 12635 Dihedral : 4.766 26.830 9460 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.56 % Allowed : 12.04 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.09), residues: 8577 helix: 1.38 (0.10), residues: 3108 sheet: 0.35 (0.11), residues: 1881 loop : -0.22 (0.10), residues: 3588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRPC3 76 HIS 0.007 0.001 HISP3 92 PHE 0.026 0.002 PHEP5 173 TYR 0.036 0.002 TYRD2 139 ARG 0.009 0.001 ARGB5 207 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17154 Ramachandran restraints generated. 8577 Oldfield, 0 Emsley, 8577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17154 Ramachandran restraints generated. 8577 Oldfield, 0 Emsley, 8577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1482 residues out of total 7775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 1283 time to evaluate : 6.228 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: 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: symmetry clash REVERT: B1 76 TRP cc_start: 0.5882 (p-90) cc_final: 0.5597 (p-90) REVERT: B2 30 MET cc_start: 0.7309 (mmm) cc_final: 0.7004 (mpp) REVERT: B2 123 TYR cc_start: 0.8048 (t80) cc_final: 0.7375 (t80) REVERT: B2 243 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7623 (mm-30) REVERT: B2 261 GLU cc_start: 0.8427 (tm-30) cc_final: 0.8226 (tm-30) REVERT: B2 309 LYS cc_start: 0.7975 (tttt) cc_final: 0.7586 (tttm) REVERT: B3 34 LYS cc_start: 0.8104 (mttt) cc_final: 0.7662 (mmmt) REVERT: B3 149 ASN cc_start: 0.7994 (t160) cc_final: 0.7657 (t0) REVERT: B3 196 PHE cc_start: 0.6448 (OUTLIER) cc_final: 0.5940 (m-80) REVERT: B3 243 GLU cc_start: 0.7549 (mp0) cc_final: 0.7309 (mp0) REVERT: B3 279 THR cc_start: 0.8723 (m) cc_final: 0.8378 (p) REVERT: B4 35 LYS cc_start: 0.7557 (mttt) cc_final: 0.7310 (mttm) REVERT: B4 179 ILE cc_start: 0.9030 (mt) cc_final: 0.8757 (mm) REVERT: B5 130 MET cc_start: 0.8039 (mmm) cc_final: 0.7805 (mmm) REVERT: B5 279 THR cc_start: 0.8759 (m) cc_final: 0.8447 (p) REVERT: C1 73 PHE cc_start: 0.6704 (m-80) cc_final: 0.6270 (m-10) REVERT: C3 76 TRP cc_start: 0.6342 (m-90) cc_final: 0.5955 (m-90) REVERT: C5 90 LYS cc_start: 0.7724 (mmtp) cc_final: 0.7457 (mmtp) REVERT: D1 40 MET cc_start: -0.2652 (tpp) cc_final: -0.2885 (ttt) REVERT: D1 262 TYR cc_start: 0.8691 (m-80) cc_final: 0.7987 (m-80) REVERT: D2 30 MET cc_start: 0.6650 (mmm) cc_final: 0.6328 (mtt) REVERT: D2 31 MET cc_start: 0.7399 (mtp) cc_final: 0.6942 (ttm) REVERT: D2 58 MET cc_start: 0.9016 (mtp) cc_final: 0.8813 (mtp) REVERT: D2 309 LYS cc_start: 0.8162 (tttt) cc_final: 0.7910 (tttp) REVERT: D3 25 ASN cc_start: 0.8669 (t0) cc_final: 0.8317 (m-40) REVERT: D3 30 MET cc_start: 0.5867 (mmm) cc_final: 0.5572 (mmm) REVERT: D3 176 GLN cc_start: 0.8172 (pp30) cc_final: 0.7808 (pp30) REVERT: D3 266 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7511 (tm-30) REVERT: D4 30 MET cc_start: 0.7153 (mmm) cc_final: 0.6048 (mmm) REVERT: D5 30 MET cc_start: 0.6729 (mmm) cc_final: 0.6493 (mmt) REVERT: D5 39 LEU cc_start: 0.7297 (OUTLIER) cc_final: 0.6978 (pp) REVERT: D5 52 MET cc_start: 0.7589 (mmt) cc_final: 0.7369 (mmt) REVERT: D5 246 THR cc_start: 0.7460 (t) cc_final: 0.7173 (m) REVERT: P1 50 GLU cc_start: 0.8883 (tt0) cc_final: 0.8634 (tp30) REVERT: P1 53 MET cc_start: 0.8807 (mtp) cc_final: 0.8585 (mtp) REVERT: P1 93 ASP cc_start: 0.9007 (t0) cc_final: 0.8728 (t0) REVERT: P1 243 MET cc_start: 0.8886 (tmm) cc_final: 0.8615 (tmm) REVERT: P1 302 LYS cc_start: 0.8700 (mtmt) cc_final: 0.8057 (pptt) REVERT: P1 383 LEU cc_start: 0.9411 (tp) cc_final: 0.9146 (tp) REVERT: P1 441 LYS cc_start: 0.8992 (tmmt) cc_final: 0.8665 (ttpp) REVERT: P1 468 GLU cc_start: 0.8896 (tp30) cc_final: 0.8392 (tp30) REVERT: P1 470 LYS cc_start: 0.9313 (mmmm) cc_final: 0.9041 (mmmt) REVERT: P1 471 LYS cc_start: 0.9008 (tttt) cc_final: 0.8673 (ttmt) REVERT: P2 50 GLU cc_start: 0.8696 (tt0) cc_final: 0.8405 (tp30) REVERT: P2 68 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8221 (mt-10) REVERT: P2 70 LYS cc_start: 0.9109 (mtpt) cc_final: 0.8866 (mtmm) REVERT: P2 93 ASP cc_start: 0.8483 (t0) cc_final: 0.8106 (t70) REVERT: P2 132 ASP cc_start: 0.8268 (t0) cc_final: 0.7573 (t0) REVERT: P2 227 LYS cc_start: 0.9026 (tppt) cc_final: 0.8664 (mtmt) REVERT: P2 239 SER cc_start: 0.9320 (m) cc_final: 0.9028 (t) REVERT: P2 302 LYS cc_start: 0.8942 (mtmt) cc_final: 0.8679 (mtmm) REVERT: P2 329 ASP cc_start: 0.8554 (OUTLIER) cc_final: 0.8282 (m-30) REVERT: P2 413 ARG cc_start: 0.8811 (ptp-170) cc_final: 0.7931 (tpp80) REVERT: P2 439 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8066 (mt-10) REVERT: P2 468 GLU cc_start: 0.9394 (tp30) cc_final: 0.8948 (tp30) REVERT: P2 473 GLU cc_start: 0.8989 (mm-30) cc_final: 0.8577 (mm-30) REVERT: P3 121 LEU cc_start: 0.9082 (tp) cc_final: 0.8825 (mt) REVERT: P3 144 LEU cc_start: 0.9479 (mt) cc_final: 0.9171 (mt) REVERT: P3 152 GLU cc_start: 0.8532 (pp20) cc_final: 0.8203 (pp20) REVERT: P3 159 ASP cc_start: 0.8749 (t70) cc_final: 0.8422 (t0) REVERT: P3 243 MET cc_start: 0.9084 (tmm) cc_final: 0.8260 (tmm) REVERT: P3 301 ARG cc_start: 0.8570 (mtm-85) cc_final: 0.8183 (mtm-85) REVERT: P3 374 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8006 (mp0) REVERT: P3 425 ARG cc_start: 0.8189 (mtm-85) cc_final: 0.7874 (mtt-85) REVERT: P3 456 MET cc_start: 0.9013 (mtt) cc_final: 0.8539 (mtt) REVERT: P3 468 GLU cc_start: 0.7966 (tp30) cc_final: 0.7249 (tp30) REVERT: P3 472 ILE cc_start: 0.8301 (mt) cc_final: 0.7642 (mt) REVERT: P4 61 LYS cc_start: 0.8431 (tttt) cc_final: 0.8045 (tmtt) REVERT: P4 89 ARG cc_start: 0.8816 (ptt180) cc_final: 0.8550 (mtm180) REVERT: P4 112 GLN cc_start: 0.8130 (mp10) cc_final: 0.7661 (mp10) REVERT: P4 125 GLU cc_start: 0.8514 (tt0) cc_final: 0.7715 (tp30) REVERT: P4 129 ASP cc_start: 0.8982 (t0) cc_final: 0.8479 (m-30) REVERT: P4 192 ARG cc_start: 0.7974 (ttt90) cc_final: 0.7653 (ttt90) REVERT: P4 274 ASP cc_start: 0.9237 (t0) cc_final: 0.8850 (t0) REVERT: P4 428 TYR cc_start: 0.8819 (m-80) cc_final: 0.8564 (m-80) REVERT: P4 435 SER cc_start: 0.8643 (t) cc_final: 0.8151 (p) REVERT: P4 471 LYS cc_start: 0.8735 (tttt) cc_final: 0.8335 (tttm) REVERT: P4 476 GLU cc_start: 0.7729 (pt0) cc_final: 0.7498 (pt0) REVERT: P5 26 ASN cc_start: 0.8615 (t0) cc_final: 0.8025 (t0) REVERT: P5 118 LYS cc_start: 0.8590 (tppt) cc_final: 0.8338 (tppt) REVERT: P5 132 ASP cc_start: 0.8326 (t0) cc_final: 0.7591 (t0) REVERT: P5 312 GLU cc_start: 0.8190 (tt0) cc_final: 0.7909 (tt0) REVERT: P5 438 GLU cc_start: 0.8616 (tp30) cc_final: 0.8211 (tp30) REVERT: P6 1 MET cc_start: 0.6870 (ttm) cc_final: 0.6561 (ttm) REVERT: P6 31 TYR cc_start: 0.9270 (t80) cc_final: 0.8689 (t80) REVERT: P6 85 MET cc_start: 0.5276 (pmm) cc_final: 0.4074 (pmm) REVERT: P6 93 ASP cc_start: 0.8544 (t0) cc_final: 0.8178 (t0) REVERT: P6 103 ASN cc_start: 0.9326 (t0) cc_final: 0.8773 (t0) REVERT: P6 124 ILE cc_start: 0.9420 (mm) cc_final: 0.9165 (tt) REVERT: P6 149 LYS cc_start: 0.9226 (pttt) cc_final: 0.8969 (pttp) REVERT: P6 154 MET cc_start: 0.8587 (ttm) cc_final: 0.8330 (ttm) REVERT: P6 161 GLU cc_start: 0.8511 (mt-10) cc_final: 0.8133 (pt0) REVERT: P6 208 ASP cc_start: 0.8312 (m-30) cc_final: 0.7697 (p0) REVERT: P6 222 ARG cc_start: 0.8135 (ttt180) cc_final: 0.7779 (ttt-90) REVERT: P6 249 SER cc_start: 0.9497 (m) cc_final: 0.9117 (t) REVERT: P6 279 MET cc_start: 0.8755 (mmm) cc_final: 0.8373 (mmm) REVERT: P6 302 LYS cc_start: 0.8780 (mtmt) cc_final: 0.8552 (pttt) REVERT: P6 327 SER cc_start: 0.9132 (m) cc_final: 0.8690 (p) REVERT: P6 347 ASP cc_start: 0.8885 (m-30) cc_final: 0.8632 (m-30) REVERT: P6 396 LYS cc_start: 0.9192 (ttmm) cc_final: 0.8685 (tppt) REVERT: P6 406 GLU cc_start: 0.9092 (OUTLIER) cc_final: 0.8774 (tm-30) REVERT: P7 24 GLU cc_start: 0.8338 (mm-30) cc_final: 0.8127 (mm-30) REVERT: P7 44 GLU cc_start: 0.8488 (mm-30) cc_final: 0.8086 (mp0) REVERT: P7 70 LYS cc_start: 0.9138 (mtpt) cc_final: 0.8845 (mtpp) REVERT: P7 93 ASP cc_start: 0.9252 (t70) cc_final: 0.8956 (t0) REVERT: P7 142 LEU cc_start: 0.9223 (tt) cc_final: 0.8937 (tt) REVERT: P7 146 ILE cc_start: 0.8738 (pt) cc_final: 0.8503 (pt) REVERT: P7 170 MET cc_start: 0.9460 (mtp) cc_final: 0.8829 (mmm) REVERT: P7 318 ASP cc_start: 0.8335 (t0) cc_final: 0.7984 (t0) REVERT: P7 406 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7284 (tt0) REVERT: P8 76 GLU cc_start: 0.7957 (tp30) cc_final: 0.7557 (tp30) REVERT: P8 177 ASP cc_start: 0.8603 (t0) cc_final: 0.8182 (t0) REVERT: P8 222 ARG cc_start: 0.7834 (tpt90) cc_final: 0.7555 (tpt170) REVERT: P8 236 GLU cc_start: 0.7934 (tt0) cc_final: 0.7661 (tt0) REVERT: P8 343 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8340 (mm-30) REVERT: P8 438 GLU cc_start: 0.8455 (mt-10) cc_final: 0.7985 (mt-10) REVERT: P9 26 ASN cc_start: 0.8640 (t0) cc_final: 0.7912 (t0) REVERT: P9 177 ASP cc_start: 0.8827 (t0) cc_final: 0.8508 (t0) REVERT: P9 227 LYS cc_start: 0.9135 (tppt) cc_final: 0.8766 (mmmt) REVERT: P9 274 ASP cc_start: 0.8814 (t70) cc_final: 0.8416 (t0) REVERT: P9 322 ARG cc_start: 0.8422 (mtp85) cc_final: 0.8124 (mtt180) REVERT: P9 376 MET cc_start: 0.9330 (mmm) cc_final: 0.8812 (mmm) REVERT: P9 463 GLN cc_start: 0.8191 (tp40) cc_final: 0.7401 (tp-100) REVERT: Q1 50 GLU cc_start: 0.8860 (tt0) cc_final: 0.8129 (tm-30) REVERT: Q1 54 ASP cc_start: 0.9139 (t0) cc_final: 0.8823 (t70) REVERT: Q1 118 LYS cc_start: 0.8753 (pttp) cc_final: 0.8516 (pttp) REVERT: Q1 159 ASP cc_start: 0.8866 (t0) cc_final: 0.8548 (t0) REVERT: Q1 258 TYR cc_start: 0.9194 (p90) cc_final: 0.8876 (p90) REVERT: Q1 296 ASP cc_start: 0.8161 (t0) cc_final: 0.7935 (t70) REVERT: Q1 358 ASN cc_start: 0.9249 (m-40) cc_final: 0.8722 (m110) REVERT: Q1 425 ARG cc_start: 0.8450 (mtm-85) cc_final: 0.8125 (ttm110) REVERT: Q1 476 GLU cc_start: 0.9103 (tp30) cc_final: 0.8750 (tp30) REVERT: Q1 477 LYS cc_start: 0.8889 (ttmm) cc_final: 0.8545 (mtmm) REVERT: Q2 22 ASN cc_start: 0.9096 (t0) cc_final: 0.8775 (t0) REVERT: Q2 50 GLU cc_start: 0.8878 (tt0) cc_final: 0.8601 (tt0) REVERT: Q2 61 LYS cc_start: 0.8597 (tttt) cc_final: 0.8252 (tptp) REVERT: Q2 72 LYS cc_start: 0.8962 (tttt) cc_final: 0.8718 (tptm) REVERT: Q2 114 GLN cc_start: 0.7794 (OUTLIER) cc_final: 0.6677 (pt0) REVERT: Q2 152 GLU cc_start: 0.8599 (pt0) cc_final: 0.8374 (pt0) REVERT: Q2 161 GLU cc_start: 0.7343 (pm20) cc_final: 0.7142 (pm20) REVERT: Q2 327 SER cc_start: 0.8937 (m) cc_final: 0.8686 (p) REVERT: Q2 359 THR cc_start: 0.9340 (m) cc_final: 0.8816 (p) REVERT: Q2 425 ARG cc_start: 0.8328 (mtm-85) cc_final: 0.7410 (mtm-85) REVERT: Q2 477 LYS cc_start: 0.8228 (tppt) cc_final: 0.8017 (tppt) REVERT: Q3 26 ASN cc_start: 0.7905 (t0) cc_final: 0.7608 (t0) REVERT: Q3 39 LEU cc_start: 0.9549 (tp) cc_final: 0.9058 (pp) REVERT: Q3 61 LYS cc_start: 0.8539 (tttt) cc_final: 0.8057 (ttpt) REVERT: Q3 76 GLU cc_start: 0.8244 (tt0) cc_final: 0.7878 (tp30) REVERT: Q3 221 ASN cc_start: 0.8155 (p0) cc_final: 0.7816 (p0) REVERT: Q3 323 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8231 (mt-10) REVERT: Q3 340 GLN cc_start: 0.8349 (mm-40) cc_final: 0.8131 (mt0) REVERT: Q3 358 ASN cc_start: 0.9250 (m-40) cc_final: 0.8919 (m110) REVERT: Q3 363 LYS cc_start: 0.9083 (tttm) cc_final: 0.8750 (tttt) REVERT: Q3 408 ILE cc_start: 0.8864 (tp) cc_final: 0.8511 (tp) outliers start: 199 outliers final: 139 residues processed: 1406 average time/residue: 0.6958 time to fit residues: 1660.4511 Evaluate side-chains 1301 residues out of total 7775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 1155 time to evaluate : 6.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B1 residue 97 THR Chi-restraints excluded: chain B1 residue 162 SER Chi-restraints excluded: chain B1 residue 169 VAL Chi-restraints excluded: chain B2 residue 54 ASN Chi-restraints excluded: chain B2 residue 188 ASP Chi-restraints excluded: chain B2 residue 234 LEU Chi-restraints excluded: chain B3 residue 23 VAL Chi-restraints excluded: chain B3 residue 27 ASP Chi-restraints excluded: chain B3 residue 196 PHE Chi-restraints excluded: chain B3 residue 245 ILE Chi-restraints excluded: chain B3 residue 250 ASP Chi-restraints excluded: chain B3 residue 272 THR Chi-restraints excluded: chain B4 residue 169 VAL Chi-restraints excluded: chain B4 residue 232 VAL Chi-restraints excluded: chain B5 residue 44 THR Chi-restraints excluded: chain B5 residue 47 ILE Chi-restraints excluded: chain B5 residue 205 LEU Chi-restraints excluded: chain B5 residue 234 LEU Chi-restraints excluded: chain B5 residue 238 ASN Chi-restraints excluded: chain B5 residue 264 ILE Chi-restraints excluded: chain C4 residue 73 PHE Chi-restraints excluded: chain C4 residue 102 THR Chi-restraints excluded: chain C5 residue 94 SER Chi-restraints excluded: chain C5 residue 99 VAL Chi-restraints excluded: chain D1 residue 159 ILE Chi-restraints excluded: chain D1 residue 201 GLN Chi-restraints excluded: chain D2 residue 111 ILE Chi-restraints excluded: chain D2 residue 190 GLU Chi-restraints excluded: chain D2 residue 294 THR Chi-restraints excluded: chain D3 residue 57 ILE Chi-restraints excluded: chain D3 residue 122 THR Chi-restraints excluded: chain D3 residue 177 ASP Chi-restraints excluded: chain D3 residue 198 SER Chi-restraints excluded: chain D3 residue 243 GLU Chi-restraints excluded: chain D3 residue 266 GLU Chi-restraints excluded: chain D4 residue 57 ILE Chi-restraints excluded: chain D4 residue 175 THR Chi-restraints excluded: chain D4 residue 177 ASP Chi-restraints excluded: chain D4 residue 206 LEU Chi-restraints excluded: chain D4 residue 214 THR Chi-restraints excluded: chain D4 residue 231 VAL Chi-restraints excluded: chain D4 residue 259 LEU Chi-restraints excluded: chain D5 residue 39 LEU Chi-restraints excluded: chain D5 residue 44 THR Chi-restraints excluded: chain D5 residue 119 LEU Chi-restraints excluded: chain D5 residue 299 LEU Chi-restraints excluded: chain P1 residue 2 LEU Chi-restraints excluded: chain P1 residue 99 SER Chi-restraints excluded: chain P1 residue 119 ASP Chi-restraints excluded: chain P1 residue 143 ASP Chi-restraints excluded: chain P1 residue 206 THR Chi-restraints excluded: chain P1 residue 211 THR Chi-restraints excluded: chain P1 residue 327 SER Chi-restraints excluded: chain P1 residue 377 LYS Chi-restraints excluded: chain P1 residue 415 ILE Chi-restraints excluded: chain P1 residue 416 ASP Chi-restraints excluded: chain P1 residue 436 LEU Chi-restraints excluded: chain P1 residue 450 ILE Chi-restraints excluded: chain P1 residue 452 GLN Chi-restraints excluded: chain P2 residue 96 SER Chi-restraints excluded: chain P2 residue 124 ILE Chi-restraints excluded: chain P2 residue 155 ILE Chi-restraints excluded: chain P2 residue 197 ASP Chi-restraints excluded: chain P2 residue 262 ILE Chi-restraints excluded: chain P2 residue 327 SER Chi-restraints excluded: chain P2 residue 329 ASP Chi-restraints excluded: chain P3 residue 23 ASP Chi-restraints excluded: chain P3 residue 43 ASN Chi-restraints excluded: chain P3 residue 111 ILE Chi-restraints excluded: chain P3 residue 116 ASP Chi-restraints excluded: chain P3 residue 135 SER Chi-restraints excluded: chain P3 residue 170 MET Chi-restraints excluded: chain P3 residue 191 LEU Chi-restraints excluded: chain P3 residue 208 ASP Chi-restraints excluded: chain P3 residue 229 THR Chi-restraints excluded: chain P3 residue 295 LEU Chi-restraints excluded: chain P3 residue 296 ASP Chi-restraints excluded: chain P3 residue 406 GLU Chi-restraints excluded: chain P4 residue 154 MET Chi-restraints excluded: chain P4 residue 206 THR Chi-restraints excluded: chain P4 residue 287 LEU Chi-restraints excluded: chain P4 residue 418 ASN Chi-restraints excluded: chain P5 residue 42 VAL Chi-restraints excluded: chain P5 residue 88 ASN Chi-restraints excluded: chain P5 residue 135 SER Chi-restraints excluded: chain P5 residue 164 LEU Chi-restraints excluded: chain P5 residue 469 VAL Chi-restraints excluded: chain P6 residue 6 GLU Chi-restraints excluded: chain P6 residue 152 GLU Chi-restraints excluded: chain P6 residue 193 THR Chi-restraints excluded: chain P6 residue 196 ILE Chi-restraints excluded: chain P6 residue 406 GLU Chi-restraints excluded: chain P6 residue 444 ILE Chi-restraints excluded: chain P7 residue 57 ARG Chi-restraints excluded: chain P7 residue 71 THR Chi-restraints excluded: chain P7 residue 99 SER Chi-restraints excluded: chain P7 residue 116 ASP Chi-restraints excluded: chain P7 residue 143 ASP Chi-restraints excluded: chain P7 residue 406 GLU Chi-restraints excluded: chain P7 residue 407 THR Chi-restraints excluded: chain P8 residue 39 LEU Chi-restraints excluded: chain P8 residue 87 ASP Chi-restraints excluded: chain P8 residue 124 ILE Chi-restraints excluded: chain P8 residue 152 GLU Chi-restraints excluded: chain P8 residue 188 VAL Chi-restraints excluded: chain P8 residue 208 ASP Chi-restraints excluded: chain P8 residue 284 ASP Chi-restraints excluded: chain P8 residue 298 VAL Chi-restraints excluded: chain P9 residue 18 ASN Chi-restraints excluded: chain P9 residue 50 GLU Chi-restraints excluded: chain P9 residue 96 SER Chi-restraints excluded: chain P9 residue 119 ASP Chi-restraints excluded: chain P9 residue 133 VAL Chi-restraints excluded: chain P9 residue 152 GLU Chi-restraints excluded: chain P9 residue 206 THR Chi-restraints excluded: chain P9 residue 409 LEU Chi-restraints excluded: chain Q1 residue 45 VAL Chi-restraints excluded: chain Q1 residue 204 VAL Chi-restraints excluded: chain Q1 residue 215 VAL Chi-restraints excluded: chain Q1 residue 229 THR Chi-restraints excluded: chain Q1 residue 284 ASP Chi-restraints excluded: chain Q1 residue 295 LEU Chi-restraints excluded: chain Q1 residue 298 VAL Chi-restraints excluded: chain Q1 residue 327 SER Chi-restraints excluded: chain Q1 residue 362 MET Chi-restraints excluded: chain Q1 residue 467 LEU Chi-restraints excluded: chain Q2 residue 96 SER Chi-restraints excluded: chain Q2 residue 114 GLN Chi-restraints excluded: chain Q2 residue 119 ASP Chi-restraints excluded: chain Q2 residue 133 VAL Chi-restraints excluded: chain Q2 residue 155 ILE Chi-restraints excluded: chain Q2 residue 170 MET Chi-restraints excluded: chain Q2 residue 298 VAL Chi-restraints excluded: chain Q2 residue 355 MET Chi-restraints excluded: chain Q2 residue 406 GLU Chi-restraints excluded: chain Q2 residue 410 LYS Chi-restraints excluded: chain Q3 residue 146 ILE Chi-restraints excluded: chain Q3 residue 158 GLN Chi-restraints excluded: chain Q3 residue 185 ILE Chi-restraints excluded: chain Q3 residue 211 THR Chi-restraints excluded: chain Q3 residue 220 THR Chi-restraints excluded: chain Q3 residue 295 LEU Chi-restraints excluded: chain Q3 residue 298 VAL Chi-restraints excluded: chain Q3 residue 317 VAL Chi-restraints excluded: chain Q3 residue 324 THR Chi-restraints excluded: chain Q3 residue 437 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 851 random chunks: chunk 764 optimal weight: 6.9990 chunk 582 optimal weight: 7.9990 chunk 401 optimal weight: 0.9990 chunk 85 optimal weight: 30.0000 chunk 369 optimal weight: 4.9990 chunk 519 optimal weight: 6.9990 chunk 776 optimal weight: 6.9990 chunk 822 optimal weight: 6.9990 chunk 405 optimal weight: 9.9990 chunk 736 optimal weight: 10.0000 chunk 221 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1 152 ASN ** B2 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2 194 ASN B2 300 HIS B3 161 GLN B4 149 ASN B4 286 GLN C4 89 GLN D1 167 ASN ** D2 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3 22 GLN D3 201 GLN D3 238 ASN ** D3 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4 28 ASN P1 178 ASN P1 452 GLN ** P3 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P5 41 ASN ** P5 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P7 233 ASN P7 422 ASN P8 41 ASN P8 411 ASN ** P9 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q2 73 ASN Q3 103 ASN ** Q3 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q3 452 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 71413 Z= 0.309 Angle : 0.566 9.971 96321 Z= 0.302 Chirality : 0.043 0.169 10525 Planarity : 0.004 0.046 12635 Dihedral : 4.676 27.799 9460 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.86 % Allowed : 13.76 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.09), residues: 8577 helix: 1.56 (0.10), residues: 3099 sheet: 0.34 (0.12), residues: 1786 loop : -0.24 (0.10), residues: 3692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRPC3 76 HIS 0.007 0.001 HISP3 92 PHE 0.026 0.002 PHEP5 173 TYR 0.035 0.002 TYRD5 139 ARG 0.006 0.000 ARGD4 241 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17154 Ramachandran restraints generated. 8577 Oldfield, 0 Emsley, 8577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17154 Ramachandran restraints generated. 8577 Oldfield, 0 Emsley, 8577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1457 residues out of total 7775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 1235 time to evaluate : 6.319 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B2 30 MET cc_start: 0.7447 (mmm) cc_final: 0.7074 (mpp) REVERT: B2 123 TYR cc_start: 0.8091 (t80) cc_final: 0.7501 (t80) REVERT: B2 161 GLN cc_start: 0.8991 (pt0) cc_final: 0.8681 (pt0) REVERT: B2 309 LYS cc_start: 0.8043 (tttt) cc_final: 0.7625 (tttm) REVERT: B3 34 LYS cc_start: 0.8143 (mttt) cc_final: 0.7595 (mmmt) REVERT: B3 103 MET cc_start: 0.6538 (ptm) cc_final: 0.5990 (ttp) REVERT: B3 149 ASN cc_start: 0.7973 (t160) cc_final: 0.7662 (t0) REVERT: B4 25 ASN cc_start: 0.8393 (t0) cc_final: 0.7332 (p0) REVERT: B4 35 LYS cc_start: 0.7507 (mttt) cc_final: 0.7187 (mttm) REVERT: B4 179 ILE cc_start: 0.9157 (mt) cc_final: 0.8891 (mm) REVERT: B5 279 THR cc_start: 0.8630 (m) cc_final: 0.8311 (p) REVERT: C1 73 PHE cc_start: 0.6916 (m-80) cc_final: 0.6421 (m-10) REVERT: C1 83 TYR cc_start: 0.7349 (m-80) cc_final: 0.7104 (m-10) REVERT: C2 75 PHE cc_start: 0.8571 (m-80) cc_final: 0.8348 (m-80) REVERT: D1 167 ASN cc_start: 0.8337 (t0) cc_final: 0.8108 (t0) REVERT: D1 262 TYR cc_start: 0.8531 (m-80) cc_final: 0.7829 (m-80) REVERT: D2 31 MET cc_start: 0.7328 (mtp) cc_final: 0.6526 (ttm) REVERT: D2 40 MET cc_start: 0.1477 (ptp) cc_final: -0.1400 (tpp) REVERT: D2 121 TYR cc_start: 0.7084 (m-10) cc_final: 0.6775 (m-80) REVERT: D2 139 TYR cc_start: 0.7368 (m-80) cc_final: 0.7167 (m-80) REVERT: D2 201 GLN cc_start: 0.8747 (mp10) cc_final: 0.8357 (mp10) REVERT: D2 309 LYS cc_start: 0.8172 (tttt) cc_final: 0.7926 (tttp) REVERT: D3 25 ASN cc_start: 0.8627 (t0) cc_final: 0.8409 (m-40) REVERT: D3 30 MET cc_start: 0.5972 (mmm) cc_final: 0.5741 (mmm) REVERT: D3 116 LYS cc_start: 0.8161 (mttm) cc_final: 0.7951 (mttm) REVERT: D3 130 MET cc_start: 0.8209 (mtt) cc_final: 0.7941 (mtp) REVERT: D3 176 GLN cc_start: 0.7984 (pp30) cc_final: 0.7718 (pp30) REVERT: D3 217 ARG cc_start: 0.6099 (mmt180) cc_final: 0.5859 (mtm180) REVERT: D3 252 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7704 (tp) REVERT: D3 266 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7529 (tm-30) REVERT: D4 30 MET cc_start: 0.7310 (mmm) cc_final: 0.6175 (mmm) REVERT: D4 207 ARG cc_start: 0.8061 (mtm180) cc_final: 0.7726 (ttt180) REVERT: D5 66 MET cc_start: 0.7325 (OUTLIER) cc_final: 0.6827 (mtp) REVERT: D5 126 PHE cc_start: 0.5493 (t80) cc_final: 0.5027 (t80) REVERT: P1 24 GLU cc_start: 0.8992 (mm-30) cc_final: 0.8622 (mt-10) REVERT: P1 50 GLU cc_start: 0.8862 (tt0) cc_final: 0.8603 (tp30) REVERT: P1 53 MET cc_start: 0.8826 (mtp) cc_final: 0.8625 (mtp) REVERT: P1 93 ASP cc_start: 0.8918 (t0) cc_final: 0.8667 (t0) REVERT: P1 302 LYS cc_start: 0.8728 (mtmt) cc_final: 0.8058 (pptt) REVERT: P1 383 LEU cc_start: 0.9432 (tp) cc_final: 0.9161 (tp) REVERT: P1 468 GLU cc_start: 0.8913 (tp30) cc_final: 0.8401 (tp30) REVERT: P1 470 LYS cc_start: 0.9322 (mmmm) cc_final: 0.9053 (mmmt) REVERT: P1 471 LYS cc_start: 0.9065 (tttt) cc_final: 0.8725 (ttmt) REVERT: P2 68 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8184 (mt-10) REVERT: P2 70 LYS cc_start: 0.9105 (mtpt) cc_final: 0.8863 (mtmm) REVERT: P2 132 ASP cc_start: 0.8240 (t0) cc_final: 0.7501 (t0) REVERT: P2 227 LYS cc_start: 0.8999 (tppt) cc_final: 0.8633 (mtmt) REVERT: P2 239 SER cc_start: 0.9309 (m) cc_final: 0.9014 (t) REVERT: P2 302 LYS cc_start: 0.8919 (mtmt) cc_final: 0.8623 (mtmm) REVERT: P2 322 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.7621 (mmt180) REVERT: P2 329 ASP cc_start: 0.8579 (OUTLIER) cc_final: 0.8317 (m-30) REVERT: P2 415 ILE cc_start: 0.9047 (tp) cc_final: 0.8812 (tt) REVERT: P2 473 GLU cc_start: 0.9187 (mm-30) cc_final: 0.8657 (mm-30) REVERT: P3 144 LEU cc_start: 0.9467 (mt) cc_final: 0.9142 (mt) REVERT: P3 152 GLU cc_start: 0.8532 (pp20) cc_final: 0.8195 (pp20) REVERT: P3 159 ASP cc_start: 0.8850 (t70) cc_final: 0.8451 (t0) REVERT: P3 243 MET cc_start: 0.9050 (tmm) cc_final: 0.8238 (tmm) REVERT: P3 302 LYS cc_start: 0.8698 (mtpt) cc_final: 0.8283 (ptpt) REVERT: P3 355 MET cc_start: 0.8423 (ttt) cc_final: 0.7858 (ttt) REVERT: P3 374 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8069 (mp0) REVERT: P3 456 MET cc_start: 0.9027 (mtt) cc_final: 0.8576 (mtt) REVERT: P3 468 GLU cc_start: 0.7915 (tp30) cc_final: 0.7613 (tp30) REVERT: P3 472 ILE cc_start: 0.8373 (mt) cc_final: 0.7900 (mt) REVERT: P3 478 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.7924 (mp0) REVERT: P4 61 LYS cc_start: 0.8530 (tttt) cc_final: 0.8225 (tmtt) REVERT: P4 112 GLN cc_start: 0.8240 (mp10) cc_final: 0.7624 (mp10) REVERT: P4 125 GLU cc_start: 0.8478 (tt0) cc_final: 0.7765 (mm-30) REVERT: P4 129 ASP cc_start: 0.8969 (t0) cc_final: 0.8486 (m-30) REVERT: P4 243 MET cc_start: 0.8712 (tmm) cc_final: 0.8220 (tmm) REVERT: P4 274 ASP cc_start: 0.9231 (t0) cc_final: 0.8869 (t0) REVERT: P4 428 TYR cc_start: 0.8835 (m-80) cc_final: 0.8584 (m-80) REVERT: P4 435 SER cc_start: 0.8660 (t) cc_final: 0.8169 (p) REVERT: P4 471 LYS cc_start: 0.8709 (tttt) cc_final: 0.8330 (tttm) REVERT: P4 476 GLU cc_start: 0.7903 (pt0) cc_final: 0.7627 (pt0) REVERT: P5 26 ASN cc_start: 0.8482 (t0) cc_final: 0.7957 (t0) REVERT: P5 132 ASP cc_start: 0.8319 (t0) cc_final: 0.7572 (t0) REVERT: P5 312 GLU cc_start: 0.8190 (tt0) cc_final: 0.7913 (tt0) REVERT: P5 347 ASP cc_start: 0.8769 (m-30) cc_final: 0.8419 (m-30) REVERT: P5 438 GLU cc_start: 0.8589 (tp30) cc_final: 0.8175 (tp30) REVERT: P5 439 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8205 (mt-10) REVERT: P6 31 TYR cc_start: 0.9279 (t80) cc_final: 0.8661 (t80) REVERT: P6 85 MET cc_start: 0.5412 (pmm) cc_final: 0.4275 (pmm) REVERT: P6 93 ASP cc_start: 0.8549 (t0) cc_final: 0.8149 (t0) REVERT: P6 103 ASN cc_start: 0.9335 (t0) cc_final: 0.8759 (t0) REVERT: P6 149 LYS cc_start: 0.9211 (pttt) cc_final: 0.8949 (pttp) REVERT: P6 154 MET cc_start: 0.8633 (ttm) cc_final: 0.8393 (ttm) REVERT: P6 161 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8091 (pt0) REVERT: P6 208 ASP cc_start: 0.8406 (m-30) cc_final: 0.7537 (p0) REVERT: P6 222 ARG cc_start: 0.8220 (ttt180) cc_final: 0.7801 (ttt-90) REVERT: P6 249 SER cc_start: 0.9460 (m) cc_final: 0.9064 (t) REVERT: P6 279 MET cc_start: 0.8751 (mmm) cc_final: 0.8335 (mmm) REVERT: P6 302 LYS cc_start: 0.8807 (mtmt) cc_final: 0.8578 (pttt) REVERT: P6 303 GLN cc_start: 0.8509 (tm130) cc_final: 0.8296 (tm-30) REVERT: P6 327 SER cc_start: 0.9089 (m) cc_final: 0.8633 (p) REVERT: P6 347 ASP cc_start: 0.8875 (m-30) cc_final: 0.8428 (m-30) REVERT: P6 406 GLU cc_start: 0.9050 (OUTLIER) cc_final: 0.8738 (tm-30) REVERT: P7 44 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8144 (mp0) REVERT: P7 70 LYS cc_start: 0.9140 (mtpt) cc_final: 0.8828 (mtpp) REVERT: P7 93 ASP cc_start: 0.9285 (t70) cc_final: 0.8957 (t0) REVERT: P7 181 GLU cc_start: 0.8352 (tm-30) cc_final: 0.8094 (tm-30) REVERT: P7 192 ARG cc_start: 0.9022 (ttp80) cc_final: 0.8792 (ttm-80) REVERT: P7 279 MET cc_start: 0.8702 (mmm) cc_final: 0.8341 (mmm) REVERT: P7 318 ASP cc_start: 0.8377 (t0) cc_final: 0.7973 (t0) REVERT: P8 1 MET cc_start: 0.3857 (tmm) cc_final: 0.3521 (tmm) REVERT: P8 76 GLU cc_start: 0.8109 (tp30) cc_final: 0.7653 (tp30) REVERT: P8 177 ASP cc_start: 0.8760 (t0) cc_final: 0.8220 (t0) REVERT: P8 236 GLU cc_start: 0.7925 (tt0) cc_final: 0.7651 (tt0) REVERT: P8 257 ASP cc_start: 0.8487 (m-30) cc_final: 0.8011 (m-30) REVERT: P8 343 GLU cc_start: 0.8833 (mm-30) cc_final: 0.8268 (mm-30) REVERT: P8 438 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8090 (mt-10) REVERT: P8 466 GLU cc_start: 0.8513 (tm-30) cc_final: 0.8241 (tm-30) REVERT: P8 467 LEU cc_start: 0.9271 (tt) cc_final: 0.8937 (pp) REVERT: P9 89 ARG cc_start: 0.8294 (mtm180) cc_final: 0.7414 (mtp180) REVERT: P9 177 ASP cc_start: 0.8837 (t0) cc_final: 0.8488 (t0) REVERT: P9 208 ASP cc_start: 0.8076 (m-30) cc_final: 0.7764 (m-30) REVERT: P9 221 ASN cc_start: 0.7981 (p0) cc_final: 0.7607 (p0) REVERT: P9 227 LYS cc_start: 0.9043 (tppt) cc_final: 0.8722 (mmmt) REVERT: P9 274 ASP cc_start: 0.8828 (t70) cc_final: 0.8444 (t0) REVERT: P9 281 ASP cc_start: 0.8342 (OUTLIER) cc_final: 0.7454 (t0) REVERT: P9 322 ARG cc_start: 0.8444 (mtp85) cc_final: 0.8109 (mtt180) REVERT: P9 376 MET cc_start: 0.9301 (mmm) cc_final: 0.8769 (mmm) REVERT: P9 463 GLN cc_start: 0.8054 (tp40) cc_final: 0.7295 (tp-100) REVERT: P9 473 GLU cc_start: 0.8959 (tp30) cc_final: 0.8728 (tp30) REVERT: Q1 50 GLU cc_start: 0.8932 (tt0) cc_final: 0.8195 (tm-30) REVERT: Q1 54 ASP cc_start: 0.9163 (t0) cc_final: 0.8797 (t70) REVERT: Q1 159 ASP cc_start: 0.8951 (t0) cc_final: 0.8645 (t0) REVERT: Q1 296 ASP cc_start: 0.8213 (t0) cc_final: 0.7970 (t70) REVERT: Q1 358 ASN cc_start: 0.9246 (m-40) cc_final: 0.8714 (m110) REVERT: Q1 425 ARG cc_start: 0.8442 (mtm-85) cc_final: 0.8113 (ttm110) REVERT: Q1 462 PHE cc_start: 0.8490 (m-80) cc_final: 0.8136 (m-80) REVERT: Q1 477 LYS cc_start: 0.8925 (ttmm) cc_final: 0.8609 (mtmm) REVERT: Q2 22 ASN cc_start: 0.9095 (t0) cc_final: 0.8781 (t0) REVERT: Q2 61 LYS cc_start: 0.8595 (tttt) cc_final: 0.8266 (tptp) REVERT: Q2 72 LYS cc_start: 0.8990 (tttt) cc_final: 0.8638 (tttp) REVERT: Q2 114 GLN cc_start: 0.7772 (OUTLIER) cc_final: 0.6767 (pt0) REVERT: Q2 239 SER cc_start: 0.9221 (m) cc_final: 0.9010 (t) REVERT: Q2 327 SER cc_start: 0.8678 (m) cc_final: 0.8398 (p) REVERT: Q2 359 THR cc_start: 0.9344 (m) cc_final: 0.8871 (p) REVERT: Q2 425 ARG cc_start: 0.8367 (mtm-85) cc_final: 0.7231 (mtm-85) REVERT: Q3 26 ASN cc_start: 0.7935 (t0) cc_final: 0.7613 (t0) REVERT: Q3 61 LYS cc_start: 0.8680 (tttt) cc_final: 0.8163 (ttpt) REVERT: Q3 76 GLU cc_start: 0.8258 (tt0) cc_final: 0.7889 (tp30) REVERT: Q3 119 ASP cc_start: 0.8955 (m-30) cc_final: 0.8691 (m-30) REVERT: Q3 161 GLU cc_start: 0.7512 (pm20) cc_final: 0.7252 (pm20) REVERT: Q3 221 ASN cc_start: 0.8005 (p0) cc_final: 0.7671 (p0) REVERT: Q3 296 ASP cc_start: 0.8169 (t0) cc_final: 0.7907 (t70) REVERT: Q3 323 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8225 (mt-10) REVERT: Q3 340 GLN cc_start: 0.8358 (mm-40) cc_final: 0.8147 (mt0) REVERT: Q3 358 ASN cc_start: 0.9241 (m-40) cc_final: 0.8913 (m110) REVERT: Q3 363 LYS cc_start: 0.9116 (tttm) cc_final: 0.8812 (tttt) REVERT: Q3 408 ILE cc_start: 0.8848 (tp) cc_final: 0.8560 (tp) outliers start: 222 outliers final: 160 residues processed: 1381 average time/residue: 0.6569 time to fit residues: 1532.2001 Evaluate side-chains 1292 residues out of total 7775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 1122 time to evaluate : 6.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B1 residue 162 SER Chi-restraints excluded: chain B1 residue 169 VAL Chi-restraints excluded: chain B1 residue 277 ASP Chi-restraints excluded: chain B2 residue 54 ASN Chi-restraints excluded: chain B2 residue 188 ASP Chi-restraints excluded: chain B2 residue 220 ASP Chi-restraints excluded: chain B2 residue 271 SER Chi-restraints excluded: chain B3 residue 23 VAL Chi-restraints excluded: chain B3 residue 27 ASP Chi-restraints excluded: chain B3 residue 245 ILE Chi-restraints excluded: chain B3 residue 250 ASP Chi-restraints excluded: chain B3 residue 272 THR Chi-restraints excluded: chain B4 residue 97 THR Chi-restraints excluded: chain B4 residue 167 ASN Chi-restraints excluded: chain B4 residue 169 VAL Chi-restraints excluded: chain B4 residue 232 VAL Chi-restraints excluded: chain B4 residue 264 ILE Chi-restraints excluded: chain B5 residue 44 THR Chi-restraints excluded: chain B5 residue 47 ILE Chi-restraints excluded: chain B5 residue 205 LEU Chi-restraints excluded: chain B5 residue 234 LEU Chi-restraints excluded: chain B5 residue 238 ASN Chi-restraints excluded: chain C4 residue 73 PHE Chi-restraints excluded: chain C4 residue 102 THR Chi-restraints excluded: chain C5 residue 94 SER Chi-restraints excluded: chain C5 residue 99 VAL Chi-restraints excluded: chain D1 residue 159 ILE Chi-restraints excluded: chain D1 residue 179 ILE Chi-restraints excluded: chain D1 residue 198 SER Chi-restraints excluded: chain D1 residue 204 SER Chi-restraints excluded: chain D1 residue 311 VAL Chi-restraints excluded: chain D2 residue 111 ILE Chi-restraints excluded: chain D2 residue 190 GLU Chi-restraints excluded: chain D2 residue 294 THR Chi-restraints excluded: chain D3 residue 57 ILE Chi-restraints excluded: chain D3 residue 122 THR Chi-restraints excluded: chain D3 residue 177 ASP Chi-restraints excluded: chain D3 residue 198 SER Chi-restraints excluded: chain D3 residue 243 GLU Chi-restraints excluded: chain D3 residue 252 LEU Chi-restraints excluded: chain D3 residue 266 GLU Chi-restraints excluded: chain D4 residue 57 ILE Chi-restraints excluded: chain D4 residue 177 ASP Chi-restraints excluded: chain D4 residue 231 VAL Chi-restraints excluded: chain D4 residue 259 LEU Chi-restraints excluded: chain D5 residue 29 VAL Chi-restraints excluded: chain D5 residue 44 THR Chi-restraints excluded: chain D5 residue 66 MET Chi-restraints excluded: chain D5 residue 119 LEU Chi-restraints excluded: chain D5 residue 273 VAL Chi-restraints excluded: chain D5 residue 299 LEU Chi-restraints excluded: chain P1 residue 2 LEU Chi-restraints excluded: chain P1 residue 18 ASN Chi-restraints excluded: chain P1 residue 54 ASP Chi-restraints excluded: chain P1 residue 96 SER Chi-restraints excluded: chain P1 residue 99 SER Chi-restraints excluded: chain P1 residue 119 ASP Chi-restraints excluded: chain P1 residue 143 ASP Chi-restraints excluded: chain P1 residue 206 THR Chi-restraints excluded: chain P1 residue 211 THR Chi-restraints excluded: chain P1 residue 327 SER Chi-restraints excluded: chain P1 residue 377 LYS Chi-restraints excluded: chain P1 residue 415 ILE Chi-restraints excluded: chain P1 residue 436 LEU Chi-restraints excluded: chain P1 residue 450 ILE Chi-restraints excluded: chain P2 residue 96 SER Chi-restraints excluded: chain P2 residue 124 ILE Chi-restraints excluded: chain P2 residue 175 ILE Chi-restraints excluded: chain P2 residue 197 ASP Chi-restraints excluded: chain P2 residue 262 ILE Chi-restraints excluded: chain P2 residue 298 VAL Chi-restraints excluded: chain P2 residue 322 ARG Chi-restraints excluded: chain P2 residue 327 SER Chi-restraints excluded: chain P2 residue 329 ASP Chi-restraints excluded: chain P3 residue 23 ASP Chi-restraints excluded: chain P3 residue 39 LEU Chi-restraints excluded: chain P3 residue 111 ILE Chi-restraints excluded: chain P3 residue 135 SER Chi-restraints excluded: chain P3 residue 170 MET Chi-restraints excluded: chain P3 residue 191 LEU Chi-restraints excluded: chain P3 residue 208 ASP Chi-restraints excluded: chain P3 residue 229 THR Chi-restraints excluded: chain P3 residue 295 LEU Chi-restraints excluded: chain P3 residue 296 ASP Chi-restraints excluded: chain P3 residue 478 GLU Chi-restraints excluded: chain P4 residue 154 MET Chi-restraints excluded: chain P4 residue 287 LEU Chi-restraints excluded: chain P4 residue 327 SER Chi-restraints excluded: chain P4 residue 339 VAL Chi-restraints excluded: chain P4 residue 362 MET Chi-restraints excluded: chain P4 residue 418 ASN Chi-restraints excluded: chain P5 residue 37 ASP Chi-restraints excluded: chain P5 residue 42 VAL Chi-restraints excluded: chain P5 residue 135 SER Chi-restraints excluded: chain P5 residue 164 LEU Chi-restraints excluded: chain P5 residue 196 ILE Chi-restraints excluded: chain P5 residue 439 GLU Chi-restraints excluded: chain P5 residue 469 VAL Chi-restraints excluded: chain P6 residue 152 GLU Chi-restraints excluded: chain P6 residue 193 THR Chi-restraints excluded: chain P6 residue 196 ILE Chi-restraints excluded: chain P6 residue 406 GLU Chi-restraints excluded: chain P6 residue 444 ILE Chi-restraints excluded: chain P7 residue 57 ARG Chi-restraints excluded: chain P7 residue 71 THR Chi-restraints excluded: chain P7 residue 116 ASP Chi-restraints excluded: chain P7 residue 133 VAL Chi-restraints excluded: chain P7 residue 143 ASP Chi-restraints excluded: chain P7 residue 188 VAL Chi-restraints excluded: chain P7 residue 327 SER Chi-restraints excluded: chain P7 residue 406 GLU Chi-restraints excluded: chain P7 residue 407 THR Chi-restraints excluded: chain P8 residue 39 LEU Chi-restraints excluded: chain P8 residue 87 ASP Chi-restraints excluded: chain P8 residue 90 VAL Chi-restraints excluded: chain P8 residue 124 ILE Chi-restraints excluded: chain P8 residue 152 GLU Chi-restraints excluded: chain P8 residue 188 VAL Chi-restraints excluded: chain P8 residue 196 ILE Chi-restraints excluded: chain P8 residue 208 ASP Chi-restraints excluded: chain P8 residue 284 ASP Chi-restraints excluded: chain P8 residue 298 VAL Chi-restraints excluded: chain P9 residue 18 ASN Chi-restraints excluded: chain P9 residue 37 ASP Chi-restraints excluded: chain P9 residue 50 GLU Chi-restraints excluded: chain P9 residue 96 SER Chi-restraints excluded: chain P9 residue 119 ASP Chi-restraints excluded: chain P9 residue 133 VAL Chi-restraints excluded: chain P9 residue 152 GLU Chi-restraints excluded: chain P9 residue 206 THR Chi-restraints excluded: chain P9 residue 281 ASP Chi-restraints excluded: chain P9 residue 409 LEU Chi-restraints excluded: chain P9 residue 436 LEU Chi-restraints excluded: chain Q1 residue 45 VAL Chi-restraints excluded: chain Q1 residue 121 LEU Chi-restraints excluded: chain Q1 residue 139 SER Chi-restraints excluded: chain Q1 residue 204 VAL Chi-restraints excluded: chain Q1 residue 215 VAL Chi-restraints excluded: chain Q1 residue 229 THR Chi-restraints excluded: chain Q1 residue 284 ASP Chi-restraints excluded: chain Q1 residue 295 LEU Chi-restraints excluded: chain Q1 residue 298 VAL Chi-restraints excluded: chain Q1 residue 327 SER Chi-restraints excluded: chain Q1 residue 362 MET Chi-restraints excluded: chain Q1 residue 467 LEU Chi-restraints excluded: chain Q2 residue 96 SER Chi-restraints excluded: chain Q2 residue 114 GLN Chi-restraints excluded: chain Q2 residue 119 ASP Chi-restraints excluded: chain Q2 residue 133 VAL Chi-restraints excluded: chain Q2 residue 155 ILE Chi-restraints excluded: chain Q2 residue 263 THR Chi-restraints excluded: chain Q2 residue 298 VAL Chi-restraints excluded: chain Q2 residue 355 MET Chi-restraints excluded: chain Q2 residue 406 GLU Chi-restraints excluded: chain Q2 residue 410 LYS Chi-restraints excluded: chain Q3 residue 96 SER Chi-restraints excluded: chain Q3 residue 124 ILE Chi-restraints excluded: chain Q3 residue 146 ILE Chi-restraints excluded: chain Q3 residue 158 GLN Chi-restraints excluded: chain Q3 residue 185 ILE Chi-restraints excluded: chain Q3 residue 211 THR Chi-restraints excluded: chain Q3 residue 220 THR Chi-restraints excluded: chain Q3 residue 295 LEU Chi-restraints excluded: chain Q3 residue 298 VAL Chi-restraints excluded: chain Q3 residue 317 VAL Chi-restraints excluded: chain Q3 residue 324 THR Chi-restraints excluded: chain Q3 residue 328 VAL Chi-restraints excluded: chain Q3 residue 406 GLU Chi-restraints excluded: chain Q3 residue 437 ILE Chi-restraints excluded: chain Q3 residue 456 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 851 random chunks: chunk 685 optimal weight: 8.9990 chunk 466 optimal weight: 20.0000 chunk 11 optimal weight: 7.9990 chunk 612 optimal weight: 6.9990 chunk 339 optimal weight: 9.9990 chunk 701 optimal weight: 20.0000 chunk 568 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 420 optimal weight: 4.9990 chunk 738 optimal weight: 0.8980 chunk 207 optimal weight: 2.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1 178 ASN ** B2 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2 201 GLN B4 286 GLN ** B5 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4 89 GLN ** D1 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 238 ASN ** D2 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3 201 GLN ** D3 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P1 178 ASN P3 136 HIS ** P3 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P5 41 ASN P6 178 ASN P7 422 ASN P8 411 ASN ** P9 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q1 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q2 73 ASN Q3 43 ASN ** Q3 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q3 452 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.4427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 71413 Z= 0.276 Angle : 0.543 10.268 96321 Z= 0.289 Chirality : 0.042 0.159 10525 Planarity : 0.003 0.045 12635 Dihedral : 4.559 27.549 9460 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.93 % Allowed : 14.56 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.09), residues: 8577 helix: 1.69 (0.10), residues: 3102 sheet: 0.28 (0.12), residues: 1786 loop : -0.23 (0.10), residues: 3689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRPC3 76 HIS 0.006 0.001 HISP3 92 PHE 0.025 0.002 PHEP5 173 TYR 0.023 0.001 TYRD1 139 ARG 0.007 0.000 ARGP1 301 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17154 Ramachandran restraints generated. 8577 Oldfield, 0 Emsley, 8577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17154 Ramachandran restraints generated. 8577 Oldfield, 0 Emsley, 8577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1405 residues out of total 7775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 1177 time to evaluate : 6.184 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: 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: B1 76 TRP cc_start: 0.5678 (p-90) cc_final: 0.5367 (p-90) REVERT: B1 79 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.7678 (mtmm) REVERT: B1 177 ASP cc_start: 0.6497 (OUTLIER) cc_final: 0.6278 (p0) REVERT: B2 30 MET cc_start: 0.7452 (mmm) cc_final: 0.7235 (mpp) REVERT: B2 89 GLN cc_start: 0.8140 (mm-40) cc_final: 0.7909 (mm-40) REVERT: B2 123 TYR cc_start: 0.8307 (t80) cc_final: 0.7525 (t80) REVERT: B3 34 LYS cc_start: 0.8253 (mttt) cc_final: 0.7557 (mmmt) REVERT: B3 103 MET cc_start: 0.6505 (ptm) cc_final: 0.6105 (ttp) REVERT: B3 149 ASN cc_start: 0.7949 (t160) cc_final: 0.7645 (t0) REVERT: B4 25 ASN cc_start: 0.8351 (t0) cc_final: 0.7289 (p0) REVERT: B4 104 ARG cc_start: 0.8236 (ptp90) cc_final: 0.7894 (ptp90) REVERT: B5 130 MET cc_start: 0.8034 (mmm) cc_final: 0.7466 (mmm) REVERT: B5 279 THR cc_start: 0.8627 (m) cc_final: 0.8324 (p) REVERT: B5 295 MET cc_start: 0.7253 (ttp) cc_final: 0.6946 (ttm) REVERT: C1 70 GLU cc_start: 0.5949 (mp0) cc_final: 0.5621 (mp0) REVERT: C1 73 PHE cc_start: 0.7102 (m-80) cc_final: 0.6595 (m-10) REVERT: D1 165 LYS cc_start: 0.7998 (ttmt) cc_final: 0.7689 (ptmt) REVERT: D1 262 TYR cc_start: 0.8490 (m-80) cc_final: 0.7894 (m-80) REVERT: D1 305 LYS cc_start: 0.7508 (mppt) cc_final: 0.7279 (mtmm) REVERT: D2 31 MET cc_start: 0.7317 (mtp) cc_final: 0.6537 (ttm) REVERT: D2 40 MET cc_start: 0.1476 (ptp) cc_final: -0.1456 (tpp) REVERT: D2 309 LYS cc_start: 0.7988 (tttt) cc_final: 0.7759 (tttp) REVERT: D3 25 ASN cc_start: 0.8628 (t0) cc_final: 0.8369 (m-40) REVERT: D3 123 TYR cc_start: 0.6289 (t80) cc_final: 0.5613 (t80) REVERT: D3 130 MET cc_start: 0.8244 (mtt) cc_final: 0.7905 (mtp) REVERT: D3 176 GLN cc_start: 0.7769 (pp30) cc_final: 0.7489 (pp30) REVERT: D3 217 ARG cc_start: 0.6183 (mmt180) cc_final: 0.5841 (mtm180) REVERT: D3 275 ASN cc_start: 0.8296 (m-40) cc_final: 0.8047 (m110) REVERT: D4 30 MET cc_start: 0.7352 (mmm) cc_final: 0.6176 (mmm) REVERT: D4 48 LEU cc_start: 0.7064 (OUTLIER) cc_final: 0.6721 (mt) REVERT: D4 194 ASN cc_start: 0.7600 (t0) cc_final: 0.7342 (t0) REVERT: D4 207 ARG cc_start: 0.7982 (mtm180) cc_final: 0.7595 (ttt180) REVERT: D5 40 MET cc_start: 0.1834 (mmm) cc_final: 0.1443 (mtm) REVERT: D5 126 PHE cc_start: 0.5594 (t80) cc_final: 0.5378 (t80) REVERT: P1 1 MET cc_start: 0.7365 (tpp) cc_final: 0.7064 (tpp) REVERT: P1 24 GLU cc_start: 0.8944 (mm-30) cc_final: 0.8605 (mt-10) REVERT: P1 50 GLU cc_start: 0.8857 (tt0) cc_final: 0.8596 (tp30) REVERT: P1 93 ASP cc_start: 0.8867 (t0) cc_final: 0.8637 (t0) REVERT: P1 243 MET cc_start: 0.8883 (tmm) cc_final: 0.8616 (tmm) REVERT: P1 301 ARG cc_start: 0.7946 (mmp80) cc_final: 0.7178 (ttm-80) REVERT: P1 302 LYS cc_start: 0.8753 (mtmt) cc_final: 0.8281 (pptt) REVERT: P1 383 LEU cc_start: 0.9423 (tp) cc_final: 0.9140 (tp) REVERT: P1 468 GLU cc_start: 0.8888 (tp30) cc_final: 0.8371 (tp30) REVERT: P1 470 LYS cc_start: 0.9306 (mmmm) cc_final: 0.9032 (mmmt) REVERT: P1 471 LYS cc_start: 0.9069 (tttt) cc_final: 0.8717 (ttmt) REVERT: P2 68 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8167 (mt-10) REVERT: P2 70 LYS cc_start: 0.9017 (mtpt) cc_final: 0.8745 (mtmm) REVERT: P2 93 ASP cc_start: 0.8600 (t70) cc_final: 0.8338 (t70) REVERT: P2 132 ASP cc_start: 0.8266 (t0) cc_final: 0.7497 (t0) REVERT: P2 182 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.7873 (mmm-85) REVERT: P2 227 LYS cc_start: 0.9002 (tppt) cc_final: 0.8629 (mtmt) REVERT: P2 239 SER cc_start: 0.9353 (m) cc_final: 0.9063 (t) REVERT: P2 302 LYS cc_start: 0.8910 (mtmt) cc_final: 0.8623 (mtmm) REVERT: P2 322 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.7631 (mmt180) REVERT: P2 329 ASP cc_start: 0.8590 (OUTLIER) cc_final: 0.8277 (m-30) REVERT: P2 415 ILE cc_start: 0.9047 (tp) cc_final: 0.8747 (tt) REVERT: P2 438 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8291 (tp30) REVERT: P3 1 MET cc_start: 0.8283 (ptp) cc_final: 0.8005 (ptp) REVERT: P3 144 LEU cc_start: 0.9462 (mt) cc_final: 0.9216 (mt) REVERT: P3 152 GLU cc_start: 0.8555 (pp20) cc_final: 0.8177 (pp20) REVERT: P3 159 ASP cc_start: 0.8883 (t70) cc_final: 0.8429 (t0) REVERT: P3 243 MET cc_start: 0.9026 (tmm) cc_final: 0.8219 (tmm) REVERT: P3 301 ARG cc_start: 0.8651 (mtm-85) cc_final: 0.8290 (mtm-85) REVERT: P3 355 MET cc_start: 0.8513 (ttt) cc_final: 0.7981 (ttt) REVERT: P3 374 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8016 (mp0) REVERT: P3 425 ARG cc_start: 0.8160 (mtm-85) cc_final: 0.7803 (mtt-85) REVERT: P3 456 MET cc_start: 0.9021 (mtt) cc_final: 0.8518 (mtt) REVERT: P3 468 GLU cc_start: 0.7603 (tp30) cc_final: 0.6793 (tp30) REVERT: P3 472 ILE cc_start: 0.8413 (mt) cc_final: 0.7788 (mt) REVERT: P3 476 GLU cc_start: 0.8460 (pp20) cc_final: 0.7976 (pp20) REVERT: P3 478 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.7928 (mp0) REVERT: P4 61 LYS cc_start: 0.8512 (tttt) cc_final: 0.8230 (tmtt) REVERT: P4 112 GLN cc_start: 0.8309 (mp10) cc_final: 0.7646 (mp10) REVERT: P4 125 GLU cc_start: 0.8511 (tt0) cc_final: 0.7779 (mm-30) REVERT: P4 129 ASP cc_start: 0.8958 (t0) cc_final: 0.8474 (m-30) REVERT: P4 170 MET cc_start: 0.9358 (mtp) cc_final: 0.9112 (ttm) REVERT: P4 192 ARG cc_start: 0.8050 (ttt90) cc_final: 0.7741 (ttt90) REVERT: P4 243 MET cc_start: 0.8721 (tmm) cc_final: 0.8142 (tmm) REVERT: P4 274 ASP cc_start: 0.9242 (t0) cc_final: 0.8901 (t0) REVERT: P4 428 TYR cc_start: 0.8871 (m-80) cc_final: 0.8621 (m-80) REVERT: P4 435 SER cc_start: 0.8671 (t) cc_final: 0.8032 (p) REVERT: P4 439 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7775 (mt-10) REVERT: P4 471 LYS cc_start: 0.8699 (tttt) cc_final: 0.8331 (tttm) REVERT: P4 476 GLU cc_start: 0.7995 (pt0) cc_final: 0.7702 (pt0) REVERT: P5 26 ASN cc_start: 0.8414 (t0) cc_final: 0.7967 (t0) REVERT: P5 41 ASN cc_start: 0.8000 (OUTLIER) cc_final: 0.7022 (t0) REVERT: P5 44 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8036 (mp0) REVERT: P5 118 LYS cc_start: 0.8381 (tppt) cc_final: 0.8142 (tppt) REVERT: P5 132 ASP cc_start: 0.8336 (t0) cc_final: 0.7508 (t0) REVERT: P5 312 GLU cc_start: 0.8151 (tt0) cc_final: 0.7880 (tt0) REVERT: P5 386 ARG cc_start: 0.9227 (OUTLIER) cc_final: 0.8905 (ttm170) REVERT: P5 438 GLU cc_start: 0.8590 (tp30) cc_final: 0.8178 (tp30) REVERT: P6 85 MET cc_start: 0.5444 (pmm) cc_final: 0.4361 (pmm) REVERT: P6 93 ASP cc_start: 0.8517 (t0) cc_final: 0.8097 (t0) REVERT: P6 103 ASN cc_start: 0.9318 (t0) cc_final: 0.8753 (t0) REVERT: P6 149 LYS cc_start: 0.9196 (pttt) cc_final: 0.8962 (pttp) REVERT: P6 154 MET cc_start: 0.8613 (ttm) cc_final: 0.8383 (ttm) REVERT: P6 208 ASP cc_start: 0.8453 (m-30) cc_final: 0.7691 (p0) REVERT: P6 249 SER cc_start: 0.9471 (m) cc_final: 0.9058 (t) REVERT: P6 279 MET cc_start: 0.8716 (mmm) cc_final: 0.8255 (mmm) REVERT: P6 302 LYS cc_start: 0.8848 (mtmt) cc_final: 0.8627 (pttt) REVERT: P6 303 GLN cc_start: 0.8606 (tm130) cc_final: 0.8340 (tm-30) REVERT: P6 327 SER cc_start: 0.9132 (m) cc_final: 0.8671 (p) REVERT: P6 347 ASP cc_start: 0.8883 (m-30) cc_final: 0.8468 (m-30) REVERT: P6 406 GLU cc_start: 0.9047 (OUTLIER) cc_final: 0.8732 (tm-30) REVERT: P7 44 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8203 (mp0) REVERT: P7 70 LYS cc_start: 0.9140 (mtpt) cc_final: 0.8810 (mtpp) REVERT: P7 93 ASP cc_start: 0.9276 (t70) cc_final: 0.8941 (t0) REVERT: P7 181 GLU cc_start: 0.8457 (tm-30) cc_final: 0.8169 (tm-30) REVERT: P7 318 ASP cc_start: 0.8394 (t0) cc_final: 0.8036 (t0) REVERT: P8 1 MET cc_start: 0.4707 (OUTLIER) cc_final: 0.4124 (tmm) REVERT: P8 76 GLU cc_start: 0.8043 (tp30) cc_final: 0.7601 (tp30) REVERT: P8 177 ASP cc_start: 0.8903 (t0) cc_final: 0.8401 (t0) REVERT: P8 192 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.8050 (tpt170) REVERT: P8 236 GLU cc_start: 0.7805 (tt0) cc_final: 0.7541 (tt0) REVERT: P8 257 ASP cc_start: 0.8482 (m-30) cc_final: 0.8017 (m-30) REVERT: P8 343 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8338 (mm-30) REVERT: P8 438 GLU cc_start: 0.8350 (mt-10) cc_final: 0.8038 (mt-10) REVERT: P8 466 GLU cc_start: 0.8512 (tm-30) cc_final: 0.8293 (tm-30) REVERT: P8 467 LEU cc_start: 0.9207 (tt) cc_final: 0.8884 (pp) REVERT: P9 208 ASP cc_start: 0.7959 (m-30) cc_final: 0.7640 (m-30) REVERT: P9 221 ASN cc_start: 0.7957 (p0) cc_final: 0.7599 (p0) REVERT: P9 227 LYS cc_start: 0.9015 (tppt) cc_final: 0.8623 (mmmt) REVERT: P9 274 ASP cc_start: 0.8827 (t70) cc_final: 0.8442 (t0) REVERT: P9 322 ARG cc_start: 0.8441 (mtp85) cc_final: 0.8030 (mtt180) REVERT: P9 376 MET cc_start: 0.9281 (mmm) cc_final: 0.8754 (mmm) REVERT: P9 452 GLN cc_start: 0.8857 (mm-40) cc_final: 0.8360 (pm20) REVERT: P9 463 GLN cc_start: 0.8003 (tp40) cc_final: 0.7215 (tp-100) REVERT: P9 473 GLU cc_start: 0.8924 (tp30) cc_final: 0.8695 (tp30) REVERT: Q1 24 GLU cc_start: 0.9204 (mm-30) cc_final: 0.8522 (mm-30) REVERT: Q1 50 GLU cc_start: 0.8877 (tt0) cc_final: 0.8126 (tm-30) REVERT: Q1 54 ASP cc_start: 0.9151 (t0) cc_final: 0.8771 (t70) REVERT: Q1 296 ASP cc_start: 0.8241 (t0) cc_final: 0.7993 (t70) REVERT: Q1 358 ASN cc_start: 0.9226 (m-40) cc_final: 0.8691 (m110) REVERT: Q1 425 ARG cc_start: 0.8562 (mtm-85) cc_final: 0.8251 (ptp90) REVERT: Q1 462 PHE cc_start: 0.8445 (m-80) cc_final: 0.8147 (m-80) REVERT: Q2 22 ASN cc_start: 0.9081 (t0) cc_final: 0.8877 (t0) REVERT: Q2 50 GLU cc_start: 0.8808 (tt0) cc_final: 0.8571 (tt0) REVERT: Q2 61 LYS cc_start: 0.8596 (tttt) cc_final: 0.8267 (tptp) REVERT: Q2 72 LYS cc_start: 0.8945 (tttt) cc_final: 0.8604 (tttm) REVERT: Q2 327 SER cc_start: 0.8637 (m) cc_final: 0.8358 (p) REVERT: Q2 359 THR cc_start: 0.9328 (m) cc_final: 0.8872 (p) REVERT: Q2 406 GLU cc_start: 0.9052 (OUTLIER) cc_final: 0.8610 (tt0) REVERT: Q3 26 ASN cc_start: 0.7901 (t0) cc_final: 0.7605 (t0) REVERT: Q3 61 LYS cc_start: 0.8682 (tttt) cc_final: 0.8166 (ttpt) REVERT: Q3 76 GLU cc_start: 0.8257 (tt0) cc_final: 0.7893 (tp30) REVERT: Q3 119 ASP cc_start: 0.8919 (m-30) cc_final: 0.8634 (m-30) REVERT: Q3 221 ASN cc_start: 0.8174 (p0) cc_final: 0.7764 (p0) REVERT: Q3 323 GLU cc_start: 0.8482 (mt-10) cc_final: 0.8269 (mt-10) REVERT: Q3 340 GLN cc_start: 0.8353 (mm-40) cc_final: 0.8141 (mt0) REVERT: Q3 358 ASN cc_start: 0.9241 (m-40) cc_final: 0.8915 (m110) REVERT: Q3 363 LYS cc_start: 0.9099 (tttm) cc_final: 0.8790 (tttt) outliers start: 228 outliers final: 172 residues processed: 1327 average time/residue: 0.6916 time to fit residues: 1555.6121 Evaluate side-chains 1294 residues out of total 7775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 1109 time to evaluate : 6.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B1 residue 79 LYS Chi-restraints excluded: chain B1 residue 162 SER Chi-restraints excluded: chain B1 residue 169 VAL Chi-restraints excluded: chain B1 residue 177 ASP Chi-restraints excluded: chain B1 residue 178 ASN Chi-restraints excluded: chain B1 residue 222 ASN Chi-restraints excluded: chain B1 residue 277 ASP Chi-restraints excluded: chain B2 residue 54 ASN Chi-restraints excluded: chain B2 residue 143 ASP Chi-restraints excluded: chain B2 residue 188 ASP Chi-restraints excluded: chain B2 residue 220 ASP Chi-restraints excluded: chain B2 residue 234 LEU Chi-restraints excluded: chain B2 residue 271 SER Chi-restraints excluded: chain B2 residue 304 ASP Chi-restraints excluded: chain B3 residue 23 VAL Chi-restraints excluded: chain B3 residue 27 ASP Chi-restraints excluded: chain B3 residue 69 THR Chi-restraints excluded: chain B3 residue 97 THR Chi-restraints excluded: chain B3 residue 177 ASP Chi-restraints excluded: chain B3 residue 245 ILE Chi-restraints excluded: chain B3 residue 272 THR Chi-restraints excluded: chain B3 residue 304 ASP Chi-restraints excluded: chain B4 residue 97 THR Chi-restraints excluded: chain B4 residue 124 SER Chi-restraints excluded: chain B4 residue 169 VAL Chi-restraints excluded: chain B4 residue 264 ILE Chi-restraints excluded: chain B4 residue 266 GLU Chi-restraints excluded: chain B5 residue 44 THR Chi-restraints excluded: chain B5 residue 47 ILE Chi-restraints excluded: chain B5 residue 162 SER Chi-restraints excluded: chain B5 residue 205 LEU Chi-restraints excluded: chain B5 residue 234 LEU Chi-restraints excluded: chain B5 residue 238 ASN Chi-restraints excluded: chain C4 residue 73 PHE Chi-restraints excluded: chain C5 residue 94 SER Chi-restraints excluded: chain C5 residue 99 VAL Chi-restraints excluded: chain D1 residue 159 ILE Chi-restraints excluded: chain D1 residue 179 ILE Chi-restraints excluded: chain D1 residue 198 SER Chi-restraints excluded: chain D1 residue 204 SER Chi-restraints excluded: chain D1 residue 311 VAL Chi-restraints excluded: chain D2 residue 111 ILE Chi-restraints excluded: chain D2 residue 190 GLU Chi-restraints excluded: chain D3 residue 57 ILE Chi-restraints excluded: chain D3 residue 122 THR Chi-restraints excluded: chain D3 residue 177 ASP Chi-restraints excluded: chain D3 residue 198 SER Chi-restraints excluded: chain D3 residue 243 GLU Chi-restraints excluded: chain D4 residue 48 LEU Chi-restraints excluded: chain D4 residue 57 ILE Chi-restraints excluded: chain D4 residue 177 ASP Chi-restraints excluded: chain D4 residue 231 VAL Chi-restraints excluded: chain D5 residue 44 THR Chi-restraints excluded: chain D5 residue 273 VAL Chi-restraints excluded: chain D5 residue 299 LEU Chi-restraints excluded: chain P1 residue 2 LEU Chi-restraints excluded: chain P1 residue 18 ASN Chi-restraints excluded: chain P1 residue 39 LEU Chi-restraints excluded: chain P1 residue 54 ASP Chi-restraints excluded: chain P1 residue 96 SER Chi-restraints excluded: chain P1 residue 99 SER Chi-restraints excluded: chain P1 residue 119 ASP Chi-restraints excluded: chain P1 residue 143 ASP Chi-restraints excluded: chain P1 residue 206 THR Chi-restraints excluded: chain P1 residue 211 THR Chi-restraints excluded: chain P1 residue 284 ASP Chi-restraints excluded: chain P1 residue 327 SER Chi-restraints excluded: chain P1 residue 377 LYS Chi-restraints excluded: chain P1 residue 415 ILE Chi-restraints excluded: chain P1 residue 436 LEU Chi-restraints excluded: chain P1 residue 450 ILE Chi-restraints excluded: chain P2 residue 96 SER Chi-restraints excluded: chain P2 residue 124 ILE Chi-restraints excluded: chain P2 residue 155 ILE Chi-restraints excluded: chain P2 residue 175 ILE Chi-restraints excluded: chain P2 residue 182 ARG Chi-restraints excluded: chain P2 residue 229 THR Chi-restraints excluded: chain P2 residue 262 ILE Chi-restraints excluded: chain P2 residue 322 ARG Chi-restraints excluded: chain P2 residue 329 ASP Chi-restraints excluded: chain P2 residue 444 ILE Chi-restraints excluded: chain P3 residue 23 ASP Chi-restraints excluded: chain P3 residue 39 LEU Chi-restraints excluded: chain P3 residue 43 ASN Chi-restraints excluded: chain P3 residue 111 ILE Chi-restraints excluded: chain P3 residue 135 SER Chi-restraints excluded: chain P3 residue 170 MET Chi-restraints excluded: chain P3 residue 191 LEU Chi-restraints excluded: chain P3 residue 208 ASP Chi-restraints excluded: chain P3 residue 229 THR Chi-restraints excluded: chain P3 residue 295 LEU Chi-restraints excluded: chain P3 residue 296 ASP Chi-restraints excluded: chain P3 residue 406 GLU Chi-restraints excluded: chain P3 residue 478 GLU Chi-restraints excluded: chain P4 residue 154 MET Chi-restraints excluded: chain P4 residue 339 VAL Chi-restraints excluded: chain P4 residue 418 ASN Chi-restraints excluded: chain P5 residue 37 ASP Chi-restraints excluded: chain P5 residue 41 ASN Chi-restraints excluded: chain P5 residue 42 VAL Chi-restraints excluded: chain P5 residue 135 SER Chi-restraints excluded: chain P5 residue 164 LEU Chi-restraints excluded: chain P5 residue 196 ILE Chi-restraints excluded: chain P5 residue 286 MET Chi-restraints excluded: chain P5 residue 339 VAL Chi-restraints excluded: chain P5 residue 386 ARG Chi-restraints excluded: chain P5 residue 469 VAL Chi-restraints excluded: chain P6 residue 26 ASN Chi-restraints excluded: chain P6 residue 152 GLU Chi-restraints excluded: chain P6 residue 170 MET Chi-restraints excluded: chain P6 residue 193 THR Chi-restraints excluded: chain P6 residue 196 ILE Chi-restraints excluded: chain P6 residue 406 GLU Chi-restraints excluded: chain P7 residue 57 ARG Chi-restraints excluded: chain P7 residue 71 THR Chi-restraints excluded: chain P7 residue 99 SER Chi-restraints excluded: chain P7 residue 116 ASP Chi-restraints excluded: chain P7 residue 133 VAL Chi-restraints excluded: chain P7 residue 143 ASP Chi-restraints excluded: chain P7 residue 188 VAL Chi-restraints excluded: chain P7 residue 239 SER Chi-restraints excluded: chain P7 residue 327 SER Chi-restraints excluded: chain P7 residue 406 GLU Chi-restraints excluded: chain P7 residue 407 THR Chi-restraints excluded: chain P8 residue 1 MET Chi-restraints excluded: chain P8 residue 39 LEU Chi-restraints excluded: chain P8 residue 87 ASP Chi-restraints excluded: chain P8 residue 90 VAL Chi-restraints excluded: chain P8 residue 124 ILE Chi-restraints excluded: chain P8 residue 152 GLU Chi-restraints excluded: chain P8 residue 188 VAL Chi-restraints excluded: chain P8 residue 192 ARG Chi-restraints excluded: chain P8 residue 196 ILE Chi-restraints excluded: chain P8 residue 208 ASP Chi-restraints excluded: chain P8 residue 284 ASP Chi-restraints excluded: chain P8 residue 298 VAL Chi-restraints excluded: chain P9 residue 18 ASN Chi-restraints excluded: chain P9 residue 37 ASP Chi-restraints excluded: chain P9 residue 50 GLU Chi-restraints excluded: chain P9 residue 96 SER Chi-restraints excluded: chain P9 residue 133 VAL Chi-restraints excluded: chain P9 residue 152 GLU Chi-restraints excluded: chain P9 residue 188 VAL Chi-restraints excluded: chain P9 residue 206 THR Chi-restraints excluded: chain P9 residue 281 ASP Chi-restraints excluded: chain P9 residue 318 ASP Chi-restraints excluded: chain P9 residue 339 VAL Chi-restraints excluded: chain P9 residue 409 LEU Chi-restraints excluded: chain Q1 residue 43 ASN Chi-restraints excluded: chain Q1 residue 45 VAL Chi-restraints excluded: chain Q1 residue 121 LEU Chi-restraints excluded: chain Q1 residue 139 SER Chi-restraints excluded: chain Q1 residue 204 VAL Chi-restraints excluded: chain Q1 residue 215 VAL Chi-restraints excluded: chain Q1 residue 229 THR Chi-restraints excluded: chain Q1 residue 284 ASP Chi-restraints excluded: chain Q1 residue 295 LEU Chi-restraints excluded: chain Q1 residue 298 VAL Chi-restraints excluded: chain Q1 residue 327 SER Chi-restraints excluded: chain Q1 residue 362 MET Chi-restraints excluded: chain Q1 residue 467 LEU Chi-restraints excluded: chain Q2 residue 96 SER Chi-restraints excluded: chain Q2 residue 119 ASP Chi-restraints excluded: chain Q2 residue 133 VAL Chi-restraints excluded: chain Q2 residue 155 ILE Chi-restraints excluded: chain Q2 residue 170 MET Chi-restraints excluded: chain Q2 residue 193 THR Chi-restraints excluded: chain Q2 residue 263 THR Chi-restraints excluded: chain Q2 residue 355 MET Chi-restraints excluded: chain Q2 residue 406 GLU Chi-restraints excluded: chain Q2 residue 410 LYS Chi-restraints excluded: chain Q3 residue 43 ASN Chi-restraints excluded: chain Q3 residue 96 SER Chi-restraints excluded: chain Q3 residue 124 ILE Chi-restraints excluded: chain Q3 residue 185 ILE Chi-restraints excluded: chain Q3 residue 211 THR Chi-restraints excluded: chain Q3 residue 220 THR Chi-restraints excluded: chain Q3 residue 295 LEU Chi-restraints excluded: chain Q3 residue 298 VAL Chi-restraints excluded: chain Q3 residue 317 VAL Chi-restraints excluded: chain Q3 residue 324 THR Chi-restraints excluded: chain Q3 residue 328 VAL Chi-restraints excluded: chain Q3 residue 406 GLU Chi-restraints excluded: chain Q3 residue 440 LEU Chi-restraints excluded: chain Q3 residue 456 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 851 random chunks: chunk 276 optimal weight: 20.0000 chunk 740 optimal weight: 5.9990 chunk 162 optimal weight: 30.0000 chunk 482 optimal weight: 7.9990 chunk 203 optimal weight: 20.0000 chunk 823 optimal weight: 7.9990 chunk 683 optimal weight: 5.9990 chunk 381 optimal weight: 10.0000 chunk 68 optimal weight: 20.0000 chunk 272 optimal weight: 20.0000 chunk 432 optimal weight: 9.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1 161 GLN B1 178 ASN B3 41 ASN ** B3 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3 282 ASN ** B4 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4 286 GLN ** B5 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4 89 GLN ** D1 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1 167 ASN ** D1 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 286 GLN ** D2 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3 59 GLN D3 201 GLN ** D3 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 152 ASN ** D5 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P1 178 ASN ** P3 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P4 270 ASN ** P5 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P6 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P7 422 ASN P8 411 ASN ** P9 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q1 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q2 73 ASN ** Q3 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.4726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 71413 Z= 0.420 Angle : 0.629 11.059 96321 Z= 0.333 Chirality : 0.044 0.187 10525 Planarity : 0.004 0.052 12635 Dihedral : 4.845 29.274 9460 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.45 % Allowed : 14.96 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.09), residues: 8577 helix: 1.44 (0.10), residues: 3110 sheet: 0.12 (0.11), residues: 1765 loop : -0.38 (0.10), residues: 3702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRPC3 76 HIS 0.007 0.002 HISP3 92 PHE 0.029 0.002 PHEP5 173 TYR 0.023 0.002 TYRB5 262 ARG 0.007 0.001 ARGP8 192 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17154 Ramachandran restraints generated. 8577 Oldfield, 0 Emsley, 8577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17154 Ramachandran restraints generated. 8577 Oldfield, 0 Emsley, 8577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1423 residues out of total 7775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 268 poor density : 1155 time to evaluate : 6.403 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B1 76 TRP cc_start: 0.5795 (p-90) cc_final: 0.5580 (p-90) REVERT: B1 79 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.8179 (mmtm) REVERT: B1 161 GLN cc_start: 0.7641 (mt0) cc_final: 0.7347 (mt0) REVERT: B2 22 GLN cc_start: 0.8043 (tp-100) cc_final: 0.7758 (tp-100) REVERT: B2 89 GLN cc_start: 0.8282 (mm-40) cc_final: 0.8036 (mm-40) REVERT: B2 123 TYR cc_start: 0.8218 (t80) cc_final: 0.7529 (t80) REVERT: B3 103 MET cc_start: 0.6698 (ptm) cc_final: 0.6383 (ttp) REVERT: B3 149 ASN cc_start: 0.8079 (t160) cc_final: 0.7838 (t0) REVERT: B3 196 PHE cc_start: 0.6787 (OUTLIER) cc_final: 0.6285 (m-80) REVERT: B3 240 LYS cc_start: 0.8865 (mmtm) cc_final: 0.8198 (tptp) REVERT: B4 25 ASN cc_start: 0.8282 (t0) cc_final: 0.7360 (p0) REVERT: B4 266 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7234 (pp20) REVERT: B5 130 MET cc_start: 0.8140 (mmm) cc_final: 0.7637 (mmm) REVERT: B5 279 THR cc_start: 0.8782 (m) cc_final: 0.8490 (p) REVERT: B5 295 MET cc_start: 0.7423 (ttp) cc_final: 0.7083 (ttm) REVERT: C1 73 PHE cc_start: 0.7271 (m-80) cc_final: 0.6741 (m-10) REVERT: C2 89 GLN cc_start: 0.8910 (mt0) cc_final: 0.8639 (mt0) REVERT: C5 71 LYS cc_start: 0.8920 (tppt) cc_final: 0.8082 (tttt) REVERT: D1 167 ASN cc_start: 0.8395 (t0) cc_final: 0.8185 (t0) REVERT: D1 262 TYR cc_start: 0.8554 (m-80) cc_final: 0.8054 (m-80) REVERT: D2 309 LYS cc_start: 0.8136 (tttt) cc_final: 0.7928 (tttp) REVERT: D3 25 ASN cc_start: 0.8654 (t0) cc_final: 0.8428 (m-40) REVERT: D3 130 MET cc_start: 0.8295 (mtt) cc_final: 0.8057 (mtp) REVERT: D3 217 ARG cc_start: 0.6476 (mmt180) cc_final: 0.5876 (mtm180) REVERT: D4 30 MET cc_start: 0.7299 (mmm) cc_final: 0.6168 (mmm) REVERT: D4 48 LEU cc_start: 0.7068 (OUTLIER) cc_final: 0.6606 (mt) REVERT: D4 207 ARG cc_start: 0.8034 (mtm180) cc_final: 0.7774 (ttt180) REVERT: D5 40 MET cc_start: 0.2260 (mmm) cc_final: 0.1970 (mtm) REVERT: D5 66 MET cc_start: 0.5455 (mtm) cc_final: 0.5253 (mtm) REVERT: D5 126 PHE cc_start: 0.5768 (t80) cc_final: 0.5563 (t80) REVERT: P1 1 MET cc_start: 0.7306 (tpp) cc_final: 0.6999 (tpp) REVERT: P1 24 GLU cc_start: 0.8984 (mm-30) cc_final: 0.8520 (mt-10) REVERT: P1 31 TYR cc_start: 0.8756 (t80) cc_final: 0.8386 (t80) REVERT: P1 50 GLU cc_start: 0.8898 (tt0) cc_final: 0.8570 (tp30) REVERT: P1 93 ASP cc_start: 0.9007 (t0) cc_final: 0.8758 (t0) REVERT: P1 243 MET cc_start: 0.8897 (tmm) cc_final: 0.8608 (tmm) REVERT: P1 302 LYS cc_start: 0.8799 (mtmt) cc_final: 0.8254 (pptt) REVERT: P1 383 LEU cc_start: 0.9460 (tp) cc_final: 0.9217 (tp) REVERT: P1 468 GLU cc_start: 0.8869 (tp30) cc_final: 0.8345 (tp30) REVERT: P1 470 LYS cc_start: 0.9303 (mmmm) cc_final: 0.9033 (mmmt) REVERT: P1 471 LYS cc_start: 0.9089 (tttt) cc_final: 0.8729 (ttmt) REVERT: P2 68 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8182 (mt-10) REVERT: P2 70 LYS cc_start: 0.9083 (mtpt) cc_final: 0.8778 (mtmm) REVERT: P2 93 ASP cc_start: 0.8586 (t70) cc_final: 0.8296 (t70) REVERT: P2 132 ASP cc_start: 0.8363 (t0) cc_final: 0.7598 (t0) REVERT: P2 227 LYS cc_start: 0.9095 (tppt) cc_final: 0.8718 (mttt) REVERT: P2 239 SER cc_start: 0.9367 (m) cc_final: 0.9051 (t) REVERT: P2 299 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8542 (tp30) REVERT: P2 322 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.7642 (mmt180) REVERT: P2 415 ILE cc_start: 0.9006 (tp) cc_final: 0.8633 (tt) REVERT: P2 438 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8356 (tp30) REVERT: P3 1 MET cc_start: 0.8290 (ptp) cc_final: 0.7904 (ptp) REVERT: P3 152 GLU cc_start: 0.8634 (pp20) cc_final: 0.8225 (pp20) REVERT: P3 159 ASP cc_start: 0.8917 (t70) cc_final: 0.8510 (t0) REVERT: P3 243 MET cc_start: 0.9038 (tmm) cc_final: 0.8236 (tmm) REVERT: P3 297 PRO cc_start: 0.9050 (Cg_endo) cc_final: 0.8736 (Cg_exo) REVERT: P3 301 ARG cc_start: 0.8728 (mtm-85) cc_final: 0.8387 (mtm-85) REVERT: P3 302 LYS cc_start: 0.8816 (ptmt) cc_final: 0.8400 (ptmt) REVERT: P3 355 MET cc_start: 0.8598 (ttt) cc_final: 0.8188 (ttt) REVERT: P3 374 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8219 (mp0) REVERT: P3 425 ARG cc_start: 0.8233 (mtm-85) cc_final: 0.7800 (mtt-85) REVERT: P3 456 MET cc_start: 0.9046 (mtt) cc_final: 0.8591 (mtt) REVERT: P3 468 GLU cc_start: 0.7740 (tp30) cc_final: 0.7337 (tp30) REVERT: P3 472 ILE cc_start: 0.8460 (mt) cc_final: 0.7967 (mt) REVERT: P4 61 LYS cc_start: 0.8548 (tttt) cc_final: 0.8282 (tmtt) REVERT: P4 77 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7737 (pp) REVERT: P4 125 GLU cc_start: 0.8507 (tt0) cc_final: 0.7800 (mm-30) REVERT: P4 129 ASP cc_start: 0.8960 (t0) cc_final: 0.8481 (m-30) REVERT: P4 274 ASP cc_start: 0.9240 (t0) cc_final: 0.8872 (t0) REVERT: P4 428 TYR cc_start: 0.8870 (m-80) cc_final: 0.8631 (m-80) REVERT: P4 435 SER cc_start: 0.8682 (t) cc_final: 0.8029 (p) REVERT: P4 439 GLU cc_start: 0.8311 (mt-10) cc_final: 0.7863 (mt-10) REVERT: P4 471 LYS cc_start: 0.8658 (tttt) cc_final: 0.8282 (tttm) REVERT: P4 476 GLU cc_start: 0.8039 (pt0) cc_final: 0.7652 (pt0) REVERT: P5 26 ASN cc_start: 0.8796 (t0) cc_final: 0.8196 (t0) REVERT: P5 44 GLU cc_start: 0.8358 (mm-30) cc_final: 0.8020 (mm-30) REVERT: P5 132 ASP cc_start: 0.8497 (t0) cc_final: 0.7622 (t0) REVERT: P5 192 ARG cc_start: 0.7900 (ttp-170) cc_final: 0.7688 (ttt180) REVERT: P5 438 GLU cc_start: 0.8614 (tp30) cc_final: 0.8187 (tp30) REVERT: P5 439 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.8162 (mt-10) REVERT: P6 6 GLU cc_start: 0.7476 (mp0) cc_final: 0.7005 (mp0) REVERT: P6 31 TYR cc_start: 0.9318 (t80) cc_final: 0.9037 (t80) REVERT: P6 85 MET cc_start: 0.5396 (pmm) cc_final: 0.4232 (pmm) REVERT: P6 93 ASP cc_start: 0.8643 (t0) cc_final: 0.8262 (t0) REVERT: P6 154 MET cc_start: 0.8672 (ttm) cc_final: 0.8455 (ttm) REVERT: P6 157 ASN cc_start: 0.8678 (t0) cc_final: 0.8218 (t0) REVERT: P6 208 ASP cc_start: 0.8495 (m-30) cc_final: 0.7711 (p0) REVERT: P6 249 SER cc_start: 0.9453 (m) cc_final: 0.9105 (t) REVERT: P6 279 MET cc_start: 0.8840 (mmm) cc_final: 0.8335 (mmm) REVERT: P6 302 LYS cc_start: 0.8881 (mtmt) cc_final: 0.8579 (pttt) REVERT: P6 303 GLN cc_start: 0.8757 (tm130) cc_final: 0.8426 (tm-30) REVERT: P6 327 SER cc_start: 0.9169 (m) cc_final: 0.8707 (p) REVERT: P6 347 ASP cc_start: 0.8971 (m-30) cc_final: 0.8548 (m-30) REVERT: P6 378 TYR cc_start: 0.8907 (t80) cc_final: 0.8584 (t80) REVERT: P6 406 GLU cc_start: 0.9061 (OUTLIER) cc_final: 0.8718 (tm-30) REVERT: P7 70 LYS cc_start: 0.9151 (mtpt) cc_final: 0.8810 (mtpp) REVERT: P7 170 MET cc_start: 0.9409 (mtp) cc_final: 0.9142 (mmm) REVERT: P7 192 ARG cc_start: 0.9028 (ttp80) cc_final: 0.8643 (ttm-80) REVERT: P7 318 ASP cc_start: 0.8465 (t0) cc_final: 0.8071 (t0) REVERT: P7 376 MET cc_start: 0.8655 (mmm) cc_final: 0.8020 (mmm) REVERT: P8 1 MET cc_start: 0.4173 (OUTLIER) cc_final: 0.3703 (tmm) REVERT: P8 76 GLU cc_start: 0.7972 (tp30) cc_final: 0.7378 (tp30) REVERT: P8 121 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8697 (mt) REVERT: P8 236 GLU cc_start: 0.7904 (tt0) cc_final: 0.7582 (mt-10) REVERT: P8 257 ASP cc_start: 0.8449 (m-30) cc_final: 0.8015 (m-30) REVERT: P8 466 GLU cc_start: 0.8543 (tm-30) cc_final: 0.8303 (tm-30) REVERT: P8 467 LEU cc_start: 0.9189 (tt) cc_final: 0.8865 (pp) REVERT: P9 177 ASP cc_start: 0.8910 (t70) cc_final: 0.8468 (t70) REVERT: P9 208 ASP cc_start: 0.8142 (m-30) cc_final: 0.7761 (m-30) REVERT: P9 221 ASN cc_start: 0.7853 (p0) cc_final: 0.7471 (p0) REVERT: P9 227 LYS cc_start: 0.8989 (tppt) cc_final: 0.8628 (mmmt) REVERT: P9 274 ASP cc_start: 0.8849 (t70) cc_final: 0.8471 (t0) REVERT: P9 302 LYS cc_start: 0.8682 (mtmt) cc_final: 0.8126 (mmtm) REVERT: P9 322 ARG cc_start: 0.8469 (mtp85) cc_final: 0.8071 (mtt180) REVERT: P9 376 MET cc_start: 0.9296 (mmm) cc_final: 0.8741 (mmm) REVERT: P9 452 GLN cc_start: 0.8867 (mm-40) cc_final: 0.8370 (pm20) REVERT: P9 463 GLN cc_start: 0.8067 (tp40) cc_final: 0.7833 (tp-100) REVERT: Q1 1 MET cc_start: 0.6000 (OUTLIER) cc_final: 0.5636 (tmm) REVERT: Q1 50 GLU cc_start: 0.8903 (tt0) cc_final: 0.8063 (tm-30) REVERT: Q1 54 ASP cc_start: 0.9133 (t0) cc_final: 0.8733 (t70) REVERT: Q1 296 ASP cc_start: 0.8282 (t0) cc_final: 0.8031 (t70) REVERT: Q1 358 ASN cc_start: 0.9248 (m-40) cc_final: 0.8732 (m110) REVERT: Q1 425 ARG cc_start: 0.8443 (mtm-85) cc_final: 0.8054 (ttm110) REVERT: Q1 462 PHE cc_start: 0.8303 (m-80) cc_final: 0.8008 (m-80) REVERT: Q2 22 ASN cc_start: 0.9098 (t0) cc_final: 0.8886 (t0) REVERT: Q2 50 GLU cc_start: 0.8821 (tt0) cc_final: 0.8577 (tt0) REVERT: Q2 61 LYS cc_start: 0.8602 (tttt) cc_final: 0.8262 (tptp) REVERT: Q2 72 LYS cc_start: 0.8967 (tttt) cc_final: 0.8660 (tttp) REVERT: Q2 132 ASP cc_start: 0.8704 (t0) cc_final: 0.8483 (t0) REVERT: Q2 327 SER cc_start: 0.8694 (m) cc_final: 0.8372 (p) REVERT: Q2 359 THR cc_start: 0.9357 (m) cc_final: 0.9001 (p) REVERT: Q2 425 ARG cc_start: 0.8341 (mtm-85) cc_final: 0.7338 (mtm-85) REVERT: Q3 26 ASN cc_start: 0.8040 (t0) cc_final: 0.7688 (t0) REVERT: Q3 61 LYS cc_start: 0.8702 (tttt) cc_final: 0.8143 (ttpt) REVERT: Q3 76 GLU cc_start: 0.8268 (tt0) cc_final: 0.7916 (tp30) REVERT: Q3 119 ASP cc_start: 0.8933 (m-30) cc_final: 0.8643 (m-30) REVERT: Q3 161 GLU cc_start: 0.7708 (pm20) cc_final: 0.7392 (pm20) REVERT: Q3 192 ARG cc_start: 0.8840 (mtp180) cc_final: 0.8635 (mtp85) REVERT: Q3 221 ASN cc_start: 0.8197 (p0) cc_final: 0.7791 (p0) REVERT: Q3 279 MET cc_start: 0.8941 (tpp) cc_final: 0.8480 (mtp) REVERT: Q3 323 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8245 (mt-10) REVERT: Q3 358 ASN cc_start: 0.9258 (m-40) cc_final: 0.9051 (m-40) REVERT: Q3 363 LYS cc_start: 0.9132 (tttm) cc_final: 0.8827 (tttt) REVERT: Q3 408 ILE cc_start: 0.8968 (tp) cc_final: 0.8620 (tp) outliers start: 268 outliers final: 208 residues processed: 1327 average time/residue: 0.6677 time to fit residues: 1497.7804 Evaluate side-chains 1312 residues out of total 7775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 1092 time to evaluate : 6.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B1 residue 79 LYS Chi-restraints excluded: chain B1 residue 162 SER Chi-restraints excluded: chain B1 residue 169 VAL Chi-restraints excluded: chain B1 residue 222 ASN Chi-restraints excluded: chain B1 residue 264 ILE Chi-restraints excluded: chain B1 residue 277 ASP Chi-restraints excluded: chain B1 residue 297 VAL Chi-restraints excluded: chain B2 residue 23 VAL Chi-restraints excluded: chain B2 residue 54 ASN Chi-restraints excluded: chain B2 residue 66 MET Chi-restraints excluded: chain B2 residue 143 ASP Chi-restraints excluded: chain B2 residue 188 ASP Chi-restraints excluded: chain B2 residue 209 ILE Chi-restraints excluded: chain B2 residue 267 THR Chi-restraints excluded: chain B2 residue 271 SER Chi-restraints excluded: chain B2 residue 304 ASP Chi-restraints excluded: chain B3 residue 23 VAL Chi-restraints excluded: chain B3 residue 27 ASP Chi-restraints excluded: chain B3 residue 45 THR Chi-restraints excluded: chain B3 residue 69 THR Chi-restraints excluded: chain B3 residue 97 THR Chi-restraints excluded: chain B3 residue 196 PHE Chi-restraints excluded: chain B3 residue 245 ILE Chi-restraints excluded: chain B3 residue 250 ASP Chi-restraints excluded: chain B3 residue 272 THR Chi-restraints excluded: chain B3 residue 304 ASP Chi-restraints excluded: chain B4 residue 97 THR Chi-restraints excluded: chain B4 residue 124 SER Chi-restraints excluded: chain B4 residue 169 VAL Chi-restraints excluded: chain B4 residue 191 LEU Chi-restraints excluded: chain B4 residue 209 ILE Chi-restraints excluded: chain B4 residue 264 ILE Chi-restraints excluded: chain B4 residue 266 GLU Chi-restraints excluded: chain B5 residue 44 THR Chi-restraints excluded: chain B5 residue 47 ILE Chi-restraints excluded: chain B5 residue 97 THR Chi-restraints excluded: chain B5 residue 162 SER Chi-restraints excluded: chain B5 residue 198 SER Chi-restraints excluded: chain B5 residue 234 LEU Chi-restraints excluded: chain B5 residue 238 ASN Chi-restraints excluded: chain C1 residue 91 ILE Chi-restraints excluded: chain C4 residue 73 PHE Chi-restraints excluded: chain C4 residue 102 THR Chi-restraints excluded: chain C5 residue 94 SER Chi-restraints excluded: chain C5 residue 99 VAL Chi-restraints excluded: chain D1 residue 66 MET Chi-restraints excluded: chain D1 residue 159 ILE Chi-restraints excluded: chain D1 residue 179 ILE Chi-restraints excluded: chain D1 residue 198 SER Chi-restraints excluded: chain D1 residue 204 SER Chi-restraints excluded: chain D1 residue 311 VAL Chi-restraints excluded: chain D2 residue 51 VAL Chi-restraints excluded: chain D2 residue 111 ILE Chi-restraints excluded: chain D2 residue 190 GLU Chi-restraints excluded: chain D3 residue 57 ILE Chi-restraints excluded: chain D3 residue 177 ASP Chi-restraints excluded: chain D3 residue 198 SER Chi-restraints excluded: chain D3 residue 243 GLU Chi-restraints excluded: chain D4 residue 48 LEU Chi-restraints excluded: chain D4 residue 57 ILE Chi-restraints excluded: chain D4 residue 111 ILE Chi-restraints excluded: chain D4 residue 119 LEU Chi-restraints excluded: chain D4 residue 175 THR Chi-restraints excluded: chain D4 residue 177 ASP Chi-restraints excluded: chain D4 residue 231 VAL Chi-restraints excluded: chain D5 residue 29 VAL Chi-restraints excluded: chain D5 residue 44 THR Chi-restraints excluded: chain D5 residue 119 LEU Chi-restraints excluded: chain D5 residue 159 ILE Chi-restraints excluded: chain D5 residue 273 VAL Chi-restraints excluded: chain D5 residue 299 LEU Chi-restraints excluded: chain P1 residue 2 LEU Chi-restraints excluded: chain P1 residue 18 ASN Chi-restraints excluded: chain P1 residue 39 LEU Chi-restraints excluded: chain P1 residue 54 ASP Chi-restraints excluded: chain P1 residue 96 SER Chi-restraints excluded: chain P1 residue 99 SER Chi-restraints excluded: chain P1 residue 119 ASP Chi-restraints excluded: chain P1 residue 143 ASP Chi-restraints excluded: chain P1 residue 194 LYS Chi-restraints excluded: chain P1 residue 206 THR Chi-restraints excluded: chain P1 residue 211 THR Chi-restraints excluded: chain P1 residue 284 ASP Chi-restraints excluded: chain P1 residue 327 SER Chi-restraints excluded: chain P1 residue 377 LYS Chi-restraints excluded: chain P1 residue 415 ILE Chi-restraints excluded: chain P1 residue 436 LEU Chi-restraints excluded: chain P1 residue 437 ILE Chi-restraints excluded: chain P1 residue 450 ILE Chi-restraints excluded: chain P2 residue 90 VAL Chi-restraints excluded: chain P2 residue 96 SER Chi-restraints excluded: chain P2 residue 124 ILE Chi-restraints excluded: chain P2 residue 155 ILE Chi-restraints excluded: chain P2 residue 182 ARG Chi-restraints excluded: chain P2 residue 197 ASP Chi-restraints excluded: chain P2 residue 229 THR Chi-restraints excluded: chain P2 residue 262 ILE Chi-restraints excluded: chain P2 residue 298 VAL Chi-restraints excluded: chain P2 residue 299 GLU Chi-restraints excluded: chain P2 residue 322 ARG Chi-restraints excluded: chain P2 residue 327 SER Chi-restraints excluded: chain P3 residue 4 VAL Chi-restraints excluded: chain P3 residue 23 ASP Chi-restraints excluded: chain P3 residue 39 LEU Chi-restraints excluded: chain P3 residue 43 ASN Chi-restraints excluded: chain P3 residue 111 ILE Chi-restraints excluded: chain P3 residue 135 SER Chi-restraints excluded: chain P3 residue 155 ILE Chi-restraints excluded: chain P3 residue 170 MET Chi-restraints excluded: chain P3 residue 191 LEU Chi-restraints excluded: chain P3 residue 208 ASP Chi-restraints excluded: chain P3 residue 229 THR Chi-restraints excluded: chain P3 residue 295 LEU Chi-restraints excluded: chain P3 residue 296 ASP Chi-restraints excluded: chain P3 residue 406 GLU Chi-restraints excluded: chain P4 residue 77 LEU Chi-restraints excluded: chain P4 residue 154 MET Chi-restraints excluded: chain P4 residue 223 THR Chi-restraints excluded: chain P4 residue 327 SER Chi-restraints excluded: chain P4 residue 339 VAL Chi-restraints excluded: chain P4 residue 418 ASN Chi-restraints excluded: chain P5 residue 37 ASP Chi-restraints excluded: chain P5 residue 42 VAL Chi-restraints excluded: chain P5 residue 85 MET Chi-restraints excluded: chain P5 residue 119 ASP Chi-restraints excluded: chain P5 residue 135 SER Chi-restraints excluded: chain P5 residue 153 LEU Chi-restraints excluded: chain P5 residue 164 LEU Chi-restraints excluded: chain P5 residue 196 ILE Chi-restraints excluded: chain P5 residue 286 MET Chi-restraints excluded: chain P5 residue 408 ILE Chi-restraints excluded: chain P5 residue 439 GLU Chi-restraints excluded: chain P5 residue 458 LEU Chi-restraints excluded: chain P5 residue 469 VAL Chi-restraints excluded: chain P6 residue 152 GLU Chi-restraints excluded: chain P6 residue 170 MET Chi-restraints excluded: chain P6 residue 193 THR Chi-restraints excluded: chain P6 residue 196 ILE Chi-restraints excluded: chain P6 residue 406 GLU Chi-restraints excluded: chain P7 residue 57 ARG Chi-restraints excluded: chain P7 residue 71 THR Chi-restraints excluded: chain P7 residue 99 SER Chi-restraints excluded: chain P7 residue 116 ASP Chi-restraints excluded: chain P7 residue 133 VAL Chi-restraints excluded: chain P7 residue 143 ASP Chi-restraints excluded: chain P7 residue 146 ILE Chi-restraints excluded: chain P7 residue 188 VAL Chi-restraints excluded: chain P7 residue 223 THR Chi-restraints excluded: chain P7 residue 239 SER Chi-restraints excluded: chain P7 residue 320 GLU Chi-restraints excluded: chain P7 residue 327 SER Chi-restraints excluded: chain P7 residue 406 GLU Chi-restraints excluded: chain P7 residue 407 THR Chi-restraints excluded: chain P8 residue 1 MET Chi-restraints excluded: chain P8 residue 62 VAL Chi-restraints excluded: chain P8 residue 87 ASP Chi-restraints excluded: chain P8 residue 90 VAL Chi-restraints excluded: chain P8 residue 121 LEU Chi-restraints excluded: chain P8 residue 124 ILE Chi-restraints excluded: chain P8 residue 152 GLU Chi-restraints excluded: chain P8 residue 188 VAL Chi-restraints excluded: chain P8 residue 196 ILE Chi-restraints excluded: chain P8 residue 208 ASP Chi-restraints excluded: chain P8 residue 284 ASP Chi-restraints excluded: chain P8 residue 298 VAL Chi-restraints excluded: chain P9 residue 18 ASN Chi-restraints excluded: chain P9 residue 37 ASP Chi-restraints excluded: chain P9 residue 50 GLU Chi-restraints excluded: chain P9 residue 96 SER Chi-restraints excluded: chain P9 residue 133 VAL Chi-restraints excluded: chain P9 residue 152 GLU Chi-restraints excluded: chain P9 residue 188 VAL Chi-restraints excluded: chain P9 residue 206 THR Chi-restraints excluded: chain P9 residue 281 ASP Chi-restraints excluded: chain P9 residue 318 ASP Chi-restraints excluded: chain P9 residue 339 VAL Chi-restraints excluded: chain P9 residue 409 LEU Chi-restraints excluded: chain P9 residue 436 LEU Chi-restraints excluded: chain Q1 residue 1 MET Chi-restraints excluded: chain Q1 residue 45 VAL Chi-restraints excluded: chain Q1 residue 121 LEU Chi-restraints excluded: chain Q1 residue 139 SER Chi-restraints excluded: chain Q1 residue 153 LEU Chi-restraints excluded: chain Q1 residue 204 VAL Chi-restraints excluded: chain Q1 residue 215 VAL Chi-restraints excluded: chain Q1 residue 229 THR Chi-restraints excluded: chain Q1 residue 284 ASP Chi-restraints excluded: chain Q1 residue 295 LEU Chi-restraints excluded: chain Q1 residue 298 VAL Chi-restraints excluded: chain Q1 residue 327 SER Chi-restraints excluded: chain Q1 residue 362 MET Chi-restraints excluded: chain Q1 residue 415 ILE Chi-restraints excluded: chain Q2 residue 96 SER Chi-restraints excluded: chain Q2 residue 119 ASP Chi-restraints excluded: chain Q2 residue 133 VAL Chi-restraints excluded: chain Q2 residue 155 ILE Chi-restraints excluded: chain Q2 residue 170 MET Chi-restraints excluded: chain Q2 residue 193 THR Chi-restraints excluded: chain Q2 residue 263 THR Chi-restraints excluded: chain Q2 residue 298 VAL Chi-restraints excluded: chain Q2 residue 355 MET Chi-restraints excluded: chain Q2 residue 406 GLU Chi-restraints excluded: chain Q2 residue 410 LYS Chi-restraints excluded: chain Q3 residue 37 ASP Chi-restraints excluded: chain Q3 residue 96 SER Chi-restraints excluded: chain Q3 residue 124 ILE Chi-restraints excluded: chain Q3 residue 153 LEU Chi-restraints excluded: chain Q3 residue 185 ILE Chi-restraints excluded: chain Q3 residue 211 THR Chi-restraints excluded: chain Q3 residue 220 THR Chi-restraints excluded: chain Q3 residue 295 LEU Chi-restraints excluded: chain Q3 residue 298 VAL Chi-restraints excluded: chain Q3 residue 317 VAL Chi-restraints excluded: chain Q3 residue 324 THR Chi-restraints excluded: chain Q3 residue 328 VAL Chi-restraints excluded: chain Q3 residue 406 GLU Chi-restraints excluded: chain Q3 residue 437 ILE Chi-restraints excluded: chain Q3 residue 440 LEU Chi-restraints excluded: chain Q3 residue 456 MET Chi-restraints excluded: chain Q3 residue 458 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 851 random chunks: chunk 793 optimal weight: 0.0770 chunk 92 optimal weight: 10.0000 chunk 469 optimal weight: 2.9990 chunk 601 optimal weight: 3.9990 chunk 465 optimal weight: 1.9990 chunk 693 optimal weight: 0.9990 chunk 459 optimal weight: 3.9990 chunk 820 optimal weight: 7.9990 chunk 513 optimal weight: 30.0000 chunk 500 optimal weight: 9.9990 chunk 378 optimal weight: 8.9990 overall best weight: 2.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4 286 GLN ** B5 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4 89 GLN ** D1 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P1 178 ASN P5 41 ASN ** P5 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P6 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P7 16 ASN P7 422 ASN P8 411 ASN ** P9 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q1 16 ASN ** Q1 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q2 73 ASN ** Q2 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q3 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q3 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.4857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 71413 Z= 0.160 Angle : 0.515 10.417 96321 Z= 0.272 Chirality : 0.040 0.232 10525 Planarity : 0.003 0.047 12635 Dihedral : 4.389 27.349 9460 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.35 % Allowed : 16.62 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.09), residues: 8577 helix: 1.87 (0.10), residues: 3095 sheet: 0.25 (0.12), residues: 1770 loop : -0.26 (0.10), residues: 3712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRPC3 76 HIS 0.005 0.001 HISP6 136 PHE 0.021 0.001 PHEP5 173 TYR 0.022 0.001 TYRB1 254 ARG 0.009 0.000 ARGB1 104 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17154 Ramachandran restraints generated. 8577 Oldfield, 0 Emsley, 8577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17154 Ramachandran restraints generated. 8577 Oldfield, 0 Emsley, 8577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1420 residues out of total 7775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 1237 time to evaluate : 6.363 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B2 30 MET cc_start: 0.7105 (mpp) cc_final: 0.6193 (mpp) REVERT: B2 89 GLN cc_start: 0.8293 (mm-40) cc_final: 0.8076 (mm-40) REVERT: B2 123 TYR cc_start: 0.8205 (t80) cc_final: 0.7472 (t80) REVERT: B3 20 LYS cc_start: 0.7515 (tptt) cc_final: 0.7262 (tptt) REVERT: B3 123 TYR cc_start: 0.6404 (t80) cc_final: 0.6197 (t80) REVERT: B4 25 ASN cc_start: 0.8296 (t0) cc_final: 0.7332 (p0) REVERT: B4 217 ARG cc_start: 0.7559 (mtt-85) cc_final: 0.7333 (mmm160) REVERT: B4 266 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7362 (pp20) REVERT: B5 40 MET cc_start: 0.6202 (mtp) cc_final: 0.5980 (ttm) REVERT: B5 279 THR cc_start: 0.8539 (m) cc_final: 0.8231 (p) REVERT: C1 73 PHE cc_start: 0.7331 (m-80) cc_final: 0.6802 (m-10) REVERT: C3 76 TRP cc_start: 0.6554 (m-90) cc_final: 0.6234 (m-90) REVERT: C5 71 LYS cc_start: 0.8826 (tppt) cc_final: 0.8051 (tttt) REVERT: C5 76 TRP cc_start: 0.6825 (m100) cc_final: 0.6342 (m100) REVERT: C5 87 GLU cc_start: 0.6681 (tp30) cc_final: 0.6443 (tp30) REVERT: D1 40 MET cc_start: -0.2322 (ttm) cc_final: -0.2824 (ttt) REVERT: D1 167 ASN cc_start: 0.8404 (t0) cc_final: 0.8136 (t0) REVERT: D1 262 TYR cc_start: 0.8518 (m-80) cc_final: 0.7920 (m-80) REVERT: D2 58 MET cc_start: 0.8786 (mtp) cc_final: 0.8297 (mtm) REVERT: D2 309 LYS cc_start: 0.8107 (tttt) cc_final: 0.7905 (tttp) REVERT: D3 25 ASN cc_start: 0.8583 (t0) cc_final: 0.8373 (m110) REVERT: D3 123 TYR cc_start: 0.6381 (t80) cc_final: 0.5886 (t80) REVERT: D3 130 MET cc_start: 0.8255 (mtt) cc_final: 0.8026 (mtp) REVERT: D3 157 LYS cc_start: 0.5568 (mttt) cc_final: 0.5115 (ptpt) REVERT: D3 217 ARG cc_start: 0.6451 (mmt180) cc_final: 0.5847 (mtm180) REVERT: D4 30 MET cc_start: 0.7113 (mmm) cc_final: 0.6292 (mmm) REVERT: D4 207 ARG cc_start: 0.7979 (mtm180) cc_final: 0.7742 (ttt180) REVERT: P1 1 MET cc_start: 0.7738 (tpp) cc_final: 0.7517 (tpp) REVERT: P1 24 GLU cc_start: 0.8960 (mm-30) cc_final: 0.8694 (mt-10) REVERT: P1 50 GLU cc_start: 0.8841 (tt0) cc_final: 0.8591 (tp30) REVERT: P1 243 MET cc_start: 0.8936 (tmm) cc_final: 0.8605 (tmm) REVERT: P1 302 LYS cc_start: 0.8772 (mtmt) cc_final: 0.8288 (pptt) REVERT: P1 383 LEU cc_start: 0.9369 (tp) cc_final: 0.9077 (tp) REVERT: P1 468 GLU cc_start: 0.8816 (tp30) cc_final: 0.8282 (tp30) REVERT: P1 470 LYS cc_start: 0.9286 (mmmm) cc_final: 0.9003 (mmmt) REVERT: P1 471 LYS cc_start: 0.9060 (tttt) cc_final: 0.8703 (ttmt) REVERT: P2 68 GLU cc_start: 0.8428 (mt-10) cc_final: 0.8135 (mt-10) REVERT: P2 70 LYS cc_start: 0.8926 (mtpt) cc_final: 0.8358 (mtmm) REVERT: P2 93 ASP cc_start: 0.8480 (t70) cc_final: 0.8078 (t0) REVERT: P2 132 ASP cc_start: 0.8230 (t0) cc_final: 0.7431 (t0) REVERT: P2 157 ASN cc_start: 0.8765 (t0) cc_final: 0.8482 (t0) REVERT: P2 182 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.8114 (mmm-85) REVERT: P2 217 ARG cc_start: 0.8753 (mtm-85) cc_final: 0.8407 (mtt90) REVERT: P2 227 LYS cc_start: 0.8981 (tppt) cc_final: 0.8612 (mtmt) REVERT: P2 239 SER cc_start: 0.9400 (m) cc_final: 0.9043 (t) REVERT: P2 288 LEU cc_start: 0.9517 (tp) cc_final: 0.9308 (tt) REVERT: P2 302 LYS cc_start: 0.8831 (mtmt) cc_final: 0.8521 (mtmm) REVERT: P2 322 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.7459 (mmt180) REVERT: P2 415 ILE cc_start: 0.9068 (tp) cc_final: 0.8741 (tt) REVERT: P3 1 MET cc_start: 0.8245 (ptp) cc_final: 0.7967 (ptp) REVERT: P3 152 GLU cc_start: 0.8446 (pp20) cc_final: 0.8012 (pp20) REVERT: P3 159 ASP cc_start: 0.8968 (t70) cc_final: 0.8534 (t0) REVERT: P3 243 MET cc_start: 0.8965 (tmm) cc_final: 0.8215 (tmm) REVERT: P3 355 MET cc_start: 0.8549 (ttt) cc_final: 0.8060 (ttt) REVERT: P3 374 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8016 (mp0) REVERT: P3 456 MET cc_start: 0.8991 (mtt) cc_final: 0.8513 (mtt) REVERT: P3 468 GLU cc_start: 0.7574 (tp30) cc_final: 0.7087 (tp30) REVERT: P3 472 ILE cc_start: 0.8428 (mt) cc_final: 0.7992 (mt) REVERT: P3 478 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.7889 (mp0) REVERT: P4 61 LYS cc_start: 0.8483 (tttt) cc_final: 0.8281 (tmtt) REVERT: P4 77 LEU cc_start: 0.7951 (tt) cc_final: 0.7658 (pp) REVERT: P4 125 GLU cc_start: 0.8505 (tt0) cc_final: 0.7651 (mm-30) REVERT: P4 129 ASP cc_start: 0.8785 (t0) cc_final: 0.8385 (m-30) REVERT: P4 192 ARG cc_start: 0.8151 (ttt90) cc_final: 0.7584 (ttt90) REVERT: P4 274 ASP cc_start: 0.9242 (t0) cc_final: 0.8929 (t0) REVERT: P4 435 SER cc_start: 0.8707 (t) cc_final: 0.8079 (p) REVERT: P4 439 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7737 (mt-10) REVERT: P4 471 LYS cc_start: 0.8682 (tttt) cc_final: 0.8319 (tttm) REVERT: P4 476 GLU cc_start: 0.8066 (pt0) cc_final: 0.7711 (pt0) REVERT: P5 26 ASN cc_start: 0.8433 (t0) cc_final: 0.7819 (t0) REVERT: P5 41 ASN cc_start: 0.7843 (t0) cc_final: 0.6948 (t0) REVERT: P5 44 GLU cc_start: 0.8386 (mm-30) cc_final: 0.7997 (mm-30) REVERT: P5 132 ASP cc_start: 0.8346 (t0) cc_final: 0.7501 (t0) REVERT: P5 312 GLU cc_start: 0.8150 (tt0) cc_final: 0.7900 (tt0) REVERT: P5 386 ARG cc_start: 0.9217 (OUTLIER) cc_final: 0.8916 (ttm170) REVERT: P6 6 GLU cc_start: 0.7134 (mp0) cc_final: 0.6675 (mp0) REVERT: P6 31 TYR cc_start: 0.9211 (t80) cc_final: 0.8873 (t80) REVERT: P6 85 MET cc_start: 0.5252 (pmm) cc_final: 0.4136 (pmm) REVERT: P6 93 ASP cc_start: 0.8500 (t0) cc_final: 0.8069 (t0) REVERT: P6 103 ASN cc_start: 0.9302 (t0) cc_final: 0.8878 (t0) REVERT: P6 208 ASP cc_start: 0.8460 (m-30) cc_final: 0.7674 (p0) REVERT: P6 227 LYS cc_start: 0.9211 (tppt) cc_final: 0.8958 (tptp) REVERT: P6 302 LYS cc_start: 0.8861 (mtmt) cc_final: 0.8646 (pttt) REVERT: P6 303 GLN cc_start: 0.8707 (tm130) cc_final: 0.8344 (tm-30) REVERT: P6 327 SER cc_start: 0.9047 (m) cc_final: 0.8579 (p) REVERT: P6 347 ASP cc_start: 0.8894 (m-30) cc_final: 0.8486 (m-30) REVERT: P7 44 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8186 (mp0) REVERT: P7 70 LYS cc_start: 0.9081 (mtpt) cc_final: 0.8840 (mtpp) REVERT: P7 93 ASP cc_start: 0.9227 (t70) cc_final: 0.8897 (t0) REVERT: P7 170 MET cc_start: 0.9406 (mtp) cc_final: 0.9125 (mmm) REVERT: P7 218 TYR cc_start: 0.8876 (m-80) cc_final: 0.8560 (m-80) REVERT: P7 318 ASP cc_start: 0.8397 (t0) cc_final: 0.8124 (t0) REVERT: P7 376 MET cc_start: 0.8719 (mmm) cc_final: 0.8158 (mmm) REVERT: P8 1 MET cc_start: 0.4532 (tmm) cc_final: 0.4004 (tmm) REVERT: P8 76 GLU cc_start: 0.7860 (tp30) cc_final: 0.7415 (tp30) REVERT: P8 176 TYR cc_start: 0.9016 (m-80) cc_final: 0.8558 (m-80) REVERT: P8 192 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.8112 (tpt170) REVERT: P8 236 GLU cc_start: 0.7785 (tt0) cc_final: 0.7583 (mt-10) REVERT: P8 257 ASP cc_start: 0.8430 (m-30) cc_final: 0.7952 (m-30) REVERT: P8 411 ASN cc_start: 0.8174 (m-40) cc_final: 0.7884 (m110) REVERT: P8 456 MET cc_start: 0.9275 (mtt) cc_final: 0.8959 (mtt) REVERT: P8 467 LEU cc_start: 0.9172 (tt) cc_final: 0.8843 (pp) REVERT: P9 177 ASP cc_start: 0.8873 (t70) cc_final: 0.8408 (t70) REVERT: P9 208 ASP cc_start: 0.7926 (m-30) cc_final: 0.7620 (m-30) REVERT: P9 221 ASN cc_start: 0.7857 (p0) cc_final: 0.7490 (p0) REVERT: P9 227 LYS cc_start: 0.8922 (tppt) cc_final: 0.8469 (mmmt) REVERT: P9 274 ASP cc_start: 0.8772 (t70) cc_final: 0.8380 (t0) REVERT: P9 302 LYS cc_start: 0.8654 (mtmt) cc_final: 0.8114 (mmtm) REVERT: P9 322 ARG cc_start: 0.8497 (mtp85) cc_final: 0.8078 (mtt180) REVERT: P9 376 MET cc_start: 0.9232 (mmm) cc_final: 0.8696 (mmm) REVERT: P9 386 ARG cc_start: 0.9114 (ttm170) cc_final: 0.8609 (mtt180) REVERT: P9 452 GLN cc_start: 0.8784 (mm-40) cc_final: 0.8355 (pm20) REVERT: P9 463 GLN cc_start: 0.8005 (tp40) cc_final: 0.7267 (tp-100) REVERT: Q1 1 MET cc_start: 0.6172 (OUTLIER) cc_final: 0.5777 (tmm) REVERT: Q1 24 GLU cc_start: 0.9153 (mm-30) cc_final: 0.8485 (mm-30) REVERT: Q1 50 GLU cc_start: 0.8766 (tt0) cc_final: 0.8050 (tm-30) REVERT: Q1 54 ASP cc_start: 0.9108 (t0) cc_final: 0.8759 (t70) REVERT: Q1 296 ASP cc_start: 0.8126 (t0) cc_final: 0.7867 (t70) REVERT: Q1 318 ASP cc_start: 0.8516 (t0) cc_final: 0.8241 (t70) REVERT: Q1 358 ASN cc_start: 0.9169 (m-40) cc_final: 0.8643 (m110) REVERT: Q1 425 ARG cc_start: 0.8539 (mtm-85) cc_final: 0.8255 (ptp90) REVERT: Q2 22 ASN cc_start: 0.9058 (t0) cc_final: 0.8841 (t0) REVERT: Q2 50 GLU cc_start: 0.8819 (tt0) cc_final: 0.8546 (tt0) REVERT: Q2 61 LYS cc_start: 0.8594 (tttt) cc_final: 0.8292 (tptp) REVERT: Q2 72 LYS cc_start: 0.8922 (tttt) cc_final: 0.8608 (tttp) REVERT: Q2 302 LYS cc_start: 0.8600 (mtmt) cc_final: 0.8059 (pttm) REVERT: Q2 359 THR cc_start: 0.9310 (m) cc_final: 0.8863 (p) REVERT: Q2 406 GLU cc_start: 0.9014 (OUTLIER) cc_final: 0.8549 (tt0) REVERT: Q2 425 ARG cc_start: 0.8251 (mtm-85) cc_final: 0.7341 (mtm-85) REVERT: Q3 26 ASN cc_start: 0.7843 (t0) cc_final: 0.7562 (t0) REVERT: Q3 61 LYS cc_start: 0.8687 (tttt) cc_final: 0.8166 (ttpt) REVERT: Q3 76 GLU cc_start: 0.8231 (tt0) cc_final: 0.7878 (tp30) REVERT: Q3 96 SER cc_start: 0.9261 (OUTLIER) cc_final: 0.9008 (p) REVERT: Q3 119 ASP cc_start: 0.8943 (m-30) cc_final: 0.8657 (m-30) REVERT: Q3 221 ASN cc_start: 0.8123 (p0) cc_final: 0.7704 (p0) REVERT: Q3 279 MET cc_start: 0.8829 (tpp) cc_final: 0.8374 (mtp) REVERT: Q3 358 ASN cc_start: 0.9242 (m-40) cc_final: 0.8941 (m110) REVERT: Q3 363 LYS cc_start: 0.9095 (tttm) cc_final: 0.8805 (tttt) REVERT: Q3 411 ASN cc_start: 0.9024 (m110) cc_final: 0.8758 (m110) REVERT: Q3 458 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9175 (tp) outliers start: 183 outliers final: 130 residues processed: 1358 average time/residue: 0.6953 time to fit residues: 1608.7111 Evaluate side-chains 1275 residues out of total 7775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 1135 time to evaluate : 6.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B1 residue 162 SER Chi-restraints excluded: chain B1 residue 169 VAL Chi-restraints excluded: chain B1 residue 222 ASN Chi-restraints excluded: chain B2 residue 54 ASN Chi-restraints excluded: chain B2 residue 143 ASP Chi-restraints excluded: chain B2 residue 220 ASP Chi-restraints excluded: chain B2 residue 267 THR Chi-restraints excluded: chain B2 residue 271 SER Chi-restraints excluded: chain B2 residue 304 ASP Chi-restraints excluded: chain B3 residue 23 VAL Chi-restraints excluded: chain B3 residue 27 ASP Chi-restraints excluded: chain B3 residue 69 THR Chi-restraints excluded: chain B3 residue 97 THR Chi-restraints excluded: chain B3 residue 177 ASP Chi-restraints excluded: chain B3 residue 245 ILE Chi-restraints excluded: chain B3 residue 272 THR Chi-restraints excluded: chain B3 residue 304 ASP Chi-restraints excluded: chain B4 residue 97 THR Chi-restraints excluded: chain B4 residue 191 LEU Chi-restraints excluded: chain B4 residue 264 ILE Chi-restraints excluded: chain B4 residue 266 GLU Chi-restraints excluded: chain B4 residue 304 ASP Chi-restraints excluded: chain B5 residue 97 THR Chi-restraints excluded: chain B5 residue 234 LEU Chi-restraints excluded: chain B5 residue 238 ASN Chi-restraints excluded: chain C2 residue 73 PHE Chi-restraints excluded: chain C4 residue 73 PHE Chi-restraints excluded: chain C4 residue 102 THR Chi-restraints excluded: chain C5 residue 94 SER Chi-restraints excluded: chain D1 residue 66 MET Chi-restraints excluded: chain D1 residue 159 ILE Chi-restraints excluded: chain D1 residue 179 ILE Chi-restraints excluded: chain D1 residue 182 LEU Chi-restraints excluded: chain D1 residue 311 VAL Chi-restraints excluded: chain D2 residue 111 ILE Chi-restraints excluded: chain D2 residue 190 GLU Chi-restraints excluded: chain D3 residue 57 ILE Chi-restraints excluded: chain D3 residue 177 ASP Chi-restraints excluded: chain D3 residue 198 SER Chi-restraints excluded: chain D3 residue 243 GLU Chi-restraints excluded: chain D3 residue 281 VAL Chi-restraints excluded: chain D4 residue 57 ILE Chi-restraints excluded: chain D4 residue 177 ASP Chi-restraints excluded: chain D4 residue 206 LEU Chi-restraints excluded: chain D4 residue 231 VAL Chi-restraints excluded: chain D4 residue 259 LEU Chi-restraints excluded: chain D5 residue 44 THR Chi-restraints excluded: chain D5 residue 273 VAL Chi-restraints excluded: chain P1 residue 2 LEU Chi-restraints excluded: chain P1 residue 18 ASN Chi-restraints excluded: chain P1 residue 39 LEU Chi-restraints excluded: chain P1 residue 54 ASP Chi-restraints excluded: chain P1 residue 96 SER Chi-restraints excluded: chain P1 residue 119 ASP Chi-restraints excluded: chain P1 residue 206 THR Chi-restraints excluded: chain P1 residue 284 ASP Chi-restraints excluded: chain P1 residue 327 SER Chi-restraints excluded: chain P1 residue 377 LYS Chi-restraints excluded: chain P1 residue 415 ILE Chi-restraints excluded: chain P1 residue 436 LEU Chi-restraints excluded: chain P1 residue 450 ILE Chi-restraints excluded: chain P2 residue 90 VAL Chi-restraints excluded: chain P2 residue 96 SER Chi-restraints excluded: chain P2 residue 182 ARG Chi-restraints excluded: chain P2 residue 322 ARG Chi-restraints excluded: chain P2 residue 327 SER Chi-restraints excluded: chain P3 residue 4 VAL Chi-restraints excluded: chain P3 residue 23 ASP Chi-restraints excluded: chain P3 residue 39 LEU Chi-restraints excluded: chain P3 residue 43 ASN Chi-restraints excluded: chain P3 residue 135 SER Chi-restraints excluded: chain P3 residue 170 MET Chi-restraints excluded: chain P3 residue 191 LEU Chi-restraints excluded: chain P3 residue 208 ASP Chi-restraints excluded: chain P3 residue 296 ASP Chi-restraints excluded: chain P3 residue 406 GLU Chi-restraints excluded: chain P3 residue 478 GLU Chi-restraints excluded: chain P4 residue 154 MET Chi-restraints excluded: chain P4 residue 327 SER Chi-restraints excluded: chain P4 residue 339 VAL Chi-restraints excluded: chain P4 residue 418 ASN Chi-restraints excluded: chain P5 residue 135 SER Chi-restraints excluded: chain P5 residue 196 ILE Chi-restraints excluded: chain P5 residue 286 MET Chi-restraints excluded: chain P5 residue 339 VAL Chi-restraints excluded: chain P5 residue 386 ARG Chi-restraints excluded: chain P5 residue 458 LEU Chi-restraints excluded: chain P5 residue 469 VAL Chi-restraints excluded: chain P6 residue 170 MET Chi-restraints excluded: chain P6 residue 193 THR Chi-restraints excluded: chain P6 residue 196 ILE Chi-restraints excluded: chain P7 residue 57 ARG Chi-restraints excluded: chain P7 residue 71 THR Chi-restraints excluded: chain P7 residue 116 ASP Chi-restraints excluded: chain P7 residue 133 VAL Chi-restraints excluded: chain P7 residue 143 ASP Chi-restraints excluded: chain P7 residue 188 VAL Chi-restraints excluded: chain P7 residue 223 THR Chi-restraints excluded: chain P7 residue 239 SER Chi-restraints excluded: chain P7 residue 327 SER Chi-restraints excluded: chain P7 residue 406 GLU Chi-restraints excluded: chain P7 residue 407 THR Chi-restraints excluded: chain P8 residue 11 THR Chi-restraints excluded: chain P8 residue 87 ASP Chi-restraints excluded: chain P8 residue 90 VAL Chi-restraints excluded: chain P8 residue 124 ILE Chi-restraints excluded: chain P8 residue 140 LEU Chi-restraints excluded: chain P8 residue 188 VAL Chi-restraints excluded: chain P8 residue 192 ARG Chi-restraints excluded: chain P8 residue 196 ILE Chi-restraints excluded: chain P8 residue 284 ASP Chi-restraints excluded: chain P8 residue 298 VAL Chi-restraints excluded: chain P9 residue 18 ASN Chi-restraints excluded: chain P9 residue 50 GLU Chi-restraints excluded: chain P9 residue 96 SER Chi-restraints excluded: chain P9 residue 152 GLU Chi-restraints excluded: chain P9 residue 188 VAL Chi-restraints excluded: chain P9 residue 206 THR Chi-restraints excluded: chain P9 residue 339 VAL Chi-restraints excluded: chain P9 residue 409 LEU Chi-restraints excluded: chain P9 residue 436 LEU Chi-restraints excluded: chain Q1 residue 1 MET Chi-restraints excluded: chain Q1 residue 215 VAL Chi-restraints excluded: chain Q1 residue 219 LEU Chi-restraints excluded: chain Q1 residue 284 ASP Chi-restraints excluded: chain Q1 residue 327 SER Chi-restraints excluded: chain Q1 residue 362 MET Chi-restraints excluded: chain Q2 residue 96 SER Chi-restraints excluded: chain Q2 residue 119 ASP Chi-restraints excluded: chain Q2 residue 170 MET Chi-restraints excluded: chain Q2 residue 406 GLU Chi-restraints excluded: chain Q3 residue 96 SER Chi-restraints excluded: chain Q3 residue 124 ILE Chi-restraints excluded: chain Q3 residue 153 LEU Chi-restraints excluded: chain Q3 residue 185 ILE Chi-restraints excluded: chain Q3 residue 211 THR Chi-restraints excluded: chain Q3 residue 295 LEU Chi-restraints excluded: chain Q3 residue 317 VAL Chi-restraints excluded: chain Q3 residue 456 MET Chi-restraints excluded: chain Q3 residue 458 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 851 random chunks: chunk 507 optimal weight: 8.9990 chunk 327 optimal weight: 9.9990 chunk 489 optimal weight: 9.9990 chunk 247 optimal weight: 30.0000 chunk 161 optimal weight: 30.0000 chunk 158 optimal weight: 9.9990 chunk 521 optimal weight: 10.0000 chunk 558 optimal weight: 4.9990 chunk 405 optimal weight: 7.9990 chunk 76 optimal weight: 30.0000 chunk 644 optimal weight: 6.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2 17 ASN B2 201 GLN ** B3 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4 286 GLN ** B5 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4 89 GLN ** D1 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3 201 GLN ** D3 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P1 178 ASN ** P3 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P5 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P6 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P7 16 ASN P7 422 ASN ** P8 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P9 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q1 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q2 73 ASN ** Q3 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q3 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.4990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 71413 Z= 0.429 Angle : 0.638 11.349 96321 Z= 0.336 Chirality : 0.044 0.213 10525 Planarity : 0.004 0.049 12635 Dihedral : 4.745 23.150 9460 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.91 % Allowed : 16.76 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.09), residues: 8577 helix: 1.53 (0.10), residues: 3119 sheet: 0.06 (0.12), residues: 1772 loop : -0.45 (0.10), residues: 3686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRPC3 76 HIS 0.007 0.001 HISP3 92 PHE 0.027 0.002 PHEP5 173 TYR 0.024 0.002 TYRB5 262 ARG 0.009 0.001 ARGP6 192 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17154 Ramachandran restraints generated. 8577 Oldfield, 0 Emsley, 8577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17154 Ramachandran restraints generated. 8577 Oldfield, 0 Emsley, 8577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1347 residues out of total 7775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 1121 time to evaluate : 6.417 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B2 22 GLN cc_start: 0.8220 (tm-30) cc_final: 0.7457 (tm-30) REVERT: B2 30 MET cc_start: 0.7418 (mpp) cc_final: 0.6572 (mpp) REVERT: B2 123 TYR cc_start: 0.8187 (t80) cc_final: 0.7414 (t80) REVERT: B2 125 GLN cc_start: 0.7845 (pm20) cc_final: 0.7609 (pm20) REVERT: B3 103 MET cc_start: 0.7097 (ttp) cc_final: 0.6609 (ttp) REVERT: B3 123 TYR cc_start: 0.7182 (t80) cc_final: 0.6967 (t80) REVERT: B4 25 ASN cc_start: 0.8340 (t0) cc_final: 0.7395 (p0) REVERT: B4 266 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7264 (pp20) REVERT: B5 130 MET cc_start: 0.7870 (mmm) cc_final: 0.7654 (mmm) REVERT: B5 279 THR cc_start: 0.8573 (m) cc_final: 0.8250 (p) REVERT: C1 73 PHE cc_start: 0.7373 (m-80) cc_final: 0.6761 (m-10) REVERT: C5 71 LYS cc_start: 0.8887 (tppt) cc_final: 0.8092 (tttt) REVERT: C5 76 TRP cc_start: 0.6986 (m100) cc_final: 0.6469 (m100) REVERT: C5 87 GLU cc_start: 0.7080 (tp30) cc_final: 0.6753 (tp30) REVERT: D1 167 ASN cc_start: 0.8528 (t0) cc_final: 0.8189 (t0) REVERT: D1 262 TYR cc_start: 0.8575 (m-80) cc_final: 0.8200 (m-80) REVERT: D2 58 MET cc_start: 0.8794 (mtp) cc_final: 0.8412 (mtm) REVERT: D3 25 ASN cc_start: 0.8634 (t0) cc_final: 0.8415 (m110) REVERT: D3 123 TYR cc_start: 0.6517 (t80) cc_final: 0.5982 (t80) REVERT: D3 217 ARG cc_start: 0.6521 (mmt180) cc_final: 0.5874 (mtm180) REVERT: D4 30 MET cc_start: 0.7277 (mmm) cc_final: 0.6180 (mmm) REVERT: D4 48 LEU cc_start: 0.6804 (OUTLIER) cc_final: 0.6275 (mt) REVERT: D5 66 MET cc_start: 0.6775 (mtm) cc_final: 0.6165 (ptp) REVERT: P1 1 MET cc_start: 0.7468 (tpp) cc_final: 0.7168 (tpp) REVERT: P1 24 GLU cc_start: 0.9005 (mm-30) cc_final: 0.8699 (mt-10) REVERT: P1 31 TYR cc_start: 0.8753 (t80) cc_final: 0.8391 (t80) REVERT: P1 50 GLU cc_start: 0.8892 (tt0) cc_final: 0.8568 (tp30) REVERT: P1 158 GLN cc_start: 0.8779 (mm-40) cc_final: 0.8523 (mp10) REVERT: P1 301 ARG cc_start: 0.7977 (mmp80) cc_final: 0.7121 (ttm-80) REVERT: P1 302 LYS cc_start: 0.8809 (mtmt) cc_final: 0.8399 (pptt) REVERT: P1 383 LEU cc_start: 0.9434 (tp) cc_final: 0.9170 (tp) REVERT: P1 468 GLU cc_start: 0.8868 (tp30) cc_final: 0.8347 (tp30) REVERT: P1 470 LYS cc_start: 0.9218 (mmmm) cc_final: 0.8955 (mmmt) REVERT: P1 471 LYS cc_start: 0.9091 (tttt) cc_final: 0.8723 (ttmt) REVERT: P2 68 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8192 (mt-10) REVERT: P2 70 LYS cc_start: 0.9064 (mtpt) cc_final: 0.8768 (mtmm) REVERT: P2 125 GLU cc_start: 0.9122 (mm-30) cc_final: 0.8884 (mm-30) REVERT: P2 132 ASP cc_start: 0.8366 (t0) cc_final: 0.7582 (t0) REVERT: P2 157 ASN cc_start: 0.8780 (t0) cc_final: 0.8461 (t0) REVERT: P2 227 LYS cc_start: 0.9077 (tppt) cc_final: 0.8696 (mttt) REVERT: P2 239 SER cc_start: 0.9447 (m) cc_final: 0.9085 (t) REVERT: P2 322 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7670 (mmt180) REVERT: P2 376 MET cc_start: 0.9044 (mmm) cc_final: 0.8683 (mmm) REVERT: P2 415 ILE cc_start: 0.9065 (tp) cc_final: 0.8711 (tt) REVERT: P3 1 MET cc_start: 0.8284 (ptp) cc_final: 0.7951 (ptp) REVERT: P3 26 ASN cc_start: 0.8555 (t0) cc_final: 0.8212 (t0) REVERT: P3 152 GLU cc_start: 0.8575 (pp20) cc_final: 0.8152 (pp20) REVERT: P3 159 ASP cc_start: 0.8979 (t70) cc_final: 0.8514 (t0) REVERT: P3 243 MET cc_start: 0.9023 (tmm) cc_final: 0.8223 (tmm) REVERT: P3 301 ARG cc_start: 0.8918 (ttm110) cc_final: 0.8366 (mtm-85) REVERT: P3 355 MET cc_start: 0.8657 (ttt) cc_final: 0.8385 (ttt) REVERT: P3 374 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8210 (mp0) REVERT: P3 456 MET cc_start: 0.9046 (mtt) cc_final: 0.8566 (mtt) REVERT: P3 468 GLU cc_start: 0.7802 (tp30) cc_final: 0.7105 (tp30) REVERT: P3 472 ILE cc_start: 0.8473 (mt) cc_final: 0.7994 (mt) REVERT: P3 478 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.7970 (mp0) REVERT: P4 61 LYS cc_start: 0.8479 (tttt) cc_final: 0.8180 (tmtt) REVERT: P4 77 LEU cc_start: 0.8017 (tt) cc_final: 0.7769 (pp) REVERT: P4 125 GLU cc_start: 0.8529 (tt0) cc_final: 0.7829 (mm-30) REVERT: P4 129 ASP cc_start: 0.8941 (t0) cc_final: 0.8471 (m-30) REVERT: P4 192 ARG cc_start: 0.8170 (ttt90) cc_final: 0.7570 (ttt90) REVERT: P4 274 ASP cc_start: 0.9254 (t0) cc_final: 0.8892 (t0) REVERT: P4 435 SER cc_start: 0.8674 (t) cc_final: 0.8017 (p) REVERT: P4 439 GLU cc_start: 0.8323 (mt-10) cc_final: 0.7869 (mt-10) REVERT: P4 471 LYS cc_start: 0.8659 (tttt) cc_final: 0.8290 (tttm) REVERT: P4 476 GLU cc_start: 0.8070 (pt0) cc_final: 0.7708 (pt0) REVERT: P5 26 ASN cc_start: 0.8778 (t0) cc_final: 0.8328 (t0) REVERT: P5 41 ASN cc_start: 0.8156 (t0) cc_final: 0.7483 (t0) REVERT: P5 44 GLU cc_start: 0.8437 (mm-30) cc_final: 0.8107 (mm-30) REVERT: P5 132 ASP cc_start: 0.8499 (t0) cc_final: 0.7613 (t0) REVERT: P5 192 ARG cc_start: 0.7936 (ttp-170) cc_final: 0.7604 (ttt180) REVERT: P5 439 GLU cc_start: 0.8348 (mt-10) cc_final: 0.7871 (mt-10) REVERT: P6 6 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.6849 (mp0) REVERT: P6 31 TYR cc_start: 0.9307 (t80) cc_final: 0.8948 (t80) REVERT: P6 93 ASP cc_start: 0.8635 (t0) cc_final: 0.8237 (t0) REVERT: P6 157 ASN cc_start: 0.8649 (t0) cc_final: 0.8192 (t0) REVERT: P6 208 ASP cc_start: 0.8504 (m-30) cc_final: 0.7710 (p0) REVERT: P6 227 LYS cc_start: 0.9248 (tppt) cc_final: 0.8983 (tptp) REVERT: P6 249 SER cc_start: 0.9487 (m) cc_final: 0.9103 (t) REVERT: P6 302 LYS cc_start: 0.8901 (mtmt) cc_final: 0.8622 (pttt) REVERT: P6 303 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.8392 (tm-30) REVERT: P6 327 SER cc_start: 0.9188 (m) cc_final: 0.8736 (p) REVERT: P6 347 ASP cc_start: 0.8888 (m-30) cc_final: 0.8507 (m-30) REVERT: P6 367 PHE cc_start: 0.7527 (t80) cc_final: 0.7197 (t80) REVERT: P6 378 TYR cc_start: 0.8851 (t80) cc_final: 0.8524 (t80) REVERT: P7 44 GLU cc_start: 0.8600 (mm-30) cc_final: 0.7977 (mp0) REVERT: P7 70 LYS cc_start: 0.9154 (mtpt) cc_final: 0.8817 (mtpp) REVERT: P7 170 MET cc_start: 0.9390 (mtp) cc_final: 0.8804 (tpp) REVERT: P7 192 ARG cc_start: 0.9005 (ttp80) cc_final: 0.8585 (ttm-80) REVERT: P7 318 ASP cc_start: 0.8436 (t0) cc_final: 0.8165 (t0) REVERT: P8 1 MET cc_start: 0.4608 (OUTLIER) cc_final: 0.4022 (tmm) REVERT: P8 76 GLU cc_start: 0.7967 (tp30) cc_final: 0.7380 (tp30) REVERT: P8 170 MET cc_start: 0.9010 (mtm) cc_final: 0.8805 (mtp) REVERT: P8 192 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.8055 (tmt-80) REVERT: P8 236 GLU cc_start: 0.7863 (tt0) cc_final: 0.7626 (mt-10) REVERT: P8 257 ASP cc_start: 0.8440 (m-30) cc_final: 0.7979 (m-30) REVERT: P8 259 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8469 (tt0) REVERT: P8 467 LEU cc_start: 0.9103 (tt) cc_final: 0.8883 (pp) REVERT: P9 177 ASP cc_start: 0.8908 (t70) cc_final: 0.8548 (t0) REVERT: P9 208 ASP cc_start: 0.8046 (m-30) cc_final: 0.7689 (m-30) REVERT: P9 221 ASN cc_start: 0.7946 (p0) cc_final: 0.7576 (p0) REVERT: P9 227 LYS cc_start: 0.8988 (tppt) cc_final: 0.8625 (mmmt) REVERT: P9 274 ASP cc_start: 0.8840 (t70) cc_final: 0.8463 (t0) REVERT: P9 302 LYS cc_start: 0.8709 (mtmt) cc_final: 0.8160 (mmtm) REVERT: P9 322 ARG cc_start: 0.8478 (mtp85) cc_final: 0.8146 (mtt180) REVERT: P9 376 MET cc_start: 0.9288 (mmm) cc_final: 0.8722 (mmm) REVERT: P9 452 GLN cc_start: 0.8822 (mm-40) cc_final: 0.8362 (pm20) REVERT: P9 463 GLN cc_start: 0.8052 (tp40) cc_final: 0.7820 (tp-100) REVERT: Q1 50 GLU cc_start: 0.8837 (tt0) cc_final: 0.8031 (tm-30) REVERT: Q1 54 ASP cc_start: 0.9129 (t0) cc_final: 0.8732 (t70) REVERT: Q1 185 ILE cc_start: 0.9240 (mt) cc_final: 0.9027 (mp) REVERT: Q1 296 ASP cc_start: 0.8257 (t0) cc_final: 0.8031 (t70) REVERT: Q1 358 ASN cc_start: 0.9245 (m-40) cc_final: 0.8724 (m110) REVERT: Q1 425 ARG cc_start: 0.8481 (mtm-85) cc_final: 0.8151 (ptp90) REVERT: Q2 22 ASN cc_start: 0.9083 (t0) cc_final: 0.8845 (t0) REVERT: Q2 50 GLU cc_start: 0.8824 (tt0) cc_final: 0.8531 (tt0) REVERT: Q2 61 LYS cc_start: 0.8597 (tttt) cc_final: 0.8264 (tptp) REVERT: Q2 72 LYS cc_start: 0.8964 (tttt) cc_final: 0.8659 (tttp) REVERT: Q2 132 ASP cc_start: 0.8708 (t0) cc_final: 0.8463 (t0) REVERT: Q2 302 LYS cc_start: 0.8701 (mtmt) cc_final: 0.8284 (pttm) REVERT: Q2 359 THR cc_start: 0.9369 (m) cc_final: 0.9039 (p) REVERT: Q2 425 ARG cc_start: 0.8286 (mtm-85) cc_final: 0.7306 (mtm-85) REVERT: Q3 26 ASN cc_start: 0.8045 (t0) cc_final: 0.7698 (t0) REVERT: Q3 61 LYS cc_start: 0.8720 (tttt) cc_final: 0.8156 (ttpt) REVERT: Q3 76 GLU cc_start: 0.8271 (tt0) cc_final: 0.7908 (tp30) REVERT: Q3 221 ASN cc_start: 0.8213 (p0) cc_final: 0.7814 (p0) REVERT: Q3 358 ASN cc_start: 0.9264 (m-40) cc_final: 0.8987 (m110) REVERT: Q3 363 LYS cc_start: 0.9189 (tttm) cc_final: 0.8943 (tttt) REVERT: Q3 408 ILE cc_start: 0.8923 (tp) cc_final: 0.8548 (tp) outliers start: 226 outliers final: 181 residues processed: 1267 average time/residue: 0.6597 time to fit residues: 1411.2321 Evaluate side-chains 1278 residues out of total 7775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 1088 time to evaluate : 6.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B1 residue 162 SER Chi-restraints excluded: chain B1 residue 169 VAL Chi-restraints excluded: chain B1 residue 222 ASN Chi-restraints excluded: chain B1 residue 264 ILE Chi-restraints excluded: chain B1 residue 277 ASP Chi-restraints excluded: chain B2 residue 54 ASN Chi-restraints excluded: chain B2 residue 143 ASP Chi-restraints excluded: chain B2 residue 220 ASP Chi-restraints excluded: chain B2 residue 267 THR Chi-restraints excluded: chain B2 residue 271 SER Chi-restraints excluded: chain B2 residue 304 ASP Chi-restraints excluded: chain B3 residue 23 VAL Chi-restraints excluded: chain B3 residue 27 ASP Chi-restraints excluded: chain B3 residue 69 THR Chi-restraints excluded: chain B3 residue 97 THR Chi-restraints excluded: chain B3 residue 177 ASP Chi-restraints excluded: chain B3 residue 245 ILE Chi-restraints excluded: chain B3 residue 272 THR Chi-restraints excluded: chain B3 residue 304 ASP Chi-restraints excluded: chain B4 residue 97 THR Chi-restraints excluded: chain B4 residue 124 SER Chi-restraints excluded: chain B4 residue 169 VAL Chi-restraints excluded: chain B4 residue 191 LEU Chi-restraints excluded: chain B4 residue 232 VAL Chi-restraints excluded: chain B4 residue 264 ILE Chi-restraints excluded: chain B4 residue 266 GLU Chi-restraints excluded: chain B4 residue 304 ASP Chi-restraints excluded: chain B5 residue 51 VAL Chi-restraints excluded: chain B5 residue 97 THR Chi-restraints excluded: chain B5 residue 162 SER Chi-restraints excluded: chain B5 residue 223 SER Chi-restraints excluded: chain B5 residue 234 LEU Chi-restraints excluded: chain C2 residue 73 PHE Chi-restraints excluded: chain C4 residue 73 PHE Chi-restraints excluded: chain C4 residue 102 THR Chi-restraints excluded: chain C5 residue 94 SER Chi-restraints excluded: chain D1 residue 159 ILE Chi-restraints excluded: chain D1 residue 162 SER Chi-restraints excluded: chain D1 residue 179 ILE Chi-restraints excluded: chain D1 residue 182 LEU Chi-restraints excluded: chain D1 residue 198 SER Chi-restraints excluded: chain D1 residue 204 SER Chi-restraints excluded: chain D1 residue 311 VAL Chi-restraints excluded: chain D2 residue 111 ILE Chi-restraints excluded: chain D2 residue 190 GLU Chi-restraints excluded: chain D3 residue 57 ILE Chi-restraints excluded: chain D3 residue 59 GLN Chi-restraints excluded: chain D3 residue 177 ASP Chi-restraints excluded: chain D3 residue 198 SER Chi-restraints excluded: chain D3 residue 243 GLU Chi-restraints excluded: chain D4 residue 48 LEU Chi-restraints excluded: chain D4 residue 57 ILE Chi-restraints excluded: chain D4 residue 163 ILE Chi-restraints excluded: chain D4 residue 169 VAL Chi-restraints excluded: chain D4 residue 175 THR Chi-restraints excluded: chain D4 residue 206 LEU Chi-restraints excluded: chain D4 residue 231 VAL Chi-restraints excluded: chain D5 residue 29 VAL Chi-restraints excluded: chain D5 residue 44 THR Chi-restraints excluded: chain D5 residue 124 SER Chi-restraints excluded: chain D5 residue 273 VAL Chi-restraints excluded: chain D5 residue 299 LEU Chi-restraints excluded: chain P1 residue 2 LEU Chi-restraints excluded: chain P1 residue 18 ASN Chi-restraints excluded: chain P1 residue 39 LEU Chi-restraints excluded: chain P1 residue 54 ASP Chi-restraints excluded: chain P1 residue 96 SER Chi-restraints excluded: chain P1 residue 99 SER Chi-restraints excluded: chain P1 residue 119 ASP Chi-restraints excluded: chain P1 residue 143 ASP Chi-restraints excluded: chain P1 residue 206 THR Chi-restraints excluded: chain P1 residue 211 THR Chi-restraints excluded: chain P1 residue 284 ASP Chi-restraints excluded: chain P1 residue 327 SER Chi-restraints excluded: chain P1 residue 377 LYS Chi-restraints excluded: chain P1 residue 415 ILE Chi-restraints excluded: chain P1 residue 436 LEU Chi-restraints excluded: chain P1 residue 450 ILE Chi-restraints excluded: chain P2 residue 90 VAL Chi-restraints excluded: chain P2 residue 96 SER Chi-restraints excluded: chain P2 residue 155 ILE Chi-restraints excluded: chain P2 residue 175 ILE Chi-restraints excluded: chain P2 residue 182 ARG Chi-restraints excluded: chain P2 residue 197 ASP Chi-restraints excluded: chain P2 residue 229 THR Chi-restraints excluded: chain P2 residue 298 VAL Chi-restraints excluded: chain P2 residue 322 ARG Chi-restraints excluded: chain P2 residue 327 SER Chi-restraints excluded: chain P3 residue 4 VAL Chi-restraints excluded: chain P3 residue 23 ASP Chi-restraints excluded: chain P3 residue 39 LEU Chi-restraints excluded: chain P3 residue 43 ASN Chi-restraints excluded: chain P3 residue 124 ILE Chi-restraints excluded: chain P3 residue 135 SER Chi-restraints excluded: chain P3 residue 170 MET Chi-restraints excluded: chain P3 residue 191 LEU Chi-restraints excluded: chain P3 residue 208 ASP Chi-restraints excluded: chain P3 residue 229 THR Chi-restraints excluded: chain P3 residue 296 ASP Chi-restraints excluded: chain P3 residue 406 GLU Chi-restraints excluded: chain P3 residue 478 GLU Chi-restraints excluded: chain P4 residue 154 MET Chi-restraints excluded: chain P4 residue 179 THR Chi-restraints excluded: chain P4 residue 223 THR Chi-restraints excluded: chain P4 residue 327 SER Chi-restraints excluded: chain P4 residue 339 VAL Chi-restraints excluded: chain P4 residue 403 LYS Chi-restraints excluded: chain P4 residue 418 ASN Chi-restraints excluded: chain P5 residue 37 ASP Chi-restraints excluded: chain P5 residue 42 VAL Chi-restraints excluded: chain P5 residue 85 MET Chi-restraints excluded: chain P5 residue 135 SER Chi-restraints excluded: chain P5 residue 153 LEU Chi-restraints excluded: chain P5 residue 170 MET Chi-restraints excluded: chain P5 residue 196 ILE Chi-restraints excluded: chain P5 residue 286 MET Chi-restraints excluded: chain P5 residue 339 VAL Chi-restraints excluded: chain P5 residue 469 VAL Chi-restraints excluded: chain P6 residue 6 GLU Chi-restraints excluded: chain P6 residue 26 ASN Chi-restraints excluded: chain P6 residue 152 GLU Chi-restraints excluded: chain P6 residue 170 MET Chi-restraints excluded: chain P6 residue 193 THR Chi-restraints excluded: chain P6 residue 196 ILE Chi-restraints excluded: chain P6 residue 263 THR Chi-restraints excluded: chain P6 residue 303 GLN Chi-restraints excluded: chain P7 residue 57 ARG Chi-restraints excluded: chain P7 residue 71 THR Chi-restraints excluded: chain P7 residue 116 ASP Chi-restraints excluded: chain P7 residue 133 VAL Chi-restraints excluded: chain P7 residue 143 ASP Chi-restraints excluded: chain P7 residue 188 VAL Chi-restraints excluded: chain P7 residue 199 THR Chi-restraints excluded: chain P7 residue 223 THR Chi-restraints excluded: chain P7 residue 239 SER Chi-restraints excluded: chain P7 residue 320 GLU Chi-restraints excluded: chain P7 residue 327 SER Chi-restraints excluded: chain P7 residue 406 GLU Chi-restraints excluded: chain P7 residue 407 THR Chi-restraints excluded: chain P8 residue 1 MET Chi-restraints excluded: chain P8 residue 87 ASP Chi-restraints excluded: chain P8 residue 90 VAL Chi-restraints excluded: chain P8 residue 124 ILE Chi-restraints excluded: chain P8 residue 177 ASP Chi-restraints excluded: chain P8 residue 188 VAL Chi-restraints excluded: chain P8 residue 192 ARG Chi-restraints excluded: chain P8 residue 196 ILE Chi-restraints excluded: chain P8 residue 208 ASP Chi-restraints excluded: chain P8 residue 259 GLU Chi-restraints excluded: chain P8 residue 284 ASP Chi-restraints excluded: chain P8 residue 298 VAL Chi-restraints excluded: chain P8 residue 380 LEU Chi-restraints excluded: chain P9 residue 18 ASN Chi-restraints excluded: chain P9 residue 50 GLU Chi-restraints excluded: chain P9 residue 96 SER Chi-restraints excluded: chain P9 residue 144 LEU Chi-restraints excluded: chain P9 residue 152 GLU Chi-restraints excluded: chain P9 residue 188 VAL Chi-restraints excluded: chain P9 residue 206 THR Chi-restraints excluded: chain P9 residue 318 ASP Chi-restraints excluded: chain P9 residue 339 VAL Chi-restraints excluded: chain P9 residue 355 MET Chi-restraints excluded: chain P9 residue 409 LEU Chi-restraints excluded: chain P9 residue 436 LEU Chi-restraints excluded: chain Q1 residue 43 ASN Chi-restraints excluded: chain Q1 residue 215 VAL Chi-restraints excluded: chain Q1 residue 229 THR Chi-restraints excluded: chain Q1 residue 284 ASP Chi-restraints excluded: chain Q1 residue 298 VAL Chi-restraints excluded: chain Q1 residue 327 SER Chi-restraints excluded: chain Q1 residue 362 MET Chi-restraints excluded: chain Q1 residue 415 ILE Chi-restraints excluded: chain Q2 residue 17 ILE Chi-restraints excluded: chain Q2 residue 96 SER Chi-restraints excluded: chain Q2 residue 119 ASP Chi-restraints excluded: chain Q2 residue 170 MET Chi-restraints excluded: chain Q2 residue 199 THR Chi-restraints excluded: chain Q2 residue 355 MET Chi-restraints excluded: chain Q2 residue 406 GLU Chi-restraints excluded: chain Q3 residue 74 LEU Chi-restraints excluded: chain Q3 residue 96 SER Chi-restraints excluded: chain Q3 residue 124 ILE Chi-restraints excluded: chain Q3 residue 153 LEU Chi-restraints excluded: chain Q3 residue 158 GLN Chi-restraints excluded: chain Q3 residue 185 ILE Chi-restraints excluded: chain Q3 residue 211 THR Chi-restraints excluded: chain Q3 residue 295 LEU Chi-restraints excluded: chain Q3 residue 317 VAL Chi-restraints excluded: chain Q3 residue 440 LEU Chi-restraints excluded: chain Q3 residue 456 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 851 random chunks: chunk 746 optimal weight: 3.9990 chunk 785 optimal weight: 0.9980 chunk 716 optimal weight: 2.9990 chunk 764 optimal weight: 6.9990 chunk 460 optimal weight: 0.1980 chunk 332 optimal weight: 0.9980 chunk 600 optimal weight: 4.9990 chunk 234 optimal weight: 3.9990 chunk 690 optimal weight: 3.9990 chunk 722 optimal weight: 4.9990 chunk 761 optimal weight: 8.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4 286 GLN ** B5 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B5 238 ASN ** D1 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 150 GLN ** D2 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3 161 GLN ** D3 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P1 178 ASN ** P3 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P5 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P6 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P7 16 ASN P7 422 ASN P8 5 ASN ** P9 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q1 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q1 418 ASN Q2 73 ASN Q2 354 HIS ** Q3 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q3 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.5111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 71413 Z= 0.159 Angle : 0.536 10.999 96321 Z= 0.280 Chirality : 0.040 0.182 10525 Planarity : 0.003 0.048 12635 Dihedral : 4.351 21.567 9460 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.14 % Allowed : 17.59 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.09), residues: 8577 helix: 1.88 (0.10), residues: 3110 sheet: 0.22 (0.12), residues: 1770 loop : -0.33 (0.10), residues: 3697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRPC3 76 HIS 0.008 0.001 HISD5 32 PHE 0.021 0.001 PHEB3 106 TYR 0.019 0.001 TYRP2 190 ARG 0.010 0.000 ARGD4 221 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17154 Ramachandran restraints generated. 8577 Oldfield, 0 Emsley, 8577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17154 Ramachandran restraints generated. 8577 Oldfield, 0 Emsley, 8577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1369 residues out of total 7775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 1203 time to evaluate : 6.259 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B1 309 LYS cc_start: 0.8204 (ttmm) cc_final: 0.7875 (tppt) REVERT: B2 30 MET cc_start: 0.7162 (mpp) cc_final: 0.6046 (mpp) REVERT: B2 123 TYR cc_start: 0.8081 (t80) cc_final: 0.7324 (t80) REVERT: B3 20 LYS cc_start: 0.7418 (tptt) cc_final: 0.7196 (tptt) REVERT: B3 103 MET cc_start: 0.7300 (ttp) cc_final: 0.7052 (ttp) REVERT: B3 177 ASP cc_start: 0.8085 (OUTLIER) cc_final: 0.7672 (p0) REVERT: B4 25 ASN cc_start: 0.8279 (t0) cc_final: 0.7357 (p0) REVERT: B4 266 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7340 (pp20) REVERT: B4 292 ARG cc_start: 0.7232 (ttp-170) cc_final: 0.7030 (ttp-170) REVERT: B5 40 MET cc_start: 0.6173 (mtp) cc_final: 0.5924 (ttm) REVERT: B5 51 VAL cc_start: 0.8593 (t) cc_final: 0.8052 (p) REVERT: B5 66 MET cc_start: 0.7404 (mmm) cc_final: 0.7199 (mmm) REVERT: B5 279 THR cc_start: 0.8451 (m) cc_final: 0.8113 (p) REVERT: C1 73 PHE cc_start: 0.7325 (m-80) cc_final: 0.6723 (m-10) REVERT: C5 71 LYS cc_start: 0.8859 (tppt) cc_final: 0.8087 (tttt) REVERT: C5 76 TRP cc_start: 0.6864 (m100) cc_final: 0.6394 (m100) REVERT: D1 30 MET cc_start: 0.5766 (tpp) cc_final: 0.5430 (tpp) REVERT: D1 40 MET cc_start: -0.2420 (ttm) cc_final: -0.3070 (ttt) REVERT: D1 262 TYR cc_start: 0.8592 (m-80) cc_final: 0.8337 (m-80) REVERT: D2 58 MET cc_start: 0.8699 (mtp) cc_final: 0.8444 (mtm) REVERT: D3 123 TYR cc_start: 0.6452 (t80) cc_final: 0.6013 (t80) REVERT: D3 157 LYS cc_start: 0.5596 (mttt) cc_final: 0.5254 (ptpt) REVERT: D3 217 ARG cc_start: 0.6549 (mmt180) cc_final: 0.5885 (mtm180) REVERT: D4 30 MET cc_start: 0.7045 (mmm) cc_final: 0.6366 (mmm) REVERT: D4 217 ARG cc_start: 0.7933 (tpp80) cc_final: 0.7462 (mtp85) REVERT: D5 207 ARG cc_start: 0.7533 (mmm-85) cc_final: 0.7324 (mmm160) REVERT: D5 216 GLU cc_start: 0.7210 (pm20) cc_final: 0.7007 (mp0) REVERT: P1 1 MET cc_start: 0.7942 (tpp) cc_final: 0.7719 (tpp) REVERT: P1 24 GLU cc_start: 0.8962 (mm-30) cc_final: 0.8620 (mt-10) REVERT: P1 50 GLU cc_start: 0.8835 (tt0) cc_final: 0.8585 (tp30) REVERT: P1 158 GLN cc_start: 0.8727 (mm-40) cc_final: 0.8478 (mp10) REVERT: P1 243 MET cc_start: 0.8917 (tmm) cc_final: 0.8595 (tmm) REVERT: P1 252 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7820 (tm-30) REVERT: P1 301 ARG cc_start: 0.7808 (mmp80) cc_final: 0.7069 (ttm-80) REVERT: P1 302 LYS cc_start: 0.8768 (mtmt) cc_final: 0.8361 (pptt) REVERT: P1 383 LEU cc_start: 0.9349 (tp) cc_final: 0.9057 (tp) REVERT: P1 468 GLU cc_start: 0.8835 (tp30) cc_final: 0.8266 (tp30) REVERT: P1 470 LYS cc_start: 0.9196 (mmmm) cc_final: 0.8927 (mmmt) REVERT: P1 471 LYS cc_start: 0.9062 (tttt) cc_final: 0.8701 (ttmt) REVERT: P2 68 GLU cc_start: 0.8372 (mt-10) cc_final: 0.8095 (mt-10) REVERT: P2 70 LYS cc_start: 0.8917 (mtpt) cc_final: 0.8361 (mtmm) REVERT: P2 132 ASP cc_start: 0.8228 (t0) cc_final: 0.7405 (t0) REVERT: P2 157 ASN cc_start: 0.8766 (t0) cc_final: 0.8466 (t0) REVERT: P2 182 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.8084 (mmm-85) REVERT: P2 217 ARG cc_start: 0.8756 (mtm-85) cc_final: 0.8484 (mtt90) REVERT: P2 227 LYS cc_start: 0.9041 (tppt) cc_final: 0.8682 (mtmt) REVERT: P2 239 SER cc_start: 0.9377 (m) cc_final: 0.9033 (t) REVERT: P2 274 ASP cc_start: 0.9003 (t0) cc_final: 0.8800 (t0) REVERT: P2 288 LEU cc_start: 0.9519 (tp) cc_final: 0.9318 (tt) REVERT: P2 322 ARG cc_start: 0.7832 (OUTLIER) cc_final: 0.7433 (mmt180) REVERT: P2 415 ILE cc_start: 0.9087 (tp) cc_final: 0.8755 (tt) REVERT: P3 1 MET cc_start: 0.8164 (ptp) cc_final: 0.7839 (ptp) REVERT: P3 26 ASN cc_start: 0.8501 (t0) cc_final: 0.8123 (t0) REVERT: P3 125 GLU cc_start: 0.8075 (tp30) cc_final: 0.7732 (tp30) REVERT: P3 144 LEU cc_start: 0.9466 (mt) cc_final: 0.9212 (mt) REVERT: P3 152 GLU cc_start: 0.8420 (pp20) cc_final: 0.8000 (pp20) REVERT: P3 159 ASP cc_start: 0.9045 (t70) cc_final: 0.8647 (t0) REVERT: P3 243 MET cc_start: 0.8943 (tmm) cc_final: 0.8225 (tmm) REVERT: P3 301 ARG cc_start: 0.8900 (ttm110) cc_final: 0.8399 (mtm-85) REVERT: P3 374 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8023 (mp0) REVERT: P3 381 PHE cc_start: 0.8434 (t80) cc_final: 0.8128 (t80) REVERT: P3 456 MET cc_start: 0.8986 (mtt) cc_final: 0.8508 (mtt) REVERT: P3 468 GLU cc_start: 0.7696 (tp30) cc_final: 0.7065 (tp30) REVERT: P3 472 ILE cc_start: 0.8445 (mt) cc_final: 0.7961 (mt) REVERT: P3 478 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.7931 (mp0) REVERT: P4 24 GLU cc_start: 0.8776 (mm-30) cc_final: 0.8278 (mm-30) REVERT: P4 61 LYS cc_start: 0.8429 (tttt) cc_final: 0.7999 (tmtt) REVERT: P4 77 LEU cc_start: 0.7942 (tt) cc_final: 0.7678 (pp) REVERT: P4 96 SER cc_start: 0.9382 (t) cc_final: 0.9108 (p) REVERT: P4 125 GLU cc_start: 0.8497 (tt0) cc_final: 0.7649 (mm-30) REVERT: P4 129 ASP cc_start: 0.8771 (t0) cc_final: 0.8375 (m-30) REVERT: P4 192 ARG cc_start: 0.8160 (ttt90) cc_final: 0.7506 (ttt90) REVERT: P4 274 ASP cc_start: 0.9239 (t0) cc_final: 0.8937 (t0) REVERT: P4 302 LYS cc_start: 0.8978 (mtmt) cc_final: 0.8288 (mtpt) REVERT: P4 403 LYS cc_start: 0.9101 (OUTLIER) cc_final: 0.8864 (tptp) REVERT: P4 435 SER cc_start: 0.8695 (t) cc_final: 0.8213 (p) REVERT: P4 471 LYS cc_start: 0.8569 (tttt) cc_final: 0.8217 (tttm) REVERT: P4 476 GLU cc_start: 0.8044 (pt0) cc_final: 0.7685 (pt0) REVERT: P5 26 ASN cc_start: 0.8466 (t0) cc_final: 0.8006 (t0) REVERT: P5 132 ASP cc_start: 0.8346 (t0) cc_final: 0.7519 (t0) REVERT: P5 312 GLU cc_start: 0.8161 (tt0) cc_final: 0.7922 (tt0) REVERT: P5 347 ASP cc_start: 0.8784 (m-30) cc_final: 0.8427 (m-30) REVERT: P5 386 ARG cc_start: 0.9214 (OUTLIER) cc_final: 0.8904 (ttm170) REVERT: P5 434 LYS cc_start: 0.8603 (mttt) cc_final: 0.8260 (mttp) REVERT: P6 31 TYR cc_start: 0.9200 (t80) cc_final: 0.8845 (t80) REVERT: P6 93 ASP cc_start: 0.8548 (t0) cc_final: 0.8121 (t0) REVERT: P6 103 ASN cc_start: 0.9282 (t0) cc_final: 0.8881 (t0) REVERT: P6 122 GLU cc_start: 0.9026 (tp30) cc_final: 0.8819 (pt0) REVERT: P6 208 ASP cc_start: 0.8485 (m-30) cc_final: 0.7674 (p0) REVERT: P6 227 LYS cc_start: 0.9234 (tppt) cc_final: 0.8961 (tptp) REVERT: P6 327 SER cc_start: 0.9016 (m) cc_final: 0.8554 (p) REVERT: P7 44 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8213 (mp0) REVERT: P7 70 LYS cc_start: 0.9048 (mtpt) cc_final: 0.8791 (mtpp) REVERT: P7 93 ASP cc_start: 0.9225 (t70) cc_final: 0.8907 (t0) REVERT: P7 142 LEU cc_start: 0.8980 (tt) cc_final: 0.8760 (tt) REVERT: P7 170 MET cc_start: 0.9386 (mtp) cc_final: 0.8801 (tpp) REVERT: P7 192 ARG cc_start: 0.9011 (ttp80) cc_final: 0.8563 (ttm-80) REVERT: P7 218 TYR cc_start: 0.8874 (m-80) cc_final: 0.8572 (m-80) REVERT: P7 318 ASP cc_start: 0.8408 (t0) cc_final: 0.8001 (t0) REVERT: P7 371 GLN cc_start: 0.6890 (mm-40) cc_final: 0.6435 (mm-40) REVERT: P7 376 MET cc_start: 0.8583 (mmm) cc_final: 0.8286 (mmm) REVERT: P7 398 LEU cc_start: 0.9233 (mp) cc_final: 0.9023 (mp) REVERT: P7 406 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7235 (tt0) REVERT: P8 1 MET cc_start: 0.4349 (OUTLIER) cc_final: 0.4008 (tmm) REVERT: P8 76 GLU cc_start: 0.8017 (tp30) cc_final: 0.7568 (tp30) REVERT: P8 176 TYR cc_start: 0.9022 (m-80) cc_final: 0.8617 (m-80) REVERT: P8 192 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.8114 (tpt170) REVERT: P8 257 ASP cc_start: 0.8409 (m-30) cc_final: 0.7910 (m-30) REVERT: P8 456 MET cc_start: 0.9232 (mtt) cc_final: 0.8946 (mtt) REVERT: P9 44 GLU cc_start: 0.8969 (mp0) cc_final: 0.8762 (mp0) REVERT: P9 177 ASP cc_start: 0.8914 (t70) cc_final: 0.8567 (t0) REVERT: P9 208 ASP cc_start: 0.7914 (m-30) cc_final: 0.7613 (m-30) REVERT: P9 221 ASN cc_start: 0.7890 (p0) cc_final: 0.7522 (p0) REVERT: P9 227 LYS cc_start: 0.8927 (tppt) cc_final: 0.8512 (mmmt) REVERT: P9 274 ASP cc_start: 0.8757 (t70) cc_final: 0.8370 (t0) REVERT: P9 302 LYS cc_start: 0.8548 (mtmt) cc_final: 0.8117 (mmtm) REVERT: P9 322 ARG cc_start: 0.8459 (mtp85) cc_final: 0.8100 (mtt180) REVERT: P9 376 MET cc_start: 0.9197 (mmm) cc_final: 0.8700 (mmm) REVERT: P9 386 ARG cc_start: 0.9108 (ttm170) cc_final: 0.8620 (mtt180) REVERT: P9 452 GLN cc_start: 0.8748 (mm-40) cc_final: 0.8365 (pm20) REVERT: P9 463 GLN cc_start: 0.7977 (tp40) cc_final: 0.7757 (tp-100) REVERT: Q1 24 GLU cc_start: 0.9186 (mm-30) cc_final: 0.8496 (mm-30) REVERT: Q1 50 GLU cc_start: 0.8770 (tt0) cc_final: 0.8038 (tm-30) REVERT: Q1 54 ASP cc_start: 0.9103 (t0) cc_final: 0.8748 (t70) REVERT: Q1 243 MET cc_start: 0.8204 (tmm) cc_final: 0.7573 (tmm) REVERT: Q1 258 TYR cc_start: 0.9091 (p90) cc_final: 0.8644 (p90) REVERT: Q1 296 ASP cc_start: 0.8119 (t0) cc_final: 0.7853 (t70) REVERT: Q1 318 ASP cc_start: 0.8509 (t0) cc_final: 0.8297 (t70) REVERT: Q1 358 ASN cc_start: 0.9155 (m-40) cc_final: 0.8640 (m110) REVERT: Q1 425 ARG cc_start: 0.8558 (mtm-85) cc_final: 0.8299 (ptp90) REVERT: Q1 438 GLU cc_start: 0.8396 (mt-10) cc_final: 0.7981 (mt-10) REVERT: Q2 22 ASN cc_start: 0.9039 (t0) cc_final: 0.8814 (t0) REVERT: Q2 50 GLU cc_start: 0.8770 (tt0) cc_final: 0.8479 (tt0) REVERT: Q2 61 LYS cc_start: 0.8591 (tttt) cc_final: 0.8247 (tptp) REVERT: Q2 72 LYS cc_start: 0.8907 (tttt) cc_final: 0.8598 (tttp) REVERT: Q2 302 LYS cc_start: 0.8589 (mtmt) cc_final: 0.8063 (pttp) REVERT: Q2 359 THR cc_start: 0.9273 (m) cc_final: 0.8878 (p) REVERT: Q2 406 GLU cc_start: 0.8967 (OUTLIER) cc_final: 0.8609 (tt0) REVERT: Q2 425 ARG cc_start: 0.8261 (mtm-85) cc_final: 0.7263 (mtm-85) REVERT: Q2 466 GLU cc_start: 0.8816 (tp30) cc_final: 0.8515 (mp0) REVERT: Q3 26 ASN cc_start: 0.7830 (t0) cc_final: 0.7555 (t0) REVERT: Q3 61 LYS cc_start: 0.8696 (tttt) cc_final: 0.8170 (ttpt) REVERT: Q3 76 GLU cc_start: 0.8228 (tt0) cc_final: 0.7870 (tp30) REVERT: Q3 96 SER cc_start: 0.9285 (OUTLIER) cc_final: 0.9044 (p) REVERT: Q3 98 ILE cc_start: 0.9230 (mt) cc_final: 0.9017 (mt) REVERT: Q3 119 ASP cc_start: 0.8927 (m-30) cc_final: 0.8715 (m-30) REVERT: Q3 192 ARG cc_start: 0.8685 (mtp85) cc_final: 0.8439 (mtp180) REVERT: Q3 258 TYR cc_start: 0.8857 (p90) cc_final: 0.8506 (p90) REVERT: Q3 279 MET cc_start: 0.8645 (tpp) cc_final: 0.8330 (mtp) REVERT: Q3 363 LYS cc_start: 0.9157 (tttm) cc_final: 0.8922 (tttt) REVERT: Q3 408 ILE cc_start: 0.8937 (tp) cc_final: 0.8577 (tp) REVERT: Q3 411 ASN cc_start: 0.8888 (m110) cc_final: 0.8636 (m110) REVERT: Q3 458 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9164 (tp) outliers start: 166 outliers final: 126 residues processed: 1307 average time/residue: 0.6696 time to fit residues: 1476.0872 Evaluate side-chains 1275 residues out of total 7775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 1136 time to evaluate : 6.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B1 residue 222 ASN Chi-restraints excluded: chain B1 residue 264 ILE Chi-restraints excluded: chain B1 residue 277 ASP Chi-restraints excluded: chain B2 residue 54 ASN Chi-restraints excluded: chain B2 residue 143 ASP Chi-restraints excluded: chain B2 residue 220 ASP Chi-restraints excluded: chain B2 residue 304 ASP Chi-restraints excluded: chain B3 residue 23 VAL Chi-restraints excluded: chain B3 residue 69 THR Chi-restraints excluded: chain B3 residue 97 THR Chi-restraints excluded: chain B3 residue 177 ASP Chi-restraints excluded: chain B3 residue 272 THR Chi-restraints excluded: chain B3 residue 304 ASP Chi-restraints excluded: chain B4 residue 97 THR Chi-restraints excluded: chain B4 residue 169 VAL Chi-restraints excluded: chain B4 residue 191 LEU Chi-restraints excluded: chain B4 residue 264 ILE Chi-restraints excluded: chain B4 residue 266 GLU Chi-restraints excluded: chain B5 residue 97 THR Chi-restraints excluded: chain B5 residue 198 SER Chi-restraints excluded: chain B5 residue 234 LEU Chi-restraints excluded: chain C2 residue 73 PHE Chi-restraints excluded: chain C4 residue 73 PHE Chi-restraints excluded: chain C4 residue 102 THR Chi-restraints excluded: chain C5 residue 94 SER Chi-restraints excluded: chain C5 residue 99 VAL Chi-restraints excluded: chain D1 residue 159 ILE Chi-restraints excluded: chain D1 residue 179 ILE Chi-restraints excluded: chain D1 residue 182 LEU Chi-restraints excluded: chain D1 residue 311 VAL Chi-restraints excluded: chain D2 residue 51 VAL Chi-restraints excluded: chain D2 residue 111 ILE Chi-restraints excluded: chain D2 residue 190 GLU Chi-restraints excluded: chain D3 residue 57 ILE Chi-restraints excluded: chain D3 residue 177 ASP Chi-restraints excluded: chain D3 residue 198 SER Chi-restraints excluded: chain D3 residue 243 GLU Chi-restraints excluded: chain D4 residue 57 ILE Chi-restraints excluded: chain D4 residue 206 LEU Chi-restraints excluded: chain D4 residue 231 VAL Chi-restraints excluded: chain D5 residue 124 SER Chi-restraints excluded: chain D5 residue 273 VAL Chi-restraints excluded: chain D5 residue 299 LEU Chi-restraints excluded: chain P1 residue 2 LEU Chi-restraints excluded: chain P1 residue 18 ASN Chi-restraints excluded: chain P1 residue 39 LEU Chi-restraints excluded: chain P1 residue 54 ASP Chi-restraints excluded: chain P1 residue 96 SER Chi-restraints excluded: chain P1 residue 119 ASP Chi-restraints excluded: chain P1 residue 284 ASP Chi-restraints excluded: chain P1 residue 377 LYS Chi-restraints excluded: chain P1 residue 415 ILE Chi-restraints excluded: chain P1 residue 436 LEU Chi-restraints excluded: chain P1 residue 450 ILE Chi-restraints excluded: chain P2 residue 90 VAL Chi-restraints excluded: chain P2 residue 96 SER Chi-restraints excluded: chain P2 residue 155 ILE Chi-restraints excluded: chain P2 residue 182 ARG Chi-restraints excluded: chain P2 residue 322 ARG Chi-restraints excluded: chain P2 residue 327 SER Chi-restraints excluded: chain P3 residue 4 VAL Chi-restraints excluded: chain P3 residue 23 ASP Chi-restraints excluded: chain P3 residue 39 LEU Chi-restraints excluded: chain P3 residue 43 ASN Chi-restraints excluded: chain P3 residue 124 ILE Chi-restraints excluded: chain P3 residue 135 SER Chi-restraints excluded: chain P3 residue 170 MET Chi-restraints excluded: chain P3 residue 191 LEU Chi-restraints excluded: chain P3 residue 296 ASP Chi-restraints excluded: chain P3 residue 406 GLU Chi-restraints excluded: chain P3 residue 478 GLU Chi-restraints excluded: chain P4 residue 154 MET Chi-restraints excluded: chain P4 residue 327 SER Chi-restraints excluded: chain P4 residue 339 VAL Chi-restraints excluded: chain P4 residue 403 LYS Chi-restraints excluded: chain P4 residue 418 ASN Chi-restraints excluded: chain P5 residue 42 VAL Chi-restraints excluded: chain P5 residue 119 ASP Chi-restraints excluded: chain P5 residue 135 SER Chi-restraints excluded: chain P5 residue 196 ILE Chi-restraints excluded: chain P5 residue 286 MET Chi-restraints excluded: chain P5 residue 339 VAL Chi-restraints excluded: chain P5 residue 386 ARG Chi-restraints excluded: chain P5 residue 458 LEU Chi-restraints excluded: chain P5 residue 469 VAL Chi-restraints excluded: chain P6 residue 6 GLU Chi-restraints excluded: chain P6 residue 170 MET Chi-restraints excluded: chain P6 residue 193 THR Chi-restraints excluded: chain P6 residue 196 ILE Chi-restraints excluded: chain P6 residue 263 THR Chi-restraints excluded: chain P7 residue 57 ARG Chi-restraints excluded: chain P7 residue 99 SER Chi-restraints excluded: chain P7 residue 116 ASP Chi-restraints excluded: chain P7 residue 133 VAL Chi-restraints excluded: chain P7 residue 143 ASP Chi-restraints excluded: chain P7 residue 188 VAL Chi-restraints excluded: chain P7 residue 239 SER Chi-restraints excluded: chain P7 residue 327 SER Chi-restraints excluded: chain P7 residue 406 GLU Chi-restraints excluded: chain P7 residue 407 THR Chi-restraints excluded: chain P8 residue 1 MET Chi-restraints excluded: chain P8 residue 11 THR Chi-restraints excluded: chain P8 residue 87 ASP Chi-restraints excluded: chain P8 residue 90 VAL Chi-restraints excluded: chain P8 residue 188 VAL Chi-restraints excluded: chain P8 residue 192 ARG Chi-restraints excluded: chain P8 residue 196 ILE Chi-restraints excluded: chain P8 residue 284 ASP Chi-restraints excluded: chain P8 residue 298 VAL Chi-restraints excluded: chain P9 residue 18 ASN Chi-restraints excluded: chain P9 residue 50 GLU Chi-restraints excluded: chain P9 residue 96 SER Chi-restraints excluded: chain P9 residue 152 GLU Chi-restraints excluded: chain P9 residue 188 VAL Chi-restraints excluded: chain P9 residue 339 VAL Chi-restraints excluded: chain P9 residue 409 LEU Chi-restraints excluded: chain Q1 residue 219 LEU Chi-restraints excluded: chain Q1 residue 284 ASP Chi-restraints excluded: chain Q1 residue 327 SER Chi-restraints excluded: chain Q1 residue 362 MET Chi-restraints excluded: chain Q2 residue 17 ILE Chi-restraints excluded: chain Q2 residue 96 SER Chi-restraints excluded: chain Q2 residue 119 ASP Chi-restraints excluded: chain Q2 residue 133 VAL Chi-restraints excluded: chain Q2 residue 170 MET Chi-restraints excluded: chain Q2 residue 199 THR Chi-restraints excluded: chain Q2 residue 263 THR Chi-restraints excluded: chain Q2 residue 406 GLU Chi-restraints excluded: chain Q2 residue 414 SER Chi-restraints excluded: chain Q2 residue 450 ILE Chi-restraints excluded: chain Q3 residue 96 SER Chi-restraints excluded: chain Q3 residue 124 ILE Chi-restraints excluded: chain Q3 residue 153 LEU Chi-restraints excluded: chain Q3 residue 185 ILE Chi-restraints excluded: chain Q3 residue 211 THR Chi-restraints excluded: chain Q3 residue 295 LEU Chi-restraints excluded: chain Q3 residue 317 VAL Chi-restraints excluded: chain Q3 residue 456 MET Chi-restraints excluded: chain Q3 residue 458 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 851 random chunks: chunk 501 optimal weight: 6.9990 chunk 808 optimal weight: 9.9990 chunk 493 optimal weight: 3.9990 chunk 383 optimal weight: 6.9990 chunk 561 optimal weight: 10.0000 chunk 847 optimal weight: 10.0000 chunk 780 optimal weight: 7.9990 chunk 675 optimal weight: 10.0000 chunk 70 optimal weight: 20.0000 chunk 521 optimal weight: 0.6980 chunk 413 optimal weight: 9.9990 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4 286 GLN ** B5 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4 89 GLN ** D1 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3 25 ASN ** D3 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P1 178 ASN ** P3 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P3 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P5 16 ASN P5 41 ASN ** P5 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P6 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P7 16 ASN P7 422 ASN ** P9 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q1 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q2 73 ASN ** Q3 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q3 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q3 358 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.5170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 71413 Z= 0.310 Angle : 0.591 10.951 96321 Z= 0.310 Chirality : 0.042 0.182 10525 Planarity : 0.004 0.049 12635 Dihedral : 4.491 21.898 9460 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.19 % Allowed : 17.58 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.09), residues: 8577 helix: 1.73 (0.10), residues: 3119 sheet: 0.13 (0.12), residues: 1775 loop : -0.38 (0.10), residues: 3683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRPC3 76 HIS 0.008 0.001 HISD5 32 PHE 0.024 0.002 PHEP5 173 TYR 0.025 0.002 TYRD1 139 ARG 0.010 0.000 ARGB1 104 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17154 Ramachandran restraints generated. 8577 Oldfield, 0 Emsley, 8577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17154 Ramachandran restraints generated. 8577 Oldfield, 0 Emsley, 8577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1307 residues out of total 7775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 1137 time to evaluate : 6.332 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B2 30 MET cc_start: 0.7296 (mpp) cc_final: 0.6290 (mpp) REVERT: B2 123 TYR cc_start: 0.8092 (t80) cc_final: 0.7459 (t80) REVERT: B2 125 GLN cc_start: 0.7681 (pm20) cc_final: 0.7430 (pm20) REVERT: B3 103 MET cc_start: 0.7156 (ttp) cc_final: 0.6732 (ttp) REVERT: B3 199 LYS cc_start: 0.7381 (tptt) cc_final: 0.7144 (tppt) REVERT: B4 25 ASN cc_start: 0.8317 (t0) cc_final: 0.7427 (p0) REVERT: B4 203 ARG cc_start: 0.8213 (ptp-170) cc_final: 0.7994 (ptm160) REVERT: B4 266 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7399 (pp20) REVERT: B5 51 VAL cc_start: 0.8650 (t) cc_final: 0.8144 (p) REVERT: B5 279 THR cc_start: 0.8436 (m) cc_final: 0.8117 (p) REVERT: C1 73 PHE cc_start: 0.7403 (m-80) cc_final: 0.6751 (m-10) REVERT: C5 71 LYS cc_start: 0.8899 (tppt) cc_final: 0.8106 (tttt) REVERT: C5 76 TRP cc_start: 0.6922 (m100) cc_final: 0.5884 (m100) REVERT: D1 30 MET cc_start: 0.5993 (tpp) cc_final: 0.5485 (ttm) REVERT: D1 40 MET cc_start: -0.2260 (ttm) cc_final: -0.2942 (ttt) REVERT: D1 262 TYR cc_start: 0.8500 (m-80) cc_final: 0.8292 (m-80) REVERT: D2 58 MET cc_start: 0.8748 (mtp) cc_final: 0.8424 (mtm) REVERT: D3 58 MET cc_start: 0.8070 (ttm) cc_final: 0.7643 (ttp) REVERT: D3 123 TYR cc_start: 0.6411 (t80) cc_final: 0.5990 (t80) REVERT: D3 157 LYS cc_start: 0.5614 (mttt) cc_final: 0.5318 (ptpt) REVERT: D3 217 ARG cc_start: 0.6525 (mmt180) cc_final: 0.5870 (mtm180) REVERT: D4 30 MET cc_start: 0.7104 (mmm) cc_final: 0.6350 (mmm) REVERT: P1 1 MET cc_start: 0.7893 (tpp) cc_final: 0.7614 (tpp) REVERT: P1 24 GLU cc_start: 0.8983 (mm-30) cc_final: 0.8611 (mt-10) REVERT: P1 50 GLU cc_start: 0.8874 (tt0) cc_final: 0.8575 (tp30) REVERT: P1 158 GLN cc_start: 0.8778 (mm-40) cc_final: 0.8571 (mp10) REVERT: P1 243 MET cc_start: 0.8909 (tmm) cc_final: 0.8591 (tmm) REVERT: P1 252 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7796 (tm-30) REVERT: P1 301 ARG cc_start: 0.7851 (mmp80) cc_final: 0.7097 (ttm-80) REVERT: P1 302 LYS cc_start: 0.8802 (mtmt) cc_final: 0.8420 (pptt) REVERT: P1 383 LEU cc_start: 0.9420 (tp) cc_final: 0.9165 (tp) REVERT: P1 468 GLU cc_start: 0.8882 (tp30) cc_final: 0.8318 (tp30) REVERT: P1 470 LYS cc_start: 0.9207 (mmmm) cc_final: 0.8927 (mmmt) REVERT: P1 471 LYS cc_start: 0.9087 (tttt) cc_final: 0.8718 (ttmt) REVERT: P2 68 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8112 (mt-10) REVERT: P2 70 LYS cc_start: 0.9007 (mtpt) cc_final: 0.8723 (mtmm) REVERT: P2 93 ASP cc_start: 0.8509 (t0) cc_final: 0.8219 (t0) REVERT: P2 132 ASP cc_start: 0.8310 (t0) cc_final: 0.7521 (t0) REVERT: P2 157 ASN cc_start: 0.8764 (t0) cc_final: 0.8432 (t0) REVERT: P2 182 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.7945 (mmm-85) REVERT: P2 227 LYS cc_start: 0.9059 (tppt) cc_final: 0.8689 (mttt) REVERT: P2 322 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7501 (mmt180) REVERT: P2 376 MET cc_start: 0.9033 (mmm) cc_final: 0.8682 (mmm) REVERT: P2 415 ILE cc_start: 0.9083 (tp) cc_final: 0.8732 (tt) REVERT: P3 1 MET cc_start: 0.8194 (ptp) cc_final: 0.7813 (ptp) REVERT: P3 26 ASN cc_start: 0.8564 (t0) cc_final: 0.8203 (t0) REVERT: P3 152 GLU cc_start: 0.8456 (pp20) cc_final: 0.8015 (pp20) REVERT: P3 159 ASP cc_start: 0.9029 (t70) cc_final: 0.8644 (t0) REVERT: P3 243 MET cc_start: 0.8981 (tmm) cc_final: 0.8208 (tmm) REVERT: P3 301 ARG cc_start: 0.8917 (ttm110) cc_final: 0.8455 (mtm-85) REVERT: P3 355 MET cc_start: 0.8118 (ttt) cc_final: 0.7726 (ttt) REVERT: P3 374 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8034 (mp0) REVERT: P3 456 MET cc_start: 0.9018 (mtt) cc_final: 0.8565 (mtt) REVERT: P3 468 GLU cc_start: 0.7735 (tp30) cc_final: 0.7138 (tp30) REVERT: P3 472 ILE cc_start: 0.8484 (mt) cc_final: 0.8039 (mt) REVERT: P3 478 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.7971 (mp0) REVERT: P4 61 LYS cc_start: 0.8488 (tttt) cc_final: 0.8252 (tmtt) REVERT: P4 77 LEU cc_start: 0.8117 (tt) cc_final: 0.7878 (pp) REVERT: P4 125 GLU cc_start: 0.8547 (tt0) cc_final: 0.7816 (mm-30) REVERT: P4 129 ASP cc_start: 0.8765 (t0) cc_final: 0.8383 (m-30) REVERT: P4 192 ARG cc_start: 0.8171 (ttt90) cc_final: 0.7512 (ttt90) REVERT: P4 274 ASP cc_start: 0.9262 (t0) cc_final: 0.8937 (t0) REVERT: P4 302 LYS cc_start: 0.8879 (mtmt) cc_final: 0.8585 (mtmm) REVERT: P4 435 SER cc_start: 0.8642 (t) cc_final: 0.8141 (p) REVERT: P4 471 LYS cc_start: 0.8668 (tttt) cc_final: 0.8292 (tttm) REVERT: P4 476 GLU cc_start: 0.8036 (pt0) cc_final: 0.7675 (pt0) REVERT: P5 26 ASN cc_start: 0.8607 (t0) cc_final: 0.8082 (t0) REVERT: P5 132 ASP cc_start: 0.8453 (t0) cc_final: 0.7610 (t0) REVERT: P5 312 GLU cc_start: 0.8189 (tt0) cc_final: 0.7943 (tt0) REVERT: P5 386 ARG cc_start: 0.9238 (OUTLIER) cc_final: 0.8907 (ttm170) REVERT: P5 434 LYS cc_start: 0.8648 (mttt) cc_final: 0.8244 (mttp) REVERT: P5 439 GLU cc_start: 0.8297 (mt-10) cc_final: 0.7831 (mt-10) REVERT: P6 31 TYR cc_start: 0.9276 (t80) cc_final: 0.8908 (t80) REVERT: P6 93 ASP cc_start: 0.8603 (t0) cc_final: 0.8163 (t0) REVERT: P6 103 ASN cc_start: 0.9338 (t0) cc_final: 0.8743 (t0) REVERT: P6 208 ASP cc_start: 0.8489 (m-30) cc_final: 0.7694 (p0) REVERT: P6 227 LYS cc_start: 0.9230 (tppt) cc_final: 0.8962 (tptp) REVERT: P6 249 SER cc_start: 0.9478 (OUTLIER) cc_final: 0.9086 (t) REVERT: P6 302 LYS cc_start: 0.4448 (pttt) cc_final: 0.4182 (pttt) REVERT: P6 327 SER cc_start: 0.9062 (m) cc_final: 0.8609 (p) REVERT: P6 378 TYR cc_start: 0.8849 (t80) cc_final: 0.8503 (t80) REVERT: P6 379 LYS cc_start: 0.8874 (mttp) cc_final: 0.8583 (mttp) REVERT: P7 44 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8197 (mp0) REVERT: P7 70 LYS cc_start: 0.9123 (mtpt) cc_final: 0.8793 (mtpp) REVERT: P7 93 ASP cc_start: 0.9306 (t70) cc_final: 0.8965 (t0) REVERT: P7 170 MET cc_start: 0.9386 (mtp) cc_final: 0.8801 (tpp) REVERT: P7 192 ARG cc_start: 0.9037 (ttp80) cc_final: 0.8609 (ttm-80) REVERT: P7 318 ASP cc_start: 0.8439 (t0) cc_final: 0.8171 (t0) REVERT: P7 371 GLN cc_start: 0.7080 (mm-40) cc_final: 0.6876 (mm-40) REVERT: P7 376 MET cc_start: 0.8600 (mmm) cc_final: 0.8349 (mmm) REVERT: P8 76 GLU cc_start: 0.8024 (tp30) cc_final: 0.7467 (tp30) REVERT: P8 192 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.8058 (tpt170) REVERT: P8 201 GLU cc_start: 0.7151 (pm20) cc_final: 0.6865 (pm20) REVERT: P8 257 ASP cc_start: 0.8442 (m-30) cc_final: 0.8003 (m-30) REVERT: P8 343 GLU cc_start: 0.8961 (mm-30) cc_final: 0.8436 (mm-30) REVERT: P8 456 MET cc_start: 0.9256 (mtt) cc_final: 0.8945 (mtt) REVERT: P9 177 ASP cc_start: 0.8861 (t70) cc_final: 0.8484 (t0) REVERT: P9 208 ASP cc_start: 0.8046 (m-30) cc_final: 0.7749 (m-30) REVERT: P9 221 ASN cc_start: 0.7930 (p0) cc_final: 0.7542 (p0) REVERT: P9 227 LYS cc_start: 0.8977 (tppt) cc_final: 0.8532 (mmmt) REVERT: P9 274 ASP cc_start: 0.8822 (t70) cc_final: 0.8440 (t0) REVERT: P9 302 LYS cc_start: 0.8591 (mtmt) cc_final: 0.8193 (mmtm) REVERT: P9 322 ARG cc_start: 0.8487 (mtp85) cc_final: 0.8141 (mtt180) REVERT: P9 376 MET cc_start: 0.9226 (mmm) cc_final: 0.8645 (mmm) REVERT: P9 452 GLN cc_start: 0.8756 (mm-40) cc_final: 0.8373 (pm20) REVERT: P9 463 GLN cc_start: 0.7997 (tp40) cc_final: 0.7770 (tp-100) REVERT: Q1 24 GLU cc_start: 0.9252 (mm-30) cc_final: 0.8893 (mm-30) REVERT: Q1 50 GLU cc_start: 0.8821 (tt0) cc_final: 0.8019 (tm-30) REVERT: Q1 54 ASP cc_start: 0.9111 (t0) cc_final: 0.8705 (t70) REVERT: Q1 93 ASP cc_start: 0.8547 (t0) cc_final: 0.8282 (t0) REVERT: Q1 243 MET cc_start: 0.8257 (tmm) cc_final: 0.7582 (tmm) REVERT: Q1 296 ASP cc_start: 0.8165 (t0) cc_final: 0.7886 (t70) REVERT: Q1 318 ASP cc_start: 0.8609 (t0) cc_final: 0.8344 (t70) REVERT: Q1 358 ASN cc_start: 0.9201 (m-40) cc_final: 0.8682 (m110) REVERT: Q1 425 ARG cc_start: 0.8538 (mtm-85) cc_final: 0.8245 (ptp90) REVERT: Q1 438 GLU cc_start: 0.8419 (mt-10) cc_final: 0.7959 (mt-10) REVERT: Q2 22 ASN cc_start: 0.9056 (t0) cc_final: 0.8814 (t0) REVERT: Q2 50 GLU cc_start: 0.8812 (tt0) cc_final: 0.8506 (tt0) REVERT: Q2 61 LYS cc_start: 0.8590 (tttt) cc_final: 0.8269 (tptp) REVERT: Q2 72 LYS cc_start: 0.8940 (tttt) cc_final: 0.8640 (tttm) REVERT: Q2 302 LYS cc_start: 0.8661 (mtmt) cc_final: 0.8124 (pttt) REVERT: Q2 359 THR cc_start: 0.9325 (m) cc_final: 0.8984 (p) REVERT: Q2 406 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8529 (tt0) REVERT: Q2 425 ARG cc_start: 0.8276 (mtm-85) cc_final: 0.7277 (mtm-85) REVERT: Q2 466 GLU cc_start: 0.8859 (tp30) cc_final: 0.8452 (mp0) REVERT: Q3 26 ASN cc_start: 0.7959 (t0) cc_final: 0.7689 (t0) REVERT: Q3 39 LEU cc_start: 0.9576 (tp) cc_final: 0.9049 (pp) REVERT: Q3 61 LYS cc_start: 0.8736 (tttt) cc_final: 0.8180 (ttpt) REVERT: Q3 76 GLU cc_start: 0.8210 (tt0) cc_final: 0.7888 (tp30) REVERT: Q3 96 SER cc_start: 0.9302 (OUTLIER) cc_final: 0.9023 (p) REVERT: Q3 192 ARG cc_start: 0.8659 (mtp85) cc_final: 0.8429 (mtp180) REVERT: Q3 243 MET cc_start: 0.8243 (tmm) cc_final: 0.7901 (tmm) REVERT: Q3 279 MET cc_start: 0.8862 (tpp) cc_final: 0.8461 (mtp) REVERT: Q3 363 LYS cc_start: 0.9168 (tttm) cc_final: 0.8928 (tttt) REVERT: Q3 408 ILE cc_start: 0.8858 (tp) cc_final: 0.8500 (tp) REVERT: Q3 411 ASN cc_start: 0.8931 (m110) cc_final: 0.8681 (m110) outliers start: 170 outliers final: 145 residues processed: 1243 average time/residue: 0.6744 time to fit residues: 1413.1131 Evaluate side-chains 1271 residues out of total 7775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 1117 time to evaluate : 6.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B1 residue 222 ASN Chi-restraints excluded: chain B1 residue 264 ILE Chi-restraints excluded: chain B1 residue 277 ASP Chi-restraints excluded: chain B2 residue 54 ASN Chi-restraints excluded: chain B2 residue 143 ASP Chi-restraints excluded: chain B2 residue 220 ASP Chi-restraints excluded: chain B2 residue 271 SER Chi-restraints excluded: chain B2 residue 304 ASP Chi-restraints excluded: chain B3 residue 23 VAL Chi-restraints excluded: chain B3 residue 69 THR Chi-restraints excluded: chain B3 residue 97 THR Chi-restraints excluded: chain B3 residue 177 ASP Chi-restraints excluded: chain B3 residue 245 ILE Chi-restraints excluded: chain B3 residue 272 THR Chi-restraints excluded: chain B3 residue 304 ASP Chi-restraints excluded: chain B4 residue 97 THR Chi-restraints excluded: chain B4 residue 169 VAL Chi-restraints excluded: chain B4 residue 191 LEU Chi-restraints excluded: chain B4 residue 264 ILE Chi-restraints excluded: chain B4 residue 266 GLU Chi-restraints excluded: chain B5 residue 97 THR Chi-restraints excluded: chain B5 residue 234 LEU Chi-restraints excluded: chain C2 residue 73 PHE Chi-restraints excluded: chain C4 residue 73 PHE Chi-restraints excluded: chain C4 residue 102 THR Chi-restraints excluded: chain C5 residue 94 SER Chi-restraints excluded: chain C5 residue 99 VAL Chi-restraints excluded: chain D1 residue 159 ILE Chi-restraints excluded: chain D1 residue 162 SER Chi-restraints excluded: chain D1 residue 179 ILE Chi-restraints excluded: chain D1 residue 182 LEU Chi-restraints excluded: chain D1 residue 311 VAL Chi-restraints excluded: chain D2 residue 111 ILE Chi-restraints excluded: chain D3 residue 57 ILE Chi-restraints excluded: chain D3 residue 59 GLN Chi-restraints excluded: chain D3 residue 177 ASP Chi-restraints excluded: chain D3 residue 198 SER Chi-restraints excluded: chain D3 residue 243 GLU Chi-restraints excluded: chain D4 residue 206 LEU Chi-restraints excluded: chain D4 residue 231 VAL Chi-restraints excluded: chain D5 residue 124 SER Chi-restraints excluded: chain D5 residue 273 VAL Chi-restraints excluded: chain D5 residue 299 LEU Chi-restraints excluded: chain P1 residue 2 LEU Chi-restraints excluded: chain P1 residue 18 ASN Chi-restraints excluded: chain P1 residue 39 LEU Chi-restraints excluded: chain P1 residue 54 ASP Chi-restraints excluded: chain P1 residue 96 SER Chi-restraints excluded: chain P1 residue 119 ASP Chi-restraints excluded: chain P1 residue 206 THR Chi-restraints excluded: chain P1 residue 284 ASP Chi-restraints excluded: chain P1 residue 377 LYS Chi-restraints excluded: chain P1 residue 415 ILE Chi-restraints excluded: chain P1 residue 436 LEU Chi-restraints excluded: chain P1 residue 450 ILE Chi-restraints excluded: chain P2 residue 90 VAL Chi-restraints excluded: chain P2 residue 96 SER Chi-restraints excluded: chain P2 residue 155 ILE Chi-restraints excluded: chain P2 residue 182 ARG Chi-restraints excluded: chain P2 residue 298 VAL Chi-restraints excluded: chain P2 residue 322 ARG Chi-restraints excluded: chain P2 residue 327 SER Chi-restraints excluded: chain P3 residue 4 VAL Chi-restraints excluded: chain P3 residue 23 ASP Chi-restraints excluded: chain P3 residue 39 LEU Chi-restraints excluded: chain P3 residue 43 ASN Chi-restraints excluded: chain P3 residue 124 ILE Chi-restraints excluded: chain P3 residue 135 SER Chi-restraints excluded: chain P3 residue 170 MET Chi-restraints excluded: chain P3 residue 191 LEU Chi-restraints excluded: chain P3 residue 296 ASP Chi-restraints excluded: chain P3 residue 317 VAL Chi-restraints excluded: chain P3 residue 406 GLU Chi-restraints excluded: chain P3 residue 478 GLU Chi-restraints excluded: chain P4 residue 154 MET Chi-restraints excluded: chain P4 residue 327 SER Chi-restraints excluded: chain P4 residue 339 VAL Chi-restraints excluded: chain P4 residue 403 LYS Chi-restraints excluded: chain P4 residue 418 ASN Chi-restraints excluded: chain P5 residue 42 VAL Chi-restraints excluded: chain P5 residue 85 MET Chi-restraints excluded: chain P5 residue 119 ASP Chi-restraints excluded: chain P5 residue 135 SER Chi-restraints excluded: chain P5 residue 164 LEU Chi-restraints excluded: chain P5 residue 170 MET Chi-restraints excluded: chain P5 residue 196 ILE Chi-restraints excluded: chain P5 residue 286 MET Chi-restraints excluded: chain P5 residue 339 VAL Chi-restraints excluded: chain P5 residue 386 ARG Chi-restraints excluded: chain P5 residue 458 LEU Chi-restraints excluded: chain P5 residue 469 VAL Chi-restraints excluded: chain P6 residue 6 GLU Chi-restraints excluded: chain P6 residue 152 GLU Chi-restraints excluded: chain P6 residue 170 MET Chi-restraints excluded: chain P6 residue 193 THR Chi-restraints excluded: chain P6 residue 196 ILE Chi-restraints excluded: chain P6 residue 249 SER Chi-restraints excluded: chain P6 residue 263 THR Chi-restraints excluded: chain P7 residue 57 ARG Chi-restraints excluded: chain P7 residue 99 SER Chi-restraints excluded: chain P7 residue 116 ASP Chi-restraints excluded: chain P7 residue 133 VAL Chi-restraints excluded: chain P7 residue 143 ASP Chi-restraints excluded: chain P7 residue 188 VAL Chi-restraints excluded: chain P7 residue 239 SER Chi-restraints excluded: chain P7 residue 320 GLU Chi-restraints excluded: chain P7 residue 327 SER Chi-restraints excluded: chain P7 residue 406 GLU Chi-restraints excluded: chain P7 residue 407 THR Chi-restraints excluded: chain P8 residue 11 THR Chi-restraints excluded: chain P8 residue 87 ASP Chi-restraints excluded: chain P8 residue 90 VAL Chi-restraints excluded: chain P8 residue 124 ILE Chi-restraints excluded: chain P8 residue 177 ASP Chi-restraints excluded: chain P8 residue 188 VAL Chi-restraints excluded: chain P8 residue 192 ARG Chi-restraints excluded: chain P8 residue 196 ILE Chi-restraints excluded: chain P8 residue 208 ASP Chi-restraints excluded: chain P8 residue 284 ASP Chi-restraints excluded: chain P8 residue 298 VAL Chi-restraints excluded: chain P8 residue 380 LEU Chi-restraints excluded: chain P9 residue 18 ASN Chi-restraints excluded: chain P9 residue 50 GLU Chi-restraints excluded: chain P9 residue 96 SER Chi-restraints excluded: chain P9 residue 152 GLU Chi-restraints excluded: chain P9 residue 188 VAL Chi-restraints excluded: chain P9 residue 339 VAL Chi-restraints excluded: chain P9 residue 409 LEU Chi-restraints excluded: chain Q1 residue 43 ASN Chi-restraints excluded: chain Q1 residue 219 LEU Chi-restraints excluded: chain Q1 residue 229 THR Chi-restraints excluded: chain Q1 residue 284 ASP Chi-restraints excluded: chain Q1 residue 327 SER Chi-restraints excluded: chain Q1 residue 362 MET Chi-restraints excluded: chain Q2 residue 17 ILE Chi-restraints excluded: chain Q2 residue 96 SER Chi-restraints excluded: chain Q2 residue 119 ASP Chi-restraints excluded: chain Q2 residue 133 VAL Chi-restraints excluded: chain Q2 residue 170 MET Chi-restraints excluded: chain Q2 residue 199 THR Chi-restraints excluded: chain Q2 residue 263 THR Chi-restraints excluded: chain Q2 residue 355 MET Chi-restraints excluded: chain Q2 residue 406 GLU Chi-restraints excluded: chain Q2 residue 414 SER Chi-restraints excluded: chain Q3 residue 96 SER Chi-restraints excluded: chain Q3 residue 124 ILE Chi-restraints excluded: chain Q3 residue 153 LEU Chi-restraints excluded: chain Q3 residue 185 ILE Chi-restraints excluded: chain Q3 residue 211 THR Chi-restraints excluded: chain Q3 residue 295 LEU Chi-restraints excluded: chain Q3 residue 317 VAL Chi-restraints excluded: chain Q3 residue 440 LEU Chi-restraints excluded: chain Q3 residue 456 MET Chi-restraints excluded: chain Q3 residue 463 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 851 random chunks: chunk 536 optimal weight: 5.9990 chunk 719 optimal weight: 10.0000 chunk 206 optimal weight: 0.6980 chunk 622 optimal weight: 9.9990 chunk 99 optimal weight: 20.0000 chunk 187 optimal weight: 0.1980 chunk 676 optimal weight: 9.9990 chunk 282 optimal weight: 30.0000 chunk 694 optimal weight: 6.9990 chunk 85 optimal weight: 30.0000 chunk 124 optimal weight: 20.0000 overall best weight: 4.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4 89 GLN ** D1 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P1 178 ASN ** P3 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P5 16 ASN P5 41 ASN ** P5 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P6 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P7 422 ASN ** P9 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q1 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q2 73 ASN ** Q3 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q3 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.136063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.095357 restraints weight = 126490.657| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.98 r_work: 0.3125 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.5234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 71413 Z= 0.282 Angle : 0.581 10.629 96321 Z= 0.304 Chirality : 0.042 0.173 10525 Planarity : 0.003 0.047 12635 Dihedral : 4.477 21.557 9460 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.28 % Allowed : 17.52 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.09), residues: 8577 helix: 1.74 (0.10), residues: 3119 sheet: 0.11 (0.12), residues: 1775 loop : -0.40 (0.10), residues: 3683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRPC3 76 HIS 0.007 0.001 HISP3 92 PHE 0.023 0.002 PHEP5 173 TYR 0.025 0.002 TYRD4 123 ARG 0.010 0.000 ARGD4 221 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22933.13 seconds wall clock time: 400 minutes 34.79 seconds (24034.79 seconds total)