Starting phenix.real_space_refine on Sun Feb 8 10:24:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9msf_48587/02_2026/9msf_48587.cif Found real_map, /net/cci-nas-00/data/ceres_data/9msf_48587/02_2026/9msf_48587.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9msf_48587/02_2026/9msf_48587.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9msf_48587/02_2026/9msf_48587.map" model { file = "/net/cci-nas-00/data/ceres_data/9msf_48587/02_2026/9msf_48587.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9msf_48587/02_2026/9msf_48587.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 111 5.49 5 Mg 2 5.21 5 S 144 5.16 5 C 26900 2.51 5 N 7495 2.21 5 O 9419 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 44073 Number of models: 1 Model: "" Number of chains: 38 Chain: "A" Number of atoms: 1979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1979 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 8, 'TRANS': 238} Chain: "B" Number of atoms: 1979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1979 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 8, 'TRANS': 238} Chain: "C" Number of atoms: 1979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1979 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 8, 'TRANS': 238} Chain: "D" Number of atoms: 1979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1979 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 8, 'TRANS': 238} Chain: "E" Number of atoms: 1979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1979 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 8, 'TRANS': 238} Chain: "F" Number of atoms: 1964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1964 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 237} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2357 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 290} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 1718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1718 Classifications: {'peptide': 223} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 213} Chain breaks: 1 Chain: "I" Number of atoms: 10567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10567 Classifications: {'peptide': 1340} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1283} Chain: "J" Number of atoms: 10524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1352, 10524 Classifications: {'peptide': 1352} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1296} Chain breaks: 2 Chain: "K" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "M" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3353 Classifications: {'peptide': 421} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 403} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "S" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 276 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "T" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 217 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "U" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 701 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "V" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 693 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 12 Unusual residues: {' MG': 1, ' ZN': 2, 'POP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "E" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 89 Classifications: {'water': 89} Link IDs: {None: 88} Chain: "H" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 45 Classifications: {'water': 45} Link IDs: {None: 44} Chain: "I" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 367 Classifications: {'water': 367} Link IDs: {None: 366} Chain: "J" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 333 Classifications: {'water': 333} Link IDs: {None: 332} Chain: "K" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "M" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 64 Classifications: {'water': 64} Link IDs: {None: 63} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "U" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "V" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 27074 SG CYS J 70 53.534 69.548 129.654 1.00 53.47 S ATOM 27088 SG CYS J 72 55.389 70.198 132.934 1.00 66.45 S ATOM 27196 SG CYS J 85 51.905 71.573 132.728 1.00 73.34 S ATOM 27220 SG CYS J 88 54.912 73.204 130.704 1.00 52.46 S ATOM 32908 SG CYS J 814 36.312 98.710 69.050 1.00 71.42 S ATOM 33473 SG CYS J 888 39.654 97.996 71.045 1.00 54.45 S ATOM 33524 SG CYS J 895 37.852 95.309 69.094 1.00 57.90 S ATOM 33545 SG CYS J 898 39.563 97.907 67.157 1.00 70.56 S Time building chain proxies: 9.50, per 1000 atoms: 0.22 Number of scatterers: 44073 At special positions: 0 Unit cell: (163.4, 171.14, 239.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 144 16.00 P 111 15.00 Mg 2 11.99 O 9419 8.00 N 7495 7.00 C 26900 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.93 Conformation dependent library (CDL) restraints added in 1.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 70 " pdb=" ZN J1504 " pdb="ZN ZN J1504 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1504 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1504 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1504 " - pdb=" SG CYS J 888 " Number of angles added : 12 10330 Ramachandran restraints generated. 5165 Oldfield, 0 Emsley, 5165 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9642 Finding SS restraints... Secondary structure from input PDB file: 226 helices and 71 sheets defined 45.2% alpha, 14.2% beta 44 base pairs and 79 stacking pairs defined. Time for finding SS restraints: 6.00 Creating SS restraints... Processing helix chain 'A' and resid 143 through 157 Processing helix chain 'A' and resid 172 through 183 Processing helix chain 'A' and resid 200 through 202 No H-bonds generated for 'chain 'A' and resid 200 through 202' Processing helix chain 'A' and resid 203 through 209 Processing helix chain 'A' and resid 225 through 230 Processing helix chain 'A' and resid 240 through 243 Processing helix chain 'A' and resid 244 through 258 removed outlier: 3.517A pdb=" N VAL A 254 " --> pdb=" O LYS A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 290 Processing helix chain 'A' and resid 293 through 301 Processing helix chain 'A' and resid 309 through 315 removed outlier: 4.518A pdb=" N LYS A 314 " --> pdb=" O ARG A 311 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N GLU A 315 " --> pdb=" O GLU A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 333 removed outlier: 3.540A pdb=" N LYS A 326 " --> pdb=" O ASN A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 350 removed outlier: 3.640A pdb=" N SER A 349 " --> pdb=" O GLU A 345 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 369 removed outlier: 3.569A pdb=" N GLU A 358 " --> pdb=" O GLY A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 384 removed outlier: 3.725A pdb=" N LEU A 380 " --> pdb=" O ASP A 376 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N CYS A 382 " --> pdb=" O GLY A 378 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LEU A 383 " --> pdb=" O GLU A 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 156 removed outlier: 3.639A pdb=" N ILE B 149 " --> pdb=" O LYS B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 184 Processing helix chain 'B' and resid 197 through 199 No H-bonds generated for 'chain 'B' and resid 197 through 199' Processing helix chain 'B' and resid 200 through 202 No H-bonds generated for 'chain 'B' and resid 200 through 202' Processing helix chain 'B' and resid 203 through 209 Processing helix chain 'B' and resid 225 through 230 Processing helix chain 'B' and resid 240 through 243 Processing helix chain 'B' and resid 244 through 249 removed outlier: 4.047A pdb=" N ALA B 249 " --> pdb=" O LEU B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 252 No H-bonds generated for 'chain 'B' and resid 250 through 252' Processing helix chain 'B' and resid 282 through 289 Processing helix chain 'B' and resid 293 through 301 removed outlier: 3.849A pdb=" N TYR B 298 " --> pdb=" O GLU B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 332 removed outlier: 3.877A pdb=" N ARG B 330 " --> pdb=" O LYS B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 350 removed outlier: 3.978A pdb=" N GLU B 345 " --> pdb=" O LYS B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 369 removed outlier: 3.552A pdb=" N GLU B 358 " --> pdb=" O GLY B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 382 removed outlier: 4.143A pdb=" N CYS B 382 " --> pdb=" O GLY B 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 156 removed outlier: 3.643A pdb=" N GLU C 148 " --> pdb=" O PRO C 144 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE C 149 " --> pdb=" O LYS C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 183 Processing helix chain 'C' and resid 203 through 209 Processing helix chain 'C' and resid 225 through 230 Processing helix chain 'C' and resid 240 through 243 removed outlier: 3.514A pdb=" N LEU C 243 " --> pdb=" O ILE C 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 240 through 243' Processing helix chain 'C' and resid 244 through 249 removed outlier: 3.758A pdb=" N ALA C 249 " --> pdb=" O LEU C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 257 removed outlier: 4.041A pdb=" N GLU C 256 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER C 257 " --> pdb=" O ARG C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 290 Processing helix chain 'C' and resid 293 through 301 removed outlier: 3.535A pdb=" N TYR C 298 " --> pdb=" O GLU C 294 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG C 299 " --> pdb=" O ASP C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 315 No H-bonds generated for 'chain 'C' and resid 313 through 315' Processing helix chain 'C' and resid 316 through 332 removed outlier: 3.816A pdb=" N ARG C 330 " --> pdb=" O LYS C 326 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS C 331 " --> pdb=" O LYS C 327 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR C 332 " --> pdb=" O PHE C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 350 removed outlier: 3.594A pdb=" N SER C 349 " --> pdb=" O GLU C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 369 removed outlier: 3.565A pdb=" N GLU C 358 " --> pdb=" O GLY C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 384 removed outlier: 5.127A pdb=" N CYS C 382 " --> pdb=" O GLU C 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 156 Processing helix chain 'D' and resid 172 through 184 Processing helix chain 'D' and resid 197 through 199 No H-bonds generated for 'chain 'D' and resid 197 through 199' Processing helix chain 'D' and resid 200 through 202 No H-bonds generated for 'chain 'D' and resid 200 through 202' Processing helix chain 'D' and resid 203 through 209 Processing helix chain 'D' and resid 225 through 230 Processing helix chain 'D' and resid 240 through 243 Processing helix chain 'D' and resid 244 through 249 removed outlier: 3.841A pdb=" N ALA D 249 " --> pdb=" O LEU D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 258 removed outlier: 4.248A pdb=" N GLU D 256 " --> pdb=" O LEU D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 290 removed outlier: 3.982A pdb=" N LYS D 288 " --> pdb=" O LYS D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 301 removed outlier: 3.780A pdb=" N TYR D 298 " --> pdb=" O GLU D 294 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG D 299 " --> pdb=" O ASP D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 313 Processing helix chain 'D' and resid 316 through 333 Processing helix chain 'D' and resid 340 through 348 removed outlier: 3.914A pdb=" N GLU D 345 " --> pdb=" O LYS D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 369 Processing helix chain 'E' and resid 143 through 157 Processing helix chain 'E' and resid 172 through 184 Processing helix chain 'E' and resid 200 through 202 No H-bonds generated for 'chain 'E' and resid 200 through 202' Processing helix chain 'E' and resid 203 through 210 Processing helix chain 'E' and resid 225 through 230 Processing helix chain 'E' and resid 246 through 250 Processing helix chain 'E' and resid 251 through 258 removed outlier: 3.570A pdb=" N ILE E 255 " --> pdb=" O LEU E 251 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLU E 256 " --> pdb=" O LEU E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 289 Processing helix chain 'E' and resid 293 through 301 Processing helix chain 'E' and resid 309 through 313 Processing helix chain 'E' and resid 317 through 333 Processing helix chain 'E' and resid 340 through 350 Processing helix chain 'E' and resid 354 through 369 Processing helix chain 'F' and resid 143 through 157 Processing helix chain 'F' and resid 172 through 184 Processing helix chain 'F' and resid 200 through 202 No H-bonds generated for 'chain 'F' and resid 200 through 202' Processing helix chain 'F' and resid 203 through 209 Processing helix chain 'F' and resid 225 through 230 Processing helix chain 'F' and resid 239 through 243 Processing helix chain 'F' and resid 244 through 258 removed outlier: 3.542A pdb=" N ALA F 249 " --> pdb=" O LEU F 245 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS F 250 " --> pdb=" O GLU F 246 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG F 253 " --> pdb=" O ALA F 249 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N VAL F 254 " --> pdb=" O LYS F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 289 Processing helix chain 'F' and resid 293 through 301 Processing helix chain 'F' and resid 309 through 313 Processing helix chain 'F' and resid 316 through 333 Processing helix chain 'F' and resid 340 through 350 removed outlier: 3.828A pdb=" N GLU F 345 " --> pdb=" O LYS F 341 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU F 346 " --> pdb=" O SER F 342 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU F 347 " --> pdb=" O ALA F 343 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU F 348 " --> pdb=" O GLN F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 370 removed outlier: 3.520A pdb=" N GLU F 358 " --> pdb=" O GLY F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 376 through 384 removed outlier: 3.909A pdb=" N LEU F 380 " --> pdb=" O ASP F 376 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LEU F 383 " --> pdb=" O GLU F 379 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 51 removed outlier: 3.604A pdb=" N THR G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA G 42 " --> pdb=" O THR G 38 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N MET G 51 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 86 Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'G' and resid 212 through 233 removed outlier: 4.274A pdb=" N ALA G 230 " --> pdb=" O GLU G 226 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N PHE G 231 " --> pdb=" O GLN G 227 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP G 233 " --> pdb=" O GLU G 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 255 Processing helix chain 'G' and resid 256 through 260 Processing helix chain 'G' and resid 263 through 273 Processing helix chain 'G' and resid 277 through 283 removed outlier: 3.660A pdb=" N GLN G 283 " --> pdb=" O GLY G 279 " (cutoff:3.500A) Processing helix chain 'G' and resid 285 through 292 Processing helix chain 'G' and resid 296 through 309 Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.525A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 87 Processing helix chain 'H' and resid 113 through 115 No H-bonds generated for 'chain 'H' and resid 113 through 115' Processing helix chain 'H' and resid 154 through 159 removed outlier: 3.516A pdb=" N THR H 157 " --> pdb=" O PRO H 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 212 through 227 Processing helix chain 'I' and resid 4 through 9 removed outlier: 3.620A pdb=" N LYS I 9 " --> pdb=" O TYR I 5 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 40 removed outlier: 3.630A pdb=" N SER I 34 " --> pdb=" O ILE I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 55 removed outlier: 3.868A pdb=" N ALA I 51 " --> pdb=" O TYR I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 206 through 213 removed outlier: 4.041A pdb=" N LEU I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 242 through 247 Processing helix chain 'I' and resid 270 through 281 Processing helix chain 'I' and resid 288 through 293 Processing helix chain 'I' and resid 318 through 327 Processing helix chain 'I' and resid 346 through 354 Processing helix chain 'I' and resid 359 through 371 removed outlier: 3.812A pdb=" N LEU I 363 " --> pdb=" O ARG I 359 " (cutoff:3.500A) Processing helix chain 'I' and resid 377 through 390 removed outlier: 3.971A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 409 Processing helix chain 'I' and resid 421 through 438 Processing helix chain 'I' and resid 455 through 479 removed outlier: 3.651A pdb=" N ARG I 470 " --> pdb=" O VAL I 466 " (cutoff:3.500A) Processing helix chain 'I' and resid 488 through 493 Processing helix chain 'I' and resid 495 through 509 removed outlier: 3.528A pdb=" N SER I 499 " --> pdb=" O ALA I 495 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER I 509 " --> pdb=" O PHE I 505 " (cutoff:3.500A) Processing helix chain 'I' and resid 519 through 528 Processing helix chain 'I' and resid 545 through 549 Processing helix chain 'I' and resid 551 through 555 Processing helix chain 'I' and resid 608 through 612 removed outlier: 3.650A pdb=" N GLY I 612 " --> pdb=" O ALA I 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 608 through 612' Processing helix chain 'I' and resid 648 through 650 No H-bonds generated for 'chain 'I' and resid 648 through 650' Processing helix chain 'I' and resid 664 through 668 Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 687 removed outlier: 4.139A pdb=" N ARG I 687 " --> pdb=" O ALA I 683 " (cutoff:3.500A) Processing helix chain 'I' and resid 704 through 712 Processing helix chain 'I' and resid 738 through 741 Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 859 through 863 Processing helix chain 'I' and resid 896 through 907 Processing helix chain 'I' and resid 942 through 981 removed outlier: 3.770A pdb=" N GLN I 955 " --> pdb=" O MET I 951 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA I 956 " --> pdb=" O GLN I 952 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE I 966 " --> pdb=" O GLU I 962 " (cutoff:3.500A) Processing helix chain 'I' and resid 986 through 992 removed outlier: 3.691A pdb=" N ASP I 990 " --> pdb=" O ALA I 986 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU I 992 " --> pdb=" O LYS I 988 " (cutoff:3.500A) Processing helix chain 'I' and resid 993 through 999 removed outlier: 3.630A pdb=" N TRP I 997 " --> pdb=" O PRO I 993 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU I 998 " --> pdb=" O ARG I 994 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU I 999 " --> pdb=" O ASP I 995 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 993 through 999' Processing helix chain 'I' and resid 1005 through 1037 removed outlier: 4.128A pdb=" N ASN I1009 " --> pdb=" O GLU I1005 " (cutoff:3.500A) Processing helix chain 'I' and resid 1081 through 1085 removed outlier: 3.502A pdb=" N MET I1085 " --> pdb=" O ILE I1082 " (cutoff:3.500A) Processing helix chain 'I' and resid 1099 through 1103 Processing helix chain 'I' and resid 1109 through 1134 removed outlier: 3.536A pdb=" N LEU I1113 " --> pdb=" O ILE I1109 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN I1134 " --> pdb=" O ALA I1130 " (cutoff:3.500A) Processing helix chain 'I' and resid 1137 through 1151 Processing helix chain 'I' and resid 1160 through 1164 removed outlier: 3.805A pdb=" N THR I1163 " --> pdb=" O ASP I1160 " (cutoff:3.500A) Processing helix chain 'I' and resid 1165 through 1176 Processing helix chain 'I' and resid 1191 through 1202 Processing helix chain 'I' and resid 1238 through 1242 Processing helix chain 'I' and resid 1271 through 1282 Processing helix chain 'I' and resid 1283 through 1292 Processing helix chain 'I' and resid 1297 through 1311 removed outlier: 3.724A pdb=" N THR I1302 " --> pdb=" O VAL I1298 " (cutoff:3.500A) Processing helix chain 'I' and resid 1320 through 1332 removed outlier: 3.795A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 11 removed outlier: 3.596A pdb=" N GLN J 11 " --> pdb=" O PHE J 7 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 33 Processing helix chain 'J' and resid 58 through 63 Processing helix chain 'J' and resid 77 through 81 Processing helix chain 'J' and resid 94 through 100 removed outlier: 3.797A pdb=" N VAL J 97 " --> pdb=" O GLN J 94 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG J 98 " --> pdb=" O THR J 95 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 119 removed outlier: 3.558A pdb=" N SER J 119 " --> pdb=" O TRP J 115 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 129 Processing helix chain 'J' and resid 131 through 140 Processing helix chain 'J' and resid 161 through 172 Processing helix chain 'J' and resid 181 through 192 removed outlier: 3.701A pdb=" N ILE J 185 " --> pdb=" O GLY J 181 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET J 192 " --> pdb=" O LEU J 188 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 208 Processing helix chain 'J' and resid 211 through 230 Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 246 through 250 Processing helix chain 'J' and resid 263 through 286 Processing helix chain 'J' and resid 288 through 308 removed outlier: 3.984A pdb=" N ASN J 294 " --> pdb=" O ILE J 290 " (cutoff:3.500A) Processing helix chain 'J' and resid 326 through 332 Processing helix chain 'J' and resid 336 through 342 removed outlier: 3.527A pdb=" N LEU J 342 " --> pdb=" O PHE J 338 " (cutoff:3.500A) Processing helix chain 'J' and resid 370 through 377 removed outlier: 3.682A pdb=" N GLU J 375 " --> pdb=" O LYS J 371 " (cutoff:3.500A) Processing helix chain 'J' and resid 377 through 388 Processing helix chain 'J' and resid 393 through 404 Processing helix chain 'J' and resid 405 through 416 removed outlier: 4.110A pdb=" N TRP J 409 " --> pdb=" O GLU J 405 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASP J 410 " --> pdb=" O ALA J 406 " (cutoff:3.500A) Processing helix chain 'J' and resid 430 through 432 No H-bonds generated for 'chain 'J' and resid 430 through 432' Processing helix chain 'J' and resid 450 through 452 No H-bonds generated for 'chain 'J' and resid 450 through 452' Processing helix chain 'J' and resid 453 through 458 Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 504 through 514 Processing helix chain 'J' and resid 529 through 539 Processing helix chain 'J' and resid 574 through 581 removed outlier: 3.879A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) Processing helix chain 'J' and resid 588 through 592 Processing helix chain 'J' and resid 597 through 613 Processing helix chain 'J' and resid 614 through 636 removed outlier: 3.905A pdb=" N GLY J 636 " --> pdb=" O ALA J 632 " (cutoff:3.500A) Processing helix chain 'J' and resid 640 through 644 Processing helix chain 'J' and resid 649 through 670 Processing helix chain 'J' and resid 674 through 702 Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 742 Processing helix chain 'J' and resid 768 through 804 removed outlier: 3.951A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N THR J 790 " --> pdb=" O THR J 786 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ASN J 792 " --> pdb=" O LEU J 788 " (cutoff:3.500A) Processing helix chain 'J' and resid 835 through 840 Processing helix chain 'J' and resid 865 through 875 Processing helix chain 'J' and resid 896 through 900 Processing helix chain 'J' and resid 914 through 925 Processing helix chain 'J' and resid 926 through 930 removed outlier: 3.799A pdb=" N LEU J 930 " --> pdb=" O GLY J 927 " (cutoff:3.500A) Processing helix chain 'J' and resid 1137 through 1147 Processing helix chain 'J' and resid 1216 through 1224 Processing helix chain 'J' and resid 1225 through 1243 removed outlier: 3.680A pdb=" N LEU J1243 " --> pdb=" O ASP J1239 " (cutoff:3.500A) Processing helix chain 'J' and resid 1250 through 1261 Processing helix chain 'J' and resid 1282 through 1294 removed outlier: 3.821A pdb=" N ALA J1294 " --> pdb=" O ARG J1290 " (cutoff:3.500A) Processing helix chain 'J' and resid 1308 through 1314 removed outlier: 3.589A pdb=" N LEU J1314 " --> pdb=" O THR J1310 " (cutoff:3.500A) Processing helix chain 'J' and resid 1318 through 1326 removed outlier: 3.727A pdb=" N PHE J1325 " --> pdb=" O SER J1321 " (cutoff:3.500A) Processing helix chain 'J' and resid 1327 through 1339 Processing helix chain 'J' and resid 1346 through 1353 Processing helix chain 'J' and resid 1359 through 1361 No H-bonds generated for 'chain 'J' and resid 1359 through 1361' Processing helix chain 'J' and resid 1362 through 1374 removed outlier: 3.589A pdb=" N ARG J1369 " --> pdb=" O TYR J1365 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA J1374 " --> pdb=" O MET J1370 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 14 Processing helix chain 'K' and resid 15 through 32 Processing helix chain 'K' and resid 45 through 56 Processing helix chain 'K' and resid 60 through 80 Processing helix chain 'M' and resid 29 through 44 Processing helix chain 'M' and resid 119 through 130 removed outlier: 3.527A pdb=" N LEU M 130 " --> pdb=" O TRP M 126 " (cutoff:3.500A) Processing helix chain 'M' and resid 134 through 147 Processing helix chain 'M' and resid 157 through 166 removed outlier: 3.556A pdb=" N ILE M 161 " --> pdb=" O PRO M 157 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLY M 166 " --> pdb=" O LEU M 162 " (cutoff:3.500A) Processing helix chain 'M' and resid 171 through 183 removed outlier: 3.902A pdb=" N VAL M 175 " --> pdb=" O ASP M 171 " (cutoff:3.500A) Processing helix chain 'M' and resid 194 through 205 removed outlier: 3.680A pdb=" N GLN M 205 " --> pdb=" O ILE M 201 " (cutoff:3.500A) Processing helix chain 'M' and resid 212 through 223 Processing helix chain 'M' and resid 224 through 229 Processing helix chain 'M' and resid 233 through 240 Processing helix chain 'M' and resid 242 through 255 Processing helix chain 'M' and resid 259 through 263 removed outlier: 3.627A pdb=" N SER M 263 " --> pdb=" O PRO M 260 " (cutoff:3.500A) Processing helix chain 'M' and resid 300 through 305 Processing helix chain 'M' and resid 312 through 351 Processing helix chain 'M' and resid 353 through 358 Processing helix chain 'M' and resid 366 through 375 removed outlier: 3.945A pdb=" N ILE M 370 " --> pdb=" O VAL M 366 " (cutoff:3.500A) Processing helix chain 'M' and resid 377 through 385 Processing helix chain 'M' and resid 400 through 403 removed outlier: 3.634A pdb=" N PHE M 403 " --> pdb=" O LYS M 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 400 through 403' Processing helix chain 'M' and resid 417 through 429 Processing helix chain 'M' and resid 438 through 448 Processing helix chain 'M' and resid 454 through 465 Processing helix chain 'M' and resid 469 through 473 Processing sheet with id=AA1, first strand: chain 'A' and resid 191 through 195 removed outlier: 6.368A pdb=" N VAL A 192 " --> pdb=" O PHE A 236 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ASP A 238 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU A 194 " --> pdb=" O ASP A 238 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 210 through 211 Processing sheet with id=AA3, first strand: chain 'A' and resid 259 through 260 Processing sheet with id=AA4, first strand: chain 'A' and resid 338 through 339 removed outlier: 7.015A pdb=" N GLY A 338 " --> pdb=" O ILE A 375 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 191 through 195 removed outlier: 6.605A pdb=" N VAL B 192 " --> pdb=" O PHE B 236 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ASP B 238 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU B 194 " --> pdb=" O ASP B 238 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N LEU B 235 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ALA B 278 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LEU B 237 " --> pdb=" O ALA B 278 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 210 through 211 Processing sheet with id=AA7, first strand: chain 'B' and resid 259 through 260 Processing sheet with id=AA8, first strand: chain 'C' and resid 191 through 195 removed outlier: 6.692A pdb=" N VAL C 192 " --> pdb=" O PHE C 236 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ASP C 238 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU C 194 " --> pdb=" O ASP C 238 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N LEU C 235 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ALA C 278 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU C 237 " --> pdb=" O ALA C 278 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY C 167 " --> pdb=" O THR C 279 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 259 through 260 Processing sheet with id=AB1, first strand: chain 'C' and resid 338 through 339 removed outlier: 7.482A pdb=" N GLY C 338 " --> pdb=" O ILE C 375 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 191 through 195 removed outlier: 6.469A pdb=" N LEU D 164 " --> pdb=" O ILE D 305 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 210 through 211 Processing sheet with id=AB4, first strand: chain 'D' and resid 259 through 261 Processing sheet with id=AB5, first strand: chain 'E' and resid 191 through 195 removed outlier: 6.379A pdb=" N VAL E 192 " --> pdb=" O PHE E 236 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ASP E 238 " --> pdb=" O VAL E 192 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU E 194 " --> pdb=" O ASP E 238 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 259 through 260 Processing sheet with id=AB7, first strand: chain 'E' and resid 338 through 339 removed outlier: 7.352A pdb=" N GLY E 338 " --> pdb=" O ILE E 375 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'F' and resid 191 through 195 removed outlier: 6.106A pdb=" N LEU F 235 " --> pdb=" O LEU F 276 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N ALA F 278 " --> pdb=" O LEU F 235 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LEU F 237 " --> pdb=" O ALA F 278 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL F 163 " --> pdb=" O ALA F 277 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N THR F 279 " --> pdb=" O VAL F 163 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE F 165 " --> pdb=" O THR F 279 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 210 through 211 Processing sheet with id=AC1, first strand: chain 'F' and resid 259 through 261 Processing sheet with id=AC2, first strand: chain 'F' and resid 338 through 339 removed outlier: 7.134A pdb=" N GLY F 338 " --> pdb=" O ILE F 375 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'G' and resid 12 through 18 removed outlier: 6.903A pdb=" N THR G 27 " --> pdb=" O VAL G 14 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ILE G 16 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LYS G 25 " --> pdb=" O ILE G 16 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N GLN G 18 " --> pdb=" O HIS G 23 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N HIS G 23 " --> pdb=" O GLN G 18 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N HIS G 23 " --> pdb=" O THR G 207 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N THR G 207 " --> pdb=" O HIS G 23 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N LYS G 25 " --> pdb=" O MET G 205 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N MET G 205 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N THR G 27 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ILE G 203 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N GLU G 29 " --> pdb=" O LEU G 201 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N LEU G 201 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LYS G 200 " --> pdb=" O VAL G 187 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N VAL G 187 " --> pdb=" O LYS G 200 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL G 202 " --> pdb=" O TYR G 185 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N TYR G 185 " --> pdb=" O VAL G 202 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLU G 204 " --> pdb=" O ILE G 183 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ILE G 183 " --> pdb=" O GLU G 204 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLU G 206 " --> pdb=" O GLU G 181 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 97 through 105 removed outlier: 7.636A pdb=" N SER G 141 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N ILE G 61 " --> pdb=" O SER G 141 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ARG G 143 " --> pdb=" O VAL G 59 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL G 59 " --> pdb=" O ARG G 143 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LYS G 145 " --> pdb=" O THR G 57 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 90 through 92 Processing sheet with id=AC6, first strand: chain 'G' and resid 108 through 111 removed outlier: 6.562A pdb=" N GLY G 108 " --> pdb=" O HIS G 132 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N HIS G 132 " --> pdb=" O GLY G 108 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL G 110 " --> pdb=" O ILE G 130 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 152 through 153 Processing sheet with id=AC8, first strand: chain 'H' and resid 13 through 20 removed outlier: 6.530A pdb=" N HIS H 23 " --> pdb=" O VAL H 19 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 97 through 105 removed outlier: 8.020A pdb=" N SER H 141 " --> pdb=" O ILE H 61 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ILE H 61 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 90 through 92 Processing sheet with id=AD2, first strand: chain 'H' and resid 108 through 111 Processing sheet with id=AD3, first strand: chain 'H' and resid 152 through 153 Processing sheet with id=AD4, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.693A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'I' and resid 59 through 60 removed outlier: 5.276A pdb=" N SER I 66 " --> pdb=" O TYR I 105 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TYR I 105 " --> pdb=" O SER I 66 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER I 72 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP I 116 " --> pdb=" O ILE I 104 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 136 through 138 Processing sheet with id=AD7, first strand: chain 'I' and resid 451 through 454 removed outlier: 3.520A pdb=" N SER I 147 " --> pdb=" O ARG I 529 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 154 through 160 removed outlier: 3.579A pdb=" N ASP I 160 " --> pdb=" O LEU I 171 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU I 171 " --> pdb=" O ASP I 160 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 227 through 231 Processing sheet with id=AE1, first strand: chain 'I' and resid 239 through 240 Processing sheet with id=AE2, first strand: chain 'I' and resid 255 through 257 removed outlier: 7.302A pdb=" N ILE I 255 " --> pdb=" O TYR I 262 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 301 through 302 removed outlier: 6.771A pdb=" N TYR I 301 " --> pdb=" O ILE I 310 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 580 through 581 removed outlier: 7.024A pdb=" N LEU I 587 " --> pdb=" O LEU I 606 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU I 606 " --> pdb=" O LEU I 587 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N THR I 589 " --> pdb=" O HIS I 604 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N HIS I 604 " --> pdb=" O THR I 589 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N TYR I 591 " --> pdb=" O GLU I 602 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N GLU I 602 " --> pdb=" O TYR I 591 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N LYS I 593 " --> pdb=" O THR I 600 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AE6, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.564A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 748 through 752 removed outlier: 6.719A pdb=" N ARG I 731 " --> pdb=" O VAL I 727 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N VAL I 727 " --> pdb=" O ARG I 731 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL I 733 " --> pdb=" O GLN I 725 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AE9, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AF1, first strand: chain 'I' and resid 1209 through 1210 removed outlier: 7.106A pdb=" N ILE I 816 " --> pdb=" O LYS I1078 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N ASN I1080 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL I 818 " --> pdb=" O ASN I1080 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU I 817 " --> pdb=" O VAL I1097 " (cutoff:3.500A) removed outlier: 8.598A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 830 through 841 removed outlier: 3.829A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 8.800A pdb=" N LYS I1057 " --> pdb=" O GLY I 926 " (cutoff:3.500A) removed outlier: 8.947A pdb=" N GLY I 926 " --> pdb=" O LYS I1057 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 849 through 850 Processing sheet with id=AF4, first strand: chain 'I' and resid 882 through 884 removed outlier: 6.781A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 1244 through 1246 Processing sheet with id=AF6, first strand: chain 'I' and resid 1269 through 1270 Processing sheet with id=AF7, first strand: chain 'I' and resid 1335 through 1340 removed outlier: 3.625A pdb=" N ALA J 19 " --> pdb=" O GLU I1340 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'J' and resid 34 through 37 removed outlier: 7.613A pdb=" N HIS J 104 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLU J 37 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N GLU J 106 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 10.034A pdb=" N LEU J 107 " --> pdb=" O PRO J 243 " (cutoff:3.500A) removed outlier: 10.591A pdb=" N SER J 109 " --> pdb=" O VAL J 241 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N VAL J 241 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'J' and resid 159 through 160 removed outlier: 6.955A pdb=" N ASP J 177 " --> pdb=" O ILE J 147 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'J' and resid 316 through 317 Processing sheet with id=AG2, first strand: chain 'J' and resid 526 through 527 Processing sheet with id=AG3, first strand: chain 'J' and resid 703 through 707 Processing sheet with id=AG4, first strand: chain 'J' and resid 809 through 811 Processing sheet with id=AG5, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AG6, first strand: chain 'J' and resid 825 through 827 removed outlier: 6.767A pdb=" N GLU J 827 " --> pdb=" O VAL J 831 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N VAL J 831 " --> pdb=" O GLU J 827 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'J' and resid 848 through 849 removed outlier: 6.624A pdb=" N VAL J 848 " --> pdb=" O LEU J 857 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'J' and resid 991 through 996 removed outlier: 6.637A pdb=" N LEU J 984 " --> pdb=" O LYS J 992 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N SER J 994 " --> pdb=" O LEU J 982 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU J 982 " --> pdb=" O SER J 994 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY J 956 " --> pdb=" O VAL J1011 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N VAL J1011 " --> pdb=" O GLY J 956 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'J' and resid 965 through 967 removed outlier: 3.822A pdb=" N LEU J 973 " --> pdb=" O LEU J1003 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'J' and resid 1034 through 1038 Processing sheet with id=AH2, first strand: chain 'J' and resid 1046 through 1047 Processing sheet with id=AH3, first strand: chain 'J' and resid 1155 through 1156 removed outlier: 6.407A pdb=" N ILE J1155 " --> pdb=" O ILE J1210 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'J' and resid 1162 through 1165 Processing sheet with id=AH5, first strand: chain 'J' and resid 1279 through 1281 Processing sheet with id=AH6, first strand: chain 'M' and resid 47 through 48 Processing sheet with id=AH7, first strand: chain 'M' and resid 284 through 289 removed outlier: 6.562A pdb=" N VAL M 276 " --> pdb=" O HIS M 391 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'M' and resid 406 through 408 1775 hydrogen bonds defined for protein. 4944 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 104 hydrogen bonds 208 hydrogen bond angles 0 basepair planarities 44 basepair parallelities 79 stacking parallelities Total time for adding SS restraints: 14.85 Time building geometry restraints manager: 5.16 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: 13353 1.34 - 1.45: 5846 1.45 - 1.57: 24306 1.57 - 1.69: 210 1.69 - 1.81: 238 Bond restraints: 43953 Sorted by residual: bond pdb=" O POP J1501 " pdb=" P2 POP J1501 " ideal model delta sigma weight residual 1.661 1.609 0.052 2.00e-02 2.50e+03 6.75e+00 bond pdb=" O POP J1501 " pdb=" P1 POP J1501 " ideal model delta sigma weight residual 1.660 1.610 0.050 2.00e-02 2.50e+03 6.23e+00 bond pdb=" O2 POP J1501 " pdb=" P1 POP J1501 " ideal model delta sigma weight residual 1.531 1.508 0.023 2.00e-02 2.50e+03 1.35e+00 bond pdb=" O1 POP J1501 " pdb=" P1 POP J1501 " ideal model delta sigma weight residual 1.531 1.508 0.023 2.00e-02 2.50e+03 1.31e+00 bond pdb=" O4 POP J1501 " pdb=" P2 POP J1501 " ideal model delta sigma weight residual 1.530 1.509 0.021 2.00e-02 2.50e+03 1.14e+00 ... (remaining 43948 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.66: 59654 3.66 - 7.32: 50 7.32 - 10.98: 2 10.98 - 14.64: 0 14.64 - 18.30: 1 Bond angle restraints: 59707 Sorted by residual: angle pdb=" P1 POP J1501 " pdb=" O POP J1501 " pdb=" P2 POP J1501 " ideal model delta sigma weight residual 139.66 121.36 18.30 3.00e+00 1.11e-01 3.72e+01 angle pdb=" C ASN D 355 " pdb=" CA ASN D 355 " pdb=" CB ASN D 355 " ideal model delta sigma weight residual 116.63 110.42 6.21 1.16e+00 7.43e-01 2.87e+01 angle pdb=" CA ASN D 355 " pdb=" C ASN D 355 " pdb=" N VAL D 356 " ideal model delta sigma weight residual 119.63 116.33 3.30 8.10e-01 1.52e+00 1.66e+01 angle pdb=" C GLU M 359 " pdb=" N GLU M 360 " pdb=" CA GLU M 360 " ideal model delta sigma weight residual 121.54 128.04 -6.50 1.91e+00 2.74e-01 1.16e+01 angle pdb=" C PRO I 698 " pdb=" N LEU I 699 " pdb=" CA LEU I 699 " ideal model delta sigma weight residual 121.54 127.76 -6.22 1.91e+00 2.74e-01 1.06e+01 ... (remaining 59702 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.53: 25325 21.53 - 43.07: 1110 43.07 - 64.60: 415 64.60 - 86.14: 15 86.14 - 107.67: 5 Dihedral angle restraints: 26870 sinusoidal: 11902 harmonic: 14968 Sorted by residual: dihedral pdb=" C5' ADP E 401 " pdb=" O5' ADP E 401 " pdb=" PA ADP E 401 " pdb=" O2A ADP E 401 " ideal model delta sinusoidal sigma weight residual -60.00 -167.67 107.67 1 2.00e+01 2.50e-03 3.13e+01 dihedral pdb=" CA SER G 49 " pdb=" C SER G 49 " pdb=" N SER G 50 " pdb=" CA SER G 50 " ideal model delta harmonic sigma weight residual -180.00 -158.01 -21.99 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA ARG H 191 " pdb=" C ARG H 191 " pdb=" N VAL H 192 " pdb=" CA VAL H 192 " ideal model delta harmonic sigma weight residual 180.00 159.00 21.00 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 26867 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 4422 0.031 - 0.062: 1611 0.062 - 0.093: 412 0.093 - 0.123: 284 0.123 - 0.154: 33 Chirality restraints: 6762 Sorted by residual: chirality pdb=" CB VAL J1255 " pdb=" CA VAL J1255 " pdb=" CG1 VAL J1255 " pdb=" CG2 VAL J1255 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.94e-01 chirality pdb=" CA VAL I 700 " pdb=" N VAL I 700 " pdb=" C VAL I 700 " pdb=" CB VAL I 700 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.55e-01 chirality pdb=" CA ILE J1090 " pdb=" N ILE J1090 " pdb=" C ILE J1090 " pdb=" CB ILE J1090 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.17e-01 ... (remaining 6759 not shown) Planarity restraints: 7403 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS J 850 " 0.037 5.00e-02 4.00e+02 5.63e-02 5.07e+00 pdb=" N PRO J 851 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO J 851 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO J 851 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU J 245 " 0.026 5.00e-02 4.00e+02 3.97e-02 2.52e+00 pdb=" N PRO J 246 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO J 246 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO J 246 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER M 392 " 0.026 5.00e-02 4.00e+02 3.91e-02 2.44e+00 pdb=" N PRO M 393 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO M 393 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO M 393 " 0.022 5.00e-02 4.00e+02 ... (remaining 7400 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 1353 2.70 - 3.25: 40696 3.25 - 3.80: 67464 3.80 - 4.35: 93558 4.35 - 4.90: 152902 Nonbonded interactions: 355973 Sorted by model distance: nonbonded pdb=" O ARG J 339 " pdb=" O HOH J1601 " model vdw 2.155 3.040 nonbonded pdb=" OG SER M 382 " pdb=" OP2 DT U 45 " model vdw 2.171 3.040 nonbonded pdb=" OD1 ASP J 462 " pdb="MG MG J1502 " model vdw 2.185 2.170 nonbonded pdb=" OG SER I 318 " pdb=" OD1 ASP I 320 " model vdw 2.204 3.040 nonbonded pdb=" O GLY G 169 " pdb=" O HOH G 401 " model vdw 2.213 3.040 ... (remaining 355968 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 139 through 280 or (resid 281 and (name N or name CA or na \ me C or name O or name CB )) or resid 282 through 384)) selection = (chain 'B' and (resid 139 through 280 or (resid 281 and (name N or name CA or na \ me C or name O or name CB )) or resid 282 through 384)) selection = (chain 'C' and (resid 139 through 280 or (resid 281 and (name N or name CA or na \ me C or name O or name CB )) or resid 282 through 384)) selection = (chain 'D' and (resid 139 through 280 or (resid 281 and (name N or name CA or na \ me C or name O or name CB )) or resid 282 through 384)) selection = (chain 'E' and (resid 139 through 280 or (resid 281 and (name N or name CA or na \ me C or name O or name CB )) or resid 282 through 384)) selection = (chain 'F' and resid 139 through 384) } 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: 5.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.760 Check model and map are aligned: 0.130 Set scattering table: 0.130 Process input model: 54.350 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.150 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:6.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 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 : 0.003 0.180 43961 Z= 0.116 Angle : 0.456 18.295 59719 Z= 0.247 Chirality : 0.039 0.154 6762 Planarity : 0.003 0.056 7403 Dihedral : 13.229 107.672 17228 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.12 % Allowed : 4.06 % Favored : 94.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.12), residues: 5165 helix: 1.18 (0.12), residues: 2110 sheet: 1.04 (0.20), residues: 623 loop : -0.47 (0.12), residues: 2432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I1301 TYR 0.013 0.001 TYR J 631 PHE 0.012 0.001 PHE J1319 TRP 0.005 0.001 TRP J 409 HIS 0.004 0.001 HIS J 777 Details of bonding type rmsd covalent geometry : bond 0.00208 (43953) covalent geometry : angle 0.45589 (59707) hydrogen bonds : bond 0.15547 ( 1877) hydrogen bonds : angle 5.63044 ( 5152) metal coordination : bond 0.12339 ( 8) metal coordination : angle 0.11438 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10330 Ramachandran restraints generated. 5165 Oldfield, 0 Emsley, 5165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10330 Ramachandran restraints generated. 5165 Oldfield, 0 Emsley, 5165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 4462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 372 time to evaluate : 1.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 ASP cc_start: 0.7550 (t0) cc_final: 0.7238 (t0) REVERT: F 243 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8199 (tt) REVERT: G 269 CYS cc_start: 0.9059 (m) cc_final: 0.8490 (m) REVERT: J 466 MET cc_start: 0.8890 (mtt) cc_final: 0.8681 (ttm) REVERT: J 747 MET cc_start: 0.8967 (mmt) cc_final: 0.8688 (mmt) REVERT: J 1040 MET cc_start: 0.4064 (mmt) cc_final: 0.3782 (mmm) REVERT: J 1210 ILE cc_start: 0.8096 (mm) cc_final: 0.7742 (mm) REVERT: M 8 ARG cc_start: 0.8132 (ptp-110) cc_final: 0.7851 (ptp90) outliers start: 50 outliers final: 12 residues processed: 415 average time/residue: 0.8700 time to fit residues: 433.3985 Evaluate side-chains 260 residues out of total 4462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 247 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain H residue 95 LYS Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 856 ASN Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain J residue 260 PHE Chi-restraints excluded: chain J residue 1255 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 394 optimal weight: 0.0040 chunk 430 optimal weight: 50.0000 chunk 41 optimal weight: 4.9990 chunk 265 optimal weight: 3.9990 chunk 497 optimal weight: 9.9990 chunk 414 optimal weight: 4.9990 chunk 310 optimal weight: 0.9980 chunk 488 optimal weight: 7.9990 chunk 366 optimal weight: 3.9990 chunk 223 optimal weight: 10.0000 chunk 516 optimal weight: 5.9990 overall best weight: 2.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 GLN H 137 ASN I1146 GLN I1288 GLN J1259 GLN K 15 ASN K 61 ASN M 406 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.088528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.053012 restraints weight = 104228.364| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 2.63 r_work: 0.2631 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2497 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 43961 Z= 0.213 Angle : 0.558 10.121 59719 Z= 0.296 Chirality : 0.043 0.200 6762 Planarity : 0.004 0.058 7403 Dihedral : 13.688 102.278 6914 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.41 % Allowed : 7.72 % Favored : 90.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.12), residues: 5165 helix: 1.20 (0.12), residues: 2161 sheet: 1.08 (0.21), residues: 590 loop : -0.49 (0.12), residues: 2414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG I 779 TYR 0.020 0.001 TYR J 631 PHE 0.016 0.001 PHE F 339 TRP 0.041 0.002 TRP F 352 HIS 0.008 0.001 HIS J 777 Details of bonding type rmsd covalent geometry : bond 0.00511 (43953) covalent geometry : angle 0.55730 (59707) hydrogen bonds : bond 0.05313 ( 1877) hydrogen bonds : angle 4.42626 ( 5152) metal coordination : bond 0.00720 ( 8) metal coordination : angle 2.09559 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10330 Ramachandran restraints generated. 5165 Oldfield, 0 Emsley, 5165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10330 Ramachandran restraints generated. 5165 Oldfield, 0 Emsley, 5165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 4462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 259 time to evaluate : 1.747 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 ILE cc_start: 0.9435 (OUTLIER) cc_final: 0.9228 (mp) REVERT: A 166 THR cc_start: 0.9219 (OUTLIER) cc_final: 0.8991 (p) REVERT: B 360 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8722 (mtpm) REVERT: D 166 THR cc_start: 0.9291 (m) cc_final: 0.9075 (p) REVERT: E 353 TYR cc_start: 0.8861 (m-80) cc_final: 0.8597 (m-80) REVERT: F 243 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8627 (tt) REVERT: F 282 ASN cc_start: 0.8759 (t0) cc_final: 0.8350 (t0) REVERT: F 374 PHE cc_start: 0.9025 (OUTLIER) cc_final: 0.8727 (t80) REVERT: H 93 GLN cc_start: 0.7659 (OUTLIER) cc_final: 0.7327 (mp10) REVERT: H 117 HIS cc_start: 0.8723 (t70) cc_final: 0.8422 (t70) REVERT: I 369 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.8147 (tmt) REVERT: I 965 GLN cc_start: 0.8444 (tm-30) cc_final: 0.8213 (tm-30) REVERT: J 330 MET cc_start: 0.9157 (mmt) cc_final: 0.8878 (mmt) REVERT: J 995 TYR cc_start: 0.6033 (m-80) cc_final: 0.5811 (m-80) REVERT: J 1189 MET cc_start: 0.7833 (tmm) cc_final: 0.7609 (tmm) REVERT: K 3 ARG cc_start: 0.8778 (mtm-85) cc_final: 0.8429 (mtt90) REVERT: K 56 GLU cc_start: 0.8489 (tp30) cc_final: 0.8044 (tm-30) REVERT: M 8 ARG cc_start: 0.8884 (ptp-110) cc_final: 0.8174 (ptp90) REVERT: M 242 LYS cc_start: 0.8722 (pttt) cc_final: 0.8486 (ttpp) REVERT: M 279 ARG cc_start: 0.8469 (mtp-110) cc_final: 0.8223 (mtm-85) outliers start: 63 outliers final: 21 residues processed: 307 average time/residue: 0.8089 time to fit residues: 302.8664 Evaluate side-chains 266 residues out of total 4462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 238 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 360 LYS Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 248 GLN Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 374 PHE Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 147 GLN Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain H residue 93 GLN Chi-restraints excluded: chain H residue 95 LYS Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 369 MET Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 909 LYS Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain J residue 260 PHE Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain M residue 294 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 431 optimal weight: 40.0000 chunk 372 optimal weight: 1.9990 chunk 403 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 217 optimal weight: 4.9990 chunk 277 optimal weight: 0.7980 chunk 501 optimal weight: 0.7980 chunk 341 optimal weight: 4.9990 chunk 343 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 GLN H 37 HIS H 137 ASN I1010 GLN K 15 ASN K 61 ASN M 406 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.089266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.053880 restraints weight = 103529.173| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 2.64 r_work: 0.2661 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2527 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 43961 Z= 0.130 Angle : 0.480 10.024 59719 Z= 0.255 Chirality : 0.040 0.165 6762 Planarity : 0.004 0.056 7403 Dihedral : 13.603 96.173 6909 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.46 % Allowed : 8.28 % Favored : 90.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.12), residues: 5165 helix: 1.51 (0.12), residues: 2152 sheet: 1.14 (0.21), residues: 593 loop : -0.41 (0.12), residues: 2420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 368 TYR 0.015 0.001 TYR J 631 PHE 0.017 0.001 PHE I1025 TRP 0.020 0.001 TRP J1193 HIS 0.005 0.001 HIS H 66 Details of bonding type rmsd covalent geometry : bond 0.00304 (43953) covalent geometry : angle 0.47959 (59707) hydrogen bonds : bond 0.04204 ( 1877) hydrogen bonds : angle 4.13385 ( 5152) metal coordination : bond 0.00429 ( 8) metal coordination : angle 2.11200 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10330 Ramachandran restraints generated. 5165 Oldfield, 0 Emsley, 5165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10330 Ramachandran restraints generated. 5165 Oldfield, 0 Emsley, 5165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 4462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 254 time to evaluate : 1.739 Fit side-chains revert: symmetry clash REVERT: E 353 TYR cc_start: 0.8820 (m-80) cc_final: 0.8502 (m-80) REVERT: F 243 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8472 (tt) REVERT: F 279 THR cc_start: 0.8087 (m) cc_final: 0.7785 (t) REVERT: F 282 ASN cc_start: 0.8753 (t0) cc_final: 0.8296 (t0) REVERT: F 374 PHE cc_start: 0.8947 (OUTLIER) cc_final: 0.8631 (t80) REVERT: G 192 VAL cc_start: 0.7634 (OUTLIER) cc_final: 0.7380 (p) REVERT: H 93 GLN cc_start: 0.7719 (OUTLIER) cc_final: 0.7334 (mp10) REVERT: H 117 HIS cc_start: 0.8769 (t70) cc_final: 0.8462 (t70) REVERT: H 205 MET cc_start: 0.9118 (OUTLIER) cc_final: 0.8707 (ttt) REVERT: I 60 GLN cc_start: 0.9096 (pt0) cc_final: 0.8828 (mt0) REVERT: I 445 ILE cc_start: 0.9007 (pt) cc_final: 0.8753 (mm) REVERT: I 1024 GLU cc_start: 0.9014 (tp30) cc_final: 0.8800 (tp30) REVERT: I 1119 MET cc_start: 0.8998 (ttt) cc_final: 0.8403 (tpt) REVERT: J 256 ASP cc_start: 0.8147 (m-30) cc_final: 0.7790 (p0) REVERT: J 330 MET cc_start: 0.9085 (mmt) cc_final: 0.8742 (mmt) REVERT: J 995 TYR cc_start: 0.6004 (m-80) cc_final: 0.5707 (m-80) REVERT: J 1040 MET cc_start: 0.2780 (mmm) cc_final: 0.2381 (mmm) REVERT: J 1189 MET cc_start: 0.7821 (tmm) cc_final: 0.7512 (tmm) REVERT: K 3 ARG cc_start: 0.8753 (mtm-85) cc_final: 0.8383 (mtt90) REVERT: M 8 ARG cc_start: 0.8848 (ptp-110) cc_final: 0.8144 (ptp90) REVERT: M 279 ARG cc_start: 0.8476 (mtp-110) cc_final: 0.8181 (mtm-85) outliers start: 65 outliers final: 24 residues processed: 302 average time/residue: 0.7345 time to fit residues: 274.2045 Evaluate side-chains 269 residues out of total 4462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 240 time to evaluate : 1.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain F residue 158 CYS Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 374 PHE Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain H residue 93 GLN Chi-restraints excluded: chain H residue 95 LYS Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 341 LEU Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 909 LYS Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain J residue 260 PHE Chi-restraints excluded: chain J residue 466 MET Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 272 VAL Chi-restraints excluded: chain M residue 294 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 120 optimal weight: 0.6980 chunk 298 optimal weight: 1.9990 chunk 338 optimal weight: 10.0000 chunk 280 optimal weight: 4.9990 chunk 121 optimal weight: 8.9990 chunk 182 optimal weight: 4.9990 chunk 86 optimal weight: 8.9990 chunk 434 optimal weight: 10.0000 chunk 82 optimal weight: 4.9990 chunk 352 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 GLN H 137 ASN ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 430 HIS K 15 ASN K 61 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.087173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.051529 restraints weight = 103790.218| |-----------------------------------------------------------------------------| r_work (start): 0.2775 rms_B_bonded: 2.63 r_work: 0.2601 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2466 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 43961 Z= 0.260 Angle : 0.559 9.996 59719 Z= 0.297 Chirality : 0.043 0.198 6762 Planarity : 0.004 0.059 7403 Dihedral : 13.688 95.081 6907 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.88 % Allowed : 8.19 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.12), residues: 5165 helix: 1.38 (0.11), residues: 2156 sheet: 1.08 (0.22), residues: 591 loop : -0.50 (0.12), residues: 2418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 313 TYR 0.020 0.001 TYR J 631 PHE 0.024 0.001 PHE I1025 TRP 0.021 0.001 TRP J1193 HIS 0.009 0.001 HIS J 777 Details of bonding type rmsd covalent geometry : bond 0.00629 (43953) covalent geometry : angle 0.55790 (59707) hydrogen bonds : bond 0.05534 ( 1877) hydrogen bonds : angle 4.30305 ( 5152) metal coordination : bond 0.00851 ( 8) metal coordination : angle 1.99577 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10330 Ramachandran restraints generated. 5165 Oldfield, 0 Emsley, 5165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10330 Ramachandran restraints generated. 5165 Oldfield, 0 Emsley, 5165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 4462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 244 time to evaluate : 1.219 Fit side-chains revert: symmetry clash REVERT: E 353 TYR cc_start: 0.8877 (m-80) cc_final: 0.8544 (m-80) REVERT: F 243 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8515 (tt) REVERT: F 279 THR cc_start: 0.8050 (m) cc_final: 0.7703 (t) REVERT: F 282 ASN cc_start: 0.8747 (t0) cc_final: 0.8266 (t0) REVERT: F 374 PHE cc_start: 0.8901 (OUTLIER) cc_final: 0.8552 (t80) REVERT: H 93 GLN cc_start: 0.7848 (OUTLIER) cc_final: 0.7413 (mp10) REVERT: H 117 HIS cc_start: 0.8791 (t70) cc_final: 0.8478 (t70) REVERT: H 205 MET cc_start: 0.9189 (OUTLIER) cc_final: 0.8823 (ttt) REVERT: I 876 GLU cc_start: 0.9039 (OUTLIER) cc_final: 0.8743 (mm-30) REVERT: J 330 MET cc_start: 0.9157 (mmt) cc_final: 0.8839 (mmt) REVERT: J 995 TYR cc_start: 0.6019 (m-80) cc_final: 0.5677 (m-80) REVERT: J 1040 MET cc_start: 0.3275 (mmm) cc_final: 0.2884 (mmm) REVERT: K 3 ARG cc_start: 0.8757 (mtm-85) cc_final: 0.8339 (mtt90) REVERT: M 8 ARG cc_start: 0.8894 (ptp-110) cc_final: 0.8208 (ptp90) REVERT: M 279 ARG cc_start: 0.8545 (mtp-110) cc_final: 0.8221 (mtm-85) outliers start: 84 outliers final: 38 residues processed: 300 average time/residue: 0.6665 time to fit residues: 248.1915 Evaluate side-chains 277 residues out of total 4462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 234 time to evaluate : 1.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain E residue 295 ASP Chi-restraints excluded: chain E residue 316 ASP Chi-restraints excluded: chain F residue 158 CYS Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 316 ASP Chi-restraints excluded: chain F residue 374 PHE Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 147 GLN Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain H residue 93 GLN Chi-restraints excluded: chain H residue 95 LYS Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 876 GLU Chi-restraints excluded: chain I residue 1101 LEU Chi-restraints excluded: chain I residue 1119 MET Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 260 PHE Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 466 MET Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 272 VAL Chi-restraints excluded: chain M residue 294 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 419 optimal weight: 6.9990 chunk 159 optimal weight: 5.9990 chunk 102 optimal weight: 0.0870 chunk 187 optimal weight: 4.9990 chunk 363 optimal weight: 1.9990 chunk 270 optimal weight: 6.9990 chunk 269 optimal weight: 1.9990 chunk 397 optimal weight: 3.9990 chunk 288 optimal weight: 4.9990 chunk 341 optimal weight: 5.9990 chunk 240 optimal weight: 5.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 GLN H 137 ASN J 430 HIS K 15 ASN K 61 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.087575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.052051 restraints weight = 103594.500| |-----------------------------------------------------------------------------| r_work (start): 0.2791 rms_B_bonded: 2.63 r_work: 0.2618 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2483 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 43961 Z= 0.197 Angle : 0.517 10.236 59719 Z= 0.275 Chirality : 0.042 0.162 6762 Planarity : 0.004 0.059 7403 Dihedral : 13.673 96.389 6907 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.66 % Allowed : 8.68 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.12), residues: 5165 helix: 1.46 (0.12), residues: 2157 sheet: 1.09 (0.22), residues: 586 loop : -0.49 (0.12), residues: 2422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG I 368 TYR 0.017 0.001 TYR J 631 PHE 0.019 0.001 PHE I1025 TRP 0.024 0.001 TRP J1193 HIS 0.006 0.001 HIS J 777 Details of bonding type rmsd covalent geometry : bond 0.00474 (43953) covalent geometry : angle 0.51647 (59707) hydrogen bonds : bond 0.04814 ( 1877) hydrogen bonds : angle 4.17077 ( 5152) metal coordination : bond 0.00580 ( 8) metal coordination : angle 2.06359 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10330 Ramachandran restraints generated. 5165 Oldfield, 0 Emsley, 5165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10330 Ramachandran restraints generated. 5165 Oldfield, 0 Emsley, 5165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 4462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 238 time to evaluate : 1.552 Fit side-chains revert: symmetry clash REVERT: E 353 TYR cc_start: 0.8872 (m-80) cc_final: 0.8545 (m-80) REVERT: F 279 THR cc_start: 0.8111 (m) cc_final: 0.7746 (t) REVERT: F 282 ASN cc_start: 0.8763 (t0) cc_final: 0.8276 (t0) REVERT: F 374 PHE cc_start: 0.8885 (OUTLIER) cc_final: 0.8550 (t80) REVERT: G 192 VAL cc_start: 0.7614 (OUTLIER) cc_final: 0.7381 (p) REVERT: H 117 HIS cc_start: 0.8827 (t70) cc_final: 0.8511 (t70) REVERT: H 205 MET cc_start: 0.9160 (OUTLIER) cc_final: 0.8813 (ttt) REVERT: I 996 ARG cc_start: 0.8639 (mmm160) cc_final: 0.8414 (mmm160) REVERT: I 1024 GLU cc_start: 0.9091 (tp30) cc_final: 0.8791 (tp30) REVERT: I 1119 MET cc_start: 0.9010 (OUTLIER) cc_final: 0.8432 (tpt) REVERT: J 330 MET cc_start: 0.9138 (mmt) cc_final: 0.8806 (mmt) REVERT: J 995 TYR cc_start: 0.5936 (m-80) cc_final: 0.5595 (m-80) REVERT: J 1040 MET cc_start: 0.3194 (mmm) cc_final: 0.2827 (mmm) REVERT: J 1189 MET cc_start: 0.7955 (tmm) cc_final: 0.7704 (tmm) REVERT: K 3 ARG cc_start: 0.8753 (mtm-85) cc_final: 0.8414 (mtt90) REVERT: M 8 ARG cc_start: 0.8886 (ptp-110) cc_final: 0.8193 (ptp90) outliers start: 74 outliers final: 38 residues processed: 293 average time/residue: 0.6522 time to fit residues: 238.0396 Evaluate side-chains 278 residues out of total 4462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 236 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain E residue 295 ASP Chi-restraints excluded: chain E residue 316 ASP Chi-restraints excluded: chain F residue 158 CYS Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 316 ASP Chi-restraints excluded: chain F residue 374 PHE Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 147 GLN Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 290 LEU Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 60 GLN Chi-restraints excluded: chain I residue 341 LEU Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 909 LYS Chi-restraints excluded: chain I residue 1101 LEU Chi-restraints excluded: chain I residue 1119 MET Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain J residue 260 PHE Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 466 MET Chi-restraints excluded: chain J residue 485 MET Chi-restraints excluded: chain J residue 525 MET Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1190 ILE Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 272 VAL Chi-restraints excluded: chain M residue 294 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 54 optimal weight: 2.9990 chunk 359 optimal weight: 0.9980 chunk 402 optimal weight: 0.4980 chunk 148 optimal weight: 3.9990 chunk 280 optimal weight: 0.9980 chunk 273 optimal weight: 10.0000 chunk 246 optimal weight: 5.9990 chunk 313 optimal weight: 0.6980 chunk 260 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 268 optimal weight: 3.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 GLN H 137 ASN I1023 HIS J 430 HIS K 15 ASN K 61 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.088565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.053280 restraints weight = 103255.740| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 2.63 r_work: 0.2650 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2516 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 43961 Z= 0.119 Angle : 0.479 10.348 59719 Z= 0.253 Chirality : 0.040 0.142 6762 Planarity : 0.003 0.059 7403 Dihedral : 13.568 94.435 6901 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.35 % Allowed : 9.45 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.12), residues: 5165 helix: 1.67 (0.12), residues: 2141 sheet: 1.01 (0.21), residues: 612 loop : -0.38 (0.12), residues: 2412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG I 368 TYR 0.015 0.001 TYR J 631 PHE 0.015 0.001 PHE J1319 TRP 0.029 0.001 TRP J1193 HIS 0.004 0.001 HIS J 777 Details of bonding type rmsd covalent geometry : bond 0.00278 (43953) covalent geometry : angle 0.47810 (59707) hydrogen bonds : bond 0.03955 ( 1877) hydrogen bonds : angle 3.98722 ( 5152) metal coordination : bond 0.00308 ( 8) metal coordination : angle 1.95395 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10330 Ramachandran restraints generated. 5165 Oldfield, 0 Emsley, 5165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10330 Ramachandran restraints generated. 5165 Oldfield, 0 Emsley, 5165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 4462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 243 time to evaluate : 1.016 Fit side-chains revert: symmetry clash REVERT: B 295 ASP cc_start: 0.9092 (OUTLIER) cc_final: 0.8709 (OUTLIER) REVERT: E 353 TYR cc_start: 0.8850 (m-80) cc_final: 0.8521 (m-80) REVERT: F 279 THR cc_start: 0.8067 (m) cc_final: 0.7739 (t) REVERT: F 282 ASN cc_start: 0.8753 (t0) cc_final: 0.8245 (t0) REVERT: F 374 PHE cc_start: 0.8904 (OUTLIER) cc_final: 0.8573 (t80) REVERT: G 192 VAL cc_start: 0.7600 (OUTLIER) cc_final: 0.7396 (p) REVERT: G 271 LYS cc_start: 0.9400 (ttmm) cc_final: 0.9086 (mmpt) REVERT: H 58 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.8303 (pm20) REVERT: H 93 GLN cc_start: 0.7707 (OUTLIER) cc_final: 0.7331 (mp10) REVERT: H 117 HIS cc_start: 0.8829 (t70) cc_final: 0.8510 (t70) REVERT: H 205 MET cc_start: 0.9115 (OUTLIER) cc_final: 0.8758 (ttt) REVERT: I 60 GLN cc_start: 0.9094 (OUTLIER) cc_final: 0.8680 (pm20) REVERT: I 378 ARG cc_start: 0.6999 (ttp80) cc_final: 0.6273 (ttp80) REVERT: I 445 ILE cc_start: 0.9100 (pt) cc_final: 0.8865 (tt) REVERT: I 1024 GLU cc_start: 0.9047 (tp30) cc_final: 0.8800 (tp30) REVERT: I 1119 MET cc_start: 0.8990 (ttt) cc_final: 0.8392 (tpt) REVERT: J 330 MET cc_start: 0.9134 (mmt) cc_final: 0.8803 (mmt) REVERT: J 913 GLU cc_start: 0.9301 (OUTLIER) cc_final: 0.8637 (mp0) REVERT: J 966 VAL cc_start: 0.6316 (OUTLIER) cc_final: 0.6029 (t) REVERT: J 995 TYR cc_start: 0.6034 (m-80) cc_final: 0.5683 (m-80) REVERT: J 1040 MET cc_start: 0.3296 (mmm) cc_final: 0.2944 (mmm) REVERT: J 1156 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8709 (tp) REVERT: K 3 ARG cc_start: 0.8736 (mtm-85) cc_final: 0.8405 (mtt90) REVERT: M 8 ARG cc_start: 0.8880 (ptp-110) cc_final: 0.8209 (ptp90) REVERT: M 279 ARG cc_start: 0.8422 (mtp-110) cc_final: 0.8221 (mtm-85) outliers start: 60 outliers final: 33 residues processed: 289 average time/residue: 0.4655 time to fit residues: 168.4125 Evaluate side-chains 277 residues out of total 4462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 235 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 374 PHE Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 147 GLN Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 290 LEU Chi-restraints excluded: chain H residue 58 GLU Chi-restraints excluded: chain H residue 93 GLN Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 60 GLN Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 909 LYS Chi-restraints excluded: chain I residue 1101 LEU Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain J residue 260 PHE Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 466 MET Chi-restraints excluded: chain J residue 670 SER Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 913 GLU Chi-restraints excluded: chain J residue 966 VAL Chi-restraints excluded: chain J residue 1156 LEU Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1190 ILE Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 272 VAL Chi-restraints excluded: chain M residue 294 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 464 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 506 optimal weight: 0.9980 chunk 496 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 225 optimal weight: 1.9990 chunk 235 optimal weight: 6.9990 chunk 290 optimal weight: 3.9990 chunk 263 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 179 optimal weight: 5.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 GLN H 137 ASN I1023 HIS J 430 HIS K 15 ASN K 61 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.088235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.052834 restraints weight = 103262.926| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 2.64 r_work: 0.2639 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2504 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 43961 Z= 0.148 Angle : 0.499 11.742 59719 Z= 0.261 Chirality : 0.040 0.143 6762 Planarity : 0.004 0.059 7403 Dihedral : 13.550 93.988 6899 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.30 % Allowed : 9.89 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.12), residues: 5165 helix: 1.70 (0.12), residues: 2146 sheet: 1.00 (0.21), residues: 617 loop : -0.38 (0.12), residues: 2402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG J 47 TYR 0.016 0.001 TYR J 631 PHE 0.015 0.001 PHE I1025 TRP 0.032 0.001 TRP J1193 HIS 0.005 0.001 HIS J 777 Details of bonding type rmsd covalent geometry : bond 0.00353 (43953) covalent geometry : angle 0.49860 (59707) hydrogen bonds : bond 0.04199 ( 1877) hydrogen bonds : angle 3.98389 ( 5152) metal coordination : bond 0.00454 ( 8) metal coordination : angle 1.86698 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10330 Ramachandran restraints generated. 5165 Oldfield, 0 Emsley, 5165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10330 Ramachandran restraints generated. 5165 Oldfield, 0 Emsley, 5165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 4462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 238 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 295 ASP cc_start: 0.9083 (OUTLIER) cc_final: 0.8720 (OUTLIER) REVERT: D 330 ARG cc_start: 0.8343 (ttp80) cc_final: 0.7847 (tmm-80) REVERT: E 353 TYR cc_start: 0.8822 (m-80) cc_final: 0.8527 (m-80) REVERT: F 279 THR cc_start: 0.8106 (m) cc_final: 0.7781 (t) REVERT: F 282 ASN cc_start: 0.8750 (t0) cc_final: 0.8252 (t0) REVERT: F 374 PHE cc_start: 0.8925 (OUTLIER) cc_final: 0.8536 (t80) REVERT: G 271 LYS cc_start: 0.9409 (ttmm) cc_final: 0.9102 (mmpt) REVERT: H 58 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.7983 (pm20) REVERT: H 93 GLN cc_start: 0.7741 (OUTLIER) cc_final: 0.7358 (mp10) REVERT: H 117 HIS cc_start: 0.8815 (t70) cc_final: 0.8504 (t70) REVERT: H 145 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8402 (ttpp) REVERT: H 205 MET cc_start: 0.9131 (OUTLIER) cc_final: 0.8790 (ttt) REVERT: I 60 GLN cc_start: 0.9106 (OUTLIER) cc_final: 0.8698 (pm20) REVERT: I 378 ARG cc_start: 0.6956 (ttp80) cc_final: 0.6236 (ttp80) REVERT: I 445 ILE cc_start: 0.9104 (pt) cc_final: 0.8861 (tt) REVERT: I 996 ARG cc_start: 0.8582 (mmm160) cc_final: 0.8306 (mmp80) REVERT: I 1024 GLU cc_start: 0.9075 (tp30) cc_final: 0.8815 (tp30) REVERT: I 1119 MET cc_start: 0.9009 (ttt) cc_final: 0.8414 (tpt) REVERT: J 256 ASP cc_start: 0.8209 (m-30) cc_final: 0.7773 (p0) REVERT: J 330 MET cc_start: 0.9129 (mmt) cc_final: 0.8783 (mmt) REVERT: J 913 GLU cc_start: 0.9314 (OUTLIER) cc_final: 0.8633 (mp0) REVERT: J 966 VAL cc_start: 0.6372 (OUTLIER) cc_final: 0.6096 (t) REVERT: J 995 TYR cc_start: 0.6061 (m-80) cc_final: 0.5696 (m-80) REVERT: J 1040 MET cc_start: 0.3674 (mmm) cc_final: 0.3340 (mmm) REVERT: K 3 ARG cc_start: 0.8751 (mtm-85) cc_final: 0.8415 (mtt90) REVERT: M 8 ARG cc_start: 0.8891 (ptp-110) cc_final: 0.8193 (ptp90) REVERT: M 279 ARG cc_start: 0.8451 (mtp-110) cc_final: 0.8242 (mtm-85) outliers start: 58 outliers final: 36 residues processed: 282 average time/residue: 0.4690 time to fit residues: 165.7834 Evaluate side-chains 279 residues out of total 4462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 235 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain E residue 316 ASP Chi-restraints excluded: chain F residue 158 CYS Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 316 ASP Chi-restraints excluded: chain F residue 374 PHE Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 147 GLN Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 290 LEU Chi-restraints excluded: chain H residue 58 GLU Chi-restraints excluded: chain H residue 93 GLN Chi-restraints excluded: chain H residue 145 LYS Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 60 GLN Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 1101 LEU Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain J residue 260 PHE Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 466 MET Chi-restraints excluded: chain J residue 485 MET Chi-restraints excluded: chain J residue 913 GLU Chi-restraints excluded: chain J residue 966 VAL Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1190 ILE Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 272 VAL Chi-restraints excluded: chain M residue 294 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 55 optimal weight: 3.9990 chunk 141 optimal weight: 9.9990 chunk 464 optimal weight: 0.9990 chunk 518 optimal weight: 7.9990 chunk 130 optimal weight: 5.9990 chunk 390 optimal weight: 0.5980 chunk 94 optimal weight: 0.8980 chunk 165 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 381 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 GLN H 137 ASN I1023 HIS J 430 HIS K 15 ASN K 61 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.089135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.053947 restraints weight = 103703.487| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 2.64 r_work: 0.2672 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2538 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.077 43961 Z= 0.102 Angle : 0.477 11.904 59719 Z= 0.249 Chirality : 0.039 0.157 6762 Planarity : 0.003 0.059 7403 Dihedral : 13.484 91.525 6899 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.01 % Allowed : 10.48 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.12), residues: 5165 helix: 1.83 (0.12), residues: 2130 sheet: 1.05 (0.21), residues: 617 loop : -0.29 (0.13), residues: 2418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG I 473 TYR 0.013 0.001 TYR J 631 PHE 0.014 0.001 PHE J1319 TRP 0.036 0.001 TRP J1193 HIS 0.003 0.001 HIS J 777 Details of bonding type rmsd covalent geometry : bond 0.00232 (43953) covalent geometry : angle 0.47641 (59707) hydrogen bonds : bond 0.03532 ( 1877) hydrogen bonds : angle 3.86288 ( 5152) metal coordination : bond 0.00277 ( 8) metal coordination : angle 1.78857 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10330 Ramachandran restraints generated. 5165 Oldfield, 0 Emsley, 5165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10330 Ramachandran restraints generated. 5165 Oldfield, 0 Emsley, 5165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 4462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 238 time to evaluate : 1.011 Fit side-chains REVERT: B 295 ASP cc_start: 0.9027 (OUTLIER) cc_final: 0.8796 (OUTLIER) REVERT: B 371 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8135 (pp20) REVERT: E 353 TYR cc_start: 0.8862 (m-80) cc_final: 0.8551 (m-80) REVERT: F 279 THR cc_start: 0.8114 (m) cc_final: 0.7811 (t) REVERT: F 282 ASN cc_start: 0.8740 (t0) cc_final: 0.8231 (t0) REVERT: F 374 PHE cc_start: 0.8930 (OUTLIER) cc_final: 0.8499 (t80) REVERT: G 271 LYS cc_start: 0.9406 (ttmm) cc_final: 0.9056 (mmpt) REVERT: H 58 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.7996 (pm20) REVERT: H 93 GLN cc_start: 0.7725 (OUTLIER) cc_final: 0.7326 (mp10) REVERT: H 145 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8447 (ttpp) REVERT: I 378 ARG cc_start: 0.7021 (ttp80) cc_final: 0.6301 (ttp80) REVERT: I 445 ILE cc_start: 0.9077 (pt) cc_final: 0.8844 (tt) REVERT: I 1010 GLN cc_start: 0.8213 (mm-40) cc_final: 0.7993 (pt0) REVERT: I 1024 GLU cc_start: 0.9044 (tp30) cc_final: 0.8743 (tp30) REVERT: I 1119 MET cc_start: 0.8939 (ttt) cc_final: 0.8384 (tpt) REVERT: J 256 ASP cc_start: 0.8191 (m-30) cc_final: 0.7799 (p0) REVERT: J 330 MET cc_start: 0.9082 (mmt) cc_final: 0.8726 (mmt) REVERT: J 913 GLU cc_start: 0.9298 (OUTLIER) cc_final: 0.8643 (mp0) REVERT: J 966 VAL cc_start: 0.6373 (OUTLIER) cc_final: 0.6091 (t) REVERT: J 995 TYR cc_start: 0.6081 (m-80) cc_final: 0.5057 (m-80) REVERT: J 1040 MET cc_start: 0.3607 (mmm) cc_final: 0.3060 (mmm) REVERT: K 3 ARG cc_start: 0.8752 (mtm-85) cc_final: 0.8421 (mtt90) REVERT: M 8 ARG cc_start: 0.8874 (ptp-110) cc_final: 0.8116 (ptp90) outliers start: 45 outliers final: 24 residues processed: 274 average time/residue: 0.4601 time to fit residues: 157.4245 Evaluate side-chains 262 residues out of total 4462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 231 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 374 PHE Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain H residue 58 GLU Chi-restraints excluded: chain H residue 93 GLN Chi-restraints excluded: chain H residue 145 LYS Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 909 LYS Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 260 PHE Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 913 GLU Chi-restraints excluded: chain J residue 966 VAL Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1190 ILE Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 272 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 11 optimal weight: 1.9990 chunk 374 optimal weight: 0.9980 chunk 313 optimal weight: 2.9990 chunk 348 optimal weight: 4.9990 chunk 446 optimal weight: 8.9990 chunk 233 optimal weight: 20.0000 chunk 68 optimal weight: 10.0000 chunk 125 optimal weight: 0.7980 chunk 207 optimal weight: 6.9990 chunk 208 optimal weight: 0.7980 chunk 470 optimal weight: 8.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 GLN H 137 ASN I1023 HIS K 15 ASN K 61 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.088555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.053245 restraints weight = 103492.950| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 2.65 r_work: 0.2651 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2517 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 43961 Z= 0.133 Angle : 0.499 12.538 59719 Z= 0.259 Chirality : 0.040 0.143 6762 Planarity : 0.004 0.075 7403 Dihedral : 13.482 90.914 6899 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.94 % Allowed : 10.66 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.12), residues: 5165 helix: 1.82 (0.12), residues: 2136 sheet: 1.03 (0.21), residues: 617 loop : -0.29 (0.13), residues: 2412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG J 47 TYR 0.016 0.001 TYR J 631 PHE 0.015 0.001 PHE J1319 TRP 0.039 0.001 TRP J1193 HIS 0.005 0.001 HIS J 777 Details of bonding type rmsd covalent geometry : bond 0.00315 (43953) covalent geometry : angle 0.49847 (59707) hydrogen bonds : bond 0.03907 ( 1877) hydrogen bonds : angle 3.89064 ( 5152) metal coordination : bond 0.00414 ( 8) metal coordination : angle 1.79094 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10330 Ramachandran restraints generated. 5165 Oldfield, 0 Emsley, 5165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10330 Ramachandran restraints generated. 5165 Oldfield, 0 Emsley, 5165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 4462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 238 time to evaluate : 1.007 Fit side-chains revert: symmetry clash REVERT: B 371 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8144 (pp20) REVERT: E 353 TYR cc_start: 0.8817 (m-80) cc_final: 0.8505 (m-80) REVERT: F 279 THR cc_start: 0.8071 (m) cc_final: 0.7752 (t) REVERT: F 282 ASN cc_start: 0.8739 (t0) cc_final: 0.8232 (t0) REVERT: G 271 LYS cc_start: 0.9409 (ttmm) cc_final: 0.9064 (mmpt) REVERT: H 58 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.7988 (pm20) REVERT: H 93 GLN cc_start: 0.7813 (OUTLIER) cc_final: 0.7412 (mp10) REVERT: H 145 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8424 (ttpp) REVERT: I 60 GLN cc_start: 0.9092 (OUTLIER) cc_final: 0.8860 (mt0) REVERT: I 378 ARG cc_start: 0.6985 (ttp80) cc_final: 0.6268 (ttp80) REVERT: I 445 ILE cc_start: 0.9090 (pt) cc_final: 0.8854 (tt) REVERT: I 996 ARG cc_start: 0.8466 (mmm160) cc_final: 0.8249 (mmp80) REVERT: I 1024 GLU cc_start: 0.9066 (tp30) cc_final: 0.8767 (tp30) REVERT: I 1119 MET cc_start: 0.8937 (ttt) cc_final: 0.8376 (tpt) REVERT: J 256 ASP cc_start: 0.8198 (m-30) cc_final: 0.7802 (p0) REVERT: J 330 MET cc_start: 0.9094 (mmt) cc_final: 0.8742 (mmt) REVERT: J 821 MET cc_start: 0.9274 (tpp) cc_final: 0.9069 (tpp) REVERT: J 913 GLU cc_start: 0.9301 (OUTLIER) cc_final: 0.8606 (mp0) REVERT: J 966 VAL cc_start: 0.6381 (OUTLIER) cc_final: 0.6100 (t) REVERT: J 1040 MET cc_start: 0.3645 (mmm) cc_final: 0.3096 (mmm) REVERT: K 3 ARG cc_start: 0.8759 (mtm-85) cc_final: 0.8432 (mtt90) REVERT: M 8 ARG cc_start: 0.8890 (ptp-110) cc_final: 0.8103 (ptp90) outliers start: 42 outliers final: 28 residues processed: 273 average time/residue: 0.4703 time to fit residues: 159.7892 Evaluate side-chains 268 residues out of total 4462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 233 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain F residue 158 CYS Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 147 GLN Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain H residue 58 GLU Chi-restraints excluded: chain H residue 93 GLN Chi-restraints excluded: chain H residue 145 LYS Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 60 GLN Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 909 LYS Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 260 PHE Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 913 GLU Chi-restraints excluded: chain J residue 966 VAL Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1190 ILE Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 272 VAL Chi-restraints excluded: chain M residue 294 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 296 optimal weight: 5.9990 chunk 172 optimal weight: 6.9990 chunk 442 optimal weight: 0.8980 chunk 454 optimal weight: 0.7980 chunk 521 optimal weight: 3.9990 chunk 395 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 509 optimal weight: 0.0070 chunk 67 optimal weight: 6.9990 chunk 250 optimal weight: 8.9990 chunk 437 optimal weight: 7.9990 overall best weight: 1.5402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 GLN H 137 ASN I1023 HIS K 15 ASN K 61 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.088517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.053258 restraints weight = 103863.542| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 2.64 r_work: 0.2651 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2515 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 43961 Z= 0.133 Angle : 0.508 14.543 59719 Z= 0.262 Chirality : 0.040 0.143 6762 Planarity : 0.004 0.058 7403 Dihedral : 13.513 90.325 6899 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.85 % Allowed : 10.95 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.12), residues: 5165 helix: 1.83 (0.12), residues: 2136 sheet: 1.01 (0.21), residues: 615 loop : -0.28 (0.13), residues: 2414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG I 473 TYR 0.016 0.001 TYR J 631 PHE 0.014 0.001 PHE J1319 TRP 0.041 0.001 TRP J1193 HIS 0.005 0.001 HIS J 777 Details of bonding type rmsd covalent geometry : bond 0.00316 (43953) covalent geometry : angle 0.50703 (59707) hydrogen bonds : bond 0.03895 ( 1877) hydrogen bonds : angle 3.88671 ( 5152) metal coordination : bond 0.00400 ( 8) metal coordination : angle 1.82026 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10330 Ramachandran restraints generated. 5165 Oldfield, 0 Emsley, 5165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10330 Ramachandran restraints generated. 5165 Oldfield, 0 Emsley, 5165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 4462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 234 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 371 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8174 (pp20) REVERT: D 330 ARG cc_start: 0.8824 (tmm-80) cc_final: 0.8538 (ttp80) REVERT: E 353 TYR cc_start: 0.8832 (m-80) cc_final: 0.8523 (m-80) REVERT: F 279 THR cc_start: 0.8085 (m) cc_final: 0.7746 (t) REVERT: F 282 ASN cc_start: 0.8732 (t0) cc_final: 0.8219 (t0) REVERT: G 271 LYS cc_start: 0.9410 (ttmm) cc_final: 0.9071 (mmpt) REVERT: H 58 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.7970 (pm20) REVERT: H 93 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.7408 (mp10) REVERT: H 145 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8423 (ttpp) REVERT: I 60 GLN cc_start: 0.9092 (OUTLIER) cc_final: 0.8858 (mt0) REVERT: I 378 ARG cc_start: 0.6984 (ttp80) cc_final: 0.6262 (ttp80) REVERT: I 445 ILE cc_start: 0.9093 (pt) cc_final: 0.8852 (tt) REVERT: I 996 ARG cc_start: 0.8491 (mmm160) cc_final: 0.8270 (mmp80) REVERT: I 1010 GLN cc_start: 0.8203 (mm-40) cc_final: 0.7985 (pt0) REVERT: I 1024 GLU cc_start: 0.9065 (tp30) cc_final: 0.8764 (tp30) REVERT: I 1119 MET cc_start: 0.8938 (ttt) cc_final: 0.8384 (tpt) REVERT: J 256 ASP cc_start: 0.8185 (m-30) cc_final: 0.7750 (p0) REVERT: J 330 MET cc_start: 0.9112 (mmt) cc_final: 0.8761 (mmt) REVERT: J 913 GLU cc_start: 0.9302 (OUTLIER) cc_final: 0.8618 (mp0) REVERT: J 966 VAL cc_start: 0.6429 (OUTLIER) cc_final: 0.6158 (t) REVERT: J 1019 ASN cc_start: 0.9209 (m-40) cc_final: 0.8886 (m110) REVERT: J 1040 MET cc_start: 0.3729 (mmm) cc_final: 0.3178 (mmm) REVERT: J 1210 ILE cc_start: 0.7750 (mp) cc_final: 0.7494 (mm) REVERT: K 3 ARG cc_start: 0.8774 (mtm-85) cc_final: 0.8442 (mtt90) REVERT: M 8 ARG cc_start: 0.8891 (ptp-110) cc_final: 0.8096 (ptp90) outliers start: 38 outliers final: 28 residues processed: 265 average time/residue: 0.4651 time to fit residues: 153.3050 Evaluate side-chains 265 residues out of total 4462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 230 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain F residue 158 CYS Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 316 ASP Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 147 GLN Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain H residue 58 GLU Chi-restraints excluded: chain H residue 93 GLN Chi-restraints excluded: chain H residue 145 LYS Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 60 GLN Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 909 LYS Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain J residue 260 PHE Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 485 MET Chi-restraints excluded: chain J residue 913 GLU Chi-restraints excluded: chain J residue 966 VAL Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1190 ILE Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 272 VAL Chi-restraints excluded: chain M residue 294 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 170 optimal weight: 2.9990 chunk 446 optimal weight: 0.0070 chunk 239 optimal weight: 0.0050 chunk 432 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 246 optimal weight: 5.9990 chunk 398 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 481 optimal weight: 0.8980 chunk 285 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 overall best weight: 1.1816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 GLN H 137 ASN I1023 HIS K 15 ASN K 61 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.089360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.054708 restraints weight = 105882.546| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 2.64 r_work: 0.2744 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 43961 Z= 0.115 Angle : 0.495 14.148 59719 Z= 0.256 Chirality : 0.040 0.144 6762 Planarity : 0.003 0.058 7403 Dihedral : 13.456 88.758 6897 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.79 % Allowed : 11.17 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.12), residues: 5165 helix: 1.91 (0.12), residues: 2125 sheet: 1.01 (0.21), residues: 623 loop : -0.24 (0.13), residues: 2417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG I 473 TYR 0.014 0.001 TYR J 631 PHE 0.014 0.001 PHE J1319 TRP 0.041 0.001 TRP J1193 HIS 0.004 0.001 HIS J 777 Details of bonding type rmsd covalent geometry : bond 0.00269 (43953) covalent geometry : angle 0.49406 (59707) hydrogen bonds : bond 0.03635 ( 1877) hydrogen bonds : angle 3.84362 ( 5152) metal coordination : bond 0.00342 ( 8) metal coordination : angle 1.79538 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17737.98 seconds wall clock time: 300 minutes 18.51 seconds (18018.51 seconds total)