Starting phenix.real_space_refine on Fri Jan 16 20:58:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z8i_14552/01_2026/7z8i_14552.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z8i_14552/01_2026/7z8i_14552.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7z8i_14552/01_2026/7z8i_14552.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z8i_14552/01_2026/7z8i_14552.map" model { file = "/net/cci-nas-00/data/ceres_data/7z8i_14552/01_2026/7z8i_14552.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z8i_14552/01_2026/7z8i_14552.cif" } resolution = 3.3 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= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 6 5.21 5 S 157 5.16 5 C 27487 2.51 5 N 7681 2.21 5 O 8082 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 89 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 43425 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 2944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2944 Classifications: {'peptide': 370} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 2956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2956 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "C" Number of atoms: 2998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2998 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "D" Number of atoms: 2956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2956 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "E" Number of atoms: 2944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2944 Classifications: {'peptide': 370} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 2223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2223 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 15, 'TRANS': 263} Chain breaks: 4 Chain: "K" Number of atoms: 2264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2264 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 267} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 2122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2122 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 9, 'TRANS': 259} Chain: "X" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 797 Classifications: {'peptide': 93} Link IDs: {'TRANS': 92} Chain: "f" Number of atoms: 5943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 720, 5943 Classifications: {'peptide': 720} Link IDs: {'PTRANS': 21, 'TRANS': 698} Chain breaks: 2 Chain: "h" Number of atoms: 2808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2808 Classifications: {'peptide': 358} Link IDs: {'PTRANS': 17, 'TRANS': 340} Chain: "j" Number of atoms: 291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 291 Classifications: {'peptide': 44} Incomplete info: {'backbone_only': 13} Link IDs: {'PTRANS': 2, 'TRANS': 41} Chain breaks: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "m" Number of atoms: 4963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4963 Classifications: {'peptide': 602} Link IDs: {'PTRANS': 17, 'TRANS': 584} Chain breaks: 2 Chain: "n" Number of atoms: 3387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3387 Classifications: {'peptide': 409} Link IDs: {'PTRANS': 11, 'TRANS': 397} Chain breaks: 2 Chain: "o" Number of atoms: 2808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2808 Classifications: {'peptide': 358} Link IDs: {'PTRANS': 17, 'TRANS': 340} Chain: "r" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 56 Classifications: {'peptide': 14} Incomplete info: {'backbone_only': 13} Link IDs: {'TRANS': 13} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "x" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 797 Classifications: {'peptide': 93} Link IDs: {'TRANS': 92} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.29, per 1000 atoms: 0.21 Number of scatterers: 43425 At special positions: 0 Unit cell: (257.612, 161.785, 189.164, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 157 16.00 P 12 15.00 Mg 6 11.99 O 8082 8.00 N 7681 7.00 C 27487 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: 3.28 Conformation dependent library (CDL) restraints added in 1.4 seconds 10632 Ramachandran restraints generated. 5316 Oldfield, 0 Emsley, 5316 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10084 Finding SS restraints... Secondary structure from input PDB file: 222 helices and 55 sheets defined 55.8% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.63 Creating SS restraints... Processing helix chain 'A' and resid 59 through 65 Processing helix chain 'A' and resid 82 through 94 removed outlier: 3.713A pdb=" N TYR A 94 " --> pdb=" O TRP A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 131 removed outlier: 3.708A pdb=" N ARG A 121 " --> pdb=" O PRO A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 150 removed outlier: 3.725A pdb=" N THR A 150 " --> pdb=" O SER A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 180 removed outlier: 3.857A pdb=" N ILE A 180 " --> pdb=" O PRO A 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 177 through 180' Processing helix chain 'A' and resid 186 through 200 Processing helix chain 'A' and resid 207 through 221 removed outlier: 3.938A pdb=" N GLU A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE A 213 " --> pdb=" O SER A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 234 removed outlier: 3.522A pdb=" N ASP A 231 " --> pdb=" O ASN A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 258 Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 264 through 269 Processing helix chain 'A' and resid 274 through 285 Processing helix chain 'A' and resid 287 through 297 removed outlier: 3.535A pdb=" N ARG A 291 " --> pdb=" O ASP A 287 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG A 292 " --> pdb=" O MET A 288 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N THR A 293 " --> pdb=" O ASP A 289 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER A 296 " --> pdb=" O ARG A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 307 removed outlier: 3.793A pdb=" N PHE A 307 " --> pdb=" O SER A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 322 Processing helix chain 'A' and resid 338 through 350 removed outlier: 3.530A pdb=" N LEU A 350 " --> pdb=" O ILE A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 356 Processing helix chain 'A' and resid 360 through 366 Processing helix chain 'A' and resid 367 through 375 removed outlier: 3.653A pdb=" N ILE A 371 " --> pdb=" O GLY A 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 65 removed outlier: 3.511A pdb=" N HIS B 65 " --> pdb=" O LYS B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.511A pdb=" N TYR B 94 " --> pdb=" O TRP B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 removed outlier: 3.662A pdb=" N ARG B 121 " --> pdb=" O PRO B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 151 Processing helix chain 'B' and resid 186 through 201 Processing helix chain 'B' and resid 207 through 221 removed outlier: 3.876A pdb=" N GLU B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE B 213 " --> pdb=" O SER B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 234 Processing helix chain 'B' and resid 253 through 258 removed outlier: 3.547A pdb=" N ALA B 258 " --> pdb=" O SER B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 263 Processing helix chain 'B' and resid 264 through 269 Processing helix chain 'B' and resid 274 through 285 Processing helix chain 'B' and resid 290 through 296 Processing helix chain 'B' and resid 302 through 307 removed outlier: 3.694A pdb=" N THR B 305 " --> pdb=" O GLY B 302 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N PHE B 307 " --> pdb=" O SER B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 322 Processing helix chain 'B' and resid 338 through 350 removed outlier: 3.670A pdb=" N LEU B 350 " --> pdb=" O ILE B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 356 Processing helix chain 'B' and resid 360 through 366 Processing helix chain 'B' and resid 367 through 376 removed outlier: 3.958A pdb=" N ILE B 371 " --> pdb=" O GLY B 367 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE B 376 " --> pdb=" O HIS B 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 9 Processing helix chain 'C' and resid 59 through 65 Processing helix chain 'C' and resid 82 through 94 removed outlier: 3.510A pdb=" N TYR C 94 " --> pdb=" O TRP C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 131 removed outlier: 3.642A pdb=" N ARG C 121 " --> pdb=" O PRO C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 151 Processing helix chain 'C' and resid 177 through 180 removed outlier: 3.516A pdb=" N ILE C 180 " --> pdb=" O PRO C 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 177 through 180' Processing helix chain 'C' and resid 186 through 201 Processing helix chain 'C' and resid 210 through 221 Processing helix chain 'C' and resid 227 through 234 removed outlier: 3.639A pdb=" N ASP C 231 " --> pdb=" O ASN C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 258 removed outlier: 3.512A pdb=" N ALA C 258 " --> pdb=" O SER C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 263 Processing helix chain 'C' and resid 264 through 269 Processing helix chain 'C' and resid 274 through 285 Processing helix chain 'C' and resid 287 through 297 removed outlier: 4.324A pdb=" N ARG C 292 " --> pdb=" O MET C 288 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N THR C 293 " --> pdb=" O ASP C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 307 removed outlier: 3.519A pdb=" N THR C 305 " --> pdb=" O GLY C 302 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N PHE C 307 " --> pdb=" O SER C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 322 Processing helix chain 'C' and resid 338 through 350 Processing helix chain 'C' and resid 351 through 356 Processing helix chain 'C' and resid 360 through 367 Processing helix chain 'C' and resid 367 through 373 removed outlier: 3.927A pdb=" N ILE C 371 " --> pdb=" O GLY C 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 65 Processing helix chain 'D' and resid 82 through 94 removed outlier: 3.542A pdb=" N MET D 86 " --> pdb=" O ASP D 82 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR D 94 " --> pdb=" O TRP D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 106 removed outlier: 3.653A pdb=" N HIS D 106 " --> pdb=" O SER D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 130 removed outlier: 3.737A pdb=" N ARG D 121 " --> pdb=" O PRO D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 151 Processing helix chain 'D' and resid 186 through 202 Processing helix chain 'D' and resid 207 through 221 Processing helix chain 'D' and resid 227 through 235 removed outlier: 4.140A pdb=" N ASP D 231 " --> pdb=" O ASN D 227 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU D 235 " --> pdb=" O ASP D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 258 removed outlier: 3.689A pdb=" N ALA D 258 " --> pdb=" O SER D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 263 Processing helix chain 'D' and resid 264 through 269 Processing helix chain 'D' and resid 274 through 285 Processing helix chain 'D' and resid 289 through 297 removed outlier: 4.609A pdb=" N THR D 293 " --> pdb=" O ASP D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 307 removed outlier: 4.006A pdb=" N PHE D 307 " --> pdb=" O SER D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 322 Processing helix chain 'D' and resid 338 through 349 Processing helix chain 'D' and resid 350 through 356 Processing helix chain 'D' and resid 360 through 367 Processing helix chain 'D' and resid 367 through 376 removed outlier: 3.817A pdb=" N ILE D 371 " --> pdb=" O GLY D 367 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N PHE D 376 " --> pdb=" O HIS D 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 65 Processing helix chain 'E' and resid 82 through 94 Processing helix chain 'E' and resid 117 through 130 removed outlier: 3.759A pdb=" N ARG E 121 " --> pdb=" O PRO E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 151 removed outlier: 3.649A pdb=" N THR E 150 " --> pdb=" O SER E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 180 removed outlier: 3.724A pdb=" N ILE E 180 " --> pdb=" O PRO E 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 177 through 180' Processing helix chain 'E' and resid 186 through 201 Processing helix chain 'E' and resid 207 through 221 removed outlier: 3.973A pdb=" N GLU E 212 " --> pdb=" O SER E 208 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE E 213 " --> pdb=" O SER E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 234 removed outlier: 3.553A pdb=" N ASP E 231 " --> pdb=" O ASN E 227 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU E 234 " --> pdb=" O LYS E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 258 removed outlier: 3.550A pdb=" N ALA E 258 " --> pdb=" O SER E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 263 Processing helix chain 'E' and resid 264 through 269 Processing helix chain 'E' and resid 274 through 286 removed outlier: 3.557A pdb=" N SER E 286 " --> pdb=" O ALA E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 289 No H-bonds generated for 'chain 'E' and resid 287 through 289' Processing helix chain 'E' and resid 290 through 296 Processing helix chain 'E' and resid 302 through 307 removed outlier: 3.576A pdb=" N THR E 305 " --> pdb=" O GLY E 302 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE E 307 " --> pdb=" O SER E 304 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 322 Processing helix chain 'E' and resid 338 through 350 Processing helix chain 'E' and resid 351 through 356 Processing helix chain 'E' and resid 360 through 367 Processing helix chain 'E' and resid 368 through 374 removed outlier: 3.660A pdb=" N HIS E 372 " --> pdb=" O ALA E 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.534A pdb=" N VAL F 93 " --> pdb=" O ILE F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 131 removed outlier: 3.626A pdb=" N ARG F 121 " --> pdb=" O PRO F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 151 Processing helix chain 'F' and resid 186 through 194 Processing helix chain 'F' and resid 216 through 221 Processing helix chain 'F' and resid 259 through 264 removed outlier: 4.266A pdb=" N PHE F 263 " --> pdb=" O PRO F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 285 Processing helix chain 'F' and resid 290 through 297 Processing helix chain 'F' and resid 302 through 307 removed outlier: 3.812A pdb=" N PHE F 307 " --> pdb=" O SER F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 322 Processing helix chain 'F' and resid 338 through 350 removed outlier: 3.824A pdb=" N LEU F 350 " --> pdb=" O ILE F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 351 through 356 Processing helix chain 'F' and resid 360 through 367 Processing helix chain 'F' and resid 367 through 374 removed outlier: 4.357A pdb=" N ILE F 371 " --> pdb=" O GLY F 367 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 23 removed outlier: 3.663A pdb=" N HIS K 23 " --> pdb=" O LYS K 19 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 41 Processing helix chain 'K' and resid 42 through 61 removed outlier: 4.402A pdb=" N GLU K 48 " --> pdb=" O ASN K 44 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N GLY K 49 " --> pdb=" O LEU K 45 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N HIS K 52 " --> pdb=" O GLU K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 117 through 136 Processing helix chain 'K' and resid 220 through 249 Processing helix chain 'K' and resid 254 through 258 removed outlier: 3.559A pdb=" N ALA K 257 " --> pdb=" O THR K 254 " (cutoff:3.500A) Processing helix chain 'K' and resid 270 through 277 Processing helix chain 'L' and resid 3 through 16 Processing helix chain 'L' and resid 20 through 30 removed outlier: 3.573A pdb=" N ASP L 30 " --> pdb=" O SER L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 31 through 34 removed outlier: 6.462A pdb=" N SER L 34 " --> pdb=" O LEU L 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 31 through 34' Processing helix chain 'L' and resid 35 through 43 Processing helix chain 'L' and resid 91 through 112 Processing helix chain 'L' and resid 208 through 244 removed outlier: 3.908A pdb=" N TYR L 232 " --> pdb=" O LEU L 228 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N PHE L 233 " --> pdb=" O ASN L 229 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N THR L 236 " --> pdb=" O TYR L 232 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG L 244 " --> pdb=" O VAL L 240 " (cutoff:3.500A) Processing helix chain 'L' and resid 248 through 269 Processing helix chain 'X' and resid 101 through 192 removed outlier: 3.617A pdb=" N ARG X 192 " --> pdb=" O GLN X 188 " (cutoff:3.500A) Processing helix chain 'f' and resid 211 through 223 Processing helix chain 'f' and resid 228 through 237 removed outlier: 6.443A pdb=" N ASP f 234 " --> pdb=" O ASP f 231 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL f 236 " --> pdb=" O GLY f 233 " (cutoff:3.500A) Processing helix chain 'f' and resid 238 through 261 removed outlier: 3.713A pdb=" N VAL f 259 " --> pdb=" O GLU f 255 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS f 261 " --> pdb=" O GLN f 257 " (cutoff:3.500A) Processing helix chain 'f' and resid 270 through 293 removed outlier: 3.552A pdb=" N GLU f 274 " --> pdb=" O THR f 270 " (cutoff:3.500A) Processing helix chain 'f' and resid 294 through 307 Processing helix chain 'f' and resid 309 through 319 removed outlier: 3.935A pdb=" N THR f 313 " --> pdb=" O ARG f 309 " (cutoff:3.500A) Processing helix chain 'f' and resid 321 through 333 Processing helix chain 'f' and resid 334 through 336 No H-bonds generated for 'chain 'f' and resid 334 through 336' Processing helix chain 'f' and resid 340 through 346 removed outlier: 3.618A pdb=" N LEU f 344 " --> pdb=" O PRO f 340 " (cutoff:3.500A) Processing helix chain 'f' and resid 349 through 365 Processing helix chain 'f' and resid 366 through 369 Processing helix chain 'f' and resid 373 through 400 Processing helix chain 'f' and resid 401 through 404 removed outlier: 3.815A pdb=" N VAL f 404 " --> pdb=" O LEU f 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 401 through 404' Processing helix chain 'f' and resid 405 through 441 removed outlier: 3.783A pdb=" N VAL f 432 " --> pdb=" O GLU f 428 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU f 433 " --> pdb=" O LYS f 429 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS f 441 " --> pdb=" O ILE f 437 " (cutoff:3.500A) Processing helix chain 'f' and resid 455 through 485 removed outlier: 4.047A pdb=" N LEU f 459 " --> pdb=" O ALA f 455 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ARG f 485 " --> pdb=" O VAL f 481 " (cutoff:3.500A) Processing helix chain 'f' and resid 513 through 533 removed outlier: 3.990A pdb=" N VAL f 533 " --> pdb=" O ASN f 529 " (cutoff:3.500A) Processing helix chain 'f' and resid 539 through 575 removed outlier: 3.834A pdb=" N VAL f 560 " --> pdb=" O ARG f 556 " (cutoff:3.500A) Processing helix chain 'f' and resid 577 through 588 removed outlier: 4.056A pdb=" N PHE f 588 " --> pdb=" O ILE f 584 " (cutoff:3.500A) Processing helix chain 'f' and resid 589 through 593 removed outlier: 3.908A pdb=" N PHE f 592 " --> pdb=" O ASN f 589 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL f 593 " --> pdb=" O ALA f 590 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 589 through 593' Processing helix chain 'f' and resid 596 through 604 removed outlier: 4.014A pdb=" N ALA f 600 " --> pdb=" O HIS f 596 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR f 604 " --> pdb=" O ALA f 600 " (cutoff:3.500A) Processing helix chain 'f' and resid 604 through 625 removed outlier: 3.595A pdb=" N VAL f 625 " --> pdb=" O ASP f 621 " (cutoff:3.500A) Processing helix chain 'f' and resid 630 through 639 removed outlier: 3.914A pdb=" N LYS f 634 " --> pdb=" O SER f 630 " (cutoff:3.500A) Processing helix chain 'f' and resid 642 through 670 Processing helix chain 'f' and resid 672 through 675 removed outlier: 3.568A pdb=" N ASN f 675 " --> pdb=" O GLY f 672 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 672 through 675' Processing helix chain 'f' and resid 676 through 693 Processing helix chain 'f' and resid 695 through 710 Processing helix chain 'f' and resid 740 through 754 removed outlier: 3.883A pdb=" N ILE f 744 " --> pdb=" O LEU f 740 " (cutoff:3.500A) Processing helix chain 'f' and resid 755 through 757 No H-bonds generated for 'chain 'f' and resid 755 through 757' Processing helix chain 'f' and resid 761 through 798 removed outlier: 3.696A pdb=" N LEU f 774 " --> pdb=" O GLN f 770 " (cutoff:3.500A) Proline residue: f 776 - end of helix removed outlier: 3.630A pdb=" N SER f 780 " --> pdb=" O PRO f 776 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG f 798 " --> pdb=" O LYS f 794 " (cutoff:3.500A) Processing helix chain 'f' and resid 799 through 804 removed outlier: 3.868A pdb=" N SER f 802 " --> pdb=" O ASN f 799 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N LEU f 803 " --> pdb=" O THR f 800 " (cutoff:3.500A) Processing helix chain 'f' and resid 805 through 821 Processing helix chain 'f' and resid 828 through 866 removed outlier: 3.978A pdb=" N GLN f 834 " --> pdb=" O ASP f 830 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU f 854 " --> pdb=" O LEU f 850 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU f 865 " --> pdb=" O VAL f 861 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N THR f 866 " --> pdb=" O ARG f 862 " (cutoff:3.500A) Processing helix chain 'f' and resid 870 through 891 Processing helix chain 'f' and resid 895 through 914 Processing helix chain 'f' and resid 1013 through 1018 Processing helix chain 'f' and resid 1019 through 1025 removed outlier: 3.850A pdb=" N LEU f1023 " --> pdb=" O ARG f1020 " (cutoff:3.500A) Processing helix chain 'h' and resid 600 through 605 Processing helix chain 'h' and resid 609 through 621 Processing helix chain 'j' and resid 358 through 373 Processing helix chain 'j' and resid 427 through 439 removed outlier: 3.527A pdb=" N PHE j 432 " --> pdb=" O VAL j 428 " (cutoff:3.500A) Processing helix chain 'm' and resid 211 through 223 Processing helix chain 'm' and resid 228 through 233 removed outlier: 4.125A pdb=" N PHE m 232 " --> pdb=" O LYS m 228 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLY m 233 " --> pdb=" O VAL m 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 228 through 233' Processing helix chain 'm' and resid 234 through 237 Processing helix chain 'm' and resid 238 through 261 removed outlier: 3.544A pdb=" N VAL m 259 " --> pdb=" O GLU m 255 " (cutoff:3.500A) Processing helix chain 'm' and resid 270 through 293 Processing helix chain 'm' and resid 294 through 307 Processing helix chain 'm' and resid 309 through 319 removed outlier: 3.766A pdb=" N THR m 313 " --> pdb=" O ARG m 309 " (cutoff:3.500A) Processing helix chain 'm' and resid 321 through 337 Proline residue: m 334 - end of helix Processing helix chain 'm' and resid 340 through 346 removed outlier: 3.725A pdb=" N LEU m 344 " --> pdb=" O PRO m 340 " (cutoff:3.500A) Processing helix chain 'm' and resid 349 through 365 Processing helix chain 'm' and resid 366 through 369 Processing helix chain 'm' and resid 373 through 400 Processing helix chain 'm' and resid 405 through 441 Processing helix chain 'm' and resid 455 through 484 removed outlier: 4.513A pdb=" N LEU m 459 " --> pdb=" O ALA m 455 " (cutoff:3.500A) Processing helix chain 'm' and resid 514 through 533 removed outlier: 4.009A pdb=" N VAL m 533 " --> pdb=" O ASN m 529 " (cutoff:3.500A) Processing helix chain 'm' and resid 539 through 575 removed outlier: 4.312A pdb=" N LEU m 572 " --> pdb=" O LEU m 568 " (cutoff:3.500A) Processing helix chain 'm' and resid 577 through 588 removed outlier: 3.615A pdb=" N MET m 581 " --> pdb=" O ASN m 577 " (cutoff:3.500A) Processing helix chain 'm' and resid 589 through 593 Processing helix chain 'm' and resid 594 through 601 removed outlier: 3.542A pdb=" N ILE m 601 " --> pdb=" O ILE m 597 " (cutoff:3.500A) Processing helix chain 'm' and resid 602 through 625 removed outlier: 4.031A pdb=" N THR m 606 " --> pdb=" O ARG m 602 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN m 607 " --> pdb=" O GLU m 603 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL m 625 " --> pdb=" O ASP m 621 " (cutoff:3.500A) Processing helix chain 'm' and resid 630 through 639 removed outlier: 3.994A pdb=" N LYS m 634 " --> pdb=" O SER m 630 " (cutoff:3.500A) Processing helix chain 'm' and resid 642 through 670 Processing helix chain 'm' and resid 672 through 676 removed outlier: 3.572A pdb=" N ASN m 675 " --> pdb=" O GLY m 672 " (cutoff:3.500A) Processing helix chain 'm' and resid 678 through 693 removed outlier: 3.721A pdb=" N LEU m 682 " --> pdb=" O GLU m 678 " (cutoff:3.500A) Processing helix chain 'm' and resid 695 through 710 Processing helix chain 'm' and resid 741 through 756 removed outlier: 3.516A pdb=" N THR m 745 " --> pdb=" O PRO m 741 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TRP m 755 " --> pdb=" O ARG m 751 " (cutoff:3.500A) Processing helix chain 'm' and resid 761 through 798 Proline residue: m 776 - end of helix Processing helix chain 'm' and resid 799 through 802 Processing helix chain 'm' and resid 805 through 821 removed outlier: 4.401A pdb=" N ALA m 821 " --> pdb=" O ALA m 817 " (cutoff:3.500A) Processing helix chain 'm' and resid 828 through 849 removed outlier: 4.273A pdb=" N GLN m 834 " --> pdb=" O ASP m 830 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA m 837 " --> pdb=" O VAL m 833 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL m 847 " --> pdb=" O PHE m 843 " (cutoff:3.500A) Processing helix chain 'n' and resid 211 through 223 Processing helix chain 'n' and resid 232 through 237 Processing helix chain 'n' and resid 238 through 261 removed outlier: 3.581A pdb=" N VAL n 259 " --> pdb=" O GLU n 255 " (cutoff:3.500A) Processing helix chain 'n' and resid 270 through 293 Processing helix chain 'n' and resid 294 through 307 Processing helix chain 'n' and resid 309 through 319 removed outlier: 3.869A pdb=" N THR n 313 " --> pdb=" O ARG n 309 " (cutoff:3.500A) Processing helix chain 'n' and resid 321 through 332 Processing helix chain 'n' and resid 332 through 338 removed outlier: 4.165A pdb=" N ASP n 338 " --> pdb=" O PRO n 334 " (cutoff:3.500A) Processing helix chain 'n' and resid 340 through 347 removed outlier: 3.928A pdb=" N LEU n 344 " --> pdb=" O PRO n 340 " (cutoff:3.500A) Processing helix chain 'n' and resid 349 through 365 Processing helix chain 'n' and resid 366 through 368 No H-bonds generated for 'chain 'n' and resid 366 through 368' Processing helix chain 'n' and resid 373 through 399 removed outlier: 3.510A pdb=" N ARG n 399 " --> pdb=" O VAL n 395 " (cutoff:3.500A) Processing helix chain 'n' and resid 400 through 404 removed outlier: 3.686A pdb=" N VAL n 404 " --> pdb=" O LEU n 401 " (cutoff:3.500A) Processing helix chain 'n' and resid 405 through 440 removed outlier: 3.674A pdb=" N PHE n 409 " --> pdb=" O ALA n 405 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG n 440 " --> pdb=" O ASP n 436 " (cutoff:3.500A) Processing helix chain 'n' and resid 456 through 485 removed outlier: 4.554A pdb=" N VAL n 479 " --> pdb=" O GLN n 475 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL n 481 " --> pdb=" O ARG n 477 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ARG n 482 " --> pdb=" O ALA n 478 " (cutoff:3.500A) Processing helix chain 'n' and resid 513 through 533 removed outlier: 4.044A pdb=" N ALA n 517 " --> pdb=" O ASP n 513 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL n 533 " --> pdb=" O ASN n 529 " (cutoff:3.500A) Processing helix chain 'n' and resid 539 through 575 removed outlier: 3.560A pdb=" N LEU n 572 " --> pdb=" O LEU n 568 " (cutoff:3.500A) Processing helix chain 'n' and resid 577 through 587 removed outlier: 3.593A pdb=" N MET n 581 " --> pdb=" O ASN n 577 " (cutoff:3.500A) Processing helix chain 'n' and resid 589 through 593 Processing helix chain 'n' and resid 597 through 617 removed outlier: 4.174A pdb=" N THR n 606 " --> pdb=" O ARG n 602 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLN n 607 " --> pdb=" O GLU n 603 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLN n 610 " --> pdb=" O THR n 606 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ARG n 611 " --> pdb=" O GLN n 607 " (cutoff:3.500A) Processing helix chain 'n' and resid 659 through 670 removed outlier: 3.808A pdb=" N VAL n 668 " --> pdb=" O ARG n 664 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU n 669 " --> pdb=" O VAL n 665 " (cutoff:3.500A) Processing helix chain 'n' and resid 672 through 675 Processing helix chain 'n' and resid 676 through 681 removed outlier: 4.438A pdb=" N LYS n 681 " --> pdb=" O VAL n 677 " (cutoff:3.500A) Processing helix chain 'o' and resid 600 through 605 Processing helix chain 'o' and resid 609 through 621 Processing helix chain 'r' and resid 427 through 439 Processing helix chain 'x' and resid 101 through 192 removed outlier: 3.677A pdb=" N ARG x 192 " --> pdb=" O GLN x 188 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 36 removed outlier: 3.850A pdb=" N ASN A 16 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A 137 " --> pdb=" O VAL A 358 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 42 Processing sheet with id=AA3, first strand: chain 'A' and resid 45 through 46 removed outlier: 3.760A pdb=" N VAL A 45 " --> pdb=" O ALA C 175 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 45 through 46 removed outlier: 3.760A pdb=" N VAL A 45 " --> pdb=" O ALA C 175 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ILE C 298 " --> pdb=" O SER C 331 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AA6, first strand: chain 'A' and resid 174 through 175 removed outlier: 3.535A pdb=" N PHE A 174 " --> pdb=" O TYR A 171 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 174 through 175 removed outlier: 3.535A pdb=" N PHE A 174 " --> pdb=" O TYR A 171 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ILE A 298 " --> pdb=" O SER A 331 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 240 through 242 Processing sheet with id=AA9, first strand: chain 'B' and resid 33 through 36 removed outlier: 7.040A pdb=" N VAL B 12 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N THR B 111 " --> pdb=" O VAL B 12 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N ILE B 14 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N SER B 140 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LEU B 110 " --> pdb=" O SER B 140 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 39 through 42 Processing sheet with id=AB2, first strand: chain 'B' and resid 45 through 46 Processing sheet with id=AB3, first strand: chain 'B' and resid 45 through 46 removed outlier: 6.229A pdb=" N ILE D 298 " --> pdb=" O SER D 331 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 75 through 76 Processing sheet with id=AB5, first strand: chain 'B' and resid 136 through 137 Processing sheet with id=AB6, first strand: chain 'B' and resid 174 through 175 Processing sheet with id=AB7, first strand: chain 'B' and resid 174 through 175 removed outlier: 6.326A pdb=" N VAL B 156 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N SER B 301 " --> pdb=" O VAL B 156 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU B 158 " --> pdb=" O SER B 301 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE B 298 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 240 through 242 Processing sheet with id=AB9, first strand: chain 'C' and resid 33 through 36 removed outlier: 4.663A pdb=" N ASN C 16 " --> pdb=" O THR C 111 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL C 108 " --> pdb=" O PHE C 138 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N SER C 140 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU C 110 " --> pdb=" O SER C 140 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 39 through 42 Processing sheet with id=AC2, first strand: chain 'C' and resid 45 through 46 Processing sheet with id=AC3, first strand: chain 'C' and resid 45 through 46 removed outlier: 6.084A pdb=" N ILE E 298 " --> pdb=" O SER E 331 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 75 through 76 Processing sheet with id=AC5, first strand: chain 'C' and resid 240 through 242 Processing sheet with id=AC6, first strand: chain 'D' and resid 33 through 36 removed outlier: 3.641A pdb=" N THR D 111 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ASN D 16 " --> pdb=" O THR D 111 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 39 through 42 Processing sheet with id=AC8, first strand: chain 'D' and resid 45 through 46 removed outlier: 3.572A pdb=" N VAL D 45 " --> pdb=" O ALA F 175 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 45 through 46 removed outlier: 3.572A pdb=" N VAL D 45 " --> pdb=" O ALA F 175 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ILE F 298 " --> pdb=" O SER F 331 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 75 through 76 Processing sheet with id=AD2, first strand: chain 'D' and resid 240 through 242 Processing sheet with id=AD3, first strand: chain 'E' and resid 33 through 36 removed outlier: 4.795A pdb=" N ASN E 16 " --> pdb=" O THR E 111 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 39 through 42 Processing sheet with id=AD5, first strand: chain 'E' and resid 75 through 76 Processing sheet with id=AD6, first strand: chain 'E' and resid 240 through 242 Processing sheet with id=AD7, first strand: chain 'F' and resid 33 through 36 removed outlier: 7.085A pdb=" N VAL F 12 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N THR F 111 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N ILE F 14 " --> pdb=" O THR F 111 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 75 through 76 Processing sheet with id=AD9, first strand: chain 'K' and resid 64 through 65 Processing sheet with id=AE1, first strand: chain 'K' and resid 86 through 89 removed outlier: 4.333A pdb=" N LYS K 97 " --> pdb=" O ASP K 107 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N ASP K 107 " --> pdb=" O LYS K 97 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ASP K 99 " --> pdb=" O ALA K 105 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ALA K 105 " --> pdb=" O ASP K 99 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 140 through 148 removed outlier: 4.035A pdb=" N GLN K 187 " --> pdb=" O THR K 180 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 48 through 52 removed outlier: 4.167A pdb=" N LYS L 48 " --> pdb=" O LEU L 61 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'f' and resid 718 through 723 Processing sheet with id=AE5, first strand: chain 'h' and resid 265 through 271 removed outlier: 7.010A pdb=" N ILE h 596 " --> pdb=" O ASN h 268 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N GLN h 270 " --> pdb=" O ILE h 594 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ILE h 594 " --> pdb=" O GLN h 270 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'h' and resid 282 through 287 removed outlier: 4.660A pdb=" N CYS h 284 " --> pdb=" O SER h 298 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'h' and resid 335 through 340 Processing sheet with id=AE8, first strand: chain 'h' and resid 384 through 392 removed outlier: 3.768A pdb=" N CYS h 386 " --> pdb=" O ILE h 401 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LYS h 406 " --> pdb=" O SER h 402 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'h' and resid 434 through 438 removed outlier: 6.696A pdb=" N GLY h 450 " --> pdb=" O THR h 435 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N MET h 437 " --> pdb=" O VAL h 448 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL h 448 " --> pdb=" O MET h 437 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'h' and resid 479 through 484 Processing sheet with id=AF2, first strand: chain 'h' and resid 527 through 532 removed outlier: 4.316A pdb=" N ARG h 548 " --> pdb=" O ASP h 544 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'm' and resid 718 through 719 removed outlier: 3.600A pdb=" N LYS m 736 " --> pdb=" O THR m 719 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'o' and resid 266 through 271 removed outlier: 7.052A pdb=" N ILE o 596 " --> pdb=" O ASN o 268 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N GLN o 270 " --> pdb=" O ILE o 594 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ILE o 594 " --> pdb=" O GLN o 270 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'o' and resid 282 through 287 removed outlier: 3.947A pdb=" N CYS o 284 " --> pdb=" O SER o 298 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'o' and resid 335 through 340 removed outlier: 3.848A pdb=" N GLN o 371 " --> pdb=" O LEU o 359 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'o' and resid 386 through 391 removed outlier: 3.691A pdb=" N CYS o 386 " --> pdb=" O ILE o 401 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'o' and resid 434 through 438 removed outlier: 6.480A pdb=" N GLY o 450 " --> pdb=" O THR o 435 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N MET o 437 " --> pdb=" O VAL o 448 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL o 448 " --> pdb=" O MET o 437 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N CYS o 460 " --> pdb=" O ILE o 468 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N ILE o 468 " --> pdb=" O CYS o 460 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'o' and resid 479 through 484 removed outlier: 6.566A pdb=" N SER o 500 " --> pdb=" O THR o 480 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ILE o 482 " --> pdb=" O VAL o 498 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL o 498 " --> pdb=" O ILE o 482 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N CYS o 484 " --> pdb=" O LEU o 496 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N LEU o 496 " --> pdb=" O CYS o 484 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'o' and resid 527 through 532 removed outlier: 3.652A pdb=" N ASP o 529 " --> pdb=" O VAL o 543 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ARG o 548 " --> pdb=" O ASP o 544 " (cutoff:3.500A) 2521 hydrogen bonds defined for protein. 7056 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.19 Time building geometry restraints manager: 4.42 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: 14355 1.34 - 1.46: 9207 1.46 - 1.58: 20477 1.58 - 1.70: 21 1.70 - 1.82: 269 Bond restraints: 44329 Sorted by residual: bond pdb=" N VAL D 164 " pdb=" CA VAL D 164 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.19e-02 7.06e+03 7.69e+00 bond pdb=" N ASP h 420 " pdb=" CA ASP h 420 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.27e-02 6.20e+03 7.61e+00 bond pdb=" N VAL B 164 " pdb=" CA VAL B 164 " ideal model delta sigma weight residual 1.459 1.491 -0.033 1.19e-02 7.06e+03 7.47e+00 bond pdb=" N VAL K 132 " pdb=" CA VAL K 132 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.21e-02 6.83e+03 7.41e+00 bond pdb=" N VAL j 428 " pdb=" CA VAL j 428 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.19e-02 7.06e+03 7.32e+00 ... (remaining 44324 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 58362 1.96 - 3.92: 1162 3.92 - 5.88: 329 5.88 - 7.84: 29 7.84 - 9.79: 5 Bond angle restraints: 59887 Sorted by residual: angle pdb=" N ASN K 84 " pdb=" CA ASN K 84 " pdb=" C ASN K 84 " ideal model delta sigma weight residual 112.25 105.81 6.44 1.36e+00 5.41e-01 2.24e+01 angle pdb=" CA GLY K 202 " pdb=" C GLY K 202 " pdb=" O GLY K 202 " ideal model delta sigma weight residual 121.04 117.49 3.55 7.90e-01 1.60e+00 2.02e+01 angle pdb=" CA ASP K 201 " pdb=" CB ASP K 201 " pdb=" CG ASP K 201 " ideal model delta sigma weight residual 112.60 116.85 -4.25 1.00e+00 1.00e+00 1.80e+01 angle pdb=" CA ASN K 84 " pdb=" CB ASN K 84 " pdb=" CG ASN K 84 " ideal model delta sigma weight residual 112.60 116.59 -3.99 1.00e+00 1.00e+00 1.59e+01 angle pdb=" C ASP K 201 " pdb=" CA ASP K 201 " pdb=" CB ASP K 201 " ideal model delta sigma weight residual 111.80 117.62 -5.82 1.46e+00 4.69e-01 1.59e+01 ... (remaining 59882 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.11: 26071 35.11 - 70.22: 663 70.22 - 105.33: 70 105.33 - 140.44: 6 140.44 - 175.56: 10 Dihedral angle restraints: 26820 sinusoidal: 11224 harmonic: 15596 Sorted by residual: dihedral pdb=" C5' ADP F 800 " pdb=" O5' ADP F 800 " pdb=" PA ADP F 800 " pdb=" O2A ADP F 800 " ideal model delta sinusoidal sigma weight residual -60.00 115.56 -175.56 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C5' ADP E 800 " pdb=" O5' ADP E 800 " pdb=" PA ADP E 800 " pdb=" O2A ADP E 800 " ideal model delta sinusoidal sigma weight residual 300.00 125.75 174.25 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O2A ADP E 800 " pdb=" O3A ADP E 800 " pdb=" PA ADP E 800 " pdb=" PB ADP E 800 " ideal model delta sinusoidal sigma weight residual -60.00 113.26 -173.26 1 2.00e+01 2.50e-03 4.78e+01 ... (remaining 26817 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 6036 0.083 - 0.165: 484 0.165 - 0.248: 2 0.248 - 0.330: 0 0.330 - 0.413: 1 Chirality restraints: 6523 Sorted by residual: chirality pdb=" CA ASP K 201 " pdb=" N ASP K 201 " pdb=" C ASP K 201 " pdb=" CB ASP K 201 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.26e+00 chirality pdb=" CA ASP x 182 " pdb=" N ASP x 182 " pdb=" C ASP x 182 " pdb=" CB ASP x 182 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA GLN h 419 " pdb=" N GLN h 419 " pdb=" C GLN h 419 " pdb=" CB GLN h 419 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.46e-01 ... (remaining 6520 not shown) Planarity restraints: 7735 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 369 " -0.216 9.50e-02 1.11e+02 9.71e-02 6.60e+00 pdb=" NE ARG F 369 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG F 369 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG F 369 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG F 369 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG n 594 " 0.042 5.00e-02 4.00e+02 6.19e-02 6.13e+00 pdb=" N PRO n 595 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO n 595 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO n 595 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE K 140 " -0.015 2.00e-02 2.50e+03 1.80e-02 5.66e+00 pdb=" CG PHE K 140 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE K 140 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE K 140 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE K 140 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE K 140 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE K 140 " -0.000 2.00e-02 2.50e+03 ... (remaining 7732 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 200 2.55 - 3.14: 33110 3.14 - 3.72: 68979 3.72 - 4.31: 94633 4.31 - 4.90: 160108 Nonbonded interactions: 357030 Sorted by model distance: nonbonded pdb=" O3B ADP A 800 " pdb="MG MG A 801 " model vdw 1.962 2.170 nonbonded pdb=" O1B ADP F 800 " pdb="MG MG F 801 " model vdw 2.024 2.170 nonbonded pdb=" O2B ADP B 800 " pdb="MG MG B 801 " model vdw 2.035 2.170 nonbonded pdb=" O2B ADP E 800 " pdb="MG MG E 801 " model vdw 2.061 2.170 nonbonded pdb=" OE1 GLN A 142 " pdb="MG MG A 801 " model vdw 2.069 2.170 ... (remaining 357025 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' selection = (chain 'B' and (resid 7 through 231 or (resid 232 and (name N or name CA or name \ C or name O or name CB )) or resid 233 through 234 or (resid 235 and (name N or \ name CA or name C or name O or name CB )) or resid 236 or (resid 237 and (name \ N or name CA or name C or name O or name CB )) or resid 238 through 801)) selection = (chain 'C' and (resid 7 through 231 or (resid 232 and (name N or name CA or name \ C or name O or name CB )) or resid 233 through 234 or (resid 235 and (name N or \ name CA or name C or name O or name CB )) or resid 236 or (resid 237 and (name \ N or name CA or name C or name O or name CB )) or resid 238 through 801)) selection = (chain 'D' and (resid 7 through 231 or (resid 232 and (name N or name CA or name \ C or name O or name CB )) or resid 233 through 234 or (resid 235 and (name N or \ name CA or name C or name O or name CB )) or resid 236 or (resid 237 and (name \ N or name CA or name C or name O or name CB )) or resid 238 through 801)) selection = chain 'E' } ncs_group { reference = chain 'X' selection = chain 'x' } ncs_group { reference = chain 'h' selection = chain 'o' } 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: 43.160 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: 0.050 Extract box with map and model: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 39.400 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 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 : 0.004 0.096 44329 Z= 0.194 Angle : 0.729 9.794 59887 Z= 0.396 Chirality : 0.043 0.413 6523 Planarity : 0.005 0.097 7735 Dihedral : 16.544 175.556 16736 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.13 % Allowed : 7.38 % Favored : 92.49 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % 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: 0.65 (0.11), residues: 5316 helix: 1.26 (0.10), residues: 2703 sheet: -0.86 (0.17), residues: 830 loop : -0.02 (0.15), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D 373 TYR 0.021 0.001 TYR C 38 PHE 0.042 0.002 PHE K 140 TRP 0.022 0.002 TRP E 357 HIS 0.010 0.001 HIS m 769 Details of bonding type rmsd covalent geometry : bond 0.00419 (44329) covalent geometry : angle 0.72896 (59887) hydrogen bonds : bond 0.13027 ( 2504) hydrogen bonds : angle 5.41037 ( 7056) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10632 Ramachandran restraints generated. 5316 Oldfield, 0 Emsley, 5316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10632 Ramachandran restraints generated. 5316 Oldfield, 0 Emsley, 5316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 4717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 404 time to evaluate : 1.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 ASP cc_start: 0.8219 (t0) cc_final: 0.7895 (t0) REVERT: D 162 ASP cc_start: 0.8997 (t70) cc_final: 0.8704 (t70) REVERT: E 284 GLN cc_start: 0.8278 (mt0) cc_final: 0.7943 (mm-40) REVERT: n 306 HIS cc_start: 0.7698 (t-90) cc_final: 0.7397 (t70) REVERT: o 336 MET cc_start: 0.7130 (mmm) cc_final: 0.6616 (mmt) outliers start: 6 outliers final: 3 residues processed: 407 average time/residue: 0.2831 time to fit residues: 186.0537 Evaluate side-chains 357 residues out of total 4717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 354 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain K residue 238 GLU Chi-restraints excluded: chain x residue 140 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 530 random chunks: chunk 394 optimal weight: 0.9990 chunk 430 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 265 optimal weight: 0.6980 chunk 523 optimal weight: 1.9990 chunk 497 optimal weight: 0.6980 chunk 414 optimal weight: 2.9990 chunk 310 optimal weight: 0.9980 chunk 488 optimal weight: 0.9990 chunk 366 optimal weight: 0.0770 chunk 223 optimal weight: 0.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 HIS A 120 ASN B 133 ASN B 166 HIS C 227 ASN D 276 HIS ** X 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 834 GLN m 311 HIS m 363 HIS m 403 HIS m 769 HIS o 417 HIS x 187 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.143100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.094709 restraints weight = 73237.080| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.03 r_work: 0.3046 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 44329 Z= 0.245 Angle : 0.599 8.512 59887 Z= 0.308 Chirality : 0.045 0.163 6523 Planarity : 0.004 0.047 7735 Dihedral : 8.447 164.738 5962 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.32 % Allowed : 8.92 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.85 (0.12), residues: 5316 helix: 1.43 (0.10), residues: 2703 sheet: -0.85 (0.17), residues: 860 loop : 0.13 (0.15), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 329 TYR 0.027 0.002 TYR C 38 PHE 0.022 0.002 PHE h 340 TRP 0.021 0.002 TRP C 357 HIS 0.012 0.001 HIS n 473 Details of bonding type rmsd covalent geometry : bond 0.00583 (44329) covalent geometry : angle 0.59943 (59887) hydrogen bonds : bond 0.04376 ( 2504) hydrogen bonds : angle 4.51571 ( 7056) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10632 Ramachandran restraints generated. 5316 Oldfield, 0 Emsley, 5316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10632 Ramachandran restraints generated. 5316 Oldfield, 0 Emsley, 5316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 4717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 378 time to evaluate : 1.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ASN cc_start: 0.7974 (OUTLIER) cc_final: 0.7617 (m-40) REVERT: E 284 GLN cc_start: 0.8713 (mt0) cc_final: 0.8291 (mm-40) REVERT: K 140 PHE cc_start: 0.7610 (m-80) cc_final: 0.7351 (m-80) REVERT: X 140 GLU cc_start: 0.7893 (pt0) cc_final: 0.7304 (tp30) REVERT: X 166 TRP cc_start: 0.7165 (m100) cc_final: 0.6821 (m100) REVERT: f 448 MET cc_start: 0.6990 (tpt) cc_final: 0.6671 (tpt) REVERT: f 635 MET cc_start: 0.6873 (mmm) cc_final: 0.6438 (mmp) REVERT: f 671 LYS cc_start: 0.6686 (tptm) cc_final: 0.6218 (tptp) REVERT: m 253 ILE cc_start: 0.9026 (OUTLIER) cc_final: 0.8573 (mt) REVERT: m 448 MET cc_start: 0.5951 (mtm) cc_final: 0.5613 (ttt) REVERT: m 521 GLU cc_start: 0.8227 (pp20) cc_final: 0.7964 (pp20) REVERT: m 604 TYR cc_start: 0.7284 (m-80) cc_final: 0.6926 (m-80) REVERT: m 662 MET cc_start: 0.8736 (mmp) cc_final: 0.8204 (mmp) REVERT: n 448 MET cc_start: 0.2951 (mmm) cc_final: 0.2661 (mmm) REVERT: n 565 THR cc_start: 0.7354 (m) cc_final: 0.7104 (p) REVERT: o 336 MET cc_start: 0.8586 (mmm) cc_final: 0.8119 (mmp) outliers start: 62 outliers final: 42 residues processed: 421 average time/residue: 0.2716 time to fit residues: 186.7277 Evaluate side-chains 391 residues out of total 4717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 347 time to evaluate : 1.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 206 HIS Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 34 CYS Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 276 SER Chi-restraints excluded: chain K residue 283 MET Chi-restraints excluded: chain L residue 13 MET Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 170 THR Chi-restraints excluded: chain L residue 176 TRP Chi-restraints excluded: chain X residue 160 GLU Chi-restraints excluded: chain X residue 187 GLN Chi-restraints excluded: chain h residue 339 THR Chi-restraints excluded: chain h residue 386 CYS Chi-restraints excluded: chain m residue 253 ILE Chi-restraints excluded: chain m residue 327 GLU Chi-restraints excluded: chain m residue 530 VAL Chi-restraints excluded: chain m residue 614 ASP Chi-restraints excluded: chain m residue 665 VAL Chi-restraints excluded: chain n residue 483 VAL Chi-restraints excluded: chain o residue 328 VAL Chi-restraints excluded: chain o residue 560 VAL Chi-restraints excluded: chain o residue 576 VAL Chi-restraints excluded: chain x residue 140 GLU Chi-restraints excluded: chain x residue 175 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 530 random chunks: chunk 306 optimal weight: 0.5980 chunk 303 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 207 optimal weight: 0.4980 chunk 49 optimal weight: 0.4980 chunk 199 optimal weight: 0.2980 chunk 288 optimal weight: 0.9980 chunk 150 optimal weight: 0.0370 chunk 334 optimal weight: 1.9990 chunk 119 optimal weight: 0.1980 chunk 407 optimal weight: 0.6980 overall best weight: 0.3058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 ASN B 133 ASN E 284 GLN ** X 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 769 HIS o 523 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.145145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.098283 restraints weight = 73853.517| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.30 r_work: 0.3049 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 44329 Z= 0.138 Angle : 0.518 7.589 59887 Z= 0.264 Chirality : 0.041 0.140 6523 Planarity : 0.004 0.042 7735 Dihedral : 8.078 164.565 5959 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.05 % Allowed : 10.44 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.09 (0.12), residues: 5316 helix: 1.68 (0.10), residues: 2695 sheet: -0.76 (0.17), residues: 851 loop : 0.17 (0.15), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 373 TYR 0.018 0.001 TYR n 527 PHE 0.018 0.001 PHE m 841 TRP 0.018 0.002 TRP C 357 HIS 0.008 0.001 HIS n 473 Details of bonding type rmsd covalent geometry : bond 0.00318 (44329) covalent geometry : angle 0.51795 (59887) hydrogen bonds : bond 0.03758 ( 2504) hydrogen bonds : angle 4.27947 ( 7056) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10632 Ramachandran restraints generated. 5316 Oldfield, 0 Emsley, 5316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10632 Ramachandran restraints generated. 5316 Oldfield, 0 Emsley, 5316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 4717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 389 time to evaluate : 1.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 GLU cc_start: 0.8363 (tp30) cc_final: 0.8066 (tp30) REVERT: E 284 GLN cc_start: 0.8718 (mt0) cc_final: 0.8334 (mm-40) REVERT: K 181 ILE cc_start: 0.6752 (OUTLIER) cc_final: 0.6262 (tp) REVERT: X 140 GLU cc_start: 0.7879 (pt0) cc_final: 0.7235 (tp30) REVERT: X 166 TRP cc_start: 0.7129 (m100) cc_final: 0.6781 (m100) REVERT: f 448 MET cc_start: 0.6952 (tpt) cc_final: 0.6647 (tpt) REVERT: f 671 LYS cc_start: 0.6684 (tptm) cc_final: 0.6168 (tptp) REVERT: h 327 TYR cc_start: 0.6851 (m-10) cc_final: 0.6583 (m-10) REVERT: h 353 TYR cc_start: 0.8045 (t80) cc_final: 0.7740 (t80) REVERT: j 357 GLU cc_start: 0.6402 (mp0) cc_final: 0.5553 (tm-30) REVERT: m 253 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8529 (mt) REVERT: m 448 MET cc_start: 0.5948 (mtm) cc_final: 0.5621 (ttt) REVERT: m 521 GLU cc_start: 0.8303 (pp20) cc_final: 0.8044 (pp20) REVERT: n 565 THR cc_start: 0.7394 (m) cc_final: 0.7148 (p) REVERT: o 336 MET cc_start: 0.8502 (mmm) cc_final: 0.8081 (mmp) outliers start: 49 outliers final: 34 residues processed: 417 average time/residue: 0.2860 time to fit residues: 192.8287 Evaluate side-chains 389 residues out of total 4717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 353 time to evaluate : 2.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 206 HIS Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 222 CYS Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 181 ILE Chi-restraints excluded: chain K residue 201 ASP Chi-restraints excluded: chain K residue 264 VAL Chi-restraints excluded: chain K residue 283 MET Chi-restraints excluded: chain L residue 13 MET Chi-restraints excluded: chain L residue 170 THR Chi-restraints excluded: chain X residue 160 GLU Chi-restraints excluded: chain X residue 187 GLN Chi-restraints excluded: chain h residue 368 THR Chi-restraints excluded: chain h residue 386 CYS Chi-restraints excluded: chain m residue 253 ILE Chi-restraints excluded: chain m residue 327 GLU Chi-restraints excluded: chain m residue 466 MET Chi-restraints excluded: chain m residue 614 ASP Chi-restraints excluded: chain m residue 665 VAL Chi-restraints excluded: chain n residue 329 VAL Chi-restraints excluded: chain n residue 483 VAL Chi-restraints excluded: chain o residue 281 VAL Chi-restraints excluded: chain o residue 560 VAL Chi-restraints excluded: chain o residue 576 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 530 random chunks: chunk 115 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 334 optimal weight: 1.9990 chunk 453 optimal weight: 0.9980 chunk 151 optimal weight: 0.9990 chunk 418 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 121 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 455 optimal weight: 0.9990 chunk 265 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 116 ASN F 276 HIS ** K 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 529 ASN ** f 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 769 HIS n 431 GLN n 596 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.141581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.093026 restraints weight = 73254.899| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.06 r_work: 0.3014 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.104 44329 Z= 0.268 Angle : 0.615 8.041 59887 Z= 0.314 Chirality : 0.045 0.172 6523 Planarity : 0.005 0.058 7735 Dihedral : 7.994 160.257 5956 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.18 % Allowed : 11.31 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.87 (0.12), residues: 5316 helix: 1.48 (0.10), residues: 2694 sheet: -0.79 (0.17), residues: 841 loop : 0.04 (0.15), residues: 1781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 264 TYR 0.026 0.002 TYR n 527 PHE 0.023 0.002 PHE K 168 TRP 0.023 0.002 TRP C 357 HIS 0.009 0.001 HIS n 473 Details of bonding type rmsd covalent geometry : bond 0.00638 (44329) covalent geometry : angle 0.61534 (59887) hydrogen bonds : bond 0.04232 ( 2504) hydrogen bonds : angle 4.42398 ( 7056) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10632 Ramachandran restraints generated. 5316 Oldfield, 0 Emsley, 5316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10632 Ramachandran restraints generated. 5316 Oldfield, 0 Emsley, 5316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 4717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 377 time to evaluate : 1.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 MET cc_start: 0.9017 (mmm) cc_final: 0.8736 (mmt) REVERT: E 284 GLN cc_start: 0.8807 (mt0) cc_final: 0.8389 (mm-40) REVERT: E 364 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7273 (pt0) REVERT: K 129 ARG cc_start: 0.7937 (mmt180) cc_final: 0.7465 (mtm-85) REVERT: K 181 ILE cc_start: 0.6580 (OUTLIER) cc_final: 0.6219 (tp) REVERT: L 4 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7602 (pm20) REVERT: L 163 ARG cc_start: 0.8049 (ttm-80) cc_final: 0.7683 (ttt90) REVERT: X 140 GLU cc_start: 0.7893 (pt0) cc_final: 0.7337 (tp30) REVERT: f 671 LYS cc_start: 0.6366 (tptm) cc_final: 0.5984 (tptp) REVERT: f 1019 TYR cc_start: 0.6775 (m-80) cc_final: 0.6244 (m-80) REVERT: h 327 TYR cc_start: 0.7031 (m-10) cc_final: 0.6819 (m-10) REVERT: h 471 MET cc_start: 0.7147 (OUTLIER) cc_final: 0.6270 (tpp) REVERT: m 253 ILE cc_start: 0.9017 (OUTLIER) cc_final: 0.8687 (mt) REVERT: n 430 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7557 (tt) REVERT: n 462 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7992 (ttm170) REVERT: n 565 THR cc_start: 0.7123 (m) cc_final: 0.6787 (p) REVERT: o 336 MET cc_start: 0.8474 (mmm) cc_final: 0.8044 (mmp) outliers start: 102 outliers final: 64 residues processed: 454 average time/residue: 0.2814 time to fit residues: 207.2252 Evaluate side-chains 429 residues out of total 4717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 358 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 206 HIS Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 222 CYS Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 34 CYS Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 222 CYS Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 34 CYS Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 181 ILE Chi-restraints excluded: chain K residue 191 VAL Chi-restraints excluded: chain K residue 201 ASP Chi-restraints excluded: chain K residue 264 VAL Chi-restraints excluded: chain K residue 276 SER Chi-restraints excluded: chain K residue 277 TYR Chi-restraints excluded: chain K residue 283 MET Chi-restraints excluded: chain L residue 4 GLN Chi-restraints excluded: chain L residue 13 MET Chi-restraints excluded: chain L residue 16 LEU Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 124 LEU Chi-restraints excluded: chain L residue 170 THR Chi-restraints excluded: chain L residue 176 TRP Chi-restraints excluded: chain X residue 160 GLU Chi-restraints excluded: chain X residue 187 GLN Chi-restraints excluded: chain f residue 344 LEU Chi-restraints excluded: chain f residue 658 LEU Chi-restraints excluded: chain h residue 339 THR Chi-restraints excluded: chain h residue 368 THR Chi-restraints excluded: chain h residue 386 CYS Chi-restraints excluded: chain h residue 471 MET Chi-restraints excluded: chain h residue 530 VAL Chi-restraints excluded: chain h residue 579 THR Chi-restraints excluded: chain m residue 253 ILE Chi-restraints excluded: chain m residue 327 GLU Chi-restraints excluded: chain m residue 404 VAL Chi-restraints excluded: chain m residue 466 MET Chi-restraints excluded: chain m residue 530 VAL Chi-restraints excluded: chain m residue 614 ASP Chi-restraints excluded: chain m residue 665 VAL Chi-restraints excluded: chain n residue 329 VAL Chi-restraints excluded: chain n residue 339 PHE Chi-restraints excluded: chain n residue 430 LEU Chi-restraints excluded: chain n residue 462 ARG Chi-restraints excluded: chain n residue 483 VAL Chi-restraints excluded: chain n residue 609 ILE Chi-restraints excluded: chain o residue 281 VAL Chi-restraints excluded: chain o residue 328 VAL Chi-restraints excluded: chain o residue 435 THR Chi-restraints excluded: chain o residue 560 VAL Chi-restraints excluded: chain o residue 562 THR Chi-restraints excluded: chain o residue 576 VAL Chi-restraints excluded: chain x residue 140 GLU Chi-restraints excluded: chain x residue 175 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 530 random chunks: chunk 506 optimal weight: 0.6980 chunk 312 optimal weight: 1.9990 chunk 265 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 126 optimal weight: 0.1980 chunk 438 optimal weight: 1.9990 chunk 116 optimal weight: 0.1980 chunk 368 optimal weight: 4.9990 chunk 92 optimal weight: 0.5980 chunk 377 optimal weight: 2.9990 chunk 426 optimal weight: 0.9990 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 227 ASN ** X 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 571 GLN m 769 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.143143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.095923 restraints weight = 73080.006| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.11 r_work: 0.3039 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 44329 Z= 0.205 Angle : 0.565 7.920 59887 Z= 0.287 Chirality : 0.043 0.175 6523 Planarity : 0.004 0.054 7735 Dihedral : 7.825 159.134 5956 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.26 % Allowed : 12.70 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.92 (0.12), residues: 5316 helix: 1.56 (0.10), residues: 2695 sheet: -0.77 (0.17), residues: 834 loop : 0.01 (0.15), residues: 1787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 373 TYR 0.024 0.002 TYR n 527 PHE 0.018 0.002 PHE m 841 TRP 0.019 0.002 TRP C 357 HIS 0.008 0.001 HIS n 473 Details of bonding type rmsd covalent geometry : bond 0.00483 (44329) covalent geometry : angle 0.56525 (59887) hydrogen bonds : bond 0.03931 ( 2504) hydrogen bonds : angle 4.34723 ( 7056) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10632 Ramachandran restraints generated. 5316 Oldfield, 0 Emsley, 5316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10632 Ramachandran restraints generated. 5316 Oldfield, 0 Emsley, 5316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 4717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 374 time to evaluate : 1.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 162 ASP cc_start: 0.8643 (t70) cc_final: 0.8297 (t0) REVERT: E 284 GLN cc_start: 0.8770 (mt0) cc_final: 0.8338 (mm-40) REVERT: E 364 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7176 (pt0) REVERT: K 59 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.8104 (tmm) REVERT: K 129 ARG cc_start: 0.7805 (mmt180) cc_final: 0.7413 (mtm-85) REVERT: L 4 GLN cc_start: 0.8095 (OUTLIER) cc_final: 0.7598 (pm20) REVERT: L 163 ARG cc_start: 0.8006 (ttm-80) cc_final: 0.7645 (ttt90) REVERT: X 140 GLU cc_start: 0.7830 (pt0) cc_final: 0.7269 (tp30) REVERT: f 528 GLU cc_start: 0.5278 (mm-30) cc_final: 0.4647 (mt-10) REVERT: f 662 MET cc_start: 0.4636 (OUTLIER) cc_final: 0.4349 (mtt) REVERT: f 671 LYS cc_start: 0.6247 (tptm) cc_final: 0.5862 (tptp) REVERT: f 1019 TYR cc_start: 0.6421 (m-80) cc_final: 0.5998 (m-80) REVERT: h 353 TYR cc_start: 0.8254 (t80) cc_final: 0.8046 (t80) REVERT: h 422 MET cc_start: 0.6982 (pmm) cc_final: 0.6694 (pmm) REVERT: h 471 MET cc_start: 0.7009 (OUTLIER) cc_final: 0.5786 (tpp) REVERT: m 253 ILE cc_start: 0.8989 (OUTLIER) cc_final: 0.8517 (mt) REVERT: m 604 TYR cc_start: 0.7538 (m-80) cc_final: 0.6800 (m-80) REVERT: n 430 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7597 (tt) REVERT: n 462 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7908 (ttm170) REVERT: n 525 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7902 (mt) REVERT: n 565 THR cc_start: 0.7172 (m) cc_final: 0.6811 (p) REVERT: o 336 MET cc_start: 0.8427 (mmm) cc_final: 0.7964 (mmp) REVERT: x 179 GLN cc_start: 0.7887 (pp30) cc_final: 0.7657 (pp30) outliers start: 106 outliers final: 74 residues processed: 453 average time/residue: 0.2759 time to fit residues: 204.0934 Evaluate side-chains 444 residues out of total 4717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 361 time to evaluate : 1.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 222 CYS Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 206 HIS Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain D residue 112 GLU Chi-restraints excluded: chain D residue 222 CYS Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 34 CYS Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 222 CYS Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 59 MET Chi-restraints excluded: chain K residue 191 VAL Chi-restraints excluded: chain K residue 217 THR Chi-restraints excluded: chain K residue 264 VAL Chi-restraints excluded: chain K residue 276 SER Chi-restraints excluded: chain K residue 277 TYR Chi-restraints excluded: chain K residue 283 MET Chi-restraints excluded: chain L residue 4 GLN Chi-restraints excluded: chain L residue 13 MET Chi-restraints excluded: chain L residue 16 LEU Chi-restraints excluded: chain L residue 124 LEU Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 170 THR Chi-restraints excluded: chain L residue 176 TRP Chi-restraints excluded: chain X residue 106 ILE Chi-restraints excluded: chain X residue 160 GLU Chi-restraints excluded: chain X residue 187 GLN Chi-restraints excluded: chain f residue 344 LEU Chi-restraints excluded: chain f residue 658 LEU Chi-restraints excluded: chain f residue 662 MET Chi-restraints excluded: chain h residue 336 MET Chi-restraints excluded: chain h residue 339 THR Chi-restraints excluded: chain h residue 368 THR Chi-restraints excluded: chain h residue 386 CYS Chi-restraints excluded: chain h residue 471 MET Chi-restraints excluded: chain h residue 530 VAL Chi-restraints excluded: chain h residue 567 VAL Chi-restraints excluded: chain m residue 253 ILE Chi-restraints excluded: chain m residue 327 GLU Chi-restraints excluded: chain m residue 338 ASP Chi-restraints excluded: chain m residue 404 VAL Chi-restraints excluded: chain m residue 466 MET Chi-restraints excluded: chain m residue 480 ILE Chi-restraints excluded: chain m residue 614 ASP Chi-restraints excluded: chain m residue 665 VAL Chi-restraints excluded: chain n residue 329 VAL Chi-restraints excluded: chain n residue 339 PHE Chi-restraints excluded: chain n residue 419 VAL Chi-restraints excluded: chain n residue 430 LEU Chi-restraints excluded: chain n residue 438 VAL Chi-restraints excluded: chain n residue 462 ARG Chi-restraints excluded: chain n residue 483 VAL Chi-restraints excluded: chain n residue 525 LEU Chi-restraints excluded: chain o residue 281 VAL Chi-restraints excluded: chain o residue 282 VAL Chi-restraints excluded: chain o residue 328 VAL Chi-restraints excluded: chain o residue 549 LEU Chi-restraints excluded: chain o residue 560 VAL Chi-restraints excluded: chain o residue 562 THR Chi-restraints excluded: chain o residue 576 VAL Chi-restraints excluded: chain x residue 140 GLU Chi-restraints excluded: chain x residue 170 VAL Chi-restraints excluded: chain x residue 175 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 530 random chunks: chunk 401 optimal weight: 0.9980 chunk 509 optimal weight: 0.9990 chunk 121 optimal weight: 0.4980 chunk 368 optimal weight: 5.9990 chunk 420 optimal weight: 0.9990 chunk 9 optimal weight: 0.4980 chunk 153 optimal weight: 0.9990 chunk 407 optimal weight: 0.9990 chunk 190 optimal weight: 0.6980 chunk 1 optimal weight: 0.1980 chunk 113 optimal weight: 0.3980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 227 ASN ** K 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 571 GLN m 769 HIS n 456 HIS o 279 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.142507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.094700 restraints weight = 73229.516| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.07 r_work: 0.3048 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 44329 Z= 0.182 Angle : 0.552 7.682 59887 Z= 0.279 Chirality : 0.042 0.187 6523 Planarity : 0.004 0.054 7735 Dihedral : 7.652 157.884 5956 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.28 % Allowed : 13.42 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.99 (0.12), residues: 5316 helix: 1.63 (0.10), residues: 2696 sheet: -0.76 (0.17), residues: 830 loop : 0.01 (0.15), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 373 TYR 0.019 0.002 TYR A 38 PHE 0.018 0.001 PHE m 841 TRP 0.020 0.002 TRP C 357 HIS 0.009 0.001 HIS n 363 Details of bonding type rmsd covalent geometry : bond 0.00428 (44329) covalent geometry : angle 0.55212 (59887) hydrogen bonds : bond 0.03801 ( 2504) hydrogen bonds : angle 4.28948 ( 7056) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10632 Ramachandran restraints generated. 5316 Oldfield, 0 Emsley, 5316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10632 Ramachandran restraints generated. 5316 Oldfield, 0 Emsley, 5316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 4717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 389 time to evaluate : 1.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 284 GLN cc_start: 0.8756 (mt0) cc_final: 0.8305 (mm-40) REVERT: E 364 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7170 (pt0) REVERT: K 59 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.8121 (tmm) REVERT: K 129 ARG cc_start: 0.7833 (mmt180) cc_final: 0.7460 (mtm-85) REVERT: L 4 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7530 (pm20) REVERT: L 163 ARG cc_start: 0.8023 (ttm-80) cc_final: 0.7687 (ttt90) REVERT: X 128 GLN cc_start: 0.6760 (mm-40) cc_final: 0.6525 (mm-40) REVERT: X 140 GLU cc_start: 0.7824 (pt0) cc_final: 0.7206 (tp30) REVERT: f 528 GLU cc_start: 0.5171 (mm-30) cc_final: 0.4599 (mt-10) REVERT: f 671 LYS cc_start: 0.6264 (tptm) cc_final: 0.5873 (tptp) REVERT: f 1019 TYR cc_start: 0.6396 (m-80) cc_final: 0.5958 (m-80) REVERT: h 353 TYR cc_start: 0.8369 (t80) cc_final: 0.8140 (t80) REVERT: h 471 MET cc_start: 0.7005 (OUTLIER) cc_final: 0.5801 (tpp) REVERT: m 253 ILE cc_start: 0.8983 (OUTLIER) cc_final: 0.8512 (mt) REVERT: n 430 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7545 (tt) REVERT: n 462 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7998 (ttm170) REVERT: n 525 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7903 (mt) REVERT: n 565 THR cc_start: 0.7317 (m) cc_final: 0.6924 (p) REVERT: o 336 MET cc_start: 0.8385 (mmm) cc_final: 0.7888 (mmp) REVERT: o 428 GLN cc_start: 0.7246 (pm20) cc_final: 0.6918 (pm20) outliers start: 107 outliers final: 81 residues processed: 470 average time/residue: 0.2730 time to fit residues: 210.5556 Evaluate side-chains 456 residues out of total 4717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 367 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 222 CYS Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 206 HIS Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 222 CYS Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain D residue 112 GLU Chi-restraints excluded: chain D residue 222 CYS Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 34 CYS Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 222 CYS Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 59 MET Chi-restraints excluded: chain K residue 191 VAL Chi-restraints excluded: chain K residue 217 THR Chi-restraints excluded: chain K residue 264 VAL Chi-restraints excluded: chain K residue 276 SER Chi-restraints excluded: chain K residue 277 TYR Chi-restraints excluded: chain K residue 283 MET Chi-restraints excluded: chain L residue 4 GLN Chi-restraints excluded: chain L residue 13 MET Chi-restraints excluded: chain L residue 16 LEU Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 124 LEU Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 170 THR Chi-restraints excluded: chain L residue 176 TRP Chi-restraints excluded: chain X residue 106 ILE Chi-restraints excluded: chain X residue 160 GLU Chi-restraints excluded: chain X residue 187 GLN Chi-restraints excluded: chain f residue 344 LEU Chi-restraints excluded: chain f residue 658 LEU Chi-restraints excluded: chain f residue 890 LEU Chi-restraints excluded: chain h residue 336 MET Chi-restraints excluded: chain h residue 339 THR Chi-restraints excluded: chain h residue 368 THR Chi-restraints excluded: chain h residue 386 CYS Chi-restraints excluded: chain h residue 402 SER Chi-restraints excluded: chain h residue 471 MET Chi-restraints excluded: chain h residue 560 VAL Chi-restraints excluded: chain h residue 567 VAL Chi-restraints excluded: chain m residue 253 ILE Chi-restraints excluded: chain m residue 327 GLU Chi-restraints excluded: chain m residue 338 ASP Chi-restraints excluded: chain m residue 404 VAL Chi-restraints excluded: chain m residue 466 MET Chi-restraints excluded: chain m residue 480 ILE Chi-restraints excluded: chain m residue 568 LEU Chi-restraints excluded: chain m residue 614 ASP Chi-restraints excluded: chain m residue 665 VAL Chi-restraints excluded: chain n residue 329 VAL Chi-restraints excluded: chain n residue 339 PHE Chi-restraints excluded: chain n residue 419 VAL Chi-restraints excluded: chain n residue 430 LEU Chi-restraints excluded: chain n residue 462 ARG Chi-restraints excluded: chain n residue 483 VAL Chi-restraints excluded: chain n residue 525 LEU Chi-restraints excluded: chain n residue 609 ILE Chi-restraints excluded: chain o residue 281 VAL Chi-restraints excluded: chain o residue 282 VAL Chi-restraints excluded: chain o residue 328 VAL Chi-restraints excluded: chain o residue 348 VAL Chi-restraints excluded: chain o residue 368 THR Chi-restraints excluded: chain o residue 435 THR Chi-restraints excluded: chain o residue 549 LEU Chi-restraints excluded: chain o residue 560 VAL Chi-restraints excluded: chain o residue 562 THR Chi-restraints excluded: chain o residue 576 VAL Chi-restraints excluded: chain x residue 140 GLU Chi-restraints excluded: chain x residue 175 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 530 random chunks: chunk 303 optimal weight: 0.5980 chunk 224 optimal weight: 1.9990 chunk 275 optimal weight: 1.9990 chunk 427 optimal weight: 1.9990 chunk 179 optimal weight: 0.2980 chunk 372 optimal weight: 0.6980 chunk 407 optimal weight: 0.9980 chunk 185 optimal weight: 0.9990 chunk 513 optimal weight: 1.9990 chunk 228 optimal weight: 0.8980 chunk 202 optimal weight: 0.0040 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 227 ASN ** K 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 571 GLN m 769 HIS n 215 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.143202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.093929 restraints weight = 74077.156| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.05 r_work: 0.3055 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 44329 Z= 0.196 Angle : 0.566 11.169 59887 Z= 0.286 Chirality : 0.043 0.250 6523 Planarity : 0.004 0.051 7735 Dihedral : 7.598 156.184 5956 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.62 % Allowed : 13.64 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.97 (0.12), residues: 5316 helix: 1.62 (0.10), residues: 2699 sheet: -0.77 (0.17), residues: 830 loop : -0.00 (0.15), residues: 1787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 373 TYR 0.022 0.002 TYR n 527 PHE 0.018 0.001 PHE m 841 TRP 0.020 0.002 TRP C 357 HIS 0.009 0.001 HIS n 363 Details of bonding type rmsd covalent geometry : bond 0.00463 (44329) covalent geometry : angle 0.56597 (59887) hydrogen bonds : bond 0.03837 ( 2504) hydrogen bonds : angle 4.29941 ( 7056) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10632 Ramachandran restraints generated. 5316 Oldfield, 0 Emsley, 5316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10632 Ramachandran restraints generated. 5316 Oldfield, 0 Emsley, 5316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 4717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 373 time to evaluate : 1.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 GLU cc_start: 0.8199 (tp30) cc_final: 0.7889 (tp30) REVERT: D 100 GLN cc_start: 0.8703 (mt0) cc_final: 0.8388 (mt0) REVERT: E 162 ASP cc_start: 0.8604 (t70) cc_final: 0.8259 (t0) REVERT: E 284 GLN cc_start: 0.8808 (mt0) cc_final: 0.8359 (mm-40) REVERT: E 364 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7225 (pt0) REVERT: K 59 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.8227 (tmm) REVERT: K 129 ARG cc_start: 0.7812 (mmt180) cc_final: 0.7483 (mtm-85) REVERT: L 4 GLN cc_start: 0.8159 (OUTLIER) cc_final: 0.7564 (pm20) REVERT: L 163 ARG cc_start: 0.8070 (ttm-80) cc_final: 0.7773 (ttt90) REVERT: X 128 GLN cc_start: 0.6823 (mm-40) cc_final: 0.6575 (mm-40) REVERT: X 140 GLU cc_start: 0.7856 (pt0) cc_final: 0.7405 (tp30) REVERT: f 286 TYR cc_start: 0.7394 (m-10) cc_final: 0.7066 (m-10) REVERT: f 448 MET cc_start: 0.7231 (tpt) cc_final: 0.6972 (tpt) REVERT: f 528 GLU cc_start: 0.5341 (mm-30) cc_final: 0.4748 (mt-10) REVERT: f 662 MET cc_start: 0.4688 (OUTLIER) cc_final: 0.4395 (mtt) REVERT: f 671 LYS cc_start: 0.6180 (tptm) cc_final: 0.5797 (tptp) REVERT: f 1019 TYR cc_start: 0.6412 (m-80) cc_final: 0.5990 (m-80) REVERT: h 353 TYR cc_start: 0.8403 (t80) cc_final: 0.8152 (t80) REVERT: h 471 MET cc_start: 0.7034 (OUTLIER) cc_final: 0.6093 (tpp) REVERT: m 253 ILE cc_start: 0.8981 (OUTLIER) cc_final: 0.8506 (mt) REVERT: n 430 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7542 (tt) REVERT: n 462 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7895 (ttm170) REVERT: n 525 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.7942 (mt) REVERT: n 565 THR cc_start: 0.7252 (m) cc_final: 0.6820 (p) REVERT: o 336 MET cc_start: 0.8409 (mmm) cc_final: 0.7853 (mmp) REVERT: o 428 GLN cc_start: 0.7156 (pm20) cc_final: 0.6876 (pm20) outliers start: 123 outliers final: 99 residues processed: 466 average time/residue: 0.2680 time to fit residues: 204.7122 Evaluate side-chains 471 residues out of total 4717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 363 time to evaluate : 1.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 222 CYS Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 206 HIS Chi-restraints excluded: chain B residue 222 CYS Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 227 ASN Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain D residue 18 SER Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 112 GLU Chi-restraints excluded: chain D residue 222 CYS Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 34 CYS Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 222 CYS Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 34 CYS Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 59 MET Chi-restraints excluded: chain K residue 191 VAL Chi-restraints excluded: chain K residue 209 HIS Chi-restraints excluded: chain K residue 217 THR Chi-restraints excluded: chain K residue 264 VAL Chi-restraints excluded: chain K residue 276 SER Chi-restraints excluded: chain K residue 277 TYR Chi-restraints excluded: chain K residue 283 MET Chi-restraints excluded: chain L residue 4 GLN Chi-restraints excluded: chain L residue 13 MET Chi-restraints excluded: chain L residue 16 LEU Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain L residue 117 SER Chi-restraints excluded: chain L residue 124 LEU Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 170 THR Chi-restraints excluded: chain L residue 176 TRP Chi-restraints excluded: chain X residue 106 ILE Chi-restraints excluded: chain X residue 160 GLU Chi-restraints excluded: chain X residue 187 GLN Chi-restraints excluded: chain f residue 344 LEU Chi-restraints excluded: chain f residue 658 LEU Chi-restraints excluded: chain f residue 662 MET Chi-restraints excluded: chain f residue 890 LEU Chi-restraints excluded: chain h residue 336 MET Chi-restraints excluded: chain h residue 339 THR Chi-restraints excluded: chain h residue 368 THR Chi-restraints excluded: chain h residue 386 CYS Chi-restraints excluded: chain h residue 402 SER Chi-restraints excluded: chain h residue 471 MET Chi-restraints excluded: chain h residue 530 VAL Chi-restraints excluded: chain h residue 560 VAL Chi-restraints excluded: chain h residue 567 VAL Chi-restraints excluded: chain m residue 253 ILE Chi-restraints excluded: chain m residue 327 GLU Chi-restraints excluded: chain m residue 338 ASP Chi-restraints excluded: chain m residue 404 VAL Chi-restraints excluded: chain m residue 466 MET Chi-restraints excluded: chain m residue 480 ILE Chi-restraints excluded: chain m residue 568 LEU Chi-restraints excluded: chain m residue 614 ASP Chi-restraints excluded: chain m residue 665 VAL Chi-restraints excluded: chain n residue 329 VAL Chi-restraints excluded: chain n residue 339 PHE Chi-restraints excluded: chain n residue 348 THR Chi-restraints excluded: chain n residue 353 ILE Chi-restraints excluded: chain n residue 419 VAL Chi-restraints excluded: chain n residue 430 LEU Chi-restraints excluded: chain n residue 438 VAL Chi-restraints excluded: chain n residue 462 ARG Chi-restraints excluded: chain n residue 466 MET Chi-restraints excluded: chain n residue 483 VAL Chi-restraints excluded: chain n residue 525 LEU Chi-restraints excluded: chain n residue 609 ILE Chi-restraints excluded: chain o residue 281 VAL Chi-restraints excluded: chain o residue 282 VAL Chi-restraints excluded: chain o residue 328 VAL Chi-restraints excluded: chain o residue 348 VAL Chi-restraints excluded: chain o residue 435 THR Chi-restraints excluded: chain o residue 549 LEU Chi-restraints excluded: chain o residue 560 VAL Chi-restraints excluded: chain o residue 562 THR Chi-restraints excluded: chain x residue 140 GLU Chi-restraints excluded: chain x residue 148 LEU Chi-restraints excluded: chain x residue 170 VAL Chi-restraints excluded: chain x residue 175 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 530 random chunks: chunk 120 optimal weight: 0.5980 chunk 458 optimal weight: 0.6980 chunk 180 optimal weight: 0.3980 chunk 60 optimal weight: 0.3980 chunk 309 optimal weight: 1.9990 chunk 424 optimal weight: 1.9990 chunk 248 optimal weight: 0.9990 chunk 262 optimal weight: 0.4980 chunk 314 optimal weight: 1.9990 chunk 116 optimal weight: 0.0970 chunk 230 optimal weight: 1.9990 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 229 GLN ** K 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 571 GLN m 769 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.143605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.094393 restraints weight = 74372.571| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.98 r_work: 0.3074 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 44329 Z= 0.165 Angle : 0.550 9.700 59887 Z= 0.277 Chirality : 0.042 0.304 6523 Planarity : 0.004 0.057 7735 Dihedral : 7.517 155.313 5956 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.52 % Allowed : 14.13 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.03 (0.12), residues: 5316 helix: 1.66 (0.10), residues: 2706 sheet: -0.73 (0.17), residues: 823 loop : 0.01 (0.15), residues: 1787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 373 TYR 0.024 0.001 TYR n 527 PHE 0.020 0.001 PHE n 592 TRP 0.020 0.002 TRP C 357 HIS 0.010 0.001 HIS n 363 Details of bonding type rmsd covalent geometry : bond 0.00387 (44329) covalent geometry : angle 0.54953 (59887) hydrogen bonds : bond 0.03711 ( 2504) hydrogen bonds : angle 4.25099 ( 7056) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10632 Ramachandran restraints generated. 5316 Oldfield, 0 Emsley, 5316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10632 Ramachandran restraints generated. 5316 Oldfield, 0 Emsley, 5316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 4717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 376 time to evaluate : 1.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 100 GLN cc_start: 0.8654 (mt0) cc_final: 0.8333 (mt0) REVERT: E 162 ASP cc_start: 0.8580 (t70) cc_final: 0.8231 (t0) REVERT: E 284 GLN cc_start: 0.8791 (mt0) cc_final: 0.8338 (mm-40) REVERT: E 364 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7222 (pt0) REVERT: K 59 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.7932 (tmm) REVERT: K 129 ARG cc_start: 0.7745 (mmt180) cc_final: 0.7413 (mtm-85) REVERT: L 4 GLN cc_start: 0.8142 (OUTLIER) cc_final: 0.7561 (pm20) REVERT: L 11 ASP cc_start: 0.8314 (OUTLIER) cc_final: 0.8092 (t70) REVERT: L 163 ARG cc_start: 0.8066 (ttm-80) cc_final: 0.7772 (ttt90) REVERT: X 128 GLN cc_start: 0.6847 (mm-40) cc_final: 0.6597 (mm-40) REVERT: X 140 GLU cc_start: 0.7839 (pt0) cc_final: 0.7400 (tp30) REVERT: f 528 GLU cc_start: 0.5310 (mm-30) cc_final: 0.4723 (mt-10) REVERT: f 662 MET cc_start: 0.4732 (OUTLIER) cc_final: 0.4441 (mtt) REVERT: f 671 LYS cc_start: 0.6433 (tptm) cc_final: 0.5999 (tptp) REVERT: h 336 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.6886 (mtp) REVERT: h 353 TYR cc_start: 0.8397 (t80) cc_final: 0.8073 (t80) REVERT: m 253 ILE cc_start: 0.8971 (OUTLIER) cc_final: 0.8496 (mt) REVERT: m 604 TYR cc_start: 0.7465 (m-80) cc_final: 0.6889 (m-80) REVERT: n 212 MET cc_start: 0.7592 (mtp) cc_final: 0.7382 (mtt) REVERT: n 430 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7526 (tt) REVERT: n 462 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7933 (ttm170) REVERT: n 565 THR cc_start: 0.7247 (m) cc_final: 0.6809 (p) REVERT: o 336 MET cc_start: 0.8380 (mmm) cc_final: 0.7800 (mmp) REVERT: o 428 GLN cc_start: 0.7339 (pm20) cc_final: 0.6995 (pm20) REVERT: x 179 GLN cc_start: 0.7574 (pp30) cc_final: 0.7347 (pp30) outliers start: 118 outliers final: 98 residues processed: 466 average time/residue: 0.2737 time to fit residues: 209.3284 Evaluate side-chains 470 residues out of total 4717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 363 time to evaluate : 1.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 222 CYS Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 206 HIS Chi-restraints excluded: chain B residue 222 CYS Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 222 CYS Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain D residue 18 SER Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 112 GLU Chi-restraints excluded: chain D residue 222 CYS Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 34 CYS Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 222 CYS Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 59 MET Chi-restraints excluded: chain K residue 191 VAL Chi-restraints excluded: chain K residue 217 THR Chi-restraints excluded: chain K residue 264 VAL Chi-restraints excluded: chain K residue 276 SER Chi-restraints excluded: chain K residue 283 MET Chi-restraints excluded: chain L residue 4 GLN Chi-restraints excluded: chain L residue 11 ASP Chi-restraints excluded: chain L residue 13 MET Chi-restraints excluded: chain L residue 16 LEU Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain L residue 117 SER Chi-restraints excluded: chain L residue 124 LEU Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 170 THR Chi-restraints excluded: chain L residue 176 TRP Chi-restraints excluded: chain X residue 106 ILE Chi-restraints excluded: chain X residue 160 GLU Chi-restraints excluded: chain X residue 187 GLN Chi-restraints excluded: chain f residue 344 LEU Chi-restraints excluded: chain f residue 488 VAL Chi-restraints excluded: chain f residue 658 LEU Chi-restraints excluded: chain f residue 662 MET Chi-restraints excluded: chain f residue 875 SER Chi-restraints excluded: chain h residue 336 MET Chi-restraints excluded: chain h residue 339 THR Chi-restraints excluded: chain h residue 368 THR Chi-restraints excluded: chain h residue 386 CYS Chi-restraints excluded: chain h residue 402 SER Chi-restraints excluded: chain h residue 530 VAL Chi-restraints excluded: chain h residue 560 VAL Chi-restraints excluded: chain h residue 567 VAL Chi-restraints excluded: chain j residue 369 LEU Chi-restraints excluded: chain m residue 253 ILE Chi-restraints excluded: chain m residue 327 GLU Chi-restraints excluded: chain m residue 338 ASP Chi-restraints excluded: chain m residue 404 VAL Chi-restraints excluded: chain m residue 466 MET Chi-restraints excluded: chain m residue 480 ILE Chi-restraints excluded: chain m residue 568 LEU Chi-restraints excluded: chain m residue 571 GLN Chi-restraints excluded: chain m residue 614 ASP Chi-restraints excluded: chain m residue 665 VAL Chi-restraints excluded: chain n residue 329 VAL Chi-restraints excluded: chain n residue 339 PHE Chi-restraints excluded: chain n residue 348 THR Chi-restraints excluded: chain n residue 353 ILE Chi-restraints excluded: chain n residue 419 VAL Chi-restraints excluded: chain n residue 430 LEU Chi-restraints excluded: chain n residue 438 VAL Chi-restraints excluded: chain n residue 462 ARG Chi-restraints excluded: chain n residue 466 MET Chi-restraints excluded: chain n residue 483 VAL Chi-restraints excluded: chain o residue 281 VAL Chi-restraints excluded: chain o residue 328 VAL Chi-restraints excluded: chain o residue 348 VAL Chi-restraints excluded: chain o residue 368 THR Chi-restraints excluded: chain o residue 435 THR Chi-restraints excluded: chain o residue 549 LEU Chi-restraints excluded: chain o residue 560 VAL Chi-restraints excluded: chain o residue 562 THR Chi-restraints excluded: chain o residue 576 VAL Chi-restraints excluded: chain x residue 148 LEU Chi-restraints excluded: chain x residue 170 VAL Chi-restraints excluded: chain x residue 175 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 530 random chunks: chunk 460 optimal weight: 2.9990 chunk 305 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 525 optimal weight: 0.5980 chunk 412 optimal weight: 2.9990 chunk 529 optimal weight: 0.8980 chunk 428 optimal weight: 2.9990 chunk 346 optimal weight: 0.9980 chunk 35 optimal weight: 0.0870 chunk 199 optimal weight: 0.2980 chunk 316 optimal weight: 4.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 227 ASN ** K 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 571 GLN m 769 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.142746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.093401 restraints weight = 73862.212| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.05 r_work: 0.3051 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 44329 Z= 0.217 Angle : 0.580 9.568 59887 Z= 0.293 Chirality : 0.043 0.304 6523 Planarity : 0.004 0.059 7735 Dihedral : 7.535 153.873 5956 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.52 % Allowed : 14.23 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.95 (0.12), residues: 5316 helix: 1.59 (0.10), residues: 2706 sheet: -0.78 (0.17), residues: 838 loop : -0.00 (0.15), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 373 TYR 0.028 0.002 TYR n 527 PHE 0.021 0.002 PHE n 592 TRP 0.020 0.002 TRP C 357 HIS 0.010 0.001 HIS n 363 Details of bonding type rmsd covalent geometry : bond 0.00516 (44329) covalent geometry : angle 0.58025 (59887) hydrogen bonds : bond 0.03881 ( 2504) hydrogen bonds : angle 4.31198 ( 7056) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10632 Ramachandran restraints generated. 5316 Oldfield, 0 Emsley, 5316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10632 Ramachandran restraints generated. 5316 Oldfield, 0 Emsley, 5316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 4717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 362 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 227 ASN cc_start: 0.7850 (OUTLIER) cc_final: 0.7622 (p0) REVERT: E 162 ASP cc_start: 0.8614 (t70) cc_final: 0.8278 (t0) REVERT: E 364 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7319 (pt0) REVERT: K 59 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.7965 (tmm) REVERT: K 129 ARG cc_start: 0.7751 (mmt180) cc_final: 0.7411 (mtm-85) REVERT: L 4 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7578 (pm20) REVERT: L 11 ASP cc_start: 0.8309 (OUTLIER) cc_final: 0.8031 (t70) REVERT: L 163 ARG cc_start: 0.8072 (ttm-80) cc_final: 0.7633 (ttt90) REVERT: X 128 GLN cc_start: 0.6846 (mm-40) cc_final: 0.6599 (mm-40) REVERT: X 140 GLU cc_start: 0.7846 (pt0) cc_final: 0.7405 (tp30) REVERT: f 286 TYR cc_start: 0.7406 (m-10) cc_final: 0.7112 (m-10) REVERT: f 528 GLU cc_start: 0.5321 (mm-30) cc_final: 0.4746 (mt-10) REVERT: f 662 MET cc_start: 0.4723 (OUTLIER) cc_final: 0.4433 (mtt) REVERT: f 671 LYS cc_start: 0.6362 (tptm) cc_final: 0.5905 (tptp) REVERT: f 1019 TYR cc_start: 0.6415 (m-80) cc_final: 0.5994 (m-80) REVERT: h 336 MET cc_start: 0.8107 (OUTLIER) cc_final: 0.6824 (mtp) REVERT: h 471 MET cc_start: 0.7057 (OUTLIER) cc_final: 0.6068 (tpp) REVERT: m 253 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8517 (mt) REVERT: n 430 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7564 (tt) REVERT: n 462 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7910 (ttm170) REVERT: n 565 THR cc_start: 0.7062 (m) cc_final: 0.6576 (p) REVERT: o 336 MET cc_start: 0.8480 (mmm) cc_final: 0.7916 (mmp) REVERT: o 428 GLN cc_start: 0.7349 (pm20) cc_final: 0.7006 (pm20) REVERT: x 179 GLN cc_start: 0.7591 (pp30) cc_final: 0.7375 (pp30) outliers start: 118 outliers final: 102 residues processed: 453 average time/residue: 0.2595 time to fit residues: 191.2764 Evaluate side-chains 471 residues out of total 4717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 358 time to evaluate : 1.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 222 CYS Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 206 HIS Chi-restraints excluded: chain B residue 222 CYS Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 222 CYS Chi-restraints excluded: chain C residue 227 ASN Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain D residue 18 SER Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 112 GLU Chi-restraints excluded: chain D residue 222 CYS Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 34 CYS Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 222 CYS Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 59 MET Chi-restraints excluded: chain K residue 191 VAL Chi-restraints excluded: chain K residue 217 THR Chi-restraints excluded: chain K residue 264 VAL Chi-restraints excluded: chain K residue 276 SER Chi-restraints excluded: chain K residue 283 MET Chi-restraints excluded: chain L residue 4 GLN Chi-restraints excluded: chain L residue 11 ASP Chi-restraints excluded: chain L residue 13 MET Chi-restraints excluded: chain L residue 16 LEU Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain L residue 117 SER Chi-restraints excluded: chain L residue 124 LEU Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 170 THR Chi-restraints excluded: chain L residue 176 TRP Chi-restraints excluded: chain X residue 106 ILE Chi-restraints excluded: chain X residue 160 GLU Chi-restraints excluded: chain X residue 187 GLN Chi-restraints excluded: chain f residue 344 LEU Chi-restraints excluded: chain f residue 488 VAL Chi-restraints excluded: chain f residue 568 LEU Chi-restraints excluded: chain f residue 658 LEU Chi-restraints excluded: chain f residue 662 MET Chi-restraints excluded: chain f residue 875 SER Chi-restraints excluded: chain f residue 890 LEU Chi-restraints excluded: chain h residue 336 MET Chi-restraints excluded: chain h residue 339 THR Chi-restraints excluded: chain h residue 368 THR Chi-restraints excluded: chain h residue 386 CYS Chi-restraints excluded: chain h residue 402 SER Chi-restraints excluded: chain h residue 471 MET Chi-restraints excluded: chain h residue 530 VAL Chi-restraints excluded: chain h residue 560 VAL Chi-restraints excluded: chain h residue 567 VAL Chi-restraints excluded: chain h residue 579 THR Chi-restraints excluded: chain j residue 369 LEU Chi-restraints excluded: chain m residue 253 ILE Chi-restraints excluded: chain m residue 327 GLU Chi-restraints excluded: chain m residue 338 ASP Chi-restraints excluded: chain m residue 404 VAL Chi-restraints excluded: chain m residue 480 ILE Chi-restraints excluded: chain m residue 568 LEU Chi-restraints excluded: chain m residue 614 ASP Chi-restraints excluded: chain m residue 665 VAL Chi-restraints excluded: chain n residue 329 VAL Chi-restraints excluded: chain n residue 339 PHE Chi-restraints excluded: chain n residue 348 THR Chi-restraints excluded: chain n residue 353 ILE Chi-restraints excluded: chain n residue 419 VAL Chi-restraints excluded: chain n residue 430 LEU Chi-restraints excluded: chain n residue 438 VAL Chi-restraints excluded: chain n residue 462 ARG Chi-restraints excluded: chain n residue 466 MET Chi-restraints excluded: chain n residue 483 VAL Chi-restraints excluded: chain n residue 609 ILE Chi-restraints excluded: chain o residue 281 VAL Chi-restraints excluded: chain o residue 328 VAL Chi-restraints excluded: chain o residue 348 VAL Chi-restraints excluded: chain o residue 368 THR Chi-restraints excluded: chain o residue 435 THR Chi-restraints excluded: chain o residue 549 LEU Chi-restraints excluded: chain o residue 560 VAL Chi-restraints excluded: chain o residue 562 THR Chi-restraints excluded: chain o residue 576 VAL Chi-restraints excluded: chain x residue 140 GLU Chi-restraints excluded: chain x residue 148 LEU Chi-restraints excluded: chain x residue 170 VAL Chi-restraints excluded: chain x residue 175 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 530 random chunks: chunk 457 optimal weight: 0.8980 chunk 429 optimal weight: 0.8980 chunk 171 optimal weight: 0.0000 chunk 112 optimal weight: 0.4980 chunk 497 optimal weight: 0.6980 chunk 169 optimal weight: 0.3980 chunk 0 optimal weight: 0.9990 chunk 95 optimal weight: 0.0770 chunk 475 optimal weight: 0.5980 chunk 310 optimal weight: 0.6980 chunk 86 optimal weight: 0.0770 overall best weight: 0.2100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 227 ASN ** K 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 209 HIS ** X 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 518 ASN m 571 GLN m 769 HIS o 394 ASN ** o 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.144745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.095725 restraints weight = 74114.255| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.92 r_work: 0.3105 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 44329 Z= 0.119 Angle : 0.528 9.432 59887 Z= 0.265 Chirality : 0.041 0.290 6523 Planarity : 0.004 0.061 7735 Dihedral : 7.370 152.916 5956 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.81 % Allowed : 14.81 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.17 (0.12), residues: 5316 helix: 1.79 (0.10), residues: 2708 sheet: -0.71 (0.17), residues: 833 loop : 0.09 (0.15), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 373 TYR 0.020 0.001 TYR K 144 PHE 0.025 0.001 PHE n 592 TRP 0.021 0.002 TRP C 357 HIS 0.011 0.001 HIS n 363 Details of bonding type rmsd covalent geometry : bond 0.00269 (44329) covalent geometry : angle 0.52801 (59887) hydrogen bonds : bond 0.03504 ( 2504) hydrogen bonds : angle 4.17592 ( 7056) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10632 Ramachandran restraints generated. 5316 Oldfield, 0 Emsley, 5316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10632 Ramachandran restraints generated. 5316 Oldfield, 0 Emsley, 5316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 4717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 386 time to evaluate : 1.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 MET cc_start: 0.8961 (mmm) cc_final: 0.8621 (mmt) REVERT: D 100 GLN cc_start: 0.8621 (mt0) cc_final: 0.8325 (mt0) REVERT: E 162 ASP cc_start: 0.8561 (t70) cc_final: 0.8208 (t0) REVERT: E 284 GLN cc_start: 0.8684 (mt0) cc_final: 0.8296 (mm-40) REVERT: E 364 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7392 (pt0) REVERT: K 59 MET cc_start: 0.8588 (OUTLIER) cc_final: 0.8014 (tmm) REVERT: K 129 ARG cc_start: 0.7646 (mmt180) cc_final: 0.7368 (mtm-85) REVERT: K 182 THR cc_start: 0.6313 (m) cc_final: 0.5834 (p) REVERT: L 4 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7530 (pm20) REVERT: L 163 ARG cc_start: 0.8060 (ttm-80) cc_final: 0.7632 (ttt90) REVERT: X 140 GLU cc_start: 0.7750 (pt0) cc_final: 0.7357 (tp30) REVERT: f 286 TYR cc_start: 0.7534 (m-10) cc_final: 0.7279 (m-10) REVERT: f 448 MET cc_start: 0.7140 (tpt) cc_final: 0.6873 (tpt) REVERT: f 528 GLU cc_start: 0.4953 (mm-30) cc_final: 0.4303 (mt-10) REVERT: f 671 LYS cc_start: 0.6343 (tptm) cc_final: 0.5867 (tptp) REVERT: h 353 TYR cc_start: 0.8394 (t80) cc_final: 0.8180 (t80) REVERT: h 471 MET cc_start: 0.7013 (OUTLIER) cc_final: 0.5855 (tpp) REVERT: m 253 ILE cc_start: 0.8936 (OUTLIER) cc_final: 0.8470 (mt) REVERT: m 604 TYR cc_start: 0.7336 (m-80) cc_final: 0.6886 (m-80) REVERT: n 430 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7505 (tt) REVERT: n 462 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7934 (ttm170) REVERT: n 565 THR cc_start: 0.7223 (m) cc_final: 0.6792 (p) REVERT: o 336 MET cc_start: 0.8353 (mmm) cc_final: 0.7778 (mmp) REVERT: o 428 GLN cc_start: 0.7305 (pm20) cc_final: 0.6964 (pm20) REVERT: x 166 TRP cc_start: 0.6266 (m100) cc_final: 0.6045 (m100) outliers start: 85 outliers final: 72 residues processed: 452 average time/residue: 0.2369 time to fit residues: 174.6841 Evaluate side-chains 445 residues out of total 4717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 366 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 222 CYS Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 206 HIS Chi-restraints excluded: chain B residue 222 CYS Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 222 CYS Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain D residue 18 SER Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 222 CYS Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 34 CYS Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 222 CYS Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 59 MET Chi-restraints excluded: chain K residue 191 VAL Chi-restraints excluded: chain K residue 217 THR Chi-restraints excluded: chain K residue 264 VAL Chi-restraints excluded: chain K residue 276 SER Chi-restraints excluded: chain K residue 283 MET Chi-restraints excluded: chain L residue 4 GLN Chi-restraints excluded: chain L residue 13 MET Chi-restraints excluded: chain L residue 16 LEU Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain L residue 124 LEU Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 170 THR Chi-restraints excluded: chain L residue 176 TRP Chi-restraints excluded: chain X residue 106 ILE Chi-restraints excluded: chain X residue 160 GLU Chi-restraints excluded: chain X residue 187 GLN Chi-restraints excluded: chain f residue 344 LEU Chi-restraints excluded: chain f residue 488 VAL Chi-restraints excluded: chain f residue 568 LEU Chi-restraints excluded: chain f residue 658 LEU Chi-restraints excluded: chain f residue 875 SER Chi-restraints excluded: chain h residue 368 THR Chi-restraints excluded: chain h residue 386 CYS Chi-restraints excluded: chain h residue 471 MET Chi-restraints excluded: chain h residue 560 VAL Chi-restraints excluded: chain h residue 567 VAL Chi-restraints excluded: chain j residue 369 LEU Chi-restraints excluded: chain m residue 253 ILE Chi-restraints excluded: chain m residue 327 GLU Chi-restraints excluded: chain m residue 338 ASP Chi-restraints excluded: chain m residue 404 VAL Chi-restraints excluded: chain m residue 480 ILE Chi-restraints excluded: chain m residue 614 ASP Chi-restraints excluded: chain m residue 665 VAL Chi-restraints excluded: chain n residue 329 VAL Chi-restraints excluded: chain n residue 339 PHE Chi-restraints excluded: chain n residue 430 LEU Chi-restraints excluded: chain n residue 438 VAL Chi-restraints excluded: chain n residue 462 ARG Chi-restraints excluded: chain n residue 466 MET Chi-restraints excluded: chain n residue 483 VAL Chi-restraints excluded: chain o residue 281 VAL Chi-restraints excluded: chain o residue 368 THR Chi-restraints excluded: chain o residue 435 THR Chi-restraints excluded: chain o residue 549 LEU Chi-restraints excluded: chain o residue 560 VAL Chi-restraints excluded: chain o residue 576 VAL Chi-restraints excluded: chain x residue 148 LEU Chi-restraints excluded: chain x residue 170 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 530 random chunks: chunk 303 optimal weight: 0.9980 chunk 526 optimal weight: 2.9990 chunk 296 optimal weight: 0.1980 chunk 135 optimal weight: 0.4980 chunk 93 optimal weight: 0.0870 chunk 42 optimal weight: 0.8980 chunk 475 optimal weight: 0.8980 chunk 431 optimal weight: 0.7980 chunk 273 optimal weight: 2.9990 chunk 233 optimal weight: 3.9990 chunk 331 optimal weight: 0.9980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN ** K 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 769 HIS ** o 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.143192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.094191 restraints weight = 74547.837| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.10 r_work: 0.3056 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 44329 Z= 0.194 Angle : 0.573 9.238 59887 Z= 0.288 Chirality : 0.043 0.287 6523 Planarity : 0.004 0.063 7735 Dihedral : 7.417 152.587 5956 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.96 % Allowed : 14.94 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.08 (0.12), residues: 5316 helix: 1.69 (0.10), residues: 2710 sheet: -0.73 (0.17), residues: 833 loop : 0.07 (0.15), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 373 TYR 0.027 0.002 TYR n 527 PHE 0.023 0.001 PHE n 592 TRP 0.021 0.002 TRP C 357 HIS 0.010 0.001 HIS n 363 Details of bonding type rmsd covalent geometry : bond 0.00462 (44329) covalent geometry : angle 0.57310 (59887) hydrogen bonds : bond 0.03782 ( 2504) hydrogen bonds : angle 4.25763 ( 7056) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14570.08 seconds wall clock time: 249 minutes 0.69 seconds (14940.69 seconds total)