Starting phenix.real_space_refine on Tue Sep 15 09:14:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5nv3_3699/09_2026/5nv3_3699.cif Found real_map, /net/cci-nas-00/data/ceres_data/5nv3_3699/09_2026/5nv3_3699.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/5nv3_3699/09_2026/5nv3_3699.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5nv3_3699/09_2026/5nv3_3699.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5nv3_3699/09_2026/5nv3_3699.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5nv3_3699/09_2026/5nv3_3699.map" model { file = "/net/cci-nas-00/data/ceres_data/5nv3_3699/09_2026/5nv3_3699.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5nv3_3699/09_2026/5nv3_3699.cif" } resolution = 3.39 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= 0.002 sd= 0.273 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 16 5.49 5 Mg 8 5.21 5 S 240 5.16 5 C 23960 2.51 5 N 6544 2.21 5 O 7048 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 67 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 37816 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3642 Classifications: {'peptide': 467} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 446} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 1063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1063 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 120} Chain: "B" Number of atoms: 3642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3642 Classifications: {'peptide': 467} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 446} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 1063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1063 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 120} Chain: "C" Number of atoms: 3642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3642 Classifications: {'peptide': 467} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 446} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 1063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1063 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 120} Chain: "D" Number of atoms: 3642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3642 Classifications: {'peptide': 467} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 446} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 1063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1063 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 120} Chain: "E" Number of atoms: 3642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3642 Classifications: {'peptide': 467} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 446} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 1063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1063 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 120} Chain: "F" Number of atoms: 3642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3642 Classifications: {'peptide': 467} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 446} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 1063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1063 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 120} Chain: "G" Number of atoms: 3642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3642 Classifications: {'peptide': 467} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 446} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 1063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1063 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 120} Chain: "H" Number of atoms: 3642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3642 Classifications: {'peptide': 467} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 446} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 1063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1063 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 120} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 128 residue: pdb=" N GLY A 464 " occ=0.40 ... (2 atoms not shown) pdb=" O GLY A 464 " occ=0.40 residue: pdb=" N ASN A 465 " occ=0.40 ... (6 atoms not shown) pdb=" ND2 ASN A 465 " occ=0.40 residue: pdb=" N ILE A 466 " occ=0.40 ... (6 atoms not shown) pdb=" CD1 ILE A 466 " occ=0.40 residue: pdb=" N THR A 467 " occ=0.40 ... (5 atoms not shown) pdb=" CG2 THR A 467 " occ=0.40 residue: pdb=" N PHE A 468 " occ=0.40 ... (9 atoms not shown) pdb=" CZ PHE A 468 " occ=0.40 residue: pdb=" N ASN A 469 " occ=0.40 ... (6 atoms not shown) pdb=" ND2 ASN A 469 " occ=0.40 residue: pdb=" N TYR A 470 " occ=0.40 ... (10 atoms not shown) pdb=" OH TYR A 470 " occ=0.40 residue: pdb=" N THR A 471 " occ=0.40 ... (5 atoms not shown) pdb=" CG2 THR A 471 " occ=0.40 residue: pdb=" N SER A 472 " occ=0.40 ... (4 atoms not shown) pdb=" OG SER A 472 " occ=0.40 residue: pdb=" N THR A 473 " occ=0.40 ... (5 atoms not shown) pdb=" CG2 THR A 473 " occ=0.40 residue: pdb=" N ASP A 474 " occ=0.40 ... (6 atoms not shown) pdb=" OD2 ASP A 474 " occ=0.40 residue: pdb=" N THR A 475 " occ=0.40 ... (5 atoms not shown) pdb=" CG2 THR A 475 " occ=0.40 ... (remaining 116 not shown) Time building chain proxies: 7.48, per 1000 atoms: 0.20 Number of scatterers: 37816 At special positions: 0 Unit cell: (132.08, 132.08, 127.92, 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 240 16.00 P 16 15.00 Mg 8 11.99 O 7048 8.00 N 6544 7.00 C 23960 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: 3.04 Conformation dependent library (CDL) restraints added in 1.3 seconds 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8656 Finding SS restraints... Secondary structure from input PDB file: 176 helices and 34 sheets defined 41.6% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 20 through 25 Processing helix chain 'A' and resid 51 through 63 removed outlier: 3.551A pdb=" N SER A 63 " --> pdb=" O VAL A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 76 removed outlier: 3.564A pdb=" N ASP A 74 " --> pdb=" O VAL A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 83 removed outlier: 3.808A pdb=" N TYR A 82 " --> pdb=" O ALA A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 114 through 123 removed outlier: 3.682A pdb=" N LEU A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 148 removed outlier: 3.537A pdb=" N LYS A 148 " --> pdb=" O VAL A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 165 removed outlier: 3.659A pdb=" N GLY A 159 " --> pdb=" O THR A 155 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG A 163 " --> pdb=" O GLY A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 198 removed outlier: 3.608A pdb=" N GLY A 188 " --> pdb=" O GLY A 184 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG A 189 " --> pdb=" O LYS A 185 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY A 198 " --> pdb=" O GLY A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 235 removed outlier: 3.582A pdb=" N LEU A 221 " --> pdb=" O ARG A 217 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET A 224 " --> pdb=" O PHE A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 263 removed outlier: 3.502A pdb=" N ARG A 254 " --> pdb=" O GLU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 287 removed outlier: 3.604A pdb=" N SER A 280 " --> pdb=" O THR A 276 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE A 281 " --> pdb=" O ALA A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 323 removed outlier: 3.607A pdb=" N ILE A 315 " --> pdb=" O SER A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 352 removed outlier: 3.549A pdb=" N TYR A 346 " --> pdb=" O THR A 342 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N CYS A 350 " --> pdb=" O TYR A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 386 No H-bonds generated for 'chain 'A' and resid 384 through 386' Processing helix chain 'A' and resid 387 through 395 removed outlier: 3.504A pdb=" N SER A 393 " --> pdb=" O HIS A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 removed outlier: 4.027A pdb=" N ILE A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 435 Processing helix chain 'A' and resid 441 through 450 Processing helix chain 'A' and resid 453 through 463 removed outlier: 3.683A pdb=" N GLU A 457 " --> pdb=" O CYS A 453 " (cutoff:3.500A) Processing helix chain 'I' and resid 15 through 30 Processing helix chain 'I' and resid 60 through 75 removed outlier: 4.173A pdb=" N VAL I 64 " --> pdb=" O ASP I 60 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET I 65 " --> pdb=" O PRO I 61 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU I 67 " --> pdb=" O GLY I 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 25 Processing helix chain 'B' and resid 51 through 63 removed outlier: 3.546A pdb=" N SER B 63 " --> pdb=" O VAL B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 76 removed outlier: 3.601A pdb=" N ASP B 74 " --> pdb=" O VAL B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 83 removed outlier: 3.800A pdb=" N TYR B 82 " --> pdb=" O ALA B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 114 through 123 removed outlier: 3.699A pdb=" N LEU B 118 " --> pdb=" O SER B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 148 removed outlier: 3.535A pdb=" N LYS B 148 " --> pdb=" O VAL B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 165 removed outlier: 3.655A pdb=" N GLY B 159 " --> pdb=" O THR B 155 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG B 163 " --> pdb=" O GLY B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 198 removed outlier: 3.592A pdb=" N GLY B 188 " --> pdb=" O GLY B 184 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG B 189 " --> pdb=" O LYS B 185 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY B 198 " --> pdb=" O GLY B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 235 removed outlier: 3.599A pdb=" N LEU B 221 " --> pdb=" O ARG B 217 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET B 224 " --> pdb=" O PHE B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 263 removed outlier: 3.503A pdb=" N ARG B 254 " --> pdb=" O GLU B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 287 removed outlier: 3.599A pdb=" N SER B 280 " --> pdb=" O THR B 276 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE B 281 " --> pdb=" O ALA B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 323 removed outlier: 3.621A pdb=" N ILE B 315 " --> pdb=" O SER B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 352 removed outlier: 3.535A pdb=" N TYR B 346 " --> pdb=" O THR B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 386 No H-bonds generated for 'chain 'B' and resid 384 through 386' Processing helix chain 'B' and resid 387 through 395 removed outlier: 3.503A pdb=" N SER B 393 " --> pdb=" O HIS B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 409 removed outlier: 4.045A pdb=" N ILE B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 435 Processing helix chain 'B' and resid 441 through 450 Processing helix chain 'B' and resid 453 through 463 removed outlier: 3.700A pdb=" N GLU B 457 " --> pdb=" O CYS B 453 " (cutoff:3.500A) Processing helix chain 'J' and resid 15 through 30 Processing helix chain 'J' and resid 60 through 75 removed outlier: 4.169A pdb=" N VAL J 64 " --> pdb=" O ASP J 60 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET J 65 " --> pdb=" O PRO J 61 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU J 67 " --> pdb=" O GLY J 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 25 Processing helix chain 'C' and resid 51 through 63 removed outlier: 3.541A pdb=" N SER C 63 " --> pdb=" O VAL C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 76 removed outlier: 3.563A pdb=" N ASP C 74 " --> pdb=" O VAL C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 83 removed outlier: 3.802A pdb=" N TYR C 82 " --> pdb=" O ALA C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 110 No H-bonds generated for 'chain 'C' and resid 108 through 110' Processing helix chain 'C' and resid 114 through 123 removed outlier: 3.698A pdb=" N LEU C 118 " --> pdb=" O SER C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 148 removed outlier: 3.542A pdb=" N LYS C 148 " --> pdb=" O VAL C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 165 removed outlier: 3.653A pdb=" N GLY C 159 " --> pdb=" O THR C 155 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG C 163 " --> pdb=" O GLY C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 198 removed outlier: 3.599A pdb=" N GLY C 188 " --> pdb=" O GLY C 184 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG C 189 " --> pdb=" O LYS C 185 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY C 198 " --> pdb=" O GLY C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 235 removed outlier: 3.599A pdb=" N LEU C 221 " --> pdb=" O ARG C 217 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N MET C 224 " --> pdb=" O PHE C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 263 Processing helix chain 'C' and resid 274 through 287 removed outlier: 3.603A pdb=" N SER C 280 " --> pdb=" O THR C 276 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE C 281 " --> pdb=" O ALA C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 323 removed outlier: 3.622A pdb=" N ILE C 315 " --> pdb=" O SER C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 352 removed outlier: 3.549A pdb=" N TYR C 346 " --> pdb=" O THR C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 386 No H-bonds generated for 'chain 'C' and resid 384 through 386' Processing helix chain 'C' and resid 387 through 395 Processing helix chain 'C' and resid 404 through 409 removed outlier: 4.035A pdb=" N ILE C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 435 Processing helix chain 'C' and resid 441 through 450 Processing helix chain 'C' and resid 453 through 463 removed outlier: 3.693A pdb=" N GLU C 457 " --> pdb=" O CYS C 453 " (cutoff:3.500A) Processing helix chain 'K' and resid 15 through 30 Processing helix chain 'K' and resid 60 through 75 removed outlier: 4.174A pdb=" N VAL K 64 " --> pdb=" O ASP K 60 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET K 65 " --> pdb=" O PRO K 61 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU K 67 " --> pdb=" O GLY K 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 25 Processing helix chain 'D' and resid 51 through 63 removed outlier: 3.540A pdb=" N SER D 63 " --> pdb=" O VAL D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 76 removed outlier: 3.607A pdb=" N ASP D 74 " --> pdb=" O VAL D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 83 removed outlier: 3.795A pdb=" N TYR D 82 " --> pdb=" O ALA D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 110 No H-bonds generated for 'chain 'D' and resid 108 through 110' Processing helix chain 'D' and resid 114 through 123 removed outlier: 3.692A pdb=" N LEU D 118 " --> pdb=" O SER D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 148 removed outlier: 3.541A pdb=" N LYS D 148 " --> pdb=" O VAL D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 165 removed outlier: 3.659A pdb=" N GLY D 159 " --> pdb=" O THR D 155 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG D 163 " --> pdb=" O GLY D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 198 removed outlier: 3.596A pdb=" N GLY D 188 " --> pdb=" O GLY D 184 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG D 189 " --> pdb=" O LYS D 185 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY D 198 " --> pdb=" O GLY D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 235 removed outlier: 3.603A pdb=" N LEU D 221 " --> pdb=" O ARG D 217 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET D 224 " --> pdb=" O PHE D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 263 Processing helix chain 'D' and resid 274 through 287 removed outlier: 3.598A pdb=" N SER D 280 " --> pdb=" O THR D 276 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE D 281 " --> pdb=" O ALA D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 323 removed outlier: 3.609A pdb=" N ILE D 315 " --> pdb=" O SER D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 352 removed outlier: 3.546A pdb=" N TYR D 346 " --> pdb=" O THR D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 386 No H-bonds generated for 'chain 'D' and resid 384 through 386' Processing helix chain 'D' and resid 387 through 395 removed outlier: 3.513A pdb=" N SER D 393 " --> pdb=" O HIS D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 409 removed outlier: 4.030A pdb=" N ILE D 408 " --> pdb=" O GLY D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 435 Processing helix chain 'D' and resid 441 through 450 Processing helix chain 'D' and resid 453 through 463 removed outlier: 3.692A pdb=" N GLU D 457 " --> pdb=" O CYS D 453 " (cutoff:3.500A) Processing helix chain 'L' and resid 15 through 30 Processing helix chain 'L' and resid 61 through 75 removed outlier: 3.646A pdb=" N MET L 65 " --> pdb=" O PRO L 61 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU L 67 " --> pdb=" O GLY L 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 25 Processing helix chain 'E' and resid 51 through 63 removed outlier: 3.534A pdb=" N SER E 63 " --> pdb=" O VAL E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 76 removed outlier: 3.589A pdb=" N ASP E 74 " --> pdb=" O VAL E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 83 removed outlier: 3.801A pdb=" N TYR E 82 " --> pdb=" O ALA E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 110 No H-bonds generated for 'chain 'E' and resid 108 through 110' Processing helix chain 'E' and resid 114 through 123 removed outlier: 3.696A pdb=" N LEU E 118 " --> pdb=" O SER E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 148 removed outlier: 3.541A pdb=" N LYS E 148 " --> pdb=" O VAL E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 165 removed outlier: 3.671A pdb=" N GLY E 159 " --> pdb=" O THR E 155 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG E 163 " --> pdb=" O GLY E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 198 removed outlier: 3.591A pdb=" N GLY E 188 " --> pdb=" O GLY E 184 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG E 189 " --> pdb=" O LYS E 185 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY E 198 " --> pdb=" O GLY E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 235 removed outlier: 3.618A pdb=" N LEU E 221 " --> pdb=" O ARG E 217 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N MET E 224 " --> pdb=" O PHE E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 263 Processing helix chain 'E' and resid 274 through 287 removed outlier: 3.591A pdb=" N SER E 280 " --> pdb=" O THR E 276 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE E 281 " --> pdb=" O ALA E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 323 removed outlier: 3.626A pdb=" N ILE E 315 " --> pdb=" O SER E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 352 removed outlier: 3.533A pdb=" N TYR E 346 " --> pdb=" O THR E 342 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 386 No H-bonds generated for 'chain 'E' and resid 384 through 386' Processing helix chain 'E' and resid 387 through 395 removed outlier: 3.506A pdb=" N SER E 393 " --> pdb=" O HIS E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 409 removed outlier: 4.026A pdb=" N ILE E 408 " --> pdb=" O GLY E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 435 removed outlier: 3.502A pdb=" N GLY E 435 " --> pdb=" O ALA E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 450 Processing helix chain 'E' and resid 453 through 463 removed outlier: 3.705A pdb=" N GLU E 457 " --> pdb=" O CYS E 453 " (cutoff:3.500A) Processing helix chain 'M' and resid 15 through 30 Processing helix chain 'M' and resid 60 through 75 removed outlier: 4.170A pdb=" N VAL M 64 " --> pdb=" O ASP M 60 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N MET M 65 " --> pdb=" O PRO M 61 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU M 67 " --> pdb=" O GLY M 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 25 Processing helix chain 'F' and resid 51 through 63 removed outlier: 3.545A pdb=" N SER F 63 " --> pdb=" O VAL F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 76 removed outlier: 3.593A pdb=" N ASP F 74 " --> pdb=" O VAL F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 83 removed outlier: 3.803A pdb=" N TYR F 82 " --> pdb=" O ALA F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 110 No H-bonds generated for 'chain 'F' and resid 108 through 110' Processing helix chain 'F' and resid 114 through 123 removed outlier: 3.691A pdb=" N LEU F 118 " --> pdb=" O SER F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 148 removed outlier: 3.520A pdb=" N LYS F 148 " --> pdb=" O VAL F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 165 removed outlier: 3.657A pdb=" N GLY F 159 " --> pdb=" O THR F 155 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG F 163 " --> pdb=" O GLY F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 198 removed outlier: 3.596A pdb=" N GLY F 188 " --> pdb=" O GLY F 184 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG F 189 " --> pdb=" O LYS F 185 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY F 198 " --> pdb=" O GLY F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 235 removed outlier: 3.599A pdb=" N LEU F 221 " --> pdb=" O ARG F 217 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET F 224 " --> pdb=" O PHE F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 263 Processing helix chain 'F' and resid 274 through 287 removed outlier: 3.587A pdb=" N SER F 280 " --> pdb=" O THR F 276 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE F 281 " --> pdb=" O ALA F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 323 removed outlier: 3.618A pdb=" N ILE F 315 " --> pdb=" O SER F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 352 removed outlier: 3.532A pdb=" N TYR F 346 " --> pdb=" O THR F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 386 No H-bonds generated for 'chain 'F' and resid 384 through 386' Processing helix chain 'F' and resid 387 through 395 removed outlier: 3.501A pdb=" N SER F 393 " --> pdb=" O HIS F 389 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 409 removed outlier: 4.036A pdb=" N ILE F 408 " --> pdb=" O GLY F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 435 Processing helix chain 'F' and resid 441 through 450 Processing helix chain 'F' and resid 453 through 463 removed outlier: 3.688A pdb=" N GLU F 457 " --> pdb=" O CYS F 453 " (cutoff:3.500A) Processing helix chain 'N' and resid 15 through 30 Processing helix chain 'N' and resid 60 through 75 removed outlier: 4.165A pdb=" N VAL N 64 " --> pdb=" O ASP N 60 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET N 65 " --> pdb=" O PRO N 61 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU N 67 " --> pdb=" O GLY N 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 25 Processing helix chain 'G' and resid 51 through 63 removed outlier: 3.548A pdb=" N SER G 63 " --> pdb=" O VAL G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 76 removed outlier: 3.599A pdb=" N ASP G 74 " --> pdb=" O VAL G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 83 removed outlier: 3.805A pdb=" N TYR G 82 " --> pdb=" O ALA G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 110 No H-bonds generated for 'chain 'G' and resid 108 through 110' Processing helix chain 'G' and resid 114 through 123 removed outlier: 3.677A pdb=" N LEU G 118 " --> pdb=" O SER G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 143 through 148 removed outlier: 3.536A pdb=" N LYS G 148 " --> pdb=" O VAL G 144 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 165 removed outlier: 3.673A pdb=" N GLY G 159 " --> pdb=" O THR G 155 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG G 163 " --> pdb=" O GLY G 159 " (cutoff:3.500A) Processing helix chain 'G' and resid 183 through 198 removed outlier: 3.599A pdb=" N GLY G 188 " --> pdb=" O GLY G 184 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG G 189 " --> pdb=" O LYS G 185 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY G 198 " --> pdb=" O GLY G 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 215 through 235 removed outlier: 3.600A pdb=" N LEU G 221 " --> pdb=" O ARG G 217 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET G 224 " --> pdb=" O PHE G 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 248 through 263 removed outlier: 3.507A pdb=" N ARG G 254 " --> pdb=" O GLU G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 274 through 287 removed outlier: 3.586A pdb=" N SER G 280 " --> pdb=" O THR G 276 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE G 281 " --> pdb=" O ALA G 277 " (cutoff:3.500A) Processing helix chain 'G' and resid 311 through 323 removed outlier: 3.609A pdb=" N ILE G 315 " --> pdb=" O SER G 311 " (cutoff:3.500A) Processing helix chain 'G' and resid 339 through 352 removed outlier: 3.530A pdb=" N TYR G 346 " --> pdb=" O THR G 342 " (cutoff:3.500A) Processing helix chain 'G' and resid 384 through 386 No H-bonds generated for 'chain 'G' and resid 384 through 386' Processing helix chain 'G' and resid 387 through 395 removed outlier: 3.512A pdb=" N SER G 393 " --> pdb=" O HIS G 389 " (cutoff:3.500A) Processing helix chain 'G' and resid 404 through 409 removed outlier: 4.019A pdb=" N ILE G 408 " --> pdb=" O GLY G 404 " (cutoff:3.500A) Processing helix chain 'G' and resid 414 through 435 Processing helix chain 'G' and resid 441 through 450 Processing helix chain 'G' and resid 453 through 463 removed outlier: 3.693A pdb=" N GLU G 457 " --> pdb=" O CYS G 453 " (cutoff:3.500A) Processing helix chain 'O' and resid 15 through 30 Processing helix chain 'O' and resid 60 through 75 removed outlier: 4.168A pdb=" N VAL O 64 " --> pdb=" O ASP O 60 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N MET O 65 " --> pdb=" O PRO O 61 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU O 67 " --> pdb=" O GLY O 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 25 Processing helix chain 'H' and resid 51 through 63 removed outlier: 3.541A pdb=" N SER H 63 " --> pdb=" O VAL H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 76 removed outlier: 3.600A pdb=" N ASP H 74 " --> pdb=" O VAL H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 83 removed outlier: 3.799A pdb=" N TYR H 82 " --> pdb=" O ALA H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 110 No H-bonds generated for 'chain 'H' and resid 108 through 110' Processing helix chain 'H' and resid 114 through 123 removed outlier: 3.686A pdb=" N LEU H 118 " --> pdb=" O SER H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 143 through 148 removed outlier: 3.528A pdb=" N LYS H 148 " --> pdb=" O VAL H 144 " (cutoff:3.500A) Processing helix chain 'H' and resid 155 through 165 removed outlier: 3.660A pdb=" N GLY H 159 " --> pdb=" O THR H 155 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG H 163 " --> pdb=" O GLY H 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 198 removed outlier: 3.599A pdb=" N GLY H 188 " --> pdb=" O GLY H 184 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG H 189 " --> pdb=" O LYS H 185 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY H 198 " --> pdb=" O GLY H 194 " (cutoff:3.500A) Processing helix chain 'H' and resid 215 through 235 removed outlier: 3.605A pdb=" N LEU H 221 " --> pdb=" O ARG H 217 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N MET H 224 " --> pdb=" O PHE H 220 " (cutoff:3.500A) Processing helix chain 'H' and resid 248 through 263 Processing helix chain 'H' and resid 274 through 287 removed outlier: 3.585A pdb=" N SER H 280 " --> pdb=" O THR H 276 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE H 281 " --> pdb=" O ALA H 277 " (cutoff:3.500A) Processing helix chain 'H' and resid 311 through 323 removed outlier: 3.608A pdb=" N ILE H 315 " --> pdb=" O SER H 311 " (cutoff:3.500A) Processing helix chain 'H' and resid 339 through 352 removed outlier: 3.543A pdb=" N TYR H 346 " --> pdb=" O THR H 342 " (cutoff:3.500A) Processing helix chain 'H' and resid 384 through 386 No H-bonds generated for 'chain 'H' and resid 384 through 386' Processing helix chain 'H' and resid 387 through 395 removed outlier: 3.509A pdb=" N SER H 393 " --> pdb=" O HIS H 389 " (cutoff:3.500A) Processing helix chain 'H' and resid 404 through 409 removed outlier: 4.022A pdb=" N ILE H 408 " --> pdb=" O GLY H 404 " (cutoff:3.500A) Processing helix chain 'H' and resid 414 through 435 Processing helix chain 'H' and resid 441 through 450 Processing helix chain 'H' and resid 453 through 463 removed outlier: 3.683A pdb=" N GLU H 457 " --> pdb=" O CYS H 453 " (cutoff:3.500A) Processing helix chain 'P' and resid 15 through 30 Processing helix chain 'P' and resid 61 through 75 removed outlier: 3.649A pdb=" N MET P 65 " --> pdb=" O PRO P 61 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU P 67 " --> pdb=" O GLY P 63 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 91 removed outlier: 5.492A pdb=" N ALA A 86 " --> pdb=" O ALA A 104 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ALA A 104 " --> pdb=" O ALA A 86 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARG A 88 " --> pdb=" O TYR A 102 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU A 39 " --> pdb=" O MET A 140 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N MET A 140 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU A 41 " --> pdb=" O GLU A 138 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 171 through 175 removed outlier: 6.692A pdb=" N LEU A 172 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N KCX A 203 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ALA A 174 " --> pdb=" O KCX A 203 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N MET A 202 " --> pdb=" O TYR A 241 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N ASN A 243 " --> pdb=" O MET A 202 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N HIS A 240 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N MET A 268 " --> pdb=" O HIS A 240 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N LEU A 242 " --> pdb=" O MET A 268 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N ASP A 270 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL A 267 " --> pdb=" O HIS A 293 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N HIS A 295 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL A 269 " --> pdb=" O HIS A 295 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU A 292 " --> pdb=" O HIS A 326 " (cutoff:3.500A) removed outlier: 8.732A pdb=" N HIS A 328 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N MET A 294 " --> pdb=" O HIS A 328 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU A 327 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N SER A 380 " --> pdb=" O LEU A 327 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 354 through 355 Processing sheet with id=AA4, first strand: chain 'I' and resid 49 through 50 removed outlier: 7.189A pdb=" N ILE I 80 " --> pdb=" O ILE I 99 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ILE I 99 " --> pdb=" O ILE I 80 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE I 82 " --> pdb=" O SER I 97 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER I 97 " --> pdb=" O ILE I 82 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ALA I 84 " --> pdb=" O THR I 95 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 109 through 115 removed outlier: 4.348A pdb=" N TYR I 123 " --> pdb=" O GLU J 115 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N HIS I 125 " --> pdb=" O ARG J 113 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ARG J 113 " --> pdb=" O HIS I 125 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE I 127 " --> pdb=" O MET J 111 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N MET J 111 " --> pdb=" O ILE I 127 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N TYR J 123 " --> pdb=" O GLU K 115 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N HIS J 125 " --> pdb=" O ARG K 113 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ARG K 113 " --> pdb=" O HIS J 125 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE J 127 " --> pdb=" O MET K 111 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N MET K 111 " --> pdb=" O ILE J 127 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N TYR K 123 " --> pdb=" O GLU L 115 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N HIS K 125 " --> pdb=" O ARG L 113 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ARG L 113 " --> pdb=" O HIS K 125 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE K 127 " --> pdb=" O MET L 111 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N MET L 111 " --> pdb=" O ILE K 127 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N TYR L 123 " --> pdb=" O GLU I 115 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N HIS L 125 " --> pdb=" O ARG I 113 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ARG I 113 " --> pdb=" O HIS L 125 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE L 127 " --> pdb=" O MET I 111 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N MET I 111 " --> pdb=" O ILE L 127 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 85 through 91 removed outlier: 5.491A pdb=" N ALA B 86 " --> pdb=" O ALA B 104 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ALA B 104 " --> pdb=" O ALA B 86 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ARG B 88 " --> pdb=" O TYR B 102 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU B 39 " --> pdb=" O MET B 140 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N MET B 140 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LEU B 41 " --> pdb=" O GLU B 138 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 171 through 175 removed outlier: 6.684A pdb=" N LEU B 172 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N KCX B 203 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ALA B 174 " --> pdb=" O KCX B 203 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N MET B 202 " --> pdb=" O TYR B 241 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N ASN B 243 " --> pdb=" O MET B 202 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N HIS B 240 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N MET B 268 " --> pdb=" O HIS B 240 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N LEU B 242 " --> pdb=" O MET B 268 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N ASP B 270 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL B 267 " --> pdb=" O HIS B 293 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N HIS B 295 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL B 269 " --> pdb=" O HIS B 295 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LEU B 292 " --> pdb=" O HIS B 326 " (cutoff:3.500A) removed outlier: 8.746A pdb=" N HIS B 328 " --> pdb=" O LEU B 292 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N MET B 294 " --> pdb=" O HIS B 328 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEU B 327 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N SER B 380 " --> pdb=" O LEU B 327 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 354 through 355 Processing sheet with id=AA9, first strand: chain 'J' and resid 49 through 50 removed outlier: 7.191A pdb=" N ILE J 80 " --> pdb=" O ILE J 99 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ILE J 99 " --> pdb=" O ILE J 80 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE J 82 " --> pdb=" O SER J 97 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER J 97 " --> pdb=" O ILE J 82 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA J 84 " --> pdb=" O THR J 95 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 85 through 91 removed outlier: 5.494A pdb=" N ALA C 86 " --> pdb=" O ALA C 104 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ALA C 104 " --> pdb=" O ALA C 86 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG C 88 " --> pdb=" O TYR C 102 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU C 39 " --> pdb=" O MET C 140 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N MET C 140 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LEU C 41 " --> pdb=" O GLU C 138 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 171 through 175 removed outlier: 6.693A pdb=" N LEU C 172 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N KCX C 203 " --> pdb=" O LEU C 172 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ALA C 174 " --> pdb=" O KCX C 203 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N MET C 202 " --> pdb=" O TYR C 241 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N ASN C 243 " --> pdb=" O MET C 202 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N HIS C 240 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N MET C 268 " --> pdb=" O HIS C 240 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N LEU C 242 " --> pdb=" O MET C 268 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N ASP C 270 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL C 267 " --> pdb=" O HIS C 293 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N HIS C 295 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL C 269 " --> pdb=" O HIS C 295 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU C 292 " --> pdb=" O HIS C 326 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N HIS C 328 " --> pdb=" O LEU C 292 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N MET C 294 " --> pdb=" O HIS C 328 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU C 327 " --> pdb=" O VAL C 378 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N SER C 380 " --> pdb=" O LEU C 327 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 354 through 355 Processing sheet with id=AB4, first strand: chain 'K' and resid 49 through 50 removed outlier: 7.198A pdb=" N ILE K 80 " --> pdb=" O ILE K 99 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ILE K 99 " --> pdb=" O ILE K 80 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE K 82 " --> pdb=" O SER K 97 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER K 97 " --> pdb=" O ILE K 82 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA K 84 " --> pdb=" O THR K 95 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 85 through 91 removed outlier: 5.485A pdb=" N ALA D 86 " --> pdb=" O ALA D 104 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ALA D 104 " --> pdb=" O ALA D 86 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ARG D 88 " --> pdb=" O TYR D 102 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LEU D 39 " --> pdb=" O MET D 140 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N MET D 140 " --> pdb=" O LEU D 39 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LEU D 41 " --> pdb=" O GLU D 138 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 171 through 175 removed outlier: 6.690A pdb=" N LEU D 172 " --> pdb=" O PHE D 201 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N KCX D 203 " --> pdb=" O LEU D 172 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ALA D 174 " --> pdb=" O KCX D 203 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N MET D 202 " --> pdb=" O TYR D 241 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N ASN D 243 " --> pdb=" O MET D 202 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N HIS D 240 " --> pdb=" O ILE D 266 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N MET D 268 " --> pdb=" O HIS D 240 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N LEU D 242 " --> pdb=" O MET D 268 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ASP D 270 " --> pdb=" O LEU D 242 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL D 267 " --> pdb=" O HIS D 293 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N HIS D 295 " --> pdb=" O VAL D 267 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL D 269 " --> pdb=" O HIS D 295 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LEU D 292 " --> pdb=" O HIS D 326 " (cutoff:3.500A) removed outlier: 8.746A pdb=" N HIS D 328 " --> pdb=" O LEU D 292 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N MET D 294 " --> pdb=" O HIS D 328 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU D 327 " --> pdb=" O VAL D 378 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N SER D 380 " --> pdb=" O LEU D 327 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 354 through 355 Processing sheet with id=AB8, first strand: chain 'L' and resid 49 through 50 removed outlier: 7.183A pdb=" N ILE L 80 " --> pdb=" O ILE L 99 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ILE L 99 " --> pdb=" O ILE L 80 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE L 82 " --> pdb=" O SER L 97 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER L 97 " --> pdb=" O ILE L 82 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ALA L 84 " --> pdb=" O THR L 95 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 85 through 91 removed outlier: 5.510A pdb=" N ALA E 86 " --> pdb=" O ALA E 104 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ALA E 104 " --> pdb=" O ALA E 86 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ARG E 88 " --> pdb=" O TYR E 102 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU E 39 " --> pdb=" O MET E 140 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N MET E 140 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU E 41 " --> pdb=" O GLU E 138 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 171 through 175 removed outlier: 6.692A pdb=" N LEU E 172 " --> pdb=" O PHE E 201 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N KCX E 203 " --> pdb=" O LEU E 172 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ALA E 174 " --> pdb=" O KCX E 203 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N MET E 202 " --> pdb=" O TYR E 241 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N ASN E 243 " --> pdb=" O MET E 202 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N HIS E 240 " --> pdb=" O ILE E 266 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N MET E 268 " --> pdb=" O HIS E 240 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N LEU E 242 " --> pdb=" O MET E 268 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ASP E 270 " --> pdb=" O LEU E 242 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL E 267 " --> pdb=" O HIS E 293 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N HIS E 295 " --> pdb=" O VAL E 267 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL E 269 " --> pdb=" O HIS E 295 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N LEU E 292 " --> pdb=" O HIS E 326 " (cutoff:3.500A) removed outlier: 8.734A pdb=" N HIS E 328 " --> pdb=" O LEU E 292 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N MET E 294 " --> pdb=" O HIS E 328 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU E 327 " --> pdb=" O VAL E 378 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N SER E 380 " --> pdb=" O LEU E 327 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 354 through 355 Processing sheet with id=AC3, first strand: chain 'M' and resid 49 through 50 removed outlier: 7.195A pdb=" N ILE M 80 " --> pdb=" O ILE M 99 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ILE M 99 " --> pdb=" O ILE M 80 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE M 82 " --> pdb=" O SER M 97 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N SER M 97 " --> pdb=" O ILE M 82 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA M 84 " --> pdb=" O THR M 95 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'M' and resid 109 through 115 removed outlier: 4.323A pdb=" N TYR M 123 " --> pdb=" O GLU P 115 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N HIS M 125 " --> pdb=" O ARG P 113 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ARG P 113 " --> pdb=" O HIS M 125 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE M 127 " --> pdb=" O MET P 111 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N MET P 111 " --> pdb=" O ILE M 127 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N TYR P 123 " --> pdb=" O GLU O 115 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N HIS P 125 " --> pdb=" O ARG O 113 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ARG O 113 " --> pdb=" O HIS P 125 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILE P 127 " --> pdb=" O MET O 111 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N MET O 111 " --> pdb=" O ILE P 127 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N TYR O 123 " --> pdb=" O GLU N 115 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N HIS O 125 " --> pdb=" O ARG N 113 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ARG N 113 " --> pdb=" O HIS O 125 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE O 127 " --> pdb=" O MET N 111 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N MET N 111 " --> pdb=" O ILE O 127 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N TYR N 123 " --> pdb=" O GLU M 115 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N HIS N 125 " --> pdb=" O ARG M 113 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ARG M 113 " --> pdb=" O HIS N 125 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE N 127 " --> pdb=" O MET M 111 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N MET M 111 " --> pdb=" O ILE N 127 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 85 through 91 removed outlier: 5.506A pdb=" N ALA F 86 " --> pdb=" O ALA F 104 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ALA F 104 " --> pdb=" O ALA F 86 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ARG F 88 " --> pdb=" O TYR F 102 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU F 39 " --> pdb=" O MET F 140 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N MET F 140 " --> pdb=" O LEU F 39 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU F 41 " --> pdb=" O GLU F 138 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 171 through 175 removed outlier: 6.685A pdb=" N LEU F 172 " --> pdb=" O PHE F 201 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N KCX F 203 " --> pdb=" O LEU F 172 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ALA F 174 " --> pdb=" O KCX F 203 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N MET F 202 " --> pdb=" O TYR F 241 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N ASN F 243 " --> pdb=" O MET F 202 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N HIS F 240 " --> pdb=" O ILE F 266 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N MET F 268 " --> pdb=" O HIS F 240 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LEU F 242 " --> pdb=" O MET F 268 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ASP F 270 " --> pdb=" O LEU F 242 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL F 267 " --> pdb=" O HIS F 293 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N HIS F 295 " --> pdb=" O VAL F 267 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL F 269 " --> pdb=" O HIS F 295 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N LEU F 292 " --> pdb=" O HIS F 326 " (cutoff:3.500A) removed outlier: 8.730A pdb=" N HIS F 328 " --> pdb=" O LEU F 292 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N MET F 294 " --> pdb=" O HIS F 328 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU F 327 " --> pdb=" O VAL F 378 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N SER F 380 " --> pdb=" O LEU F 327 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 354 through 355 Processing sheet with id=AC8, first strand: chain 'N' and resid 49 through 50 removed outlier: 7.193A pdb=" N ILE N 80 " --> pdb=" O ILE N 99 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ILE N 99 " --> pdb=" O ILE N 80 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE N 82 " --> pdb=" O SER N 97 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER N 97 " --> pdb=" O ILE N 82 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ALA N 84 " --> pdb=" O THR N 95 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 85 through 91 removed outlier: 5.509A pdb=" N ALA G 86 " --> pdb=" O ALA G 104 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ALA G 104 " --> pdb=" O ALA G 86 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ARG G 88 " --> pdb=" O TYR G 102 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU G 39 " --> pdb=" O MET G 140 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N MET G 140 " --> pdb=" O LEU G 39 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LEU G 41 " --> pdb=" O GLU G 138 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 171 through 175 removed outlier: 6.690A pdb=" N LEU G 172 " --> pdb=" O PHE G 201 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N KCX G 203 " --> pdb=" O LEU G 172 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ALA G 174 " --> pdb=" O KCX G 203 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N MET G 202 " --> pdb=" O TYR G 241 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N ASN G 243 " --> pdb=" O MET G 202 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N HIS G 240 " --> pdb=" O ILE G 266 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N MET G 268 " --> pdb=" O HIS G 240 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N LEU G 242 " --> pdb=" O MET G 268 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ASP G 270 " --> pdb=" O LEU G 242 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL G 267 " --> pdb=" O HIS G 293 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N HIS G 295 " --> pdb=" O VAL G 267 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL G 269 " --> pdb=" O HIS G 295 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N LEU G 292 " --> pdb=" O HIS G 326 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N HIS G 328 " --> pdb=" O LEU G 292 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N MET G 294 " --> pdb=" O HIS G 328 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU G 327 " --> pdb=" O VAL G 378 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N SER G 380 " --> pdb=" O LEU G 327 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 354 through 355 Processing sheet with id=AD3, first strand: chain 'O' and resid 49 through 50 removed outlier: 7.186A pdb=" N ILE O 80 " --> pdb=" O ILE O 99 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ILE O 99 " --> pdb=" O ILE O 80 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE O 82 " --> pdb=" O SER O 97 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER O 97 " --> pdb=" O ILE O 82 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA O 84 " --> pdb=" O THR O 95 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 85 through 91 removed outlier: 5.499A pdb=" N ALA H 86 " --> pdb=" O ALA H 104 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ALA H 104 " --> pdb=" O ALA H 86 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ARG H 88 " --> pdb=" O TYR H 102 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU H 39 " --> pdb=" O MET H 140 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N MET H 140 " --> pdb=" O LEU H 39 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU H 41 " --> pdb=" O GLU H 138 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 171 through 175 removed outlier: 6.693A pdb=" N LEU H 172 " --> pdb=" O PHE H 201 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N KCX H 203 " --> pdb=" O LEU H 172 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ALA H 174 " --> pdb=" O KCX H 203 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N MET H 202 " --> pdb=" O TYR H 241 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N ASN H 243 " --> pdb=" O MET H 202 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N HIS H 240 " --> pdb=" O ILE H 266 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N MET H 268 " --> pdb=" O HIS H 240 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N LEU H 242 " --> pdb=" O MET H 268 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N ASP H 270 " --> pdb=" O LEU H 242 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL H 267 " --> pdb=" O HIS H 293 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N HIS H 295 " --> pdb=" O VAL H 267 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL H 269 " --> pdb=" O HIS H 295 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N LEU H 292 " --> pdb=" O HIS H 326 " (cutoff:3.500A) removed outlier: 8.729A pdb=" N HIS H 328 " --> pdb=" O LEU H 292 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N MET H 294 " --> pdb=" O HIS H 328 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU H 327 " --> pdb=" O VAL H 378 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N SER H 380 " --> pdb=" O LEU H 327 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 354 through 355 Processing sheet with id=AD7, first strand: chain 'P' and resid 49 through 50 removed outlier: 7.187A pdb=" N ILE P 80 " --> pdb=" O ILE P 99 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ILE P 99 " --> pdb=" O ILE P 80 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE P 82 " --> pdb=" O SER P 97 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER P 97 " --> pdb=" O ILE P 82 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ALA P 84 " --> pdb=" O THR P 95 " (cutoff:3.500A) 1468 hydrogen bonds defined for protein. 4188 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: 7.93 Time building geometry restraints manager: 4.11 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: 12256 1.34 - 1.46: 4862 1.46 - 1.57: 21186 1.57 - 1.69: 16 1.69 - 1.81: 408 Bond restraints: 38728 Sorted by residual: bond pdb=" CX KCX G 203 " pdb=" OQ1 KCX G 203 " ideal model delta sigma weight residual 1.250 1.330 -0.080 2.00e-02 2.50e+03 1.61e+01 bond pdb=" CX KCX F 203 " pdb=" OQ1 KCX F 203 " ideal model delta sigma weight residual 1.250 1.330 -0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" CX KCX E 203 " pdb=" OQ1 KCX E 203 " ideal model delta sigma weight residual 1.250 1.330 -0.080 2.00e-02 2.50e+03 1.59e+01 bond pdb=" CX KCX B 203 " pdb=" OQ2 KCX B 203 " ideal model delta sigma weight residual 1.251 1.331 -0.080 2.00e-02 2.50e+03 1.59e+01 bond pdb=" CX KCX H 203 " pdb=" OQ1 KCX H 203 " ideal model delta sigma weight residual 1.250 1.330 -0.080 2.00e-02 2.50e+03 1.59e+01 ... (remaining 38723 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 47136 1.92 - 3.84: 4853 3.84 - 5.76: 460 5.76 - 7.68: 83 7.68 - 9.60: 12 Bond angle restraints: 52544 Sorted by residual: angle pdb=" C ASP C 339 " pdb=" N PRO C 340 " pdb=" CA PRO C 340 " ideal model delta sigma weight residual 119.84 125.45 -5.61 1.25e+00 6.40e-01 2.02e+01 angle pdb=" C ASP A 339 " pdb=" N PRO A 340 " pdb=" CA PRO A 340 " ideal model delta sigma weight residual 119.84 125.45 -5.61 1.25e+00 6.40e-01 2.02e+01 angle pdb=" C ASP G 339 " pdb=" N PRO G 340 " pdb=" CA PRO G 340 " ideal model delta sigma weight residual 119.84 125.42 -5.58 1.25e+00 6.40e-01 1.99e+01 angle pdb=" C ASP B 339 " pdb=" N PRO B 340 " pdb=" CA PRO B 340 " ideal model delta sigma weight residual 119.84 125.38 -5.54 1.25e+00 6.40e-01 1.97e+01 angle pdb=" C ASP H 339 " pdb=" N PRO H 340 " pdb=" CA PRO H 340 " ideal model delta sigma weight residual 119.84 125.34 -5.50 1.25e+00 6.40e-01 1.93e+01 ... (remaining 52539 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.40: 22336 35.40 - 70.79: 460 70.79 - 106.19: 4 106.19 - 141.58: 4 141.58 - 176.98: 4 Dihedral angle restraints: 22808 sinusoidal: 9200 harmonic: 13608 Sorted by residual: dihedral pdb=" C3 CAP A1001 " pdb=" C CAP A1001 " pdb=" C2 CAP A1001 " pdb=" O6 CAP A1001 " ideal model delta sinusoidal sigma weight residual 81.86 -101.16 -176.98 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C3 CAP C1001 " pdb=" C CAP C1001 " pdb=" C2 CAP C1001 " pdb=" O6 CAP C1001 " ideal model delta sinusoidal sigma weight residual 81.86 -101.18 -176.95 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C3 CAP B1001 " pdb=" C CAP B1001 " pdb=" C2 CAP B1001 " pdb=" O6 CAP B1001 " ideal model delta sinusoidal sigma weight residual 81.86 -101.57 -176.57 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 22805 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 4468 0.079 - 0.158: 981 0.158 - 0.237: 137 0.237 - 0.316: 14 0.316 - 0.394: 16 Chirality restraints: 5616 Sorted by residual: chirality pdb=" CA TYR G 87 " pdb=" N TYR G 87 " pdb=" C TYR G 87 " pdb=" CB TYR G 87 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.89e+00 chirality pdb=" CA TYR A 87 " pdb=" N TYR A 87 " pdb=" C TYR A 87 " pdb=" CB TYR A 87 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.84e+00 chirality pdb=" CA TYR F 87 " pdb=" N TYR F 87 " pdb=" C TYR F 87 " pdb=" CB TYR F 87 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.82e+00 ... (remaining 5613 not shown) Planarity restraints: 6800 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 359 " -0.022 5.00e-02 4.00e+02 3.34e-02 1.78e+00 pdb=" N PRO C 360 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO C 360 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 360 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 359 " 0.022 5.00e-02 4.00e+02 3.32e-02 1.76e+00 pdb=" N PRO A 360 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 360 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 360 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 359 " 0.021 5.00e-02 4.00e+02 3.16e-02 1.59e+00 pdb=" N PRO D 360 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO D 360 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 360 " 0.018 5.00e-02 4.00e+02 ... (remaining 6797 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 288 2.71 - 3.26: 33127 3.26 - 3.81: 59653 3.81 - 4.35: 85034 4.35 - 4.90: 136612 Nonbonded interactions: 314714 Sorted by model distance: nonbonded pdb=" OQ2 KCX A 203 " pdb="MG MG A1002 " model vdw 2.164 2.170 nonbonded pdb=" OQ2 KCX C 203 " pdb="MG MG C1002 " model vdw 2.169 2.170 nonbonded pdb=" OQ2 KCX D 203 " pdb="MG MG D1002 " model vdw 2.199 2.170 nonbonded pdb=" OQ1 KCX H 203 " pdb="MG MG H1002 " model vdw 2.202 2.170 nonbonded pdb=" OQ1 KCX G 203 " pdb="MG MG G1002 " model vdw 2.211 2.170 ... (remaining 314709 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: 0.14 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } 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=0.40 max=1.00 mean=0.98 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: 2.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 32.700 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.110 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: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1582 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 38728 Z= 0.486 Angle : 1.218 9.597 52544 Z= 0.793 Chirality : 0.068 0.394 5616 Planarity : 0.004 0.033 6800 Dihedral : 14.589 176.981 14152 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.65 % Favored : 94.19 % Rotamer: Outliers : 0.94 % Allowed : 5.36 % Favored : 93.70 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.82 (0.10), residues: 4712 helix: -2.40 (0.08), residues: 1688 sheet: -0.28 (0.17), residues: 784 loop : -1.97 (0.11), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 119 TYR 0.015 0.001 TYR E 87 PHE 0.014 0.002 PHE A 213 TRP 0.012 0.001 TRP K 48 HIS 0.005 0.001 HIS C 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00731 / 0.49 (38728) covalent geometry : angle 1.21761 / 0.79 (52544) hydrogen bonds : bond 0.31273 / 20.54 ( 1468) hydrogen bonds : angle 8.45880 / 5.89 ( 4188) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 3936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 648 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 THR cc_start: 0.3669 (p) cc_final: 0.3344 (p) REVERT: A 44 ILE cc_start: 0.2658 (mt) cc_final: 0.2416 (pt) REVERT: A 99 TYR cc_start: 0.3042 (m-80) cc_final: 0.2747 (m-80) REVERT: A 129 PHE cc_start: 0.1030 (m-80) cc_final: 0.0725 (m-80) REVERT: A 283 GLU cc_start: 0.2358 (tt0) cc_final: 0.2018 (mp0) REVERT: A 306 LYS cc_start: 0.3676 (ttpt) cc_final: 0.3265 (tptt) REVERT: I 50 MET cc_start: 0.4406 (mtt) cc_final: 0.3718 (mmt) REVERT: I 112 GLU cc_start: 0.2459 (mt-10) cc_final: 0.2081 (mp0) REVERT: B 36 THR cc_start: 0.3600 (p) cc_final: 0.3065 (p) REVERT: B 99 TYR cc_start: 0.2950 (m-80) cc_final: 0.2647 (m-80) REVERT: B 133 LYS cc_start: 0.3273 (tptp) cc_final: 0.3073 (mtmm) REVERT: B 283 GLU cc_start: 0.2370 (tt0) cc_final: 0.2023 (mp0) REVERT: B 306 LYS cc_start: 0.3622 (ttpt) cc_final: 0.3195 (tptt) REVERT: J 50 MET cc_start: 0.4543 (mtt) cc_final: 0.3812 (mmt) REVERT: J 112 GLU cc_start: 0.2467 (mt-10) cc_final: 0.2072 (mp0) REVERT: C 36 THR cc_start: 0.3589 (p) cc_final: 0.3026 (p) REVERT: C 44 ILE cc_start: 0.2675 (mt) cc_final: 0.2442 (pt) REVERT: C 99 TYR cc_start: 0.2972 (m-80) cc_final: 0.2683 (m-80) REVERT: C 129 PHE cc_start: 0.0985 (m-80) cc_final: 0.0678 (m-80) REVERT: C 133 LYS cc_start: 0.3270 (tptp) cc_final: 0.3068 (mtmm) REVERT: C 306 LYS cc_start: 0.3579 (ttpt) cc_final: 0.3185 (tptt) REVERT: C 457 GLU cc_start: 0.2482 (tt0) cc_final: 0.2277 (mt-10) REVERT: K 50 MET cc_start: 0.4560 (mtt) cc_final: 0.3851 (mmt) REVERT: K 112 GLU cc_start: 0.2461 (mt-10) cc_final: 0.2084 (mp0) REVERT: D 20 LYS cc_start: 0.1417 (mttt) cc_final: 0.1177 (ttpt) REVERT: D 36 THR cc_start: 0.3234 (p) cc_final: 0.2582 (p) REVERT: D 99 TYR cc_start: 0.2995 (m-80) cc_final: 0.2677 (m-80) REVERT: D 129 PHE cc_start: 0.1109 (m-80) cc_final: 0.0881 (m-80) REVERT: D 133 LYS cc_start: 0.3266 (tptp) cc_final: 0.3064 (mtmm) REVERT: D 283 GLU cc_start: 0.2389 (tt0) cc_final: 0.2040 (mp0) REVERT: D 306 LYS cc_start: 0.3616 (ttpt) cc_final: 0.3213 (tptt) REVERT: L 50 MET cc_start: 0.4508 (mtt) cc_final: 0.3803 (mmt) REVERT: L 112 GLU cc_start: 0.2467 (mt-10) cc_final: 0.2094 (mp0) REVERT: E 20 LYS cc_start: 0.1141 (mttt) cc_final: 0.0906 (ttpt) REVERT: E 36 THR cc_start: 0.3314 (p) cc_final: 0.2768 (p) REVERT: E 44 ILE cc_start: 0.2566 (mt) cc_final: 0.2364 (pt) REVERT: E 99 TYR cc_start: 0.2940 (m-80) cc_final: 0.2622 (m-80) REVERT: E 129 PHE cc_start: 0.0955 (m-80) cc_final: 0.0585 (m-80) REVERT: E 306 LYS cc_start: 0.3541 (ttpt) cc_final: 0.3125 (tptt) REVERT: E 457 GLU cc_start: 0.2702 (tt0) cc_final: 0.2486 (mt-10) REVERT: M 50 MET cc_start: 0.4404 (mtt) cc_final: 0.3698 (mmt) REVERT: M 112 GLU cc_start: 0.2454 (mt-10) cc_final: 0.2080 (mp0) REVERT: F 36 THR cc_start: 0.3452 (p) cc_final: 0.2922 (p) REVERT: F 99 TYR cc_start: 0.2944 (m-80) cc_final: 0.2640 (m-80) REVERT: F 129 PHE cc_start: 0.1039 (m-80) cc_final: 0.0668 (m-80) REVERT: F 306 LYS cc_start: 0.3576 (ttpt) cc_final: 0.3159 (tptt) REVERT: F 457 GLU cc_start: 0.2640 (tt0) cc_final: 0.2438 (mt-10) REVERT: N 50 MET cc_start: 0.4301 (mtt) cc_final: 0.3593 (mmt) REVERT: N 112 GLU cc_start: 0.2444 (mt-10) cc_final: 0.2072 (mp0) REVERT: G 36 THR cc_start: 0.3174 (p) cc_final: 0.2861 (p) REVERT: G 44 ILE cc_start: 0.2531 (mt) cc_final: 0.2322 (pt) REVERT: G 99 TYR cc_start: 0.2940 (m-80) cc_final: 0.2626 (m-80) REVERT: G 129 PHE cc_start: 0.1018 (m-80) cc_final: 0.0609 (m-80) REVERT: G 306 LYS cc_start: 0.3573 (ttpt) cc_final: 0.3157 (tptt) REVERT: G 457 GLU cc_start: 0.2884 (tt0) cc_final: 0.2637 (mt-10) REVERT: O 50 MET cc_start: 0.4314 (mtt) cc_final: 0.3611 (mmt) REVERT: O 112 GLU cc_start: 0.2415 (mt-10) cc_final: 0.2051 (mp0) REVERT: H 20 LYS cc_start: 0.1140 (mttt) cc_final: 0.0902 (ttpt) REVERT: H 36 THR cc_start: 0.3168 (p) cc_final: 0.2858 (p) REVERT: H 99 TYR cc_start: 0.3008 (m-80) cc_final: 0.2692 (m-80) REVERT: H 129 PHE cc_start: 0.1034 (m-80) cc_final: 0.0722 (m-80) REVERT: H 133 LYS cc_start: 0.3205 (tptp) cc_final: 0.2993 (mtmm) REVERT: H 306 LYS cc_start: 0.3555 (ttpt) cc_final: 0.3146 (tptt) REVERT: H 457 GLU cc_start: 0.2734 (tt0) cc_final: 0.2488 (mt-10) REVERT: P 50 MET cc_start: 0.4324 (mtt) cc_final: 0.3646 (mmt) REVERT: P 112 GLU cc_start: 0.2449 (mt-10) cc_final: 0.2055 (mp0) outliers start: 37 outliers final: 8 residues processed: 678 average time/residue: 0.2469 time to fit residues: 268.0190 Evaluate side-chains 441 residues out of total 3936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 433 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain H residue 281 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 432 optimal weight: 1.9990 chunk 197 optimal weight: 0.6980 chunk 388 optimal weight: 5.9990 chunk 455 optimal weight: 5.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 5.9990 chunk 248 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 61.6386 > 50:) chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 HIS A 288 ASN A 295 HIS A 387 GLN A 415 GLN I 22 GLN I 37 HIS B 215 HIS B 288 ASN B 387 GLN B 415 GLN J 22 GLN J 37 HIS C 215 HIS C 288 ASN C 295 HIS C 387 GLN C 415 GLN K 22 GLN K 37 HIS D 215 HIS D 288 ASN D 295 HIS D 387 GLN D 415 GLN L 22 GLN L 37 HIS E 215 HIS E 288 ASN E 295 HIS E 387 GLN E 415 GLN M 22 GLN M 37 HIS F 215 HIS F 288 ASN F 387 GLN F 415 GLN N 22 GLN N 37 HIS G 215 HIS G 288 ASN G 387 GLN O 22 GLN O 37 HIS H 215 HIS H 288 ASN H 387 GLN H 415 GLN P 22 GLN P 37 HIS Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.175160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.142176 restraints weight = 266101.849| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 6.19 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3373 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3373 r_free = 0.3373 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3369 r_free = 0.3369 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 159 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3369 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 38728 Z= 0.137 Angle : 0.596 7.243 52544 Z= 0.307 Chirality : 0.043 0.174 5616 Planarity : 0.005 0.035 6800 Dihedral : 7.305 175.181 5408 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.86 % Allowed : 7.57 % Favored : 91.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 (0.11), residues: 4712 helix: 0.10 (0.11), residues: 1760 sheet: 0.05 (0.17), residues: 880 loop : -1.49 (0.12), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 219 TYR 0.017 0.002 TYR A 346 PHE 0.016 0.002 PHE H 213 TRP 0.013 0.002 TRP A 318 HIS 0.005 0.001 HIS D 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (38728) covalent geometry : angle 0.59577 / 0.31 (52544) hydrogen bonds : bond 0.04153 / 2.72 ( 1468) hydrogen bonds : angle 4.50466 / 3.12 ( 4188) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 3936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 514 time to evaluate : 1.164 Fit side-chains REVERT: A 252 MET cc_start: 0.8071 (ttt) cc_final: 0.7782 (ttm) REVERT: A 283 GLU cc_start: 0.6885 (tt0) cc_final: 0.6571 (mp0) REVERT: A 286 ARG cc_start: 0.6978 (tpp80) cc_final: 0.6689 (tpm170) REVERT: A 306 LYS cc_start: 0.8341 (ttpt) cc_final: 0.7623 (tptt) REVERT: A 371 ASP cc_start: 0.6762 (m-30) cc_final: 0.6527 (m-30) REVERT: A 447 ARG cc_start: 0.6144 (mtt90) cc_final: 0.5853 (mtp180) REVERT: I 50 MET cc_start: 0.7282 (mtt) cc_final: 0.6722 (mmt) REVERT: I 112 GLU cc_start: 0.6792 (mt-10) cc_final: 0.6552 (mp0) REVERT: B 36 THR cc_start: 0.8126 (p) cc_final: 0.7810 (p) REVERT: B 41 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8561 (tp) REVERT: B 252 MET cc_start: 0.8037 (ttt) cc_final: 0.7716 (ttm) REVERT: B 283 GLU cc_start: 0.6921 (tt0) cc_final: 0.6576 (mp0) REVERT: B 286 ARG cc_start: 0.6890 (tpp80) cc_final: 0.6587 (tpm170) REVERT: B 306 LYS cc_start: 0.8301 (ttpt) cc_final: 0.7705 (tptt) REVERT: B 366 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7347 (mt-10) REVERT: B 447 ARG cc_start: 0.6020 (mtt90) cc_final: 0.5637 (mtp180) REVERT: J 50 MET cc_start: 0.7129 (mtt) cc_final: 0.6613 (mmt) REVERT: J 78 ARG cc_start: 0.8583 (mtp85) cc_final: 0.8368 (mtp85) REVERT: J 112 GLU cc_start: 0.6695 (mt-10) cc_final: 0.6442 (mp0) REVERT: C 36 THR cc_start: 0.7918 (p) cc_final: 0.7594 (p) REVERT: C 73 THR cc_start: 0.6881 (p) cc_final: 0.6561 (p) REVERT: C 249 MET cc_start: 0.7566 (tpp) cc_final: 0.7314 (mmm) REVERT: C 252 MET cc_start: 0.8162 (ttt) cc_final: 0.7870 (ttm) REVERT: C 253 TYR cc_start: 0.7811 (m-10) cc_final: 0.7605 (m-10) REVERT: C 283 GLU cc_start: 0.7061 (tt0) cc_final: 0.6482 (mp0) REVERT: C 286 ARG cc_start: 0.6857 (tpp80) cc_final: 0.6553 (tpm170) REVERT: C 306 LYS cc_start: 0.8286 (ttpt) cc_final: 0.7666 (tptt) REVERT: C 366 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7384 (mt-10) REVERT: C 447 ARG cc_start: 0.6152 (mtt90) cc_final: 0.5735 (mtp180) REVERT: K 50 MET cc_start: 0.7111 (mtt) cc_final: 0.6534 (mmt) REVERT: K 78 ARG cc_start: 0.8580 (mtp85) cc_final: 0.8363 (mtp85) REVERT: K 112 GLU cc_start: 0.6680 (mt-10) cc_final: 0.6414 (mp0) REVERT: D 20 LYS cc_start: 0.6329 (mttt) cc_final: 0.5633 (mtmt) REVERT: D 249 MET cc_start: 0.7605 (tpp) cc_final: 0.7325 (mmm) REVERT: D 252 MET cc_start: 0.8099 (ttt) cc_final: 0.7815 (ttm) REVERT: D 253 TYR cc_start: 0.7851 (m-10) cc_final: 0.7634 (m-10) REVERT: D 283 GLU cc_start: 0.7150 (tt0) cc_final: 0.6707 (mp0) REVERT: D 286 ARG cc_start: 0.6975 (tpp80) cc_final: 0.6638 (tpm170) REVERT: D 306 LYS cc_start: 0.8279 (ttpt) cc_final: 0.7529 (tptt) REVERT: D 366 GLU cc_start: 0.7407 (mt-10) cc_final: 0.7162 (mt-10) REVERT: D 447 ARG cc_start: 0.6063 (mtt90) cc_final: 0.5748 (mtp180) REVERT: L 39 ASP cc_start: 0.7424 (p0) cc_final: 0.7199 (p0) REVERT: L 50 MET cc_start: 0.7173 (mtt) cc_final: 0.6666 (mmt) REVERT: L 78 ARG cc_start: 0.8619 (mtp85) cc_final: 0.8318 (mtp85) REVERT: L 112 GLU cc_start: 0.6685 (mt-10) cc_final: 0.6405 (mp0) REVERT: E 20 LYS cc_start: 0.6310 (mttt) cc_final: 0.5579 (mtmt) REVERT: E 36 THR cc_start: 0.7942 (p) cc_final: 0.7606 (p) REVERT: E 249 MET cc_start: 0.7082 (mmm) cc_final: 0.6845 (mmm) REVERT: E 252 MET cc_start: 0.8161 (ttt) cc_final: 0.7769 (ttm) REVERT: E 253 TYR cc_start: 0.8014 (m-10) cc_final: 0.7662 (m-10) REVERT: E 283 GLU cc_start: 0.7024 (tt0) cc_final: 0.6732 (mp0) REVERT: E 286 ARG cc_start: 0.6948 (tpp80) cc_final: 0.6648 (tpm170) REVERT: E 306 LYS cc_start: 0.8236 (ttpt) cc_final: 0.7658 (tptt) REVERT: E 366 GLU cc_start: 0.7618 (mt-10) cc_final: 0.7363 (mt-10) REVERT: E 371 ASP cc_start: 0.6401 (m-30) cc_final: 0.6136 (m-30) REVERT: E 447 ARG cc_start: 0.6086 (mtt90) cc_final: 0.5680 (mtp180) REVERT: M 50 MET cc_start: 0.7196 (mtt) cc_final: 0.6601 (mmt) REVERT: M 78 ARG cc_start: 0.8583 (mtp85) cc_final: 0.8353 (mtp85) REVERT: F 36 THR cc_start: 0.8011 (p) cc_final: 0.7686 (p) REVERT: F 196 LYS cc_start: 0.8010 (tttt) cc_final: 0.7622 (tttm) REVERT: F 249 MET cc_start: 0.7019 (mmm) cc_final: 0.6739 (mmm) REVERT: F 252 MET cc_start: 0.8123 (ttt) cc_final: 0.7814 (ttm) REVERT: F 253 TYR cc_start: 0.7866 (m-10) cc_final: 0.7536 (m-10) REVERT: F 283 GLU cc_start: 0.6911 (tt0) cc_final: 0.6605 (mp0) REVERT: F 286 ARG cc_start: 0.7001 (tpp80) cc_final: 0.6680 (tpm170) REVERT: F 306 LYS cc_start: 0.8191 (ttpt) cc_final: 0.7554 (tptt) REVERT: F 366 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7288 (mt-10) REVERT: F 447 ARG cc_start: 0.6100 (mtt90) cc_final: 0.5657 (mtp180) REVERT: N 50 MET cc_start: 0.7262 (mtt) cc_final: 0.6665 (mmt) REVERT: N 78 ARG cc_start: 0.8567 (mtp85) cc_final: 0.8354 (mtp85) REVERT: N 112 GLU cc_start: 0.6602 (mt-10) cc_final: 0.6327 (mp0) REVERT: G 20 LYS cc_start: 0.6221 (mttt) cc_final: 0.5217 (mtmt) REVERT: G 34 LYS cc_start: 0.6184 (tptm) cc_final: 0.5980 (tptp) REVERT: G 196 LYS cc_start: 0.7989 (tttt) cc_final: 0.7624 (tttm) REVERT: G 252 MET cc_start: 0.7988 (ttt) cc_final: 0.7653 (ttm) REVERT: G 283 GLU cc_start: 0.6843 (tt0) cc_final: 0.6470 (mp0) REVERT: G 286 ARG cc_start: 0.6946 (tpp80) cc_final: 0.6650 (tpm170) REVERT: G 306 LYS cc_start: 0.8381 (ttpt) cc_final: 0.7771 (tptt) REVERT: G 371 ASP cc_start: 0.6611 (m-30) cc_final: 0.6356 (m-30) REVERT: O 50 MET cc_start: 0.7235 (mtt) cc_final: 0.6705 (mmt) REVERT: O 112 GLU cc_start: 0.6662 (mt-10) cc_final: 0.6460 (mp0) REVERT: H 20 LYS cc_start: 0.6090 (mttt) cc_final: 0.5369 (mtmt) REVERT: H 196 LYS cc_start: 0.7912 (tttt) cc_final: 0.7582 (tttm) REVERT: H 252 MET cc_start: 0.7989 (ttt) cc_final: 0.7709 (ttm) REVERT: H 283 GLU cc_start: 0.7035 (tt0) cc_final: 0.6682 (mp0) REVERT: H 286 ARG cc_start: 0.7004 (tpp80) cc_final: 0.6695 (tpm170) REVERT: H 306 LYS cc_start: 0.8191 (ttpt) cc_final: 0.7569 (tptt) REVERT: H 366 GLU cc_start: 0.7445 (mt-10) cc_final: 0.7180 (mt-10) REVERT: H 447 ARG cc_start: 0.5932 (mtt90) cc_final: 0.5719 (mtp180) REVERT: P 50 MET cc_start: 0.7110 (mtt) cc_final: 0.6559 (mmt) outliers start: 34 outliers final: 25 residues processed: 548 average time/residue: 0.2782 time to fit residues: 232.7814 Evaluate side-chains 474 residues out of total 3936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 448 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain J residue 38 THR Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 342 THR Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain F residue 264 SER Chi-restraints excluded: chain F residue 342 THR Chi-restraints excluded: chain N residue 38 THR Chi-restraints excluded: chain G residue 264 SER Chi-restraints excluded: chain G residue 342 THR Chi-restraints excluded: chain O residue 38 THR Chi-restraints excluded: chain H residue 264 SER Chi-restraints excluded: chain H residue 342 THR Chi-restraints excluded: chain P residue 38 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 424 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 4.9990 chunk 456 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 258 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 144 optimal weight: 4.9990 chunk 386 optimal weight: 0.0030 overall best weight: 1.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 326 HIS A 421 ASN A 433 ASN B 326 HIS B 421 ASN B 433 ASN C 326 HIS C 421 ASN C 433 ASN ** D 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 326 HIS D 421 ASN D 433 ASN L 18 GLN E 326 HIS E 421 ASN E 433 ASN F 326 HIS F 421 ASN G 415 GLN G 421 ASN G 433 ASN ** H 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 421 ASN H 433 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.164344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.129567 restraints weight = 269306.424| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 6.32 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3229 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 159 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 218 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3227 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 38728 Z= 0.165 Angle : 0.637 6.787 52544 Z= 0.323 Chirality : 0.044 0.142 5616 Planarity : 0.005 0.041 6800 Dihedral : 7.489 179.708 5392 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.88 % Allowed : 9.17 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.61 (0.11), residues: 4712 helix: 0.61 (0.12), residues: 1768 sheet: 0.08 (0.17), residues: 816 loop : -1.48 (0.12), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 304 TYR 0.023 0.002 TYR H 241 PHE 0.016 0.003 PHE A 201 TRP 0.009 0.001 TRP I 75 HIS 0.006 0.001 HIS F 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.17 (38728) covalent geometry : angle 0.63743 / 0.32 (52544) hydrogen bonds : bond 0.04471 / 2.94 ( 1468) hydrogen bonds : angle 4.51971 / 3.11 ( 4188) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 3936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 537 time to evaluate : 1.405 Fit side-chains REVERT: A 73 THR cc_start: 0.6757 (OUTLIER) cc_final: 0.6291 (p) REVERT: A 129 PHE cc_start: 0.7063 (OUTLIER) cc_final: 0.5976 (m-80) REVERT: A 207 ASN cc_start: 0.8521 (p0) cc_final: 0.8299 (p0) REVERT: A 249 MET cc_start: 0.7886 (tpp) cc_final: 0.7684 (mmm) REVERT: A 252 MET cc_start: 0.8060 (ttt) cc_final: 0.7688 (ttm) REVERT: A 306 LYS cc_start: 0.8452 (ttpt) cc_final: 0.7857 (tptt) REVERT: A 361 ARG cc_start: 0.7183 (mtt90) cc_final: 0.6951 (mtt90) REVERT: A 373 ARG cc_start: 0.7829 (mmt90) cc_final: 0.7043 (mtm-85) REVERT: A 447 ARG cc_start: 0.6026 (mtt90) cc_final: 0.5555 (mtp180) REVERT: I 50 MET cc_start: 0.7415 (mtt) cc_final: 0.7169 (mtm) REVERT: I 108 SER cc_start: 0.7596 (p) cc_final: 0.7347 (m) REVERT: I 112 GLU cc_start: 0.6960 (mt-10) cc_final: 0.6532 (mp0) REVERT: B 35 ASP cc_start: 0.6184 (m-30) cc_final: 0.5909 (m-30) REVERT: B 73 THR cc_start: 0.6746 (OUTLIER) cc_final: 0.6284 (p) REVERT: B 129 PHE cc_start: 0.7078 (OUTLIER) cc_final: 0.6021 (m-80) REVERT: B 207 ASN cc_start: 0.8461 (p0) cc_final: 0.8210 (p0) REVERT: B 283 GLU cc_start: 0.7165 (tt0) cc_final: 0.6631 (mp0) REVERT: B 306 LYS cc_start: 0.8435 (ttpt) cc_final: 0.7776 (tppt) REVERT: B 373 ARG cc_start: 0.7743 (mmt90) cc_final: 0.6973 (mtm-85) REVERT: B 447 ARG cc_start: 0.6216 (mtt90) cc_final: 0.5734 (mtp180) REVERT: J 108 SER cc_start: 0.7676 (p) cc_final: 0.7450 (m) REVERT: J 112 GLU cc_start: 0.6925 (mt-10) cc_final: 0.6551 (mp0) REVERT: C 35 ASP cc_start: 0.6207 (m-30) cc_final: 0.5922 (m-30) REVERT: C 73 THR cc_start: 0.6749 (OUTLIER) cc_final: 0.6328 (p) REVERT: C 129 PHE cc_start: 0.6926 (OUTLIER) cc_final: 0.5845 (m-80) REVERT: C 207 ASN cc_start: 0.8502 (p0) cc_final: 0.8233 (p0) REVERT: C 252 MET cc_start: 0.8228 (ttt) cc_final: 0.7829 (ttm) REVERT: C 283 GLU cc_start: 0.7043 (tt0) cc_final: 0.6472 (mp0) REVERT: C 286 ARG cc_start: 0.6962 (tpp80) cc_final: 0.6213 (tpm170) REVERT: C 306 LYS cc_start: 0.8410 (ttpt) cc_final: 0.7807 (tptt) REVERT: C 447 ARG cc_start: 0.6075 (mtt90) cc_final: 0.5638 (mtp180) REVERT: K 50 MET cc_start: 0.7381 (mtt) cc_final: 0.7143 (mtm) REVERT: K 108 SER cc_start: 0.7677 (p) cc_final: 0.7386 (m) REVERT: K 112 GLU cc_start: 0.6897 (mt-10) cc_final: 0.6526 (mp0) REVERT: D 20 LYS cc_start: 0.6589 (mttt) cc_final: 0.5692 (mtmt) REVERT: D 73 THR cc_start: 0.6658 (OUTLIER) cc_final: 0.6185 (p) REVERT: D 108 ILE cc_start: 0.7924 (pt) cc_final: 0.7387 (tp) REVERT: D 129 PHE cc_start: 0.6957 (OUTLIER) cc_final: 0.5894 (m-80) REVERT: D 283 GLU cc_start: 0.7211 (tt0) cc_final: 0.6722 (mp0) REVERT: D 306 LYS cc_start: 0.8391 (ttpt) cc_final: 0.7769 (tptt) REVERT: D 361 ARG cc_start: 0.7212 (mtt90) cc_final: 0.6951 (mtt90) REVERT: D 373 ARG cc_start: 0.7684 (mmt90) cc_final: 0.6920 (mtm-85) REVERT: D 447 ARG cc_start: 0.6238 (mtt90) cc_final: 0.5766 (mtp180) REVERT: L 108 SER cc_start: 0.7640 (p) cc_final: 0.7394 (m) REVERT: L 112 GLU cc_start: 0.6927 (mt-10) cc_final: 0.6592 (mp0) REVERT: E 35 ASP cc_start: 0.6306 (m-30) cc_final: 0.5912 (m-30) REVERT: E 36 THR cc_start: 0.8275 (p) cc_final: 0.8034 (p) REVERT: E 73 THR cc_start: 0.6864 (OUTLIER) cc_final: 0.6377 (p) REVERT: E 83 ARG cc_start: 0.6180 (mtt180) cc_final: 0.5966 (mtm180) REVERT: E 129 PHE cc_start: 0.7001 (OUTLIER) cc_final: 0.5929 (m-80) REVERT: E 207 ASN cc_start: 0.8508 (p0) cc_final: 0.8298 (p0) REVERT: E 283 GLU cc_start: 0.7169 (tt0) cc_final: 0.6607 (mp0) REVERT: E 306 LYS cc_start: 0.8446 (ttpt) cc_final: 0.7832 (tptt) REVERT: E 361 ARG cc_start: 0.6648 (ttm170) cc_final: 0.6418 (ttm170) REVERT: E 373 ARG cc_start: 0.7740 (mmt90) cc_final: 0.6915 (mtm-85) REVERT: E 447 ARG cc_start: 0.6301 (mtt90) cc_final: 0.5796 (mtp180) REVERT: M 50 MET cc_start: 0.7387 (mtt) cc_final: 0.7123 (mtm) REVERT: M 108 SER cc_start: 0.7679 (p) cc_final: 0.7366 (m) REVERT: F 35 ASP cc_start: 0.6299 (m-30) cc_final: 0.5914 (m-30) REVERT: F 36 THR cc_start: 0.8247 (p) cc_final: 0.8025 (p) REVERT: F 73 THR cc_start: 0.6863 (OUTLIER) cc_final: 0.6405 (p) REVERT: F 129 PHE cc_start: 0.7132 (OUTLIER) cc_final: 0.6042 (m-80) REVERT: F 207 ASN cc_start: 0.8300 (p0) cc_final: 0.8054 (p0) REVERT: F 283 GLU cc_start: 0.7090 (tt0) cc_final: 0.6581 (mp0) REVERT: F 306 LYS cc_start: 0.8384 (ttpt) cc_final: 0.7758 (tptt) REVERT: F 361 ARG cc_start: 0.7254 (mtt90) cc_final: 0.6992 (mtt90) REVERT: F 373 ARG cc_start: 0.7880 (mmt90) cc_final: 0.7095 (mtm-85) REVERT: F 447 ARG cc_start: 0.6216 (mtt90) cc_final: 0.5737 (mtp180) REVERT: N 50 MET cc_start: 0.7466 (mtt) cc_final: 0.7227 (mtm) REVERT: N 108 SER cc_start: 0.7734 (p) cc_final: 0.7489 (m) REVERT: N 112 GLU cc_start: 0.6913 (mt-10) cc_final: 0.6552 (mp0) REVERT: G 20 LYS cc_start: 0.6353 (mttt) cc_final: 0.5265 (mtmt) REVERT: G 73 THR cc_start: 0.7039 (OUTLIER) cc_final: 0.6582 (p) REVERT: G 102 TYR cc_start: 0.8546 (m-80) cc_final: 0.8329 (m-80) REVERT: G 129 PHE cc_start: 0.6967 (OUTLIER) cc_final: 0.5848 (m-80) REVERT: G 207 ASN cc_start: 0.8407 (p0) cc_final: 0.8093 (p0) REVERT: G 249 MET cc_start: 0.7453 (mmm) cc_final: 0.7129 (mmm) REVERT: G 306 LYS cc_start: 0.8413 (ttpt) cc_final: 0.7797 (tptt) REVERT: G 373 ARG cc_start: 0.7790 (mmt90) cc_final: 0.6955 (mtm-85) REVERT: O 108 SER cc_start: 0.7643 (p) cc_final: 0.7398 (m) REVERT: O 112 GLU cc_start: 0.6886 (mt-10) cc_final: 0.6466 (mp0) REVERT: H 20 LYS cc_start: 0.6540 (mttt) cc_final: 0.5685 (mtmt) REVERT: H 73 THR cc_start: 0.6745 (OUTLIER) cc_final: 0.6265 (p) REVERT: H 129 PHE cc_start: 0.7079 (OUTLIER) cc_final: 0.5974 (m-80) REVERT: H 133 LYS cc_start: 0.8081 (OUTLIER) cc_final: 0.7560 (mtmm) REVERT: H 283 GLU cc_start: 0.7155 (tt0) cc_final: 0.6558 (mp0) REVERT: H 306 LYS cc_start: 0.8296 (ttpt) cc_final: 0.7702 (tptt) REVERT: H 373 ARG cc_start: 0.7784 (mmt90) cc_final: 0.6975 (mtm-85) REVERT: H 447 ARG cc_start: 0.6454 (mtt90) cc_final: 0.5982 (mtp180) REVERT: P 50 MET cc_start: 0.7504 (mtt) cc_final: 0.7213 (mtm) REVERT: P 108 SER cc_start: 0.7669 (p) cc_final: 0.7363 (m) outliers start: 74 outliers final: 46 residues processed: 597 average time/residue: 0.2434 time to fit residues: 229.7422 Evaluate side-chains 515 residues out of total 3936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 452 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 355 ASN Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain J residue 38 THR Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 129 PHE Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain D residue 355 ASN Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 129 PHE Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 342 THR Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 129 PHE Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 342 THR Chi-restraints excluded: chain F residue 355 ASN Chi-restraints excluded: chain F residue 357 VAL Chi-restraints excluded: chain N residue 38 THR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 129 PHE Chi-restraints excluded: chain G residue 265 VAL Chi-restraints excluded: chain G residue 342 THR Chi-restraints excluded: chain G residue 355 ASN Chi-restraints excluded: chain G residue 357 VAL Chi-restraints excluded: chain O residue 38 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 129 PHE Chi-restraints excluded: chain H residue 133 LYS Chi-restraints excluded: chain H residue 265 VAL Chi-restraints excluded: chain H residue 281 ILE Chi-restraints excluded: chain H residue 342 THR Chi-restraints excluded: chain H residue 355 ASN Chi-restraints excluded: chain H residue 357 VAL Chi-restraints excluded: chain P residue 38 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 48 optimal weight: 1.9990 chunk 316 optimal weight: 0.7980 chunk 409 optimal weight: 0.9980 chunk 128 optimal weight: 3.9990 chunk 272 optimal weight: 8.9990 chunk 361 optimal weight: 1.9990 chunk 414 optimal weight: 0.0070 chunk 308 optimal weight: 2.9990 chunk 461 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 158 optimal weight: 9.9990 overall best weight: 1.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 326 HIS A 415 GLN B 415 GLN C 326 HIS C 415 GLN D 415 GLN E 326 HIS E 415 GLN F 326 HIS F 415 GLN G 415 GLN H 415 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.163679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.128705 restraints weight = 265056.002| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 6.07 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3220 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3220 r_free = 0.3220 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 218 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3220 r_free = 0.3220 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 172 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3220 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 38728 Z= 0.132 Angle : 0.564 5.803 52544 Z= 0.286 Chirality : 0.042 0.137 5616 Planarity : 0.004 0.037 6800 Dihedral : 7.280 178.352 5392 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.74 % Allowed : 11.03 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.31 (0.12), residues: 4712 helix: 0.94 (0.12), residues: 1760 sheet: 0.29 (0.18), residues: 800 loop : -1.39 (0.12), residues: 2152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 361 TYR 0.011 0.001 TYR N 47 PHE 0.013 0.002 PHE D 100 TRP 0.006 0.001 TRP J 51 HIS 0.004 0.001 HIS E 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.13 (38728) covalent geometry : angle 0.56396 / 0.29 (52544) hydrogen bonds : bond 0.03582 / 2.35 ( 1468) hydrogen bonds : angle 4.31896 / 2.99 ( 4188) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 3936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 480 time to evaluate : 1.395 Fit side-chains REVERT: A 73 THR cc_start: 0.6792 (p) cc_final: 0.6338 (p) REVERT: A 108 ILE cc_start: 0.7599 (OUTLIER) cc_final: 0.7273 (tp) REVERT: A 129 PHE cc_start: 0.7208 (OUTLIER) cc_final: 0.6183 (m-80) REVERT: A 207 ASN cc_start: 0.8615 (p0) cc_final: 0.8377 (p0) REVERT: A 252 MET cc_start: 0.8055 (ttt) cc_final: 0.7729 (ttm) REVERT: A 306 LYS cc_start: 0.8511 (ttpt) cc_final: 0.7876 (tptt) REVERT: A 371 ASP cc_start: 0.6480 (m-30) cc_final: 0.6241 (m-30) REVERT: A 447 ARG cc_start: 0.6218 (mtt90) cc_final: 0.5716 (mtp180) REVERT: A 460 LEU cc_start: 0.7394 (mt) cc_final: 0.7178 (mt) REVERT: I 50 MET cc_start: 0.7414 (mtt) cc_final: 0.6751 (mmt) REVERT: I 108 SER cc_start: 0.7834 (p) cc_final: 0.7489 (m) REVERT: I 112 GLU cc_start: 0.6812 (mt-10) cc_final: 0.6553 (mp0) REVERT: B 35 ASP cc_start: 0.6121 (m-30) cc_final: 0.5814 (m-30) REVERT: B 41 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8665 (tp) REVERT: B 73 THR cc_start: 0.6765 (OUTLIER) cc_final: 0.6315 (p) REVERT: B 129 PHE cc_start: 0.7185 (OUTLIER) cc_final: 0.6192 (m-80) REVERT: B 252 MET cc_start: 0.8086 (ttt) cc_final: 0.7726 (ttm) REVERT: B 306 LYS cc_start: 0.8526 (ttpt) cc_final: 0.7839 (tptt) REVERT: B 373 ARG cc_start: 0.7727 (mmt90) cc_final: 0.6969 (mtm-85) REVERT: B 447 ARG cc_start: 0.6228 (mtt90) cc_final: 0.5731 (mtp180) REVERT: B 460 LEU cc_start: 0.7488 (mt) cc_final: 0.7262 (mt) REVERT: J 50 MET cc_start: 0.7486 (mtt) cc_final: 0.6794 (mmt) REVERT: J 108 SER cc_start: 0.7814 (p) cc_final: 0.7554 (m) REVERT: J 112 GLU cc_start: 0.7073 (mt-10) cc_final: 0.6713 (mp0) REVERT: C 35 ASP cc_start: 0.6162 (m-30) cc_final: 0.5828 (m-30) REVERT: C 73 THR cc_start: 0.6675 (OUTLIER) cc_final: 0.6231 (p) REVERT: C 129 PHE cc_start: 0.7031 (OUTLIER) cc_final: 0.5995 (m-80) REVERT: C 205 ASP cc_start: 0.7705 (t70) cc_final: 0.7396 (t0) REVERT: C 252 MET cc_start: 0.8234 (ttt) cc_final: 0.7856 (ttm) REVERT: C 286 ARG cc_start: 0.7224 (tpp80) cc_final: 0.6269 (tpm170) REVERT: C 306 LYS cc_start: 0.8428 (ttpt) cc_final: 0.7745 (tptt) REVERT: C 447 ARG cc_start: 0.6243 (mtt90) cc_final: 0.5777 (mtp180) REVERT: K 39 ASP cc_start: 0.7686 (p0) cc_final: 0.7439 (p0) REVERT: K 50 MET cc_start: 0.7514 (mtt) cc_final: 0.6818 (mmt) REVERT: K 108 SER cc_start: 0.7859 (p) cc_final: 0.7575 (m) REVERT: K 112 GLU cc_start: 0.6774 (mt-10) cc_final: 0.6420 (mp0) REVERT: D 20 LYS cc_start: 0.6412 (mttt) cc_final: 0.5573 (mtmt) REVERT: D 35 ASP cc_start: 0.6395 (m-30) cc_final: 0.6059 (m-30) REVERT: D 73 THR cc_start: 0.6719 (OUTLIER) cc_final: 0.6288 (p) REVERT: D 129 PHE cc_start: 0.7067 (OUTLIER) cc_final: 0.6090 (m-80) REVERT: D 252 MET cc_start: 0.8144 (ttt) cc_final: 0.7811 (ttm) REVERT: D 306 LYS cc_start: 0.8473 (ttpt) cc_final: 0.7833 (tptt) REVERT: D 447 ARG cc_start: 0.6273 (mtt90) cc_final: 0.5786 (mtp180) REVERT: D 460 LEU cc_start: 0.7411 (mt) cc_final: 0.7205 (mt) REVERT: L 39 ASP cc_start: 0.7769 (p0) cc_final: 0.7522 (p0) REVERT: L 50 MET cc_start: 0.7414 (mtt) cc_final: 0.6697 (mmt) REVERT: L 108 SER cc_start: 0.7901 (p) cc_final: 0.7567 (m) REVERT: L 112 GLU cc_start: 0.6870 (mt-10) cc_final: 0.6525 (mp0) REVERT: E 35 ASP cc_start: 0.6186 (m-30) cc_final: 0.5866 (m-30) REVERT: E 73 THR cc_start: 0.6753 (OUTLIER) cc_final: 0.6293 (p) REVERT: E 108 ILE cc_start: 0.7599 (OUTLIER) cc_final: 0.7245 (tp) REVERT: E 129 PHE cc_start: 0.7092 (OUTLIER) cc_final: 0.6107 (m-80) REVERT: E 207 ASN cc_start: 0.8600 (p0) cc_final: 0.8346 (p0) REVERT: E 252 MET cc_start: 0.8130 (ttt) cc_final: 0.7821 (ttm) REVERT: E 306 LYS cc_start: 0.8483 (ttpt) cc_final: 0.7770 (tptt) REVERT: E 373 ARG cc_start: 0.7902 (mmt90) cc_final: 0.7121 (mtm-85) REVERT: E 447 ARG cc_start: 0.6167 (mtt90) cc_final: 0.5658 (mtp180) REVERT: E 460 LEU cc_start: 0.7529 (mt) cc_final: 0.7317 (mt) REVERT: M 39 ASP cc_start: 0.7655 (p0) cc_final: 0.7407 (p0) REVERT: M 50 MET cc_start: 0.7458 (mtt) cc_final: 0.6751 (mmt) REVERT: M 108 SER cc_start: 0.7971 (p) cc_final: 0.7632 (m) REVERT: F 35 ASP cc_start: 0.6120 (m-30) cc_final: 0.5783 (m-30) REVERT: F 73 THR cc_start: 0.6851 (OUTLIER) cc_final: 0.6379 (p) REVERT: F 129 PHE cc_start: 0.7184 (OUTLIER) cc_final: 0.6170 (m-80) REVERT: F 252 MET cc_start: 0.8180 (ttt) cc_final: 0.7852 (ttm) REVERT: F 306 LYS cc_start: 0.8469 (ttpt) cc_final: 0.7814 (tptt) REVERT: F 373 ARG cc_start: 0.7740 (mmt90) cc_final: 0.6897 (mtm-85) REVERT: F 447 ARG cc_start: 0.6229 (mtt90) cc_final: 0.5731 (mtp180) REVERT: N 108 SER cc_start: 0.7886 (p) cc_final: 0.7606 (m) REVERT: N 112 GLU cc_start: 0.6865 (mt-10) cc_final: 0.6534 (mp0) REVERT: G 20 LYS cc_start: 0.6311 (mttt) cc_final: 0.5114 (mmtt) REVERT: G 73 THR cc_start: 0.6905 (OUTLIER) cc_final: 0.6437 (p) REVERT: G 102 TYR cc_start: 0.8528 (m-80) cc_final: 0.8308 (m-80) REVERT: G 129 PHE cc_start: 0.7141 (OUTLIER) cc_final: 0.6143 (m-80) REVERT: G 249 MET cc_start: 0.7459 (mmm) cc_final: 0.7087 (mmm) REVERT: G 252 MET cc_start: 0.7965 (ttt) cc_final: 0.7667 (ttm) REVERT: G 306 LYS cc_start: 0.8545 (ttpt) cc_final: 0.7857 (tptt) REVERT: G 373 ARG cc_start: 0.7756 (mmt90) cc_final: 0.6890 (mtm-85) REVERT: O 50 MET cc_start: 0.7439 (mtt) cc_final: 0.6730 (mmt) REVERT: O 108 SER cc_start: 0.7825 (p) cc_final: 0.7497 (m) REVERT: O 112 GLU cc_start: 0.6923 (mt-10) cc_final: 0.6566 (mp0) REVERT: H 73 THR cc_start: 0.6708 (OUTLIER) cc_final: 0.6282 (p) REVERT: H 83 ARG cc_start: 0.6505 (mtm180) cc_final: 0.6165 (mtp85) REVERT: H 108 ILE cc_start: 0.7499 (OUTLIER) cc_final: 0.7109 (tp) REVERT: H 129 PHE cc_start: 0.7175 (OUTLIER) cc_final: 0.6172 (m-80) REVERT: H 133 LYS cc_start: 0.8064 (OUTLIER) cc_final: 0.7519 (mtmm) REVERT: H 252 MET cc_start: 0.8124 (ttt) cc_final: 0.7823 (ttm) REVERT: H 306 LYS cc_start: 0.8453 (ttpt) cc_final: 0.7837 (tptt) REVERT: H 371 ASP cc_start: 0.6504 (m-30) cc_final: 0.6228 (m-30) REVERT: H 373 ARG cc_start: 0.7734 (mmt90) cc_final: 0.6982 (mtm-85) REVERT: H 447 ARG cc_start: 0.6240 (mtt90) cc_final: 0.5715 (mtp180) REVERT: P 50 MET cc_start: 0.7411 (mtt) cc_final: 0.6765 (mmt) REVERT: P 108 SER cc_start: 0.7853 (p) cc_final: 0.7486 (m) outliers start: 108 outliers final: 68 residues processed: 547 average time/residue: 0.2514 time to fit residues: 217.7271 Evaluate side-chains 555 residues out of total 3936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 467 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 355 ASN Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain J residue 38 THR Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 129 PHE Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain D residue 355 ASN Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 129 PHE Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain E residue 342 THR Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 105 VAL Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain F residue 129 PHE Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 342 THR Chi-restraints excluded: chain F residue 355 ASN Chi-restraints excluded: chain F residue 356 THR Chi-restraints excluded: chain F residue 357 VAL Chi-restraints excluded: chain N residue 38 THR Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 129 PHE Chi-restraints excluded: chain G residue 342 THR Chi-restraints excluded: chain G residue 355 ASN Chi-restraints excluded: chain G residue 356 THR Chi-restraints excluded: chain G residue 357 VAL Chi-restraints excluded: chain O residue 38 THR Chi-restraints excluded: chain O residue 105 VAL Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 108 ILE Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain H residue 129 PHE Chi-restraints excluded: chain H residue 133 LYS Chi-restraints excluded: chain H residue 342 THR Chi-restraints excluded: chain H residue 355 ASN Chi-restraints excluded: chain H residue 356 THR Chi-restraints excluded: chain H residue 357 VAL Chi-restraints excluded: chain P residue 38 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 50 optimal weight: 0.7980 chunk 373 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 460 optimal weight: 7.9990 chunk 435 optimal weight: 2.9990 chunk 350 optimal weight: 1.9990 chunk 169 optimal weight: 0.8980 chunk 241 optimal weight: 0.9990 chunk 286 optimal weight: 4.9990 chunk 51 optimal weight: 0.3980 chunk 181 optimal weight: 4.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 326 HIS ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 326 HIS F 326 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.164184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.129153 restraints weight = 265791.662| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 6.18 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3217 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 172 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 183 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3217 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 38728 Z= 0.121 Angle : 0.544 6.143 52544 Z= 0.275 Chirality : 0.042 0.131 5616 Planarity : 0.004 0.049 6800 Dihedral : 7.147 177.672 5392 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.28 % Allowed : 11.79 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.13 (0.12), residues: 4712 helix: 1.12 (0.12), residues: 1760 sheet: 0.32 (0.18), residues: 800 loop : -1.28 (0.12), residues: 2152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 361 TYR 0.012 0.001 TYR J 47 PHE 0.012 0.002 PHE C 100 TRP 0.006 0.001 TRP H 216 HIS 0.004 0.001 HIS G 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.12 (38728) covalent geometry : angle 0.54420 / 0.28 (52544) hydrogen bonds : bond 0.03437 / 2.26 ( 1468) hydrogen bonds : angle 4.20664 / 2.91 ( 4188) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 3936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 478 time to evaluate : 1.331 Fit side-chains REVERT: A 73 THR cc_start: 0.6617 (OUTLIER) cc_final: 0.6150 (p) REVERT: A 83 ARG cc_start: 0.6933 (mtp85) cc_final: 0.6723 (mtm180) REVERT: A 108 ILE cc_start: 0.7818 (OUTLIER) cc_final: 0.7274 (tp) REVERT: A 129 PHE cc_start: 0.7252 (OUTLIER) cc_final: 0.6179 (m-80) REVERT: A 207 ASN cc_start: 0.8748 (p0) cc_final: 0.8497 (p0) REVERT: A 252 MET cc_start: 0.8029 (ttt) cc_final: 0.7690 (ttm) REVERT: A 306 LYS cc_start: 0.8488 (ttpt) cc_final: 0.7747 (tptt) REVERT: A 447 ARG cc_start: 0.6298 (mtt90) cc_final: 0.5787 (mtp180) REVERT: A 460 LEU cc_start: 0.7299 (mt) cc_final: 0.7074 (mt) REVERT: I 39 ASP cc_start: 0.7812 (p0) cc_final: 0.7549 (p0) REVERT: I 50 MET cc_start: 0.7357 (mtt) cc_final: 0.6763 (mmt) REVERT: I 108 SER cc_start: 0.7831 (p) cc_final: 0.7466 (m) REVERT: I 112 GLU cc_start: 0.6919 (mt-10) cc_final: 0.6564 (mp0) REVERT: B 35 ASP cc_start: 0.6072 (m-30) cc_final: 0.5754 (m-30) REVERT: B 41 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8577 (tp) REVERT: B 73 THR cc_start: 0.6889 (OUTLIER) cc_final: 0.6417 (p) REVERT: B 83 ARG cc_start: 0.7021 (mtp85) cc_final: 0.6820 (mtm180) REVERT: B 129 PHE cc_start: 0.7096 (OUTLIER) cc_final: 0.6087 (m-80) REVERT: B 252 MET cc_start: 0.8199 (ttt) cc_final: 0.7858 (ttm) REVERT: B 306 LYS cc_start: 0.8577 (ttpt) cc_final: 0.7797 (tptt) REVERT: B 373 ARG cc_start: 0.7715 (mmt90) cc_final: 0.6938 (mtm-85) REVERT: B 447 ARG cc_start: 0.6188 (mtt90) cc_final: 0.5688 (mtp180) REVERT: B 460 LEU cc_start: 0.7435 (mt) cc_final: 0.7190 (mt) REVERT: J 50 MET cc_start: 0.7427 (mtt) cc_final: 0.6793 (mmt) REVERT: J 108 SER cc_start: 0.7723 (p) cc_final: 0.7449 (m) REVERT: J 112 GLU cc_start: 0.6828 (mt-10) cc_final: 0.6563 (mp0) REVERT: C 35 ASP cc_start: 0.6025 (m-30) cc_final: 0.5699 (m-30) REVERT: C 73 THR cc_start: 0.6677 (OUTLIER) cc_final: 0.6219 (p) REVERT: C 83 ARG cc_start: 0.6943 (mtp85) cc_final: 0.6737 (mtm180) REVERT: C 129 PHE cc_start: 0.7107 (OUTLIER) cc_final: 0.6069 (m-80) REVERT: C 252 MET cc_start: 0.8203 (ttt) cc_final: 0.7796 (ttm) REVERT: C 286 ARG cc_start: 0.7145 (tpp80) cc_final: 0.6204 (tpm170) REVERT: C 306 LYS cc_start: 0.8518 (ttpt) cc_final: 0.7753 (tptt) REVERT: C 447 ARG cc_start: 0.6222 (mtt90) cc_final: 0.5729 (mtp180) REVERT: K 50 MET cc_start: 0.7405 (mtt) cc_final: 0.6828 (mmt) REVERT: K 108 SER cc_start: 0.7799 (p) cc_final: 0.7480 (m) REVERT: K 112 GLU cc_start: 0.6870 (mt-10) cc_final: 0.6500 (mp0) REVERT: D 20 LYS cc_start: 0.6463 (mttt) cc_final: 0.5631 (mtmt) REVERT: D 35 ASP cc_start: 0.6322 (m-30) cc_final: 0.5951 (m-30) REVERT: D 73 THR cc_start: 0.6687 (OUTLIER) cc_final: 0.6209 (p) REVERT: D 83 ARG cc_start: 0.7007 (mtp85) cc_final: 0.6739 (mtm180) REVERT: D 129 PHE cc_start: 0.7191 (OUTLIER) cc_final: 0.6200 (m-80) REVERT: D 252 MET cc_start: 0.8116 (ttt) cc_final: 0.7815 (ttm) REVERT: D 306 LYS cc_start: 0.8488 (ttpt) cc_final: 0.7742 (tptt) REVERT: D 447 ARG cc_start: 0.6277 (mtt90) cc_final: 0.5764 (mtp180) REVERT: L 39 ASP cc_start: 0.7370 (p0) cc_final: 0.7116 (p0) REVERT: L 50 MET cc_start: 0.7352 (mtt) cc_final: 0.6719 (mmt) REVERT: L 108 SER cc_start: 0.7857 (p) cc_final: 0.7492 (m) REVERT: L 112 GLU cc_start: 0.6840 (mt-10) cc_final: 0.6482 (mp0) REVERT: E 35 ASP cc_start: 0.6094 (m-30) cc_final: 0.5786 (m-30) REVERT: E 73 THR cc_start: 0.6745 (OUTLIER) cc_final: 0.6289 (p) REVERT: E 108 ILE cc_start: 0.7586 (OUTLIER) cc_final: 0.7097 (tp) REVERT: E 129 PHE cc_start: 0.7151 (OUTLIER) cc_final: 0.6169 (m-80) REVERT: E 252 MET cc_start: 0.8133 (ttt) cc_final: 0.7765 (ttm) REVERT: E 306 LYS cc_start: 0.8552 (ttpt) cc_final: 0.7781 (tptt) REVERT: E 373 ARG cc_start: 0.7801 (mmt90) cc_final: 0.6991 (mtm-85) REVERT: E 447 ARG cc_start: 0.6318 (mtt90) cc_final: 0.5800 (mtp180) REVERT: M 39 ASP cc_start: 0.7516 (p0) cc_final: 0.7272 (p0) REVERT: M 50 MET cc_start: 0.7501 (mtt) cc_final: 0.6835 (mmt) REVERT: M 108 SER cc_start: 0.7940 (p) cc_final: 0.7542 (m) REVERT: F 35 ASP cc_start: 0.5915 (m-30) cc_final: 0.5564 (m-30) REVERT: F 73 THR cc_start: 0.6797 (OUTLIER) cc_final: 0.6325 (p) REVERT: F 129 PHE cc_start: 0.7185 (OUTLIER) cc_final: 0.6175 (m-80) REVERT: F 252 MET cc_start: 0.8210 (ttt) cc_final: 0.7821 (ttm) REVERT: F 286 ARG cc_start: 0.7742 (tpm170) cc_final: 0.7455 (tpm170) REVERT: F 306 LYS cc_start: 0.8505 (ttpt) cc_final: 0.7732 (tptt) REVERT: F 373 ARG cc_start: 0.7797 (mmt90) cc_final: 0.6997 (mtm-85) REVERT: F 447 ARG cc_start: 0.6188 (mtt90) cc_final: 0.5658 (mtp180) REVERT: N 50 MET cc_start: 0.7328 (mtt) cc_final: 0.6651 (mmt) REVERT: N 108 SER cc_start: 0.7816 (p) cc_final: 0.7487 (m) REVERT: N 112 GLU cc_start: 0.6824 (mt-10) cc_final: 0.6489 (mp0) REVERT: G 20 LYS cc_start: 0.6379 (mttt) cc_final: 0.5148 (mmtt) REVERT: G 73 THR cc_start: 0.6761 (OUTLIER) cc_final: 0.6307 (p) REVERT: G 129 PHE cc_start: 0.7116 (OUTLIER) cc_final: 0.6090 (m-80) REVERT: G 249 MET cc_start: 0.7515 (mmm) cc_final: 0.7166 (mmm) REVERT: G 252 MET cc_start: 0.8164 (ttt) cc_final: 0.7873 (ttm) REVERT: G 306 LYS cc_start: 0.8557 (ttpt) cc_final: 0.7774 (tptt) REVERT: G 373 ARG cc_start: 0.7804 (mmt90) cc_final: 0.6966 (mtm-85) REVERT: O 50 MET cc_start: 0.7399 (mtt) cc_final: 0.6908 (mmt) REVERT: O 108 SER cc_start: 0.7795 (p) cc_final: 0.7422 (m) REVERT: O 112 GLU cc_start: 0.7011 (mt-10) cc_final: 0.6556 (mp0) REVERT: H 73 THR cc_start: 0.6742 (OUTLIER) cc_final: 0.6276 (p) REVERT: H 108 ILE cc_start: 0.7525 (OUTLIER) cc_final: 0.7120 (tp) REVERT: H 129 PHE cc_start: 0.7125 (OUTLIER) cc_final: 0.6132 (m-80) REVERT: H 133 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7714 (mtmm) REVERT: H 252 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7799 (ttm) REVERT: H 306 LYS cc_start: 0.8393 (ttpt) cc_final: 0.7642 (tptt) REVERT: H 371 ASP cc_start: 0.6252 (m-30) cc_final: 0.6005 (m-30) REVERT: H 373 ARG cc_start: 0.7843 (mmt90) cc_final: 0.7058 (mtm-85) REVERT: H 447 ARG cc_start: 0.6137 (mtt90) cc_final: 0.5643 (mtp180) REVERT: P 50 MET cc_start: 0.7453 (mtt) cc_final: 0.6802 (mmt) REVERT: P 108 SER cc_start: 0.7830 (p) cc_final: 0.7427 (m) outliers start: 129 outliers final: 83 residues processed: 565 average time/residue: 0.2466 time to fit residues: 221.9223 Evaluate side-chains 572 residues out of total 3936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 467 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain I residue 88 THR Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 355 ASN Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain J residue 38 THR Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 88 THR Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 129 PHE Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain D residue 355 ASN Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 88 THR Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 129 PHE Chi-restraints excluded: chain E residue 196 LYS Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 342 THR Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 88 THR Chi-restraints excluded: chain M residue 111 MET Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain F residue 129 PHE Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 342 THR Chi-restraints excluded: chain F residue 355 ASN Chi-restraints excluded: chain F residue 356 THR Chi-restraints excluded: chain N residue 38 THR Chi-restraints excluded: chain N residue 88 THR Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 129 PHE Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 342 THR Chi-restraints excluded: chain G residue 355 ASN Chi-restraints excluded: chain G residue 356 THR Chi-restraints excluded: chain G residue 357 VAL Chi-restraints excluded: chain O residue 38 THR Chi-restraints excluded: chain O residue 88 THR Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 108 ILE Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain H residue 129 PHE Chi-restraints excluded: chain H residue 133 LYS Chi-restraints excluded: chain H residue 252 MET Chi-restraints excluded: chain H residue 265 VAL Chi-restraints excluded: chain H residue 342 THR Chi-restraints excluded: chain H residue 355 ASN Chi-restraints excluded: chain H residue 356 THR Chi-restraints excluded: chain H residue 357 VAL Chi-restraints excluded: chain P residue 38 THR Chi-restraints excluded: chain P residue 88 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 222 optimal weight: 4.9990 chunk 161 optimal weight: 10.0000 chunk 312 optimal weight: 2.9990 chunk 327 optimal weight: 10.0000 chunk 104 optimal weight: 2.9990 chunk 282 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 chunk 226 optimal weight: 0.9990 chunk 443 optimal weight: 9.9990 chunk 266 optimal weight: 3.9990 chunk 133 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 326 HIS ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 402 GLN ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 326 HIS ** G 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.159684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.124989 restraints weight = 269081.494| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 6.09 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3172 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 183 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 167 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3171 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 38728 Z= 0.180 Angle : 0.632 6.829 52544 Z= 0.318 Chirality : 0.045 0.139 5616 Planarity : 0.005 0.060 6800 Dihedral : 7.474 179.407 5392 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.46 % Allowed : 12.02 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.33 (0.12), residues: 4712 helix: 0.86 (0.12), residues: 1760 sheet: 0.19 (0.18), residues: 800 loop : -1.29 (0.12), residues: 2152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 361 TYR 0.015 0.002 TYR L 47 PHE 0.014 0.002 PHE C 100 TRP 0.008 0.001 TRP A 216 HIS 0.005 0.002 HIS F 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.18 (38728) covalent geometry : angle 0.63157 / 0.32 (52544) hydrogen bonds : bond 0.04097 / 2.71 ( 1468) hydrogen bonds : angle 4.54502 / 3.14 ( 4188) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 3936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 442 time to evaluate : 1.450 Fit side-chains REVERT: A 73 THR cc_start: 0.6748 (OUTLIER) cc_final: 0.6276 (p) REVERT: A 129 PHE cc_start: 0.7320 (OUTLIER) cc_final: 0.6300 (m-80) REVERT: A 207 ASN cc_start: 0.8708 (p0) cc_final: 0.8474 (p0) REVERT: A 306 LYS cc_start: 0.8467 (ttpt) cc_final: 0.7648 (tptt) REVERT: A 447 ARG cc_start: 0.6220 (mtt90) cc_final: 0.5664 (mtp180) REVERT: I 50 MET cc_start: 0.7390 (mtt) cc_final: 0.6786 (mmt) REVERT: I 108 SER cc_start: 0.7844 (p) cc_final: 0.7449 (m) REVERT: B 35 ASP cc_start: 0.6384 (m-30) cc_final: 0.6095 (m-30) REVERT: B 73 THR cc_start: 0.6977 (OUTLIER) cc_final: 0.6455 (p) REVERT: B 129 PHE cc_start: 0.7254 (OUTLIER) cc_final: 0.6270 (m-80) REVERT: B 283 GLU cc_start: 0.6964 (tt0) cc_final: 0.6533 (mp0) REVERT: B 306 LYS cc_start: 0.8610 (ttpt) cc_final: 0.7762 (tptt) REVERT: B 368 ASP cc_start: 0.7106 (t70) cc_final: 0.6900 (t70) REVERT: B 447 ARG cc_start: 0.6152 (mtt90) cc_final: 0.5617 (mtp180) REVERT: J 50 MET cc_start: 0.7352 (mtt) cc_final: 0.6768 (mmt) REVERT: J 108 SER cc_start: 0.7763 (p) cc_final: 0.7459 (m) REVERT: C 35 ASP cc_start: 0.6396 (m-30) cc_final: 0.6109 (m-30) REVERT: C 73 THR cc_start: 0.6974 (OUTLIER) cc_final: 0.6464 (p) REVERT: C 83 ARG cc_start: 0.7001 (mtp85) cc_final: 0.6772 (mtm180) REVERT: C 129 PHE cc_start: 0.7344 (OUTLIER) cc_final: 0.6353 (m-80) REVERT: C 283 GLU cc_start: 0.6863 (tt0) cc_final: 0.6442 (mp0) REVERT: C 286 ARG cc_start: 0.7287 (tpp80) cc_final: 0.6308 (tpm170) REVERT: C 306 LYS cc_start: 0.8540 (ttpt) cc_final: 0.7710 (tptt) REVERT: C 447 ARG cc_start: 0.6213 (mtt90) cc_final: 0.5589 (mtp180) REVERT: C 457 GLU cc_start: 0.6188 (tt0) cc_final: 0.5729 (tt0) REVERT: K 50 MET cc_start: 0.7453 (mtt) cc_final: 0.6915 (mmt) REVERT: K 108 SER cc_start: 0.7859 (p) cc_final: 0.7524 (m) REVERT: D 35 ASP cc_start: 0.6409 (m-30) cc_final: 0.6069 (m-30) REVERT: D 73 THR cc_start: 0.6790 (OUTLIER) cc_final: 0.6283 (p) REVERT: D 129 PHE cc_start: 0.7289 (OUTLIER) cc_final: 0.6266 (m-80) REVERT: D 283 GLU cc_start: 0.7170 (tt0) cc_final: 0.6703 (mp0) REVERT: D 306 LYS cc_start: 0.8585 (ttpt) cc_final: 0.7768 (tptt) REVERT: D 368 ASP cc_start: 0.7116 (t70) cc_final: 0.6915 (t70) REVERT: D 447 ARG cc_start: 0.6417 (mtt90) cc_final: 0.5841 (mtp180) REVERT: D 457 GLU cc_start: 0.6327 (tt0) cc_final: 0.5879 (tt0) REVERT: L 50 MET cc_start: 0.7395 (mtt) cc_final: 0.6910 (mmt) REVERT: L 108 SER cc_start: 0.7781 (p) cc_final: 0.7437 (m) REVERT: E 35 ASP cc_start: 0.6170 (m-30) cc_final: 0.5824 (m-30) REVERT: E 73 THR cc_start: 0.6875 (OUTLIER) cc_final: 0.6425 (p) REVERT: E 129 PHE cc_start: 0.7241 (OUTLIER) cc_final: 0.6265 (m-80) REVERT: E 283 GLU cc_start: 0.7091 (tt0) cc_final: 0.6684 (mp0) REVERT: E 306 LYS cc_start: 0.8572 (ttpt) cc_final: 0.7754 (tptt) REVERT: E 447 ARG cc_start: 0.6228 (mtt90) cc_final: 0.5643 (mtp180) REVERT: E 457 GLU cc_start: 0.6284 (tt0) cc_final: 0.5836 (tt0) REVERT: E 460 LEU cc_start: 0.7532 (mt) cc_final: 0.7313 (mt) REVERT: M 50 MET cc_start: 0.7524 (mtt) cc_final: 0.7010 (mmt) REVERT: M 108 SER cc_start: 0.7936 (p) cc_final: 0.7501 (m) REVERT: F 35 ASP cc_start: 0.6286 (m-30) cc_final: 0.5965 (m-30) REVERT: F 73 THR cc_start: 0.6916 (OUTLIER) cc_final: 0.6442 (p) REVERT: F 108 ILE cc_start: 0.7842 (OUTLIER) cc_final: 0.7246 (tp) REVERT: F 129 PHE cc_start: 0.7371 (OUTLIER) cc_final: 0.6334 (m-80) REVERT: F 252 MET cc_start: 0.8109 (OUTLIER) cc_final: 0.7757 (ttm) REVERT: F 283 GLU cc_start: 0.7146 (tt0) cc_final: 0.6702 (mp0) REVERT: F 306 LYS cc_start: 0.8503 (ttpt) cc_final: 0.7653 (tptt) REVERT: F 447 ARG cc_start: 0.6247 (mtt90) cc_final: 0.5648 (mtp180) REVERT: F 457 GLU cc_start: 0.6329 (tt0) cc_final: 0.5859 (tt0) REVERT: N 50 MET cc_start: 0.7307 (mtt) cc_final: 0.6675 (mmt) REVERT: N 108 SER cc_start: 0.7852 (p) cc_final: 0.7508 (m) REVERT: G 73 THR cc_start: 0.6752 (OUTLIER) cc_final: 0.6228 (p) REVERT: G 108 ILE cc_start: 0.7811 (OUTLIER) cc_final: 0.7237 (tp) REVERT: G 129 PHE cc_start: 0.7199 (OUTLIER) cc_final: 0.6205 (m-80) REVERT: G 249 MET cc_start: 0.7259 (mmm) cc_final: 0.6986 (mmm) REVERT: G 283 GLU cc_start: 0.6975 (tt0) cc_final: 0.6548 (mp0) REVERT: G 306 LYS cc_start: 0.8528 (ttpt) cc_final: 0.7665 (tptt) REVERT: G 457 GLU cc_start: 0.6145 (tt0) cc_final: 0.5688 (tt0) REVERT: O 50 MET cc_start: 0.7496 (mtt) cc_final: 0.6967 (mmt) REVERT: O 108 SER cc_start: 0.7793 (p) cc_final: 0.7419 (m) REVERT: H 73 THR cc_start: 0.7003 (OUTLIER) cc_final: 0.6509 (p) REVERT: H 129 PHE cc_start: 0.7167 (OUTLIER) cc_final: 0.6179 (m-80) REVERT: H 283 GLU cc_start: 0.7143 (tt0) cc_final: 0.6710 (mp0) REVERT: H 306 LYS cc_start: 0.8519 (ttpt) cc_final: 0.7713 (tptt) REVERT: H 447 ARG cc_start: 0.6261 (mtt90) cc_final: 0.5572 (mtp180) REVERT: H 457 GLU cc_start: 0.6273 (tt0) cc_final: 0.5822 (tt0) REVERT: P 50 MET cc_start: 0.7446 (mtt) cc_final: 0.6926 (mmt) REVERT: P 108 SER cc_start: 0.7855 (p) cc_final: 0.7463 (m) outliers start: 136 outliers final: 96 residues processed: 547 average time/residue: 0.2407 time to fit residues: 212.1849 Evaluate side-chains 540 residues out of total 3936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 425 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain I residue 88 THR Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 355 ASN Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain J residue 38 THR Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 88 THR Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 129 PHE Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain D residue 355 ASN Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 88 THR Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 129 PHE Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain E residue 342 THR Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 88 THR Chi-restraints excluded: chain M residue 105 VAL Chi-restraints excluded: chain M residue 111 MET Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 129 PHE Chi-restraints excluded: chain F residue 207 ASN Chi-restraints excluded: chain F residue 252 MET Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 342 THR Chi-restraints excluded: chain F residue 355 ASN Chi-restraints excluded: chain F residue 356 THR Chi-restraints excluded: chain F residue 357 VAL Chi-restraints excluded: chain N residue 38 THR Chi-restraints excluded: chain N residue 88 THR Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 129 PHE Chi-restraints excluded: chain G residue 207 ASN Chi-restraints excluded: chain G residue 265 VAL Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain G residue 342 THR Chi-restraints excluded: chain G residue 355 ASN Chi-restraints excluded: chain G residue 356 THR Chi-restraints excluded: chain G residue 357 VAL Chi-restraints excluded: chain O residue 38 THR Chi-restraints excluded: chain O residue 88 THR Chi-restraints excluded: chain O residue 105 VAL Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 108 ILE Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 129 PHE Chi-restraints excluded: chain H residue 252 MET Chi-restraints excluded: chain H residue 265 VAL Chi-restraints excluded: chain H residue 342 THR Chi-restraints excluded: chain H residue 355 ASN Chi-restraints excluded: chain H residue 356 THR Chi-restraints excluded: chain H residue 357 VAL Chi-restraints excluded: chain P residue 38 THR Chi-restraints excluded: chain P residue 88 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 31 optimal weight: 2.9990 chunk 412 optimal weight: 4.9990 chunk 280 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 368 optimal weight: 0.7980 chunk 430 optimal weight: 1.9990 chunk 204 optimal weight: 2.9990 chunk 363 optimal weight: 0.7980 chunk 422 optimal weight: 1.9990 chunk 401 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 326 HIS ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.161693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.126640 restraints weight = 267891.534| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 6.12 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3199 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 167 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 160 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3199 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.4124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 38728 Z= 0.139 Angle : 0.573 6.935 52544 Z= 0.288 Chirality : 0.043 0.129 5616 Planarity : 0.004 0.041 6800 Dihedral : 7.264 179.857 5392 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.58 % Allowed : 12.53 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.18 (0.12), residues: 4712 helix: 1.03 (0.12), residues: 1760 sheet: 0.20 (0.18), residues: 800 loop : -1.23 (0.12), residues: 2152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 361 TYR 0.014 0.001 TYR J 47 PHE 0.012 0.002 PHE C 100 TRP 0.007 0.001 TRP H 216 HIS 0.004 0.001 HIS G 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.14 (38728) covalent geometry : angle 0.57277 / 0.29 (52544) hydrogen bonds : bond 0.03661 / 2.41 ( 1468) hydrogen bonds : angle 4.38525 / 3.04 ( 4188) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 3936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 456 time to evaluate : 1.184 Fit side-chains REVERT: A 73 THR cc_start: 0.6750 (OUTLIER) cc_final: 0.6243 (p) REVERT: A 129 PHE cc_start: 0.7389 (OUTLIER) cc_final: 0.6326 (m-80) REVERT: A 207 ASN cc_start: 0.8748 (p0) cc_final: 0.8487 (p0) REVERT: A 283 GLU cc_start: 0.7133 (tt0) cc_final: 0.6629 (mp0) REVERT: A 306 LYS cc_start: 0.8490 (ttpt) cc_final: 0.8013 (ttpp) REVERT: A 447 ARG cc_start: 0.6319 (mtt90) cc_final: 0.5677 (mtp180) REVERT: A 457 GLU cc_start: 0.6152 (tt0) cc_final: 0.5677 (tt0) REVERT: I 39 ASP cc_start: 0.7625 (p0) cc_final: 0.7335 (p0) REVERT: I 50 MET cc_start: 0.7522 (mtt) cc_final: 0.7031 (mmt) REVERT: I 108 SER cc_start: 0.7907 (p) cc_final: 0.7538 (m) REVERT: B 35 ASP cc_start: 0.6377 (m-30) cc_final: 0.5995 (m-30) REVERT: B 41 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8606 (tp) REVERT: B 73 THR cc_start: 0.6984 (OUTLIER) cc_final: 0.6453 (p) REVERT: B 83 ARG cc_start: 0.7058 (mtp85) cc_final: 0.6857 (mtm180) REVERT: B 129 PHE cc_start: 0.7430 (OUTLIER) cc_final: 0.6407 (m-80) REVERT: B 283 GLU cc_start: 0.7180 (tt0) cc_final: 0.6854 (mp0) REVERT: B 306 LYS cc_start: 0.8552 (ttpt) cc_final: 0.8074 (ttpp) REVERT: B 447 ARG cc_start: 0.6277 (mtt90) cc_final: 0.5763 (mtp180) REVERT: J 39 ASP cc_start: 0.7588 (p0) cc_final: 0.7354 (p0) REVERT: J 50 MET cc_start: 0.7533 (mtt) cc_final: 0.7012 (mmt) REVERT: J 108 SER cc_start: 0.7845 (p) cc_final: 0.7515 (m) REVERT: C 35 ASP cc_start: 0.6226 (m-30) cc_final: 0.5857 (m-30) REVERT: C 73 THR cc_start: 0.6992 (OUTLIER) cc_final: 0.6516 (p) REVERT: C 83 ARG cc_start: 0.7089 (mtp85) cc_final: 0.6850 (mtm180) REVERT: C 129 PHE cc_start: 0.7463 (OUTLIER) cc_final: 0.6389 (m-80) REVERT: C 205 ASP cc_start: 0.7596 (OUTLIER) cc_final: 0.6873 (t0) REVERT: C 286 ARG cc_start: 0.7355 (tpp80) cc_final: 0.6376 (tpm170) REVERT: C 306 LYS cc_start: 0.8605 (ttpt) cc_final: 0.8086 (ttpp) REVERT: C 447 ARG cc_start: 0.6403 (mtt90) cc_final: 0.5834 (mtp180) REVERT: K 39 ASP cc_start: 0.7639 (p0) cc_final: 0.7400 (p0) REVERT: K 50 MET cc_start: 0.7421 (mtt) cc_final: 0.6948 (mmt) REVERT: K 108 SER cc_start: 0.7944 (p) cc_final: 0.7572 (m) REVERT: D 35 ASP cc_start: 0.6319 (m-30) cc_final: 0.5985 (m-30) REVERT: D 73 THR cc_start: 0.6878 (OUTLIER) cc_final: 0.6381 (p) REVERT: D 83 ARG cc_start: 0.6968 (mtp85) cc_final: 0.6762 (mtm180) REVERT: D 108 ILE cc_start: 0.7704 (OUTLIER) cc_final: 0.7164 (tp) REVERT: D 128 SER cc_start: 0.8010 (OUTLIER) cc_final: 0.7423 (t) REVERT: D 129 PHE cc_start: 0.7396 (OUTLIER) cc_final: 0.6470 (m-80) REVERT: D 306 LYS cc_start: 0.8477 (ttpt) cc_final: 0.7976 (ttpp) REVERT: D 447 ARG cc_start: 0.6297 (mtt90) cc_final: 0.5804 (mtp180) REVERT: L 39 ASP cc_start: 0.7662 (p0) cc_final: 0.7400 (p0) REVERT: L 50 MET cc_start: 0.7419 (mtt) cc_final: 0.6924 (mmt) REVERT: L 108 SER cc_start: 0.7813 (p) cc_final: 0.7439 (m) REVERT: E 35 ASP cc_start: 0.6425 (m-30) cc_final: 0.6078 (m-30) REVERT: E 73 THR cc_start: 0.6784 (OUTLIER) cc_final: 0.6360 (p) REVERT: E 129 PHE cc_start: 0.7308 (OUTLIER) cc_final: 0.6331 (m-80) REVERT: E 283 GLU cc_start: 0.7087 (tt0) cc_final: 0.6597 (mp0) REVERT: E 306 LYS cc_start: 0.8409 (ttpt) cc_final: 0.7907 (ttpp) REVERT: E 447 ARG cc_start: 0.6299 (mtt90) cc_final: 0.5729 (mtp180) REVERT: E 457 GLU cc_start: 0.6176 (tt0) cc_final: 0.5743 (tt0) REVERT: E 460 LEU cc_start: 0.7446 (mt) cc_final: 0.7235 (mt) REVERT: M 50 MET cc_start: 0.7418 (mtt) cc_final: 0.6953 (mmt) REVERT: M 108 SER cc_start: 0.8009 (p) cc_final: 0.7561 (m) REVERT: F 35 ASP cc_start: 0.6358 (m-30) cc_final: 0.5979 (m-30) REVERT: F 73 THR cc_start: 0.6973 (OUTLIER) cc_final: 0.6502 (p) REVERT: F 129 PHE cc_start: 0.7432 (OUTLIER) cc_final: 0.6433 (m-80) REVERT: F 133 LYS cc_start: 0.8066 (OUTLIER) cc_final: 0.7696 (mtmm) REVERT: F 205 ASP cc_start: 0.7486 (OUTLIER) cc_final: 0.6782 (t0) REVERT: F 306 LYS cc_start: 0.8572 (ttpt) cc_final: 0.7731 (tptt) REVERT: F 447 ARG cc_start: 0.6264 (mtt90) cc_final: 0.5734 (mtp180) REVERT: N 50 MET cc_start: 0.7533 (mtt) cc_final: 0.6926 (mmt) REVERT: N 108 SER cc_start: 0.7942 (p) cc_final: 0.7559 (m) REVERT: G 73 THR cc_start: 0.6793 (OUTLIER) cc_final: 0.6313 (p) REVERT: G 108 ILE cc_start: 0.7702 (OUTLIER) cc_final: 0.7107 (tp) REVERT: G 129 PHE cc_start: 0.7250 (OUTLIER) cc_final: 0.6237 (m-80) REVERT: G 249 MET cc_start: 0.7354 (mmm) cc_final: 0.7080 (mmm) REVERT: G 283 GLU cc_start: 0.6962 (tt0) cc_final: 0.6457 (mp0) REVERT: G 306 LYS cc_start: 0.8483 (ttpt) cc_final: 0.7985 (ttpp) REVERT: G 457 GLU cc_start: 0.6085 (tt0) cc_final: 0.5635 (tt0) REVERT: O 50 MET cc_start: 0.7484 (mtt) cc_final: 0.6979 (mmt) REVERT: O 108 SER cc_start: 0.7926 (p) cc_final: 0.7531 (m) REVERT: H 73 THR cc_start: 0.6832 (OUTLIER) cc_final: 0.6333 (p) REVERT: H 129 PHE cc_start: 0.7420 (OUTLIER) cc_final: 0.6393 (m-80) REVERT: H 306 LYS cc_start: 0.8477 (ttpt) cc_final: 0.7995 (ttpp) REVERT: H 428 MET cc_start: 0.7846 (mmm) cc_final: 0.7426 (mmt) REVERT: H 447 ARG cc_start: 0.6528 (mtt90) cc_final: 0.5940 (mtp180) REVERT: P 39 ASP cc_start: 0.7845 (p0) cc_final: 0.7605 (p0) REVERT: P 50 MET cc_start: 0.7476 (mtt) cc_final: 0.6971 (mmt) REVERT: P 108 SER cc_start: 0.7922 (p) cc_final: 0.7506 (m) outliers start: 141 outliers final: 103 residues processed: 549 average time/residue: 0.2395 time to fit residues: 211.6313 Evaluate side-chains 567 residues out of total 3936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 441 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain I residue 88 THR Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 355 ASN Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain J residue 38 THR Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 88 THR Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 129 PHE Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain D residue 355 ASN Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 88 THR Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 129 PHE Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 342 THR Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 88 THR Chi-restraints excluded: chain M residue 105 VAL Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 129 PHE Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 205 ASP Chi-restraints excluded: chain F residue 207 ASN Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 342 THR Chi-restraints excluded: chain F residue 355 ASN Chi-restraints excluded: chain F residue 356 THR Chi-restraints excluded: chain F residue 357 VAL Chi-restraints excluded: chain N residue 38 THR Chi-restraints excluded: chain N residue 88 THR Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 129 PHE Chi-restraints excluded: chain G residue 207 ASN Chi-restraints excluded: chain G residue 265 VAL Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain G residue 342 THR Chi-restraints excluded: chain G residue 355 ASN Chi-restraints excluded: chain G residue 356 THR Chi-restraints excluded: chain G residue 357 VAL Chi-restraints excluded: chain O residue 38 THR Chi-restraints excluded: chain O residue 88 THR Chi-restraints excluded: chain O residue 105 VAL Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 108 ILE Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain H residue 129 PHE Chi-restraints excluded: chain H residue 265 VAL Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain H residue 342 THR Chi-restraints excluded: chain H residue 355 ASN Chi-restraints excluded: chain H residue 356 THR Chi-restraints excluded: chain H residue 357 VAL Chi-restraints excluded: chain P residue 38 THR Chi-restraints excluded: chain P residue 88 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 342 optimal weight: 4.9990 chunk 320 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 313 optimal weight: 6.9990 chunk 252 optimal weight: 0.9990 chunk 423 optimal weight: 2.9990 chunk 444 optimal weight: 5.9990 chunk 170 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 373 optimal weight: 0.5980 chunk 166 optimal weight: 1.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 326 HIS ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.160095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.125257 restraints weight = 269523.030| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 6.24 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3180 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 160 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 175 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3180 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.4242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 38728 Z= 0.158 Angle : 0.605 7.752 52544 Z= 0.303 Chirality : 0.044 0.131 5616 Planarity : 0.005 0.041 6800 Dihedral : 7.279 177.704 5392 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.79 % Allowed : 12.60 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.24 (0.12), residues: 4712 helix: 0.94 (0.12), residues: 1760 sheet: 0.08 (0.19), residues: 752 loop : -1.15 (0.12), residues: 2200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 361 TYR 0.015 0.002 TYR K 47 PHE 0.013 0.002 PHE C 100 TRP 0.008 0.001 TRP D 216 HIS 0.005 0.001 HIS A 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.16 (38728) covalent geometry : angle 0.60529 / 0.30 (52544) hydrogen bonds : bond 0.03868 / 2.55 ( 1468) hydrogen bonds : angle 4.51447 / 3.12 ( 4188) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 3936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 442 time to evaluate : 1.285 Fit side-chains REVERT: A 73 THR cc_start: 0.6858 (OUTLIER) cc_final: 0.6389 (p) REVERT: A 128 SER cc_start: 0.7961 (t) cc_final: 0.7410 (t) REVERT: A 129 PHE cc_start: 0.7371 (OUTLIER) cc_final: 0.6329 (m-80) REVERT: A 207 ASN cc_start: 0.8802 (p0) cc_final: 0.8546 (p0) REVERT: A 283 GLU cc_start: 0.7090 (tt0) cc_final: 0.6597 (mp0) REVERT: A 306 LYS cc_start: 0.8400 (ttpt) cc_final: 0.7937 (ttpp) REVERT: A 447 ARG cc_start: 0.6333 (mtt90) cc_final: 0.5683 (mtp180) REVERT: A 457 GLU cc_start: 0.6173 (tt0) cc_final: 0.5718 (tt0) REVERT: I 50 MET cc_start: 0.7539 (mtt) cc_final: 0.7052 (mmt) REVERT: I 108 SER cc_start: 0.7886 (p) cc_final: 0.7480 (m) REVERT: B 35 ASP cc_start: 0.6477 (m-30) cc_final: 0.6134 (m-30) REVERT: B 41 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8686 (tp) REVERT: B 83 ARG cc_start: 0.7133 (mtp85) cc_final: 0.6920 (mtm180) REVERT: B 128 SER cc_start: 0.8037 (t) cc_final: 0.7469 (t) REVERT: B 129 PHE cc_start: 0.7419 (OUTLIER) cc_final: 0.6442 (m-80) REVERT: B 283 GLU cc_start: 0.6911 (tt0) cc_final: 0.6437 (mp0) REVERT: B 306 LYS cc_start: 0.8455 (ttpt) cc_final: 0.8003 (ttpp) REVERT: B 447 ARG cc_start: 0.6232 (mtt90) cc_final: 0.5630 (mtp180) REVERT: J 50 MET cc_start: 0.7482 (mtt) cc_final: 0.7007 (mmt) REVERT: J 108 SER cc_start: 0.7839 (p) cc_final: 0.7486 (m) REVERT: C 35 ASP cc_start: 0.6386 (m-30) cc_final: 0.6053 (m-30) REVERT: C 73 THR cc_start: 0.6802 (OUTLIER) cc_final: 0.6275 (p) REVERT: C 83 ARG cc_start: 0.7056 (mtp85) cc_final: 0.6850 (mtm180) REVERT: C 108 ILE cc_start: 0.7658 (OUTLIER) cc_final: 0.7084 (tp) REVERT: C 129 PHE cc_start: 0.7439 (OUTLIER) cc_final: 0.6364 (m-80) REVERT: C 283 GLU cc_start: 0.6992 (tt0) cc_final: 0.6543 (mp0) REVERT: C 286 ARG cc_start: 0.7374 (tpp80) cc_final: 0.6323 (tpm170) REVERT: C 306 LYS cc_start: 0.8357 (ttpt) cc_final: 0.7889 (ttpp) REVERT: C 447 ARG cc_start: 0.6108 (mtt90) cc_final: 0.5467 (mtp180) REVERT: C 457 GLU cc_start: 0.6203 (tt0) cc_final: 0.5734 (tt0) REVERT: K 50 MET cc_start: 0.7468 (mtt) cc_final: 0.6993 (mmt) REVERT: K 108 SER cc_start: 0.7891 (p) cc_final: 0.7518 (m) REVERT: D 35 ASP cc_start: 0.6318 (m-30) cc_final: 0.5999 (m-30) REVERT: D 73 THR cc_start: 0.6983 (OUTLIER) cc_final: 0.6465 (p) REVERT: D 83 ARG cc_start: 0.6985 (mtp85) cc_final: 0.6767 (mtm180) REVERT: D 108 ILE cc_start: 0.7785 (OUTLIER) cc_final: 0.7129 (tp) REVERT: D 128 SER cc_start: 0.7981 (t) cc_final: 0.7421 (t) REVERT: D 129 PHE cc_start: 0.7301 (OUTLIER) cc_final: 0.6256 (m-80) REVERT: D 283 GLU cc_start: 0.7050 (tt0) cc_final: 0.6525 (mp0) REVERT: D 306 LYS cc_start: 0.8353 (ttpt) cc_final: 0.7852 (ttpp) REVERT: D 447 ARG cc_start: 0.6366 (mtt90) cc_final: 0.5708 (mtp180) REVERT: D 457 GLU cc_start: 0.6181 (tt0) cc_final: 0.5750 (tt0) REVERT: L 50 MET cc_start: 0.7496 (mtt) cc_final: 0.7024 (mmt) REVERT: L 108 SER cc_start: 0.7788 (p) cc_final: 0.7442 (m) REVERT: E 35 ASP cc_start: 0.6515 (m-30) cc_final: 0.6151 (m-30) REVERT: E 73 THR cc_start: 0.6725 (OUTLIER) cc_final: 0.6251 (p) REVERT: E 128 SER cc_start: 0.7976 (t) cc_final: 0.7387 (t) REVERT: E 129 PHE cc_start: 0.7322 (OUTLIER) cc_final: 0.6359 (m-80) REVERT: E 283 GLU cc_start: 0.7133 (tt0) cc_final: 0.6623 (mp0) REVERT: E 306 LYS cc_start: 0.8318 (ttpt) cc_final: 0.7833 (ttpp) REVERT: E 447 ARG cc_start: 0.6467 (mtt90) cc_final: 0.5819 (mtp180) REVERT: E 457 GLU cc_start: 0.6225 (tt0) cc_final: 0.5762 (tt0) REVERT: M 50 MET cc_start: 0.7460 (mtt) cc_final: 0.6958 (mmt) REVERT: M 108 SER cc_start: 0.7957 (p) cc_final: 0.7521 (m) REVERT: F 35 ASP cc_start: 0.6499 (m-30) cc_final: 0.6167 (m-30) REVERT: F 73 THR cc_start: 0.6760 (OUTLIER) cc_final: 0.6280 (p) REVERT: F 108 ILE cc_start: 0.7899 (OUTLIER) cc_final: 0.7292 (tp) REVERT: F 129 PHE cc_start: 0.7379 (OUTLIER) cc_final: 0.6300 (m-80) REVERT: F 133 LYS cc_start: 0.7981 (OUTLIER) cc_final: 0.7603 (mtmm) REVERT: F 205 ASP cc_start: 0.7645 (OUTLIER) cc_final: 0.6960 (t0) REVERT: F 283 GLU cc_start: 0.7100 (tt0) cc_final: 0.6577 (mp0) REVERT: F 306 LYS cc_start: 0.8322 (ttpt) cc_final: 0.7831 (ttpp) REVERT: F 336 LEU cc_start: 0.5949 (OUTLIER) cc_final: 0.5508 (mp) REVERT: F 447 ARG cc_start: 0.6381 (mtt90) cc_final: 0.5740 (mtp180) REVERT: F 457 GLU cc_start: 0.6149 (tt0) cc_final: 0.5701 (tt0) REVERT: N 50 MET cc_start: 0.7443 (mtt) cc_final: 0.6953 (mmt) REVERT: N 108 SER cc_start: 0.7873 (p) cc_final: 0.7483 (m) REVERT: G 73 THR cc_start: 0.6931 (OUTLIER) cc_final: 0.6409 (p) REVERT: G 108 ILE cc_start: 0.7733 (OUTLIER) cc_final: 0.7133 (tp) REVERT: G 129 PHE cc_start: 0.7418 (OUTLIER) cc_final: 0.6411 (m-80) REVERT: G 205 ASP cc_start: 0.7485 (OUTLIER) cc_final: 0.6767 (t0) REVERT: G 249 MET cc_start: 0.7411 (mmm) cc_final: 0.7130 (mmm) REVERT: G 283 GLU cc_start: 0.7172 (tt0) cc_final: 0.6660 (mp0) REVERT: G 306 LYS cc_start: 0.8342 (ttpt) cc_final: 0.7850 (ttpp) REVERT: G 457 GLU cc_start: 0.6187 (tt0) cc_final: 0.5707 (tt0) REVERT: O 50 MET cc_start: 0.7461 (mtt) cc_final: 0.6999 (mmt) REVERT: O 108 SER cc_start: 0.7790 (p) cc_final: 0.7396 (m) REVERT: H 73 THR cc_start: 0.6769 (OUTLIER) cc_final: 0.6260 (p) REVERT: H 128 SER cc_start: 0.7992 (t) cc_final: 0.7422 (t) REVERT: H 129 PHE cc_start: 0.7279 (OUTLIER) cc_final: 0.6279 (m-80) REVERT: H 283 GLU cc_start: 0.7156 (tt0) cc_final: 0.6609 (mp0) REVERT: H 306 LYS cc_start: 0.8424 (ttpt) cc_final: 0.7970 (ttpp) REVERT: H 336 LEU cc_start: 0.5775 (OUTLIER) cc_final: 0.5343 (mp) REVERT: H 428 MET cc_start: 0.7772 (mmm) cc_final: 0.7425 (mmt) REVERT: H 447 ARG cc_start: 0.6309 (mtt90) cc_final: 0.5691 (mtp180) REVERT: H 457 GLU cc_start: 0.6153 (tt0) cc_final: 0.5682 (tt0) REVERT: P 50 MET cc_start: 0.7433 (mtt) cc_final: 0.6958 (mmt) REVERT: P 108 SER cc_start: 0.7917 (p) cc_final: 0.7512 (m) outliers start: 149 outliers final: 111 residues processed: 549 average time/residue: 0.2369 time to fit residues: 211.0566 Evaluate side-chains 571 residues out of total 3936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 435 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain I residue 88 THR Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 355 ASN Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain J residue 38 THR Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 88 THR Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 129 PHE Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain D residue 355 ASN Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 88 THR Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 129 PHE Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 342 THR Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 88 THR Chi-restraints excluded: chain M residue 105 VAL Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 129 PHE Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 205 ASP Chi-restraints excluded: chain F residue 207 ASN Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 336 LEU Chi-restraints excluded: chain F residue 342 THR Chi-restraints excluded: chain F residue 355 ASN Chi-restraints excluded: chain F residue 356 THR Chi-restraints excluded: chain F residue 357 VAL Chi-restraints excluded: chain N residue 38 THR Chi-restraints excluded: chain N residue 88 THR Chi-restraints excluded: chain N residue 105 VAL Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 129 PHE Chi-restraints excluded: chain G residue 205 ASP Chi-restraints excluded: chain G residue 207 ASN Chi-restraints excluded: chain G residue 265 VAL Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain G residue 336 LEU Chi-restraints excluded: chain G residue 342 THR Chi-restraints excluded: chain G residue 355 ASN Chi-restraints excluded: chain G residue 356 THR Chi-restraints excluded: chain G residue 357 VAL Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain O residue 38 THR Chi-restraints excluded: chain O residue 88 THR Chi-restraints excluded: chain O residue 105 VAL Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 108 ILE Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 129 PHE Chi-restraints excluded: chain H residue 265 VAL Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain H residue 336 LEU Chi-restraints excluded: chain H residue 342 THR Chi-restraints excluded: chain H residue 355 ASN Chi-restraints excluded: chain H residue 356 THR Chi-restraints excluded: chain H residue 357 VAL Chi-restraints excluded: chain P residue 38 THR Chi-restraints excluded: chain P residue 88 THR Chi-restraints excluded: chain P residue 105 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 360 optimal weight: 0.9980 chunk 445 optimal weight: 3.9990 chunk 32 optimal weight: 0.0670 chunk 97 optimal weight: 0.6980 chunk 290 optimal weight: 9.9990 chunk 113 optimal weight: 4.9990 chunk 122 optimal weight: 7.9990 chunk 411 optimal weight: 8.9990 chunk 72 optimal weight: 0.9980 chunk 278 optimal weight: 4.9990 chunk 229 optimal weight: 0.7980 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 326 HIS ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.165292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.130418 restraints weight = 265005.805| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 6.17 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3243 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 175 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 184 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3243 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 38728 Z= 0.103 Angle : 0.520 6.455 52544 Z= 0.262 Chirality : 0.041 0.126 5616 Planarity : 0.004 0.041 6800 Dihedral : 6.901 176.432 5392 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.97 % Allowed : 13.77 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.10 (0.12), residues: 4712 helix: 1.32 (0.13), residues: 1760 sheet: 0.27 (0.18), residues: 800 loop : -1.07 (0.13), residues: 2152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 361 TYR 0.011 0.001 TYR A 26 PHE 0.011 0.001 PHE C 100 TRP 0.007 0.001 TRP G 216 HIS 0.003 0.001 HIS I 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.10 (38728) covalent geometry : angle 0.51994 / 0.26 (52544) hydrogen bonds : bond 0.03157 / 2.08 ( 1468) hydrogen bonds : angle 4.17481 / 2.90 ( 4188) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 3936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 467 time to evaluate : 1.138 Fit side-chains REVERT: A 73 THR cc_start: 0.6844 (OUTLIER) cc_final: 0.6329 (p) REVERT: A 128 SER cc_start: 0.8015 (t) cc_final: 0.7423 (t) REVERT: A 129 PHE cc_start: 0.7309 (OUTLIER) cc_final: 0.6215 (m-80) REVERT: A 207 ASN cc_start: 0.8703 (p0) cc_final: 0.8434 (p0) REVERT: A 306 LYS cc_start: 0.8433 (ttpt) cc_final: 0.7863 (tttp) REVERT: A 447 ARG cc_start: 0.6395 (mtt90) cc_final: 0.5803 (mtp180) REVERT: I 39 ASP cc_start: 0.7644 (p0) cc_final: 0.7393 (p0) REVERT: I 50 MET cc_start: 0.7499 (mtt) cc_final: 0.7090 (mmt) REVERT: I 108 SER cc_start: 0.7821 (p) cc_final: 0.7402 (m) REVERT: B 41 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8694 (tp) REVERT: B 73 THR cc_start: 0.6900 (OUTLIER) cc_final: 0.6367 (p) REVERT: B 83 ARG cc_start: 0.6985 (mtp85) cc_final: 0.6733 (mtm180) REVERT: B 128 SER cc_start: 0.7898 (t) cc_final: 0.7350 (t) REVERT: B 129 PHE cc_start: 0.7309 (OUTLIER) cc_final: 0.6284 (m-80) REVERT: B 306 LYS cc_start: 0.8353 (ttpt) cc_final: 0.7894 (ttpp) REVERT: B 447 ARG cc_start: 0.6305 (mtt90) cc_final: 0.5726 (mtp180) REVERT: J 50 MET cc_start: 0.7491 (mtt) cc_final: 0.7042 (mmt) REVERT: J 108 SER cc_start: 0.7833 (p) cc_final: 0.7438 (m) REVERT: C 73 THR cc_start: 0.6906 (OUTLIER) cc_final: 0.6389 (p) REVERT: C 108 ILE cc_start: 0.7626 (OUTLIER) cc_final: 0.7200 (tp) REVERT: C 129 PHE cc_start: 0.7297 (OUTLIER) cc_final: 0.6232 (m-80) REVERT: C 286 ARG cc_start: 0.7292 (tpp80) cc_final: 0.6340 (tpm170) REVERT: C 306 LYS cc_start: 0.8388 (ttpt) cc_final: 0.7936 (ttpp) REVERT: C 447 ARG cc_start: 0.6434 (mtt90) cc_final: 0.5847 (mtp180) REVERT: K 39 ASP cc_start: 0.7645 (p0) cc_final: 0.7425 (p0) REVERT: K 50 MET cc_start: 0.7387 (mtt) cc_final: 0.6984 (mmt) REVERT: K 108 SER cc_start: 0.7867 (p) cc_final: 0.7471 (m) REVERT: D 73 THR cc_start: 0.6710 (OUTLIER) cc_final: 0.6199 (p) REVERT: D 83 ARG cc_start: 0.6942 (mtp85) cc_final: 0.6696 (mtm180) REVERT: D 108 ILE cc_start: 0.7652 (OUTLIER) cc_final: 0.7188 (tp) REVERT: D 128 SER cc_start: 0.8010 (t) cc_final: 0.7441 (t) REVERT: D 129 PHE cc_start: 0.7291 (OUTLIER) cc_final: 0.6240 (m-80) REVERT: D 306 LYS cc_start: 0.8256 (ttpt) cc_final: 0.7784 (ttpp) REVERT: D 447 ARG cc_start: 0.6410 (mtt90) cc_final: 0.5793 (mtp180) REVERT: L 39 ASP cc_start: 0.7634 (p0) cc_final: 0.7384 (p0) REVERT: L 50 MET cc_start: 0.7327 (mtt) cc_final: 0.6967 (mmt) REVERT: L 108 SER cc_start: 0.7829 (p) cc_final: 0.7421 (m) REVERT: E 73 THR cc_start: 0.6696 (p) cc_final: 0.6220 (p) REVERT: E 128 SER cc_start: 0.7885 (t) cc_final: 0.7302 (t) REVERT: E 129 PHE cc_start: 0.7249 (OUTLIER) cc_final: 0.6226 (m-80) REVERT: E 283 GLU cc_start: 0.6949 (tt0) cc_final: 0.6746 (mp0) REVERT: E 306 LYS cc_start: 0.8319 (ttpt) cc_final: 0.7741 (tttp) REVERT: E 447 ARG cc_start: 0.6460 (mtt90) cc_final: 0.5848 (mtp180) REVERT: E 457 GLU cc_start: 0.6255 (tt0) cc_final: 0.5792 (tt0) REVERT: M 39 ASP cc_start: 0.7608 (p0) cc_final: 0.7382 (p0) REVERT: M 50 MET cc_start: 0.7330 (mtt) cc_final: 0.6974 (mmt) REVERT: M 108 SER cc_start: 0.7979 (p) cc_final: 0.7516 (m) REVERT: F 73 THR cc_start: 0.6775 (OUTLIER) cc_final: 0.6264 (p) REVERT: F 108 ILE cc_start: 0.7831 (OUTLIER) cc_final: 0.7246 (tp) REVERT: F 129 PHE cc_start: 0.7309 (OUTLIER) cc_final: 0.6261 (m-80) REVERT: F 133 LYS cc_start: 0.7876 (OUTLIER) cc_final: 0.7322 (mtmm) REVERT: F 283 GLU cc_start: 0.6979 (tt0) cc_final: 0.6721 (mp0) REVERT: F 306 LYS cc_start: 0.8266 (ttpt) cc_final: 0.7777 (ttpp) REVERT: F 447 ARG cc_start: 0.6332 (mtt90) cc_final: 0.5688 (mtp180) REVERT: F 457 GLU cc_start: 0.6072 (tt0) cc_final: 0.5614 (tt0) REVERT: N 50 MET cc_start: 0.7415 (mtt) cc_final: 0.7012 (mmt) REVERT: N 108 SER cc_start: 0.7852 (p) cc_final: 0.7426 (m) REVERT: G 73 THR cc_start: 0.6757 (OUTLIER) cc_final: 0.6266 (p) REVERT: G 108 ILE cc_start: 0.7836 (OUTLIER) cc_final: 0.7321 (tp) REVERT: G 129 PHE cc_start: 0.7333 (OUTLIER) cc_final: 0.6275 (m-80) REVERT: G 249 MET cc_start: 0.7373 (mmm) cc_final: 0.7057 (mmm) REVERT: G 306 LYS cc_start: 0.8325 (ttpt) cc_final: 0.7863 (ttpp) REVERT: O 39 ASP cc_start: 0.7670 (p0) cc_final: 0.7386 (p0) REVERT: O 50 MET cc_start: 0.7415 (mtt) cc_final: 0.6988 (mmt) REVERT: O 108 SER cc_start: 0.7818 (p) cc_final: 0.7370 (m) REVERT: H 73 THR cc_start: 0.6686 (OUTLIER) cc_final: 0.6157 (p) REVERT: H 128 SER cc_start: 0.7910 (t) cc_final: 0.7368 (t) REVERT: H 129 PHE cc_start: 0.7329 (OUTLIER) cc_final: 0.6308 (m-80) REVERT: H 283 GLU cc_start: 0.7001 (tt0) cc_final: 0.6753 (mp0) REVERT: H 306 LYS cc_start: 0.8363 (ttpt) cc_final: 0.7920 (ttpp) REVERT: H 336 LEU cc_start: 0.5639 (OUTLIER) cc_final: 0.5222 (mp) REVERT: H 447 ARG cc_start: 0.6375 (mtt90) cc_final: 0.5717 (mtp180) REVERT: H 457 GLU cc_start: 0.6117 (tt0) cc_final: 0.5663 (tt0) REVERT: P 39 ASP cc_start: 0.7731 (p0) cc_final: 0.7497 (p0) REVERT: P 50 MET cc_start: 0.7530 (mtt) cc_final: 0.7091 (mmt) REVERT: P 108 SER cc_start: 0.7895 (p) cc_final: 0.7495 (m) outliers start: 117 outliers final: 86 residues processed: 542 average time/residue: 0.2429 time to fit residues: 213.6034 Evaluate side-chains 559 residues out of total 3936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 451 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain I residue 88 THR Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 355 ASN Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain J residue 38 THR Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 88 THR Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 129 PHE Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain D residue 355 ASN Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 88 THR Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 129 PHE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 342 THR Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 88 THR Chi-restraints excluded: chain M residue 105 VAL Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 129 PHE Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 342 THR Chi-restraints excluded: chain F residue 355 ASN Chi-restraints excluded: chain F residue 356 THR Chi-restraints excluded: chain F residue 357 VAL Chi-restraints excluded: chain N residue 38 THR Chi-restraints excluded: chain N residue 88 THR Chi-restraints excluded: chain N residue 105 VAL Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 129 PHE Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain G residue 336 LEU Chi-restraints excluded: chain G residue 342 THR Chi-restraints excluded: chain G residue 355 ASN Chi-restraints excluded: chain G residue 357 VAL Chi-restraints excluded: chain O residue 38 THR Chi-restraints excluded: chain O residue 88 THR Chi-restraints excluded: chain O residue 105 VAL Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 108 ILE Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 129 PHE Chi-restraints excluded: chain H residue 265 VAL Chi-restraints excluded: chain H residue 336 LEU Chi-restraints excluded: chain H residue 342 THR Chi-restraints excluded: chain H residue 355 ASN Chi-restraints excluded: chain H residue 356 THR Chi-restraints excluded: chain P residue 38 THR Chi-restraints excluded: chain P residue 88 THR Chi-restraints excluded: chain P residue 105 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 46 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 163 optimal weight: 3.9990 chunk 448 optimal weight: 7.9990 chunk 260 optimal weight: 4.9990 chunk 250 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 282 optimal weight: 0.8980 chunk 149 optimal weight: 0.7980 chunk 361 optimal weight: 0.0020 overall best weight: 1.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.161032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.126578 restraints weight = 269480.631| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 6.23 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3188 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 184 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 182 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (14 function evaluations) r_final: 0.3188 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.4300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 38728 Z= 0.159 Angle : 0.600 8.500 52544 Z= 0.299 Chirality : 0.044 0.131 5616 Planarity : 0.005 0.044 6800 Dihedral : 7.057 175.587 5392 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.18 % Allowed : 13.54 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.06 (0.12), residues: 4712 helix: 1.11 (0.12), residues: 1760 sheet: 0.17 (0.19), residues: 752 loop : -1.06 (0.13), residues: 2200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 361 TYR 0.015 0.002 TYR P 47 PHE 0.013 0.002 PHE C 100 TRP 0.008 0.001 TRP G 216 HIS 0.005 0.001 HIS E 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.16 (38728) covalent geometry : angle 0.59988 / 0.30 (52544) hydrogen bonds : bond 0.03831 / 2.53 ( 1468) hydrogen bonds : angle 4.44325 / 3.08 ( 4188) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 3936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 435 time to evaluate : 1.354 Fit side-chains REVERT: A 73 THR cc_start: 0.6792 (OUTLIER) cc_final: 0.6303 (p) REVERT: A 128 SER cc_start: 0.8057 (t) cc_final: 0.7492 (t) REVERT: A 129 PHE cc_start: 0.7304 (OUTLIER) cc_final: 0.6221 (m-80) REVERT: A 207 ASN cc_start: 0.8760 (p0) cc_final: 0.8500 (p0) REVERT: A 283 GLU cc_start: 0.7075 (tt0) cc_final: 0.6678 (mp0) REVERT: A 306 LYS cc_start: 0.8336 (ttpt) cc_final: 0.7860 (ttpp) REVERT: A 447 ARG cc_start: 0.6337 (mtt90) cc_final: 0.5740 (mtp180) REVERT: I 50 MET cc_start: 0.7478 (mtt) cc_final: 0.7034 (mmt) REVERT: I 108 SER cc_start: 0.7849 (p) cc_final: 0.7438 (m) REVERT: B 35 ASP cc_start: 0.6492 (m-30) cc_final: 0.6149 (m-30) REVERT: B 83 ARG cc_start: 0.7038 (mtp85) cc_final: 0.6823 (mtm180) REVERT: B 128 SER cc_start: 0.7867 (t) cc_final: 0.7347 (t) REVERT: B 129 PHE cc_start: 0.7331 (OUTLIER) cc_final: 0.6268 (m-80) REVERT: B 283 GLU cc_start: 0.6899 (tt0) cc_final: 0.6527 (mp0) REVERT: B 306 LYS cc_start: 0.8314 (ttpt) cc_final: 0.7821 (ttpp) REVERT: B 447 ARG cc_start: 0.6203 (mtt90) cc_final: 0.5598 (mtp180) REVERT: J 50 MET cc_start: 0.7436 (mtt) cc_final: 0.6959 (mmt) REVERT: J 108 SER cc_start: 0.7723 (p) cc_final: 0.7382 (m) REVERT: C 35 ASP cc_start: 0.6481 (m-30) cc_final: 0.6173 (m-30) REVERT: C 73 THR cc_start: 0.7006 (OUTLIER) cc_final: 0.6498 (p) REVERT: C 108 ILE cc_start: 0.7700 (OUTLIER) cc_final: 0.7207 (tp) REVERT: C 129 PHE cc_start: 0.7288 (OUTLIER) cc_final: 0.6149 (m-80) REVERT: C 283 GLU cc_start: 0.7108 (tt0) cc_final: 0.6603 (mp0) REVERT: C 286 ARG cc_start: 0.7433 (tpp80) cc_final: 0.6364 (tpm170) REVERT: C 306 LYS cc_start: 0.8321 (ttpt) cc_final: 0.7822 (ttpp) REVERT: C 447 ARG cc_start: 0.6291 (mtt90) cc_final: 0.5646 (mtp180) REVERT: C 457 GLU cc_start: 0.6143 (tt0) cc_final: 0.5646 (tt0) REVERT: K 50 MET cc_start: 0.7439 (mtt) cc_final: 0.7016 (mmt) REVERT: K 108 SER cc_start: 0.7880 (p) cc_final: 0.7467 (m) REVERT: D 35 ASP cc_start: 0.6341 (m-30) cc_final: 0.6015 (m-30) REVERT: D 73 THR cc_start: 0.6868 (OUTLIER) cc_final: 0.6324 (p) REVERT: D 83 ARG cc_start: 0.7112 (mtp85) cc_final: 0.6855 (mtm180) REVERT: D 108 ILE cc_start: 0.7551 (OUTLIER) cc_final: 0.7065 (tp) REVERT: D 128 SER cc_start: 0.7932 (t) cc_final: 0.7385 (t) REVERT: D 129 PHE cc_start: 0.7234 (OUTLIER) cc_final: 0.6167 (m-80) REVERT: D 283 GLU cc_start: 0.7010 (tt0) cc_final: 0.6482 (mp0) REVERT: D 306 LYS cc_start: 0.8301 (ttpt) cc_final: 0.7782 (ttpp) REVERT: D 447 ARG cc_start: 0.6481 (mtt90) cc_final: 0.5841 (mtp180) REVERT: D 457 GLU cc_start: 0.6141 (tt0) cc_final: 0.5661 (tt0) REVERT: L 50 MET cc_start: 0.7471 (mtt) cc_final: 0.7051 (mmt) REVERT: L 108 SER cc_start: 0.7859 (p) cc_final: 0.7489 (m) REVERT: E 35 ASP cc_start: 0.6357 (m-30) cc_final: 0.6022 (m-30) REVERT: E 73 THR cc_start: 0.6750 (OUTLIER) cc_final: 0.6322 (p) REVERT: E 128 SER cc_start: 0.8046 (t) cc_final: 0.7459 (t) REVERT: E 129 PHE cc_start: 0.7314 (OUTLIER) cc_final: 0.6270 (m-80) REVERT: E 283 GLU cc_start: 0.6970 (tt0) cc_final: 0.6381 (mp0) REVERT: E 306 LYS cc_start: 0.8228 (ttpt) cc_final: 0.7719 (ttpp) REVERT: E 447 ARG cc_start: 0.6258 (mtt90) cc_final: 0.5656 (mtp180) REVERT: E 457 GLU cc_start: 0.6213 (tt0) cc_final: 0.5752 (tt0) REVERT: M 50 MET cc_start: 0.7408 (mtt) cc_final: 0.7003 (mmt) REVERT: M 108 SER cc_start: 0.7979 (p) cc_final: 0.7533 (m) REVERT: F 35 ASP cc_start: 0.6332 (m-30) cc_final: 0.6025 (m-30) REVERT: F 73 THR cc_start: 0.6837 (OUTLIER) cc_final: 0.6329 (p) REVERT: F 108 ILE cc_start: 0.7817 (OUTLIER) cc_final: 0.7204 (tp) REVERT: F 128 SER cc_start: 0.7919 (t) cc_final: 0.7387 (t) REVERT: F 129 PHE cc_start: 0.7370 (OUTLIER) cc_final: 0.6336 (m-80) REVERT: F 133 LYS cc_start: 0.7874 (OUTLIER) cc_final: 0.7506 (mtmm) REVERT: F 283 GLU cc_start: 0.6947 (tt0) cc_final: 0.6450 (mp0) REVERT: F 306 LYS cc_start: 0.8303 (ttpt) cc_final: 0.7791 (ttpp) REVERT: F 336 LEU cc_start: 0.5740 (OUTLIER) cc_final: 0.5334 (mp) REVERT: F 447 ARG cc_start: 0.6414 (mtt90) cc_final: 0.5771 (mtp180) REVERT: F 457 GLU cc_start: 0.6163 (tt0) cc_final: 0.5700 (tt0) REVERT: N 50 MET cc_start: 0.7337 (mtt) cc_final: 0.6901 (mmt) REVERT: N 108 SER cc_start: 0.7841 (p) cc_final: 0.7432 (m) REVERT: G 108 ILE cc_start: 0.7779 (OUTLIER) cc_final: 0.7227 (tp) REVERT: G 129 PHE cc_start: 0.7238 (OUTLIER) cc_final: 0.6206 (m-80) REVERT: G 205 ASP cc_start: 0.7460 (OUTLIER) cc_final: 0.6733 (t0) REVERT: G 249 MET cc_start: 0.7334 (mmm) cc_final: 0.7035 (mmm) REVERT: G 283 GLU cc_start: 0.6882 (tt0) cc_final: 0.6570 (mp0) REVERT: G 306 LYS cc_start: 0.8250 (ttpt) cc_final: 0.7740 (ttpp) REVERT: G 457 GLU cc_start: 0.6066 (tt0) cc_final: 0.5611 (tt0) REVERT: O 50 MET cc_start: 0.7458 (mtt) cc_final: 0.7017 (mmt) REVERT: O 108 SER cc_start: 0.7762 (p) cc_final: 0.7386 (m) REVERT: H 73 THR cc_start: 0.6844 (OUTLIER) cc_final: 0.6335 (p) REVERT: H 128 SER cc_start: 0.7903 (t) cc_final: 0.7323 (t) REVERT: H 129 PHE cc_start: 0.7305 (OUTLIER) cc_final: 0.6277 (m-80) REVERT: H 283 GLU cc_start: 0.6937 (tt0) cc_final: 0.6529 (mp0) REVERT: H 306 LYS cc_start: 0.8395 (ttpt) cc_final: 0.7924 (ttpp) REVERT: H 336 LEU cc_start: 0.5759 (OUTLIER) cc_final: 0.5330 (mp) REVERT: H 447 ARG cc_start: 0.6298 (mtt90) cc_final: 0.5783 (mtp180) REVERT: H 457 GLU cc_start: 0.6169 (tt0) cc_final: 0.5692 (tt0) REVERT: P 50 MET cc_start: 0.7423 (mtt) cc_final: 0.6981 (mmt) REVERT: P 108 SER cc_start: 0.7809 (p) cc_final: 0.7429 (m) outliers start: 125 outliers final: 99 residues processed: 530 average time/residue: 0.2355 time to fit residues: 201.8181 Evaluate side-chains 554 residues out of total 3936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 433 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain I residue 88 THR Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 355 ASN Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain J residue 38 THR Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 88 THR Chi-restraints excluded: chain K residue 105 VAL Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 129 PHE Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain D residue 355 ASN Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 88 THR Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 129 PHE Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 342 THR Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 88 THR Chi-restraints excluded: chain M residue 105 VAL Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 129 PHE Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 336 LEU Chi-restraints excluded: chain F residue 342 THR Chi-restraints excluded: chain F residue 355 ASN Chi-restraints excluded: chain F residue 356 THR Chi-restraints excluded: chain F residue 357 VAL Chi-restraints excluded: chain N residue 38 THR Chi-restraints excluded: chain N residue 88 THR Chi-restraints excluded: chain N residue 105 VAL Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 129 PHE Chi-restraints excluded: chain G residue 205 ASP Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain G residue 336 LEU Chi-restraints excluded: chain G residue 342 THR Chi-restraints excluded: chain G residue 355 ASN Chi-restraints excluded: chain G residue 356 THR Chi-restraints excluded: chain G residue 357 VAL Chi-restraints excluded: chain O residue 38 THR Chi-restraints excluded: chain O residue 88 THR Chi-restraints excluded: chain O residue 105 VAL Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 108 ILE Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 129 PHE Chi-restraints excluded: chain H residue 265 VAL Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain H residue 336 LEU Chi-restraints excluded: chain H residue 342 THR Chi-restraints excluded: chain H residue 355 ASN Chi-restraints excluded: chain H residue 356 THR Chi-restraints excluded: chain P residue 38 THR Chi-restraints excluded: chain P residue 88 THR Chi-restraints excluded: chain P residue 105 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 63 optimal weight: 2.9990 chunk 280 optimal weight: 4.9990 chunk 170 optimal weight: 2.9990 chunk 417 optimal weight: 1.9990 chunk 276 optimal weight: 0.5980 chunk 104 optimal weight: 6.9990 chunk 409 optimal weight: 5.9990 chunk 308 optimal weight: 3.9990 chunk 300 optimal weight: 0.7980 chunk 147 optimal weight: 5.9990 chunk 227 optimal weight: 6.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 402 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.158329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.123933 restraints weight = 271271.284| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 6.12 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3168 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 182 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 188 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3168 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.4427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 38728 Z= 0.186 Angle : 0.652 9.758 52544 Z= 0.324 Chirality : 0.045 0.138 5616 Planarity : 0.005 0.047 6800 Dihedral : 7.256 176.412 5392 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.38 % Allowed : 13.31 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.31 (0.12), residues: 4712 helix: 0.86 (0.12), residues: 1760 sheet: -0.17 (0.18), residues: 832 loop : -1.09 (0.13), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 361 TYR 0.017 0.002 TYR J 47 PHE 0.014 0.002 PHE A 100 TRP 0.010 0.001 TRP B 216 HIS 0.006 0.002 HIS B 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.19 (38728) covalent geometry : angle 0.65205 / 0.32 (52544) hydrogen bonds : bond 0.04174 / 2.76 ( 1468) hydrogen bonds : angle 4.68151 / 3.24 ( 4188) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6265.18 seconds wall clock time: 109 minutes 8.21 seconds (6548.21 seconds total)