Starting phenix.real_space_refine on Sun Feb 8 00:00:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ln9_63229/02_2026/9ln9_63229.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ln9_63229/02_2026/9ln9_63229.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ln9_63229/02_2026/9ln9_63229.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ln9_63229/02_2026/9ln9_63229.map" model { file = "/net/cci-nas-00/data/ceres_data/9ln9_63229/02_2026/9ln9_63229.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ln9_63229/02_2026/9ln9_63229.cif" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.010 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 42 5.49 5 Mg 14 5.21 5 S 190 5.16 5 C 23779 2.51 5 N 6377 2.21 5 O 7224 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 37626 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 2292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2292 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 13, 'TRANS': 276} Chain breaks: 1 Chain: "B" Number of atoms: 2313 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 291, 2302 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 13, 'TRANS': 277} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 291, 2302 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 13, 'TRANS': 277} Chain breaks: 1 bond proxies already assigned to first conformer: 2327 Chain: "C" Number of atoms: 2325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2325 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 13, 'TRANS': 280} Chain breaks: 1 Chain: "D" Number of atoms: 2333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2333 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 13, 'TRANS': 281} Chain breaks: 1 Chain: "E" Number of atoms: 2316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2316 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 13, 'TRANS': 279} Chain breaks: 1 Chain: "F" Number of atoms: 2316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2316 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 13, 'TRANS': 279} Chain breaks: 1 Chain: "G" Number of atoms: 2316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2316 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 13, 'TRANS': 279} Chain breaks: 1 Chain: "H" Number of atoms: 2316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2316 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 13, 'TRANS': 279} Chain breaks: 1 Chain: "I" Number of atoms: 2316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2316 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 13, 'TRANS': 279} Chain breaks: 1 Chain: "J" Number of atoms: 2324 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 293, 2316 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 13, 'TRANS': 279} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 293, 2316 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 13, 'TRANS': 279} Chain breaks: 1 bond proxies already assigned to first conformer: 2344 Chain: "K" Number of atoms: 2324 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 293, 2316 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 13, 'TRANS': 279} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 293, 2316 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 13, 'TRANS': 279} Chain breaks: 1 bond proxies already assigned to first conformer: 2344 Chain: "L" Number of atoms: 2324 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 293, 2316 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 13, 'TRANS': 279} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 293, 2316 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 13, 'TRANS': 279} Chain breaks: 1 bond proxies already assigned to first conformer: 2344 Chain: "M" Number of atoms: 2324 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 293, 2316 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 13, 'TRANS': 279} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 293, 2316 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 13, 'TRANS': 279} Chain breaks: 1 bond proxies already assigned to first conformer: 2344 Chain: "N" Number of atoms: 2324 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 293, 2316 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 13, 'TRANS': 279} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 293, 2316 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 13, 'TRANS': 279} Chain breaks: 1 bond proxies already assigned to first conformer: 2344 Chain: "O" Number of atoms: 2254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2254 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 13, 'TRANS': 272} Chain breaks: 1 Chain: "P" Number of atoms: 2316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2316 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 13, 'TRANS': 279} Chain breaks: 1 Chain: "Q" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 145 Classifications: {'peptide': 29} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'TRANS': 28} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'UNK:plan-1': 29} Unresolved non-hydrogen planarities: 29 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG B 74 " occ=0.69 ... (20 atoms not shown) pdb=" NH2BARG B 74 " occ=0.31 Time building chain proxies: 11.34, per 1000 atoms: 0.30 Number of scatterers: 37626 At special positions: 0 Unit cell: (158.26, 133.25, 163.18, 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 190 16.00 P 42 15.00 Mg 14 11.99 O 7224 8.00 N 6377 7.00 C 23779 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: 2.94 Conformation dependent library (CDL) restraints added in 2.0 seconds 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8980 Finding SS restraints... Secondary structure from input PDB file: 271 helices and 17 sheets defined 60.8% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 43 through 61 Processing helix chain 'A' and resid 70 through 78 Processing helix chain 'A' and resid 89 through 93 Processing helix chain 'A' and resid 96 through 107 Processing helix chain 'A' and resid 107 through 113 Processing helix chain 'A' and resid 139 through 149 Processing helix chain 'A' and resid 168 through 184 Processing helix chain 'A' and resid 193 through 198 removed outlier: 3.905A pdb=" N PHE A 197 " --> pdb=" O GLN A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 221 removed outlier: 4.148A pdb=" N ASP A 221 " --> pdb=" O MET A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 241 Processing helix chain 'A' and resid 242 through 248 Processing helix chain 'A' and resid 259 through 271 Processing helix chain 'A' and resid 282 through 290 Processing helix chain 'A' and resid 294 through 319 removed outlier: 5.487A pdb=" N GLU A 312 " --> pdb=" O ASP A 308 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N TYR A 313 " --> pdb=" O ALA A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 347 removed outlier: 3.724A pdb=" N PHE A 344 " --> pdb=" O LYS A 340 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LYS A 347 " --> pdb=" O ASP A 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 61 Processing helix chain 'B' and resid 70 through 77 removed outlier: 3.667A pdb=" N THR B 75 " --> pdb=" O ALA B 71 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU B 77 " --> pdb=" O GLU B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 80 No H-bonds generated for 'chain 'B' and resid 78 through 80' Processing helix chain 'B' and resid 89 through 93 Processing helix chain 'B' and resid 96 through 107 Processing helix chain 'B' and resid 108 through 113 Processing helix chain 'B' and resid 113 through 118 removed outlier: 3.823A pdb=" N TYR B 117 " --> pdb=" O MET B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 149 Processing helix chain 'B' and resid 158 through 163 Processing helix chain 'B' and resid 168 through 184 Processing helix chain 'B' and resid 193 through 198 removed outlier: 4.159A pdb=" N PHE B 197 " --> pdb=" O GLN B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 221 Processing helix chain 'B' and resid 242 through 248 Processing helix chain 'B' and resid 259 through 271 Processing helix chain 'B' and resid 282 through 290 Processing helix chain 'B' and resid 294 through 320 removed outlier: 5.069A pdb=" N GLU B 312 " --> pdb=" O ASP B 308 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N TYR B 313 " --> pdb=" O ALA B 309 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN B 319 " --> pdb=" O LYS B 315 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU B 320 " --> pdb=" O GLN B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 348 removed outlier: 4.037A pdb=" N PHE B 344 " --> pdb=" O LYS B 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 61 Processing helix chain 'C' and resid 62 through 66 removed outlier: 3.986A pdb=" N GLU C 66 " --> pdb=" O ALA C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 78 Processing helix chain 'C' and resid 89 through 93 Processing helix chain 'C' and resid 96 through 107 Processing helix chain 'C' and resid 107 through 113 Processing helix chain 'C' and resid 120 through 124 removed outlier: 3.977A pdb=" N GLN C 124 " --> pdb=" O PRO C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 150 Processing helix chain 'C' and resid 158 through 163 Processing helix chain 'C' and resid 168 through 184 Processing helix chain 'C' and resid 193 through 198 removed outlier: 4.340A pdb=" N PHE C 197 " --> pdb=" O GLN C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 221 Processing helix chain 'C' and resid 242 through 247 Processing helix chain 'C' and resid 259 through 271 Processing helix chain 'C' and resid 282 through 290 Processing helix chain 'C' and resid 294 through 310 Processing helix chain 'C' and resid 310 through 320 Processing helix chain 'C' and resid 341 through 346 Processing helix chain 'D' and resid 44 through 61 Processing helix chain 'D' and resid 62 through 66 removed outlier: 3.618A pdb=" N ALA D 65 " --> pdb=" O PRO D 62 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLU D 66 " --> pdb=" O ALA D 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 66' Processing helix chain 'D' and resid 70 through 77 Processing helix chain 'D' and resid 82 through 86 Processing helix chain 'D' and resid 89 through 93 Processing helix chain 'D' and resid 96 through 106 Processing helix chain 'D' and resid 107 through 113 Processing helix chain 'D' and resid 115 through 119 removed outlier: 3.779A pdb=" N SER D 118 " --> pdb=" O GLU D 115 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ASN D 119 " --> pdb=" O VAL D 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 115 through 119' Processing helix chain 'D' and resid 138 through 149 Processing helix chain 'D' and resid 168 through 184 removed outlier: 3.658A pdb=" N LYS D 172 " --> pdb=" O GLY D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 198 removed outlier: 4.128A pdb=" N PHE D 197 " --> pdb=" O GLN D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 221 Processing helix chain 'D' and resid 242 through 248 Processing helix chain 'D' and resid 259 through 271 Processing helix chain 'D' and resid 282 through 290 Processing helix chain 'D' and resid 294 through 310 Processing helix chain 'D' and resid 310 through 320 Processing helix chain 'D' and resid 340 through 348 removed outlier: 4.057A pdb=" N PHE D 344 " --> pdb=" O LYS D 340 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU D 348 " --> pdb=" O PHE D 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 61 Processing helix chain 'E' and resid 62 through 65 Processing helix chain 'E' and resid 70 through 77 Processing helix chain 'E' and resid 96 through 106 Processing helix chain 'E' and resid 107 through 113 Processing helix chain 'E' and resid 138 through 150 Processing helix chain 'E' and resid 158 through 163 Processing helix chain 'E' and resid 168 through 184 removed outlier: 3.698A pdb=" N LYS E 172 " --> pdb=" O GLY E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 198 removed outlier: 4.186A pdb=" N PHE E 197 " --> pdb=" O GLN E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 221 Processing helix chain 'E' and resid 242 through 248 Processing helix chain 'E' and resid 259 through 271 Processing helix chain 'E' and resid 282 through 290 removed outlier: 3.925A pdb=" N ILE E 286 " --> pdb=" O ASP E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 310 Processing helix chain 'E' and resid 311 through 320 Processing helix chain 'E' and resid 340 through 348 removed outlier: 4.180A pdb=" N PHE E 344 " --> pdb=" O LYS E 340 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYS E 347 " --> pdb=" O ASP E 343 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 61 Processing helix chain 'F' and resid 62 through 65 Processing helix chain 'F' and resid 70 through 78 removed outlier: 3.601A pdb=" N SER F 78 " --> pdb=" O ARG F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 86 Processing helix chain 'F' and resid 89 through 93 Processing helix chain 'F' and resid 96 through 107 Processing helix chain 'F' and resid 107 through 113 Processing helix chain 'F' and resid 138 through 150 Processing helix chain 'F' and resid 158 through 163 Processing helix chain 'F' and resid 168 through 184 Processing helix chain 'F' and resid 193 through 198 removed outlier: 4.147A pdb=" N PHE F 197 " --> pdb=" O GLN F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 221 Processing helix chain 'F' and resid 237 through 241 Processing helix chain 'F' and resid 242 through 248 Processing helix chain 'F' and resid 259 through 271 Processing helix chain 'F' and resid 282 through 290 Processing helix chain 'F' and resid 294 through 320 removed outlier: 5.149A pdb=" N GLU F 312 " --> pdb=" O ASP F 308 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N TYR F 313 " --> pdb=" O ALA F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 347 removed outlier: 3.827A pdb=" N PHE F 344 " --> pdb=" O LYS F 340 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LYS F 347 " --> pdb=" O ASP F 343 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 61 Processing helix chain 'G' and resid 62 through 65 Processing helix chain 'G' and resid 70 through 77 Processing helix chain 'G' and resid 89 through 93 removed outlier: 3.649A pdb=" N ILE G 93 " --> pdb=" O PHE G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 107 Processing helix chain 'G' and resid 107 through 113 Processing helix chain 'G' and resid 113 through 118 removed outlier: 3.767A pdb=" N TYR G 117 " --> pdb=" O MET G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 150 Processing helix chain 'G' and resid 158 through 162 Processing helix chain 'G' and resid 168 through 184 removed outlier: 3.540A pdb=" N LYS G 172 " --> pdb=" O GLY G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 193 through 198 removed outlier: 4.010A pdb=" N PHE G 197 " --> pdb=" O GLN G 193 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 220 Processing helix chain 'G' and resid 242 through 248 Processing helix chain 'G' and resid 259 through 271 Processing helix chain 'G' and resid 282 through 290 removed outlier: 3.509A pdb=" N ILE G 286 " --> pdb=" O ASP G 282 " (cutoff:3.500A) Processing helix chain 'G' and resid 294 through 310 Processing helix chain 'G' and resid 310 through 320 Processing helix chain 'G' and resid 340 through 348 removed outlier: 3.823A pdb=" N PHE G 344 " --> pdb=" O LYS G 340 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS G 347 " --> pdb=" O ASP G 343 " (cutoff:3.500A) Processing helix chain 'H' and resid 44 through 61 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 70 through 77 Processing helix chain 'H' and resid 89 through 93 removed outlier: 3.582A pdb=" N ILE H 93 " --> pdb=" O PHE H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 107 Processing helix chain 'H' and resid 107 through 113 Processing helix chain 'H' and resid 115 through 120 removed outlier: 3.700A pdb=" N SER H 118 " --> pdb=" O GLU H 115 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ASN H 119 " --> pdb=" O VAL H 116 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER H 120 " --> pdb=" O TYR H 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 115 through 120' Processing helix chain 'H' and resid 138 through 149 Processing helix chain 'H' and resid 168 through 184 Processing helix chain 'H' and resid 193 through 198 removed outlier: 4.148A pdb=" N PHE H 197 " --> pdb=" O GLN H 193 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 221 Processing helix chain 'H' and resid 237 through 241 Processing helix chain 'H' and resid 242 through 248 Processing helix chain 'H' and resid 259 through 271 Processing helix chain 'H' and resid 282 through 290 Processing helix chain 'H' and resid 294 through 320 removed outlier: 5.408A pdb=" N GLU H 312 " --> pdb=" O ASP H 308 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N TYR H 313 " --> pdb=" O ALA H 309 " (cutoff:3.500A) Processing helix chain 'H' and resid 340 through 347 removed outlier: 3.786A pdb=" N PHE H 344 " --> pdb=" O LYS H 340 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LYS H 347 " --> pdb=" O ASP H 343 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 61 Processing helix chain 'I' and resid 62 through 65 Processing helix chain 'I' and resid 70 through 77 Processing helix chain 'I' and resid 89 through 93 removed outlier: 3.626A pdb=" N ILE I 93 " --> pdb=" O PHE I 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 96 through 107 Processing helix chain 'I' and resid 107 through 113 Processing helix chain 'I' and resid 138 through 150 Processing helix chain 'I' and resid 158 through 162 Processing helix chain 'I' and resid 168 through 184 Processing helix chain 'I' and resid 193 through 198 removed outlier: 4.093A pdb=" N PHE I 197 " --> pdb=" O GLN I 193 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 221 Processing helix chain 'I' and resid 242 through 248 Processing helix chain 'I' and resid 259 through 271 Processing helix chain 'I' and resid 282 through 290 Processing helix chain 'I' and resid 294 through 320 removed outlier: 5.134A pdb=" N GLU I 312 " --> pdb=" O ASP I 308 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N TYR I 313 " --> pdb=" O ALA I 309 " (cutoff:3.500A) Processing helix chain 'I' and resid 340 through 348 removed outlier: 3.864A pdb=" N PHE I 344 " --> pdb=" O LYS I 340 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS I 347 " --> pdb=" O ASP I 343 " (cutoff:3.500A) Processing helix chain 'J' and resid 44 through 61 Processing helix chain 'J' and resid 62 through 65 Processing helix chain 'J' and resid 70 through 78 Processing helix chain 'J' and resid 89 through 93 Processing helix chain 'J' and resid 96 through 107 Processing helix chain 'J' and resid 107 through 113 Processing helix chain 'J' and resid 116 through 120 removed outlier: 4.378A pdb=" N ASN J 119 " --> pdb=" O VAL J 116 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER J 120 " --> pdb=" O TYR J 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 116 through 120' Processing helix chain 'J' and resid 138 through 149 Processing helix chain 'J' and resid 168 through 184 Processing helix chain 'J' and resid 193 through 198 removed outlier: 4.107A pdb=" N PHE J 197 " --> pdb=" O GLN J 193 " (cutoff:3.500A) Processing helix chain 'J' and resid 206 through 221 Processing helix chain 'J' and resid 242 through 248 Processing helix chain 'J' and resid 259 through 271 Processing helix chain 'J' and resid 282 through 290 removed outlier: 4.281A pdb=" N ILE J 286 " --> pdb=" O ASP J 282 " (cutoff:3.500A) Processing helix chain 'J' and resid 294 through 310 Processing helix chain 'J' and resid 310 through 320 Processing helix chain 'J' and resid 340 through 348 removed outlier: 3.899A pdb=" N PHE J 344 " --> pdb=" O LYS J 340 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 61 Processing helix chain 'K' and resid 62 through 65 Processing helix chain 'K' and resid 70 through 78 removed outlier: 3.799A pdb=" N SER K 78 " --> pdb=" O ARG K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 89 through 93 Processing helix chain 'K' and resid 96 through 107 Processing helix chain 'K' and resid 107 through 113 Processing helix chain 'K' and resid 138 through 149 Processing helix chain 'K' and resid 168 through 184 Processing helix chain 'K' and resid 193 through 198 removed outlier: 4.021A pdb=" N PHE K 197 " --> pdb=" O GLN K 193 " (cutoff:3.500A) Processing helix chain 'K' and resid 206 through 221 Processing helix chain 'K' and resid 242 through 248 Processing helix chain 'K' and resid 259 through 271 Processing helix chain 'K' and resid 282 through 290 removed outlier: 3.719A pdb=" N ILE K 286 " --> pdb=" O ASP K 282 " (cutoff:3.500A) Processing helix chain 'K' and resid 294 through 310 Processing helix chain 'K' and resid 310 through 320 Processing helix chain 'K' and resid 340 through 346 removed outlier: 3.940A pdb=" N PHE K 344 " --> pdb=" O LYS K 340 " (cutoff:3.500A) Processing helix chain 'L' and resid 44 through 61 Processing helix chain 'L' and resid 62 through 65 Processing helix chain 'L' and resid 70 through 77 Processing helix chain 'L' and resid 89 through 93 Processing helix chain 'L' and resid 96 through 107 Processing helix chain 'L' and resid 108 through 113 Processing helix chain 'L' and resid 115 through 124 removed outlier: 4.204A pdb=" N ASN L 119 " --> pdb=" O VAL L 116 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N SER L 120 " --> pdb=" O TYR L 117 " (cutoff:3.500A) Proline residue: L 121 - end of helix removed outlier: 4.090A pdb=" N GLN L 124 " --> pdb=" O PRO L 121 " (cutoff:3.500A) Processing helix chain 'L' and resid 138 through 149 Processing helix chain 'L' and resid 168 through 184 Processing helix chain 'L' and resid 193 through 198 removed outlier: 4.215A pdb=" N PHE L 197 " --> pdb=" O GLN L 193 " (cutoff:3.500A) Processing helix chain 'L' and resid 206 through 221 Processing helix chain 'L' and resid 237 through 241 Processing helix chain 'L' and resid 242 through 248 Processing helix chain 'L' and resid 259 through 271 Processing helix chain 'L' and resid 283 through 290 Processing helix chain 'L' and resid 294 through 310 Processing helix chain 'L' and resid 310 through 320 Processing helix chain 'L' and resid 340 through 348 removed outlier: 3.900A pdb=" N PHE L 344 " --> pdb=" O LYS L 340 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS L 347 " --> pdb=" O ASP L 343 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 61 Processing helix chain 'M' and resid 62 through 65 Processing helix chain 'M' and resid 70 through 78 Processing helix chain 'M' and resid 82 through 86 Processing helix chain 'M' and resid 96 through 107 Processing helix chain 'M' and resid 107 through 113 Processing helix chain 'M' and resid 113 through 118 removed outlier: 3.908A pdb=" N TYR M 117 " --> pdb=" O MET M 113 " (cutoff:3.500A) Processing helix chain 'M' and resid 139 through 150 removed outlier: 3.602A pdb=" N SER M 150 " --> pdb=" O LEU M 146 " (cutoff:3.500A) Processing helix chain 'M' and resid 168 through 184 removed outlier: 3.756A pdb=" N LYS M 172 " --> pdb=" O GLY M 168 " (cutoff:3.500A) Processing helix chain 'M' and resid 193 through 198 removed outlier: 4.015A pdb=" N PHE M 197 " --> pdb=" O GLN M 193 " (cutoff:3.500A) Processing helix chain 'M' and resid 206 through 221 Processing helix chain 'M' and resid 242 through 248 Processing helix chain 'M' and resid 259 through 271 Processing helix chain 'M' and resid 282 through 290 removed outlier: 4.003A pdb=" N ILE M 286 " --> pdb=" O ASP M 282 " (cutoff:3.500A) Processing helix chain 'M' and resid 294 through 319 removed outlier: 5.305A pdb=" N GLU M 312 " --> pdb=" O ASP M 308 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N TYR M 313 " --> pdb=" O ALA M 309 " (cutoff:3.500A) Processing helix chain 'M' and resid 340 through 348 removed outlier: 3.667A pdb=" N PHE M 344 " --> pdb=" O LYS M 340 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS M 347 " --> pdb=" O ASP M 343 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 61 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 70 through 78 Processing helix chain 'N' and resid 82 through 86 Processing helix chain 'N' and resid 96 through 107 Processing helix chain 'N' and resid 107 through 113 Processing helix chain 'N' and resid 138 through 149 Processing helix chain 'N' and resid 158 through 163 Processing helix chain 'N' and resid 168 through 184 Processing helix chain 'N' and resid 206 through 221 Processing helix chain 'N' and resid 237 through 241 Processing helix chain 'N' and resid 242 through 248 Processing helix chain 'N' and resid 259 through 271 Processing helix chain 'N' and resid 282 through 290 Processing helix chain 'N' and resid 294 through 310 Processing helix chain 'N' and resid 311 through 320 Processing helix chain 'N' and resid 340 through 348 removed outlier: 3.753A pdb=" N PHE N 344 " --> pdb=" O LYS N 340 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS N 347 " --> pdb=" O ASP N 343 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 61 Processing helix chain 'O' and resid 62 through 65 Processing helix chain 'O' and resid 70 through 78 removed outlier: 3.530A pdb=" N SER O 78 " --> pdb=" O ARG O 74 " (cutoff:3.500A) Processing helix chain 'O' and resid 89 through 93 Processing helix chain 'O' and resid 96 through 107 Processing helix chain 'O' and resid 107 through 113 Processing helix chain 'O' and resid 138 through 150 removed outlier: 3.554A pdb=" N SER O 150 " --> pdb=" O LEU O 146 " (cutoff:3.500A) Processing helix chain 'O' and resid 158 through 163 Processing helix chain 'O' and resid 169 through 184 Processing helix chain 'O' and resid 193 through 198 removed outlier: 4.041A pdb=" N PHE O 197 " --> pdb=" O GLN O 193 " (cutoff:3.500A) Processing helix chain 'O' and resid 206 through 221 Processing helix chain 'O' and resid 242 through 248 Processing helix chain 'O' and resid 259 through 271 Processing helix chain 'O' and resid 282 through 290 removed outlier: 3.597A pdb=" N ILE O 286 " --> pdb=" O ASP O 282 " (cutoff:3.500A) Processing helix chain 'O' and resid 294 through 315 removed outlier: 5.270A pdb=" N GLU O 312 " --> pdb=" O ASP O 308 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N TYR O 313 " --> pdb=" O ALA O 309 " (cutoff:3.500A) Processing helix chain 'O' and resid 340 through 347 removed outlier: 3.679A pdb=" N PHE O 344 " --> pdb=" O LYS O 340 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS O 347 " --> pdb=" O ASP O 343 " (cutoff:3.500A) Processing helix chain 'P' and resid 44 through 61 Processing helix chain 'P' and resid 62 through 65 Processing helix chain 'P' and resid 70 through 78 Processing helix chain 'P' and resid 82 through 86 Processing helix chain 'P' and resid 89 through 93 removed outlier: 3.670A pdb=" N ILE P 93 " --> pdb=" O PHE P 90 " (cutoff:3.500A) Processing helix chain 'P' and resid 96 through 107 Processing helix chain 'P' and resid 107 through 113 Processing helix chain 'P' and resid 120 through 124 removed outlier: 3.931A pdb=" N GLN P 124 " --> pdb=" O PRO P 121 " (cutoff:3.500A) Processing helix chain 'P' and resid 140 through 149 Processing helix chain 'P' and resid 168 through 184 removed outlier: 4.051A pdb=" N LYS P 172 " --> pdb=" O GLY P 168 " (cutoff:3.500A) Processing helix chain 'P' and resid 193 through 198 removed outlier: 3.663A pdb=" N PHE P 197 " --> pdb=" O GLN P 193 " (cutoff:3.500A) Processing helix chain 'P' and resid 206 through 221 removed outlier: 3.518A pdb=" N ASP P 221 " --> pdb=" O MET P 217 " (cutoff:3.500A) Processing helix chain 'P' and resid 242 through 249 Processing helix chain 'P' and resid 259 through 271 Processing helix chain 'P' and resid 282 through 290 removed outlier: 4.146A pdb=" N ILE P 286 " --> pdb=" O ASP P 282 " (cutoff:3.500A) Processing helix chain 'P' and resid 294 through 310 Processing helix chain 'P' and resid 310 through 320 removed outlier: 3.557A pdb=" N GLN P 319 " --> pdb=" O LYS P 315 " (cutoff:3.500A) Processing helix chain 'P' and resid 340 through 348 removed outlier: 3.721A pdb=" N PHE P 344 " --> pdb=" O LYS P 340 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 129 through 132 removed outlier: 5.998A pdb=" N LEU A 130 " --> pdb=" O PHE A 253 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 153 through 155 removed outlier: 6.255A pdb=" N ASN A 153 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N PHE A 190 " --> pdb=" O ASN A 153 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ILE A 155 " --> pdb=" O PHE A 190 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N ILE A 232 " --> pdb=" O CYS A 187 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N ILE A 189 " --> pdb=" O ILE A 232 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 154 through 156 removed outlier: 5.985A pdb=" N ILE B 155 " --> pdb=" O PHE B 190 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ASP B 192 " --> pdb=" O ILE B 155 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ILE B 189 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ALA B 234 " --> pdb=" O ILE B 189 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ILE B 191 " --> pdb=" O ALA B 234 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR B 235 " --> pdb=" O LEU B 131 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N GLY B 128 " --> pdb=" O LYS B 251 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N PHE B 253 " --> pdb=" O GLY B 128 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LEU B 130 " --> pdb=" O PHE B 253 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 80 through 81 removed outlier: 3.866A pdb=" N PHE C 154 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA C 234 " --> pdb=" O ILE C 191 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL C 129 " --> pdb=" O GLY C 233 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N THR C 235 " --> pdb=" O VAL C 129 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU C 131 " --> pdb=" O THR C 235 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N GLY C 128 " --> pdb=" O LYS C 251 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N PHE C 253 " --> pdb=" O GLY C 128 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU C 130 " --> pdb=" O PHE C 253 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 80 through 81 removed outlier: 3.888A pdb=" N PHE D 154 " --> pdb=" O VAL D 81 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ASN D 153 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N PHE D 190 " --> pdb=" O ASN D 153 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ILE D 155 " --> pdb=" O PHE D 190 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ASP D 192 " --> pdb=" O ILE D 155 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA D 234 " --> pdb=" O ILE D 191 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N VAL D 129 " --> pdb=" O GLY D 233 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N THR D 235 " --> pdb=" O VAL D 129 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N LEU D 131 " --> pdb=" O THR D 235 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLY D 128 " --> pdb=" O LYS D 251 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N PHE D 253 " --> pdb=" O GLY D 128 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU D 130 " --> pdb=" O PHE D 253 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 80 through 81 removed outlier: 3.859A pdb=" N PHE E 154 " --> pdb=" O VAL E 81 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ASN E 153 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N PHE E 190 " --> pdb=" O ASN E 153 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ILE E 155 " --> pdb=" O PHE E 190 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N ASP E 192 " --> pdb=" O ILE E 155 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA E 234 " --> pdb=" O ILE E 191 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N VAL E 129 " --> pdb=" O GLY E 233 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N THR E 235 " --> pdb=" O VAL E 129 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N LEU E 131 " --> pdb=" O THR E 235 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLY E 128 " --> pdb=" O LYS E 251 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N PHE E 253 " --> pdb=" O GLY E 128 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LEU E 130 " --> pdb=" O PHE E 253 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 153 through 156 removed outlier: 6.024A pdb=" N ASN F 153 " --> pdb=" O ILE F 188 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N PHE F 190 " --> pdb=" O ASN F 153 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ILE F 155 " --> pdb=" O PHE F 190 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ASP F 192 " --> pdb=" O ILE F 155 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA F 234 " --> pdb=" O ILE F 191 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N VAL F 129 " --> pdb=" O GLY F 233 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N THR F 235 " --> pdb=" O VAL F 129 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N LEU F 131 " --> pdb=" O THR F 235 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLY F 128 " --> pdb=" O LYS F 251 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N PHE F 253 " --> pdb=" O GLY F 128 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU F 130 " --> pdb=" O PHE F 253 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 80 through 81 removed outlier: 4.013A pdb=" N PHE G 154 " --> pdb=" O VAL G 81 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA G 234 " --> pdb=" O ILE G 191 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLY G 128 " --> pdb=" O LYS G 251 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N PHE G 253 " --> pdb=" O GLY G 128 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU G 130 " --> pdb=" O PHE G 253 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 80 through 81 removed outlier: 3.996A pdb=" N PHE H 154 " --> pdb=" O VAL H 81 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ASN H 153 " --> pdb=" O ILE H 188 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N PHE H 190 " --> pdb=" O ASN H 153 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ILE H 155 " --> pdb=" O PHE H 190 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N ASP H 192 " --> pdb=" O ILE H 155 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N ILE H 157 " --> pdb=" O ASP H 192 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA H 234 " --> pdb=" O ILE H 191 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL H 129 " --> pdb=" O GLY H 233 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N THR H 235 " --> pdb=" O VAL H 129 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N LEU H 131 " --> pdb=" O THR H 235 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLY H 128 " --> pdb=" O LYS H 251 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N PHE H 253 " --> pdb=" O GLY H 128 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU H 130 " --> pdb=" O PHE H 253 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 80 through 81 removed outlier: 3.801A pdb=" N PHE I 154 " --> pdb=" O VAL I 81 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ASN I 153 " --> pdb=" O ILE I 188 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N PHE I 190 " --> pdb=" O ASN I 153 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ILE I 155 " --> pdb=" O PHE I 190 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N ASP I 192 " --> pdb=" O ILE I 155 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA I 234 " --> pdb=" O ILE I 191 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL I 129 " --> pdb=" O GLY I 233 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLY I 128 " --> pdb=" O LYS I 251 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N PHE I 253 " --> pdb=" O GLY I 128 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU I 130 " --> pdb=" O PHE I 253 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 80 through 81 removed outlier: 3.952A pdb=" N PHE J 154 " --> pdb=" O VAL J 81 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ASN J 153 " --> pdb=" O ILE J 188 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N PHE J 190 " --> pdb=" O ASN J 153 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ILE J 155 " --> pdb=" O PHE J 190 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ASP J 192 " --> pdb=" O ILE J 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA J 234 " --> pdb=" O ILE J 191 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLY J 128 " --> pdb=" O LYS J 251 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N PHE J 253 " --> pdb=" O GLY J 128 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU J 130 " --> pdb=" O PHE J 253 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 80 through 81 removed outlier: 3.827A pdb=" N PHE K 154 " --> pdb=" O VAL K 81 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ASN K 153 " --> pdb=" O ILE K 188 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N PHE K 190 " --> pdb=" O ASN K 153 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ILE K 155 " --> pdb=" O PHE K 190 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ASP K 192 " --> pdb=" O ILE K 155 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA K 234 " --> pdb=" O ILE K 191 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLY K 128 " --> pdb=" O LYS K 251 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N PHE K 253 " --> pdb=" O GLY K 128 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU K 130 " --> pdb=" O PHE K 253 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 80 through 81 removed outlier: 3.858A pdb=" N PHE L 154 " --> pdb=" O VAL L 81 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA L 234 " --> pdb=" O ILE L 191 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLY L 128 " --> pdb=" O LYS L 251 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N PHE L 253 " --> pdb=" O GLY L 128 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU L 130 " --> pdb=" O PHE L 253 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 80 through 81 removed outlier: 3.817A pdb=" N PHE M 154 " --> pdb=" O VAL M 81 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLY M 128 " --> pdb=" O LYS M 251 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N PHE M 253 " --> pdb=" O GLY M 128 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU M 130 " --> pdb=" O PHE M 253 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 80 through 81 removed outlier: 3.763A pdb=" N PHE N 154 " --> pdb=" O VAL N 81 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA N 234 " --> pdb=" O ILE N 191 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL N 129 " --> pdb=" O GLY N 233 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N THR N 235 " --> pdb=" O VAL N 129 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU N 131 " --> pdb=" O THR N 235 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLY N 128 " --> pdb=" O LYS N 251 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N PHE N 253 " --> pdb=" O GLY N 128 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU N 130 " --> pdb=" O PHE N 253 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'O' and resid 80 through 81 removed outlier: 4.037A pdb=" N PHE O 154 " --> pdb=" O VAL O 81 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ASN O 153 " --> pdb=" O ILE O 188 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N PHE O 190 " --> pdb=" O ASN O 153 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ILE O 155 " --> pdb=" O PHE O 190 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N CYS O 187 " --> pdb=" O MET O 230 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ILE O 232 " --> pdb=" O CYS O 187 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ILE O 189 " --> pdb=" O ILE O 232 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLY O 128 " --> pdb=" O LYS O 251 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N PHE O 253 " --> pdb=" O GLY O 128 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU O 130 " --> pdb=" O PHE O 253 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'P' and resid 80 through 81 removed outlier: 4.099A pdb=" N PHE P 154 " --> pdb=" O VAL P 81 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N ASN P 153 " --> pdb=" O ILE P 188 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N PHE P 190 " --> pdb=" O ASN P 153 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ILE P 155 " --> pdb=" O PHE P 190 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ASP P 192 " --> pdb=" O ILE P 155 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N ILE P 157 " --> pdb=" O ASP P 192 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N MET P 230 " --> pdb=" O CYS P 187 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA P 234 " --> pdb=" O ILE P 191 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL P 129 " --> pdb=" O GLY P 233 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N GLY P 128 " --> pdb=" O LYS P 251 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N PHE P 253 " --> pdb=" O GLY P 128 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LEU P 130 " --> pdb=" O PHE P 253 " (cutoff:3.500A) 1808 hydrogen bonds defined for protein. 5233 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: 6.46 Time building geometry restraints manager: 3.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9491 1.33 - 1.46: 7152 1.46 - 1.58: 21193 1.58 - 1.70: 69 1.70 - 1.83: 332 Bond restraints: 38237 Sorted by residual: bond pdb=" C4 ATP B 401 " pdb=" C5 ATP B 401 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.93e+01 bond pdb=" C4 ATP N 401 " pdb=" C5 ATP N 401 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.86e+01 bond pdb=" C4 ATP M 401 " pdb=" C5 ATP M 401 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.61e+01 bond pdb=" C4 ATP L 401 " pdb=" C5 ATP L 401 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.56e+01 bond pdb=" C4 ATP A 401 " pdb=" C5 ATP A 401 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.49e+01 ... (remaining 38232 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.93: 51171 3.93 - 7.86: 381 7.86 - 11.79: 68 11.79 - 15.71: 12 15.71 - 19.64: 15 Bond angle restraints: 51647 Sorted by residual: angle pdb=" PB ATP K 401 " pdb=" O3B ATP K 401 " pdb=" PG ATP K 401 " ideal model delta sigma weight residual 139.87 120.23 19.64 1.00e+00 1.00e+00 3.86e+02 angle pdb=" PB ATP A 401 " pdb=" O3B ATP A 401 " pdb=" PG ATP A 401 " ideal model delta sigma weight residual 139.87 120.28 19.59 1.00e+00 1.00e+00 3.84e+02 angle pdb=" PB ATP G 401 " pdb=" O3B ATP G 401 " pdb=" PG ATP G 401 " ideal model delta sigma weight residual 139.87 120.36 19.51 1.00e+00 1.00e+00 3.81e+02 angle pdb=" PB ATP L 401 " pdb=" O3B ATP L 401 " pdb=" PG ATP L 401 " ideal model delta sigma weight residual 139.87 120.60 19.27 1.00e+00 1.00e+00 3.71e+02 angle pdb=" PB ATP B 401 " pdb=" O3B ATP B 401 " pdb=" PG ATP B 401 " ideal model delta sigma weight residual 139.87 121.11 18.76 1.00e+00 1.00e+00 3.52e+02 ... (remaining 51642 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 19596 18.01 - 36.02: 3088 36.02 - 54.03: 1025 54.03 - 72.04: 245 72.04 - 90.05: 69 Dihedral angle restraints: 24023 sinusoidal: 10244 harmonic: 13779 Sorted by residual: dihedral pdb=" C UNK Q 21 " pdb=" N UNK Q 21 " pdb=" CA UNK Q 21 " pdb=" CB UNK Q 21 " ideal model delta harmonic sigma weight residual -122.60 -138.67 16.07 0 2.50e+00 1.60e-01 4.13e+01 dihedral pdb=" N UNK Q 21 " pdb=" C UNK Q 21 " pdb=" CA UNK Q 21 " pdb=" CB UNK Q 21 " ideal model delta harmonic sigma weight residual 122.80 138.03 -15.23 0 2.50e+00 1.60e-01 3.71e+01 dihedral pdb=" CA LEU I 184 " pdb=" C LEU I 184 " pdb=" N GLN I 185 " pdb=" CA GLN I 185 " ideal model delta harmonic sigma weight residual 180.00 -153.03 -26.97 0 5.00e+00 4.00e-02 2.91e+01 ... (remaining 24020 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.154: 5873 0.154 - 0.309: 40 0.309 - 0.463: 4 0.463 - 0.618: 0 0.618 - 0.772: 1 Chirality restraints: 5918 Sorted by residual: chirality pdb=" CA UNK Q 21 " pdb=" N UNK Q 21 " pdb=" C UNK Q 21 " pdb=" CB UNK Q 21 " both_signs ideal model delta sigma weight residual False 2.52 1.75 0.77 2.00e-01 2.50e+01 1.49e+01 chirality pdb=" CA UNK Q 14 " pdb=" N UNK Q 14 " pdb=" C UNK Q 14 " pdb=" CB UNK Q 14 " both_signs ideal model delta sigma weight residual False 2.52 2.13 0.39 2.00e-01 2.50e+01 3.76e+00 chirality pdb=" CA UNK Q 20 " pdb=" N UNK Q 20 " pdb=" C UNK Q 20 " pdb=" CB UNK Q 20 " both_signs ideal model delta sigma weight residual False 2.52 2.18 0.34 2.00e-01 2.50e+01 2.94e+00 ... (remaining 5915 not shown) Planarity restraints: 6491 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG K 337 " 0.067 5.00e-02 4.00e+02 1.01e-01 1.62e+01 pdb=" N PRO K 338 " -0.174 5.00e-02 4.00e+02 pdb=" CA PRO K 338 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO K 338 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA UNK Q 21 " 0.019 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C UNK Q 21 " -0.067 2.00e-02 2.50e+03 pdb=" O UNK Q 21 " 0.025 2.00e-02 2.50e+03 pdb=" N UNK Q 22 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG I 337 " 0.062 5.00e-02 4.00e+02 9.28e-02 1.38e+01 pdb=" N PRO I 338 " -0.160 5.00e-02 4.00e+02 pdb=" CA PRO I 338 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO I 338 " 0.050 5.00e-02 4.00e+02 ... (remaining 6488 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 101 2.39 - 3.02: 19516 3.02 - 3.64: 61315 3.64 - 4.27: 94494 4.27 - 4.90: 155272 Nonbonded interactions: 330698 Sorted by model distance: nonbonded pdb=" O1G ATP N 401 " pdb="MG MG N 402 " model vdw 1.759 2.170 nonbonded pdb=" O1G ATP F 401 " pdb="MG MG F 402 " model vdw 1.827 2.170 nonbonded pdb=" O3B ATP M 401 " pdb="MG MG M 402 " model vdw 1.847 2.170 nonbonded pdb=" O2G ATP C 401 " pdb="MG MG C 402 " model vdw 1.896 2.170 nonbonded pdb=" OG1 THR C 140 " pdb="MG MG C 402 " model vdw 2.006 2.170 ... (remaining 330693 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 44 through 73 or resid 75 through 315 or resid 337 through \ 349)) selection = (chain 'B' and (resid 44 through 73 or resid 75 through 315 or resid 337 through \ 349)) selection = (chain 'C' and (resid 44 through 73 or resid 75 through 315 or resid 337 through \ 349)) selection = (chain 'D' and (resid 44 through 73 or resid 75 through 315 or resid 337 through \ 349)) selection = (chain 'E' and (resid 44 through 73 or resid 75 through 315 or resid 337 through \ 349)) selection = (chain 'F' and (resid 44 through 73 or resid 75 through 315 or resid 337 through \ 349)) selection = (chain 'G' and (resid 44 through 73 or resid 75 through 315 or resid 337 through \ 349)) selection = (chain 'H' and (resid 44 through 73 or resid 75 through 315 or resid 337 through \ 349)) selection = (chain 'I' and (resid 44 through 73 or resid 75 through 315 or resid 337 through \ 349)) selection = (chain 'J' and (resid 44 through 73 or resid 75 through 315 or resid 337 through \ 349)) selection = (chain 'K' and (resid 44 through 73 or resid 75 through 315 or resid 337 through \ 349)) selection = (chain 'L' and (resid 44 through 73 or resid 75 through 315 or resid 337 through \ 349)) selection = (chain 'M' and (resid 44 through 73 or resid 75 through 315 or resid 337 through \ 349)) selection = (chain 'N' and (resid 44 through 73 or resid 75 through 315 or resid 337 through \ 349)) selection = (chain 'O' and (resid 44 through 73 or resid 75 through 349)) selection = (chain 'P' and (resid 44 through 73 or resid 75 through 315 or resid 337 through \ 349)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 28.320 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: 0.020 Extract box with map and model: 1.790 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 35.760 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 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 : 0.005 0.083 38237 Z= 0.317 Angle : 0.925 19.642 51647 Z= 0.594 Chirality : 0.050 0.772 5918 Planarity : 0.005 0.101 6491 Dihedral : 20.030 90.053 15043 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.93 % Allowed : 33.81 % Favored : 64.26 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.12), residues: 4623 helix: 0.39 (0.10), residues: 2515 sheet: -0.47 (0.29), residues: 356 loop : 0.04 (0.15), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 44 TYR 0.029 0.001 TYR F 313 PHE 0.021 0.002 PHE J 197 TRP 0.012 0.001 TRP E 166 HIS 0.007 0.001 HIS J 206 Details of bonding type rmsd covalent geometry : bond 0.00483 (38237) covalent geometry : angle 0.92522 (51647) hydrogen bonds : bond 0.15770 ( 1808) hydrogen bonds : angle 6.06631 ( 5233) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 4129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 606 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 85 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7571 (mt-10) REVERT: F 115 GLU cc_start: 0.7629 (pm20) cc_final: 0.7323 (pm20) REVERT: F 119 ASN cc_start: 0.8112 (OUTLIER) cc_final: 0.7420 (t0) REVERT: F 308 ASP cc_start: 0.7855 (t0) cc_final: 0.7602 (m-30) REVERT: F 350 MET cc_start: 0.6782 (mmp) cc_final: 0.6272 (mmp) REVERT: H 346 LYS cc_start: 0.8464 (mtmt) cc_final: 0.8038 (mtmt) REVERT: I 163 MET cc_start: 0.8961 (mmm) cc_final: 0.8622 (mtp) REVERT: K 346 LYS cc_start: 0.8217 (ptpt) cc_final: 0.7801 (pttt) REVERT: L 247 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.7281 (ppt90) REVERT: M 350 MET cc_start: 0.5021 (mtm) cc_final: 0.4369 (tmt) REVERT: O 96 LEU cc_start: 0.7316 (mt) cc_final: 0.6875 (mt) REVERT: O 217 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.8472 (ttp) outliers start: 78 outliers final: 53 residues processed: 669 average time/residue: 0.7201 time to fit residues: 589.1833 Evaluate side-chains 603 residues out of total 4129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 547 time to evaluate : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 70 ASP Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 137 CYS Chi-restraints excluded: chain E residue 161 SER Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain F residue 119 ASN Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 236 ASN Chi-restraints excluded: chain F residue 247 ARG Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 231 ILE Chi-restraints excluded: chain G residue 260 SER Chi-restraints excluded: chain H residue 170 SER Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 203 SER Chi-restraints excluded: chain H residue 209 THR Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain I residue 161 SER Chi-restraints excluded: chain I residue 177 MET Chi-restraints excluded: chain I residue 224 LEU Chi-restraints excluded: chain J residue 80 ILE Chi-restraints excluded: chain J residue 88 ILE Chi-restraints excluded: chain J residue 149 GLU Chi-restraints excluded: chain J residue 276 LEU Chi-restraints excluded: chain K residue 184 LEU Chi-restraints excluded: chain L residue 224 LEU Chi-restraints excluded: chain L residue 247 ARG Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain N residue 209 THR Chi-restraints excluded: chain N residue 255 VAL Chi-restraints excluded: chain N residue 341 THR Chi-restraints excluded: chain O residue 80 ILE Chi-restraints excluded: chain O residue 217 MET Chi-restraints excluded: chain O residue 291 LYS Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 102 ASP Chi-restraints excluded: chain P residue 163 MET Chi-restraints excluded: chain P residue 170 SER Chi-restraints excluded: chain P residue 235 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 432 optimal weight: 10.0000 chunk 197 optimal weight: 0.8980 chunk 388 optimal weight: 3.9990 chunk 455 optimal weight: 4.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.0470 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.1980 chunk 401 optimal weight: 5.9990 overall best weight: 1.2282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 ASN B 185 GLN C 50 GLN C 119 ASN ** E 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 236 ASN G 316 GLN I 225 ASN K 289 ASN L 225 ASN M 182 ASN ** M 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 239 ASN M 284 GLN N 104 HIS O 53 GLN O 182 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.167938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.124437 restraints weight = 80833.835| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.81 r_work: 0.3106 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3108 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3108 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.0873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 38237 Z= 0.151 Angle : 0.580 10.245 51647 Z= 0.286 Chirality : 0.042 0.250 5918 Planarity : 0.004 0.069 6491 Dihedral : 11.545 87.453 5631 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.91 % Allowed : 31.08 % Favored : 65.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.13), residues: 4623 helix: 0.87 (0.10), residues: 2614 sheet: -0.64 (0.28), residues: 363 loop : 0.39 (0.16), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 263 TYR 0.017 0.001 TYR J 313 PHE 0.012 0.001 PHE G 197 TRP 0.008 0.001 TRP B 220 HIS 0.005 0.001 HIS E 206 Details of bonding type rmsd covalent geometry : bond 0.00352 (38237) covalent geometry : angle 0.58018 (51647) hydrogen bonds : bond 0.03855 ( 1808) hydrogen bonds : angle 4.70204 ( 5233) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 756 residues out of total 4129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 596 time to evaluate : 2.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 MET cc_start: 0.5878 (OUTLIER) cc_final: 0.5157 (mpt) REVERT: B 163 MET cc_start: 0.7247 (OUTLIER) cc_final: 0.6188 (mtp) REVERT: B 284 GLN cc_start: 0.8464 (tp40) cc_final: 0.8065 (tp-100) REVERT: B 288 ASP cc_start: 0.8347 (OUTLIER) cc_final: 0.8046 (m-30) REVERT: C 85 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7628 (mt-10) REVERT: D 52 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8342 (mt) REVERT: D 243 ASP cc_start: 0.8021 (t0) cc_final: 0.7798 (t0) REVERT: D 276 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8264 (mp) REVERT: D 315 LYS cc_start: 0.7572 (mtpm) cc_final: 0.7200 (pttp) REVERT: E 105 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7967 (pt0) REVERT: E 283 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8746 (tt) REVERT: F 115 GLU cc_start: 0.7672 (pm20) cc_final: 0.7423 (pm20) REVERT: F 308 ASP cc_start: 0.8104 (OUTLIER) cc_final: 0.7859 (m-30) REVERT: G 311 LYS cc_start: 0.8422 (ptpp) cc_final: 0.8217 (ptpp) REVERT: H 278 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7748 (mp0) REVERT: I 163 MET cc_start: 0.8884 (mmm) cc_final: 0.8573 (mtp) REVERT: K 337 ARG cc_start: 0.7174 (ptt90) cc_final: 0.6863 (ppt170) REVERT: K 346 LYS cc_start: 0.8225 (ptpt) cc_final: 0.7799 (pttt) REVERT: M 200 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7928 (tm-30) REVERT: M 316 GLN cc_start: 0.6937 (mt0) cc_final: 0.6591 (tm-30) REVERT: M 350 MET cc_start: 0.4995 (mtm) cc_final: 0.4545 (tmt) REVERT: O 96 LEU cc_start: 0.7119 (mt) cc_final: 0.6656 (mt) REVERT: O 228 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.6899 (mtp85) REVERT: P 169 GLU cc_start: 0.6002 (tp30) cc_final: 0.5778 (mm-30) outliers start: 160 outliers final: 53 residues processed: 698 average time/residue: 0.7111 time to fit residues: 610.4088 Evaluate side-chains 621 residues out of total 4129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 558 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 236 ASN Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 275 LYS Chi-restraints excluded: chain F residue 308 ASP Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain G residue 347 LYS Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain H residue 209 THR Chi-restraints excluded: chain H residue 224 LEU Chi-restraints excluded: chain H residue 256 SER Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain H residue 278 GLU Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 146 LEU Chi-restraints excluded: chain J residue 246 LEU Chi-restraints excluded: chain K residue 177 MET Chi-restraints excluded: chain K residue 204 THR Chi-restraints excluded: chain K residue 224 LEU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 137 CYS Chi-restraints excluded: chain L residue 177 MET Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain M residue 200 GLU Chi-restraints excluded: chain N residue 101 SER Chi-restraints excluded: chain O residue 74 ARG Chi-restraints excluded: chain O residue 88 ILE Chi-restraints excluded: chain O residue 106 SER Chi-restraints excluded: chain O residue 157 ILE Chi-restraints excluded: chain O residue 207 GLU Chi-restraints excluded: chain O residue 228 ARG Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 155 ILE Chi-restraints excluded: chain P residue 163 MET Chi-restraints excluded: chain P residue 205 ASP Chi-restraints excluded: chain P residue 235 THR Chi-restraints excluded: chain P residue 255 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 217 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 459 optimal weight: 20.0000 chunk 334 optimal weight: 7.9990 chunk 268 optimal weight: 2.9990 chunk 365 optimal weight: 1.9990 chunk 356 optimal weight: 0.0980 chunk 316 optimal weight: 3.9990 chunk 30 optimal weight: 8.9990 chunk 294 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 289 ASN ** E 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 236 ASN G 284 GLN G 319 GLN I 225 ASN K 193 GLN K 289 ASN L 225 ASN L 236 ASN M 182 ASN ** M 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 239 ASN M 284 GLN N 104 HIS O 182 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.167530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.123660 restraints weight = 71734.130| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.65 r_work: 0.3090 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2874 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2874 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 38237 Z= 0.153 Angle : 0.556 10.767 51647 Z= 0.271 Chirality : 0.041 0.185 5918 Planarity : 0.004 0.061 6491 Dihedral : 11.185 84.007 5548 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 4.76 % Allowed : 30.26 % Favored : 64.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.13), residues: 4623 helix: 1.17 (0.10), residues: 2599 sheet: -1.13 (0.25), residues: 432 loop : 0.61 (0.16), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 263 TYR 0.011 0.001 TYR M 313 PHE 0.024 0.001 PHE A 178 TRP 0.008 0.001 TRP B 220 HIS 0.006 0.001 HIS E 206 Details of bonding type rmsd covalent geometry : bond 0.00362 (38237) covalent geometry : angle 0.55618 (51647) hydrogen bonds : bond 0.03349 ( 1808) hydrogen bonds : angle 4.49633 ( 5233) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 792 residues out of total 4129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 195 poor density : 597 time to evaluate : 1.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 MET cc_start: 0.5838 (OUTLIER) cc_final: 0.5111 (mpt) REVERT: A 219 LEU cc_start: 0.6426 (OUTLIER) cc_final: 0.5559 (mt) REVERT: A 228 ARG cc_start: 0.3747 (mtp180) cc_final: 0.3430 (ptm160) REVERT: B 282 ASP cc_start: 0.7233 (t0) cc_final: 0.7022 (t0) REVERT: B 288 ASP cc_start: 0.8380 (OUTLIER) cc_final: 0.8123 (m-30) REVERT: C 85 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7553 (mt-10) REVERT: C 348 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8136 (mp) REVERT: D 52 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8279 (mt) REVERT: D 276 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8242 (mp) REVERT: D 315 LYS cc_start: 0.7578 (mtpm) cc_final: 0.7103 (pttp) REVERT: D 350 MET cc_start: 0.6755 (mmp) cc_final: 0.4340 (ttm) REVERT: E 105 GLU cc_start: 0.8451 (mm-30) cc_final: 0.7980 (pt0) REVERT: E 200 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.7794 (tm-30) REVERT: F 115 GLU cc_start: 0.7794 (pm20) cc_final: 0.7524 (pm20) REVERT: F 159 MET cc_start: 0.8301 (mmm) cc_final: 0.8067 (mmm) REVERT: G 91 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.8475 (mp-120) REVERT: G 199 ARG cc_start: 0.9210 (OUTLIER) cc_final: 0.8366 (ttp-170) REVERT: G 311 LYS cc_start: 0.8361 (ptpp) cc_final: 0.8126 (ptpp) REVERT: H 280 GLU cc_start: 0.7652 (tm-30) cc_final: 0.7134 (tm-30) REVERT: H 346 LYS cc_start: 0.8692 (mttt) cc_final: 0.8151 (mtmt) REVERT: I 163 MET cc_start: 0.9004 (OUTLIER) cc_final: 0.8767 (mtp) REVERT: I 272 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7787 (pttm) REVERT: K 141 MET cc_start: 0.8949 (OUTLIER) cc_final: 0.8714 (mtp) REVERT: K 261 ASP cc_start: 0.8548 (t0) cc_final: 0.8157 (t0) REVERT: K 337 ARG cc_start: 0.7237 (ptt90) cc_final: 0.7012 (ppt-90) REVERT: K 346 LYS cc_start: 0.8157 (ptpt) cc_final: 0.7753 (pttt) REVERT: M 184 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8686 (mt) REVERT: M 316 GLN cc_start: 0.6855 (mt0) cc_final: 0.6479 (tm-30) REVERT: M 350 MET cc_start: 0.5098 (mtm) cc_final: 0.4480 (tmt) REVERT: N 205 ASP cc_start: 0.8541 (OUTLIER) cc_final: 0.8259 (t0) REVERT: O 228 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.6877 (mtp85) REVERT: P 142 LEU cc_start: 0.6074 (OUTLIER) cc_final: 0.5790 (mm) REVERT: P 207 GLU cc_start: 0.4453 (OUTLIER) cc_final: 0.3956 (pt0) outliers start: 195 outliers final: 51 residues processed: 728 average time/residue: 0.6732 time to fit residues: 600.0977 Evaluate side-chains 615 residues out of total 4129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 547 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 312 GLU Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 200 GLU Chi-restraints excluded: chain E residue 236 ASN Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 161 SER Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 91 GLN Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain G residue 199 ARG Chi-restraints excluded: chain G residue 347 LYS Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain H residue 177 MET Chi-restraints excluded: chain H residue 207 GLU Chi-restraints excluded: chain H residue 224 LEU Chi-restraints excluded: chain H residue 236 ASN Chi-restraints excluded: chain H residue 256 SER Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain I residue 115 GLU Chi-restraints excluded: chain I residue 163 MET Chi-restraints excluded: chain I residue 236 ASN Chi-restraints excluded: chain I residue 272 LYS Chi-restraints excluded: chain I residue 336 ILE Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 146 LEU Chi-restraints excluded: chain J residue 276 LEU Chi-restraints excluded: chain K residue 141 MET Chi-restraints excluded: chain K residue 204 THR Chi-restraints excluded: chain K residue 274 THR Chi-restraints excluded: chain K residue 340 LYS Chi-restraints excluded: chain L residue 137 CYS Chi-restraints excluded: chain L residue 177 MET Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain N residue 82 THR Chi-restraints excluded: chain N residue 205 ASP Chi-restraints excluded: chain N residue 209 THR Chi-restraints excluded: chain O residue 74 ARG Chi-restraints excluded: chain O residue 88 ILE Chi-restraints excluded: chain O residue 228 ARG Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 142 LEU Chi-restraints excluded: chain P residue 155 ILE Chi-restraints excluded: chain P residue 163 MET Chi-restraints excluded: chain P residue 207 GLU Chi-restraints excluded: chain P residue 290 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 362 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 335 optimal weight: 0.9980 chunk 5 optimal weight: 8.9990 chunk 115 optimal weight: 5.9990 chunk 237 optimal weight: 0.8980 chunk 13 optimal weight: 8.9990 chunk 81 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 245 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 91 GLN ** E 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 236 ASN G 119 ASN G 284 GLN I 225 ASN L 225 ASN M 182 ASN ** M 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 239 ASN M 284 GLN N 104 HIS O 182 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.168332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.122196 restraints weight = 78832.204| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.36 r_work: 0.3154 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2951 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2951 r_free = 0.2951 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2951 r_free = 0.2951 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2951 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 38237 Z= 0.128 Angle : 0.543 9.920 51647 Z= 0.265 Chirality : 0.041 0.214 5918 Planarity : 0.004 0.065 6491 Dihedral : 10.992 89.240 5544 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 4.42 % Allowed : 31.18 % Favored : 64.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.13), residues: 4623 helix: 1.29 (0.11), residues: 2628 sheet: -1.13 (0.24), residues: 432 loop : 0.82 (0.17), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 263 TYR 0.020 0.001 TYR J 313 PHE 0.016 0.001 PHE A 178 TRP 0.008 0.001 TRP A 220 HIS 0.006 0.001 HIS E 206 Details of bonding type rmsd covalent geometry : bond 0.00298 (38237) covalent geometry : angle 0.54308 (51647) hydrogen bonds : bond 0.03089 ( 1808) hydrogen bonds : angle 4.39696 ( 5233) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 769 residues out of total 4129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 588 time to evaluate : 1.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.5970 (mmm) cc_final: 0.5651 (tpt) REVERT: A 163 MET cc_start: 0.5843 (OUTLIER) cc_final: 0.5150 (mpt) REVERT: A 177 MET cc_start: 0.5075 (ptm) cc_final: 0.4742 (pmt) REVERT: B 215 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.6618 (tp30) REVERT: B 282 ASP cc_start: 0.7212 (t0) cc_final: 0.6998 (t0) REVERT: C 348 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.7976 (mp) REVERT: D 52 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8273 (mt) REVERT: D 315 LYS cc_start: 0.7548 (mtpm) cc_final: 0.7066 (pttp) REVERT: D 350 MET cc_start: 0.6593 (mmp) cc_final: 0.4263 (ttm) REVERT: E 105 GLU cc_start: 0.8387 (mm-30) cc_final: 0.7950 (pt0) REVERT: E 200 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.7818 (tm-30) REVERT: E 283 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8615 (tt) REVERT: F 115 GLU cc_start: 0.7753 (pm20) cc_final: 0.7477 (pm20) REVERT: F 119 ASN cc_start: 0.8171 (OUTLIER) cc_final: 0.7407 (t0) REVERT: G 91 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.8433 (mp-120) REVERT: G 199 ARG cc_start: 0.9177 (OUTLIER) cc_final: 0.8300 (ttp-170) REVERT: G 311 LYS cc_start: 0.8331 (ptpp) cc_final: 0.8000 (ptpp) REVERT: H 66 GLU cc_start: 0.6310 (OUTLIER) cc_final: 0.5818 (mp0) REVERT: H 82 THR cc_start: 0.9211 (OUTLIER) cc_final: 0.9002 (m) REVERT: H 280 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7012 (tm-30) REVERT: H 346 LYS cc_start: 0.8685 (mttt) cc_final: 0.8123 (mtmt) REVERT: I 113 MET cc_start: 0.8908 (ptp) cc_final: 0.8679 (ptm) REVERT: J 291 LYS cc_start: 0.8621 (mtmt) cc_final: 0.8188 (mptt) REVERT: K 261 ASP cc_start: 0.8438 (t0) cc_final: 0.8053 (t0) REVERT: K 337 ARG cc_start: 0.7221 (ptt90) cc_final: 0.6785 (ppt170) REVERT: K 346 LYS cc_start: 0.8118 (ptpt) cc_final: 0.7707 (pttt) REVERT: M 184 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8659 (mt) REVERT: M 200 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.8073 (tm-30) REVERT: M 316 GLN cc_start: 0.6856 (OUTLIER) cc_final: 0.6484 (tm-30) REVERT: N 164 ASP cc_start: 0.7886 (t0) cc_final: 0.7546 (t0) REVERT: N 205 ASP cc_start: 0.8482 (OUTLIER) cc_final: 0.8234 (t0) REVERT: N 282 ASP cc_start: 0.6943 (t0) cc_final: 0.6654 (p0) REVERT: N 285 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8471 (tm) REVERT: P 142 LEU cc_start: 0.6070 (OUTLIER) cc_final: 0.5769 (mm) outliers start: 181 outliers final: 66 residues processed: 700 average time/residue: 0.6712 time to fit residues: 580.3170 Evaluate side-chains 632 residues out of total 4129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 548 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 303 ARG Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 312 GLU Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 200 GLU Chi-restraints excluded: chain E residue 236 ASN Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 119 ASN Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 91 GLN Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain G residue 199 ARG Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 347 LYS Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 70 ASP Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 177 MET Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 207 GLU Chi-restraints excluded: chain H residue 224 LEU Chi-restraints excluded: chain H residue 236 ASN Chi-restraints excluded: chain H residue 256 SER Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain H residue 280 GLU Chi-restraints excluded: chain H residue 312 GLU Chi-restraints excluded: chain H residue 342 LYS Chi-restraints excluded: chain I residue 115 GLU Chi-restraints excluded: chain I residue 177 MET Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 246 LEU Chi-restraints excluded: chain J residue 261 ASP Chi-restraints excluded: chain J residue 276 LEU Chi-restraints excluded: chain K residue 184 LEU Chi-restraints excluded: chain K residue 204 THR Chi-restraints excluded: chain K residue 224 LEU Chi-restraints excluded: chain K residue 274 THR Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 137 CYS Chi-restraints excluded: chain L residue 177 MET Chi-restraints excluded: chain L residue 247 ARG Chi-restraints excluded: chain M residue 91 GLN Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain M residue 200 GLU Chi-restraints excluded: chain M residue 204 THR Chi-restraints excluded: chain M residue 316 GLN Chi-restraints excluded: chain M residue 339 LEU Chi-restraints excluded: chain N residue 82 THR Chi-restraints excluded: chain N residue 205 ASP Chi-restraints excluded: chain N residue 209 THR Chi-restraints excluded: chain N residue 255 VAL Chi-restraints excluded: chain N residue 285 LEU Chi-restraints excluded: chain O residue 74 ARG Chi-restraints excluded: chain O residue 88 ILE Chi-restraints excluded: chain P residue 142 LEU Chi-restraints excluded: chain P residue 155 ILE Chi-restraints excluded: chain P residue 179 SER Chi-restraints excluded: chain P residue 235 THR Chi-restraints excluded: chain P residue 254 LEU Chi-restraints excluded: chain P residue 290 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 450 optimal weight: 5.9990 chunk 312 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 241 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 204 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 324 optimal weight: 2.9990 chunk 283 optimal weight: 0.9980 chunk 217 optimal weight: 0.5980 chunk 165 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 289 ASN ** E 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 236 ASN G 284 GLN G 319 GLN I 225 ASN L 193 GLN L 225 ASN M 182 ASN M 185 GLN M 239 ASN M 284 GLN N 104 HIS N 171 ASN O 182 ASN P 171 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.168942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.124917 restraints weight = 80133.861| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.99 r_work: 0.3091 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3058 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3058 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 38237 Z= 0.123 Angle : 0.540 9.904 51647 Z= 0.262 Chirality : 0.041 0.169 5918 Planarity : 0.003 0.061 6491 Dihedral : 10.856 89.984 5539 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.06 % Allowed : 31.80 % Favored : 64.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.13), residues: 4623 helix: 1.52 (0.11), residues: 2539 sheet: -0.90 (0.26), residues: 377 loop : 0.47 (0.16), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 60 TYR 0.017 0.001 TYR M 264 PHE 0.015 0.001 PHE A 178 TRP 0.008 0.001 TRP B 220 HIS 0.005 0.000 HIS E 206 Details of bonding type rmsd covalent geometry : bond 0.00289 (38237) covalent geometry : angle 0.54026 (51647) hydrogen bonds : bond 0.02977 ( 1808) hydrogen bonds : angle 4.34601 ( 5233) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 739 residues out of total 4129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 574 time to evaluate : 1.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.6122 (mmm) cc_final: 0.5856 (tpt) REVERT: A 163 MET cc_start: 0.5810 (OUTLIER) cc_final: 0.5018 (mpt) REVERT: A 177 MET cc_start: 0.5130 (ptm) cc_final: 0.4791 (pmt) REVERT: A 215 GLU cc_start: 0.6173 (OUTLIER) cc_final: 0.5787 (pp20) REVERT: A 219 LEU cc_start: 0.6202 (OUTLIER) cc_final: 0.5270 (mt) REVERT: A 228 ARG cc_start: 0.3825 (mtp180) cc_final: 0.3475 (ptm160) REVERT: B 215 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.6588 (tp30) REVERT: B 282 ASP cc_start: 0.7174 (t0) cc_final: 0.6968 (t0) REVERT: C 47 LYS cc_start: 0.6561 (OUTLIER) cc_final: 0.6284 (mptt) REVERT: C 348 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7958 (mp) REVERT: D 315 LYS cc_start: 0.7526 (mtpm) cc_final: 0.7067 (pttp) REVERT: D 350 MET cc_start: 0.6424 (mmp) cc_final: 0.4176 (ttm) REVERT: E 105 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7860 (pt0) REVERT: E 200 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.7741 (tm-30) REVERT: E 243 ASP cc_start: 0.7832 (m-30) cc_final: 0.7428 (m-30) REVERT: E 283 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8548 (tt) REVERT: F 115 GLU cc_start: 0.7677 (pm20) cc_final: 0.7427 (pm20) REVERT: F 119 ASN cc_start: 0.8142 (OUTLIER) cc_final: 0.7380 (t0) REVERT: F 163 MET cc_start: 0.8090 (mmm) cc_final: 0.7814 (mtt) REVERT: F 167 TYR cc_start: 0.9054 (t80) cc_final: 0.8393 (t80) REVERT: G 199 ARG cc_start: 0.9103 (OUTLIER) cc_final: 0.8161 (ttp-170) REVERT: G 311 LYS cc_start: 0.8310 (ptpp) cc_final: 0.8087 (ptpp) REVERT: H 236 ASN cc_start: 0.8790 (OUTLIER) cc_final: 0.8424 (p0) REVERT: H 280 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.6982 (tm-30) REVERT: H 346 LYS cc_start: 0.8615 (mttt) cc_final: 0.8057 (mtmt) REVERT: I 113 MET cc_start: 0.8835 (ptp) cc_final: 0.8590 (ptm) REVERT: I 163 MET cc_start: 0.8927 (OUTLIER) cc_final: 0.8675 (mtp) REVERT: K 261 ASP cc_start: 0.8315 (t0) cc_final: 0.7915 (t0) REVERT: K 291 LYS cc_start: 0.8124 (mmmt) cc_final: 0.7889 (mmmt) REVERT: K 337 ARG cc_start: 0.7153 (ptt90) cc_final: 0.6843 (ppt170) REVERT: K 346 LYS cc_start: 0.8079 (ptpt) cc_final: 0.7686 (pttt) REVERT: L 337 ARG cc_start: 0.7764 (ttp80) cc_final: 0.7439 (ttp80) REVERT: M 184 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8566 (mt) REVERT: M 200 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7942 (tm-30) REVERT: M 316 GLN cc_start: 0.6864 (mt0) cc_final: 0.6480 (tm-30) REVERT: N 205 ASP cc_start: 0.8437 (OUTLIER) cc_final: 0.8177 (t0) REVERT: N 282 ASP cc_start: 0.6875 (t0) cc_final: 0.6545 (p0) REVERT: N 285 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8424 (tm) REVERT: O 228 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.6766 (mtp85) REVERT: P 142 LEU cc_start: 0.6094 (OUTLIER) cc_final: 0.5817 (mm) outliers start: 165 outliers final: 68 residues processed: 683 average time/residue: 0.6933 time to fit residues: 579.8812 Evaluate side-chains 633 residues out of total 4129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 546 time to evaluate : 1.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 303 ARG Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 47 LYS Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 312 GLU Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 200 GLU Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 236 ASN Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 119 ASN Chi-restraints excluded: chain F residue 161 SER Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 275 LYS Chi-restraints excluded: chain G residue 45 GLU Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain G residue 199 ARG Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 347 LYS Chi-restraints excluded: chain H residue 70 ASP Chi-restraints excluded: chain H residue 177 MET Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 207 GLU Chi-restraints excluded: chain H residue 236 ASN Chi-restraints excluded: chain H residue 256 SER Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain H residue 280 GLU Chi-restraints excluded: chain H residue 342 LYS Chi-restraints excluded: chain I residue 115 GLU Chi-restraints excluded: chain I residue 163 MET Chi-restraints excluded: chain I residue 177 MET Chi-restraints excluded: chain I residue 224 LEU Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 276 LEU Chi-restraints excluded: chain K residue 184 LEU Chi-restraints excluded: chain K residue 204 THR Chi-restraints excluded: chain K residue 212 LEU Chi-restraints excluded: chain K residue 224 LEU Chi-restraints excluded: chain K residue 274 THR Chi-restraints excluded: chain K residue 340 LYS Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 137 CYS Chi-restraints excluded: chain L residue 177 MET Chi-restraints excluded: chain L residue 224 LEU Chi-restraints excluded: chain L residue 247 ARG Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain M residue 200 GLU Chi-restraints excluded: chain M residue 204 THR Chi-restraints excluded: chain M residue 339 LEU Chi-restraints excluded: chain N residue 82 THR Chi-restraints excluded: chain N residue 101 SER Chi-restraints excluded: chain N residue 205 ASP Chi-restraints excluded: chain N residue 209 THR Chi-restraints excluded: chain N residue 255 VAL Chi-restraints excluded: chain N residue 285 LEU Chi-restraints excluded: chain O residue 74 ARG Chi-restraints excluded: chain O residue 80 ILE Chi-restraints excluded: chain O residue 228 ARG Chi-restraints excluded: chain P residue 142 LEU Chi-restraints excluded: chain P residue 155 ILE Chi-restraints excluded: chain P residue 235 THR Chi-restraints excluded: chain P residue 254 LEU Chi-restraints excluded: chain P residue 290 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 451 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 355 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 201 optimal weight: 0.9980 chunk 294 optimal weight: 0.0770 chunk 72 optimal weight: 4.9990 chunk 223 optimal weight: 1.9990 chunk 434 optimal weight: 8.9990 overall best weight: 1.3742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 91 GLN ** E 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 236 ASN G 236 ASN G 284 GLN I 225 ASN I 316 GLN L 225 ASN M 182 ASN M 239 ASN M 284 GLN N 104 HIS O 182 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.167263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.118743 restraints weight = 83936.119| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.52 r_work: 0.3101 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2956 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2956 r_free = 0.2956 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2956 r_free = 0.2956 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2956 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 38237 Z= 0.152 Angle : 0.557 10.557 51647 Z= 0.270 Chirality : 0.041 0.206 5918 Planarity : 0.004 0.063 6491 Dihedral : 10.786 88.979 5539 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.96 % Allowed : 32.05 % Favored : 63.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.13), residues: 4623 helix: 1.36 (0.11), residues: 2631 sheet: -0.83 (0.26), residues: 388 loop : 0.78 (0.16), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 60 TYR 0.020 0.001 TYR J 313 PHE 0.014 0.001 PHE A 178 TRP 0.008 0.001 TRP B 220 HIS 0.006 0.001 HIS E 206 Details of bonding type rmsd covalent geometry : bond 0.00363 (38237) covalent geometry : angle 0.55745 (51647) hydrogen bonds : bond 0.03078 ( 1808) hydrogen bonds : angle 4.35141 ( 5233) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 737 residues out of total 4129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 576 time to evaluate : 1.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.6168 (mmm) cc_final: 0.5932 (tpt) REVERT: A 163 MET cc_start: 0.5673 (OUTLIER) cc_final: 0.4887 (mpt) REVERT: A 177 MET cc_start: 0.5072 (ptm) cc_final: 0.4762 (pmt) REVERT: A 215 GLU cc_start: 0.6144 (OUTLIER) cc_final: 0.5924 (pp20) REVERT: A 228 ARG cc_start: 0.3717 (mtp180) cc_final: 0.3425 (ptm160) REVERT: B 215 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.6552 (tp30) REVERT: B 282 ASP cc_start: 0.7189 (t0) cc_final: 0.6951 (t0) REVERT: C 47 LYS cc_start: 0.6489 (OUTLIER) cc_final: 0.6264 (mptt) REVERT: D 315 LYS cc_start: 0.7452 (mtpm) cc_final: 0.6948 (pttp) REVERT: D 350 MET cc_start: 0.6503 (mmp) cc_final: 0.4207 (ttm) REVERT: E 105 GLU cc_start: 0.8436 (mm-30) cc_final: 0.7875 (pt0) REVERT: E 200 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.7792 (tm-30) REVERT: E 243 ASP cc_start: 0.8032 (m-30) cc_final: 0.7806 (m-30) REVERT: E 283 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8475 (tt) REVERT: F 115 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7494 (pm20) REVERT: F 119 ASN cc_start: 0.8228 (OUTLIER) cc_final: 0.7518 (t160) REVERT: G 199 ARG cc_start: 0.9175 (OUTLIER) cc_final: 0.8263 (ttp-170) REVERT: G 311 LYS cc_start: 0.8202 (ptpp) cc_final: 0.7899 (pttm) REVERT: H 280 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.6853 (tm-30) REVERT: I 113 MET cc_start: 0.8868 (ptp) cc_final: 0.8578 (ptm) REVERT: I 163 MET cc_start: 0.8996 (OUTLIER) cc_final: 0.7981 (mtm) REVERT: I 272 LYS cc_start: 0.7822 (pttm) cc_final: 0.7461 (pttm) REVERT: J 342 LYS cc_start: 0.7723 (tptt) cc_final: 0.7407 (tmtt) REVERT: K 261 ASP cc_start: 0.8385 (t0) cc_final: 0.7957 (t0) REVERT: K 346 LYS cc_start: 0.8073 (ptpt) cc_final: 0.7663 (pttt) REVERT: L 337 ARG cc_start: 0.7813 (ttp80) cc_final: 0.7389 (ttp80) REVERT: M 184 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8564 (mt) REVERT: M 200 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.8029 (tm-30) REVERT: M 316 GLN cc_start: 0.6822 (OUTLIER) cc_final: 0.6417 (tm-30) REVERT: N 205 ASP cc_start: 0.8471 (OUTLIER) cc_final: 0.8225 (t0) REVERT: N 282 ASP cc_start: 0.6813 (t0) cc_final: 0.6505 (p0) REVERT: N 285 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8383 (tm) REVERT: O 200 GLU cc_start: 0.7592 (mm-30) cc_final: 0.7354 (mm-30) REVERT: O 228 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.6757 (mtp85) REVERT: P 142 LEU cc_start: 0.5997 (OUTLIER) cc_final: 0.5747 (mm) REVERT: P 144 LYS cc_start: 0.5278 (OUTLIER) cc_final: 0.5066 (tmtm) outliers start: 161 outliers final: 74 residues processed: 681 average time/residue: 0.7089 time to fit residues: 591.7521 Evaluate side-chains 635 residues out of total 4129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 542 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 303 ARG Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 47 LYS Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 243 ASP Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 312 GLU Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 200 GLU Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 236 ASN Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 115 GLU Chi-restraints excluded: chain F residue 119 ASN Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 275 LYS Chi-restraints excluded: chain G residue 45 GLU Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain G residue 199 ARG Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 347 LYS Chi-restraints excluded: chain H residue 177 MET Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 207 GLU Chi-restraints excluded: chain H residue 224 LEU Chi-restraints excluded: chain H residue 236 ASN Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 256 SER Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain H residue 280 GLU Chi-restraints excluded: chain H residue 342 LYS Chi-restraints excluded: chain I residue 115 GLU Chi-restraints excluded: chain I residue 163 MET Chi-restraints excluded: chain I residue 177 MET Chi-restraints excluded: chain I residue 224 LEU Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 246 LEU Chi-restraints excluded: chain J residue 276 LEU Chi-restraints excluded: chain K residue 177 MET Chi-restraints excluded: chain K residue 204 THR Chi-restraints excluded: chain K residue 274 THR Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 137 CYS Chi-restraints excluded: chain L residue 177 MET Chi-restraints excluded: chain L residue 224 LEU Chi-restraints excluded: chain L residue 230 MET Chi-restraints excluded: chain L residue 247 ARG Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain M residue 177 MET Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain M residue 200 GLU Chi-restraints excluded: chain M residue 204 THR Chi-restraints excluded: chain M residue 316 GLN Chi-restraints excluded: chain M residue 339 LEU Chi-restraints excluded: chain N residue 82 THR Chi-restraints excluded: chain N residue 101 SER Chi-restraints excluded: chain N residue 205 ASP Chi-restraints excluded: chain N residue 209 THR Chi-restraints excluded: chain N residue 255 VAL Chi-restraints excluded: chain N residue 285 LEU Chi-restraints excluded: chain O residue 74 ARG Chi-restraints excluded: chain O residue 80 ILE Chi-restraints excluded: chain O residue 88 ILE Chi-restraints excluded: chain O residue 228 ARG Chi-restraints excluded: chain P residue 142 LEU Chi-restraints excluded: chain P residue 144 LYS Chi-restraints excluded: chain P residue 155 ILE Chi-restraints excluded: chain P residue 157 ILE Chi-restraints excluded: chain P residue 290 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 41 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 237 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 448 optimal weight: 6.9990 chunk 456 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 74 optimal weight: 0.0060 chunk 408 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 chunk 405 optimal weight: 10.0000 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 289 ASN D 91 GLN ** E 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 236 ASN G 119 ASN G 284 GLN G 319 GLN I 225 ASN ** K 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 225 ASN M 182 ASN M 239 ASN M 284 GLN N 104 HIS O 182 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.168912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.125244 restraints weight = 72254.113| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.56 r_work: 0.3127 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2927 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2927 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 38237 Z= 0.121 Angle : 0.552 10.249 51647 Z= 0.267 Chirality : 0.041 0.187 5918 Planarity : 0.003 0.062 6491 Dihedral : 10.659 88.932 5539 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.67 % Allowed : 32.41 % Favored : 63.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.13), residues: 4623 helix: 1.53 (0.11), residues: 2504 sheet: -0.81 (0.27), residues: 380 loop : 0.69 (0.16), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 349 TYR 0.018 0.001 TYR D 264 PHE 0.013 0.001 PHE A 178 TRP 0.006 0.001 TRP B 220 HIS 0.005 0.000 HIS E 206 Details of bonding type rmsd covalent geometry : bond 0.00285 (38237) covalent geometry : angle 0.55226 (51647) hydrogen bonds : bond 0.02924 ( 1808) hydrogen bonds : angle 4.32386 ( 5233) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 4129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 565 time to evaluate : 1.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 MET cc_start: 0.5703 (OUTLIER) cc_final: 0.4955 (mpt) REVERT: A 177 MET cc_start: 0.5069 (ptm) cc_final: 0.4755 (pmt) REVERT: A 215 GLU cc_start: 0.6121 (OUTLIER) cc_final: 0.5770 (pp20) REVERT: A 219 LEU cc_start: 0.6037 (OUTLIER) cc_final: 0.5139 (mt) REVERT: A 228 ARG cc_start: 0.3730 (mtp180) cc_final: 0.3462 (ptm160) REVERT: B 282 ASP cc_start: 0.7254 (t0) cc_final: 0.7019 (t0) REVERT: C 47 LYS cc_start: 0.6642 (OUTLIER) cc_final: 0.6410 (mptt) REVERT: C 350 MET cc_start: 0.4350 (tpp) cc_final: 0.3818 (tmt) REVERT: D 141 MET cc_start: 0.9133 (mmm) cc_final: 0.8756 (mtm) REVERT: D 315 LYS cc_start: 0.7518 (mtpm) cc_final: 0.7008 (pttp) REVERT: D 350 MET cc_start: 0.6473 (mmp) cc_final: 0.4208 (ttm) REVERT: E 105 GLU cc_start: 0.8463 (mm-30) cc_final: 0.7934 (pt0) REVERT: E 200 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.7958 (tm-30) REVERT: E 243 ASP cc_start: 0.8076 (m-30) cc_final: 0.7667 (m-30) REVERT: E 283 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8527 (tt) REVERT: F 115 GLU cc_start: 0.7780 (pm20) cc_final: 0.7489 (pm20) REVERT: F 119 ASN cc_start: 0.8180 (OUTLIER) cc_final: 0.7492 (t160) REVERT: G 198 LEU cc_start: 0.9034 (mt) cc_final: 0.8827 (mp) REVERT: G 199 ARG cc_start: 0.9193 (OUTLIER) cc_final: 0.8269 (ttp-170) REVERT: G 311 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7935 (pttm) REVERT: H 236 ASN cc_start: 0.8890 (OUTLIER) cc_final: 0.8542 (p0) REVERT: H 280 GLU cc_start: 0.7553 (tm-30) cc_final: 0.6918 (tm-30) REVERT: H 346 LYS cc_start: 0.8593 (mttt) cc_final: 0.8022 (mtmt) REVERT: I 113 MET cc_start: 0.8891 (ptp) cc_final: 0.8620 (ptm) REVERT: I 163 MET cc_start: 0.9011 (OUTLIER) cc_final: 0.8782 (mtp) REVERT: K 261 ASP cc_start: 0.8431 (t0) cc_final: 0.8028 (t0) REVERT: K 346 LYS cc_start: 0.8085 (ptpt) cc_final: 0.7683 (pttt) REVERT: L 337 ARG cc_start: 0.7825 (ttp80) cc_final: 0.7426 (ttp80) REVERT: M 184 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8649 (mt) REVERT: M 200 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8105 (tm-30) REVERT: M 316 GLN cc_start: 0.6849 (OUTLIER) cc_final: 0.6448 (tm-30) REVERT: N 205 ASP cc_start: 0.8449 (OUTLIER) cc_final: 0.8217 (t0) REVERT: N 282 ASP cc_start: 0.6774 (t0) cc_final: 0.6529 (p0) REVERT: N 285 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8403 (tm) REVERT: O 200 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7434 (mm-30) REVERT: O 228 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.6862 (mtp85) REVERT: P 142 LEU cc_start: 0.5973 (OUTLIER) cc_final: 0.5728 (mm) REVERT: P 144 LYS cc_start: 0.5248 (OUTLIER) cc_final: 0.5025 (tmtm) outliers start: 149 outliers final: 71 residues processed: 667 average time/residue: 0.7030 time to fit residues: 572.9657 Evaluate side-chains 632 residues out of total 4129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 542 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 303 ARG Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 47 LYS Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 312 GLU Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 200 GLU Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 236 ASN Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 119 ASN Chi-restraints excluded: chain F residue 161 SER Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 177 MET Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain G residue 199 ARG Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 311 LYS Chi-restraints excluded: chain G residue 347 LYS Chi-restraints excluded: chain H residue 177 MET Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 207 GLU Chi-restraints excluded: chain H residue 209 THR Chi-restraints excluded: chain H residue 236 ASN Chi-restraints excluded: chain H residue 256 SER Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain I residue 115 GLU Chi-restraints excluded: chain I residue 163 MET Chi-restraints excluded: chain I residue 177 MET Chi-restraints excluded: chain J residue 246 LEU Chi-restraints excluded: chain J residue 276 LEU Chi-restraints excluded: chain K residue 137 CYS Chi-restraints excluded: chain K residue 177 MET Chi-restraints excluded: chain K residue 204 THR Chi-restraints excluded: chain K residue 274 THR Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 177 MET Chi-restraints excluded: chain L residue 224 LEU Chi-restraints excluded: chain L residue 247 ARG Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain M residue 177 MET Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain M residue 200 GLU Chi-restraints excluded: chain M residue 204 THR Chi-restraints excluded: chain M residue 316 GLN Chi-restraints excluded: chain M residue 339 LEU Chi-restraints excluded: chain N residue 82 THR Chi-restraints excluded: chain N residue 101 SER Chi-restraints excluded: chain N residue 205 ASP Chi-restraints excluded: chain N residue 209 THR Chi-restraints excluded: chain N residue 255 VAL Chi-restraints excluded: chain N residue 285 LEU Chi-restraints excluded: chain O residue 74 ARG Chi-restraints excluded: chain O residue 80 ILE Chi-restraints excluded: chain O residue 88 ILE Chi-restraints excluded: chain O residue 228 ARG Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 82 THR Chi-restraints excluded: chain P residue 142 LEU Chi-restraints excluded: chain P residue 144 LYS Chi-restraints excluded: chain P residue 155 ILE Chi-restraints excluded: chain P residue 254 LEU Chi-restraints excluded: chain P residue 290 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 330 optimal weight: 3.9990 chunk 253 optimal weight: 0.3980 chunk 351 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 198 optimal weight: 0.8980 chunk 293 optimal weight: 0.9990 chunk 247 optimal weight: 0.1980 chunk 143 optimal weight: 0.5980 chunk 395 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 289 optimal weight: 1.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 91 GLN ** E 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 236 ASN G 284 GLN I 225 ASN L 225 ASN M 53 GLN M 182 ASN M 239 ASN M 284 GLN N 104 HIS O 182 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.170060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.125245 restraints weight = 76212.273| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.67 r_work: 0.3137 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2965 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2965 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 38237 Z= 0.113 Angle : 0.551 13.241 51647 Z= 0.266 Chirality : 0.041 0.195 5918 Planarity : 0.003 0.062 6491 Dihedral : 10.500 89.850 5539 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.33 % Allowed : 32.94 % Favored : 63.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.13), residues: 4623 helix: 1.60 (0.11), residues: 2559 sheet: -0.43 (0.29), residues: 320 loop : 0.48 (0.16), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 263 TYR 0.023 0.001 TYR J 313 PHE 0.013 0.001 PHE A 178 TRP 0.006 0.001 TRP N 166 HIS 0.005 0.000 HIS E 206 Details of bonding type rmsd covalent geometry : bond 0.00264 (38237) covalent geometry : angle 0.55126 (51647) hydrogen bonds : bond 0.02853 ( 1808) hydrogen bonds : angle 4.27047 ( 5233) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 711 residues out of total 4129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 576 time to evaluate : 1.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 MET cc_start: 0.5752 (OUTLIER) cc_final: 0.4936 (mpt) REVERT: A 215 GLU cc_start: 0.6095 (OUTLIER) cc_final: 0.5763 (pp20) REVERT: A 219 LEU cc_start: 0.5947 (OUTLIER) cc_final: 0.5050 (mt) REVERT: A 228 ARG cc_start: 0.3745 (mtp180) cc_final: 0.3440 (ptm160) REVERT: B 282 ASP cc_start: 0.7308 (t0) cc_final: 0.7052 (t0) REVERT: C 47 LYS cc_start: 0.6681 (OUTLIER) cc_final: 0.6450 (mptt) REVERT: C 308 ASP cc_start: 0.8632 (t0) cc_final: 0.8259 (t0) REVERT: C 350 MET cc_start: 0.4569 (tpp) cc_final: 0.4092 (tmt) REVERT: D 315 LYS cc_start: 0.7511 (mtpm) cc_final: 0.7001 (pttp) REVERT: D 350 MET cc_start: 0.6336 (mmp) cc_final: 0.4122 (ttm) REVERT: E 105 GLU cc_start: 0.8443 (mm-30) cc_final: 0.7918 (pt0) REVERT: E 200 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.7960 (tm-30) REVERT: E 243 ASP cc_start: 0.8071 (m-30) cc_final: 0.7850 (m-30) REVERT: E 283 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8499 (tt) REVERT: F 113 MET cc_start: 0.8979 (mtp) cc_final: 0.8705 (mtt) REVERT: F 115 GLU cc_start: 0.7806 (pm20) cc_final: 0.7506 (pm20) REVERT: F 119 ASN cc_start: 0.8174 (OUTLIER) cc_final: 0.7490 (t160) REVERT: F 167 TYR cc_start: 0.9112 (t80) cc_final: 0.8475 (t80) REVERT: F 308 ASP cc_start: 0.8371 (t0) cc_final: 0.8079 (m-30) REVERT: G 198 LEU cc_start: 0.9039 (mt) cc_final: 0.8809 (mp) REVERT: G 199 ARG cc_start: 0.9191 (OUTLIER) cc_final: 0.8264 (ttp-170) REVERT: G 311 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.7930 (pttm) REVERT: H 280 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.6951 (tm-30) REVERT: H 315 LYS cc_start: 0.8015 (mtpt) cc_final: 0.7606 (ttpt) REVERT: H 342 LYS cc_start: 0.7851 (mppt) cc_final: 0.7147 (mmmt) REVERT: H 346 LYS cc_start: 0.8607 (mttt) cc_final: 0.8122 (mtmt) REVERT: I 113 MET cc_start: 0.8892 (ptp) cc_final: 0.8570 (ptm) REVERT: I 163 MET cc_start: 0.8995 (OUTLIER) cc_final: 0.8781 (mtp) REVERT: I 275 LYS cc_start: 0.8811 (mttt) cc_final: 0.8175 (mtpt) REVERT: K 261 ASP cc_start: 0.8412 (t0) cc_final: 0.7988 (t0) REVERT: K 337 ARG cc_start: 0.7235 (ptt90) cc_final: 0.6763 (ppt170) REVERT: K 346 LYS cc_start: 0.8053 (ptpt) cc_final: 0.7665 (pttt) REVERT: L 252 ARG cc_start: 0.8497 (mtm-85) cc_final: 0.8291 (mtm180) REVERT: L 337 ARG cc_start: 0.7848 (ttp80) cc_final: 0.7461 (ttp80) REVERT: M 184 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8595 (mt) REVERT: M 200 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.8036 (tm-30) REVERT: M 316 GLN cc_start: 0.6829 (OUTLIER) cc_final: 0.6429 (tm-30) REVERT: N 285 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8382 (tm) REVERT: O 163 MET cc_start: 0.5242 (OUTLIER) cc_final: 0.5012 (tpt) REVERT: O 164 ASP cc_start: 0.7363 (t0) cc_final: 0.7050 (t0) REVERT: O 200 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7432 (mm-30) REVERT: P 142 LEU cc_start: 0.5993 (OUTLIER) cc_final: 0.5768 (mm) REVERT: P 144 LYS cc_start: 0.5242 (OUTLIER) cc_final: 0.5026 (tmtm) REVERT: P 350 MET cc_start: 0.0600 (mpm) cc_final: 0.0201 (ppp) outliers start: 135 outliers final: 67 residues processed: 668 average time/residue: 0.7014 time to fit residues: 576.4045 Evaluate side-chains 638 residues out of total 4129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 553 time to evaluate : 1.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 303 ARG Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 47 LYS Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 200 GLU Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 236 ASN Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain F residue 119 ASN Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 118 SER Chi-restraints excluded: chain G residue 177 MET Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain G residue 199 ARG Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 311 LYS Chi-restraints excluded: chain G residue 347 LYS Chi-restraints excluded: chain H residue 177 MET Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 207 GLU Chi-restraints excluded: chain H residue 209 THR Chi-restraints excluded: chain H residue 236 ASN Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 256 SER Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain H residue 280 GLU Chi-restraints excluded: chain I residue 115 GLU Chi-restraints excluded: chain I residue 163 MET Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 246 LEU Chi-restraints excluded: chain J residue 276 LEU Chi-restraints excluded: chain K residue 137 CYS Chi-restraints excluded: chain K residue 177 MET Chi-restraints excluded: chain K residue 184 LEU Chi-restraints excluded: chain K residue 204 THR Chi-restraints excluded: chain K residue 350 MET Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 137 CYS Chi-restraints excluded: chain L residue 224 LEU Chi-restraints excluded: chain L residue 247 ARG Chi-restraints excluded: chain M residue 73 GLU Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain M residue 177 MET Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain M residue 200 GLU Chi-restraints excluded: chain M residue 204 THR Chi-restraints excluded: chain M residue 316 GLN Chi-restraints excluded: chain M residue 339 LEU Chi-restraints excluded: chain N residue 82 THR Chi-restraints excluded: chain N residue 101 SER Chi-restraints excluded: chain N residue 209 THR Chi-restraints excluded: chain N residue 255 VAL Chi-restraints excluded: chain N residue 285 LEU Chi-restraints excluded: chain O residue 74 ARG Chi-restraints excluded: chain O residue 80 ILE Chi-restraints excluded: chain O residue 163 MET Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 142 LEU Chi-restraints excluded: chain P residue 144 LYS Chi-restraints excluded: chain P residue 155 ILE Chi-restraints excluded: chain P residue 254 LEU Chi-restraints excluded: chain P residue 290 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 235 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 380 optimal weight: 20.0000 chunk 360 optimal weight: 2.9990 chunk 300 optimal weight: 2.9990 chunk 361 optimal weight: 4.9990 chunk 205 optimal weight: 1.9990 chunk 189 optimal weight: 0.9990 chunk 11 optimal weight: 10.0000 chunk 445 optimal weight: 2.9990 chunk 152 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 HIS D 91 GLN ** E 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 236 ASN G 284 GLN G 319 GLN I 225 ASN L 225 ASN M 182 ASN M 206 HIS M 239 ASN M 284 GLN N 104 HIS O 182 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.167076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.118818 restraints weight = 88591.564| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.69 r_work: 0.3081 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2937 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2937 r_free = 0.2937 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2937 r_free = 0.2937 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2937 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 38237 Z= 0.178 Angle : 0.600 16.358 51647 Z= 0.289 Chirality : 0.042 0.207 5918 Planarity : 0.004 0.062 6491 Dihedral : 10.648 89.118 5539 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.80 % Allowed : 33.57 % Favored : 63.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.13), residues: 4623 helix: 1.36 (0.11), residues: 2631 sheet: -0.78 (0.26), residues: 389 loop : 0.94 (0.17), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 263 TYR 0.020 0.001 TYR D 264 PHE 0.014 0.001 PHE J 197 TRP 0.009 0.001 TRP B 220 HIS 0.006 0.001 HIS E 206 Details of bonding type rmsd covalent geometry : bond 0.00428 (38237) covalent geometry : angle 0.60046 (51647) hydrogen bonds : bond 0.03154 ( 1808) hydrogen bonds : angle 4.36698 ( 5233) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 4129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 553 time to evaluate : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 MET cc_start: 0.5657 (OUTLIER) cc_final: 0.4811 (mpt) REVERT: A 177 MET cc_start: 0.4930 (ptm) cc_final: 0.4605 (pmt) REVERT: A 215 GLU cc_start: 0.6108 (OUTLIER) cc_final: 0.5703 (pp20) REVERT: A 219 LEU cc_start: 0.5956 (OUTLIER) cc_final: 0.5067 (mt) REVERT: A 228 ARG cc_start: 0.3788 (mtp180) cc_final: 0.3470 (ptm160) REVERT: B 282 ASP cc_start: 0.7203 (t0) cc_final: 0.6964 (t0) REVERT: B 288 ASP cc_start: 0.8075 (m-30) cc_final: 0.7638 (m-30) REVERT: C 47 LYS cc_start: 0.6650 (OUTLIER) cc_final: 0.6414 (mptt) REVERT: C 308 ASP cc_start: 0.8639 (t0) cc_final: 0.8293 (t0) REVERT: C 350 MET cc_start: 0.4542 (tpp) cc_final: 0.3969 (tmt) REVERT: D 113 MET cc_start: 0.8502 (mtp) cc_final: 0.8235 (mtp) REVERT: D 276 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8217 (mp) REVERT: D 315 LYS cc_start: 0.7505 (mtpm) cc_final: 0.7001 (pttp) REVERT: D 350 MET cc_start: 0.6487 (mmp) cc_final: 0.4253 (ttm) REVERT: E 105 GLU cc_start: 0.8498 (mm-30) cc_final: 0.7929 (pt0) REVERT: E 200 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.7837 (tm-30) REVERT: E 243 ASP cc_start: 0.8064 (m-30) cc_final: 0.7831 (m-30) REVERT: E 283 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8451 (tt) REVERT: E 350 MET cc_start: 0.5612 (mmm) cc_final: 0.2974 (mtp) REVERT: F 113 MET cc_start: 0.8934 (mtp) cc_final: 0.8668 (mtt) REVERT: F 115 GLU cc_start: 0.7843 (pm20) cc_final: 0.7538 (pm20) REVERT: F 119 ASN cc_start: 0.8227 (OUTLIER) cc_final: 0.7530 (t160) REVERT: G 199 ARG cc_start: 0.9200 (OUTLIER) cc_final: 0.8281 (ttp-170) REVERT: G 311 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7942 (pttm) REVERT: H 280 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7019 (tm-30) REVERT: H 342 LYS cc_start: 0.7839 (mppt) cc_final: 0.7112 (mmmt) REVERT: H 343 ASP cc_start: 0.8301 (m-30) cc_final: 0.8045 (m-30) REVERT: H 346 LYS cc_start: 0.8577 (mttt) cc_final: 0.7957 (mtmt) REVERT: I 113 MET cc_start: 0.8874 (ptp) cc_final: 0.8573 (ptm) REVERT: I 163 MET cc_start: 0.9005 (OUTLIER) cc_final: 0.8014 (mtm) REVERT: K 261 ASP cc_start: 0.8397 (t0) cc_final: 0.7957 (t0) REVERT: M 159 MET cc_start: 0.8140 (mmm) cc_final: 0.7938 (tpt) REVERT: M 184 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8613 (mt) REVERT: M 200 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8061 (tm-30) REVERT: M 316 GLN cc_start: 0.6833 (mt0) cc_final: 0.6446 (tm-30) REVERT: O 163 MET cc_start: 0.5350 (OUTLIER) cc_final: 0.5106 (tpt) REVERT: O 164 ASP cc_start: 0.7522 (t0) cc_final: 0.7098 (t0) REVERT: O 200 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7445 (mm-30) REVERT: P 142 LEU cc_start: 0.5980 (OUTLIER) cc_final: 0.5746 (mm) REVERT: P 144 LYS cc_start: 0.5205 (OUTLIER) cc_final: 0.4980 (tmtm) REVERT: P 350 MET cc_start: 0.0491 (mpm) cc_final: 0.0203 (ppp) outliers start: 113 outliers final: 68 residues processed: 626 average time/residue: 0.6538 time to fit residues: 500.6962 Evaluate side-chains 620 residues out of total 4129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 535 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 47 LYS Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 200 GLU Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 236 ASN Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 119 ASN Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 118 SER Chi-restraints excluded: chain G residue 177 MET Chi-restraints excluded: chain G residue 199 ARG Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 311 LYS Chi-restraints excluded: chain G residue 347 LYS Chi-restraints excluded: chain H residue 177 MET Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 207 GLU Chi-restraints excluded: chain H residue 209 THR Chi-restraints excluded: chain H residue 236 ASN Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 256 SER Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain H residue 280 GLU Chi-restraints excluded: chain I residue 115 GLU Chi-restraints excluded: chain I residue 163 MET Chi-restraints excluded: chain I residue 236 ASN Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 246 LEU Chi-restraints excluded: chain J residue 276 LEU Chi-restraints excluded: chain K residue 137 CYS Chi-restraints excluded: chain K residue 204 THR Chi-restraints excluded: chain K residue 274 THR Chi-restraints excluded: chain K residue 350 MET Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 137 CYS Chi-restraints excluded: chain L residue 224 LEU Chi-restraints excluded: chain L residue 247 ARG Chi-restraints excluded: chain M residue 73 GLU Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain M residue 177 MET Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain M residue 200 GLU Chi-restraints excluded: chain M residue 204 THR Chi-restraints excluded: chain M residue 339 LEU Chi-restraints excluded: chain N residue 82 THR Chi-restraints excluded: chain N residue 101 SER Chi-restraints excluded: chain N residue 209 THR Chi-restraints excluded: chain N residue 255 VAL Chi-restraints excluded: chain O residue 74 ARG Chi-restraints excluded: chain O residue 80 ILE Chi-restraints excluded: chain O residue 163 MET Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 142 LEU Chi-restraints excluded: chain P residue 144 LYS Chi-restraints excluded: chain P residue 155 ILE Chi-restraints excluded: chain P residue 254 LEU Chi-restraints excluded: chain P residue 290 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 309 optimal weight: 5.9990 chunk 435 optimal weight: 6.9990 chunk 66 optimal weight: 0.0570 chunk 51 optimal weight: 0.7980 chunk 318 optimal weight: 2.9990 chunk 335 optimal weight: 0.9990 chunk 394 optimal weight: 0.8980 chunk 47 optimal weight: 8.9990 chunk 142 optimal weight: 0.9980 chunk 455 optimal weight: 3.9990 chunk 234 optimal weight: 3.9990 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 91 GLN ** E 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 236 ASN G 119 ASN G 284 GLN H 119 ASN I 225 ASN L 225 ASN M 182 ASN M 239 ASN M 284 GLN N 104 HIS O 182 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.168909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.124890 restraints weight = 68464.743| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.44 r_work: 0.3135 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3012 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3012 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 38237 Z= 0.124 Angle : 0.578 14.906 51647 Z= 0.278 Chirality : 0.041 0.208 5918 Planarity : 0.004 0.061 6491 Dihedral : 10.534 88.049 5539 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.46 % Allowed : 34.03 % Favored : 63.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.13), residues: 4623 helix: 1.56 (0.11), residues: 2552 sheet: -1.01 (0.23), residues: 479 loop : 1.00 (0.17), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 263 TYR 0.022 0.001 TYR J 313 PHE 0.014 0.001 PHE J 197 TRP 0.006 0.001 TRP I 166 HIS 0.006 0.000 HIS E 206 Details of bonding type rmsd covalent geometry : bond 0.00294 (38237) covalent geometry : angle 0.57799 (51647) hydrogen bonds : bond 0.02947 ( 1808) hydrogen bonds : angle 4.32770 ( 5233) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 4129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 552 time to evaluate : 1.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 MET cc_start: 0.5779 (OUTLIER) cc_final: 0.4903 (mpt) REVERT: A 215 GLU cc_start: 0.6130 (OUTLIER) cc_final: 0.5743 (pp20) REVERT: A 219 LEU cc_start: 0.5968 (OUTLIER) cc_final: 0.5095 (mt) REVERT: A 228 ARG cc_start: 0.3846 (mtp180) cc_final: 0.3520 (ptm160) REVERT: B 282 ASP cc_start: 0.7246 (t0) cc_final: 0.7035 (t0) REVERT: C 171 ASN cc_start: 0.8330 (m-40) cc_final: 0.7931 (m-40) REVERT: C 308 ASP cc_start: 0.8668 (t0) cc_final: 0.8307 (t0) REVERT: C 350 MET cc_start: 0.4566 (tpp) cc_final: 0.4082 (tmt) REVERT: D 315 LYS cc_start: 0.7585 (mtpm) cc_final: 0.7116 (pttp) REVERT: D 350 MET cc_start: 0.6345 (mmp) cc_final: 0.4349 (ttm) REVERT: E 105 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8025 (pt0) REVERT: E 200 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.7931 (tm-30) REVERT: E 283 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8579 (tt) REVERT: F 113 MET cc_start: 0.9000 (mtp) cc_final: 0.8760 (mtt) REVERT: F 115 GLU cc_start: 0.7771 (pm20) cc_final: 0.7528 (pm20) REVERT: F 119 ASN cc_start: 0.8105 (OUTLIER) cc_final: 0.7453 (t160) REVERT: G 199 ARG cc_start: 0.9183 (OUTLIER) cc_final: 0.8293 (ttp-170) REVERT: G 311 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.8045 (ptpp) REVERT: H 236 ASN cc_start: 0.8902 (OUTLIER) cc_final: 0.8545 (p0) REVERT: H 280 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7100 (tm-30) REVERT: H 308 ASP cc_start: 0.8298 (p0) cc_final: 0.7806 (p0) REVERT: H 315 LYS cc_start: 0.8081 (mtpt) cc_final: 0.7706 (ttpt) REVERT: H 342 LYS cc_start: 0.7851 (mppt) cc_final: 0.7160 (mmmt) REVERT: H 346 LYS cc_start: 0.8658 (mttt) cc_final: 0.8047 (mtmt) REVERT: I 113 MET cc_start: 0.8929 (ptp) cc_final: 0.8646 (ptm) REVERT: I 163 MET cc_start: 0.8997 (OUTLIER) cc_final: 0.8777 (mtp) REVERT: I 272 LYS cc_start: 0.7920 (pttm) cc_final: 0.7553 (pttm) REVERT: I 275 LYS cc_start: 0.8809 (mttt) cc_final: 0.8220 (mtpt) REVERT: J 342 LYS cc_start: 0.7797 (tptm) cc_final: 0.7591 (tppp) REVERT: K 261 ASP cc_start: 0.8448 (t0) cc_final: 0.8035 (t0) REVERT: L 113 MET cc_start: 0.8956 (mtm) cc_final: 0.8641 (ptp) REVERT: L 337 ARG cc_start: 0.7829 (ttp80) cc_final: 0.7457 (ttp80) REVERT: M 184 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8689 (mt) REVERT: M 200 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8159 (tm-30) REVERT: M 316 GLN cc_start: 0.6930 (mt0) cc_final: 0.6505 (tm-30) REVERT: O 163 MET cc_start: 0.5598 (OUTLIER) cc_final: 0.5361 (tpt) REVERT: O 164 ASP cc_start: 0.7385 (t0) cc_final: 0.7070 (t0) REVERT: O 200 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7507 (mm-30) REVERT: P 142 LEU cc_start: 0.5938 (OUTLIER) cc_final: 0.5710 (mm) REVERT: P 144 LYS cc_start: 0.5209 (OUTLIER) cc_final: 0.4986 (tmtm) outliers start: 99 outliers final: 65 residues processed: 617 average time/residue: 0.7021 time to fit residues: 530.4523 Evaluate side-chains 620 residues out of total 4129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 539 time to evaluate : 1.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 200 GLU Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 236 ASN Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 119 ASN Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 118 SER Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain G residue 199 ARG Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 311 LYS Chi-restraints excluded: chain G residue 347 LYS Chi-restraints excluded: chain H residue 177 MET Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 207 GLU Chi-restraints excluded: chain H residue 209 THR Chi-restraints excluded: chain H residue 224 LEU Chi-restraints excluded: chain H residue 236 ASN Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 256 SER Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain H residue 280 GLU Chi-restraints excluded: chain I residue 115 GLU Chi-restraints excluded: chain I residue 163 MET Chi-restraints excluded: chain I residue 224 LEU Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 246 LEU Chi-restraints excluded: chain J residue 276 LEU Chi-restraints excluded: chain K residue 137 CYS Chi-restraints excluded: chain K residue 204 THR Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 137 CYS Chi-restraints excluded: chain L residue 224 LEU Chi-restraints excluded: chain L residue 247 ARG Chi-restraints excluded: chain M residue 73 GLU Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain M residue 177 MET Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain M residue 200 GLU Chi-restraints excluded: chain M residue 204 THR Chi-restraints excluded: chain M residue 339 LEU Chi-restraints excluded: chain N residue 82 THR Chi-restraints excluded: chain N residue 101 SER Chi-restraints excluded: chain N residue 209 THR Chi-restraints excluded: chain N residue 255 VAL Chi-restraints excluded: chain O residue 74 ARG Chi-restraints excluded: chain O residue 80 ILE Chi-restraints excluded: chain O residue 163 MET Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 142 LEU Chi-restraints excluded: chain P residue 144 LYS Chi-restraints excluded: chain P residue 155 ILE Chi-restraints excluded: chain P residue 157 ILE Chi-restraints excluded: chain P residue 254 LEU Chi-restraints excluded: chain P residue 290 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 155 optimal weight: 0.0670 chunk 316 optimal weight: 1.9990 chunk 191 optimal weight: 0.6980 chunk 139 optimal weight: 2.9990 chunk 50 optimal weight: 0.0010 chunk 287 optimal weight: 2.9990 chunk 364 optimal weight: 3.9990 chunk 271 optimal weight: 0.6980 chunk 333 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 349 optimal weight: 1.9990 overall best weight: 0.4524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 91 GLN E 206 HIS F 236 ASN G 284 GLN G 319 GLN ** H 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 225 ASN L 225 ASN M 182 ASN M 239 ASN M 284 GLN N 104 HIS O 182 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.171329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.121006 restraints weight = 72133.550| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.76 r_work: 0.3145 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2992 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2992 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 38237 Z= 0.111 Angle : 0.571 14.097 51647 Z= 0.275 Chirality : 0.041 0.210 5918 Planarity : 0.004 0.062 6491 Dihedral : 10.346 89.918 5539 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.39 % Allowed : 34.34 % Favored : 63.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.13), residues: 4623 helix: 1.62 (0.11), residues: 2552 sheet: -0.78 (0.27), residues: 380 loop : 0.79 (0.16), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 248 TYR 0.024 0.001 TYR D 264 PHE 0.012 0.001 PHE G 197 TRP 0.005 0.001 TRP E 166 HIS 0.006 0.000 HIS E 206 Details of bonding type rmsd covalent geometry : bond 0.00259 (38237) covalent geometry : angle 0.57084 (51647) hydrogen bonds : bond 0.02820 ( 1808) hydrogen bonds : angle 4.25347 ( 5233) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19745.94 seconds wall clock time: 336 minutes 6.31 seconds (20166.31 seconds total)