Starting phenix.real_space_refine on Thu Feb 5 09:28:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l3u_62789/02_2026/9l3u_62789.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l3u_62789/02_2026/9l3u_62789.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9l3u_62789/02_2026/9l3u_62789.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l3u_62789/02_2026/9l3u_62789.map" model { file = "/net/cci-nas-00/data/ceres_data/9l3u_62789/02_2026/9l3u_62789.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l3u_62789/02_2026/9l3u_62789.cif" } resolution = 2.96 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= 0.012 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 21 5.49 5 Mg 7 5.21 5 S 81 5.16 5 C 10327 2.51 5 N 2765 2.21 5 O 3151 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s 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: 16352 Number of models: 1 Model: "" Number of chains: 15 Chain: "H" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 75 Classifications: {'peptide': 15} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'TRANS': 14} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'UNK:plan-1': 15} Unresolved non-hydrogen planarities: 15 Chain: "A" Number of atoms: 2199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2199 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 13, 'TRANS': 265} Chain breaks: 1 Chain: "B" 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: "C" 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: "D" Number of atoms: 2336 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 294, 2325 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 13, 'TRANS': 280} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 294, 2325 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 13, 'TRANS': 280} Chain breaks: 1 bond proxies already assigned to first conformer: 2350 Chain: "E" 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: "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: 2264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2264 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 13, 'TRANS': 273} Chain breaks: 1 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: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 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} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AARG C 74 " occ=0.42 ... (20 atoms not shown) pdb=" NH2BARG C 74 " occ=0.58 residue: pdb=" N AARG D 60 " occ=0.42 ... (20 atoms not shown) pdb=" NH2BARG D 60 " occ=0.58 Time building chain proxies: 4.70, per 1000 atoms: 0.29 Number of scatterers: 16352 At special positions: 0 Unit cell: (113.98, 136.94, 136.53, 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 81 16.00 P 21 15.00 Mg 7 11.99 O 3151 8.00 N 2765 7.00 C 10327 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: 1.29 Conformation dependent library (CDL) restraints added in 905.8 milliseconds 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3896 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 7 sheets defined 62.6% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 52 through 61 Processing helix chain 'A' and resid 62 through 65 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 120 through 124 Processing helix chain 'A' and resid 138 through 151 removed outlier: 4.483A pdb=" N GLY A 151 " --> pdb=" O ALA A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 163 Processing helix chain 'A' and resid 168 through 184 removed outlier: 3.518A pdb=" N LYS A 172 " --> pdb=" O GLY A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 198 removed outlier: 3.808A pdb=" N PHE A 197 " --> pdb=" O GLN A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 221 Processing helix chain 'A' and resid 237 through 241 Processing helix chain 'A' and resid 242 through 249 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 310 Processing helix chain 'A' and resid 310 through 316 Processing helix chain 'A' and resid 340 through 346 removed outlier: 3.640A pdb=" N PHE A 344 " --> pdb=" O LYS A 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 61 Processing helix chain 'B' and resid 70 through 77 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 107 through 113 Processing helix chain 'B' and resid 113 through 118 removed outlier: 3.832A pdb=" N TYR B 117 " --> pdb=" O MET B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 150 Processing helix chain 'B' and resid 158 through 163 removed outlier: 3.603A pdb=" N ILE B 162 " --> pdb=" O ARG B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 184 Processing helix chain 'B' and resid 193 through 198 removed outlier: 4.060A 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 237 through 241 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 310 removed outlier: 3.577A pdb=" N ASP B 308 " --> pdb=" O GLU B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 319 Processing helix chain 'B' and resid 340 through 347 removed outlier: 3.678A pdb=" N PHE B 344 " --> pdb=" O LYS B 340 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS B 347 " --> pdb=" O ASP B 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 61 Processing helix chain 'C' and resid 62 through 65 Processing helix chain 'C' and resid 70 through 78 removed outlier: 3.800A pdb=" N SER C 78 " --> pdb=" O AARG C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 93 removed outlier: 3.567A pdb=" N ILE C 93 " --> pdb=" O PHE C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 106 Processing helix chain 'C' and resid 107 through 113 Processing helix chain 'C' and resid 113 through 118 Processing helix chain 'C' and resid 138 through 149 Processing helix chain 'C' and resid 168 through 184 Processing helix chain 'C' and resid 193 through 198 removed outlier: 4.201A 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 237 through 241 Processing helix chain 'C' and resid 242 through 248 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 removed outlier: 3.770A pdb=" N ASP C 308 " --> pdb=" O GLU C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 320 removed outlier: 3.572A pdb=" N GLN C 316 " --> pdb=" O GLU C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 348 removed outlier: 4.217A pdb=" N LYS C 347 " --> pdb=" O ASP C 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 61 Processing helix chain 'D' and resid 62 through 65 removed outlier: 3.680A pdb=" N ALA D 65 " --> pdb=" O PRO D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 65' Processing helix chain 'D' and resid 70 through 78 removed outlier: 3.830A pdb=" N SER D 78 " --> pdb=" O ARG D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 93 Processing helix chain 'D' and resid 96 through 107 Processing helix chain 'D' and resid 107 through 113 Processing helix chain 'D' and resid 113 through 118 Processing helix chain 'D' and resid 138 through 150 Processing helix chain 'D' and resid 158 through 163 Processing helix chain 'D' and resid 168 through 184 Processing helix chain 'D' and resid 193 through 198 removed outlier: 4.198A 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 237 through 241 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 removed outlier: 3.535A pdb=" N ILE D 286 " --> pdb=" O ASP D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 310 Processing helix chain 'D' and resid 310 through 320 removed outlier: 3.584A pdb=" N GLN D 319 " --> pdb=" O LYS D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 346 removed outlier: 3.850A pdb=" N PHE D 344 " --> pdb=" O LYS D 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 61 Processing helix chain 'E' and resid 70 through 78 removed outlier: 3.840A pdb=" N SER E 78 " --> pdb=" O ARG E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 86 Processing helix chain 'E' and resid 89 through 93 Processing helix chain 'E' and resid 96 through 113 removed outlier: 5.313A pdb=" N TYR E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) Proline residue: E 110 - end of helix Processing helix chain 'E' and resid 113 through 118 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 Processing helix chain 'E' and resid 193 through 198 removed outlier: 4.266A 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 237 through 241 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: 3.644A 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 312 through 321 Processing helix chain 'E' and resid 340 through 346 removed outlier: 3.633A pdb=" N PHE E 344 " --> pdb=" O LYS E 340 " (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 77 Processing helix chain 'F' and resid 89 through 93 Processing helix chain 'F' and resid 96 through 106 Processing helix chain 'F' and resid 107 through 113 Processing helix chain 'F' and resid 113 through 118 removed outlier: 3.839A pdb=" N TYR F 117 " --> pdb=" O MET F 113 " (cutoff:3.500A) 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: 4.120A 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 309 Processing helix chain 'F' and resid 310 through 319 Processing helix chain 'F' and resid 340 through 347 removed outlier: 4.045A pdb=" N LYS F 347 " --> pdb=" O ASP F 343 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 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: 3.687A 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 108 through 113 Processing helix chain 'G' and resid 138 through 150 Processing helix chain 'G' and resid 158 through 163 Processing helix chain 'G' and resid 168 through 184 Processing helix chain 'G' and resid 206 through 222 removed outlier: 3.714A pdb=" N GLY G 222 " --> pdb=" O THR G 218 " (cutoff:3.500A) Processing helix chain 'G' and resid 242 through 248 Processing helix chain 'G' and resid 259 through 271 Processing helix chain 'G' and resid 283 through 290 Processing helix chain 'G' and resid 294 through 310 removed outlier: 3.704A pdb=" N ASP G 308 " --> pdb=" O GLU G 304 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA G 309 " --> pdb=" O ALA G 305 " (cutoff:3.500A) Processing helix chain 'G' and resid 310 through 319 removed outlier: 3.946A pdb=" N LYS G 317 " --> pdb=" O TYR G 313 " (cutoff:3.500A) Processing helix chain 'G' and resid 341 through 346 removed outlier: 3.828A pdb=" N THR G 345 " --> pdb=" O THR G 341 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 81 removed outlier: 3.635A pdb=" N PHE A 154 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ASN A 153 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N PHE A 190 " --> pdb=" O ASN A 153 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE A 155 " --> pdb=" O PHE A 190 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N ASP A 192 " --> pdb=" O ILE A 155 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N ILE A 157 " --> pdb=" O ASP A 192 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 153 through 155 removed outlier: 6.207A pdb=" N ASN B 153 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N PHE B 190 " --> pdb=" O ASN B 153 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE B 155 " --> pdb=" O PHE B 190 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N ASP B 192 " --> pdb=" O ILE B 155 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLY B 128 " --> pdb=" O LYS B 251 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N PHE B 253 " --> pdb=" O GLY B 128 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LEU B 130 " --> pdb=" O PHE B 253 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 80 through 81 removed outlier: 4.098A pdb=" N PHE C 154 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA C 234 " --> pdb=" O ILE C 191 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLY C 128 " --> pdb=" O LYS C 251 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N PHE C 253 " --> pdb=" O GLY C 128 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU C 130 " --> pdb=" O PHE C 253 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 80 through 81 removed outlier: 4.149A pdb=" N PHE D 154 " --> pdb=" O VAL D 81 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N GLY D 128 " --> pdb=" O LYS D 251 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N PHE D 253 " --> pdb=" O GLY D 128 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU D 130 " --> pdb=" O PHE D 253 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 80 through 81 removed outlier: 4.007A pdb=" N PHE E 154 " --> pdb=" O VAL E 81 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N CYS E 187 " --> pdb=" O MET E 230 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N ILE E 232 " --> pdb=" O CYS E 187 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ILE E 189 " --> pdb=" O ILE E 232 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ALA E 234 " --> pdb=" O ILE E 189 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE E 191 " --> pdb=" O ALA E 234 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLY E 128 " --> pdb=" O LYS E 251 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N PHE E 253 " --> pdb=" O GLY E 128 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU E 130 " --> pdb=" O PHE E 253 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 80 through 81 removed outlier: 4.135A pdb=" N PHE F 154 " --> pdb=" O VAL F 81 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ASN F 153 " --> pdb=" O ILE F 188 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N PHE F 190 " --> pdb=" O ASN F 153 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ILE F 155 " --> pdb=" O PHE F 190 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N ASP F 192 " --> pdb=" O ILE F 155 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N ILE F 157 " --> pdb=" O ASP F 192 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA F 234 " --> pdb=" O ILE F 191 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLY F 128 " --> pdb=" O LYS F 251 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N PHE F 253 " --> pdb=" O GLY F 128 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU F 130 " --> pdb=" O PHE F 253 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 80 through 81 removed outlier: 3.717A pdb=" N PHE G 154 " --> pdb=" O VAL G 81 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ASN G 153 " --> pdb=" O ILE G 188 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N PHE G 190 " --> pdb=" O ASN G 153 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE G 155 " --> pdb=" O PHE G 190 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N ASP G 192 " --> pdb=" O ILE G 155 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ILE G 232 " --> pdb=" O CYS G 187 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ILE G 189 " --> pdb=" O ILE G 232 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N ALA G 234 " --> pdb=" O ILE G 189 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ILE G 191 " --> pdb=" O ALA G 234 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N VAL G 129 " --> pdb=" O GLY G 233 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N PHE G 253 " --> pdb=" O GLY G 128 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU G 130 " --> pdb=" O PHE G 253 " (cutoff:3.500A) 809 hydrogen bonds defined for protein. 2330 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: 2.80 Time building geometry restraints manager: 1.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5269 1.34 - 1.46: 3150 1.46 - 1.58: 8037 1.58 - 1.70: 22 1.70 - 1.82: 141 Bond restraints: 16619 Sorted by residual: bond pdb=" N ASP G 195 " pdb=" CA ASP G 195 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.26e-02 6.30e+03 6.34e+00 bond pdb=" N ARG E 60 " pdb=" CA ARG E 60 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.20e-02 6.94e+03 5.89e+00 bond pdb=" N ASP C 343 " pdb=" CA ASP C 343 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.19e-02 7.06e+03 4.44e+00 bond pdb=" N LEU G 77 " pdb=" CA LEU G 77 " ideal model delta sigma weight residual 1.457 1.479 -0.022 1.35e-02 5.49e+03 2.74e+00 bond pdb=" CA ASP B 84 " pdb=" CB ASP B 84 " ideal model delta sigma weight residual 1.530 1.556 -0.026 1.69e-02 3.50e+03 2.32e+00 ... (remaining 16614 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 22140 2.55 - 5.10: 237 5.10 - 7.65: 58 7.65 - 10.20: 14 10.20 - 12.75: 9 Bond angle restraints: 22458 Sorted by residual: angle pdb=" CB MET B 112 " pdb=" CG MET B 112 " pdb=" SD MET B 112 " ideal model delta sigma weight residual 112.70 125.45 -12.75 3.00e+00 1.11e-01 1.80e+01 angle pdb=" CA LYS E 342 " pdb=" CB LYS E 342 " pdb=" CG LYS E 342 " ideal model delta sigma weight residual 114.10 122.29 -8.19 2.00e+00 2.50e-01 1.68e+01 angle pdb=" C PRO B 83 " pdb=" N ASP B 84 " pdb=" CA ASP B 84 " ideal model delta sigma weight residual 121.54 129.12 -7.58 1.91e+00 2.74e-01 1.57e+01 angle pdb=" N ASN D 119 " pdb=" CA ASN D 119 " pdb=" C ASN D 119 " ideal model delta sigma weight residual 114.56 109.70 4.86 1.27e+00 6.20e-01 1.46e+01 angle pdb=" CA TYR F 313 " pdb=" CB TYR F 313 " pdb=" CG TYR F 313 " ideal model delta sigma weight residual 113.90 120.56 -6.66 1.80e+00 3.09e-01 1.37e+01 ... (remaining 22453 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 8374 17.99 - 35.98: 1418 35.98 - 53.97: 481 53.97 - 71.96: 123 71.96 - 89.96: 42 Dihedral angle restraints: 10438 sinusoidal: 4460 harmonic: 5978 Sorted by residual: dihedral pdb=" CA LEU B 184 " pdb=" C LEU B 184 " pdb=" N GLN B 185 " pdb=" CA GLN B 185 " ideal model delta harmonic sigma weight residual -180.00 -155.25 -24.75 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA LEU C 184 " pdb=" C LEU C 184 " pdb=" N GLN C 185 " pdb=" CA GLN C 185 " ideal model delta harmonic sigma weight residual -180.00 -156.31 -23.69 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA LEU D 184 " pdb=" C LEU D 184 " pdb=" N GLN D 185 " pdb=" CA GLN D 185 " ideal model delta harmonic sigma weight residual -180.00 -156.38 -23.62 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 10435 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1972 0.048 - 0.096: 434 0.096 - 0.144: 155 0.144 - 0.192: 6 0.192 - 0.240: 5 Chirality restraints: 2572 Sorted by residual: chirality pdb=" CG LEU G 219 " pdb=" CB LEU G 219 " pdb=" CD1 LEU G 219 " pdb=" CD2 LEU G 219 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CB ILE G 155 " pdb=" CA ILE G 155 " pdb=" CG1 ILE G 155 " pdb=" CG2 ILE G 155 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CB ILE G 191 " pdb=" CA ILE G 191 " pdb=" CG1 ILE G 191 " pdb=" CG2 ILE G 191 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 2569 not shown) Planarity restraints: 2818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 133 " -0.075 5.00e-02 4.00e+02 1.12e-01 2.02e+01 pdb=" N PRO A 134 " 0.194 5.00e-02 4.00e+02 pdb=" CA PRO A 134 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO A 134 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 60 " -0.268 9.50e-02 1.11e+02 1.20e-01 8.85e+00 pdb=" NE ARG E 60 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG E 60 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG E 60 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG E 60 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP E 288 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.16e+00 pdb=" CG ASP E 288 " -0.043 2.00e-02 2.50e+03 pdb=" OD1 ASP E 288 " 0.016 2.00e-02 2.50e+03 pdb=" OD2 ASP E 288 " 0.015 2.00e-02 2.50e+03 ... (remaining 2815 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 201 2.59 - 3.17: 13365 3.17 - 3.75: 28038 3.75 - 4.32: 38142 4.32 - 4.90: 62832 Nonbonded interactions: 142578 Sorted by model distance: nonbonded pdb=" OG1 THR D 140 " pdb="MG MG C 402 " model vdw 2.018 2.170 nonbonded pdb=" OG1 THR B 140 " pdb="MG MG B 402 " model vdw 2.022 2.170 nonbonded pdb="MG MG B 403 " pdb=" O3G ATP C 401 " model vdw 2.032 2.170 nonbonded pdb=" OG1 THR F 140 " pdb="MG MG F 402 " model vdw 2.034 2.170 nonbonded pdb="MG MG C 402 " pdb=" O1G ATP D 401 " model vdw 2.044 2.170 ... (remaining 142573 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 51 through 59 or resid 61 through 73 or resid 75 through 3 \ 48)) selection = (chain 'B' and (resid 51 through 59 or resid 61 through 73 or resid 75 through 3 \ 16 or resid 337 through 348)) selection = (chain 'C' and (resid 51 through 59 or resid 61 through 73 or resid 75 through 3 \ 16 or resid 337 through 348)) selection = (chain 'D' and (resid 51 through 59 or resid 61 through 73 or resid 75 through 3 \ 16 or resid 337 through 348)) selection = (chain 'E' and (resid 51 through 59 or resid 61 through 73 or resid 75 through 3 \ 16 or resid 337 through 348)) selection = (chain 'F' and (resid 51 through 59 or resid 61 through 73 or resid 75 through 3 \ 16 or resid 337 through 348)) selection = (chain 'G' and (resid 51 through 59 or resid 61 through 73 or resid 75 through 3 \ 16 or resid 318 or resid 338 through 348)) } 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: 15.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 1.090 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 16.680 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.030 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:6.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16619 Z= 0.166 Angle : 0.748 12.745 22458 Z= 0.361 Chirality : 0.045 0.240 2572 Planarity : 0.006 0.120 2818 Dihedral : 20.977 89.956 6542 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.62 % Allowed : 36.18 % Favored : 61.20 % 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: 0.06 (0.18), residues: 2007 helix: 0.29 (0.15), residues: 1067 sheet: -0.64 (0.42), residues: 166 loop : 0.08 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 158 TYR 0.026 0.001 TYR G 132 PHE 0.016 0.001 PHE A 154 TRP 0.012 0.001 TRP G 54 HIS 0.003 0.001 HIS C 104 Details of bonding type rmsd covalent geometry : bond 0.00381 (16619) covalent geometry : angle 0.74848 (22458) hydrogen bonds : bond 0.19066 ( 809) hydrogen bonds : angle 6.38893 ( 2330) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 242 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.7668 (mtm-85) cc_final: 0.6969 (ptt-90) REVERT: G 163 MET cc_start: 0.7582 (mmt) cc_final: 0.7286 (mmt) REVERT: G 193 GLN cc_start: 0.7643 (OUTLIER) cc_final: 0.6109 (mp10) outliers start: 47 outliers final: 38 residues processed: 284 average time/residue: 0.5537 time to fit residues: 175.9022 Evaluate side-chains 265 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 226 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 337 ARG Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 294 SER Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 247 ARG Chi-restraints excluded: chain E residue 268 SER Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 137 CYS Chi-restraints excluded: chain F residue 236 ASN Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 97 ASP Chi-restraints excluded: chain G residue 161 SER Chi-restraints excluded: chain G residue 193 GLN Chi-restraints excluded: chain G residue 254 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 20.0000 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.0870 chunk 130 optimal weight: 0.2980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 20.0000 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 6.9990 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 GLN C 50 GLN E 91 GLN F 50 GLN G 153 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.176422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.134003 restraints weight = 37291.970| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 5.86 r_work: 0.2992 rms_B_bonded: 5.32 restraints_weight: 2.0000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2871 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2871 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.0952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16619 Z= 0.131 Angle : 0.565 9.359 22458 Z= 0.277 Chirality : 0.041 0.145 2572 Planarity : 0.004 0.074 2818 Dihedral : 12.246 85.284 2497 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 4.52 % Allowed : 32.72 % Favored : 62.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.19), residues: 2007 helix: 1.00 (0.16), residues: 1109 sheet: -0.71 (0.39), residues: 174 loop : 0.33 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 263 TYR 0.016 0.001 TYR C 264 PHE 0.013 0.001 PHE A 154 TRP 0.004 0.001 TRP C 220 HIS 0.002 0.000 HIS E 206 Details of bonding type rmsd covalent geometry : bond 0.00301 (16619) covalent geometry : angle 0.56452 (22458) hydrogen bonds : bond 0.03777 ( 809) hydrogen bonds : angle 4.63607 ( 2330) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 252 time to evaluate : 0.693 Fit side-chains REVERT: A 113 MET cc_start: 0.7882 (ptp) cc_final: 0.7666 (ptp) REVERT: A 237 ARG cc_start: 0.7556 (mtm-85) cc_final: 0.6984 (ptt-90) REVERT: A 240 ASP cc_start: 0.8216 (OUTLIER) cc_final: 0.7974 (m-30) REVERT: D 74 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7608 (mtp-110) REVERT: F 91 GLN cc_start: 0.8495 (pm20) cc_final: 0.8247 (mp10) REVERT: F 163 MET cc_start: 0.8688 (OUTLIER) cc_final: 0.8213 (mtt) REVERT: F 273 ASP cc_start: 0.7154 (t0) cc_final: 0.6898 (t0) REVERT: F 288 ASP cc_start: 0.8438 (m-30) cc_final: 0.8086 (m-30) REVERT: G 60 ARG cc_start: 0.4444 (OUTLIER) cc_final: 0.4145 (ptm-80) REVERT: G 163 MET cc_start: 0.7108 (mmt) cc_final: 0.6713 (mmt) REVERT: G 267 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.7187 (mm) REVERT: G 297 ASP cc_start: 0.7501 (m-30) cc_final: 0.7186 (m-30) REVERT: G 342 LYS cc_start: 0.6987 (pttt) cc_final: 0.6431 (pmtt) outliers start: 81 outliers final: 21 residues processed: 306 average time/residue: 0.4955 time to fit residues: 171.2167 Evaluate side-chains 270 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 244 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain D residue 74 ARG Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 247 ARG Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 163 MET Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 312 GLU Chi-restraints excluded: chain G residue 60 ARG Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 267 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 129 optimal weight: 0.8980 chunk 14 optimal weight: 6.9990 chunk 198 optimal weight: 9.9990 chunk 80 optimal weight: 8.9990 chunk 82 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 195 optimal weight: 5.9990 chunk 74 optimal weight: 0.7980 chunk 199 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN B 91 GLN C 50 GLN E 91 GLN E 236 ASN G 193 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.174508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.131348 restraints weight = 40599.026| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 6.10 r_work: 0.2955 rms_B_bonded: 5.47 restraints_weight: 2.0000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2802 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2802 r_free = 0.2802 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2802 r_free = 0.2802 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2802 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16619 Z= 0.161 Angle : 0.560 12.928 22458 Z= 0.274 Chirality : 0.042 0.157 2572 Planarity : 0.004 0.061 2818 Dihedral : 11.811 87.258 2449 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 5.02 % Allowed : 32.55 % Favored : 62.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.19), residues: 2007 helix: 1.20 (0.16), residues: 1115 sheet: -0.71 (0.38), residues: 177 loop : 0.37 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 199 TYR 0.018 0.001 TYR C 264 PHE 0.018 0.001 PHE G 281 TRP 0.008 0.001 TRP C 220 HIS 0.002 0.001 HIS E 206 Details of bonding type rmsd covalent geometry : bond 0.00384 (16619) covalent geometry : angle 0.55987 (22458) hydrogen bonds : bond 0.03615 ( 809) hydrogen bonds : angle 4.44356 ( 2330) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 249 time to evaluate : 0.607 Fit side-chains REVERT: A 60 ARG cc_start: 0.5264 (OUTLIER) cc_final: 0.5026 (ptp-170) REVERT: D 74 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.7646 (mtp-110) REVERT: D 285 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8430 (tm) REVERT: E 284 GLN cc_start: 0.8318 (tp40) cc_final: 0.8023 (tp40) REVERT: F 91 GLN cc_start: 0.8466 (pm20) cc_final: 0.8160 (mp10) REVERT: F 163 MET cc_start: 0.8756 (OUTLIER) cc_final: 0.7909 (mmm) REVERT: F 273 ASP cc_start: 0.7122 (t0) cc_final: 0.6833 (t0) REVERT: F 288 ASP cc_start: 0.8438 (OUTLIER) cc_final: 0.8105 (m-30) REVERT: G 60 ARG cc_start: 0.4428 (OUTLIER) cc_final: 0.4155 (ptm-80) REVERT: G 193 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7282 (mp-120) REVERT: G 198 LEU cc_start: 0.6685 (OUTLIER) cc_final: 0.6415 (pp) REVERT: G 201 ARG cc_start: 0.4785 (OUTLIER) cc_final: 0.4414 (ptp-110) REVERT: G 223 LEU cc_start: 0.7081 (OUTLIER) cc_final: 0.6747 (tm) REVERT: G 267 LEU cc_start: 0.7558 (OUTLIER) cc_final: 0.7105 (mm) REVERT: G 297 ASP cc_start: 0.7409 (m-30) cc_final: 0.7154 (m-30) REVERT: G 307 LEU cc_start: 0.5951 (OUTLIER) cc_final: 0.5622 (mm) REVERT: G 311 LYS cc_start: 0.5765 (OUTLIER) cc_final: 0.5518 (mmpt) REVERT: G 342 LYS cc_start: 0.6943 (pttt) cc_final: 0.6428 (pmtt) outliers start: 90 outliers final: 30 residues processed: 305 average time/residue: 0.5215 time to fit residues: 178.9739 Evaluate side-chains 284 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 241 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 284 GLN Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 74 ARG Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 118 SER Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 247 ARG Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 163 MET Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 288 ASP Chi-restraints excluded: chain F residue 312 GLU Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain G residue 60 ARG Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 164 ASP Chi-restraints excluded: chain G residue 169 GLU Chi-restraints excluded: chain G residue 193 GLN Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 201 ARG Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 213 LYS Chi-restraints excluded: chain G residue 223 LEU Chi-restraints excluded: chain G residue 267 LEU Chi-restraints excluded: chain G residue 307 LEU Chi-restraints excluded: chain G residue 311 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 114 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 160 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 189 optimal weight: 6.9990 chunk 69 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 chunk 105 optimal weight: 4.9990 chunk 173 optimal weight: 6.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN B 91 GLN F 50 GLN G 193 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.172690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.128095 restraints weight = 30280.778| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 4.41 r_work: 0.2927 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2844 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2844 r_free = 0.2844 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 = 0.2844 r_free = 0.2844 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2844 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16619 Z= 0.178 Angle : 0.576 13.235 22458 Z= 0.280 Chirality : 0.042 0.194 2572 Planarity : 0.004 0.053 2818 Dihedral : 11.690 83.970 2448 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 5.30 % Allowed : 32.39 % Favored : 62.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.19), residues: 2007 helix: 1.29 (0.16), residues: 1109 sheet: -0.78 (0.38), residues: 175 loop : 0.42 (0.24), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 199 TYR 0.017 0.001 TYR C 264 PHE 0.015 0.001 PHE G 281 TRP 0.008 0.001 TRP C 220 HIS 0.002 0.001 HIS C 104 Details of bonding type rmsd covalent geometry : bond 0.00431 (16619) covalent geometry : angle 0.57634 (22458) hydrogen bonds : bond 0.03450 ( 809) hydrogen bonds : angle 4.40102 ( 2330) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 247 time to evaluate : 0.673 Fit side-chains REVERT: A 60 ARG cc_start: 0.5284 (OUTLIER) cc_final: 0.5020 (ptp-170) REVERT: A 237 ARG cc_start: 0.7523 (mtm-85) cc_final: 0.7004 (ptt-90) REVERT: B 340 LYS cc_start: 0.7573 (mtmt) cc_final: 0.7337 (mtmt) REVERT: D 74 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.7656 (mtp-110) REVERT: D 285 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8491 (tm) REVERT: E 47 LYS cc_start: 0.8053 (OUTLIER) cc_final: 0.7262 (mptt) REVERT: E 144 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8412 (mttt) REVERT: E 284 GLN cc_start: 0.8415 (tp40) cc_final: 0.8030 (tp40) REVERT: E 288 ASP cc_start: 0.8136 (m-30) cc_final: 0.7875 (m-30) REVERT: F 73 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7878 (mt-10) REVERT: F 91 GLN cc_start: 0.8402 (pm20) cc_final: 0.8111 (mp10) REVERT: F 273 ASP cc_start: 0.7112 (t0) cc_final: 0.6863 (t0) REVERT: F 288 ASP cc_start: 0.8376 (OUTLIER) cc_final: 0.8078 (m-30) REVERT: G 60 ARG cc_start: 0.4384 (OUTLIER) cc_final: 0.4146 (ptm-80) REVERT: G 77 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7412 (mm) REVERT: G 198 LEU cc_start: 0.6785 (OUTLIER) cc_final: 0.6521 (pp) REVERT: G 201 ARG cc_start: 0.4810 (OUTLIER) cc_final: 0.4447 (ptp-110) REVERT: G 223 LEU cc_start: 0.7076 (OUTLIER) cc_final: 0.6740 (tm) REVERT: G 307 LEU cc_start: 0.6113 (OUTLIER) cc_final: 0.5890 (mm) REVERT: G 342 LYS cc_start: 0.6996 (pttt) cc_final: 0.6455 (pmtt) outliers start: 95 outliers final: 30 residues processed: 310 average time/residue: 0.5258 time to fit residues: 182.4984 Evaluate side-chains 287 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 244 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 74 ARG Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 118 SER Chi-restraints excluded: chain E residue 144 LYS Chi-restraints excluded: chain E residue 247 ARG Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 288 ASP Chi-restraints excluded: chain F residue 312 GLU Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain G residue 60 ARG Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 140 THR Chi-restraints excluded: chain G residue 164 ASP Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 201 ARG Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 213 LYS Chi-restraints excluded: chain G residue 223 LEU Chi-restraints excluded: chain G residue 307 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 106 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 176 optimal weight: 30.0000 chunk 148 optimal weight: 0.0670 chunk 56 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 185 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 2 optimal weight: 8.9990 overall best weight: 3.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN B 91 GLN F 50 GLN G 104 HIS G 185 GLN G 193 GLN G 226 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.169404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.124127 restraints weight = 37238.525| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 5.05 r_work: 0.2837 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2873 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2873 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 16619 Z= 0.258 Angle : 0.636 13.236 22458 Z= 0.310 Chirality : 0.045 0.189 2572 Planarity : 0.004 0.053 2818 Dihedral : 11.814 80.963 2448 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 6.08 % Allowed : 31.61 % Favored : 62.32 % 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: 1.02 (0.19), residues: 2007 helix: 1.22 (0.16), residues: 1100 sheet: -0.98 (0.35), residues: 213 loop : 0.59 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 247 TYR 0.014 0.001 TYR G 132 PHE 0.015 0.002 PHE G 281 TRP 0.014 0.002 TRP C 220 HIS 0.003 0.001 HIS D 104 Details of bonding type rmsd covalent geometry : bond 0.00628 (16619) covalent geometry : angle 0.63558 (22458) hydrogen bonds : bond 0.03768 ( 809) hydrogen bonds : angle 4.50613 ( 2330) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 238 time to evaluate : 0.677 Fit side-chains REVERT: A 60 ARG cc_start: 0.5221 (OUTLIER) cc_final: 0.4973 (ptp-170) REVERT: A 237 ARG cc_start: 0.7556 (mtm-85) cc_final: 0.7080 (ptt-90) REVERT: B 108 ILE cc_start: 0.8999 (OUTLIER) cc_final: 0.8653 (mm) REVERT: D 74 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.7718 (mtp-110) REVERT: D 285 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8447 (tm) REVERT: D 312 GLU cc_start: 0.7520 (pm20) cc_final: 0.7000 (tm-30) REVERT: E 47 LYS cc_start: 0.8003 (OUTLIER) cc_final: 0.7229 (mttt) REVERT: E 144 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8506 (mttp) REVERT: E 284 GLN cc_start: 0.8454 (tp40) cc_final: 0.7763 (tp40) REVERT: E 288 ASP cc_start: 0.8125 (m-30) cc_final: 0.7685 (m-30) REVERT: E 312 GLU cc_start: 0.7513 (mm-30) cc_final: 0.7240 (tm-30) REVERT: F 73 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7975 (mt-10) REVERT: F 159 MET cc_start: 0.8220 (mmp) cc_final: 0.8012 (mmp) REVERT: F 163 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.7658 (mmm) REVERT: F 165 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.7865 (ttpp) REVERT: F 273 ASP cc_start: 0.7231 (t0) cc_final: 0.6968 (t0) REVERT: F 288 ASP cc_start: 0.8421 (OUTLIER) cc_final: 0.8079 (m-30) REVERT: G 60 ARG cc_start: 0.4418 (OUTLIER) cc_final: 0.4103 (ptm-80) REVERT: G 77 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7511 (mm) REVERT: G 185 GLN cc_start: 0.6483 (OUTLIER) cc_final: 0.6265 (tp-100) REVERT: G 198 LEU cc_start: 0.6729 (OUTLIER) cc_final: 0.6470 (pp) REVERT: G 201 ARG cc_start: 0.4750 (OUTLIER) cc_final: 0.4448 (ptp-110) REVERT: G 223 LEU cc_start: 0.7144 (OUTLIER) cc_final: 0.6789 (tm) REVERT: G 307 LEU cc_start: 0.6150 (OUTLIER) cc_final: 0.5825 (mm) REVERT: G 311 LYS cc_start: 0.5933 (OUTLIER) cc_final: 0.5600 (mmpt) REVERT: G 342 LYS cc_start: 0.6955 (pttt) cc_final: 0.6441 (pmtt) outliers start: 109 outliers final: 39 residues processed: 312 average time/residue: 0.5933 time to fit residues: 206.4804 Evaluate side-chains 289 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 232 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 74 ARG Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 118 SER Chi-restraints excluded: chain E residue 144 LYS Chi-restraints excluded: chain E residue 247 ARG Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 163 MET Chi-restraints excluded: chain F residue 165 LYS Chi-restraints excluded: chain F residue 236 ASN Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 276 LEU Chi-restraints excluded: chain F residue 288 ASP Chi-restraints excluded: chain F residue 312 GLU Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain G residue 60 ARG Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 140 THR Chi-restraints excluded: chain G residue 183 LYS Chi-restraints excluded: chain G residue 185 GLN Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 201 ARG Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 213 LYS Chi-restraints excluded: chain G residue 223 LEU Chi-restraints excluded: chain G residue 267 LEU Chi-restraints excluded: chain G residue 307 LEU Chi-restraints excluded: chain G residue 311 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 112 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 66 optimal weight: 0.2980 chunk 43 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 42 optimal weight: 0.9980 chunk 198 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 115 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 225 ASN B 91 GLN C 50 GLN F 50 GLN G 193 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.172807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.128244 restraints weight = 34988.516| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 4.64 r_work: 0.2925 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2841 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 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 = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2841 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16619 Z= 0.129 Angle : 0.563 12.069 22458 Z= 0.273 Chirality : 0.041 0.181 2572 Planarity : 0.003 0.049 2818 Dihedral : 11.539 79.604 2448 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 4.96 % Allowed : 32.66 % Favored : 62.37 % 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: 1.24 (0.19), residues: 2007 helix: 1.41 (0.16), residues: 1090 sheet: -0.90 (0.36), residues: 188 loop : 0.62 (0.24), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 248 TYR 0.013 0.001 TYR B 264 PHE 0.013 0.001 PHE F 197 TRP 0.008 0.001 TRP C 220 HIS 0.002 0.000 HIS E 206 Details of bonding type rmsd covalent geometry : bond 0.00304 (16619) covalent geometry : angle 0.56275 (22458) hydrogen bonds : bond 0.03161 ( 809) hydrogen bonds : angle 4.38757 ( 2330) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 253 time to evaluate : 0.598 Fit side-chains REVERT: A 60 ARG cc_start: 0.5206 (OUTLIER) cc_final: 0.4937 (ptp-170) REVERT: A 158 ARG cc_start: 0.7288 (mtm180) cc_final: 0.6829 (mtm-85) REVERT: A 221 ASP cc_start: 0.8776 (OUTLIER) cc_final: 0.8527 (t70) REVERT: A 237 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.7168 (ptt-90) REVERT: C 350 MET cc_start: 0.5484 (tpp) cc_final: 0.5257 (tpp) REVERT: D 74 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.7636 (mtp-110) REVERT: D 285 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8500 (tm) REVERT: E 144 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8465 (mttp) REVERT: E 284 GLN cc_start: 0.8486 (tp40) cc_final: 0.7789 (tp40) REVERT: E 288 ASP cc_start: 0.8104 (m-30) cc_final: 0.7678 (m-30) REVERT: E 312 GLU cc_start: 0.7430 (mm-30) cc_final: 0.7203 (tm-30) REVERT: F 236 ASN cc_start: 0.8776 (OUTLIER) cc_final: 0.8422 (p0) REVERT: F 273 ASP cc_start: 0.7110 (t0) cc_final: 0.6825 (t0) REVERT: F 288 ASP cc_start: 0.8389 (OUTLIER) cc_final: 0.8138 (m-30) REVERT: G 77 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7501 (mm) REVERT: G 185 GLN cc_start: 0.6336 (OUTLIER) cc_final: 0.5967 (tt0) REVERT: G 198 LEU cc_start: 0.6725 (OUTLIER) cc_final: 0.6484 (pp) REVERT: G 201 ARG cc_start: 0.4774 (OUTLIER) cc_final: 0.4434 (ptp-110) REVERT: G 223 LEU cc_start: 0.7096 (OUTLIER) cc_final: 0.6760 (tm) REVERT: G 272 LYS cc_start: 0.6544 (mmtt) cc_final: 0.6339 (pttt) REVERT: G 342 LYS cc_start: 0.6982 (pttt) cc_final: 0.6468 (pmtt) outliers start: 89 outliers final: 33 residues processed: 308 average time/residue: 0.5521 time to fit residues: 190.4503 Evaluate side-chains 294 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 248 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 74 ARG Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 118 SER Chi-restraints excluded: chain E residue 144 LYS Chi-restraints excluded: chain E residue 247 ARG Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 236 ASN Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 288 ASP Chi-restraints excluded: chain F residue 312 GLU Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 140 THR Chi-restraints excluded: chain G residue 164 ASP Chi-restraints excluded: chain G residue 169 GLU Chi-restraints excluded: chain G residue 183 LYS Chi-restraints excluded: chain G residue 185 GLN Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 201 ARG Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 223 LEU Chi-restraints excluded: chain G residue 267 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 62 optimal weight: 4.9990 chunk 144 optimal weight: 6.9990 chunk 83 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 153 optimal weight: 4.9990 chunk 112 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 89 optimal weight: 0.5980 chunk 54 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 225 ASN B 91 GLN C 50 GLN E 225 ASN E 236 ASN F 50 GLN G 193 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.175336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.130715 restraints weight = 32285.062| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 4.50 r_work: 0.2981 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2915 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2915 r_free = 0.2915 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2915 r_free = 0.2915 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2915 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16619 Z= 0.125 Angle : 0.571 14.404 22458 Z= 0.273 Chirality : 0.042 0.207 2572 Planarity : 0.003 0.049 2818 Dihedral : 11.414 79.134 2446 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.46 % Allowed : 33.33 % Favored : 62.21 % 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 (0.19), residues: 2007 helix: 1.46 (0.16), residues: 1097 sheet: -0.88 (0.36), residues: 187 loop : 0.66 (0.24), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 60 TYR 0.019 0.001 TYR C 264 PHE 0.012 0.001 PHE G 281 TRP 0.005 0.001 TRP F 54 HIS 0.002 0.000 HIS E 206 Details of bonding type rmsd covalent geometry : bond 0.00296 (16619) covalent geometry : angle 0.57103 (22458) hydrogen bonds : bond 0.03044 ( 809) hydrogen bonds : angle 4.32117 ( 2330) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 258 time to evaluate : 0.692 Fit side-chains REVERT: A 60 ARG cc_start: 0.5210 (OUTLIER) cc_final: 0.4934 (ptp-170) REVERT: A 221 ASP cc_start: 0.8752 (OUTLIER) cc_final: 0.8476 (t70) REVERT: A 237 ARG cc_start: 0.7615 (OUTLIER) cc_final: 0.7226 (ptt-90) REVERT: D 74 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.7608 (mtp-110) REVERT: D 285 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8480 (tm) REVERT: D 312 GLU cc_start: 0.7448 (pm20) cc_final: 0.7065 (tm-30) REVERT: E 47 LYS cc_start: 0.8074 (OUTLIER) cc_final: 0.7266 (mptt) REVERT: E 144 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8430 (mttt) REVERT: E 284 GLN cc_start: 0.8507 (tp40) cc_final: 0.7738 (tp40) REVERT: E 288 ASP cc_start: 0.8088 (m-30) cc_final: 0.7626 (m-30) REVERT: E 312 GLU cc_start: 0.7434 (mm-30) cc_final: 0.7218 (tm-30) REVERT: F 236 ASN cc_start: 0.8725 (OUTLIER) cc_final: 0.8348 (p0) REVERT: F 273 ASP cc_start: 0.7118 (t0) cc_final: 0.6840 (t0) REVERT: F 288 ASP cc_start: 0.8397 (OUTLIER) cc_final: 0.8145 (m-30) REVERT: G 185 GLN cc_start: 0.6547 (OUTLIER) cc_final: 0.5942 (tt0) REVERT: G 198 LEU cc_start: 0.6698 (OUTLIER) cc_final: 0.6457 (pp) REVERT: G 201 ARG cc_start: 0.4800 (OUTLIER) cc_final: 0.4452 (ptp-110) REVERT: G 223 LEU cc_start: 0.7065 (OUTLIER) cc_final: 0.6732 (tm) REVERT: G 311 LYS cc_start: 0.6001 (OUTLIER) cc_final: 0.5601 (mmpt) REVERT: G 342 LYS cc_start: 0.6966 (pttt) cc_final: 0.6439 (pmtt) outliers start: 80 outliers final: 35 residues processed: 302 average time/residue: 0.5866 time to fit residues: 198.0033 Evaluate side-chains 296 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 247 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 74 ARG Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 118 SER Chi-restraints excluded: chain E residue 144 LYS Chi-restraints excluded: chain E residue 247 ARG Chi-restraints excluded: chain E residue 350 MET Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 113 MET Chi-restraints excluded: chain F residue 177 MET Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 236 ASN Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 288 ASP Chi-restraints excluded: chain F residue 312 GLU Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 140 THR Chi-restraints excluded: chain G residue 164 ASP Chi-restraints excluded: chain G residue 185 GLN Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 201 ARG Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 223 LEU Chi-restraints excluded: chain G residue 267 LEU Chi-restraints excluded: chain G residue 311 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 34 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 90 optimal weight: 0.0980 chunk 16 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 68 optimal weight: 0.4980 chunk 12 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 192 optimal weight: 20.0000 chunk 105 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 225 ASN B 91 GLN C 50 GLN E 225 ASN E 236 ASN F 50 GLN G 193 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.174276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.128677 restraints weight = 28099.718| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 3.80 r_work: 0.2966 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2891 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2891 r_free = 0.2891 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 = 0.2891 r_free = 0.2891 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2891 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16619 Z= 0.140 Angle : 0.583 13.518 22458 Z= 0.279 Chirality : 0.042 0.218 2572 Planarity : 0.003 0.049 2818 Dihedral : 11.342 80.011 2446 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.79 % Allowed : 34.17 % Favored : 62.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.19), residues: 2007 helix: 1.49 (0.16), residues: 1097 sheet: -0.79 (0.35), residues: 198 loop : 0.69 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 248 TYR 0.019 0.001 TYR C 264 PHE 0.013 0.001 PHE A 154 TRP 0.006 0.001 TRP C 166 HIS 0.002 0.001 HIS E 206 Details of bonding type rmsd covalent geometry : bond 0.00335 (16619) covalent geometry : angle 0.58320 (22458) hydrogen bonds : bond 0.03074 ( 809) hydrogen bonds : angle 4.31894 ( 2330) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 239 time to evaluate : 0.677 Fit side-chains REVERT: A 60 ARG cc_start: 0.5180 (OUTLIER) cc_final: 0.4903 (ptp-170) REVERT: A 221 ASP cc_start: 0.8775 (OUTLIER) cc_final: 0.8514 (t70) REVERT: A 237 ARG cc_start: 0.7586 (OUTLIER) cc_final: 0.7224 (ptt-90) REVERT: D 74 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7579 (mtp-110) REVERT: D 204 THR cc_start: 0.9066 (OUTLIER) cc_final: 0.8793 (t) REVERT: D 285 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8500 (tm) REVERT: D 312 GLU cc_start: 0.7416 (pm20) cc_final: 0.7004 (tm-30) REVERT: E 47 LYS cc_start: 0.8080 (OUTLIER) cc_final: 0.7280 (mptt) REVERT: E 144 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8412 (mttt) REVERT: E 284 GLN cc_start: 0.8499 (tp40) cc_final: 0.7789 (tp40) REVERT: E 288 ASP cc_start: 0.8063 (m-30) cc_final: 0.7628 (m-30) REVERT: F 236 ASN cc_start: 0.8701 (OUTLIER) cc_final: 0.8322 (p0) REVERT: F 273 ASP cc_start: 0.7089 (t0) cc_final: 0.6837 (t0) REVERT: F 288 ASP cc_start: 0.8359 (OUTLIER) cc_final: 0.8112 (m-30) REVERT: G 185 GLN cc_start: 0.6487 (OUTLIER) cc_final: 0.5838 (tt0) REVERT: G 198 LEU cc_start: 0.6686 (OUTLIER) cc_final: 0.6452 (pp) REVERT: G 201 ARG cc_start: 0.4827 (OUTLIER) cc_final: 0.4481 (ptp-110) REVERT: G 223 LEU cc_start: 0.7050 (OUTLIER) cc_final: 0.6731 (tm) REVERT: G 342 LYS cc_start: 0.6991 (pttt) cc_final: 0.6474 (pmtt) outliers start: 68 outliers final: 35 residues processed: 276 average time/residue: 0.5802 time to fit residues: 178.9287 Evaluate side-chains 286 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 237 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 74 ARG Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 118 SER Chi-restraints excluded: chain E residue 144 LYS Chi-restraints excluded: chain E residue 247 ARG Chi-restraints excluded: chain E residue 350 MET Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 113 MET Chi-restraints excluded: chain F residue 177 MET Chi-restraints excluded: chain F residue 236 ASN Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 288 ASP Chi-restraints excluded: chain F residue 312 GLU Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 140 THR Chi-restraints excluded: chain G residue 164 ASP Chi-restraints excluded: chain G residue 169 GLU Chi-restraints excluded: chain G residue 185 GLN Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 201 ARG Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 223 LEU Chi-restraints excluded: chain G residue 267 LEU Chi-restraints excluded: chain G residue 270 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 91 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 127 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 168 optimal weight: 0.4980 chunk 53 optimal weight: 3.9990 chunk 162 optimal weight: 0.0980 chunk 74 optimal weight: 0.8980 chunk 163 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 225 ASN B 91 GLN E 236 ASN F 50 GLN G 193 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.174339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.130202 restraints weight = 33949.174| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 4.47 r_work: 0.3033 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2890 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 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 = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2890 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16619 Z= 0.121 Angle : 0.576 13.133 22458 Z= 0.274 Chirality : 0.042 0.225 2572 Planarity : 0.003 0.049 2818 Dihedral : 11.223 81.087 2446 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.51 % Allowed : 34.56 % Favored : 61.93 % 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: 1.40 (0.19), residues: 2007 helix: 1.53 (0.16), residues: 1097 sheet: -0.89 (0.35), residues: 204 loop : 0.77 (0.25), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 248 TYR 0.018 0.001 TYR C 264 PHE 0.012 0.001 PHE A 154 TRP 0.006 0.001 TRP D 166 HIS 0.002 0.000 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00286 (16619) covalent geometry : angle 0.57594 (22458) hydrogen bonds : bond 0.02962 ( 809) hydrogen bonds : angle 4.28804 ( 2330) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 238 time to evaluate : 0.677 Fit side-chains REVERT: A 60 ARG cc_start: 0.5184 (OUTLIER) cc_final: 0.4905 (ptp-170) REVERT: A 158 ARG cc_start: 0.7069 (mtm180) cc_final: 0.6572 (mtm-85) REVERT: A 221 ASP cc_start: 0.8775 (OUTLIER) cc_final: 0.8505 (t70) REVERT: A 237 ARG cc_start: 0.7594 (OUTLIER) cc_final: 0.7247 (ptt-90) REVERT: D 204 THR cc_start: 0.9050 (OUTLIER) cc_final: 0.8782 (t) REVERT: D 285 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8455 (tm) REVERT: D 312 GLU cc_start: 0.7461 (pm20) cc_final: 0.6999 (tm-30) REVERT: E 47 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7290 (mptt) REVERT: E 144 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8440 (mttt) REVERT: E 284 GLN cc_start: 0.8482 (tp40) cc_final: 0.7611 (tp40) REVERT: E 288 ASP cc_start: 0.8058 (m-30) cc_final: 0.7567 (m-30) REVERT: F 236 ASN cc_start: 0.8664 (OUTLIER) cc_final: 0.8261 (p0) REVERT: F 273 ASP cc_start: 0.7077 (t0) cc_final: 0.6806 (t0) REVERT: F 288 ASP cc_start: 0.8380 (OUTLIER) cc_final: 0.8141 (m-30) REVERT: G 163 MET cc_start: 0.7281 (mmt) cc_final: 0.6884 (mmt) REVERT: G 185 GLN cc_start: 0.6496 (OUTLIER) cc_final: 0.6290 (mp10) REVERT: G 198 LEU cc_start: 0.6641 (OUTLIER) cc_final: 0.6436 (pp) REVERT: G 223 LEU cc_start: 0.7032 (OUTLIER) cc_final: 0.6707 (tm) REVERT: G 311 LYS cc_start: 0.6061 (OUTLIER) cc_final: 0.5623 (mmpt) REVERT: G 342 LYS cc_start: 0.6942 (pttt) cc_final: 0.6433 (pmtt) outliers start: 63 outliers final: 32 residues processed: 273 average time/residue: 0.5744 time to fit residues: 175.0263 Evaluate side-chains 277 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 232 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 118 SER Chi-restraints excluded: chain E residue 144 LYS Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 247 ARG Chi-restraints excluded: chain E residue 350 MET Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 177 MET Chi-restraints excluded: chain F residue 236 ASN Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 288 ASP Chi-restraints excluded: chain F residue 312 GLU Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 140 THR Chi-restraints excluded: chain G residue 185 GLN Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 223 LEU Chi-restraints excluded: chain G residue 267 LEU Chi-restraints excluded: chain G residue 311 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 125 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 120 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 2 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 chunk 182 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 225 ASN B 91 GLN C 50 GLN E 236 ASN F 50 GLN G 53 GLN G 193 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.175179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.130159 restraints weight = 33665.165| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 4.45 r_work: 0.3003 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2883 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2883 r_free = 0.2883 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2883 r_free = 0.2883 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2883 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16619 Z= 0.131 Angle : 0.586 12.923 22458 Z= 0.279 Chirality : 0.042 0.228 2572 Planarity : 0.003 0.050 2818 Dihedral : 11.159 83.506 2446 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.01 % Allowed : 35.51 % Favored : 61.48 % 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: 1.43 (0.19), residues: 2007 helix: 1.55 (0.16), residues: 1097 sheet: -0.71 (0.37), residues: 186 loop : 0.69 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 60 TYR 0.018 0.001 TYR C 264 PHE 0.010 0.001 PHE G 281 TRP 0.006 0.001 TRP F 54 HIS 0.002 0.000 HIS E 206 Details of bonding type rmsd covalent geometry : bond 0.00313 (16619) covalent geometry : angle 0.58649 (22458) hydrogen bonds : bond 0.02968 ( 809) hydrogen bonds : angle 4.26832 ( 2330) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 235 time to evaluate : 0.704 Fit side-chains REVERT: A 158 ARG cc_start: 0.7045 (mtm180) cc_final: 0.6551 (mtm-85) REVERT: A 221 ASP cc_start: 0.8764 (OUTLIER) cc_final: 0.8497 (t70) REVERT: A 237 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.7304 (ptt-90) REVERT: D 74 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.7561 (mtp-110) REVERT: D 204 THR cc_start: 0.9057 (OUTLIER) cc_final: 0.8786 (t) REVERT: D 312 GLU cc_start: 0.7452 (pm20) cc_final: 0.6980 (tm-30) REVERT: E 47 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7252 (mptt) REVERT: E 144 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8439 (mttt) REVERT: E 284 GLN cc_start: 0.8499 (tp40) cc_final: 0.7630 (tp40) REVERT: E 288 ASP cc_start: 0.8073 (m-30) cc_final: 0.7578 (m-30) REVERT: F 236 ASN cc_start: 0.8688 (OUTLIER) cc_final: 0.8264 (p0) REVERT: F 273 ASP cc_start: 0.7047 (t0) cc_final: 0.6787 (t0) REVERT: F 288 ASP cc_start: 0.8387 (OUTLIER) cc_final: 0.8145 (m-30) REVERT: G 163 MET cc_start: 0.7275 (mmt) cc_final: 0.6894 (mmt) REVERT: G 185 GLN cc_start: 0.6525 (OUTLIER) cc_final: 0.6278 (mp10) REVERT: G 223 LEU cc_start: 0.7023 (OUTLIER) cc_final: 0.6701 (tm) REVERT: G 311 LYS cc_start: 0.6039 (OUTLIER) cc_final: 0.5623 (mmpt) REVERT: G 342 LYS cc_start: 0.6942 (pttt) cc_final: 0.6430 (pmtt) outliers start: 54 outliers final: 26 residues processed: 266 average time/residue: 0.5799 time to fit residues: 172.2623 Evaluate side-chains 268 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 231 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 74 ARG Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 144 LYS Chi-restraints excluded: chain E residue 247 ARG Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 177 MET Chi-restraints excluded: chain F residue 236 ASN Chi-restraints excluded: chain F residue 288 ASP Chi-restraints excluded: chain F residue 312 GLU Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 140 THR Chi-restraints excluded: chain G residue 185 GLN Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 223 LEU Chi-restraints excluded: chain G residue 267 LEU Chi-restraints excluded: chain G residue 311 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 106 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 123 optimal weight: 0.0770 chunk 67 optimal weight: 3.9990 chunk 196 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 194 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 225 ASN B 91 GLN C 50 GLN F 50 GLN G 185 GLN G 193 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.176465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.131206 restraints weight = 29756.879| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 3.87 r_work: 0.3026 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2936 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2936 r_free = 0.2936 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2936 r_free = 0.2936 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2936 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16619 Z= 0.120 Angle : 0.576 12.669 22458 Z= 0.273 Chirality : 0.042 0.213 2572 Planarity : 0.003 0.050 2818 Dihedral : 11.074 85.500 2443 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.62 % Allowed : 36.01 % Favored : 61.37 % 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: 1.49 (0.19), residues: 2007 helix: 1.60 (0.16), residues: 1097 sheet: -0.67 (0.37), residues: 187 loop : 0.71 (0.25), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 248 TYR 0.019 0.001 TYR C 264 PHE 0.012 0.001 PHE A 154 TRP 0.006 0.001 TRP D 166 HIS 0.002 0.000 HIS E 206 Details of bonding type rmsd covalent geometry : bond 0.00284 (16619) covalent geometry : angle 0.57599 (22458) hydrogen bonds : bond 0.02878 ( 809) hydrogen bonds : angle 4.22844 ( 2330) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7202.11 seconds wall clock time: 123 minutes 20.34 seconds (7400.34 seconds total)