Starting phenix.real_space_refine on Mon Apr 6 13:28:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lv9_63416/04_2026/9lv9_63416.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lv9_63416/04_2026/9lv9_63416.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lv9_63416/04_2026/9lv9_63416.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lv9_63416/04_2026/9lv9_63416.map" model { file = "/net/cci-nas-00/data/ceres_data/9lv9_63416/04_2026/9lv9_63416.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lv9_63416/04_2026/9lv9_63416.cif" } resolution = 3.17 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= 0.009 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 24 5.49 5 Mg 8 5.21 5 S 93 5.16 5 C 12005 2.51 5 N 3231 2.21 5 O 3660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19021 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 2311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2311 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 13, 'TRANS': 279} Chain breaks: 1 Chain: "B" Number of atoms: 2338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2338 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 14, 'TRANS': 282} Chain breaks: 1 Chain: "C" Number of atoms: 2338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2338 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 13, 'TRANS': 282} Chain breaks: 1 Chain: "D" Number of atoms: 2355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2355 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 14, 'TRANS': 284} Chain breaks: 1 Chain: "E" Number of atoms: 2330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2330 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 13, 'TRANS': 281} Chain breaks: 1 Chain: "F" Number of atoms: 2327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2327 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 13, 'TRANS': 281} Chain breaks: 1 Chain: "G" Number of atoms: 2346 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 296, 2338 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 13, 'TRANS': 282} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 296, 2338 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 13, 'TRANS': 282} Chain breaks: 1 bond proxies already assigned to first conformer: 2366 Chain: "H" Number of atoms: 2325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2325 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 13, 'TRANS': 280} Chain breaks: 1 Chain: "I" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 95 Classifications: {'peptide': 19} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'TRANS': 18} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'UNK:plan-1': 19} Unresolved non-hydrogen planarities: 19 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.65, per 1000 atoms: 0.24 Number of scatterers: 19021 At special positions: 0 Unit cell: (138.17, 136.53, 133.66, 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 93 16.00 P 24 15.00 Mg 8 11.99 O 3660 8.00 N 3231 7.00 C 12005 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: 1.65 Conformation dependent library (CDL) restraints added in 721.8 milliseconds 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4528 Finding SS restraints... Secondary structure from input PDB file: 145 helices and 8 sheets defined 63.8% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 43 through 61 Processing helix chain 'A' and resid 62 through 66 removed outlier: 3.751A pdb=" N GLU A 66 " --> pdb=" O ALA A 63 " (cutoff:3.500A) 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 113 through 118 removed outlier: 3.877A pdb=" N TYR A 117 " --> pdb=" O MET A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 150 removed outlier: 3.522A pdb=" N SER A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 163 removed outlier: 3.842A pdb=" N ILE A 162 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N MET A 163 " --> pdb=" O MET A 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 158 through 163' Processing helix chain 'A' and resid 168 through 184 removed outlier: 3.563A pdb=" N LYS A 172 " --> pdb=" O GLY A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 198 removed outlier: 3.789A 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 242 through 248 removed outlier: 3.515A pdb=" N ARG A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 271 Processing helix chain 'A' and resid 282 through 290 removed outlier: 4.029A pdb=" N ILE A 286 " --> pdb=" O ASP A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 310 Processing helix chain 'A' and resid 310 through 319 Processing helix chain 'A' and resid 340 through 348 removed outlier: 3.606A pdb=" N LYS A 347 " --> pdb=" O ASP A 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 61 Processing helix chain 'B' and resid 62 through 67 removed outlier: 3.553A pdb=" N ALA B 65 " --> pdb=" O PRO B 62 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU B 66 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL B 67 " --> pdb=" O LEU B 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 62 through 67' Processing helix chain 'B' and resid 70 through 78 Processing helix chain 'B' and resid 82 through 86 Processing helix chain 'B' and resid 89 through 93 Processing helix chain 'B' and resid 96 through 113 removed outlier: 5.291A pdb=" N TYR B 109 " --> pdb=" O GLU B 105 " (cutoff:3.500A) Proline residue: B 110 - end of helix Processing helix chain 'B' and resid 113 through 118 removed outlier: 3.858A pdb=" N TYR B 117 " --> pdb=" O MET B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 150 removed outlier: 3.632A pdb=" N SER B 150 " --> pdb=" O LEU B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 184 Processing helix chain 'B' and resid 193 through 198 removed outlier: 3.865A 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 removed outlier: 3.696A pdb=" N ARG B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 271 Processing helix chain 'B' and resid 282 through 290 removed outlier: 4.049A pdb=" N ILE B 286 " --> pdb=" O ASP B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 310 Processing helix chain 'B' and resid 310 through 319 Processing helix chain 'B' and resid 340 through 348 removed outlier: 3.687A pdb=" N PHE B 344 " --> pdb=" O LYS B 340 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS B 347 " --> pdb=" O ASP B 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 61 Processing helix chain 'C' and resid 62 through 67 removed outlier: 3.854A pdb=" N GLU C 66 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL C 67 " --> pdb=" O LEU C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 78 Processing helix chain 'C' and resid 82 through 86 Processing helix chain 'C' and resid 96 through 107 Processing helix chain 'C' and resid 107 through 113 Processing helix chain 'C' and resid 116 through 120 removed outlier: 4.444A pdb=" N ASN C 119 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER C 120 " --> pdb=" O TYR C 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 116 through 120' Processing helix chain 'C' and resid 138 through 150 removed outlier: 3.649A pdb=" N SER C 150 " --> pdb=" O LEU C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 163 Processing helix chain 'C' and resid 168 through 184 removed outlier: 3.539A pdb=" N LYS C 172 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 198 removed outlier: 3.942A 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 247 Processing helix chain 'C' and resid 259 through 271 Processing helix chain 'C' and resid 282 through 290 removed outlier: 4.289A pdb=" N ILE C 286 " --> pdb=" O ASP C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 319 removed outlier: 5.173A pdb=" N GLU C 312 " --> pdb=" O ASP C 308 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N TYR C 313 " --> pdb=" O ALA C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 348 removed outlier: 3.930A pdb=" N PHE C 344 " --> pdb=" O LYS C 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 61 Processing helix chain 'D' and resid 62 through 67 removed outlier: 4.215A pdb=" N GLU D 66 " --> pdb=" O ALA D 63 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL D 67 " --> pdb=" O LEU D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 78 Processing helix chain 'D' and resid 82 through 86 Processing helix chain 'D' and resid 89 through 93 Processing helix chain 'D' and resid 96 through 113 removed outlier: 5.052A pdb=" N TYR D 109 " --> pdb=" O GLU D 105 " (cutoff:3.500A) Proline residue: D 110 - end of helix Processing helix chain 'D' and resid 113 through 118 removed outlier: 4.043A pdb=" N TYR D 117 " --> pdb=" O MET D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 149 Processing helix chain 'D' and resid 158 through 163 removed outlier: 3.619A pdb=" N ILE D 162 " --> pdb=" O ARG D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 184 Processing helix chain 'D' and resid 193 through 198 removed outlier: 4.133A 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 removed outlier: 3.620A pdb=" N ARG D 248 " --> pdb=" O ALA D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 271 Processing helix chain 'D' and resid 282 through 290 removed outlier: 4.223A pdb=" N ILE D 286 " --> pdb=" O ASP D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 319 removed outlier: 5.045A pdb=" N GLU D 312 " --> pdb=" O ASP D 308 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N TYR D 313 " --> pdb=" O ALA D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 348 removed outlier: 4.159A pdb=" N PHE D 344 " --> pdb=" O LYS D 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 61 Processing helix chain 'E' and resid 62 through 67 removed outlier: 3.962A pdb=" N GLU E 66 " --> pdb=" O ALA E 63 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL E 67 " --> pdb=" O LEU E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 78 Processing helix chain 'E' and resid 82 through 86 Processing helix chain 'E' and resid 96 through 107 Processing helix chain 'E' and resid 107 through 113 Processing helix chain 'E' and resid 120 through 124 removed outlier: 4.040A pdb=" N GLN E 124 " --> pdb=" O PRO E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 149 Processing helix chain 'E' and resid 168 through 184 Processing helix chain 'E' and resid 193 through 198 removed outlier: 4.223A pdb=" N PHE E 197 " --> pdb=" O GLN E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 221 Processing helix chain 'E' and resid 242 through 247 Processing helix chain 'E' and resid 259 through 271 Processing helix chain 'E' and resid 282 through 290 removed outlier: 4.336A 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 310 through 320 Processing helix chain 'E' and resid 340 through 348 removed outlier: 3.765A pdb=" N LYS E 347 " --> pdb=" O ASP E 343 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 61 Processing helix chain 'F' and resid 62 through 67 removed outlier: 4.017A pdb=" N GLU F 66 " --> pdb=" O ALA F 63 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL F 67 " --> pdb=" O LEU F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 78 Processing helix chain 'F' and resid 82 through 86 Processing helix chain 'F' and resid 89 through 93 Processing helix chain 'F' and resid 96 through 107 Processing helix chain 'F' and resid 107 through 113 Processing helix chain 'F' and resid 120 through 124 removed outlier: 4.063A pdb=" N GLN F 124 " --> pdb=" O PRO F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 149 Processing helix chain 'F' and resid 158 through 163 removed outlier: 3.566A pdb=" N ILE F 162 " --> pdb=" O ARG F 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 184 Processing helix chain 'F' and resid 193 through 198 removed outlier: 4.056A 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 removed outlier: 3.725A pdb=" N ARG F 248 " --> pdb=" O ALA F 244 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 271 Processing helix chain 'F' and resid 283 through 290 Processing helix chain 'F' and resid 294 through 310 Processing helix chain 'F' and resid 310 through 319 Processing helix chain 'F' and resid 340 through 348 removed outlier: 3.753A pdb=" N PHE F 344 " --> pdb=" O LYS F 340 " (cutoff:3.500A) Processing helix chain 'G' and resid 43 through 61 Processing helix chain 'G' and resid 62 through 66 removed outlier: 4.108A pdb=" N GLU G 66 " --> pdb=" O ALA G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 78 Processing helix chain 'G' and resid 82 through 86 Processing helix chain 'G' and resid 96 through 108 Processing helix chain 'G' and resid 108 through 113 Processing helix chain 'G' and resid 138 through 149 Processing helix chain 'G' and resid 158 through 163 Processing helix chain 'G' and resid 168 through 184 Processing helix chain 'G' and resid 193 through 198 removed outlier: 4.309A pdb=" N PHE G 197 " --> pdb=" O GLN G 193 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 221 Processing helix chain 'G' and resid 237 through 241 removed outlier: 3.655A pdb=" N ASP G 240 " --> pdb=" O ARG G 237 " (cutoff:3.500A) Processing helix chain 'G' and resid 242 through 248 removed outlier: 3.690A pdb=" N ARG G 248 " --> pdb=" O ALA G 244 " (cutoff:3.500A) Processing helix chain 'G' and resid 259 through 271 Processing helix chain 'G' and resid 283 through 290 removed outlier: 3.727A pdb=" N THR G 290 " --> pdb=" O ILE G 286 " (cutoff:3.500A) Processing helix chain 'G' and resid 294 through 310 Processing helix chain 'G' and resid 310 through 320 Processing helix chain 'G' and resid 340 through 348 removed outlier: 3.693A pdb=" N PHE G 344 " --> pdb=" O LYS G 340 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS G 347 " --> pdb=" O ASP G 343 " (cutoff:3.500A) Processing helix chain 'H' and resid 44 through 61 Processing helix chain 'H' and resid 62 through 66 removed outlier: 3.904A pdb=" N GLU H 66 " --> pdb=" O ALA H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 78 Processing helix chain 'H' and resid 82 through 86 Processing helix chain 'H' and resid 89 through 93 Processing helix chain 'H' and resid 96 through 107 Processing helix chain 'H' and resid 107 through 113 Processing helix chain 'H' and resid 116 through 120 removed outlier: 4.085A pdb=" N ASN H 119 " --> pdb=" O VAL H 116 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER H 120 " --> pdb=" O TYR H 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 116 through 120' Processing helix chain 'H' and resid 138 through 150 Processing helix chain 'H' and resid 158 through 163 removed outlier: 3.949A pdb=" N ILE H 162 " --> pdb=" O ARG H 158 " (cutoff:3.500A) Processing helix chain 'H' and resid 168 through 184 Processing helix chain 'H' and resid 193 through 198 removed outlier: 3.998A pdb=" N PHE H 197 " --> pdb=" O GLN H 193 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 226 removed outlier: 3.549A pdb=" N ASP H 221 " --> pdb=" O MET H 217 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY H 222 " --> pdb=" O THR H 218 " (cutoff:3.500A) Processing helix chain 'H' and resid 242 through 247 Processing helix chain 'H' and resid 259 through 271 Processing helix chain 'H' and resid 282 through 290 removed outlier: 4.165A pdb=" N ILE H 286 " --> pdb=" O ASP H 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 294 through 320 removed outlier: 5.341A pdb=" N GLU H 312 " --> pdb=" O ASP H 308 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N TYR H 313 " --> pdb=" O ALA H 309 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN H 319 " --> pdb=" O LYS H 315 " (cutoff:3.500A) Processing helix chain 'H' and resid 340 through 348 removed outlier: 3.593A pdb=" N PHE H 344 " --> pdb=" O LYS H 340 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 81 removed outlier: 3.651A pdb=" N PHE A 154 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ASN A 153 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N PHE A 190 " --> pdb=" O ASN A 153 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ILE A 155 " --> pdb=" O PHE A 190 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ASP A 192 " --> pdb=" O ILE A 155 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N ILE A 157 " --> pdb=" O ASP A 192 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N CYS A 187 " --> pdb=" O MET A 230 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ILE A 232 " --> pdb=" O CYS A 187 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE A 189 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N ALA A 234 " --> pdb=" O ILE A 189 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ILE A 191 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N GLY A 128 " --> pdb=" O LYS A 251 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N PHE A 253 " --> pdb=" O GLY A 128 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU A 130 " --> pdb=" O PHE A 253 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 80 through 81 removed outlier: 3.633A pdb=" N PHE B 154 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N ASN B 153 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N PHE B 190 " --> pdb=" O ASN B 153 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ILE B 155 " --> pdb=" O PHE B 190 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ASP B 192 " --> pdb=" O ILE B 155 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ILE B 157 " --> pdb=" O ASP B 192 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N CYS B 187 " --> pdb=" O MET B 230 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N ILE B 232 " --> pdb=" O CYS B 187 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ILE B 189 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N ALA B 234 " --> pdb=" O ILE B 189 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE B 191 " --> pdb=" O ALA B 234 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLY B 128 " --> pdb=" O LYS B 251 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N PHE B 253 " --> pdb=" O GLY B 128 " (cutoff:3.500A) removed outlier: 6.446A 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: 3.696A pdb=" N PHE C 154 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ASN C 153 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N PHE C 190 " --> pdb=" O ASN C 153 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE C 155 " --> pdb=" O PHE C 190 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ASP C 192 " --> pdb=" O ILE C 155 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N ILE C 157 " --> pdb=" O ASP C 192 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA C 234 " --> pdb=" O ILE C 191 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N GLY C 128 " --> pdb=" O LYS C 251 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N PHE C 253 " --> pdb=" O GLY C 128 " (cutoff:3.500A) removed outlier: 6.613A 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: 3.794A pdb=" N PHE D 154 " --> pdb=" O VAL D 81 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET D 230 " --> pdb=" O CYS D 187 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA D 234 " --> pdb=" O ILE D 191 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLY D 128 " --> pdb=" O LYS D 251 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N PHE D 253 " --> pdb=" O GLY D 128 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU D 130 " --> pdb=" O PHE D 253 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 153 through 157 removed outlier: 4.173A pdb=" N ASP E 192 " --> pdb=" O ILE E 157 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA E 234 " --> pdb=" O ILE E 191 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N VAL E 129 " --> pdb=" O GLY E 233 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N THR E 235 " --> pdb=" O VAL E 129 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LEU E 131 " --> pdb=" O THR E 235 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLY E 128 " --> pdb=" O LYS E 251 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N PHE E 253 " --> pdb=" O GLY E 128 " (cutoff:3.500A) removed outlier: 6.380A 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: 3.779A pdb=" N PHE F 154 " --> pdb=" O VAL F 81 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N ASN F 153 " --> pdb=" O ILE F 188 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N PHE F 190 " --> pdb=" O ASN F 153 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ILE F 155 " --> pdb=" O PHE F 190 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ASP F 192 " --> pdb=" O ILE F 155 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N CYS F 187 " --> pdb=" O MET F 230 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ILE F 232 " --> pdb=" O CYS F 187 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ILE F 189 " --> pdb=" O ILE F 232 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N ALA F 234 " --> pdb=" O ILE F 189 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ILE F 191 " --> pdb=" O ALA F 234 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N GLY F 128 " --> pdb=" O LYS F 251 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N PHE F 253 " --> pdb=" O GLY F 128 " (cutoff:3.500A) removed outlier: 6.447A 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: 3.673A pdb=" N PHE G 154 " --> pdb=" O VAL G 81 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA G 234 " --> pdb=" O ILE G 191 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLY G 128 " --> pdb=" O LYS G 251 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N PHE G 253 " --> pdb=" O GLY G 128 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU G 130 " --> pdb=" O PHE G 253 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 153 through 155 removed outlier: 6.099A pdb=" N ASN H 153 " --> pdb=" O ILE H 188 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N PHE H 190 " --> pdb=" O ASN H 153 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ILE H 155 " --> pdb=" O PHE H 190 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ASP H 192 " --> pdb=" O ILE H 155 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N CYS H 187 " --> pdb=" O MET H 230 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ILE H 232 " --> pdb=" O CYS H 187 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE H 189 " --> pdb=" O ILE H 232 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N ALA H 234 " --> pdb=" O ILE H 189 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ILE H 191 " --> pdb=" O ALA H 234 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N GLY H 128 " --> pdb=" O LYS H 251 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N PHE H 253 " --> pdb=" O GLY H 128 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU H 130 " --> pdb=" O PHE H 253 " (cutoff:3.500A) 935 hydrogen bonds defined for protein. 2678 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: 2.93 Time building geometry restraints manager: 2.18 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: 6021 1.34 - 1.46: 3213 1.46 - 1.58: 9901 1.58 - 1.70: 30 1.70 - 1.82: 162 Bond restraints: 19327 Sorted by residual: bond pdb=" N ASP E 273 " pdb=" CA ASP E 273 " ideal model delta sigma weight residual 1.457 1.483 -0.025 1.29e-02 6.01e+03 3.84e+00 bond pdb=" N ASP H 273 " pdb=" CA ASP H 273 " ideal model delta sigma weight residual 1.457 1.478 -0.020 1.29e-02 6.01e+03 2.48e+00 bond pdb=" CB PHE H 281 " pdb=" CG PHE H 281 " ideal model delta sigma weight residual 1.502 1.537 -0.035 2.30e-02 1.89e+03 2.25e+00 bond pdb=" C ARG G 199 " pdb=" O ARG G 199 " ideal model delta sigma weight residual 1.234 1.216 0.018 1.24e-02 6.50e+03 2.12e+00 bond pdb=" C ASP G 195 " pdb=" O ASP G 195 " ideal model delta sigma weight residual 1.237 1.221 0.016 1.17e-02 7.31e+03 1.89e+00 ... (remaining 19322 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.10: 25869 3.10 - 6.21: 201 6.21 - 9.31: 24 9.31 - 12.42: 2 12.42 - 15.52: 1 Bond angle restraints: 26097 Sorted by residual: angle pdb=" N ASN A 239 " pdb=" CA ASN A 239 " pdb=" C ASN A 239 " ideal model delta sigma weight residual 111.28 116.01 -4.73 1.09e+00 8.42e-01 1.88e+01 angle pdb=" N ASN E 239 " pdb=" CA ASN E 239 " pdb=" C ASN E 239 " ideal model delta sigma weight residual 111.28 115.57 -4.29 1.09e+00 8.42e-01 1.55e+01 angle pdb=" N THR E 235 " pdb=" CA THR E 235 " pdb=" C THR E 235 " ideal model delta sigma weight residual 109.24 115.65 -6.41 1.67e+00 3.59e-01 1.47e+01 angle pdb=" N MET H 230 " pdb=" CA MET H 230 " pdb=" C MET H 230 " ideal model delta sigma weight residual 109.24 114.98 -5.74 1.51e+00 4.39e-01 1.45e+01 angle pdb=" N ARG H 228 " pdb=" CA ARG H 228 " pdb=" C ARG H 228 " ideal model delta sigma weight residual 112.26 117.27 -5.01 1.32e+00 5.74e-01 1.44e+01 ... (remaining 26092 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.01: 10050 17.01 - 34.02: 1494 34.02 - 51.03: 475 51.03 - 68.05: 99 68.05 - 85.06: 35 Dihedral angle restraints: 12153 sinusoidal: 5200 harmonic: 6953 Sorted by residual: 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 -158.38 -21.62 0 5.00e+00 4.00e-02 1.87e+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 -158.49 -21.51 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA LEU E 184 " pdb=" C LEU E 184 " pdb=" N GLN E 185 " pdb=" CA GLN E 185 " ideal model delta harmonic sigma weight residual -180.00 -160.42 -19.58 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 12150 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 2611 0.068 - 0.136: 347 0.136 - 0.204: 16 0.204 - 0.272: 4 0.272 - 0.339: 3 Chirality restraints: 2981 Sorted by residual: chirality pdb=" CG LEU E 267 " pdb=" CB LEU E 267 " pdb=" CD1 LEU E 267 " pdb=" CD2 LEU E 267 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.88e+00 chirality pdb=" CG LEU H 307 " pdb=" CB LEU H 307 " pdb=" CD1 LEU H 307 " pdb=" CD2 LEU H 307 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" CA ASN H 225 " pdb=" N ASN H 225 " pdb=" C ASN H 225 " pdb=" CB ASN H 225 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.22e+00 ... (remaining 2978 not shown) Planarity restraints: 3275 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY F 133 " 0.068 5.00e-02 4.00e+02 1.03e-01 1.71e+01 pdb=" N PRO F 134 " -0.179 5.00e-02 4.00e+02 pdb=" CA PRO F 134 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO F 134 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER F 120 " 0.058 5.00e-02 4.00e+02 8.91e-02 1.27e+01 pdb=" N PRO F 121 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO F 121 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO F 121 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 61 " 0.045 5.00e-02 4.00e+02 6.85e-02 7.50e+00 pdb=" N PRO B 62 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO B 62 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 62 " 0.038 5.00e-02 4.00e+02 ... (remaining 3272 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 191 2.62 - 3.19: 16270 3.19 - 3.76: 32313 3.76 - 4.33: 43321 4.33 - 4.90: 71512 Nonbonded interactions: 163607 Sorted by model distance: nonbonded pdb=" O3G ATP H 401 " pdb="MG MG H 402 " model vdw 2.049 2.170 nonbonded pdb=" OG1 THR H 140 " pdb="MG MG H 402 " model vdw 2.060 2.170 nonbonded pdb=" OG1 THR G 140 " pdb="MG MG G 402 " model vdw 2.067 2.170 nonbonded pdb=" OG1 THR C 140 " pdb="MG MG C 402 " model vdw 2.080 2.170 nonbonded pdb=" O3G ATP G 401 " pdb="MG MG G 402 " model vdw 2.080 2.170 ... (remaining 163602 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 43 through 73 or resid 75 through 402)) selection = (chain 'B' and (resid 43 through 73 or resid 75 through 319 or resid 337 through \ 402)) selection = (chain 'C' and (resid 43 through 73 or resid 75 through 319 or resid 337 through \ 349 or resid 401 through 402)) selection = (chain 'D' and (resid 43 through 73 or resid 75 through 319 or resid 337 through \ 349 or resid 401 through 402)) selection = (chain 'E' and (resid 43 through 73 or resid 75 through 319 or resid 337 through \ 402)) selection = (chain 'F' and (resid 43 through 73 or resid 75 through 319 or resid 337 through \ 349 or resid 401 through 402)) selection = (chain 'G' and (resid 43 through 73 or resid 75 through 319 or resid 337 through \ 349 or resid 401 through 402)) selection = (chain 'H' and (resid 43 through 73 or resid 75 through 319 or resid 337 through \ 349 or resid 401 through 402)) } 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=0.50 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: 8.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.190 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 17.330 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19327 Z= 0.167 Angle : 0.721 15.522 26097 Z= 0.370 Chirality : 0.046 0.339 2981 Planarity : 0.005 0.103 3275 Dihedral : 18.037 85.056 7625 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.10 % Allowed : 21.25 % Favored : 78.66 % 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: 0.31 (0.17), residues: 2334 helix: 0.36 (0.14), residues: 1322 sheet: -0.61 (0.34), residues: 247 loop : 0.57 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG H 337 TYR 0.030 0.002 TYR H 313 PHE 0.014 0.002 PHE A 197 TRP 0.008 0.001 TRP G 166 HIS 0.004 0.001 HIS E 206 Details of bonding type rmsd covalent geometry : bond 0.00336 (19327) covalent geometry : angle 0.72110 (26097) hydrogen bonds : bond 0.14987 ( 935) hydrogen bonds : angle 5.64604 ( 2678) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 321 time to evaluate : 0.777 Fit side-chains revert: symmetry clash REVERT: A 191 ILE cc_start: 0.7880 (mt) cc_final: 0.7678 (pt) REVERT: B 124 GLN cc_start: 0.8150 (pm20) cc_final: 0.7927 (pm20) REVERT: C 47 LYS cc_start: 0.8548 (mtpp) cc_final: 0.8324 (mttp) REVERT: D 221 ASP cc_start: 0.8441 (t0) cc_final: 0.8140 (m-30) REVERT: E 221 ASP cc_start: 0.7692 (t0) cc_final: 0.7429 (t0) REVERT: G 124 GLN cc_start: 0.7900 (pm20) cc_final: 0.7543 (pm20) REVERT: H 312 GLU cc_start: 0.6809 (tp30) cc_final: 0.6441 (tt0) REVERT: H 337 ARG cc_start: 0.8220 (ttp80) cc_final: 0.8017 (ptm-80) outliers start: 2 outliers final: 1 residues processed: 322 average time/residue: 0.1513 time to fit residues: 72.8926 Evaluate side-chains 285 residues out of total 2083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 284 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 184 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.0870 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 10.0000 overall best weight: 1.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 GLN B 236 ASN C 50 GLN C 53 GLN D 236 ASN E 236 ASN F 284 GLN G 50 GLN ** G 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 GLN H 206 HIS H 289 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.151033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.112560 restraints weight = 33678.446| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.76 r_work: 0.3156 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3154 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3154 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 19327 Z= 0.177 Angle : 0.565 11.542 26097 Z= 0.279 Chirality : 0.041 0.187 2981 Planarity : 0.004 0.076 3275 Dihedral : 11.103 89.775 2828 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.87 % Allowed : 20.14 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.18), residues: 2334 helix: 1.08 (0.15), residues: 1331 sheet: -0.84 (0.32), residues: 255 loop : 0.86 (0.24), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 337 TYR 0.012 0.001 TYR C 167 PHE 0.016 0.001 PHE G 178 TRP 0.007 0.001 TRP E 220 HIS 0.002 0.001 HIS E 206 Details of bonding type rmsd covalent geometry : bond 0.00418 (19327) covalent geometry : angle 0.56537 (26097) hydrogen bonds : bond 0.03555 ( 935) hydrogen bonds : angle 4.33275 ( 2678) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 313 time to evaluate : 0.774 Fit side-chains REVERT: B 124 GLN cc_start: 0.8361 (pm20) cc_final: 0.8143 (pm20) REVERT: C 47 LYS cc_start: 0.8553 (mtpp) cc_final: 0.8321 (mttp) REVERT: C 342 LYS cc_start: 0.8679 (mmmt) cc_final: 0.8418 (tptt) REVERT: D 221 ASP cc_start: 0.8460 (t0) cc_final: 0.8087 (m-30) REVERT: D 262 GLN cc_start: 0.7586 (mp10) cc_final: 0.7153 (mp10) REVERT: D 337 ARG cc_start: 0.7799 (tmm-80) cc_final: 0.7565 (tmm-80) REVERT: E 74 ARG cc_start: 0.7714 (mtm-85) cc_final: 0.7399 (mtp85) REVERT: F 284 GLN cc_start: 0.7882 (tp40) cc_final: 0.7492 (tp-100) REVERT: G 124 GLN cc_start: 0.8076 (pm20) cc_final: 0.7681 (pm20) REVERT: G 289 ASN cc_start: 0.8891 (m110) cc_final: 0.8686 (m110) REVERT: G 337 ARG cc_start: 0.8639 (ttp80) cc_final: 0.8150 (ptm160) outliers start: 39 outliers final: 14 residues processed: 338 average time/residue: 0.1492 time to fit residues: 76.8062 Evaluate side-chains 296 residues out of total 2083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 282 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain F residue 113 MET Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 224 LEU Chi-restraints excluded: chain H residue 307 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 64 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 205 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 67 optimal weight: 0.9980 chunk 145 optimal weight: 20.0000 chunk 165 optimal weight: 0.5980 chunk 134 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 GLN C 289 ASN ** G 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 GLN H 289 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.153290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.115201 restraints weight = 33801.579| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.77 r_work: 0.3171 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3171 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3171 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19327 Z= 0.128 Angle : 0.517 10.581 26097 Z= 0.253 Chirality : 0.040 0.157 2981 Planarity : 0.003 0.061 3275 Dihedral : 10.885 87.915 2826 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.69 % Allowed : 20.53 % Favored : 76.79 % 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: 1.39 (0.18), residues: 2334 helix: 1.45 (0.15), residues: 1314 sheet: -0.80 (0.33), residues: 242 loop : 0.83 (0.23), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 337 TYR 0.009 0.001 TYR C 167 PHE 0.011 0.001 PHE G 178 TRP 0.007 0.001 TRP B 166 HIS 0.002 0.001 HIS D 104 Details of bonding type rmsd covalent geometry : bond 0.00306 (19327) covalent geometry : angle 0.51688 (26097) hydrogen bonds : bond 0.03142 ( 935) hydrogen bonds : angle 4.18033 ( 2678) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 294 time to evaluate : 0.764 Fit side-chains REVERT: A 196 SER cc_start: 0.8528 (OUTLIER) cc_final: 0.8284 (m) REVERT: C 47 LYS cc_start: 0.8557 (mtpp) cc_final: 0.8327 (mttp) REVERT: C 80 ILE cc_start: 0.9133 (OUTLIER) cc_final: 0.8872 (tt) REVERT: C 342 LYS cc_start: 0.8717 (mmmt) cc_final: 0.8507 (tptp) REVERT: D 102 ASP cc_start: 0.8942 (t70) cc_final: 0.8281 (t0) REVERT: D 221 ASP cc_start: 0.8375 (t0) cc_final: 0.8007 (t0) REVERT: D 262 GLN cc_start: 0.7575 (mp10) cc_final: 0.7060 (mp10) REVERT: D 337 ARG cc_start: 0.7805 (tmm-80) cc_final: 0.7545 (tmm-80) REVERT: F 284 GLN cc_start: 0.7919 (tp40) cc_final: 0.7531 (tp-100) REVERT: G 106 SER cc_start: 0.8117 (m) cc_final: 0.7881 (p) REVERT: G 337 ARG cc_start: 0.8577 (ttp80) cc_final: 0.8292 (ptm160) outliers start: 56 outliers final: 19 residues processed: 336 average time/residue: 0.1354 time to fit residues: 70.2239 Evaluate side-chains 305 residues out of total 2083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 284 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain F residue 113 MET Chi-restraints excluded: chain F residue 288 ASP Chi-restraints excluded: chain H residue 70 ASP Chi-restraints excluded: chain H residue 127 SER Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 218 THR Chi-restraints excluded: chain H residue 224 LEU Chi-restraints excluded: chain H residue 235 THR Chi-restraints excluded: chain H residue 307 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 156 optimal weight: 0.0370 chunk 187 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 149 optimal weight: 5.9990 chunk 219 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 201 optimal weight: 3.9990 chunk 170 optimal weight: 0.5980 chunk 104 optimal weight: 0.8980 chunk 87 optimal weight: 7.9990 overall best weight: 1.1060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 236 ASN G 53 GLN ** G 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 GLN H 289 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.151926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.113921 restraints weight = 35737.315| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.83 r_work: 0.3160 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3157 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3157 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19327 Z= 0.127 Angle : 0.513 10.784 26097 Z= 0.249 Chirality : 0.040 0.214 2981 Planarity : 0.003 0.054 3275 Dihedral : 10.662 86.313 2826 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.64 % Allowed : 20.38 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.18), residues: 2334 helix: 1.58 (0.15), residues: 1318 sheet: -1.01 (0.32), residues: 259 loop : 1.02 (0.24), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 337 TYR 0.006 0.001 TYR C 167 PHE 0.011 0.001 PHE G 178 TRP 0.006 0.001 TRP B 166 HIS 0.002 0.000 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00304 (19327) covalent geometry : angle 0.51264 (26097) hydrogen bonds : bond 0.02923 ( 935) hydrogen bonds : angle 4.10958 ( 2678) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 298 time to evaluate : 0.799 Fit side-chains REVERT: A 196 SER cc_start: 0.8511 (OUTLIER) cc_final: 0.8280 (m) REVERT: B 80 ILE cc_start: 0.8801 (OUTLIER) cc_final: 0.8535 (tt) REVERT: C 47 LYS cc_start: 0.8551 (mtpp) cc_final: 0.8314 (mttp) REVERT: C 80 ILE cc_start: 0.9148 (OUTLIER) cc_final: 0.8885 (tt) REVERT: C 342 LYS cc_start: 0.8738 (mmmt) cc_final: 0.8536 (tptp) REVERT: D 102 ASP cc_start: 0.8938 (t70) cc_final: 0.8310 (t0) REVERT: D 221 ASP cc_start: 0.8363 (t0) cc_final: 0.7981 (t70) REVERT: D 337 ARG cc_start: 0.7804 (tmm-80) cc_final: 0.7537 (tmm-80) REVERT: F 284 GLN cc_start: 0.7909 (tp40) cc_final: 0.7494 (tp-100) REVERT: G 106 SER cc_start: 0.8127 (m) cc_final: 0.7889 (p) REVERT: G 288 ASP cc_start: 0.8221 (m-30) cc_final: 0.7670 (m-30) REVERT: G 289 ASN cc_start: 0.8951 (m110) cc_final: 0.8677 (m110) REVERT: H 224 LEU cc_start: 0.7438 (OUTLIER) cc_final: 0.7059 (tp) outliers start: 55 outliers final: 26 residues processed: 337 average time/residue: 0.1394 time to fit residues: 72.2569 Evaluate side-chains 307 residues out of total 2083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 277 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain F residue 113 MET Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 288 ASP Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain H residue 127 SER Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 224 LEU Chi-restraints excluded: chain H residue 235 THR Chi-restraints excluded: chain H residue 307 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 133 optimal weight: 0.7980 chunk 146 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 176 optimal weight: 10.0000 chunk 100 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 160 optimal weight: 1.9990 chunk 216 optimal weight: 0.9990 chunk 230 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 262 GLN ** G 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 GLN H 289 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.150859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.113199 restraints weight = 27444.073| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.36 r_work: 0.3154 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3012 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3012 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19327 Z= 0.163 Angle : 0.536 10.487 26097 Z= 0.260 Chirality : 0.041 0.193 2981 Planarity : 0.003 0.050 3275 Dihedral : 10.619 86.512 2826 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.07 % Allowed : 20.62 % Favored : 76.31 % 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: 1.54 (0.18), residues: 2334 helix: 1.54 (0.15), residues: 1335 sheet: -0.61 (0.34), residues: 224 loop : 0.86 (0.24), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 44 TYR 0.008 0.001 TYR G 109 PHE 0.016 0.001 PHE G 178 TRP 0.007 0.001 TRP D 220 HIS 0.002 0.001 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00398 (19327) covalent geometry : angle 0.53567 (26097) hydrogen bonds : bond 0.03044 ( 935) hydrogen bonds : angle 4.14286 ( 2678) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 291 time to evaluate : 0.752 Fit side-chains REVERT: A 156 SER cc_start: 0.9069 (t) cc_final: 0.8692 (p) REVERT: A 196 SER cc_start: 0.8543 (OUTLIER) cc_final: 0.8330 (m) REVERT: B 80 ILE cc_start: 0.8935 (OUTLIER) cc_final: 0.8651 (tt) REVERT: C 47 LYS cc_start: 0.8583 (mtpp) cc_final: 0.8350 (mttp) REVERT: C 80 ILE cc_start: 0.9223 (OUTLIER) cc_final: 0.8943 (tt) REVERT: C 200 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8329 (tm-30) REVERT: C 314 ILE cc_start: 0.8637 (OUTLIER) cc_final: 0.7956 (tp) REVERT: D 58 VAL cc_start: 0.8438 (t) cc_final: 0.8092 (m) REVERT: D 102 ASP cc_start: 0.9012 (t70) cc_final: 0.8406 (t0) REVERT: D 221 ASP cc_start: 0.8517 (t0) cc_final: 0.8214 (t70) REVERT: D 262 GLN cc_start: 0.7672 (mp10) cc_final: 0.7093 (mp10) REVERT: D 337 ARG cc_start: 0.7841 (tmm-80) cc_final: 0.7536 (tmm-80) REVERT: E 224 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8283 (mm) REVERT: F 284 GLN cc_start: 0.7934 (tp40) cc_final: 0.7524 (tp-100) REVERT: F 312 GLU cc_start: 0.7774 (mp0) cc_final: 0.7574 (mp0) REVERT: G 106 SER cc_start: 0.8225 (m) cc_final: 0.7929 (p) REVERT: G 288 ASP cc_start: 0.8301 (m-30) cc_final: 0.7764 (m-30) REVERT: H 224 LEU cc_start: 0.7376 (OUTLIER) cc_final: 0.7053 (tp) REVERT: H 307 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8526 (mm) outliers start: 64 outliers final: 33 residues processed: 335 average time/residue: 0.1289 time to fit residues: 67.3049 Evaluate side-chains 324 residues out of total 2083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 283 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 124 GLN Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 236 ASN Chi-restraints excluded: chain F residue 113 MET Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain F residue 288 ASP Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain H residue 127 SER Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 218 THR Chi-restraints excluded: chain H residue 224 LEU Chi-restraints excluded: chain H residue 235 THR Chi-restraints excluded: chain H residue 307 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 136 optimal weight: 0.1980 chunk 97 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 169 optimal weight: 6.9990 chunk 75 optimal weight: 0.8980 chunk 108 optimal weight: 0.7980 chunk 102 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 21 optimal weight: 8.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 289 ASN ** G 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 GLN H 289 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.152810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.114347 restraints weight = 35327.627| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.70 r_work: 0.3170 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3183 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3183 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19327 Z= 0.109 Angle : 0.506 11.167 26097 Z= 0.245 Chirality : 0.040 0.179 2981 Planarity : 0.003 0.046 3275 Dihedral : 10.455 87.617 2826 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.40 % Allowed : 21.49 % Favored : 76.12 % 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: 1.66 (0.18), residues: 2334 helix: 1.69 (0.15), residues: 1316 sheet: -0.77 (0.33), residues: 237 loop : 0.94 (0.23), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 337 TYR 0.006 0.001 TYR E 167 PHE 0.013 0.001 PHE H 197 TRP 0.006 0.001 TRP B 166 HIS 0.001 0.000 HIS G 206 Details of bonding type rmsd covalent geometry : bond 0.00257 (19327) covalent geometry : angle 0.50643 (26097) hydrogen bonds : bond 0.02769 ( 935) hydrogen bonds : angle 4.06825 ( 2678) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 303 time to evaluate : 0.767 Fit side-chains REVERT: A 156 SER cc_start: 0.8993 (t) cc_final: 0.8590 (p) REVERT: B 80 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.8519 (tt) REVERT: C 80 ILE cc_start: 0.9143 (OUTLIER) cc_final: 0.8867 (tt) REVERT: C 200 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8167 (tm-30) REVERT: C 314 ILE cc_start: 0.8602 (OUTLIER) cc_final: 0.7927 (tp) REVERT: D 102 ASP cc_start: 0.8906 (t70) cc_final: 0.8328 (t0) REVERT: D 221 ASP cc_start: 0.8320 (t0) cc_final: 0.7974 (t70) REVERT: D 337 ARG cc_start: 0.7848 (tmm-80) cc_final: 0.7608 (tmm-80) REVERT: E 224 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8176 (mm) REVERT: F 284 GLN cc_start: 0.7904 (tp40) cc_final: 0.7446 (tp-100) REVERT: F 312 GLU cc_start: 0.7766 (mp0) cc_final: 0.7528 (mp0) REVERT: G 106 SER cc_start: 0.8135 (m) cc_final: 0.7898 (p) REVERT: G 288 ASP cc_start: 0.8208 (m-30) cc_final: 0.7651 (m-30) REVERT: G 289 ASN cc_start: 0.8974 (m110) cc_final: 0.8743 (m110) REVERT: H 224 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.7059 (tp) REVERT: H 248 ARG cc_start: 0.7890 (mtt90) cc_final: 0.7577 (mtt90) REVERT: H 307 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8469 (mm) outliers start: 50 outliers final: 28 residues processed: 335 average time/residue: 0.1413 time to fit residues: 73.3235 Evaluate side-chains 324 residues out of total 2083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 289 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 80 ILE 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 B residue 230 MET Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain F residue 113 MET Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 218 THR Chi-restraints excluded: chain H residue 224 LEU Chi-restraints excluded: chain H residue 307 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 217 optimal weight: 0.0970 chunk 225 optimal weight: 7.9990 chunk 196 optimal weight: 0.6980 chunk 221 optimal weight: 0.9990 chunk 182 optimal weight: 0.9980 chunk 151 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 195 optimal weight: 0.8980 chunk 193 optimal weight: 0.0070 chunk 187 optimal weight: 3.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 ASN G 53 GLN ** G 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 GLN H 226 ASN H 289 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.156570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.117364 restraints weight = 33822.780| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.73 r_work: 0.3186 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3197 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3197 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 19327 Z= 0.102 Angle : 0.502 10.936 26097 Z= 0.244 Chirality : 0.039 0.150 2981 Planarity : 0.003 0.044 3275 Dihedral : 10.335 89.329 2826 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.16 % Allowed : 21.68 % Favored : 76.16 % 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: 1.81 (0.18), residues: 2334 helix: 1.78 (0.15), residues: 1319 sheet: -0.71 (0.34), residues: 228 loop : 1.05 (0.24), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 318 TYR 0.009 0.001 TYR E 167 PHE 0.014 0.001 PHE H 197 TRP 0.005 0.001 TRP B 166 HIS 0.001 0.000 HIS B 104 Details of bonding type rmsd covalent geometry : bond 0.00239 (19327) covalent geometry : angle 0.50239 (26097) hydrogen bonds : bond 0.02651 ( 935) hydrogen bonds : angle 3.99439 ( 2678) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 312 time to evaluate : 0.819 Fit side-chains REVERT: A 191 ILE cc_start: 0.8103 (mt) cc_final: 0.7822 (pt) REVERT: B 80 ILE cc_start: 0.8736 (OUTLIER) cc_final: 0.8482 (tt) REVERT: C 80 ILE cc_start: 0.9102 (OUTLIER) cc_final: 0.8836 (tt) REVERT: C 200 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8180 (tm-30) REVERT: C 314 ILE cc_start: 0.8635 (OUTLIER) cc_final: 0.7964 (tp) REVERT: D 102 ASP cc_start: 0.8891 (t70) cc_final: 0.8370 (t0) REVERT: D 221 ASP cc_start: 0.8316 (t0) cc_final: 0.7940 (m-30) REVERT: D 262 GLN cc_start: 0.7506 (mp10) cc_final: 0.7144 (mp10) REVERT: D 337 ARG cc_start: 0.7840 (tmm-80) cc_final: 0.7619 (tmm-80) REVERT: F 284 GLN cc_start: 0.7885 (tp40) cc_final: 0.7387 (tp-100) REVERT: F 312 GLU cc_start: 0.7813 (mp0) cc_final: 0.7586 (mp0) REVERT: G 106 SER cc_start: 0.8099 (m) cc_final: 0.7883 (p) REVERT: G 288 ASP cc_start: 0.8221 (m-30) cc_final: 0.7653 (m-30) REVERT: H 224 LEU cc_start: 0.7299 (OUTLIER) cc_final: 0.7065 (tp) REVERT: H 248 ARG cc_start: 0.7902 (mtt90) cc_final: 0.7646 (mtt90) REVERT: H 307 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8467 (mm) outliers start: 45 outliers final: 22 residues processed: 341 average time/residue: 0.1359 time to fit residues: 72.0980 Evaluate side-chains 325 residues out of total 2083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 297 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain F residue 113 MET Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 224 LEU Chi-restraints excluded: chain H residue 235 THR Chi-restraints excluded: chain H residue 307 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 152 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 215 optimal weight: 7.9990 chunk 117 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 128 optimal weight: 0.9990 chunk 142 optimal weight: 9.9990 chunk 170 optimal weight: 0.5980 chunk 182 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 289 ASN ** G 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 GLN H 289 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.154393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.115671 restraints weight = 30330.644| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.57 r_work: 0.3172 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3179 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3179 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19327 Z= 0.133 Angle : 0.526 11.399 26097 Z= 0.253 Chirality : 0.040 0.257 2981 Planarity : 0.003 0.043 3275 Dihedral : 10.322 88.950 2826 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.21 % Allowed : 21.58 % Favored : 76.21 % 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: 1.81 (0.18), residues: 2334 helix: 1.75 (0.15), residues: 1322 sheet: -0.73 (0.33), residues: 237 loop : 1.13 (0.24), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 44 TYR 0.014 0.001 TYR H 167 PHE 0.015 0.001 PHE H 197 TRP 0.005 0.001 TRP B 220 HIS 0.001 0.000 HIS A 206 Details of bonding type rmsd covalent geometry : bond 0.00322 (19327) covalent geometry : angle 0.52568 (26097) hydrogen bonds : bond 0.02800 ( 935) hydrogen bonds : angle 4.04860 ( 2678) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 297 time to evaluate : 0.696 Fit side-chains REVERT: A 141 MET cc_start: 0.7596 (ttm) cc_final: 0.7332 (ttm) REVERT: B 80 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8531 (tt) REVERT: C 80 ILE cc_start: 0.9150 (OUTLIER) cc_final: 0.8870 (tt) REVERT: C 200 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8163 (tm-30) REVERT: C 314 ILE cc_start: 0.8662 (OUTLIER) cc_final: 0.7995 (tp) REVERT: D 102 ASP cc_start: 0.8881 (t70) cc_final: 0.8356 (t0) REVERT: D 221 ASP cc_start: 0.8308 (OUTLIER) cc_final: 0.7965 (t70) REVERT: D 262 GLN cc_start: 0.7512 (mp10) cc_final: 0.6993 (mp10) REVERT: D 337 ARG cc_start: 0.7890 (tmm-80) cc_final: 0.7574 (tmm-80) REVERT: F 284 GLN cc_start: 0.7879 (tp40) cc_final: 0.7451 (tp-100) REVERT: F 312 GLU cc_start: 0.7812 (mp0) cc_final: 0.7585 (mp0) REVERT: G 106 SER cc_start: 0.8168 (m) cc_final: 0.7880 (p) REVERT: H 102 ASP cc_start: 0.8773 (t0) cc_final: 0.8424 (t0) REVERT: H 248 ARG cc_start: 0.7917 (mtt90) cc_final: 0.7662 (mtt90) REVERT: H 307 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8489 (mm) outliers start: 46 outliers final: 32 residues processed: 326 average time/residue: 0.1334 time to fit residues: 67.8257 Evaluate side-chains 325 residues out of total 2083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 287 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 80 ILE 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 B residue 230 MET Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain F residue 113 MET Chi-restraints excluded: chain F residue 217 MET Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 221 ASP Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 223 LEU Chi-restraints excluded: chain H residue 235 THR Chi-restraints excluded: chain H residue 236 ASN Chi-restraints excluded: chain H residue 307 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 110 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 203 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 160 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 124 optimal weight: 0.0070 chunk 221 optimal weight: 9.9990 overall best weight: 1.1804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 289 ASN ** G 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 GLN H 289 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.152183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.113607 restraints weight = 35368.166| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.71 r_work: 0.3161 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3168 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3168 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19327 Z= 0.131 Angle : 0.529 11.183 26097 Z= 0.255 Chirality : 0.040 0.262 2981 Planarity : 0.003 0.043 3275 Dihedral : 10.324 88.913 2826 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.25 % Allowed : 21.49 % Favored : 76.26 % 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: 1.80 (0.18), residues: 2334 helix: 1.71 (0.15), residues: 1340 sheet: -0.63 (0.34), residues: 222 loop : 1.09 (0.24), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 44 TYR 0.017 0.001 TYR E 167 PHE 0.015 0.001 PHE H 197 TRP 0.005 0.001 TRP B 166 HIS 0.001 0.000 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00317 (19327) covalent geometry : angle 0.52860 (26097) hydrogen bonds : bond 0.02800 ( 935) hydrogen bonds : angle 4.07989 ( 2678) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 286 time to evaluate : 0.796 Fit side-chains REVERT: A 141 MET cc_start: 0.7636 (ttm) cc_final: 0.7361 (ttm) REVERT: B 80 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8535 (tt) REVERT: C 80 ILE cc_start: 0.9147 (OUTLIER) cc_final: 0.8873 (tt) REVERT: C 200 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8180 (tm-30) REVERT: D 102 ASP cc_start: 0.8869 (t70) cc_final: 0.8362 (t0) REVERT: D 221 ASP cc_start: 0.8321 (OUTLIER) cc_final: 0.7993 (t70) REVERT: D 262 GLN cc_start: 0.7509 (mp10) cc_final: 0.6994 (mp10) REVERT: D 337 ARG cc_start: 0.7895 (tmm-80) cc_final: 0.7589 (tmm-80) REVERT: F 284 GLN cc_start: 0.7888 (tp40) cc_final: 0.7462 (tp-100) REVERT: F 312 GLU cc_start: 0.7823 (mp0) cc_final: 0.7603 (mp0) REVERT: G 106 SER cc_start: 0.8172 (m) cc_final: 0.7890 (p) REVERT: H 248 ARG cc_start: 0.7913 (mtt90) cc_final: 0.7652 (mtt90) REVERT: H 307 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8514 (mm) outliers start: 47 outliers final: 32 residues processed: 315 average time/residue: 0.1369 time to fit residues: 67.2841 Evaluate side-chains 323 residues out of total 2083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 286 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 80 ILE 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 B residue 230 MET Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain F residue 113 MET Chi-restraints excluded: chain F residue 217 MET Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 221 ASP Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 218 THR Chi-restraints excluded: chain H residue 223 LEU Chi-restraints excluded: chain H residue 235 THR Chi-restraints excluded: chain H residue 236 ASN Chi-restraints excluded: chain H residue 307 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 93 optimal weight: 1.9990 chunk 200 optimal weight: 8.9990 chunk 106 optimal weight: 0.7980 chunk 134 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 115 optimal weight: 9.9990 chunk 80 optimal weight: 1.9990 chunk 192 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 142 optimal weight: 10.0000 chunk 223 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 289 ASN ** G 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 GLN H 289 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.152257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.115130 restraints weight = 27233.111| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.36 r_work: 0.3194 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3052 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3052 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 19327 Z= 0.124 Angle : 0.528 11.328 26097 Z= 0.255 Chirality : 0.040 0.257 2981 Planarity : 0.003 0.042 3275 Dihedral : 10.301 89.134 2826 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.97 % Allowed : 22.11 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.18), residues: 2334 helix: 1.72 (0.15), residues: 1339 sheet: -0.63 (0.34), residues: 222 loop : 1.11 (0.24), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 318 TYR 0.017 0.001 TYR E 167 PHE 0.015 0.001 PHE H 197 TRP 0.006 0.001 TRP B 166 HIS 0.002 0.000 HIS G 104 Details of bonding type rmsd covalent geometry : bond 0.00304 (19327) covalent geometry : angle 0.52821 (26097) hydrogen bonds : bond 0.02766 ( 935) hydrogen bonds : angle 4.07281 ( 2678) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 298 time to evaluate : 0.741 Fit side-chains REVERT: A 141 MET cc_start: 0.7685 (ttm) cc_final: 0.7413 (ttm) REVERT: A 199 ARG cc_start: 0.7987 (ttp80) cc_final: 0.7480 (ttm170) REVERT: B 80 ILE cc_start: 0.8841 (OUTLIER) cc_final: 0.8579 (tt) REVERT: C 80 ILE cc_start: 0.9169 (OUTLIER) cc_final: 0.8899 (tt) REVERT: C 200 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8338 (tm-30) REVERT: D 102 ASP cc_start: 0.8943 (t70) cc_final: 0.8448 (t0) REVERT: D 221 ASP cc_start: 0.8492 (OUTLIER) cc_final: 0.8158 (t70) REVERT: D 262 GLN cc_start: 0.7582 (mp10) cc_final: 0.7048 (mp10) REVERT: D 337 ARG cc_start: 0.7872 (tmm-80) cc_final: 0.7543 (tmm-80) REVERT: F 284 GLN cc_start: 0.7896 (tp40) cc_final: 0.7439 (tp-100) REVERT: F 312 GLU cc_start: 0.7880 (mp0) cc_final: 0.7674 (mp0) REVERT: G 106 SER cc_start: 0.8218 (m) cc_final: 0.7936 (p) REVERT: G 275 LYS cc_start: 0.8208 (tptt) cc_final: 0.7883 (mmmt) REVERT: H 102 ASP cc_start: 0.8838 (t0) cc_final: 0.8508 (t0) REVERT: H 169 GLU cc_start: 0.8026 (tp30) cc_final: 0.7688 (tp30) REVERT: H 248 ARG cc_start: 0.8001 (mtt90) cc_final: 0.7717 (mtt90) REVERT: H 307 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8556 (mm) outliers start: 41 outliers final: 32 residues processed: 321 average time/residue: 0.1358 time to fit residues: 67.2683 Evaluate side-chains 328 residues out of total 2083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 291 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 80 ILE 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 B residue 230 MET Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain F residue 113 MET Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 221 ASP Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 218 THR Chi-restraints excluded: chain H residue 223 LEU Chi-restraints excluded: chain H residue 235 THR Chi-restraints excluded: chain H residue 307 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 227 optimal weight: 0.8980 chunk 110 optimal weight: 5.9990 chunk 24 optimal weight: 30.0000 chunk 85 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 166 optimal weight: 0.0670 chunk 26 optimal weight: 7.9990 chunk 82 optimal weight: 0.2980 chunk 228 optimal weight: 1.9990 chunk 214 optimal weight: 5.9990 overall best weight: 0.8320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 ASN C 289 ASN ** G 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 GLN H 289 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.153325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.114995 restraints weight = 35394.014| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.71 r_work: 0.3179 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3186 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3186 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19327 Z= 0.116 Angle : 0.530 11.145 26097 Z= 0.257 Chirality : 0.040 0.252 2981 Planarity : 0.003 0.042 3275 Dihedral : 10.251 88.582 2826 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.97 % Allowed : 22.35 % Favored : 75.68 % 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: 1.86 (0.18), residues: 2334 helix: 1.75 (0.15), residues: 1337 sheet: -0.64 (0.34), residues: 222 loop : 1.14 (0.24), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 44 TYR 0.016 0.001 TYR E 167 PHE 0.014 0.001 PHE H 197 TRP 0.006 0.001 TRP B 166 HIS 0.002 0.000 HIS G 104 Details of bonding type rmsd covalent geometry : bond 0.00280 (19327) covalent geometry : angle 0.52993 (26097) hydrogen bonds : bond 0.02717 ( 935) hydrogen bonds : angle 4.06070 ( 2678) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7741.06 seconds wall clock time: 132 minutes 32.13 seconds (7952.13 seconds total)