Starting phenix.real_space_refine on Mon Apr 6 00:04:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m5c_63641/04_2026/9m5c_63641.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m5c_63641/04_2026/9m5c_63641.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9m5c_63641/04_2026/9m5c_63641.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m5c_63641/04_2026/9m5c_63641.map" model { file = "/net/cci-nas-00/data/ceres_data/9m5c_63641/04_2026/9m5c_63641.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m5c_63641/04_2026/9m5c_63641.cif" } resolution = 3.11 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 18 5.49 5 Mg 6 5.21 5 S 71 5.16 5 C 9036 2.51 5 N 2424 2.21 5 O 2748 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s 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: 14303 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2300 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 13, 'TRANS': 277} Chain breaks: 1 Chain: "F" Number of atoms: 2319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2319 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 13, 'TRANS': 279} Chain breaks: 1 Chain: "E" Number of atoms: 2342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2342 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 13, 'TRANS': 282} Chain breaks: 1 Chain: "D" Number of atoms: 2367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2367 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 13, 'TRANS': 286} Chain breaks: 1 Chain: "C" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2360 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 13, 'TRANS': 285} Chain breaks: 1 Chain: "B" Number of atoms: 2343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2343 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 13, 'TRANS': 283} Chain breaks: 1 Chain: "G" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 80 Classifications: {'peptide': 16} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'TRANS': 15} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'UNK:plan-1': 16} Unresolved non-hydrogen planarities: 16 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: "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: "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: "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: "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: "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} Time building chain proxies: 3.00, per 1000 atoms: 0.21 Number of scatterers: 14303 At special positions: 0 Unit cell: (96.35, 130.79, 138.17, 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 71 16.00 P 18 15.00 Mg 6 11.99 O 2748 8.00 N 2424 7.00 C 9036 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: 1.06 Conformation dependent library (CDL) restraints added in 415.7 milliseconds 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3410 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 6 sheets defined 63.3% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 43 through 61 removed outlier: 3.791A pdb=" N LYS A 47 " --> pdb=" O SER A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 67 removed outlier: 3.655A pdb=" N GLU A 66 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL A 67 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 77 Processing helix chain 'A' and resid 89 through 93 Processing helix chain 'A' and resid 96 through 113 removed outlier: 5.177A pdb=" N TYR A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Proline residue: A 110 - end of helix Processing helix chain 'A' and resid 115 through 119 removed outlier: 3.538A pdb=" N SER A 118 " --> pdb=" O GLU A 115 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ASN A 119 " --> pdb=" O VAL A 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 115 through 119' Processing helix chain 'A' and resid 120 through 124 Processing helix chain 'A' and resid 138 through 151 removed outlier: 3.694A pdb=" N SER A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 163 Processing helix chain 'A' and resid 168 through 184 removed outlier: 3.506A pdb=" N LYS A 172 " --> pdb=" O GLY A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 198 removed outlier: 3.667A 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: 4.065A 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 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: 3.938A pdb=" N LYS A 347 " --> pdb=" O ASP A 343 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 61 Processing helix chain 'F' and resid 62 through 65 Processing helix chain 'F' and resid 70 through 77 Processing helix chain 'F' and resid 89 through 93 Processing helix chain 'F' and resid 96 through 107 Processing helix chain 'F' and resid 107 through 113 Processing helix chain 'F' and resid 113 through 118 removed outlier: 3.568A pdb=" N TYR F 117 " --> pdb=" O MET F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 149 Processing helix chain 'F' and resid 158 through 163 removed outlier: 3.871A 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 206 through 224 removed outlier: 3.810A pdb=" N GLY F 222 " --> pdb=" O THR F 218 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU F 224 " --> pdb=" O TRP F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 249 Processing helix chain 'F' and resid 259 through 271 Processing helix chain 'F' and resid 283 through 290 removed outlier: 3.777A pdb=" N THR F 290 " --> pdb=" O ILE F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 320 removed outlier: 4.754A pdb=" N GLU F 312 " --> pdb=" O ASP F 308 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N TYR F 313 " --> pdb=" O ALA F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 348 removed outlier: 3.653A pdb=" N LYS F 347 " --> pdb=" O ASP F 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 61 Processing helix chain 'E' and resid 62 through 66 removed outlier: 3.619A pdb=" N ALA E 65 " --> pdb=" O PRO E 62 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU E 66 " --> pdb=" O ALA E 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 66' Processing helix chain 'E' and resid 70 through 78 removed outlier: 3.764A pdb=" N SER E 78 " --> pdb=" O ARG E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 86 Processing helix chain 'E' and resid 89 through 93 Processing helix chain 'E' and resid 96 through 107 Processing helix chain 'E' and resid 107 through 113 Processing helix chain 'E' and resid 120 through 124 removed outlier: 3.962A pdb=" N GLN E 124 " --> pdb=" O PRO E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 150 Processing helix chain 'E' and resid 158 through 163 Processing helix chain 'E' and resid 168 through 184 Processing helix chain 'E' and resid 193 through 198 removed outlier: 4.163A pdb=" N PHE E 197 " --> pdb=" O GLN E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 221 Processing helix chain 'E' and resid 242 through 248 Processing helix chain 'E' and resid 259 through 271 Processing helix chain 'E' and resid 282 through 290 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 347 removed outlier: 3.572A pdb=" N PHE E 344 " --> pdb=" O LYS E 340 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS E 347 " --> pdb=" O ASP E 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 61 Processing helix chain 'D' and resid 62 through 66 removed outlier: 3.626A pdb=" N GLU D 66 " --> pdb=" O ALA D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 77 Processing helix chain 'D' and resid 82 through 86 Processing helix chain 'D' and resid 89 through 93 removed outlier: 3.590A pdb=" N ILE D 93 " --> pdb=" O PHE D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 107 Processing helix chain 'D' and resid 107 through 113 Processing helix chain 'D' and resid 138 through 150 removed outlier: 3.515A pdb=" N SER D 150 " --> pdb=" O LEU D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 163 removed outlier: 3.710A pdb=" N ILE D 162 " --> pdb=" O ARG D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 184 removed outlier: 3.684A pdb=" N LYS D 172 " --> pdb=" O GLY D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 198 removed outlier: 4.229A 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 247 Processing helix chain 'D' and resid 259 through 271 Processing helix chain 'D' and resid 282 through 290 removed outlier: 3.616A pdb=" N ILE D 286 " --> pdb=" O ASP D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 310 Processing helix chain 'D' and resid 310 through 321 Processing helix chain 'D' and resid 340 through 348 removed outlier: 3.764A pdb=" N PHE D 344 " --> pdb=" O LYS D 340 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS D 347 " --> pdb=" O ASP D 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 61 Processing helix chain 'C' and resid 62 through 65 Processing helix chain 'C' and resid 70 through 77 Processing helix chain 'C' and resid 89 through 93 removed outlier: 3.514A pdb=" N ILE C 93 " --> pdb=" O PHE C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 107 Processing helix chain 'C' and resid 107 through 113 Processing helix chain 'C' and resid 120 through 124 Processing helix chain 'C' and resid 138 through 150 Processing helix chain 'C' and resid 158 through 163 Processing helix chain 'C' and resid 168 through 184 Processing helix chain 'C' and resid 193 through 198 removed outlier: 4.302A pdb=" N PHE C 197 " --> pdb=" O GLN C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 221 Processing helix chain 'C' and resid 237 through 241 Processing helix chain 'C' and resid 242 through 248 Processing helix chain 'C' and resid 259 through 271 Processing helix chain 'C' and resid 282 through 290 removed outlier: 3.726A pdb=" N ILE C 286 " --> pdb=" O ASP C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 310 Processing helix chain 'C' and resid 310 through 320 Processing helix chain 'C' and resid 340 through 346 removed outlier: 3.602A pdb=" N PHE C 344 " --> pdb=" O LYS C 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 61 Processing helix chain 'B' and resid 62 through 65 Processing helix chain 'B' and resid 70 through 77 Processing helix chain 'B' and resid 89 through 93 Processing helix chain 'B' and resid 96 through 107 Processing helix chain 'B' and resid 107 through 113 Processing helix chain 'B' and resid 113 through 118 removed outlier: 3.645A pdb=" N TYR B 117 " --> pdb=" O MET B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 124 removed outlier: 3.745A pdb=" N GLN B 124 " --> pdb=" O PRO B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 150 removed outlier: 3.532A pdb=" N SER B 150 " --> pdb=" O LEU B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 163 removed outlier: 3.639A pdb=" N ILE B 162 " --> pdb=" O ARG B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 184 removed outlier: 3.596A pdb=" N LYS B 172 " --> pdb=" O GLY B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 198 removed outlier: 4.147A pdb=" N PHE B 197 " --> pdb=" O GLN B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 221 Processing helix chain 'B' and resid 242 through 248 Processing helix chain 'B' and resid 259 through 271 Processing helix chain 'B' and resid 282 through 290 removed outlier: 3.991A 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 320 removed outlier: 3.625A pdb=" N LEU B 320 " --> pdb=" O GLN B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 348 removed outlier: 3.553A pdb=" N LYS B 347 " --> pdb=" O ASP B 343 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 81 removed outlier: 4.188A pdb=" N PHE A 154 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ASN A 153 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N PHE A 190 " --> pdb=" O ASN A 153 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE A 155 " --> pdb=" O PHE A 190 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N ASP A 192 " --> pdb=" O ILE A 155 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N ILE A 157 " --> pdb=" O ASP A 192 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N CYS A 187 " --> pdb=" O MET A 230 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ILE A 232 " --> pdb=" O CYS A 187 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ILE A 189 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ALA A 234 " --> pdb=" O ILE A 189 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE A 191 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N GLY A 128 " --> pdb=" O LYS A 251 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N PHE A 253 " --> pdb=" O GLY A 128 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU A 130 " --> pdb=" O PHE A 253 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 80 through 81 removed outlier: 3.667A pdb=" N PHE F 154 " --> pdb=" O VAL F 81 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ASN F 153 " --> pdb=" O ILE F 188 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N PHE F 190 " --> pdb=" O ASN F 153 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ILE F 155 " --> pdb=" O PHE F 190 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N CYS F 187 " --> pdb=" O MET F 230 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ILE F 232 " --> pdb=" O CYS F 187 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N ILE F 189 " --> pdb=" O ILE F 232 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ALA F 234 " --> pdb=" O ILE F 189 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE F 191 " --> pdb=" O ALA F 234 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL F 129 " --> pdb=" O GLY F 233 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N THR F 235 " --> pdb=" O VAL F 129 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU F 131 " --> pdb=" O THR F 235 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLY F 128 " --> pdb=" O LYS F 251 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N PHE F 253 " --> pdb=" O GLY F 128 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU F 130 " --> pdb=" O PHE F 253 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 80 through 81 removed outlier: 4.113A pdb=" N PHE E 154 " --> pdb=" O VAL E 81 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA E 234 " --> pdb=" O ILE E 191 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N VAL E 129 " --> pdb=" O GLY E 233 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N THR E 235 " --> pdb=" O VAL E 129 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU E 131 " --> pdb=" O THR E 235 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLY E 128 " --> pdb=" O LYS E 251 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N PHE E 253 " --> pdb=" O GLY E 128 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU E 130 " --> pdb=" O PHE E 253 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 80 through 81 removed outlier: 3.969A pdb=" N PHE D 154 " --> pdb=" O VAL D 81 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA D 234 " --> pdb=" O ILE D 191 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLY D 128 " --> pdb=" O LYS D 251 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N PHE D 253 " --> pdb=" O GLY D 128 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N LEU D 130 " --> pdb=" O PHE D 253 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 80 through 81 removed outlier: 4.035A pdb=" N PHE C 154 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ASN C 153 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N PHE C 190 " --> pdb=" O ASN C 153 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE C 155 " --> pdb=" O PHE C 190 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N ASP C 192 " --> pdb=" O ILE C 155 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA C 234 " --> pdb=" O ILE C 191 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLY C 128 " --> pdb=" O LYS C 251 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N PHE C 253 " --> pdb=" O GLY C 128 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU C 130 " --> pdb=" O PHE C 253 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 80 through 81 removed outlier: 4.197A pdb=" N PHE B 154 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ASN B 153 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N PHE B 190 " --> pdb=" O ASN B 153 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ILE B 155 " --> pdb=" O PHE B 190 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ASP B 192 " --> pdb=" O ILE B 155 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA B 234 " --> pdb=" O ILE B 191 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N VAL B 129 " --> pdb=" O GLY B 233 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N THR B 235 " --> pdb=" O VAL B 129 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N LEU B 131 " --> pdb=" O THR B 235 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N GLY B 128 " --> pdb=" O LYS B 251 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N PHE B 253 " --> pdb=" O GLY B 128 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU B 130 " --> pdb=" O PHE B 253 " (cutoff:3.500A) 693 hydrogen bonds defined for protein. 1992 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: 2.28 Time building geometry restraints manager: 1.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3626 1.33 - 1.45: 2473 1.45 - 1.58: 8278 1.58 - 1.70: 30 1.70 - 1.82: 124 Bond restraints: 14531 Sorted by residual: bond pdb=" C4 ATP A 401 " pdb=" C5 ATP A 401 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.81e+01 bond pdb=" C4 ATP F 401 " pdb=" C5 ATP F 401 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.56e+01 bond pdb=" C4 ATP C 401 " pdb=" C5 ATP C 401 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.48e+01 bond pdb=" C4 ATP B 401 " pdb=" C5 ATP B 401 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.40e+01 bond pdb=" C4 ATP E 401 " pdb=" C5 ATP E 401 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.25e+01 ... (remaining 14526 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.98: 19445 3.98 - 7.96: 136 7.96 - 11.94: 29 11.94 - 15.92: 4 15.92 - 19.90: 8 Bond angle restraints: 19622 Sorted by residual: angle pdb=" PB ATP B 401 " pdb=" O3B ATP B 401 " pdb=" PG ATP B 401 " ideal model delta sigma weight residual 139.87 119.97 19.90 1.00e+00 1.00e+00 3.96e+02 angle pdb=" PB ATP A 401 " pdb=" O3B ATP A 401 " pdb=" PG ATP A 401 " ideal model delta sigma weight residual 139.87 120.71 19.16 1.00e+00 1.00e+00 3.67e+02 angle pdb=" PB ATP F 401 " pdb=" O3B ATP F 401 " pdb=" PG ATP F 401 " ideal model delta sigma weight residual 139.87 121.29 18.58 1.00e+00 1.00e+00 3.45e+02 angle pdb=" PB ATP C 401 " pdb=" O3B ATP C 401 " pdb=" PG ATP C 401 " ideal model delta sigma weight residual 139.87 122.18 17.69 1.00e+00 1.00e+00 3.13e+02 angle pdb=" PB ATP D 401 " pdb=" O3B ATP D 401 " pdb=" PG ATP D 401 " ideal model delta sigma weight residual 139.87 122.31 17.56 1.00e+00 1.00e+00 3.08e+02 ... (remaining 19617 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 7707 17.91 - 35.82: 1088 35.82 - 53.74: 289 53.74 - 71.65: 35 71.65 - 89.56: 20 Dihedral angle restraints: 9139 sinusoidal: 3908 harmonic: 5231 Sorted by residual: dihedral pdb=" CA LEU B 184 " pdb=" C LEU B 184 " pdb=" N GLN B 185 " pdb=" CA GLN B 185 " ideal model delta harmonic sigma weight residual 180.00 -157.11 -22.89 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA LEU D 184 " pdb=" C LEU D 184 " pdb=" N GLN D 185 " pdb=" CA GLN D 185 " ideal model delta harmonic sigma weight residual -180.00 -158.08 -21.92 0 5.00e+00 4.00e-02 1.92e+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 -158.74 -21.26 0 5.00e+00 4.00e-02 1.81e+01 ... (remaining 9136 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1821 0.054 - 0.109: 329 0.109 - 0.163: 83 0.163 - 0.217: 14 0.217 - 0.271: 3 Chirality restraints: 2250 Sorted by residual: chirality pdb=" CA ILE C 155 " pdb=" N ILE C 155 " pdb=" C ILE C 155 " pdb=" CB ILE C 155 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CA ILE E 155 " pdb=" N ILE E 155 " pdb=" C ILE E 155 " pdb=" CB ILE E 155 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA ILE D 155 " pdb=" N ILE D 155 " pdb=" C ILE D 155 " pdb=" CB ILE D 155 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 2247 not shown) Planarity restraints: 2457 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 125 " -0.056 5.00e-02 4.00e+02 8.55e-02 1.17e+01 pdb=" N PRO A 126 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO A 126 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 126 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 82 " 0.053 5.00e-02 4.00e+02 7.69e-02 9.46e+00 pdb=" N PRO A 83 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO A 83 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 83 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG F 337 " 0.048 5.00e-02 4.00e+02 7.23e-02 8.37e+00 pdb=" N PRO F 338 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO F 338 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO F 338 " 0.040 5.00e-02 4.00e+02 ... (remaining 2454 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 135 2.61 - 3.19: 12139 3.19 - 3.76: 24173 3.76 - 4.33: 32501 4.33 - 4.90: 53893 Nonbonded interactions: 122841 Sorted by model distance: nonbonded pdb=" OG1 THR B 140 " pdb="MG MG B 402 " model vdw 2.043 2.170 nonbonded pdb=" OG1 THR E 140 " pdb="MG MG E 402 " model vdw 2.045 2.170 nonbonded pdb=" OG1 THR D 140 " pdb="MG MG D 402 " model vdw 2.056 2.170 nonbonded pdb=" OG1 THR F 140 " pdb="MG MG F 402 " model vdw 2.067 2.170 nonbonded pdb=" OG1 THR A 140 " pdb="MG MG A 402 " model vdw 2.090 2.170 ... (remaining 122836 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 44 through 402) selection = (chain 'B' and (resid 44 through 319 or resid 336 through 349 or resid 401 throu \ gh 402)) selection = (chain 'C' and (resid 44 through 319 or resid 336 through 349 or resid 401 throu \ gh 402)) selection = (chain 'D' and (resid 44 through 319 or resid 336 through 349 or resid 401 throu \ gh 402)) selection = (chain 'E' and (resid 44 through 319 or resid 336 through 349 or resid 401 throu \ gh 402)) selection = (chain 'F' and (resid 44 through 319 or resid 336 through 349 or resid 401 throu \ gh 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 13.410 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: 0.720 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.050 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 14531 Z= 0.354 Angle : 0.944 19.904 19622 Z= 0.652 Chirality : 0.047 0.271 2250 Planarity : 0.005 0.086 2457 Dihedral : 17.524 89.559 5729 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.57 % Allowed : 23.26 % 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: 0.60 (0.19), residues: 1752 helix: 0.71 (0.16), residues: 929 sheet: -0.30 (0.46), residues: 134 loop : 0.34 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 228 TYR 0.015 0.001 TYR B 313 PHE 0.019 0.002 PHE C 154 TRP 0.005 0.001 TRP C 166 HIS 0.002 0.001 HIS D 206 Details of bonding type rmsd covalent geometry : bond 0.00495 (14531) covalent geometry : angle 0.94404 (19622) hydrogen bonds : bond 0.15339 ( 693) hydrogen bonds : angle 5.83292 ( 1992) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 238 time to evaluate : 0.688 Fit side-chains revert: symmetry clash REVERT: A 199 ARG cc_start: 0.7893 (ttm-80) cc_final: 0.7384 (ttm-80) REVERT: F 53 GLN cc_start: 0.8477 (mt0) cc_final: 0.7942 (tt0) REVERT: F 342 LYS cc_start: 0.8367 (ttpt) cc_final: 0.8110 (tmmt) REVERT: D 284 GLN cc_start: 0.8377 (tp40) cc_final: 0.7777 (tp-100) REVERT: D 288 ASP cc_start: 0.8411 (m-30) cc_final: 0.8009 (m-30) REVERT: D 304 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7845 (mm-30) REVERT: D 308 ASP cc_start: 0.8458 (m-30) cc_final: 0.8160 (m-30) REVERT: D 338 PRO cc_start: 0.8558 (Cg_exo) cc_final: 0.8129 (Cg_endo) REVERT: D 350 MET cc_start: 0.5953 (ptp) cc_final: 0.5535 (ptt) outliers start: 9 outliers final: 4 residues processed: 242 average time/residue: 0.1187 time to fit residues: 42.3880 Evaluate side-chains 229 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 225 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain F residue 191 ILE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 184 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 316 GLN ** B 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.182682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.134314 restraints weight = 17392.601| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.28 r_work: 0.3285 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.0880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14531 Z= 0.147 Angle : 0.537 6.343 19622 Z= 0.268 Chirality : 0.040 0.144 2250 Planarity : 0.004 0.056 2457 Dihedral : 10.800 89.255 2130 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.42 % Allowed : 22.82 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.20), residues: 1752 helix: 1.33 (0.17), residues: 942 sheet: -0.50 (0.44), residues: 141 loop : 0.75 (0.25), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 228 TYR 0.009 0.001 TYR E 264 PHE 0.008 0.001 PHE C 154 TRP 0.005 0.001 TRP C 220 HIS 0.002 0.001 HIS D 206 Details of bonding type rmsd covalent geometry : bond 0.00345 (14531) covalent geometry : angle 0.53747 (19622) hydrogen bonds : bond 0.03530 ( 693) hydrogen bonds : angle 4.46003 ( 1992) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 234 time to evaluate : 0.602 Fit side-chains revert: symmetry clash REVERT: A 199 ARG cc_start: 0.8295 (ttm-80) cc_final: 0.7841 (ttm-80) REVERT: F 53 GLN cc_start: 0.8401 (mt0) cc_final: 0.7769 (tt0) REVERT: F 158 ARG cc_start: 0.7973 (mtm-85) cc_final: 0.7719 (mtm110) REVERT: F 247 ARG cc_start: 0.7492 (mtm110) cc_final: 0.7282 (mtm110) REVERT: D 284 GLN cc_start: 0.8484 (tp40) cc_final: 0.7761 (tp-100) REVERT: D 288 ASP cc_start: 0.8616 (m-30) cc_final: 0.8039 (m-30) REVERT: D 308 ASP cc_start: 0.8717 (m-30) cc_final: 0.8465 (m-30) REVERT: D 338 PRO cc_start: 0.8619 (Cg_exo) cc_final: 0.8225 (Cg_endo) REVERT: D 348 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8001 (mm) REVERT: D 350 MET cc_start: 0.5967 (ptp) cc_final: 0.5504 (ptt) REVERT: C 273 ASP cc_start: 0.6867 (m-30) cc_final: 0.6555 (t0) REVERT: C 342 LYS cc_start: 0.8226 (mtmm) cc_final: 0.7909 (mmtt) outliers start: 38 outliers final: 19 residues processed: 260 average time/residue: 0.1192 time to fit residues: 44.8131 Evaluate side-chains 234 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 214 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 194 ILE Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 236 ASN Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 230 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 132 optimal weight: 1.9990 chunk 108 optimal weight: 0.5980 chunk 158 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 75 optimal weight: 0.6980 chunk 137 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 7 optimal weight: 0.2980 chunk 72 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 289 ASN ** B 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.183314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.134213 restraints weight = 17453.034| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.66 r_work: 0.3299 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14531 Z= 0.108 Angle : 0.496 7.392 19622 Z= 0.245 Chirality : 0.039 0.205 2250 Planarity : 0.003 0.049 2457 Dihedral : 10.349 81.105 2121 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.36 % Allowed : 23.07 % Favored : 74.57 % 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: 1.59 (0.20), residues: 1752 helix: 1.65 (0.17), residues: 942 sheet: -0.49 (0.45), residues: 128 loop : 0.70 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 228 TYR 0.014 0.001 TYR E 264 PHE 0.013 0.001 PHE B 344 TRP 0.004 0.001 TRP C 166 HIS 0.002 0.001 HIS D 206 Details of bonding type rmsd covalent geometry : bond 0.00249 (14531) covalent geometry : angle 0.49556 (19622) hydrogen bonds : bond 0.03032 ( 693) hydrogen bonds : angle 4.22076 ( 1992) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 228 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 199 ARG cc_start: 0.8183 (ttm-80) cc_final: 0.7680 (ttm-80) REVERT: F 53 GLN cc_start: 0.8355 (mt0) cc_final: 0.7788 (tt0) REVERT: F 219 LEU cc_start: 0.8587 (mm) cc_final: 0.8310 (mm) REVERT: F 350 MET cc_start: 0.4252 (tpp) cc_final: 0.3854 (tpt) REVERT: D 284 GLN cc_start: 0.8387 (tp40) cc_final: 0.7949 (tp-100) REVERT: D 304 GLU cc_start: 0.8279 (mm-30) cc_final: 0.8019 (mm-30) REVERT: D 308 ASP cc_start: 0.8557 (m-30) cc_final: 0.8277 (m-30) REVERT: D 350 MET cc_start: 0.5973 (ptp) cc_final: 0.5528 (ptt) outliers start: 37 outliers final: 22 residues processed: 252 average time/residue: 0.1030 time to fit residues: 39.2189 Evaluate side-chains 234 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 212 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 191 ILE Chi-restraints excluded: chain F residue 194 ILE Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 308 ASP Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 236 ASN Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 204 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 82 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 55 optimal weight: 10.0000 chunk 155 optimal weight: 0.8980 chunk 117 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 chunk 158 optimal weight: 0.5980 chunk 145 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 69 optimal weight: 0.0970 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 124 GLN C 316 GLN ** B 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.182399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.125732 restraints weight = 17344.323| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.63 r_work: 0.3267 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14531 Z= 0.118 Angle : 0.495 6.149 19622 Z= 0.244 Chirality : 0.039 0.138 2250 Planarity : 0.003 0.047 2457 Dihedral : 10.104 84.365 2121 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.70 % Allowed : 22.43 % Favored : 73.87 % 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 (0.21), residues: 1752 helix: 1.84 (0.17), residues: 936 sheet: -0.55 (0.43), residues: 138 loop : 0.86 (0.25), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 158 TYR 0.017 0.001 TYR E 264 PHE 0.009 0.001 PHE B 197 TRP 0.004 0.001 TRP C 166 HIS 0.002 0.000 HIS D 206 Details of bonding type rmsd covalent geometry : bond 0.00281 (14531) covalent geometry : angle 0.49504 (19622) hydrogen bonds : bond 0.02817 ( 693) hydrogen bonds : angle 4.11750 ( 1992) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 231 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 199 ARG cc_start: 0.8254 (ttm-80) cc_final: 0.7689 (ttm-80) REVERT: F 53 GLN cc_start: 0.8350 (mt0) cc_final: 0.7896 (tt0) REVERT: F 219 LEU cc_start: 0.8578 (mm) cc_final: 0.8212 (mm) REVERT: F 248 ARG cc_start: 0.7964 (mpt180) cc_final: 0.7755 (mpt180) REVERT: F 350 MET cc_start: 0.4534 (tpp) cc_final: 0.4048 (tpt) REVERT: D 284 GLN cc_start: 0.8439 (tp40) cc_final: 0.7950 (tp-100) REVERT: D 291 LYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7455 (mttm) REVERT: D 304 GLU cc_start: 0.8458 (mm-30) cc_final: 0.8166 (mm-30) REVERT: D 308 ASP cc_start: 0.8735 (m-30) cc_final: 0.8443 (m-30) REVERT: D 348 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7975 (mm) REVERT: D 350 MET cc_start: 0.6118 (ptp) cc_final: 0.5672 (ptt) REVERT: C 342 LYS cc_start: 0.8143 (mtmm) cc_final: 0.7769 (mmtt) outliers start: 58 outliers final: 30 residues processed: 266 average time/residue: 0.1150 time to fit residues: 45.9294 Evaluate side-chains 250 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 218 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 191 ILE Chi-restraints excluded: chain F residue 194 ILE Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 308 ASP Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 236 ASN Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 124 GLN Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 291 LYS Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 204 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 90 optimal weight: 1.9990 chunk 4 optimal weight: 0.0060 chunk 87 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 57 optimal weight: 6.9990 chunk 63 optimal weight: 0.9980 chunk 107 optimal weight: 0.5980 chunk 48 optimal weight: 0.4980 chunk 25 optimal weight: 20.0000 chunk 175 optimal weight: 9.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.182370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.125713 restraints weight = 17315.718| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.63 r_work: 0.3281 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14531 Z= 0.106 Angle : 0.493 7.569 19622 Z= 0.243 Chirality : 0.039 0.137 2250 Planarity : 0.003 0.046 2457 Dihedral : 10.056 88.631 2121 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.31 % Allowed : 23.39 % Favored : 73.30 % 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: 1.84 (0.21), residues: 1752 helix: 1.85 (0.17), residues: 952 sheet: -0.65 (0.45), residues: 129 loop : 0.88 (0.25), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 252 TYR 0.022 0.001 TYR E 264 PHE 0.009 0.001 PHE B 197 TRP 0.004 0.001 TRP C 166 HIS 0.003 0.001 HIS D 206 Details of bonding type rmsd covalent geometry : bond 0.00247 (14531) covalent geometry : angle 0.49264 (19622) hydrogen bonds : bond 0.02710 ( 693) hydrogen bonds : angle 4.08725 ( 1992) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 236 time to evaluate : 0.410 Fit side-chains revert: symmetry clash REVERT: A 199 ARG cc_start: 0.8245 (ttm-80) cc_final: 0.7677 (ttm-80) REVERT: F 53 GLN cc_start: 0.8327 (mt0) cc_final: 0.7907 (tt0) REVERT: F 219 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8188 (mm) REVERT: F 248 ARG cc_start: 0.8007 (mpt180) cc_final: 0.7770 (mpt180) REVERT: F 350 MET cc_start: 0.4518 (tpp) cc_final: 0.4020 (tpt) REVERT: E 113 MET cc_start: 0.8494 (mtt) cc_final: 0.8271 (mtt) REVERT: E 346 LYS cc_start: 0.8098 (ttpt) cc_final: 0.7821 (mtpt) REVERT: D 284 GLN cc_start: 0.8427 (tp40) cc_final: 0.7932 (tp-100) REVERT: D 291 LYS cc_start: 0.7982 (OUTLIER) cc_final: 0.7442 (mttm) REVERT: D 348 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.8001 (mm) REVERT: C 342 LYS cc_start: 0.8118 (mtmm) cc_final: 0.7800 (mmtt) outliers start: 52 outliers final: 31 residues processed: 272 average time/residue: 0.1242 time to fit residues: 49.1818 Evaluate side-chains 248 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 214 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 84 ASP Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 191 ILE Chi-restraints excluded: chain F residue 194 ILE Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 236 ASN Chi-restraints excluded: chain D residue 124 GLN Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 291 LYS Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 204 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 86 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 141 optimal weight: 0.0870 chunk 140 optimal weight: 0.9990 chunk 18 optimal weight: 0.3980 chunk 148 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 172 optimal weight: 0.9980 chunk 15 optimal weight: 9.9990 chunk 130 optimal weight: 0.6980 chunk 30 optimal weight: 4.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 316 GLN ** B 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.183541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.126930 restraints weight = 17297.513| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.68 r_work: 0.3285 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14531 Z= 0.107 Angle : 0.495 6.702 19622 Z= 0.244 Chirality : 0.039 0.136 2250 Planarity : 0.003 0.045 2457 Dihedral : 9.942 89.138 2121 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.00 % Allowed : 23.26 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.21), residues: 1752 helix: 1.93 (0.17), residues: 947 sheet: -0.51 (0.47), residues: 125 loop : 0.91 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 252 TYR 0.021 0.001 TYR E 264 PHE 0.009 0.001 PHE B 197 TRP 0.006 0.001 TRP E 166 HIS 0.004 0.001 HIS D 206 Details of bonding type rmsd covalent geometry : bond 0.00252 (14531) covalent geometry : angle 0.49458 (19622) hydrogen bonds : bond 0.02646 ( 693) hydrogen bonds : angle 4.03576 ( 1992) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 221 time to evaluate : 0.627 Fit side-chains revert: symmetry clash REVERT: A 199 ARG cc_start: 0.8264 (ttm-80) cc_final: 0.7683 (ttm-80) REVERT: A 252 ARG cc_start: 0.5820 (mtm-85) cc_final: 0.5528 (mtm-85) REVERT: F 53 GLN cc_start: 0.8266 (mt0) cc_final: 0.7904 (tt0) REVERT: F 219 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8209 (mm) REVERT: F 350 MET cc_start: 0.4591 (tpp) cc_final: 0.4092 (tpt) REVERT: E 346 LYS cc_start: 0.8068 (ttpt) cc_final: 0.7820 (mtpt) REVERT: D 284 GLN cc_start: 0.8424 (tp40) cc_final: 0.7930 (tp-100) REVERT: D 291 LYS cc_start: 0.7974 (OUTLIER) cc_final: 0.7441 (mttm) REVERT: D 304 GLU cc_start: 0.8456 (mm-30) cc_final: 0.8139 (mm-30) REVERT: D 348 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7981 (mm) REVERT: C 342 LYS cc_start: 0.8117 (mtmm) cc_final: 0.7819 (mmtt) outliers start: 47 outliers final: 34 residues processed: 250 average time/residue: 0.1107 time to fit residues: 41.7527 Evaluate side-chains 250 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 213 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 84 ASP Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 191 ILE Chi-restraints excluded: chain F residue 194 ILE Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 236 ASN Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 124 GLN Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 291 LYS Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 204 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 99 optimal weight: 0.0050 chunk 3 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 174 optimal weight: 0.9990 chunk 145 optimal weight: 8.9990 chunk 89 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 95 optimal weight: 0.3980 chunk 139 optimal weight: 0.8980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.182741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.134416 restraints weight = 17356.468| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.46 r_work: 0.3279 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14531 Z= 0.109 Angle : 0.499 8.472 19622 Z= 0.244 Chirality : 0.039 0.173 2250 Planarity : 0.003 0.045 2457 Dihedral : 9.846 87.446 2121 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.06 % Allowed : 23.39 % Favored : 73.55 % 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: 1.96 (0.21), residues: 1752 helix: 1.95 (0.17), residues: 945 sheet: -0.51 (0.46), residues: 125 loop : 0.91 (0.25), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 74 TYR 0.023 0.001 TYR E 264 PHE 0.013 0.001 PHE F 245 TRP 0.004 0.001 TRP C 166 HIS 0.003 0.001 HIS D 206 Details of bonding type rmsd covalent geometry : bond 0.00258 (14531) covalent geometry : angle 0.49929 (19622) hydrogen bonds : bond 0.02634 ( 693) hydrogen bonds : angle 4.02892 ( 1992) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 222 time to evaluate : 0.577 Fit side-chains revert: symmetry clash REVERT: A 199 ARG cc_start: 0.8196 (ttm-80) cc_final: 0.7621 (ttm-80) REVERT: A 252 ARG cc_start: 0.5727 (mtm-85) cc_final: 0.5440 (mtm-85) REVERT: F 217 MET cc_start: 0.7809 (mmp) cc_final: 0.7154 (mmp) REVERT: F 219 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8273 (mm) REVERT: F 248 ARG cc_start: 0.7900 (mtt90) cc_final: 0.7369 (mpt90) REVERT: F 350 MET cc_start: 0.4465 (tpp) cc_final: 0.4048 (tpt) REVERT: E 346 LYS cc_start: 0.8028 (ttpt) cc_final: 0.7810 (mtpt) REVERT: D 115 GLU cc_start: 0.7642 (mp0) cc_final: 0.7335 (pm20) REVERT: D 146 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8835 (mp) REVERT: D 284 GLN cc_start: 0.8369 (tp40) cc_final: 0.7896 (tp-100) REVERT: D 291 LYS cc_start: 0.7934 (OUTLIER) cc_final: 0.7377 (mttm) REVERT: D 304 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7955 (mm-30) REVERT: D 348 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7932 (mm) REVERT: C 342 LYS cc_start: 0.8136 (mtmm) cc_final: 0.7846 (mmtt) outliers start: 48 outliers final: 30 residues processed: 254 average time/residue: 0.1113 time to fit residues: 42.3539 Evaluate side-chains 250 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 216 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 84 ASP Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 191 ILE Chi-restraints excluded: chain F residue 194 ILE Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 236 ASN Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 124 GLN Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 291 LYS Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 204 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 112 optimal weight: 7.9990 chunk 160 optimal weight: 0.0970 chunk 97 optimal weight: 0.9980 chunk 171 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 98 optimal weight: 0.5980 chunk 141 optimal weight: 0.7980 chunk 55 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 289 ASN ** B 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.183613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.135652 restraints weight = 17322.998| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.39 r_work: 0.3273 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14531 Z= 0.111 Angle : 0.505 9.047 19622 Z= 0.246 Chirality : 0.039 0.185 2250 Planarity : 0.003 0.045 2457 Dihedral : 9.775 86.720 2121 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.25 % Allowed : 23.33 % Favored : 73.42 % 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: 2.03 (0.21), residues: 1752 helix: 2.00 (0.17), residues: 944 sheet: -0.51 (0.46), residues: 125 loop : 0.97 (0.25), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 74 TYR 0.018 0.001 TYR E 264 PHE 0.009 0.001 PHE B 197 TRP 0.004 0.001 TRP C 166 HIS 0.003 0.001 HIS D 206 Details of bonding type rmsd covalent geometry : bond 0.00262 (14531) covalent geometry : angle 0.50501 (19622) hydrogen bonds : bond 0.02611 ( 693) hydrogen bonds : angle 3.99291 ( 1992) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 228 time to evaluate : 0.633 Fit side-chains revert: symmetry clash REVERT: A 162 ILE cc_start: 0.7125 (OUTLIER) cc_final: 0.6602 (tp) REVERT: A 199 ARG cc_start: 0.8225 (ttm-80) cc_final: 0.7681 (ttm-80) REVERT: A 252 ARG cc_start: 0.5788 (mtm-85) cc_final: 0.5505 (mtm-85) REVERT: F 80 ILE cc_start: 0.8801 (OUTLIER) cc_final: 0.8542 (pt) REVERT: F 217 MET cc_start: 0.7674 (mmp) cc_final: 0.6652 (mmp) REVERT: F 219 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8374 (mm) REVERT: F 350 MET cc_start: 0.4445 (tpp) cc_final: 0.4067 (tpt) REVERT: E 346 LYS cc_start: 0.8027 (ttpt) cc_final: 0.7818 (mtpt) REVERT: D 146 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8872 (mp) REVERT: D 284 GLN cc_start: 0.8384 (tp40) cc_final: 0.7937 (tp-100) REVERT: D 291 LYS cc_start: 0.7957 (OUTLIER) cc_final: 0.7393 (mttm) REVERT: D 304 GLU cc_start: 0.8283 (mm-30) cc_final: 0.7956 (mm-30) REVERT: D 348 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7971 (mm) REVERT: C 342 LYS cc_start: 0.8160 (mtmm) cc_final: 0.7882 (mmtt) outliers start: 51 outliers final: 36 residues processed: 256 average time/residue: 0.1315 time to fit residues: 48.4937 Evaluate side-chains 257 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 215 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 84 ASP Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 191 ILE Chi-restraints excluded: chain F residue 194 ILE Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 236 ASN Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 124 GLN Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 291 LYS Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 289 ASN Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 204 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 59 optimal weight: 3.9990 chunk 21 optimal weight: 7.9990 chunk 80 optimal weight: 0.9980 chunk 132 optimal weight: 0.9980 chunk 130 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 152 optimal weight: 5.9990 chunk 134 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 289 ASN ** B 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.181506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.131552 restraints weight = 17264.948| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.45 r_work: 0.3270 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14531 Z= 0.136 Angle : 0.537 10.274 19622 Z= 0.260 Chirality : 0.040 0.248 2250 Planarity : 0.003 0.045 2457 Dihedral : 9.833 86.927 2121 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.80 % Allowed : 23.71 % Favored : 73.49 % 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: 1.99 (0.21), residues: 1752 helix: 1.97 (0.17), residues: 947 sheet: -0.56 (0.44), residues: 138 loop : 0.99 (0.25), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 248 TYR 0.022 0.001 TYR B 167 PHE 0.013 0.001 PHE F 245 TRP 0.005 0.001 TRP C 220 HIS 0.003 0.001 HIS D 206 Details of bonding type rmsd covalent geometry : bond 0.00330 (14531) covalent geometry : angle 0.53693 (19622) hydrogen bonds : bond 0.02701 ( 693) hydrogen bonds : angle 4.02493 ( 1992) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 220 time to evaluate : 0.616 Fit side-chains revert: symmetry clash REVERT: A 162 ILE cc_start: 0.7141 (OUTLIER) cc_final: 0.6587 (tp) REVERT: A 199 ARG cc_start: 0.8283 (ttm-80) cc_final: 0.7719 (ttm-80) REVERT: F 217 MET cc_start: 0.7585 (mmp) cc_final: 0.6870 (mmp) REVERT: F 219 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8232 (mm) REVERT: F 350 MET cc_start: 0.4592 (tpp) cc_final: 0.4172 (tpt) REVERT: E 346 LYS cc_start: 0.8044 (ttpt) cc_final: 0.7831 (mtpt) REVERT: D 146 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8921 (mp) REVERT: D 284 GLN cc_start: 0.8463 (tp40) cc_final: 0.7989 (tp-100) REVERT: D 304 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8172 (mm-30) REVERT: D 348 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7895 (mm) outliers start: 44 outliers final: 34 residues processed: 241 average time/residue: 0.1092 time to fit residues: 39.7675 Evaluate side-chains 257 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 219 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 84 ASP Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 191 ILE Chi-restraints excluded: chain F residue 194 ILE Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 236 ASN Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 124 GLN Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 204 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 153 optimal weight: 0.0870 chunk 78 optimal weight: 0.9990 chunk 58 optimal weight: 10.0000 chunk 70 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 123 optimal weight: 0.7980 chunk 125 optimal weight: 0.9980 chunk 138 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 148 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 119 ASN C 289 ASN C 316 GLN ** B 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.182677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.133479 restraints weight = 17300.432| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.36 r_work: 0.3290 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14531 Z= 0.107 Angle : 0.522 8.918 19622 Z= 0.252 Chirality : 0.039 0.188 2250 Planarity : 0.003 0.046 2457 Dihedral : 9.712 86.345 2121 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.55 % Allowed : 23.96 % Favored : 73.49 % 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: 2.09 (0.21), residues: 1752 helix: 2.09 (0.17), residues: 930 sheet: -0.64 (0.46), residues: 128 loop : 0.99 (0.25), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 252 TYR 0.021 0.001 TYR B 167 PHE 0.008 0.001 PHE C 154 TRP 0.005 0.001 TRP C 166 HIS 0.003 0.000 HIS D 206 Details of bonding type rmsd covalent geometry : bond 0.00254 (14531) covalent geometry : angle 0.52188 (19622) hydrogen bonds : bond 0.02588 ( 693) hydrogen bonds : angle 3.98492 ( 1992) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 226 time to evaluate : 1.075 Fit side-chains revert: symmetry clash REVERT: A 162 ILE cc_start: 0.7113 (OUTLIER) cc_final: 0.6566 (tp) REVERT: A 199 ARG cc_start: 0.8307 (ttm-80) cc_final: 0.7774 (ttm-80) REVERT: F 217 MET cc_start: 0.7522 (mmp) cc_final: 0.6781 (mmp) REVERT: F 219 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8317 (mm) REVERT: D 119 ASN cc_start: 0.7801 (OUTLIER) cc_final: 0.7408 (t0) REVERT: D 146 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8955 (mp) REVERT: D 284 GLN cc_start: 0.8455 (tp40) cc_final: 0.7996 (tp-100) REVERT: D 304 GLU cc_start: 0.8444 (mm-30) cc_final: 0.8150 (mm-30) REVERT: D 348 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7923 (mm) REVERT: C 342 LYS cc_start: 0.8179 (mtmm) cc_final: 0.7773 (mmtt) outliers start: 40 outliers final: 32 residues processed: 244 average time/residue: 0.1119 time to fit residues: 40.9477 Evaluate side-chains 257 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 220 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 84 ASP Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 191 ILE Chi-restraints excluded: chain F residue 194 ILE Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 236 ASN Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 119 ASN Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 204 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 106 optimal weight: 4.9990 chunk 96 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 45 optimal weight: 8.9990 chunk 100 optimal weight: 0.0370 chunk 158 optimal weight: 0.9990 chunk 163 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 31 optimal weight: 0.0980 chunk 71 optimal weight: 0.9990 chunk 147 optimal weight: 7.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 119 ASN ** B 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.183114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.133972 restraints weight = 17368.134| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.35 r_work: 0.3290 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14531 Z= 0.105 Angle : 0.524 9.019 19622 Z= 0.253 Chirality : 0.039 0.203 2250 Planarity : 0.003 0.046 2457 Dihedral : 9.659 85.692 2121 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.80 % Allowed : 23.77 % Favored : 73.42 % 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: 2.12 (0.21), residues: 1752 helix: 2.09 (0.17), residues: 936 sheet: -0.61 (0.46), residues: 128 loop : 1.04 (0.25), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 252 TYR 0.019 0.001 TYR E 264 PHE 0.008 0.001 PHE C 344 TRP 0.005 0.001 TRP C 166 HIS 0.002 0.000 HIS D 206 Details of bonding type rmsd covalent geometry : bond 0.00247 (14531) covalent geometry : angle 0.52361 (19622) hydrogen bonds : bond 0.02567 ( 693) hydrogen bonds : angle 3.96109 ( 1992) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5560.17 seconds wall clock time: 95 minutes 21.47 seconds (5721.47 seconds total)