Starting phenix.real_space_refine on Sat Oct 11 12:44:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v2o_42918/10_2025/8v2o_42918.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v2o_42918/10_2025/8v2o_42918.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v2o_42918/10_2025/8v2o_42918.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v2o_42918/10_2025/8v2o_42918.map" model { file = "/net/cci-nas-00/data/ceres_data/8v2o_42918/10_2025/8v2o_42918.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v2o_42918/10_2025/8v2o_42918.cif" } resolution = 2.45 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= 0.012 sd= 0.166 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 10 5.49 5 Mg 5 5.21 5 S 105 5.16 5 C 9245 2.51 5 N 2470 2.21 5 O 2825 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14660 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2904 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2904 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2904 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2904 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2904 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.47, per 1000 atoms: 0.24 Number of scatterers: 14660 At special positions: 0 Unit cell: (81.32, 104.86, 192.6, 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 105 16.00 P 10 15.00 Mg 5 11.99 O 2825 8.00 N 2470 7.00 C 9245 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: 1.15 Conformation dependent library (CDL) restraints added in 661.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3440 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 30 sheets defined 49.5% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 91 Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.854A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 181 through 193 Processing helix chain 'A' and resid 194 through 197 Processing helix chain 'A' and resid 202 through 217 removed outlier: 3.648A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.597A pdb=" N CYS A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 289 through 295 Processing helix chain 'A' and resid 301 through 306 removed outlier: 4.239A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 337 through 348 Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 368 through 372 removed outlier: 3.626A pdb=" N HIS A 371 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 91 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.850A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 removed outlier: 3.520A pdb=" N GLY B 146 " --> pdb=" O LEU B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 181 through 193 Processing helix chain 'B' and resid 194 through 197 Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.733A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.637A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 286 through 288 No H-bonds generated for 'chain 'B' and resid 286 through 288' Processing helix chain 'B' and resid 289 through 295 Processing helix chain 'B' and resid 302 through 306 removed outlier: 4.015A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 337 through 348 Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 369 through 374 removed outlier: 3.504A pdb=" N CYS B 374 " --> pdb=" O VAL B 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 91 Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.850A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 removed outlier: 3.544A pdb=" N GLY C 146 " --> pdb=" O LEU C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 193 Processing helix chain 'C' and resid 194 through 197 Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.623A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.599A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 286 through 295 removed outlier: 3.727A pdb=" N ARG C 290 " --> pdb=" O ASP C 286 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LYS C 291 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 306 removed outlier: 4.031A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 337 through 348 Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 369 through 374 removed outlier: 3.526A pdb=" N CYS C 374 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 91 Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.501A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.850A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 Processing helix chain 'D' and resid 172 through 175 removed outlier: 3.504A pdb=" N ILE D 175 " --> pdb=" O PRO D 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 172 through 175' Processing helix chain 'D' and resid 181 through 193 Processing helix chain 'D' and resid 194 through 197 Processing helix chain 'D' and resid 202 through 217 removed outlier: 3.682A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.599A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 286 through 295 removed outlier: 3.604A pdb=" N ARG D 290 " --> pdb=" O ASP D 286 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LYS D 291 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ASP D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 306 removed outlier: 4.000A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 337 through 348 Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 369 through 374 Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 91 Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.501A pdb=" N HIS E 101 " --> pdb=" O PRO E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.833A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 146 Processing helix chain 'E' and resid 172 through 175 Processing helix chain 'E' and resid 181 through 193 Processing helix chain 'E' and resid 194 through 197 Processing helix chain 'E' and resid 202 through 217 removed outlier: 3.648A pdb=" N GLU E 207 " --> pdb=" O THR E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 233 Processing helix chain 'E' and resid 252 through 257 removed outlier: 3.638A pdb=" N CYS E 257 " --> pdb=" O GLU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 262 Processing helix chain 'E' and resid 263 through 268 Processing helix chain 'E' and resid 273 through 284 Processing helix chain 'E' and resid 286 through 295 removed outlier: 3.612A pdb=" N ARG E 290 " --> pdb=" O ASP E 286 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LYS E 291 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N ASP E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 306 removed outlier: 4.065A pdb=" N TYR E 306 " --> pdb=" O THR E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 337 through 348 Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 369 through 374 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.533A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 178 removed outlier: 6.388A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 176 through 178 removed outlier: 4.172A pdb=" N GLN C 41 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.517A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'B' and resid 176 through 178 removed outlier: 6.473A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 176 through 178 removed outlier: 4.193A pdb=" N GLN D 41 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.578A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'C' and resid 176 through 178 removed outlier: 6.407A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 176 through 178 removed outlier: 4.229A pdb=" N GLN E 41 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.570A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AC5, first strand: chain 'D' and resid 169 through 170 removed outlier: 6.289A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC7, first strand: chain 'E' and resid 29 through 32 removed outlier: 6.501A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AD1, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AD2, first strand: chain 'E' and resid 169 through 170 removed outlier: 6.476A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 238 through 241 727 hydrogen bonds defined for protein. 1845 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: 2.72 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4770 1.34 - 1.47: 3444 1.47 - 1.59: 6574 1.59 - 1.71: 17 1.71 - 1.84: 180 Bond restraints: 14985 Sorted by residual: bond pdb=" CB PRO B 367 " pdb=" CG PRO B 367 " ideal model delta sigma weight residual 1.492 1.639 -0.147 5.00e-02 4.00e+02 8.65e+00 bond pdb=" CG PRO B 367 " pdb=" CD PRO B 367 " ideal model delta sigma weight residual 1.503 1.404 0.099 3.40e-02 8.65e+02 8.49e+00 bond pdb=" CE1 HIC A 73 " pdb=" NE2 HIC A 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.85e+00 bond pdb=" CB PRO A 367 " pdb=" CG PRO A 367 " ideal model delta sigma weight residual 1.492 1.632 -0.140 5.00e-02 4.00e+02 7.80e+00 bond pdb=" CE1 HIC B 73 " pdb=" NE2 HIC B 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.70e+00 ... (remaining 14980 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.55: 20177 3.55 - 7.10: 140 7.10 - 10.65: 16 10.65 - 14.20: 3 14.20 - 17.75: 4 Bond angle restraints: 20340 Sorted by residual: angle pdb=" CA PRO B 367 " pdb=" N PRO B 367 " pdb=" CD PRO B 367 " ideal model delta sigma weight residual 112.00 95.15 16.85 1.40e+00 5.10e-01 1.45e+02 angle pdb=" CA PRO A 367 " pdb=" N PRO A 367 " pdb=" CD PRO A 367 " ideal model delta sigma weight residual 112.00 96.41 15.59 1.40e+00 5.10e-01 1.24e+02 angle pdb=" CB MET A 305 " pdb=" CG MET A 305 " pdb=" SD MET A 305 " ideal model delta sigma weight residual 112.70 130.45 -17.75 3.00e+00 1.11e-01 3.50e+01 angle pdb=" N PRO B 367 " pdb=" CD PRO B 367 " pdb=" CG PRO B 367 " ideal model delta sigma weight residual 103.20 95.01 8.19 1.50e+00 4.44e-01 2.98e+01 angle pdb=" CA PRO D 367 " pdb=" N PRO D 367 " pdb=" CD PRO D 367 " ideal model delta sigma weight residual 112.00 104.70 7.30 1.40e+00 5.10e-01 2.72e+01 ... (remaining 20335 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.77: 8765 34.77 - 69.54: 235 69.54 - 104.31: 10 104.31 - 139.08: 5 139.08 - 173.85: 5 Dihedral angle restraints: 9020 sinusoidal: 3645 harmonic: 5375 Sorted by residual: dihedral pdb=" C5' ADP B 401 " pdb=" O5' ADP B 401 " pdb=" PA ADP B 401 " pdb=" O2A ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 113.86 -173.85 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C5' ADP A 401 " pdb=" O5' ADP A 401 " pdb=" PA ADP A 401 " pdb=" O2A ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 113.57 -173.57 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 113.21 -173.21 1 2.00e+01 2.50e-03 4.78e+01 ... (remaining 9017 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1661 0.047 - 0.094: 407 0.094 - 0.141: 161 0.141 - 0.188: 17 0.188 - 0.235: 4 Chirality restraints: 2250 Sorted by residual: chirality pdb=" CB ILE B 151 " pdb=" CA ILE B 151 " pdb=" CG1 ILE B 151 " pdb=" CG2 ILE B 151 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CB ILE E 151 " pdb=" CA ILE E 151 " pdb=" CG1 ILE E 151 " pdb=" CG2 ILE E 151 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CB ILE A 151 " pdb=" CA ILE A 151 " pdb=" CG1 ILE A 151 " pdb=" CG2 ILE A 151 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 2247 not shown) Planarity restraints: 2605 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 366 " -0.144 5.00e-02 4.00e+02 2.00e-01 6.41e+01 pdb=" N PRO B 367 " 0.345 5.00e-02 4.00e+02 pdb=" CA PRO B 367 " -0.112 5.00e-02 4.00e+02 pdb=" CD PRO B 367 " -0.089 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 366 " 0.141 5.00e-02 4.00e+02 1.98e-01 6.26e+01 pdb=" N PRO A 367 " -0.341 5.00e-02 4.00e+02 pdb=" CA PRO A 367 " 0.111 5.00e-02 4.00e+02 pdb=" CD PRO A 367 " 0.089 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 366 " -0.115 5.00e-02 4.00e+02 1.71e-01 4.70e+01 pdb=" N PRO D 367 " 0.296 5.00e-02 4.00e+02 pdb=" CA PRO D 367 " -0.097 5.00e-02 4.00e+02 pdb=" CD PRO D 367 " -0.084 5.00e-02 4.00e+02 ... (remaining 2602 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3151 2.78 - 3.31: 12362 3.31 - 3.84: 25472 3.84 - 4.37: 31011 4.37 - 4.90: 52240 Nonbonded interactions: 124236 Sorted by model distance: nonbonded pdb=" O1B ADP E 401 " pdb="MG MG E 402 " model vdw 2.253 2.170 nonbonded pdb=" O GLN D 314 " pdb=" OG1 THR D 318 " model vdw 2.312 3.040 nonbonded pdb=" O GLN A 314 " pdb=" OG1 THR A 318 " model vdw 2.319 3.040 nonbonded pdb=" O GLN E 314 " pdb=" OG1 THR E 318 " model vdw 2.320 3.040 nonbonded pdb=" O GLN B 314 " pdb=" OG1 THR B 318 " model vdw 2.320 3.040 ... (remaining 124231 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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=1.00 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: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 14.440 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.147 14985 Z= 0.186 Angle : 0.800 17.746 20340 Z= 0.411 Chirality : 0.049 0.235 2250 Planarity : 0.009 0.200 2605 Dihedral : 15.842 173.854 5580 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.70 % Allowed : 12.10 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.34 (0.18), residues: 1835 helix: -1.65 (0.15), residues: 775 sheet: 0.28 (0.27), residues: 375 loop : -0.33 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG C 372 TYR 0.010 0.001 TYR D 306 PHE 0.014 0.001 PHE C 255 TRP 0.008 0.002 TRP E 356 HIS 0.004 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00436 (14985) covalent geometry : angle 0.80031 (20340) hydrogen bonds : bond 0.17767 ( 711) hydrogen bonds : angle 6.93030 ( 1845) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 0.506 Fit side-chains REVERT: D 246 GLN cc_start: 0.9107 (mt0) cc_final: 0.8750 (mp10) outliers start: 11 outliers final: 5 residues processed: 126 average time/residue: 0.8690 time to fit residues: 117.1679 Evaluate side-chains 120 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 115 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 260 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 10.0000 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN B 49 GLN C 41 GLN D 41 GLN E 41 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.056659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2509 r_free = 0.2509 target = 0.041682 restraints weight = 33010.195| |-----------------------------------------------------------------------------| r_work (start): 0.2490 rms_B_bonded: 2.51 r_work: 0.2350 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2220 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 14985 Z= 0.321 Angle : 0.677 7.473 20340 Z= 0.328 Chirality : 0.049 0.198 2250 Planarity : 0.006 0.113 2605 Dihedral : 9.847 149.038 2095 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.40 % Allowed : 9.17 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.20), residues: 1835 helix: -0.04 (0.18), residues: 770 sheet: 0.56 (0.29), residues: 325 loop : 0.57 (0.25), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 372 TYR 0.008 0.001 TYR E 188 PHE 0.017 0.002 PHE E 262 TRP 0.011 0.002 TRP E 340 HIS 0.005 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00747 (14985) covalent geometry : angle 0.67742 (20340) hydrogen bonds : bond 0.03822 ( 711) hydrogen bonds : angle 4.79759 ( 1845) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 0.662 Fit side-chains REVERT: A 176 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8359 (mtt) REVERT: D 246 GLN cc_start: 0.8949 (mt0) cc_final: 0.8576 (mt0) REVERT: D 314 GLN cc_start: 0.9097 (OUTLIER) cc_final: 0.8421 (tt0) REVERT: E 132 MET cc_start: 0.9245 (tmm) cc_final: 0.9021 (ppp) outliers start: 22 outliers final: 5 residues processed: 123 average time/residue: 0.9545 time to fit residues: 125.4189 Evaluate side-chains 114 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain E residue 45 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 9 optimal weight: 7.9990 chunk 129 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 87 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 175 optimal weight: 0.9990 chunk 111 optimal weight: 7.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 137 GLN B 49 GLN C 41 GLN D 41 GLN D 162 ASN E 41 GLN E 246 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.058498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2559 r_free = 0.2559 target = 0.043622 restraints weight = 33123.285| |-----------------------------------------------------------------------------| r_work (start): 0.2540 rms_B_bonded: 2.53 r_work: 0.2400 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2268 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14985 Z= 0.130 Angle : 0.557 6.252 20340 Z= 0.264 Chirality : 0.044 0.163 2250 Planarity : 0.005 0.088 2605 Dihedral : 8.271 127.391 2093 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.34 % Allowed : 9.55 % Favored : 89.11 % 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 aren not related in a simple way. whole: 0.89 (0.20), residues: 1835 helix: 0.66 (0.19), residues: 770 sheet: 0.61 (0.29), residues: 325 loop : 0.76 (0.25), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 372 TYR 0.005 0.001 TYR B 69 PHE 0.008 0.001 PHE B 255 TRP 0.011 0.001 TRP C 79 HIS 0.004 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00304 (14985) covalent geometry : angle 0.55668 (20340) hydrogen bonds : bond 0.02867 ( 711) hydrogen bonds : angle 4.47057 ( 1845) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 0.592 Fit side-chains REVERT: A 246 GLN cc_start: 0.8195 (mp10) cc_final: 0.7977 (mp10) REVERT: A 354 GLN cc_start: 0.8855 (pm20) cc_final: 0.8557 (pm20) REVERT: A 355 MET cc_start: 0.9282 (mtm) cc_final: 0.9049 (mtp) REVERT: C 246 GLN cc_start: 0.9064 (mt0) cc_final: 0.8766 (mt0) REVERT: C 354 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.8547 (pm20) REVERT: D 176 MET cc_start: 0.9193 (mtm) cc_final: 0.8812 (mtm) REVERT: D 246 GLN cc_start: 0.9021 (mt0) cc_final: 0.8580 (mt0) REVERT: E 132 MET cc_start: 0.9199 (tmm) cc_final: 0.8933 (ppp) REVERT: E 246 GLN cc_start: 0.8921 (OUTLIER) cc_final: 0.8700 (mp10) outliers start: 21 outliers final: 3 residues processed: 124 average time/residue: 0.9976 time to fit residues: 131.8368 Evaluate side-chains 117 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 112 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain E residue 246 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 129 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 160 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 169 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 133 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 chunk 41 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN B 49 GLN C 41 GLN D 41 GLN E 41 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.055423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2481 r_free = 0.2481 target = 0.040740 restraints weight = 33216.233| |-----------------------------------------------------------------------------| r_work (start): 0.2465 rms_B_bonded: 2.46 r_work: 0.2326 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2196 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 14985 Z= 0.317 Angle : 0.646 7.181 20340 Z= 0.313 Chirality : 0.049 0.190 2250 Planarity : 0.005 0.073 2605 Dihedral : 7.463 111.529 2090 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.85 % Allowed : 9.04 % Favored : 89.11 % 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 aren not related in a simple way. whole: 0.99 (0.20), residues: 1835 helix: 0.80 (0.20), residues: 770 sheet: 0.60 (0.28), residues: 325 loop : 0.78 (0.25), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 372 TYR 0.007 0.001 TYR D 133 PHE 0.014 0.002 PHE C 262 TRP 0.013 0.002 TRP C 79 HIS 0.005 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00745 (14985) covalent geometry : angle 0.64634 (20340) hydrogen bonds : bond 0.03504 ( 711) hydrogen bonds : angle 4.56090 ( 1845) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 114 time to evaluate : 0.616 Fit side-chains REVERT: A 176 MET cc_start: 0.8919 (OUTLIER) cc_final: 0.8384 (mtt) REVERT: A 246 GLN cc_start: 0.8207 (mp10) cc_final: 0.8007 (mp10) REVERT: A 354 GLN cc_start: 0.8901 (pm20) cc_final: 0.8596 (pm20) REVERT: A 355 MET cc_start: 0.9459 (mtm) cc_final: 0.9003 (mtp) REVERT: B 176 MET cc_start: 0.9063 (mtp) cc_final: 0.8826 (mmm) REVERT: B 314 GLN cc_start: 0.8977 (OUTLIER) cc_final: 0.8262 (tt0) REVERT: C 246 GLN cc_start: 0.8942 (mt0) cc_final: 0.8573 (mt0) REVERT: C 354 GLN cc_start: 0.8958 (OUTLIER) cc_final: 0.8575 (pm20) REVERT: D 176 MET cc_start: 0.9200 (OUTLIER) cc_final: 0.8840 (mtm) REVERT: D 246 GLN cc_start: 0.8910 (mt0) cc_final: 0.8559 (mt0) REVERT: D 314 GLN cc_start: 0.9033 (OUTLIER) cc_final: 0.8320 (tt0) REVERT: D 372 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.8198 (ptp-110) REVERT: E 246 GLN cc_start: 0.8856 (OUTLIER) cc_final: 0.8643 (mp10) outliers start: 29 outliers final: 5 residues processed: 127 average time/residue: 0.9810 time to fit residues: 132.9585 Evaluate side-chains 126 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 372 ARG Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 246 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 72 optimal weight: 1.9990 chunk 152 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 chunk 153 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 168 optimal weight: 0.7980 chunk 179 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN C 41 GLN D 41 GLN E 41 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.057829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2538 r_free = 0.2538 target = 0.042945 restraints weight = 32787.314| |-----------------------------------------------------------------------------| r_work (start): 0.2522 rms_B_bonded: 2.52 r_work: 0.2382 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2250 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14985 Z= 0.123 Angle : 0.551 6.121 20340 Z= 0.262 Chirality : 0.044 0.168 2250 Planarity : 0.004 0.065 2605 Dihedral : 6.793 96.596 2090 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.27 % Allowed : 9.94 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.21), residues: 1835 helix: 1.12 (0.20), residues: 770 sheet: 0.68 (0.29), residues: 325 loop : 0.88 (0.25), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 372 TYR 0.006 0.001 TYR B 294 PHE 0.007 0.001 PHE D 127 TRP 0.013 0.002 TRP C 79 HIS 0.003 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00288 (14985) covalent geometry : angle 0.55106 (20340) hydrogen bonds : bond 0.02668 ( 711) hydrogen bonds : angle 4.34126 ( 1845) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 0.584 Fit side-chains REVERT: A 246 GLN cc_start: 0.8318 (mp10) cc_final: 0.8055 (mp10) REVERT: A 354 GLN cc_start: 0.8867 (pm20) cc_final: 0.8539 (pm20) REVERT: A 355 MET cc_start: 0.9370 (mtm) cc_final: 0.8960 (mtp) REVERT: B 176 MET cc_start: 0.9083 (mtp) cc_final: 0.8880 (mmm) REVERT: C 246 GLN cc_start: 0.9023 (mt0) cc_final: 0.8660 (mt0) REVERT: D 95 ARG cc_start: 0.9015 (mtp85) cc_final: 0.8776 (mtt-85) REVERT: D 246 GLN cc_start: 0.8969 (mt0) cc_final: 0.8562 (mt0) outliers start: 20 outliers final: 5 residues processed: 124 average time/residue: 0.9908 time to fit residues: 131.0182 Evaluate side-chains 121 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 116 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain E residue 45 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 21 optimal weight: 10.0000 chunk 134 optimal weight: 0.2980 chunk 44 optimal weight: 5.9990 chunk 119 optimal weight: 0.2980 chunk 42 optimal weight: 1.9990 chunk 170 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 160 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 108 optimal weight: 8.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN C 41 GLN D 41 GLN E 41 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.058088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2553 r_free = 0.2553 target = 0.043397 restraints weight = 32614.834| |-----------------------------------------------------------------------------| r_work (start): 0.2539 rms_B_bonded: 2.48 r_work: 0.2398 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2265 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14985 Z= 0.115 Angle : 0.541 6.169 20340 Z= 0.256 Chirality : 0.043 0.151 2250 Planarity : 0.004 0.056 2605 Dihedral : 6.366 87.010 2090 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.96 % Allowed : 10.76 % Favored : 88.28 % 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 aren not related in a simple way. whole: 1.35 (0.21), residues: 1835 helix: 1.16 (0.19), residues: 800 sheet: 0.73 (0.29), residues: 325 loop : 0.91 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 372 TYR 0.005 0.001 TYR C 143 PHE 0.007 0.001 PHE B 255 TRP 0.012 0.001 TRP C 79 HIS 0.003 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00269 (14985) covalent geometry : angle 0.54138 (20340) hydrogen bonds : bond 0.02529 ( 711) hydrogen bonds : angle 4.24243 ( 1845) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.539 Fit side-chains REVERT: A 176 MET cc_start: 0.8872 (OUTLIER) cc_final: 0.8375 (mtt) REVERT: A 246 GLN cc_start: 0.8291 (mp10) cc_final: 0.8027 (mp10) REVERT: A 305 MET cc_start: 0.9081 (OUTLIER) cc_final: 0.8711 (mmm) REVERT: A 354 GLN cc_start: 0.8843 (pm20) cc_final: 0.8526 (pm20) REVERT: A 355 MET cc_start: 0.9357 (mtm) cc_final: 0.8943 (mtp) REVERT: C 246 GLN cc_start: 0.9023 (mt0) cc_final: 0.8612 (mt0) REVERT: D 95 ARG cc_start: 0.8996 (mtp85) cc_final: 0.8759 (mtt-85) REVERT: D 246 GLN cc_start: 0.8951 (mt0) cc_final: 0.8528 (mt0) REVERT: E 354 GLN cc_start: 0.9127 (pm20) cc_final: 0.8853 (pp30) outliers start: 15 outliers final: 3 residues processed: 121 average time/residue: 0.9724 time to fit residues: 125.8323 Evaluate side-chains 120 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 115 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain E residue 45 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 131 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 chunk 181 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 102 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 16 optimal weight: 0.2980 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN B 49 GLN C 41 GLN D 41 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.056882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2533 r_free = 0.2533 target = 0.042318 restraints weight = 32491.222| |-----------------------------------------------------------------------------| r_work (start): 0.2493 rms_B_bonded: 2.44 r_work: 0.2354 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2223 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 14985 Z= 0.220 Angle : 0.590 6.313 20340 Z= 0.283 Chirality : 0.046 0.169 2250 Planarity : 0.004 0.063 2605 Dihedral : 6.596 92.104 2090 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.21 % Allowed : 10.51 % Favored : 88.28 % 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 aren not related in a simple way. whole: 1.26 (0.20), residues: 1835 helix: 1.07 (0.19), residues: 800 sheet: 0.71 (0.28), residues: 325 loop : 0.88 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 372 TYR 0.007 0.001 TYR E 188 PHE 0.011 0.001 PHE C 262 TRP 0.012 0.002 TRP C 79 HIS 0.005 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00517 (14985) covalent geometry : angle 0.59021 (20340) hydrogen bonds : bond 0.03031 ( 711) hydrogen bonds : angle 4.33751 ( 1845) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.661 Fit side-chains REVERT: A 176 MET cc_start: 0.8903 (OUTLIER) cc_final: 0.8401 (mtt) REVERT: A 246 GLN cc_start: 0.8292 (mp10) cc_final: 0.8007 (mp10) REVERT: A 305 MET cc_start: 0.9113 (OUTLIER) cc_final: 0.8821 (mmm) REVERT: A 354 GLN cc_start: 0.8845 (pm20) cc_final: 0.8517 (pm20) REVERT: A 355 MET cc_start: 0.9447 (mtm) cc_final: 0.8980 (mtp) REVERT: C 107 GLU cc_start: 0.9070 (OUTLIER) cc_final: 0.8826 (tt0) REVERT: C 314 GLN cc_start: 0.8982 (OUTLIER) cc_final: 0.7929 (tp40) REVERT: D 95 ARG cc_start: 0.8994 (mtp85) cc_final: 0.8772 (mtt-85) REVERT: D 176 MET cc_start: 0.9213 (mtm) cc_final: 0.8852 (mtm) REVERT: D 246 GLN cc_start: 0.8917 (mt0) cc_final: 0.8543 (mt0) REVERT: D 314 GLN cc_start: 0.9030 (OUTLIER) cc_final: 0.8302 (tt0) REVERT: E 354 GLN cc_start: 0.9040 (pm20) cc_final: 0.8799 (pp30) outliers start: 19 outliers final: 3 residues processed: 125 average time/residue: 0.9740 time to fit residues: 129.8526 Evaluate side-chains 122 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 114 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain E residue 45 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 30 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 146 optimal weight: 4.9990 chunk 111 optimal weight: 10.0000 chunk 124 optimal weight: 0.8980 chunk 11 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 172 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 159 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN C 41 GLN D 41 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.056940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2538 r_free = 0.2538 target = 0.042467 restraints weight = 32821.599| |-----------------------------------------------------------------------------| r_work (start): 0.2499 rms_B_bonded: 2.44 r_work: 0.2360 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2230 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14985 Z= 0.198 Angle : 0.582 6.436 20340 Z= 0.278 Chirality : 0.046 0.168 2250 Planarity : 0.004 0.061 2605 Dihedral : 6.590 93.252 2090 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.83 % Allowed : 11.02 % Favored : 88.15 % 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 aren not related in a simple way. whole: 1.28 (0.21), residues: 1835 helix: 1.11 (0.19), residues: 800 sheet: 0.67 (0.28), residues: 325 loop : 0.88 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 372 TYR 0.008 0.001 TYR D 133 PHE 0.009 0.001 PHE C 262 TRP 0.012 0.002 TRP C 79 HIS 0.004 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00467 (14985) covalent geometry : angle 0.58152 (20340) hydrogen bonds : bond 0.02875 ( 711) hydrogen bonds : angle 4.32057 ( 1845) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.636 Fit side-chains REVERT: A 137 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.8106 (mt0) REVERT: A 176 MET cc_start: 0.8898 (OUTLIER) cc_final: 0.8394 (mtt) REVERT: A 246 GLN cc_start: 0.8284 (mp10) cc_final: 0.7981 (mp10) REVERT: A 305 MET cc_start: 0.9112 (OUTLIER) cc_final: 0.8822 (mmm) REVERT: A 354 GLN cc_start: 0.8857 (pm20) cc_final: 0.8519 (pm20) REVERT: A 355 MET cc_start: 0.9444 (mtm) cc_final: 0.8967 (mtp) REVERT: C 107 GLU cc_start: 0.9080 (OUTLIER) cc_final: 0.8807 (tt0) REVERT: D 95 ARG cc_start: 0.8992 (mtp85) cc_final: 0.8775 (mtt-85) REVERT: D 176 MET cc_start: 0.9218 (mtm) cc_final: 0.8754 (mtm) REVERT: D 246 GLN cc_start: 0.8907 (mt0) cc_final: 0.8518 (mt0) REVERT: D 314 GLN cc_start: 0.9019 (OUTLIER) cc_final: 0.8285 (tt0) REVERT: E 354 GLN cc_start: 0.8995 (pm20) cc_final: 0.8791 (pp30) outliers start: 13 outliers final: 3 residues processed: 123 average time/residue: 0.9574 time to fit residues: 125.5081 Evaluate side-chains 123 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 115 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain E residue 45 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 181 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 160 optimal weight: 3.9990 chunk 67 optimal weight: 0.5980 chunk 177 optimal weight: 5.9990 chunk 156 optimal weight: 0.6980 chunk 134 optimal weight: 0.0570 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN C 41 GLN D 41 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.058526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2561 r_free = 0.2561 target = 0.043760 restraints weight = 32829.203| |-----------------------------------------------------------------------------| r_work (start): 0.2545 rms_B_bonded: 2.51 r_work: 0.2403 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2271 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14985 Z= 0.099 Angle : 0.544 6.461 20340 Z= 0.258 Chirality : 0.043 0.160 2250 Planarity : 0.004 0.059 2605 Dihedral : 6.185 85.336 2090 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.51 % Allowed : 11.40 % Favored : 88.09 % 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 aren not related in a simple way. whole: 1.44 (0.21), residues: 1835 helix: 1.26 (0.19), residues: 800 sheet: 0.72 (0.29), residues: 325 loop : 0.96 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 372 TYR 0.008 0.001 TYR A 143 PHE 0.007 0.001 PHE C 255 TRP 0.013 0.001 TRP C 79 HIS 0.003 0.000 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00230 (14985) covalent geometry : angle 0.54408 (20340) hydrogen bonds : bond 0.02448 ( 711) hydrogen bonds : angle 4.19523 ( 1845) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 0.549 Fit side-chains REVERT: A 137 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7961 (mm-40) REVERT: A 246 GLN cc_start: 0.8335 (mp10) cc_final: 0.8025 (mp10) REVERT: A 305 MET cc_start: 0.9051 (OUTLIER) cc_final: 0.8799 (mmm) REVERT: A 354 GLN cc_start: 0.8850 (pm20) cc_final: 0.8520 (pm20) REVERT: A 355 MET cc_start: 0.9376 (mtm) cc_final: 0.8901 (mtp) REVERT: C 107 GLU cc_start: 0.9090 (OUTLIER) cc_final: 0.8845 (tt0) REVERT: C 246 GLN cc_start: 0.9047 (mt0) cc_final: 0.8549 (mp10) REVERT: C 372 ARG cc_start: 0.8871 (mtm110) cc_final: 0.8636 (ttp-110) REVERT: D 95 ARG cc_start: 0.8959 (mtp85) cc_final: 0.8742 (mtt-85) REVERT: D 176 MET cc_start: 0.9194 (mtm) cc_final: 0.8832 (mtm) REVERT: D 246 GLN cc_start: 0.8956 (mt0) cc_final: 0.8543 (mt0) REVERT: E 246 GLN cc_start: 0.9022 (mt0) cc_final: 0.8626 (mp10) outliers start: 8 outliers final: 2 residues processed: 122 average time/residue: 0.9111 time to fit residues: 118.8030 Evaluate side-chains 123 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 118 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain E residue 45 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 20 optimal weight: 8.9990 chunk 44 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 6 optimal weight: 0.3980 chunk 119 optimal weight: 0.7980 chunk 78 optimal weight: 7.9990 chunk 138 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN B 49 GLN C 41 GLN D 41 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.057933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2546 r_free = 0.2546 target = 0.043169 restraints weight = 32575.181| |-----------------------------------------------------------------------------| r_work (start): 0.2532 rms_B_bonded: 2.49 r_work: 0.2390 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2258 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14985 Z= 0.136 Angle : 0.560 6.494 20340 Z= 0.266 Chirality : 0.044 0.149 2250 Planarity : 0.004 0.058 2605 Dihedral : 6.115 83.627 2090 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.45 % Allowed : 11.59 % Favored : 87.96 % 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 aren not related in a simple way. whole: 1.45 (0.21), residues: 1835 helix: 1.24 (0.19), residues: 805 sheet: 0.81 (0.30), residues: 315 loop : 0.94 (0.25), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG E 372 TYR 0.007 0.001 TYR A 143 PHE 0.006 0.001 PHE C 262 TRP 0.011 0.001 TRP E 79 HIS 0.003 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00322 (14985) covalent geometry : angle 0.56027 (20340) hydrogen bonds : bond 0.02557 ( 711) hydrogen bonds : angle 4.20141 ( 1845) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 118 time to evaluate : 0.598 Fit side-chains REVERT: A 137 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.8039 (mm-40) REVERT: A 246 GLN cc_start: 0.8317 (mp10) cc_final: 0.8011 (mp10) REVERT: A 305 MET cc_start: 0.9056 (OUTLIER) cc_final: 0.8810 (mmm) REVERT: A 354 GLN cc_start: 0.8887 (pm20) cc_final: 0.8541 (pm20) REVERT: A 355 MET cc_start: 0.9395 (mtm) cc_final: 0.8905 (mtp) REVERT: C 107 GLU cc_start: 0.9019 (OUTLIER) cc_final: 0.8781 (tt0) REVERT: C 246 GLN cc_start: 0.9043 (mt0) cc_final: 0.8526 (mp10) REVERT: C 372 ARG cc_start: 0.8883 (mtm110) cc_final: 0.8653 (ttp-110) REVERT: D 95 ARG cc_start: 0.8986 (mtp85) cc_final: 0.8777 (mtt-85) REVERT: D 176 MET cc_start: 0.9207 (mtm) cc_final: 0.8894 (mtm) REVERT: D 246 GLN cc_start: 0.8948 (mt0) cc_final: 0.8517 (mt0) outliers start: 7 outliers final: 2 residues processed: 121 average time/residue: 0.9322 time to fit residues: 120.5776 Evaluate side-chains 122 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 117 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain E residue 45 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 2 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 58 optimal weight: 6.9990 chunk 96 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 156 optimal weight: 0.4980 chunk 29 optimal weight: 4.9990 chunk 82 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN B 49 GLN C 41 GLN D 41 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.058780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2571 r_free = 0.2571 target = 0.044079 restraints weight = 32462.087| |-----------------------------------------------------------------------------| r_work (start): 0.2556 rms_B_bonded: 2.49 r_work: 0.2414 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2283 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14985 Z= 0.100 Angle : 0.549 8.676 20340 Z= 0.258 Chirality : 0.043 0.153 2250 Planarity : 0.004 0.057 2605 Dihedral : 5.898 79.361 2090 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.51 % Allowed : 11.46 % Favored : 88.03 % 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 aren not related in a simple way. whole: 1.52 (0.21), residues: 1835 helix: 1.32 (0.19), residues: 805 sheet: 0.82 (0.30), residues: 315 loop : 0.97 (0.25), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 372 TYR 0.007 0.001 TYR C 143 PHE 0.006 0.001 PHE C 255 TRP 0.012 0.001 TRP C 79 HIS 0.003 0.000 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00234 (14985) covalent geometry : angle 0.54855 (20340) hydrogen bonds : bond 0.02389 ( 711) hydrogen bonds : angle 4.15052 ( 1845) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5035.25 seconds wall clock time: 86 minutes 34.86 seconds (5194.86 seconds total)