Starting phenix.real_space_refine on Fri Jun 13 04:59:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v2o_42918/06_2025/8v2o_42918.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v2o_42918/06_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_42918/06_2025/8v2o_42918.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v2o_42918/06_2025/8v2o_42918.map" model { file = "/net/cci-nas-00/data/ceres_data/8v2o_42918/06_2025/8v2o_42918.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v2o_42918/06_2025/8v2o_42918.cif" } resolution = 2.45 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.23, per 1000 atoms: 0.63 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: 3.55 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 2.14 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: 5.30 Time building geometry restraints manager: 4.29 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: 0.03 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: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.610 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 36.580 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.670 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.008 0.002 TRP E 356 HIS 0.004 0.001 HIS C 161 PHE 0.014 0.001 PHE C 255 TYR 0.010 0.001 TYR D 306 ARG 0.023 0.001 ARG C 372 Details of bonding type rmsd hydrogen bonds : bond 0.17767 ( 711) hydrogen bonds : angle 6.93030 ( 1845) covalent geometry : bond 0.00436 (14985) covalent geometry : angle 0.80031 (20340) *********************** 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 : 1.516 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: 1.7990 time to fit residues: 243.7951 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 : 1.686 ------------------------------------------------------------------------------- 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 156 optimal weight: 6.9990 chunk 140 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 94 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 chunk 145 optimal weight: 7.9990 chunk 56 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 chunk 107 optimal weight: 0.7980 chunk 168 optimal weight: 7.9990 overall best weight: 3.7186 ------------------------------------------------------------------------------- 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 = 0.2858 r_free = 0.2858 target = 0.056579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2514 r_free = 0.2514 target = 0.041795 restraints weight = 33013.338| |-----------------------------------------------------------------------------| r_work (start): 0.2495 rms_B_bonded: 2.47 r_work: 0.2357 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2228 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 14985 Z= 0.304 Angle : 0.673 7.378 20340 Z= 0.327 Chirality : 0.048 0.190 2250 Planarity : 0.006 0.117 2605 Dihedral : 9.765 148.261 2095 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.34 % Allowed : 9.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.20), residues: 1835 helix: 0.00 (0.18), residues: 770 sheet: 0.55 (0.29), residues: 325 loop : 0.57 (0.24), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 340 HIS 0.006 0.001 HIS B 161 PHE 0.018 0.002 PHE C 262 TYR 0.008 0.001 TYR E 188 ARG 0.011 0.001 ARG C 372 Details of bonding type rmsd hydrogen bonds : bond 0.03815 ( 711) hydrogen bonds : angle 4.76923 ( 1845) covalent geometry : bond 0.00702 (14985) covalent geometry : angle 0.67331 (20340) *********************** 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 132 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 1.585 Fit side-chains REVERT: A 176 MET cc_start: 0.8896 (OUTLIER) cc_final: 0.8356 (mtt) REVERT: B 227 MET cc_start: 0.8745 (mmm) cc_final: 0.8498 (mmm) REVERT: D 246 GLN cc_start: 0.8945 (mt0) cc_final: 0.8574 (mt0) REVERT: D 314 GLN cc_start: 0.9098 (OUTLIER) cc_final: 0.8412 (tt0) outliers start: 21 outliers final: 5 residues processed: 122 average time/residue: 1.9416 time to fit residues: 253.5519 Evaluate side-chains 115 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 108 time to evaluate : 1.677 ------------------------------------------------------------------------------- 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 23 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 174 optimal weight: 0.0770 chunk 141 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 143 optimal weight: 0.9990 overall best weight: 1.8146 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.057612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2542 r_free = 0.2542 target = 0.042882 restraints weight = 33088.612| |-----------------------------------------------------------------------------| r_work (start): 0.2523 rms_B_bonded: 2.49 r_work: 0.2385 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2254 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14985 Z= 0.161 Angle : 0.569 6.386 20340 Z= 0.271 Chirality : 0.045 0.174 2250 Planarity : 0.005 0.090 2605 Dihedral : 8.192 124.278 2093 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.34 % Allowed : 9.62 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.20), residues: 1835 helix: 0.65 (0.19), residues: 770 sheet: 0.58 (0.29), residues: 325 loop : 0.76 (0.25), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 79 HIS 0.003 0.001 HIS C 161 PHE 0.008 0.001 PHE C 262 TYR 0.005 0.001 TYR E 188 ARG 0.010 0.000 ARG E 372 Details of bonding type rmsd hydrogen bonds : bond 0.03042 ( 711) hydrogen bonds : angle 4.50123 ( 1845) covalent geometry : bond 0.00376 (14985) covalent geometry : angle 0.56860 (20340) *********************** 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 136 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 1.583 Fit side-chains REVERT: A 354 GLN cc_start: 0.8858 (pm20) cc_final: 0.8572 (pm20) REVERT: A 355 MET cc_start: 0.9360 (mtm) cc_final: 0.9054 (mtp) REVERT: B 227 MET cc_start: 0.8777 (mmm) cc_final: 0.8391 (mmm) REVERT: C 246 GLN cc_start: 0.9020 (mt0) cc_final: 0.8689 (mt0) REVERT: C 354 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.8525 (pm20) REVERT: D 176 MET cc_start: 0.9216 (mtm) cc_final: 0.8811 (mtm) REVERT: D 246 GLN cc_start: 0.8991 (mt0) cc_final: 0.8588 (mt0) REVERT: E 246 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.8664 (mp10) outliers start: 21 outliers final: 3 residues processed: 123 average time/residue: 2.0030 time to fit residues: 263.8614 Evaluate side-chains 116 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 111 time to evaluate : 1.660 ------------------------------------------------------------------------------- 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 49 optimal weight: 6.9990 chunk 91 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 34 optimal weight: 8.9990 chunk 177 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 174 optimal weight: 0.4980 chunk 50 optimal weight: 0.6980 chunk 128 optimal weight: 4.9990 chunk 76 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.2908 r_free = 0.2908 target = 0.058844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2578 r_free = 0.2578 target = 0.044251 restraints weight = 32423.847| |-----------------------------------------------------------------------------| r_work (start): 0.2561 rms_B_bonded: 2.48 r_work: 0.2424 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2294 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14985 Z= 0.100 Angle : 0.534 5.730 20340 Z= 0.251 Chirality : 0.043 0.152 2250 Planarity : 0.004 0.076 2605 Dihedral : 6.711 99.023 2090 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.08 % Allowed : 9.81 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.20), residues: 1835 helix: 0.94 (0.19), residues: 795 sheet: 0.65 (0.29), residues: 325 loop : 0.87 (0.25), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 79 HIS 0.003 0.000 HIS A 161 PHE 0.007 0.001 PHE B 255 TYR 0.005 0.001 TYR D 69 ARG 0.011 0.000 ARG E 372 Details of bonding type rmsd hydrogen bonds : bond 0.02502 ( 711) hydrogen bonds : angle 4.30608 ( 1845) covalent geometry : bond 0.00229 (14985) covalent geometry : angle 0.53382 (20340) *********************** 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 133 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 1.538 Fit side-chains REVERT: A 246 GLN cc_start: 0.8123 (mp10) cc_final: 0.7776 (pm20) REVERT: A 354 GLN cc_start: 0.8831 (pm20) cc_final: 0.8465 (pm20) REVERT: A 355 MET cc_start: 0.9283 (mtm) cc_final: 0.9019 (mtp) REVERT: B 227 MET cc_start: 0.8813 (mmm) cc_final: 0.8320 (mmm) REVERT: C 246 GLN cc_start: 0.9055 (mt0) cc_final: 0.8676 (mt0) REVERT: D 176 MET cc_start: 0.9224 (mtm) cc_final: 0.8884 (mtm) REVERT: D 246 GLN cc_start: 0.9016 (mt0) cc_final: 0.8557 (mt0) outliers start: 17 outliers final: 3 residues processed: 120 average time/residue: 2.0812 time to fit residues: 267.6317 Evaluate side-chains 117 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 114 time to evaluate : 1.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 355 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 26 optimal weight: 0.7980 chunk 146 optimal weight: 10.0000 chunk 71 optimal weight: 8.9990 chunk 129 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 41 optimal weight: 0.0670 chunk 170 optimal weight: 0.7980 chunk 134 optimal weight: 0.0980 chunk 163 optimal weight: 0.8980 chunk 119 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- 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 = 0.2934 r_free = 0.2934 target = 0.059973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.045210 restraints weight = 32636.052| |-----------------------------------------------------------------------------| r_work (start): 0.2589 rms_B_bonded: 2.52 r_work: 0.2450 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2321 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14985 Z= 0.086 Angle : 0.522 6.111 20340 Z= 0.244 Chirality : 0.042 0.133 2250 Planarity : 0.004 0.065 2605 Dihedral : 5.937 78.457 2090 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.21 % Allowed : 9.81 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.21), residues: 1835 helix: 1.25 (0.20), residues: 795 sheet: 0.73 (0.30), residues: 325 loop : 0.96 (0.25), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 79 HIS 0.003 0.000 HIS A 161 PHE 0.007 0.001 PHE B 255 TYR 0.006 0.001 TYR D 306 ARG 0.009 0.000 ARG C 372 Details of bonding type rmsd hydrogen bonds : bond 0.02305 ( 711) hydrogen bonds : angle 4.18151 ( 1845) covalent geometry : bond 0.00198 (14985) covalent geometry : angle 0.52164 (20340) *********************** 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 136 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 1.665 Fit side-chains REVERT: A 246 GLN cc_start: 0.8075 (mp10) cc_final: 0.7636 (pm20) REVERT: A 354 GLN cc_start: 0.8809 (pm20) cc_final: 0.8516 (pm20) REVERT: A 355 MET cc_start: 0.9239 (mtm) cc_final: 0.8970 (mtp) REVERT: B 227 MET cc_start: 0.8801 (mmm) cc_final: 0.8351 (mmm) REVERT: C 246 GLN cc_start: 0.9091 (mt0) cc_final: 0.8740 (mt0) REVERT: D 176 MET cc_start: 0.9241 (OUTLIER) cc_final: 0.8982 (mtm) REVERT: D 246 GLN cc_start: 0.9030 (mt0) cc_final: 0.8586 (mt0) REVERT: E 44 MET cc_start: 0.9251 (mtt) cc_final: 0.8756 (mtt) REVERT: E 314 GLN cc_start: 0.8947 (OUTLIER) cc_final: 0.8324 (tp40) outliers start: 19 outliers final: 4 residues processed: 124 average time/residue: 1.9358 time to fit residues: 257.5604 Evaluate side-chains 122 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 116 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain E residue 314 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 169 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 chunk 34 optimal weight: 9.9990 chunk 45 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 chunk 140 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 113 optimal weight: 0.6980 overall best weight: 1.7182 ------------------------------------------------------------------------------- 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 = 0.2889 r_free = 0.2889 target = 0.057991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2549 r_free = 0.2549 target = 0.043222 restraints weight = 32785.256| |-----------------------------------------------------------------------------| r_work (start): 0.2533 rms_B_bonded: 2.50 r_work: 0.2394 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2263 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14985 Z= 0.152 Angle : 0.556 9.486 20340 Z= 0.262 Chirality : 0.044 0.149 2250 Planarity : 0.004 0.069 2605 Dihedral : 6.111 83.350 2090 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.08 % Allowed : 10.25 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.21), residues: 1835 helix: 1.39 (0.20), residues: 770 sheet: 0.74 (0.29), residues: 325 loop : 0.95 (0.25), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 79 HIS 0.004 0.001 HIS C 161 PHE 0.008 0.001 PHE C 262 TYR 0.007 0.001 TYR E 188 ARG 0.011 0.000 ARG C 372 Details of bonding type rmsd hydrogen bonds : bond 0.02680 ( 711) hydrogen bonds : angle 4.22558 ( 1845) covalent geometry : bond 0.00357 (14985) covalent geometry : angle 0.55634 (20340) *********************** 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 133 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 1.733 Fit side-chains REVERT: A 137 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.8193 (mm-40) REVERT: A 176 MET cc_start: 0.8885 (OUTLIER) cc_final: 0.8376 (mtt) REVERT: A 246 GLN cc_start: 0.8137 (mp10) cc_final: 0.7660 (pm20) REVERT: A 305 MET cc_start: 0.9244 (mmm) cc_final: 0.8986 (mmm) REVERT: A 354 GLN cc_start: 0.8829 (pm20) cc_final: 0.8535 (pm20) REVERT: A 355 MET cc_start: 0.9341 (mtm) cc_final: 0.8912 (mtp) REVERT: C 246 GLN cc_start: 0.9001 (mt0) cc_final: 0.8659 (mt0) REVERT: D 246 GLN cc_start: 0.8981 (mt0) cc_final: 0.8570 (mt0) REVERT: E 314 GLN cc_start: 0.8985 (OUTLIER) cc_final: 0.8436 (tp40) outliers start: 17 outliers final: 4 residues processed: 120 average time/residue: 1.8698 time to fit residues: 241.1240 Evaluate side-chains 121 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 114 time to evaluate : 1.727 ------------------------------------------------------------------------------- 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 B residue 45 VAL Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain E residue 314 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 82 optimal weight: 0.9980 chunk 127 optimal weight: 0.0670 chunk 76 optimal weight: 0.9990 chunk 181 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 chunk 147 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 99 optimal weight: 0.6980 chunk 148 optimal weight: 8.9990 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 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 = 0.2902 r_free = 0.2902 target = 0.058546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2565 r_free = 0.2565 target = 0.043831 restraints weight = 32937.997| |-----------------------------------------------------------------------------| r_work (start): 0.2550 rms_B_bonded: 2.50 r_work: 0.2411 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2280 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14985 Z= 0.117 Angle : 0.539 8.064 20340 Z= 0.253 Chirality : 0.043 0.142 2250 Planarity : 0.004 0.063 2605 Dihedral : 6.007 81.436 2090 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.02 % Allowed : 10.45 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.21), residues: 1835 helix: 1.42 (0.20), residues: 775 sheet: 0.84 (0.30), residues: 315 loop : 0.97 (0.25), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 79 HIS 0.003 0.001 HIS C 161 PHE 0.007 0.001 PHE B 255 TYR 0.007 0.001 TYR C 143 ARG 0.012 0.000 ARG C 372 Details of bonding type rmsd hydrogen bonds : bond 0.02506 ( 711) hydrogen bonds : angle 4.18995 ( 1845) covalent geometry : bond 0.00273 (14985) covalent geometry : angle 0.53921 (20340) *********************** 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 132 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 1.764 Fit side-chains REVERT: A 176 MET cc_start: 0.8884 (OUTLIER) cc_final: 0.8380 (mtt) REVERT: A 246 GLN cc_start: 0.8126 (mp10) cc_final: 0.7636 (pm20) REVERT: A 305 MET cc_start: 0.9294 (mmm) cc_final: 0.9002 (mmm) REVERT: A 354 GLN cc_start: 0.8820 (pm20) cc_final: 0.8515 (pm20) REVERT: A 355 MET cc_start: 0.9326 (mtm) cc_final: 0.8908 (mtp) REVERT: C 246 GLN cc_start: 0.9054 (mt0) cc_final: 0.8680 (mt0) REVERT: C 354 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8490 (pm20) REVERT: D 246 GLN cc_start: 0.8998 (mt0) cc_final: 0.8561 (mt0) REVERT: D 314 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.8285 (tt0) REVERT: E 314 GLN cc_start: 0.8980 (OUTLIER) cc_final: 0.8412 (tp40) REVERT: E 354 GLN cc_start: 0.9098 (pp30) cc_final: 0.8542 (pp30) outliers start: 16 outliers final: 3 residues processed: 123 average time/residue: 1.9408 time to fit residues: 256.0287 Evaluate side-chains 121 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 114 time to evaluate : 1.769 ------------------------------------------------------------------------------- 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 354 GLN Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain E residue 314 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 100 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 175 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 69 optimal weight: 0.3980 chunk 48 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 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 = 0.2881 r_free = 0.2881 target = 0.057256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2546 r_free = 0.2546 target = 0.042679 restraints weight = 32704.987| |-----------------------------------------------------------------------------| r_work (start): 0.2503 rms_B_bonded: 2.46 r_work: 0.2364 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2233 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14985 Z= 0.205 Angle : 0.588 7.506 20340 Z= 0.280 Chirality : 0.046 0.166 2250 Planarity : 0.004 0.061 2605 Dihedral : 6.345 88.358 2090 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.96 % Allowed : 10.83 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.21), residues: 1835 helix: 1.34 (0.20), residues: 770 sheet: 0.69 (0.29), residues: 325 loop : 0.98 (0.25), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 79 HIS 0.004 0.001 HIS B 161 PHE 0.010 0.001 PHE C 262 TYR 0.007 0.001 TYR E 188 ARG 0.017 0.001 ARG C 372 Details of bonding type rmsd hydrogen bonds : bond 0.02955 ( 711) hydrogen bonds : angle 4.30428 ( 1845) covalent geometry : bond 0.00480 (14985) covalent geometry : angle 0.58796 (20340) *********************** 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: 15 poor density : 113 time to evaluate : 1.553 Fit side-chains REVERT: A 176 MET cc_start: 0.8879 (OUTLIER) cc_final: 0.8380 (mtt) REVERT: A 246 GLN cc_start: 0.8119 (mp10) cc_final: 0.7895 (mp10) REVERT: A 354 GLN cc_start: 0.8846 (pm20) cc_final: 0.8521 (pm20) REVERT: A 355 MET cc_start: 0.9432 (mtm) cc_final: 0.8987 (mtp) REVERT: C 246 GLN cc_start: 0.8973 (mt0) cc_final: 0.8600 (mt0) REVERT: C 354 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.8520 (pm20) REVERT: D 246 GLN cc_start: 0.8925 (mt0) cc_final: 0.8508 (mt0) REVERT: D 314 GLN cc_start: 0.9000 (OUTLIER) cc_final: 0.8282 (tt0) REVERT: E 314 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.8424 (tp40) REVERT: E 354 GLN cc_start: 0.9106 (pp30) cc_final: 0.8643 (pp30) outliers start: 15 outliers final: 3 residues processed: 120 average time/residue: 1.9365 time to fit residues: 248.6374 Evaluate side-chains 120 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 113 time to evaluate : 1.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain E residue 314 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 81 optimal weight: 0.9980 chunk 160 optimal weight: 3.9990 chunk 174 optimal weight: 0.0770 chunk 59 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 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 = 0.2915 r_free = 0.2915 target = 0.059156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2579 r_free = 0.2579 target = 0.044404 restraints weight = 32481.648| |-----------------------------------------------------------------------------| r_work (start): 0.2563 rms_B_bonded: 2.51 r_work: 0.2424 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2294 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14985 Z= 0.098 Angle : 0.536 6.461 20340 Z= 0.252 Chirality : 0.043 0.140 2250 Planarity : 0.004 0.060 2605 Dihedral : 5.916 79.694 2090 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.51 % Allowed : 11.15 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.21), residues: 1835 helix: 1.32 (0.20), residues: 805 sheet: 0.84 (0.30), residues: 315 loop : 1.00 (0.25), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 79 HIS 0.003 0.000 HIS C 161 PHE 0.007 0.001 PHE D 255 TYR 0.005 0.001 TYR B 294 ARG 0.016 0.000 ARG C 372 Details of bonding type rmsd hydrogen bonds : bond 0.02363 ( 711) hydrogen bonds : angle 4.18208 ( 1845) covalent geometry : bond 0.00229 (14985) covalent geometry : angle 0.53650 (20340) *********************** 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 123 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 115 time to evaluate : 1.580 Fit side-chains REVERT: A 246 GLN cc_start: 0.8169 (mp10) cc_final: 0.7922 (mp10) REVERT: A 305 MET cc_start: 0.8985 (mmp) cc_final: 0.8761 (mmm) REVERT: A 354 GLN cc_start: 0.8850 (pm20) cc_final: 0.8529 (pm20) REVERT: A 355 MET cc_start: 0.9351 (mtm) cc_final: 0.8986 (mtp) REVERT: C 246 GLN cc_start: 0.9077 (mt0) cc_final: 0.8716 (mt0) REVERT: C 354 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8491 (pm20) REVERT: D 95 ARG cc_start: 0.8977 (mtp85) cc_final: 0.8739 (mtt-85) REVERT: D 246 GLN cc_start: 0.8986 (mt0) cc_final: 0.8507 (mt0) REVERT: E 314 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.8401 (tp40) REVERT: E 354 GLN cc_start: 0.9084 (pp30) cc_final: 0.8624 (pp30) outliers start: 8 outliers final: 2 residues processed: 118 average time/residue: 1.9545 time to fit residues: 247.6098 Evaluate side-chains 118 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 114 time to evaluate : 2.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain E residue 314 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 102 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 chunk 180 optimal weight: 7.9990 chunk 31 optimal weight: 0.8980 chunk 131 optimal weight: 0.7980 chunk 148 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 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 = 0.057984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2553 r_free = 0.2553 target = 0.043315 restraints weight = 32787.198| |-----------------------------------------------------------------------------| r_work (start): 0.2539 rms_B_bonded: 2.48 r_work: 0.2398 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2268 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14985 Z= 0.141 Angle : 0.555 7.845 20340 Z= 0.262 Chirality : 0.044 0.147 2250 Planarity : 0.004 0.060 2605 Dihedral : 5.951 80.854 2090 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.51 % Allowed : 11.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.21), residues: 1835 helix: 1.36 (0.20), residues: 800 sheet: 0.79 (0.29), residues: 325 loop : 1.02 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 79 HIS 0.004 0.001 HIS C 161 PHE 0.007 0.001 PHE C 262 TYR 0.005 0.001 TYR E 188 ARG 0.016 0.000 ARG C 372 Details of bonding type rmsd hydrogen bonds : bond 0.02584 ( 711) hydrogen bonds : angle 4.20283 ( 1845) covalent geometry : bond 0.00332 (14985) covalent geometry : angle 0.55483 (20340) ********************** 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 122 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 114 time to evaluate : 1.579 Fit side-chains REVERT: A 246 GLN cc_start: 0.8156 (mp10) cc_final: 0.7505 (pm20) REVERT: A 305 MET cc_start: 0.9062 (mmp) cc_final: 0.8753 (mmm) REVERT: A 354 GLN cc_start: 0.8851 (pm20) cc_final: 0.8529 (pm20) REVERT: A 355 MET cc_start: 0.9397 (mtm) cc_final: 0.8987 (mtp) REVERT: C 246 GLN cc_start: 0.9055 (mt0) cc_final: 0.8676 (mt0) REVERT: C 354 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.8506 (pm20) REVERT: D 246 GLN cc_start: 0.8971 (mt0) cc_final: 0.8515 (mt0) REVERT: D 314 GLN cc_start: 0.9005 (OUTLIER) cc_final: 0.8277 (tt0) REVERT: E 132 MET cc_start: 0.9202 (ttp) cc_final: 0.8859 (ppp) REVERT: E 314 GLN cc_start: 0.8974 (OUTLIER) cc_final: 0.8474 (tp40) REVERT: E 354 GLN cc_start: 0.9081 (pp30) cc_final: 0.8645 (pp30) outliers start: 8 outliers final: 3 residues processed: 117 average time/residue: 2.1508 time to fit residues: 270.4230 Evaluate side-chains 119 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 113 time to evaluate : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain E residue 314 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 47 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 165 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 82 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 86 optimal weight: 0.9980 chunk 144 optimal weight: 0.4980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 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 = 0.2915 r_free = 0.2915 target = 0.059144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.044528 restraints weight = 32435.304| |-----------------------------------------------------------------------------| r_work (start): 0.2568 rms_B_bonded: 2.48 r_work: 0.2429 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2299 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 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 : 0.002 0.042 14985 Z= 0.100 Angle : 0.538 7.768 20340 Z= 0.252 Chirality : 0.043 0.136 2250 Planarity : 0.004 0.060 2605 Dihedral : 5.721 76.286 2090 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.45 % Allowed : 11.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.21), residues: 1835 helix: 1.40 (0.20), residues: 805 sheet: 0.88 (0.30), residues: 315 loop : 1.02 (0.25), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 79 HIS 0.003 0.000 HIS C 161 PHE 0.006 0.001 PHE D 255 TYR 0.005 0.001 TYR E 362 ARG 0.014 0.000 ARG C 372 Details of bonding type rmsd hydrogen bonds : bond 0.02350 ( 711) hydrogen bonds : angle 4.14644 ( 1845) covalent geometry : bond 0.00236 (14985) covalent geometry : angle 0.53808 (20340) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11013.30 seconds wall clock time: 191 minutes 43.60 seconds (11503.60 seconds total)