Starting phenix.real_space_refine on Mon Jan 20 03:48:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v2o_42918/01_2025/8v2o_42918.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v2o_42918/01_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_42918/01_2025/8v2o_42918.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v2o_42918/01_2025/8v2o_42918.map" model { file = "/net/cci-nas-00/data/ceres_data/8v2o_42918/01_2025/8v2o_42918.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v2o_42918/01_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 8.82, per 1000 atoms: 0.60 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: 3.64 Conformation dependent library (CDL) restraints added in 2.0 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: 2.23 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: 5.74 Time building geometry restraints manager: 4.24 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: 0.860 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: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 35.260 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.070 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:12.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.530 ------------------------------------------------------------------------------- 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= 0.279 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 *********************** 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 : 1.659 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: 1.8600 time to fit residues: 251.7339 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 : 1.653 ------------------------------------------------------------------------------- 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 = 0.2861 r_free = 0.2861 target = 0.056772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2512 r_free = 0.2512 target = 0.041811 restraints weight = 33026.575| |-----------------------------------------------------------------------------| r_work (start): 0.2494 rms_B_bonded: 2.51 r_work: 0.2354 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2223 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 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= 0.455 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 *********************** 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 : 1.717 Fit side-chains REVERT: A 176 MET cc_start: 0.8898 (OUTLIER) cc_final: 0.8359 (mtt) REVERT: B 227 MET cc_start: 0.8746 (mmm) cc_final: 0.8499 (mmm) REVERT: D 246 GLN cc_start: 0.8949 (mt0) cc_final: 0.8578 (mt0) REVERT: D 314 GLN cc_start: 0.9100 (OUTLIER) cc_final: 0.8419 (tt0) outliers start: 21 outliers final: 5 residues processed: 122 average time/residue: 1.9618 time to fit residues: 256.2560 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 : 1.659 ------------------------------------------------------------------------------- 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: 0.8980 chunk 174 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 143 optimal weight: 0.7980 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.2893 r_free = 0.2893 target = 0.058304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2560 r_free = 0.2560 target = 0.043584 restraints weight = 32982.061| |-----------------------------------------------------------------------------| r_work (start): 0.2541 rms_B_bonded: 2.49 r_work: 0.2404 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2273 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1445 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= 0.194 Angle : 0.554 6.191 20340 Z= 0.263 Chirality : 0.044 0.169 2250 Planarity : 0.005 0.090 2605 Dihedral : 8.115 124.356 2093 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.40 % Allowed : 9.43 % Favored : 89.17 % 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: 0.96 (0.20), residues: 1835 helix: 0.73 (0.19), residues: 765 sheet: 0.60 (0.29), residues: 325 loop : 0.81 (0.24), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 79 HIS 0.004 0.001 HIS C 161 PHE 0.008 0.001 PHE B 255 TYR 0.005 0.001 TYR B 69 ARG 0.009 0.000 ARG E 372 *********************** 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: 22 poor density : 114 time to evaluate : 1.575 Fit side-chains REVERT: A 354 GLN cc_start: 0.8848 (pm20) cc_final: 0.8548 (pm20) REVERT: A 355 MET cc_start: 0.9289 (mtm) cc_final: 0.9038 (mtp) REVERT: B 227 MET cc_start: 0.8779 (mmm) cc_final: 0.8385 (mmm) REVERT: C 246 GLN cc_start: 0.9059 (mt0) cc_final: 0.8751 (mt0) REVERT: C 354 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.8543 (pm20) REVERT: D 176 MET cc_start: 0.9196 (mtm) cc_final: 0.8806 (mtm) REVERT: D 246 GLN cc_start: 0.9012 (mt0) cc_final: 0.8589 (mt0) outliers start: 22 outliers final: 3 residues processed: 122 average time/residue: 1.9793 time to fit residues: 258.2272 Evaluate side-chains 115 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 111 time to evaluate : 1.727 ------------------------------------------------------------------------------- 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 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: 5.9990 chunk 89 optimal weight: 0.9990 chunk 34 optimal weight: 10.0000 chunk 177 optimal weight: 4.9990 chunk 52 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 174 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 128 optimal weight: 4.9990 chunk 76 optimal weight: 0.5980 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 = 0.2874 r_free = 0.2874 target = 0.057372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2534 r_free = 0.2534 target = 0.042655 restraints weight = 32619.425| |-----------------------------------------------------------------------------| r_work (start): 0.2519 rms_B_bonded: 2.47 r_work: 0.2381 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2250 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14985 Z= 0.253 Angle : 0.565 6.206 20340 Z= 0.268 Chirality : 0.045 0.165 2250 Planarity : 0.004 0.075 2605 Dihedral : 6.922 103.390 2090 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.34 % Allowed : 9.17 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.17 (0.21), residues: 1835 helix: 0.99 (0.20), residues: 770 sheet: 0.66 (0.29), residues: 325 loop : 0.84 (0.25), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 79 HIS 0.004 0.001 HIS B 161 PHE 0.009 0.001 PHE C 262 TYR 0.006 0.001 TYR E 188 ARG 0.011 0.001 ARG E 372 *********************** 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 134 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 1.783 Fit side-chains REVERT: A 176 MET cc_start: 0.8897 (OUTLIER) cc_final: 0.8390 (mtt) REVERT: A 354 GLN cc_start: 0.8881 (pm20) cc_final: 0.8579 (pm20) REVERT: A 355 MET cc_start: 0.9390 (mtm) cc_final: 0.9060 (mtp) REVERT: B 227 MET cc_start: 0.8817 (mmm) cc_final: 0.8450 (mmm) REVERT: C 246 GLN cc_start: 0.9025 (mt0) cc_final: 0.8666 (mt0) REVERT: D 246 GLN cc_start: 0.8980 (mt0) cc_final: 0.8572 (mt0) REVERT: E 44 MET cc_start: 0.9374 (OUTLIER) cc_final: 0.8750 (mtt) REVERT: E 314 GLN cc_start: 0.9023 (OUTLIER) cc_final: 0.8453 (tp40) outliers start: 21 outliers final: 4 residues processed: 121 average time/residue: 1.9732 time to fit residues: 255.3670 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 : 1.562 ------------------------------------------------------------------------------- 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 D residue 45 VAL Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 314 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 26 optimal weight: 0.2980 chunk 146 optimal weight: 8.9990 chunk 71 optimal weight: 7.9990 chunk 129 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 170 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 163 optimal weight: 9.9990 chunk 119 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- 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 = 0.2880 r_free = 0.2880 target = 0.057291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2543 r_free = 0.2543 target = 0.042686 restraints weight = 32796.461| |-----------------------------------------------------------------------------| r_work (start): 0.2502 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: 4.39 restraints_weight: 0.2500 r_work (final): 0.2233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1740 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= 0.309 Angle : 0.580 6.615 20340 Z= 0.278 Chirality : 0.046 0.170 2250 Planarity : 0.004 0.065 2605 Dihedral : 6.773 95.042 2090 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.53 % Allowed : 9.36 % 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: 1.13 (0.20), residues: 1835 helix: 0.93 (0.19), residues: 800 sheet: 0.66 (0.28), residues: 325 loop : 0.84 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 79 HIS 0.004 0.001 HIS D 161 PHE 0.010 0.001 PHE C 262 TYR 0.006 0.001 TYR E 188 ARG 0.011 0.000 ARG E 372 *********************** 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 137 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 113 time to evaluate : 1.591 Fit side-chains REVERT: A 305 MET cc_start: 0.9129 (OUTLIER) cc_final: 0.8787 (mmm) REVERT: A 354 GLN cc_start: 0.8863 (pm20) cc_final: 0.8542 (pm20) REVERT: A 355 MET cc_start: 0.9391 (mtm) cc_final: 0.8971 (mtp) REVERT: B 227 MET cc_start: 0.8784 (mmm) cc_final: 0.8380 (mmm) REVERT: C 246 GLN cc_start: 0.8969 (mt0) cc_final: 0.8616 (mt0) REVERT: C 314 GLN cc_start: 0.8961 (OUTLIER) cc_final: 0.7904 (tp40) REVERT: D 95 ARG cc_start: 0.9011 (mtp85) cc_final: 0.8763 (mtt-85) REVERT: D 246 GLN cc_start: 0.8938 (mt0) cc_final: 0.8544 (mt0) REVERT: D 314 GLN cc_start: 0.8998 (OUTLIER) cc_final: 0.8298 (tt0) REVERT: E 44 MET cc_start: 0.9294 (OUTLIER) cc_final: 0.8624 (mtt) REVERT: E 314 GLN cc_start: 0.8998 (OUTLIER) cc_final: 0.8428 (tp40) outliers start: 24 outliers final: 5 residues processed: 123 average time/residue: 2.0016 time to fit residues: 263.3630 Evaluate side-chains 124 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain E residue 44 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: 5.9990 chunk 55 optimal weight: 0.9990 chunk 34 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 132 optimal weight: 0.8980 chunk 38 optimal weight: 8.9990 chunk 140 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 58 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 = 0.2878 r_free = 0.2878 target = 0.057609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2537 r_free = 0.2537 target = 0.042829 restraints weight = 32762.734| |-----------------------------------------------------------------------------| r_work (start): 0.2522 rms_B_bonded: 2.50 r_work: 0.2382 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2251 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1756 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= 0.216 Angle : 0.553 6.043 20340 Z= 0.262 Chirality : 0.044 0.158 2250 Planarity : 0.004 0.058 2605 Dihedral : 6.507 90.431 2090 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.53 % Allowed : 9.55 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.26 (0.20), residues: 1835 helix: 1.07 (0.19), residues: 800 sheet: 0.69 (0.29), residues: 325 loop : 0.89 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 79 HIS 0.003 0.001 HIS A 161 PHE 0.007 0.001 PHE C 262 TYR 0.005 0.001 TYR E 188 ARG 0.010 0.000 ARG C 372 *********************** 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 138 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 1.568 Fit side-chains REVERT: A 176 MET cc_start: 0.8877 (OUTLIER) cc_final: 0.8374 (mtt) REVERT: A 305 MET cc_start: 0.9120 (OUTLIER) cc_final: 0.8797 (mmm) REVERT: A 354 GLN cc_start: 0.8859 (pm20) cc_final: 0.8537 (pm20) REVERT: A 355 MET cc_start: 0.9375 (mtm) cc_final: 0.8947 (mtp) REVERT: B 176 MET cc_start: 0.9121 (OUTLIER) cc_final: 0.8836 (mtm) REVERT: C 246 GLN cc_start: 0.8989 (mt0) cc_final: 0.8568 (mt0) REVERT: D 95 ARG cc_start: 0.8996 (mtp85) cc_final: 0.8753 (mtt-85) REVERT: D 176 MET cc_start: 0.9204 (mtm) cc_final: 0.8852 (mtm) REVERT: D 246 GLN cc_start: 0.8948 (mt0) cc_final: 0.8539 (mt0) REVERT: D 314 GLN cc_start: 0.8982 (OUTLIER) cc_final: 0.8272 (tt0) REVERT: E 314 GLN cc_start: 0.8981 (OUTLIER) cc_final: 0.8360 (tp40) REVERT: E 354 GLN cc_start: 0.9094 (OUTLIER) cc_final: 0.8800 (pp30) outliers start: 24 outliers final: 4 residues processed: 123 average time/residue: 1.9649 time to fit residues: 258.7891 Evaluate side-chains 125 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 1.669 ------------------------------------------------------------------------------- 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 44 MET Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 354 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 82 optimal weight: 0.7980 chunk 127 optimal weight: 0.7980 chunk 76 optimal weight: 0.6980 chunk 181 optimal weight: 5.9990 chunk 110 optimal weight: 0.9990 chunk 21 optimal weight: 9.9990 chunk 147 optimal weight: 7.9990 chunk 17 optimal weight: 8.9990 chunk 9 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 148 optimal weight: 7.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 = 0.2883 r_free = 0.2883 target = 0.057834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2541 r_free = 0.2541 target = 0.042989 restraints weight = 32914.116| |-----------------------------------------------------------------------------| r_work (start): 0.2525 rms_B_bonded: 2.51 r_work: 0.2387 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2257 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1791 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= 0.209 Angle : 0.550 5.877 20340 Z= 0.260 Chirality : 0.044 0.152 2250 Planarity : 0.004 0.062 2605 Dihedral : 6.293 86.428 2090 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.02 % Allowed : 10.51 % Favored : 88.47 % 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: 1.37 (0.21), residues: 1835 helix: 1.18 (0.19), residues: 800 sheet: 0.71 (0.29), residues: 325 loop : 0.93 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 79 HIS 0.003 0.001 HIS A 161 PHE 0.007 0.001 PHE B 255 TYR 0.005 0.001 TYR E 188 ARG 0.012 0.000 ARG C 372 *********************** 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 : 1.640 Fit side-chains REVERT: A 176 MET cc_start: 0.8879 (OUTLIER) cc_final: 0.8373 (mtt) REVERT: A 305 MET cc_start: 0.9107 (OUTLIER) cc_final: 0.8804 (mmm) REVERT: A 354 GLN cc_start: 0.8850 (pm20) cc_final: 0.8523 (pm20) REVERT: A 355 MET cc_start: 0.9369 (mtm) cc_final: 0.8939 (mtp) REVERT: C 246 GLN cc_start: 0.9031 (mt0) cc_final: 0.8657 (mt0) REVERT: C 354 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.8496 (pm20) REVERT: D 95 ARG cc_start: 0.8986 (mtp85) cc_final: 0.8747 (mtt-85) REVERT: D 176 MET cc_start: 0.9229 (mtm) cc_final: 0.8782 (mtm) REVERT: D 246 GLN cc_start: 0.8958 (mt0) cc_final: 0.8520 (mt0) REVERT: D 314 GLN cc_start: 0.8988 (OUTLIER) cc_final: 0.8268 (tt0) REVERT: E 314 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.8357 (tp40) REVERT: E 354 GLN cc_start: 0.9011 (OUTLIER) cc_final: 0.8787 (pp30) outliers start: 16 outliers final: 4 residues processed: 120 average time/residue: 1.9728 time to fit residues: 253.2274 Evaluate side-chains 125 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 1.564 ------------------------------------------------------------------------------- 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 44 MET Chi-restraints excluded: chain B residue 355 MET 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 Chi-restraints excluded: chain E residue 354 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 100 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 175 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 59 optimal weight: 5.9990 chunk 88 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 = 0.2895 r_free = 0.2895 target = 0.058296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2557 r_free = 0.2557 target = 0.043551 restraints weight = 32627.703| |-----------------------------------------------------------------------------| r_work (start): 0.2542 rms_B_bonded: 2.50 r_work: 0.2401 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2269 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 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 : 0.003 0.038 14985 Z= 0.183 Angle : 0.543 6.490 20340 Z= 0.257 Chirality : 0.044 0.144 2250 Planarity : 0.004 0.060 2605 Dihedral : 6.088 82.442 2090 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.96 % Allowed : 10.70 % 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: 1.46 (0.21), residues: 1835 helix: 1.26 (0.19), residues: 800 sheet: 0.73 (0.29), residues: 325 loop : 0.97 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 79 HIS 0.003 0.001 HIS C 161 PHE 0.006 0.001 PHE D 255 TYR 0.006 0.001 TYR C 143 ARG 0.013 0.000 ARG C 372 *********************** 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 135 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 1.445 Fit side-chains REVERT: A 137 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.8214 (mm-40) REVERT: A 176 MET cc_start: 0.8897 (OUTLIER) cc_final: 0.8411 (mtt) REVERT: A 305 MET cc_start: 0.9071 (OUTLIER) cc_final: 0.8794 (mmm) REVERT: A 354 GLN cc_start: 0.8842 (pm20) cc_final: 0.8517 (pm20) REVERT: A 355 MET cc_start: 0.9361 (mtm) cc_final: 0.8964 (mtp) REVERT: C 246 GLN cc_start: 0.9052 (mt0) cc_final: 0.8655 (mt0) REVERT: C 354 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.8482 (pm20) REVERT: D 95 ARG cc_start: 0.9001 (mtp85) cc_final: 0.8769 (mtt-85) REVERT: D 176 MET cc_start: 0.9233 (mtm) cc_final: 0.8810 (mtm) REVERT: D 246 GLN cc_start: 0.8979 (mt0) cc_final: 0.8524 (mt0) REVERT: D 314 GLN cc_start: 0.9010 (OUTLIER) cc_final: 0.8283 (tt0) REVERT: E 246 GLN cc_start: 0.8950 (mp10) cc_final: 0.8664 (mp10) REVERT: E 314 GLN cc_start: 0.9003 (OUTLIER) cc_final: 0.8350 (tp40) REVERT: E 354 GLN cc_start: 0.9005 (OUTLIER) cc_final: 0.8785 (pp30) outliers start: 15 outliers final: 4 residues processed: 125 average time/residue: 1.9558 time to fit residues: 262.2792 Evaluate side-chains 130 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 1.703 ------------------------------------------------------------------------------- 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 B residue 44 MET Chi-restraints excluded: chain B residue 355 MET 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 Chi-restraints excluded: chain E residue 354 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 81 optimal weight: 1.9990 chunk 160 optimal weight: 0.8980 chunk 174 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 = 0.2896 r_free = 0.2896 target = 0.058334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2559 r_free = 0.2559 target = 0.043615 restraints weight = 32530.837| |-----------------------------------------------------------------------------| r_work (start): 0.2545 rms_B_bonded: 2.49 r_work: 0.2406 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2275 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.1823 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= 0.186 Angle : 0.549 7.566 20340 Z= 0.259 Chirality : 0.044 0.142 2250 Planarity : 0.004 0.058 2605 Dihedral : 6.016 81.324 2090 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % 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: 1.47 (0.21), residues: 1835 helix: 1.25 (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 TRP 0.012 0.001 TRP C 79 HIS 0.003 0.001 HIS A 161 PHE 0.006 0.001 PHE D 255 TYR 0.010 0.001 TYR C 143 ARG 0.016 0.000 ARG C 372 *********************** 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 133 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 1.658 Fit side-chains REVERT: A 137 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.8076 (mm-40) REVERT: A 176 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.8390 (mtt) REVERT: A 305 MET cc_start: 0.9058 (OUTLIER) cc_final: 0.8805 (mmm) REVERT: A 354 GLN cc_start: 0.8848 (pm20) cc_final: 0.8522 (pm20) REVERT: A 355 MET cc_start: 0.9373 (mtm) cc_final: 0.8973 (mtp) REVERT: C 246 GLN cc_start: 0.9030 (mt0) cc_final: 0.8626 (mt0) REVERT: C 354 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.8501 (pm20) REVERT: D 95 ARG cc_start: 0.8997 (mtp85) cc_final: 0.8768 (mtt-85) REVERT: D 176 MET cc_start: 0.9235 (mtm) cc_final: 0.8805 (mtm) REVERT: D 246 GLN cc_start: 0.8981 (mt0) cc_final: 0.8518 (mt0) REVERT: D 314 GLN cc_start: 0.9012 (OUTLIER) cc_final: 0.8283 (tt0) REVERT: E 246 GLN cc_start: 0.8942 (mp10) cc_final: 0.8712 (mp10) REVERT: E 314 GLN cc_start: 0.8998 (OUTLIER) cc_final: 0.8407 (tp40) REVERT: E 354 GLN cc_start: 0.8987 (OUTLIER) cc_final: 0.8783 (pp30) outliers start: 15 outliers final: 5 residues processed: 122 average time/residue: 1.9268 time to fit residues: 252.3240 Evaluate side-chains 130 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 118 time to evaluate : 1.613 ------------------------------------------------------------------------------- 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 B residue 44 MET Chi-restraints excluded: chain B residue 355 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 Chi-restraints excluded: chain E residue 354 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 102 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 180 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 131 optimal weight: 4.9990 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: 8.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 = 0.2872 r_free = 0.2872 target = 0.056869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2534 r_free = 0.2534 target = 0.042272 restraints weight = 32727.506| |-----------------------------------------------------------------------------| r_work (start): 0.2493 rms_B_bonded: 2.45 r_work: 0.2353 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2223 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 14985 Z= 0.367 Angle : 0.608 7.094 20340 Z= 0.292 Chirality : 0.047 0.169 2250 Planarity : 0.004 0.058 2605 Dihedral : 6.421 89.210 2090 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.83 % Allowed : 10.96 % 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: 1.30 (0.21), residues: 1835 helix: 1.12 (0.19), residues: 800 sheet: 0.65 (0.28), residues: 325 loop : 0.90 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 79 HIS 0.005 0.001 HIS B 161 PHE 0.011 0.001 PHE C 262 TYR 0.008 0.001 TYR A 143 ARG 0.017 0.001 ARG C 372 ********************** 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 127 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 1.585 Fit side-chains REVERT: A 137 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.7984 (mm-40) REVERT: A 176 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.8384 (mtt) REVERT: A 305 MET cc_start: 0.9088 (OUTLIER) cc_final: 0.8785 (mmm) REVERT: A 354 GLN cc_start: 0.8888 (pm20) cc_final: 0.8539 (pm20) REVERT: A 355 MET cc_start: 0.9460 (mtm) cc_final: 0.8990 (mtp) REVERT: B 176 MET cc_start: 0.9074 (mtp) cc_final: 0.8718 (mmm) REVERT: C 246 GLN cc_start: 0.8946 (mt0) cc_final: 0.8571 (mt0) REVERT: C 354 GLN cc_start: 0.8886 (OUTLIER) cc_final: 0.8499 (pm20) REVERT: D 95 ARG cc_start: 0.8986 (mtp85) cc_final: 0.8767 (mtt-85) REVERT: D 176 MET cc_start: 0.9242 (mtm) cc_final: 0.8826 (mtm) REVERT: D 246 GLN cc_start: 0.8917 (mt0) cc_final: 0.8501 (mt0) REVERT: D 314 GLN cc_start: 0.9022 (OUTLIER) cc_final: 0.8289 (tt0) REVERT: E 314 GLN cc_start: 0.9011 (OUTLIER) cc_final: 0.8420 (tp40) REVERT: E 354 GLN cc_start: 0.8958 (pm20) cc_final: 0.8637 (pp30) outliers start: 13 outliers final: 5 residues processed: 117 average time/residue: 1.9404 time to fit residues: 243.6660 Evaluate side-chains 125 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 1.746 ------------------------------------------------------------------------------- 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 B residue 44 MET Chi-restraints excluded: chain B residue 355 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 47 optimal weight: 0.9980 chunk 118 optimal weight: 0.3980 chunk 165 optimal weight: 0.6980 chunk 31 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 74 optimal weight: 8.9990 chunk 86 optimal weight: 0.8980 chunk 144 optimal weight: 2.9990 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 E 41 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.058574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2567 r_free = 0.2567 target = 0.043894 restraints weight = 32722.660| |-----------------------------------------------------------------------------| r_work (start): 0.2552 rms_B_bonded: 2.49 r_work: 0.2413 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2283 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1876 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= 0.154 Angle : 0.545 6.911 20340 Z= 0.258 Chirality : 0.043 0.169 2250 Planarity : 0.004 0.058 2605 Dihedral : 6.039 82.568 2090 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % 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 (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: 1.30 (0.19), residues: 800 sheet: 0.71 (0.29), residues: 325 loop : 1.00 (0.25), residues: 710 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 0.006 0.001 PHE D 255 TYR 0.009 0.001 TYR C 143 ARG 0.016 0.000 ARG C 372 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10093.89 seconds wall clock time: 179 minutes 17.93 seconds (10757.93 seconds total)