Starting phenix.real_space_refine on Thu Jul 2 23:10:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pqm_71786/07_2026/9pqm_71786.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pqm_71786/07_2026/9pqm_71786.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9pqm_71786/07_2026/9pqm_71786.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pqm_71786/07_2026/9pqm_71786.map" model { file = "/net/cci-nas-00/data/ceres_data/9pqm_71786/07_2026/9pqm_71786.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pqm_71786/07_2026/9pqm_71786.cif" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 18 5.49 5 Mg 6 5.21 5 S 36 5.16 5 C 6756 2.51 5 N 1758 2.21 5 O 1938 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10512 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1720 Classifications: {'peptide': 207} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 199} Chain: "B" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1720 Classifications: {'peptide': 207} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 199} Chain: "C" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1720 Classifications: {'peptide': 207} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 199} Chain: "D" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1720 Classifications: {'peptide': 207} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 199} Chain: "E" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1720 Classifications: {'peptide': 207} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 199} Chain: "F" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1720 Classifications: {'peptide': 207} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 199} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'AGS': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.58, per 1000 atoms: 0.25 Number of scatterers: 10512 At special positions: 0 Unit cell: (113.4, 118.44, 86.52, 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 36 16.00 P 18 15.00 Mg 6 11.99 O 1938 8.00 N 1758 7.00 C 6756 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: 0.99 Conformation dependent library (CDL) restraints added in 366.0 milliseconds 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2316 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 22 sheets defined 46.5% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 133 through 140 Processing helix chain 'A' and resid 144 through 162 removed outlier: 3.571A pdb=" N LYS A 153 " --> pdb=" O ILE A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 196 removed outlier: 3.807A pdb=" N ASN A 196 " --> pdb=" O GLU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 238 removed outlier: 3.706A pdb=" N ARG A 236 " --> pdb=" O SER A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 271 removed outlier: 3.818A pdb=" N PHE A 271 " --> pdb=" O PRO A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 293 removed outlier: 3.646A pdb=" N LEU A 289 " --> pdb=" O LYS A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 323 Processing helix chain 'B' and resid 122 through 132 Processing helix chain 'B' and resid 133 through 141 Processing helix chain 'B' and resid 144 through 162 Processing helix chain 'B' and resid 182 through 195 Processing helix chain 'B' and resid 224 through 228 Processing helix chain 'B' and resid 231 through 238 removed outlier: 4.283A pdb=" N LEU B 235 " --> pdb=" O TRP B 231 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG B 236 " --> pdb=" O SER B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 271 Processing helix chain 'B' and resid 285 through 293 Processing helix chain 'B' and resid 307 through 323 Processing helix chain 'C' and resid 122 through 132 Processing helix chain 'C' and resid 133 through 140 Processing helix chain 'C' and resid 144 through 162 removed outlier: 3.656A pdb=" N VAL C 160 " --> pdb=" O ASN C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 195 Processing helix chain 'C' and resid 224 through 228 Processing helix chain 'C' and resid 231 through 238 removed outlier: 4.324A pdb=" N LEU C 235 " --> pdb=" O TRP C 231 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG C 236 " --> pdb=" O SER C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 272 Processing helix chain 'C' and resid 285 through 294 removed outlier: 3.517A pdb=" N LEU C 289 " --> pdb=" O LYS C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 323 Processing helix chain 'D' and resid 122 through 132 Processing helix chain 'D' and resid 133 through 141 Processing helix chain 'D' and resid 144 through 162 Processing helix chain 'D' and resid 182 through 195 removed outlier: 3.542A pdb=" N ALA D 187 " --> pdb=" O LYS D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 238 removed outlier: 3.631A pdb=" N ARG D 236 " --> pdb=" O SER D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 271 removed outlier: 3.989A pdb=" N PHE D 271 " --> pdb=" O PRO D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 294 Processing helix chain 'D' and resid 307 through 323 Processing helix chain 'E' and resid 122 through 132 Processing helix chain 'E' and resid 133 through 140 Processing helix chain 'E' and resid 144 through 162 removed outlier: 3.537A pdb=" N LYS E 153 " --> pdb=" O ILE E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 195 Processing helix chain 'E' and resid 224 through 228 Processing helix chain 'E' and resid 231 through 239 removed outlier: 4.283A pdb=" N LEU E 235 " --> pdb=" O TRP E 231 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG E 236 " --> pdb=" O SER E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 271 removed outlier: 3.708A pdb=" N PHE E 271 " --> pdb=" O PRO E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 293 Processing helix chain 'E' and resid 307 through 323 Processing helix chain 'F' and resid 122 through 132 Processing helix chain 'F' and resid 133 through 140 Processing helix chain 'F' and resid 144 through 162 removed outlier: 3.634A pdb=" N VAL F 160 " --> pdb=" O ASN F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 195 Processing helix chain 'F' and resid 224 through 228 Processing helix chain 'F' and resid 232 through 239 removed outlier: 3.653A pdb=" N ARG F 236 " --> pdb=" O SER F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 266 through 271 removed outlier: 3.858A pdb=" N PHE F 271 " --> pdb=" O PRO F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 293 Processing helix chain 'F' and resid 307 through 323 Processing sheet with id=AA1, first strand: chain 'A' and resid 199 through 201 removed outlier: 6.075A pdb=" N TRP A 200 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ASP A 221 " --> pdb=" O TRP A 200 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ALA A 218 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N THR A 262 " --> pdb=" O ALA A 218 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ILE A 220 " --> pdb=" O THR A 262 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N TYR A 302 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N TRP A 174 " --> pdb=" O TYR A 302 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N PHE A 304 " --> pdb=" O TRP A 174 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LYS A 176 " --> pdb=" O PHE A 304 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 244 through 247 Processing sheet with id=AA3, first strand: chain 'A' and resid 273 through 274 Processing sheet with id=AA4, first strand: chain 'A' and resid 294 through 295 Processing sheet with id=AA5, first strand: chain 'B' and resid 199 through 201 removed outlier: 6.262A pdb=" N TRP B 200 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ALA B 218 " --> pdb=" O ILE B 260 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N THR B 262 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ILE B 220 " --> pdb=" O THR B 262 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY B 177 " --> pdb=" O SER B 263 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 244 through 247 Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 274 removed outlier: 3.514A pdb=" N TRP B 273 " --> pdb=" O ILE B 281 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 294 through 295 Processing sheet with id=AA9, first strand: chain 'C' and resid 200 through 201 removed outlier: 6.277A pdb=" N TRP C 200 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU C 171 " --> pdb=" O ILE C 259 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N VAL C 261 " --> pdb=" O LEU C 171 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU C 173 " --> pdb=" O VAL C 261 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N SER C 263 " --> pdb=" O LEU C 173 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N PHE C 175 " --> pdb=" O SER C 263 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N TYR C 302 " --> pdb=" O ILE C 172 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TRP C 174 " --> pdb=" O TYR C 302 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N PHE C 304 " --> pdb=" O TRP C 174 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LYS C 176 " --> pdb=" O PHE C 304 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 244 through 247 Processing sheet with id=AB2, first strand: chain 'C' and resid 273 through 274 Processing sheet with id=AB3, first strand: chain 'D' and resid 199 through 201 removed outlier: 6.076A pdb=" N TRP D 200 " --> pdb=" O ILE D 219 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ASP D 221 " --> pdb=" O TRP D 200 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ALA D 218 " --> pdb=" O ILE D 260 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N THR D 262 " --> pdb=" O ALA D 218 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE D 220 " --> pdb=" O THR D 262 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU D 171 " --> pdb=" O ILE D 259 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N VAL D 261 " --> pdb=" O LEU D 171 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU D 173 " --> pdb=" O VAL D 261 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N TYR D 302 " --> pdb=" O ILE D 172 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N TRP D 174 " --> pdb=" O TYR D 302 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N PHE D 304 " --> pdb=" O TRP D 174 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LYS D 176 " --> pdb=" O PHE D 304 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'D' and resid 244 through 247 removed outlier: 3.543A pdb=" N GLY D 250 " --> pdb=" O VAL D 247 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 273 through 274 Processing sheet with id=AB6, first strand: chain 'E' and resid 199 through 201 removed outlier: 5.876A pdb=" N TRP E 200 " --> pdb=" O ILE E 219 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ASP E 221 " --> pdb=" O TRP E 200 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU E 171 " --> pdb=" O ILE E 259 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N VAL E 261 " --> pdb=" O LEU E 171 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU E 173 " --> pdb=" O VAL E 261 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N TYR E 302 " --> pdb=" O ILE E 172 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N TRP E 174 " --> pdb=" O TYR E 302 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N PHE E 304 " --> pdb=" O TRP E 174 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LYS E 176 " --> pdb=" O PHE E 304 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 244 through 247 Processing sheet with id=AB8, first strand: chain 'E' and resid 273 through 274 Processing sheet with id=AB9, first strand: chain 'E' and resid 294 through 295 Processing sheet with id=AC1, first strand: chain 'F' and resid 199 through 201 removed outlier: 5.975A pdb=" N TRP F 200 " --> pdb=" O ILE F 219 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU F 171 " --> pdb=" O ILE F 259 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N VAL F 261 " --> pdb=" O LEU F 171 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU F 173 " --> pdb=" O VAL F 261 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N TYR F 302 " --> pdb=" O ILE F 172 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TRP F 174 " --> pdb=" O TYR F 302 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N PHE F 304 " --> pdb=" O TRP F 174 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LYS F 176 " --> pdb=" O PHE F 304 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 244 through 247 Processing sheet with id=AC3, first strand: chain 'F' and resid 273 through 274 Processing sheet with id=AC4, first strand: chain 'F' and resid 294 through 295 419 hydrogen bonds defined for protein. 1191 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: 1.59 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 3432 1.36 - 1.51: 3636 1.51 - 1.65: 3624 1.65 - 1.80: 53 1.80 - 1.94: 13 Bond restraints: 10758 Sorted by residual: bond pdb=" O3B AGS E 402 " pdb=" PB AGS E 402 " ideal model delta sigma weight residual 1.673 1.571 0.102 2.00e-02 2.50e+03 2.62e+01 bond pdb=" O3A AGS D 401 " pdb=" PA AGS D 401 " ideal model delta sigma weight residual 1.664 1.564 0.100 2.00e-02 2.50e+03 2.49e+01 bond pdb=" O3B AGS B 401 " pdb=" PB AGS B 401 " ideal model delta sigma weight residual 1.673 1.575 0.098 2.00e-02 2.50e+03 2.39e+01 bond pdb=" O3B AGS F 401 " pdb=" PB AGS F 401 " ideal model delta sigma weight residual 1.673 1.576 0.097 2.00e-02 2.50e+03 2.37e+01 bond pdb=" O3B AGS E 401 " pdb=" PB AGS E 401 " ideal model delta sigma weight residual 1.673 1.576 0.097 2.00e-02 2.50e+03 2.35e+01 ... (remaining 10753 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 14235 2.15 - 4.30: 242 4.30 - 6.45: 43 6.45 - 8.60: 24 8.60 - 10.75: 18 Bond angle restraints: 14562 Sorted by residual: angle pdb=" PB AGS E 402 " pdb=" O3B AGS E 402 " pdb=" PG AGS E 402 " ideal model delta sigma weight residual 129.21 118.46 10.75 3.00e+00 1.11e-01 1.28e+01 angle pdb=" O3A AGS E 402 " pdb=" PB AGS E 402 " pdb=" O3B AGS E 402 " ideal model delta sigma weight residual 100.38 110.82 -10.44 3.00e+00 1.11e-01 1.21e+01 angle pdb=" O3A AGS D 401 " pdb=" PB AGS D 401 " pdb=" O3B AGS D 401 " ideal model delta sigma weight residual 100.38 110.65 -10.27 3.00e+00 1.11e-01 1.17e+01 angle pdb=" PB AGS E 401 " pdb=" O3B AGS E 401 " pdb=" PG AGS E 401 " ideal model delta sigma weight residual 129.21 118.97 10.24 3.00e+00 1.11e-01 1.17e+01 angle pdb=" O3A AGS B 401 " pdb=" PB AGS B 401 " pdb=" O3B AGS B 401 " ideal model delta sigma weight residual 100.38 110.52 -10.14 3.00e+00 1.11e-01 1.14e+01 ... (remaining 14557 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.39: 5974 22.39 - 44.78: 417 44.78 - 67.17: 84 67.17 - 89.56: 49 89.56 - 111.95: 4 Dihedral angle restraints: 6528 sinusoidal: 2934 harmonic: 3594 Sorted by residual: dihedral pdb=" CA GLN A 215 " pdb=" C GLN A 215 " pdb=" N PRO A 216 " pdb=" CA PRO A 216 " ideal model delta harmonic sigma weight residual -180.00 -152.64 -27.36 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA ASN E 133 " pdb=" C ASN E 133 " pdb=" N LEU E 134 " pdb=" CA LEU E 134 " ideal model delta harmonic sigma weight residual -180.00 -157.98 -22.02 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA GLN E 246 " pdb=" C GLN E 246 " pdb=" N VAL E 247 " pdb=" CA VAL E 247 " ideal model delta harmonic sigma weight residual 180.00 159.80 20.20 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 6525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1278 0.061 - 0.123: 220 0.123 - 0.184: 20 0.184 - 0.246: 0 0.246 - 0.307: 6 Chirality restraints: 1524 Sorted by residual: chirality pdb=" C3' AGS E 401 " pdb=" C2' AGS E 401 " pdb=" C4' AGS E 401 " pdb=" O3' AGS E 401 " both_signs ideal model delta sigma weight residual False -2.37 -2.68 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" C3' AGS F 401 " pdb=" C2' AGS F 401 " pdb=" C4' AGS F 401 " pdb=" O3' AGS F 401 " both_signs ideal model delta sigma weight residual False -2.37 -2.67 0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" C3' AGS D 401 " pdb=" C2' AGS D 401 " pdb=" C4' AGS D 401 " pdb=" O3' AGS D 401 " both_signs ideal model delta sigma weight residual False -2.37 -2.66 0.29 2.00e-01 2.50e+01 2.10e+00 ... (remaining 1521 not shown) Planarity restraints: 1818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 241 " -0.021 2.00e-02 2.50e+03 2.21e-02 9.77e+00 pdb=" CG TYR C 241 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 TYR C 241 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR C 241 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR C 241 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR C 241 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR C 241 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR C 241 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN E 255 " 0.026 5.00e-02 4.00e+02 3.94e-02 2.49e+00 pdb=" N PRO E 256 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO E 256 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO E 256 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 150 " -0.138 9.50e-02 1.11e+02 6.18e-02 2.48e+00 pdb=" NE ARG F 150 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG F 150 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG F 150 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG F 150 " -0.003 2.00e-02 2.50e+03 ... (remaining 1815 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 64 2.48 - 3.09: 7231 3.09 - 3.69: 14850 3.69 - 4.30: 23553 4.30 - 4.90: 39351 Nonbonded interactions: 85049 Sorted by model distance: nonbonded pdb=" OG1 THR F 184 " pdb="MG MG F 402 " model vdw 1.875 2.170 nonbonded pdb="MG MG C 401 " pdb=" O3G AGS D 401 " model vdw 1.901 2.170 nonbonded pdb=" O3G AGS A 401 " pdb="MG MG A 402 " model vdw 1.901 2.170 nonbonded pdb=" O3G AGS B 401 " pdb="MG MG B 402 " model vdw 1.912 2.170 nonbonded pdb=" O3G AGS E 402 " pdb="MG MG E 403 " model vdw 1.946 2.170 ... (remaining 85044 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 121 through 327) selection = (chain 'B' and resid 121 through 327) selection = (chain 'C' and resid 121 through 327) selection = (chain 'D' and resid 121 through 327) selection = (chain 'E' and resid 121 through 327) selection = (chain 'F' and resid 121 through 327) } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.780 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 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 : 0.008 0.102 10758 Z= 0.343 Angle : 0.853 10.746 14562 Z= 0.417 Chirality : 0.048 0.307 1524 Planarity : 0.005 0.062 1818 Dihedral : 17.097 111.949 4212 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.09 % Allowed : 0.55 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.24), residues: 1230 helix: 1.08 (0.22), residues: 534 sheet: 0.66 (0.40), residues: 174 loop : 0.22 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 236 TYR 0.053 0.002 TYR C 241 PHE 0.021 0.002 PHE B 209 TRP 0.019 0.002 TRP A 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00765 / 0.34 (10758) covalent geometry : angle 0.85297 / 0.42 (14562) hydrogen bonds : bond 0.15842 / 10.24 ( 419) hydrogen bonds : angle 7.01792 / 4.98 ( 1191) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 258 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: B 297 ASP cc_start: 0.8373 (m-30) cc_final: 0.7961 (t0) REVERT: D 166 LYS cc_start: 0.8902 (mmtp) cc_final: 0.8578 (mmmt) REVERT: D 201 MET cc_start: 0.9006 (ttm) cc_final: 0.8779 (ttt) REVERT: D 222 ASP cc_start: 0.7510 (m-30) cc_final: 0.7102 (p0) REVERT: D 224 ARG cc_start: 0.7632 (mtm-85) cc_final: 0.7303 (mtm-85) REVERT: D 248 LYS cc_start: 0.8636 (ttmt) cc_final: 0.8331 (ttpp) REVERT: D 269 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8165 (mm-30) REVERT: D 321 TYR cc_start: 0.9046 (t80) cc_final: 0.8792 (t80) REVERT: E 297 ASP cc_start: 0.8260 (m-30) cc_final: 0.8028 (t0) REVERT: F 290 THR cc_start: 0.8945 (m) cc_final: 0.8729 (p) REVERT: F 297 ASP cc_start: 0.8363 (m-30) cc_final: 0.8133 (t0) outliers start: 1 outliers final: 0 residues processed: 259 average time/residue: 0.1227 time to fit residues: 42.6352 Evaluate side-chains 172 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.0070 chunk 51 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 GLN B 203 ASN D 131 ASN D 303 ASN F 303 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.116331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.095850 restraints weight = 18010.868| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.69 r_work: 0.3186 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10758 Z= 0.108 Angle : 0.490 6.175 14562 Z= 0.257 Chirality : 0.042 0.177 1524 Planarity : 0.003 0.033 1818 Dihedral : 9.647 69.530 1572 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.28 % Allowed : 5.86 % Favored : 92.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.24), residues: 1230 helix: 1.49 (0.22), residues: 540 sheet: 0.65 (0.38), residues: 174 loop : 0.41 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 123 TYR 0.011 0.001 TYR A 241 PHE 0.015 0.001 PHE F 194 TRP 0.026 0.001 TRP F 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (10758) covalent geometry : angle 0.49025 / 0.26 (14562) hydrogen bonds : bond 0.03839 / 2.58 ( 419) hydrogen bonds : angle 5.11846 / 3.61 ( 1191) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 199 time to evaluate : 0.438 Fit side-chains revert: symmetry clash REVERT: B 297 ASP cc_start: 0.8268 (m-30) cc_final: 0.7958 (t0) REVERT: C 327 MET cc_start: 0.6653 (mtm) cc_final: 0.6416 (mtt) REVERT: D 131 ASN cc_start: 0.9158 (m-40) cc_final: 0.8877 (m-40) REVERT: D 166 LYS cc_start: 0.8949 (mmtp) cc_final: 0.8533 (mmmt) REVERT: D 248 LYS cc_start: 0.8618 (ttmt) cc_final: 0.8254 (ttpp) REVERT: D 269 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8005 (mm-30) REVERT: D 273 TRP cc_start: 0.5733 (p-90) cc_final: 0.5498 (p-90) REVERT: D 321 TYR cc_start: 0.8852 (t80) cc_final: 0.8541 (t80) REVERT: E 165 ASP cc_start: 0.8742 (m-30) cc_final: 0.8533 (m-30) REVERT: E 290 THR cc_start: 0.8909 (m) cc_final: 0.8703 (p) REVERT: E 297 ASP cc_start: 0.8341 (m-30) cc_final: 0.8134 (t0) REVERT: F 290 THR cc_start: 0.8859 (m) cc_final: 0.8505 (p) outliers start: 14 outliers final: 10 residues processed: 206 average time/residue: 0.1028 time to fit residues: 30.2232 Evaluate side-chains 175 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 165 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 215 GLN Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain F residue 225 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 93 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 94 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 39 optimal weight: 8.9990 chunk 22 optimal weight: 6.9990 chunk 116 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 246 GLN D 242 ASN D 303 ASN ** E 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.113806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.093266 restraints weight = 18075.864| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.71 r_work: 0.3154 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10758 Z= 0.131 Angle : 0.471 5.199 14562 Z= 0.250 Chirality : 0.042 0.160 1524 Planarity : 0.003 0.032 1818 Dihedral : 8.297 57.566 1572 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.37 % Allowed : 7.51 % Favored : 91.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.24), residues: 1230 helix: 1.79 (0.23), residues: 504 sheet: 0.51 (0.38), residues: 174 loop : 0.39 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 224 TYR 0.011 0.001 TYR C 295 PHE 0.011 0.001 PHE F 194 TRP 0.021 0.001 TRP F 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (10758) covalent geometry : angle 0.47112 / 0.25 (14562) hydrogen bonds : bond 0.03880 / 2.60 ( 419) hydrogen bonds : angle 4.94235 / 3.49 ( 1191) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 170 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: B 297 ASP cc_start: 0.8329 (m-30) cc_final: 0.7985 (t0) REVERT: C 275 ASN cc_start: 0.7115 (t0) cc_final: 0.6870 (t0) REVERT: D 166 LYS cc_start: 0.9022 (mmtp) cc_final: 0.8562 (mmmt) REVERT: D 248 LYS cc_start: 0.8531 (ttmt) cc_final: 0.8178 (ttpp) REVERT: D 269 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8022 (mm-30) REVERT: D 321 TYR cc_start: 0.8927 (t80) cc_final: 0.8664 (t80) REVERT: E 282 GLU cc_start: 0.8239 (pp20) cc_final: 0.7751 (pp20) REVERT: E 297 ASP cc_start: 0.8353 (m-30) cc_final: 0.8120 (t0) REVERT: F 290 THR cc_start: 0.8899 (m) cc_final: 0.8571 (p) REVERT: F 297 ASP cc_start: 0.8462 (m-30) cc_final: 0.8196 (t0) outliers start: 15 outliers final: 11 residues processed: 175 average time/residue: 0.0984 time to fit residues: 25.2950 Evaluate side-chains 170 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 159 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain F residue 165 ASP Chi-restraints excluded: chain F residue 225 LYS Chi-restraints excluded: chain F residue 226 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 36 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 57 optimal weight: 0.0870 chunk 15 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 131 ASN D 242 ASN ** E 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 246 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.115252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.094855 restraints weight = 18256.139| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.72 r_work: 0.3179 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10758 Z= 0.095 Angle : 0.442 7.412 14562 Z= 0.232 Chirality : 0.040 0.159 1524 Planarity : 0.003 0.032 1818 Dihedral : 7.304 50.947 1572 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.37 % Allowed : 8.88 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.24), residues: 1230 helix: 2.02 (0.23), residues: 504 sheet: 0.46 (0.38), residues: 174 loop : 0.46 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 224 TYR 0.009 0.001 TYR D 295 PHE 0.011 0.001 PHE F 194 TRP 0.023 0.001 TRP F 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 (10758) covalent geometry : angle 0.44176 / 0.23 (14562) hydrogen bonds : bond 0.03324 / 2.24 ( 419) hydrogen bonds : angle 4.71760 / 3.32 ( 1191) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 176 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 230 GLU cc_start: 0.8166 (pt0) cc_final: 0.7952 (pt0) REVERT: B 297 ASP cc_start: 0.8303 (m-30) cc_final: 0.7986 (t0) REVERT: D 166 LYS cc_start: 0.9035 (mmtp) cc_final: 0.8598 (mmmt) REVERT: D 248 LYS cc_start: 0.8501 (ttmt) cc_final: 0.8199 (ttpp) REVERT: D 269 GLU cc_start: 0.8371 (mt-10) cc_final: 0.7965 (mm-30) REVERT: D 321 TYR cc_start: 0.8921 (t80) cc_final: 0.8651 (t80) REVERT: E 290 THR cc_start: 0.8927 (m) cc_final: 0.8725 (p) REVERT: E 297 ASP cc_start: 0.8285 (m-30) cc_final: 0.8062 (t0) REVERT: F 290 THR cc_start: 0.8895 (m) cc_final: 0.8596 (p) REVERT: F 297 ASP cc_start: 0.8470 (m-30) cc_final: 0.8248 (t0) outliers start: 15 outliers final: 8 residues processed: 184 average time/residue: 0.0917 time to fit residues: 24.7169 Evaluate side-chains 174 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 166 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain F residue 225 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 119 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 80 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 131 ASN D 159 GLN ** E 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 275 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.111730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.091096 restraints weight = 18299.635| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.73 r_work: 0.3121 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10758 Z= 0.168 Angle : 0.490 6.021 14562 Z= 0.259 Chirality : 0.042 0.156 1524 Planarity : 0.003 0.034 1818 Dihedral : 7.662 56.110 1572 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.56 % Allowed : 9.43 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.24), residues: 1230 helix: 1.92 (0.23), residues: 504 sheet: 1.43 (0.48), residues: 114 loop : 0.29 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 224 TYR 0.011 0.001 TYR D 295 PHE 0.010 0.001 PHE B 223 TRP 0.026 0.001 TRP D 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 (10758) covalent geometry : angle 0.49026 / 0.26 (14562) hydrogen bonds : bond 0.04131 / 2.78 ( 419) hydrogen bonds : angle 4.82589 / 3.39 ( 1191) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 174 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 297 ASP cc_start: 0.8373 (m-30) cc_final: 0.7993 (t0) REVERT: D 166 LYS cc_start: 0.9046 (mmtp) cc_final: 0.8602 (mmmt) REVERT: D 248 LYS cc_start: 0.8464 (ttmt) cc_final: 0.8178 (ttpp) REVERT: D 269 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8066 (mm-30) REVERT: D 321 TYR cc_start: 0.8978 (t80) cc_final: 0.8740 (t80) REVERT: E 297 ASP cc_start: 0.8310 (m-30) cc_final: 0.8028 (t0) REVERT: F 290 THR cc_start: 0.8955 (m) cc_final: 0.8592 (p) REVERT: F 297 ASP cc_start: 0.8533 (m-30) cc_final: 0.8250 (t0) outliers start: 17 outliers final: 14 residues processed: 182 average time/residue: 0.0876 time to fit residues: 23.8617 Evaluate side-chains 182 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 168 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain F residue 225 LYS Chi-restraints excluded: chain F residue 226 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 11 optimal weight: 0.8980 chunk 94 optimal weight: 0.0270 chunk 99 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 10 optimal weight: 0.3980 chunk 106 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 44 optimal weight: 0.4980 chunk 20 optimal weight: 3.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 196 ASN D 131 ASN D 159 GLN ** E 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.115215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.094912 restraints weight = 18208.260| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.71 r_work: 0.3185 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10758 Z= 0.085 Angle : 0.432 7.323 14562 Z= 0.227 Chirality : 0.040 0.158 1524 Planarity : 0.003 0.033 1818 Dihedral : 6.543 48.710 1572 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.73 % Allowed : 11.54 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.24), residues: 1230 helix: 1.95 (0.22), residues: 540 sheet: 1.40 (0.49), residues: 114 loop : 0.35 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 123 TYR 0.010 0.001 TYR D 295 PHE 0.009 0.001 PHE F 194 TRP 0.024 0.001 TRP F 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00183 / 0.08 (10758) covalent geometry : angle 0.43179 / 0.23 (14562) hydrogen bonds : bond 0.03141 / 2.12 ( 419) hydrogen bonds : angle 4.59264 / 3.23 ( 1191) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 182 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 297 ASP cc_start: 0.8316 (m-30) cc_final: 0.7998 (t0) REVERT: D 166 LYS cc_start: 0.9090 (mmtp) cc_final: 0.8616 (mmmt) REVERT: D 248 LYS cc_start: 0.8452 (ttmt) cc_final: 0.8137 (ttpp) REVERT: D 269 GLU cc_start: 0.8383 (mt-10) cc_final: 0.7979 (mm-30) REVERT: D 321 TYR cc_start: 0.8932 (t80) cc_final: 0.8693 (t80) REVERT: E 290 THR cc_start: 0.8910 (m) cc_final: 0.8663 (p) REVERT: E 297 ASP cc_start: 0.8273 (m-30) cc_final: 0.8034 (t0) REVERT: F 290 THR cc_start: 0.8919 (m) cc_final: 0.8591 (p) REVERT: F 297 ASP cc_start: 0.8470 (m-30) cc_final: 0.8236 (t0) outliers start: 8 outliers final: 6 residues processed: 185 average time/residue: 0.0823 time to fit residues: 22.8281 Evaluate side-chains 173 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 167 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain E residue 179 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 84 optimal weight: 0.8980 chunk 19 optimal weight: 9.9990 chunk 96 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 115 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 196 ASN D 131 ASN D 159 GLN ** E 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.116039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.095972 restraints weight = 18153.446| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.66 r_work: 0.3205 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10758 Z= 0.117 Angle : 0.455 7.407 14562 Z= 0.240 Chirality : 0.041 0.156 1524 Planarity : 0.003 0.034 1818 Dihedral : 6.654 51.074 1572 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.10 % Allowed : 11.54 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.24), residues: 1230 helix: 2.21 (0.23), residues: 504 sheet: 1.33 (0.49), residues: 114 loop : 0.36 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 123 TYR 0.013 0.001 TYR D 295 PHE 0.009 0.001 PHE F 194 TRP 0.022 0.001 TRP F 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (10758) covalent geometry : angle 0.45475 / 0.24 (14562) hydrogen bonds : bond 0.03439 / 2.32 ( 419) hydrogen bonds : angle 4.59646 / 3.23 ( 1191) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 174 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 297 ASP cc_start: 0.8269 (m-30) cc_final: 0.8009 (t0) REVERT: D 166 LYS cc_start: 0.9049 (mmtp) cc_final: 0.8657 (mmmt) REVERT: D 248 LYS cc_start: 0.8437 (ttmt) cc_final: 0.8193 (ttpp) REVERT: D 269 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8032 (mm-30) REVERT: D 321 TYR cc_start: 0.8976 (t80) cc_final: 0.8737 (t80) REVERT: E 290 THR cc_start: 0.8977 (m) cc_final: 0.8717 (p) REVERT: F 290 THR cc_start: 0.8989 (m) cc_final: 0.8657 (p) REVERT: F 297 ASP cc_start: 0.8414 (m-30) cc_final: 0.8178 (t0) outliers start: 12 outliers final: 11 residues processed: 179 average time/residue: 0.0792 time to fit residues: 21.3414 Evaluate side-chains 182 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 171 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain F residue 225 LYS Chi-restraints excluded: chain F residue 226 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 7 optimal weight: 0.0980 chunk 93 optimal weight: 0.9990 chunk 101 optimal weight: 4.9990 chunk 78 optimal weight: 0.0980 chunk 45 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 9 optimal weight: 0.2980 chunk 92 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 119 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 overall best weight: 0.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 196 ASN D 131 ASN ** E 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.116722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.097037 restraints weight = 18072.876| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.62 r_work: 0.3257 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10758 Z= 0.085 Angle : 0.434 7.490 14562 Z= 0.228 Chirality : 0.040 0.157 1524 Planarity : 0.003 0.035 1818 Dihedral : 6.264 50.798 1572 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.19 % Allowed : 11.90 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.24), residues: 1230 helix: 2.14 (0.22), residues: 540 sheet: 1.36 (0.49), residues: 114 loop : 0.42 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 123 TYR 0.011 0.001 TYR D 295 PHE 0.008 0.001 PHE F 194 TRP 0.032 0.001 TRP F 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00186 / 0.08 (10758) covalent geometry : angle 0.43422 / 0.23 (14562) hydrogen bonds : bond 0.02978 / 2.01 ( 419) hydrogen bonds : angle 4.47008 / 3.14 ( 1191) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 181 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 297 ASP cc_start: 0.8314 (m-30) cc_final: 0.8082 (t0) REVERT: C 275 ASN cc_start: 0.7014 (t0) cc_final: 0.6769 (t0) REVERT: D 146 ILE cc_start: 0.8422 (OUTLIER) cc_final: 0.8134 (mp) REVERT: D 166 LYS cc_start: 0.9058 (mmtp) cc_final: 0.8647 (mmmt) REVERT: D 196 ASN cc_start: 0.8179 (t0) cc_final: 0.7960 (t0) REVERT: D 248 LYS cc_start: 0.8474 (ttmt) cc_final: 0.8113 (ttpp) REVERT: D 269 GLU cc_start: 0.8341 (mt-10) cc_final: 0.7965 (mm-30) REVERT: D 273 TRP cc_start: 0.6078 (p-90) cc_final: 0.5853 (p-90) REVERT: D 321 TYR cc_start: 0.8940 (t80) cc_final: 0.8696 (t80) REVERT: E 290 THR cc_start: 0.8915 (m) cc_final: 0.8709 (p) REVERT: F 290 THR cc_start: 0.8968 (m) cc_final: 0.8705 (p) REVERT: F 297 ASP cc_start: 0.8398 (m-30) cc_final: 0.8191 (t0) outliers start: 13 outliers final: 10 residues processed: 184 average time/residue: 0.0708 time to fit residues: 20.0052 Evaluate side-chains 182 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 171 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain F residue 225 LYS Chi-restraints excluded: chain F residue 226 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 20 optimal weight: 9.9990 chunk 76 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 117 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 87 optimal weight: 0.0000 chunk 70 optimal weight: 0.0870 overall best weight: 1.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 196 ASN D 131 ASN F 203 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.113658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.093431 restraints weight = 18431.126| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.66 r_work: 0.3176 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10758 Z= 0.171 Angle : 0.499 7.864 14562 Z= 0.262 Chirality : 0.043 0.156 1524 Planarity : 0.004 0.047 1818 Dihedral : 7.010 55.081 1572 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.28 % Allowed : 11.90 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.24), residues: 1230 helix: 1.93 (0.22), residues: 540 sheet: 1.25 (0.49), residues: 114 loop : 0.36 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 123 TYR 0.012 0.001 TYR D 295 PHE 0.010 0.001 PHE B 223 TRP 0.031 0.001 TRP F 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 (10758) covalent geometry : angle 0.49928 / 0.26 (14562) hydrogen bonds : bond 0.03983 / 2.68 ( 419) hydrogen bonds : angle 4.65421 / 3.27 ( 1191) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 169 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 297 ASP cc_start: 0.8368 (m-30) cc_final: 0.8148 (t0) REVERT: D 146 ILE cc_start: 0.8618 (OUTLIER) cc_final: 0.8346 (mp) REVERT: D 248 LYS cc_start: 0.8465 (ttmt) cc_final: 0.8203 (ttpp) REVERT: D 269 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8059 (mm-30) REVERT: D 321 TYR cc_start: 0.8977 (t80) cc_final: 0.8720 (t80) REVERT: F 290 THR cc_start: 0.9034 (m) cc_final: 0.8791 (p) REVERT: F 297 ASP cc_start: 0.8474 (m-30) cc_final: 0.8240 (t0) outliers start: 14 outliers final: 12 residues processed: 175 average time/residue: 0.0692 time to fit residues: 18.6325 Evaluate side-chains 178 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 165 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain F residue 225 LYS Chi-restraints excluded: chain F residue 226 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 45 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 109 optimal weight: 5.9990 chunk 102 optimal weight: 0.3980 chunk 88 optimal weight: 0.9990 chunk 77 optimal weight: 0.0040 chunk 84 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 196 ASN D 131 ASN ** E 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.117314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.097209 restraints weight = 18093.310| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.66 r_work: 0.3225 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10758 Z= 0.094 Angle : 0.456 7.711 14562 Z= 0.238 Chirality : 0.040 0.156 1524 Planarity : 0.003 0.039 1818 Dihedral : 6.424 49.439 1572 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.10 % Allowed : 12.09 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.24), residues: 1230 helix: 2.06 (0.22), residues: 540 sheet: 1.26 (0.49), residues: 114 loop : 0.41 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 123 TYR 0.011 0.001 TYR D 295 PHE 0.008 0.001 PHE F 194 TRP 0.035 0.001 TRP F 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.09 (10758) covalent geometry : angle 0.45613 / 0.24 (14562) hydrogen bonds : bond 0.03155 / 2.14 ( 419) hydrogen bonds : angle 4.47612 / 3.15 ( 1191) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 172 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 297 ASP cc_start: 0.8332 (m-30) cc_final: 0.8109 (t0) REVERT: C 275 ASN cc_start: 0.7010 (t0) cc_final: 0.6773 (t0) REVERT: D 146 ILE cc_start: 0.8428 (OUTLIER) cc_final: 0.8144 (mp) REVERT: D 166 LYS cc_start: 0.9012 (mmtp) cc_final: 0.8605 (mmmt) REVERT: D 248 LYS cc_start: 0.8470 (ttmt) cc_final: 0.8236 (ttpp) REVERT: D 269 GLU cc_start: 0.8370 (mt-10) cc_final: 0.7985 (mm-30) REVERT: D 321 TYR cc_start: 0.8922 (t80) cc_final: 0.8669 (t80) REVERT: E 290 THR cc_start: 0.8918 (m) cc_final: 0.8684 (p) REVERT: F 297 ASP cc_start: 0.8438 (m-30) cc_final: 0.8235 (t0) outliers start: 12 outliers final: 10 residues processed: 176 average time/residue: 0.0817 time to fit residues: 21.8724 Evaluate side-chains 181 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 170 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain F residue 225 LYS Chi-restraints excluded: chain F residue 226 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 118 optimal weight: 0.4980 chunk 25 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 86 optimal weight: 0.8980 chunk 69 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 44 optimal weight: 0.3980 chunk 74 optimal weight: 0.0270 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 196 ASN D 131 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.118343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.098161 restraints weight = 18246.130| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.69 r_work: 0.3255 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10758 Z= 0.085 Angle : 0.443 7.748 14562 Z= 0.231 Chirality : 0.040 0.156 1524 Planarity : 0.003 0.045 1818 Dihedral : 6.100 49.407 1572 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.01 % Allowed : 12.36 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.24), residues: 1230 helix: 2.19 (0.22), residues: 540 sheet: 1.32 (0.49), residues: 114 loop : 0.42 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 123 TYR 0.011 0.001 TYR C 295 PHE 0.008 0.001 PHE F 194 TRP 0.036 0.001 TRP F 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00188 / 0.09 (10758) covalent geometry : angle 0.44257 / 0.23 (14562) hydrogen bonds : bond 0.02888 / 1.96 ( 419) hydrogen bonds : angle 4.37949 / 3.08 ( 1191) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2100.12 seconds wall clock time: 36 minutes 50.87 seconds (2210.87 seconds total)