Starting phenix.real_space_refine on Wed Mar 4 04:24:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pqm_71786/03_2026/9pqm_71786.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pqm_71786/03_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_71786/03_2026/9pqm_71786.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pqm_71786/03_2026/9pqm_71786.map" model { file = "/net/cci-nas-00/data/ceres_data/9pqm_71786/03_2026/9pqm_71786.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pqm_71786/03_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-5986/lib/python3.9/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: 2.41, per 1000 atoms: 0.23 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: 0.83 Conformation dependent library (CDL) restraints added in 495.1 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: 0.31 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: 1.48 Time building geometry restraints manager: 1.13 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=" N GLU E 269 " pdb=" CA GLU E 269 " ideal model delta sigma weight residual 1.456 1.483 -0.026 1.31e-02 5.83e+03 4.01e+00 bond pdb=" CD GLU D 315 " pdb=" OE1 GLU D 315 " ideal model delta sigma weight residual 1.249 1.219 0.030 1.90e-02 2.77e+03 2.49e+00 bond pdb=" CA ASP C 210 " pdb=" CB ASP C 210 " ideal model delta sigma weight residual 1.529 1.511 0.018 1.66e-02 3.63e+03 1.19e+00 bond pdb=" CA ASP D 222 " pdb=" C ASP D 222 " ideal model delta sigma weight residual 1.532 1.522 0.010 9.60e-03 1.09e+04 1.15e+00 bond pdb=" CE1 PHE D 251 " pdb=" CZ PHE D 251 " ideal model delta sigma weight residual 1.382 1.350 0.032 3.00e-02 1.11e+03 1.12e+00 ... (remaining 10753 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 13494 1.18 - 2.37: 915 2.37 - 3.55: 113 3.55 - 4.74: 32 4.74 - 5.92: 8 Bond angle restraints: 14562 Sorted by residual: angle pdb=" C GLN F 255 " pdb=" CA GLN F 255 " pdb=" CB GLN F 255 " ideal model delta sigma weight residual 111.21 106.81 4.40 1.31e+00 5.83e-01 1.13e+01 angle pdb=" C TRP C 254 " pdb=" N GLN C 255 " pdb=" CA GLN C 255 " ideal model delta sigma weight residual 122.28 118.86 3.42 1.02e+00 9.61e-01 1.12e+01 angle pdb=" C GLN C 255 " pdb=" CA GLN C 255 " pdb=" CB GLN C 255 " ideal model delta sigma weight residual 111.11 107.12 3.99 1.28e+00 6.10e-01 9.71e+00 angle pdb=" N GLU D 315 " pdb=" CA GLU D 315 " pdb=" CB GLU D 315 " ideal model delta sigma weight residual 110.12 114.54 -4.42 1.47e+00 4.63e-01 9.06e+00 angle pdb=" CA GLN C 255 " pdb=" C GLN C 255 " pdb=" N PRO C 256 " ideal model delta sigma weight residual 117.84 120.75 -2.91 9.70e-01 1.06e+00 9.02e+00 ... (remaining 14557 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.44: 6191 30.44 - 60.88: 207 60.88 - 91.33: 18 91.33 - 121.77: 1 121.77 - 152.21: 3 Dihedral angle restraints: 6420 sinusoidal: 2826 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=" O1A AGS E 402 " pdb=" O3A AGS E 402 " pdb=" PA AGS E 402 " pdb=" PB AGS E 402 " ideal model delta sinusoidal sigma weight residual -67.73 84.48 -152.21 1 3.00e+01 1.11e-03 2.01e+01 dihedral pdb=" O1A AGS A 401 " pdb=" O3A AGS A 401 " pdb=" PA AGS A 401 " pdb=" PB AGS A 401 " ideal model delta sinusoidal sigma weight residual -67.73 82.80 -150.53 1 3.00e+01 1.11e-03 2.00e+01 ... (remaining 6417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 818 0.030 - 0.059: 464 0.059 - 0.089: 153 0.089 - 0.119: 71 0.119 - 0.148: 30 Chirality restraints: 1536 Sorted by residual: chirality pdb=" CA PRO A 216 " pdb=" N PRO A 216 " pdb=" C PRO A 216 " pdb=" CB PRO A 216 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.49e-01 chirality pdb=" CA ILE F 172 " pdb=" N ILE F 172 " pdb=" C ILE F 172 " pdb=" CB ILE F 172 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.41e-01 chirality pdb=" PA AGS E 401 " pdb=" O2A AGS E 401 " pdb=" O3A AGS E 401 " pdb=" O5' AGS E 401 " both_signs ideal model delta sigma weight residual True 3.18 3.04 0.15 2.00e-01 2.50e+01 5.39e-01 ... (remaining 1533 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.220 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: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.410 Find NCS groups from input model: 0.200 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 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 : 0.006 0.043 10758 Z= 0.264 Angle : 0.657 5.923 14562 Z= 0.378 Chirality : 0.045 0.148 1536 Planarity : 0.005 0.062 1818 Dihedral : 14.585 152.212 4104 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 covalent geometry : bond 0.00627 (10758) covalent geometry : angle 0.65711 (14562) hydrogen bonds : bond 0.15842 ( 419) hydrogen bonds : angle 7.01792 ( 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 : 0.393 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: 0.1175 time to fit residues: 40.4066 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 : 0.400 ------------------------------------------------------------------------------- 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: 0.6980 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: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN A 303 ASN B 203 ASN D 131 ASN D 303 ASN F 303 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.114878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.094271 restraints weight = 18080.038| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.70 r_work: 0.3165 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10758 Z= 0.114 Angle : 0.518 6.624 14562 Z= 0.278 Chirality : 0.042 0.137 1536 Planarity : 0.004 0.039 1818 Dihedral : 11.351 145.514 1464 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.56 % Allowed : 5.86 % Favored : 92.58 % 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: 1.27 (0.24), residues: 1230 helix: 1.52 (0.23), residues: 504 sheet: 0.57 (0.38), residues: 174 loop : 0.45 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 123 TYR 0.015 0.001 TYR A 295 PHE 0.013 0.001 PHE F 194 TRP 0.028 0.001 TRP F 273 Details of bonding type rmsd covalent geometry : bond 0.00242 (10758) covalent geometry : angle 0.51848 (14562) hydrogen bonds : bond 0.04441 ( 419) hydrogen bonds : angle 5.38769 ( 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 208 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 191 time to evaluate : 0.457 Fit side-chains REVERT: B 297 ASP cc_start: 0.8289 (m-30) cc_final: 0.7997 (t0) REVERT: D 166 LYS cc_start: 0.8956 (mmtp) cc_final: 0.8516 (mmmt) REVERT: D 248 LYS cc_start: 0.8544 (ttmt) cc_final: 0.8211 (ttpp) REVERT: D 269 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8053 (mm-30) REVERT: D 321 TYR cc_start: 0.8869 (t80) cc_final: 0.8589 (t80) REVERT: E 165 ASP cc_start: 0.8776 (m-30) cc_final: 0.8526 (m-30) REVERT: F 290 THR cc_start: 0.8855 (m) cc_final: 0.8498 (p) REVERT: F 297 ASP cc_start: 0.8532 (m-30) cc_final: 0.8256 (t0) outliers start: 17 outliers final: 12 residues processed: 200 average time/residue: 0.0924 time to fit residues: 26.5963 Evaluate side-chains 176 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 164 time to evaluate : 0.366 ------------------------------------------------------------------------------- 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 A residue 303 ASN Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 310 ASP Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain F residue 225 LYS Chi-restraints excluded: chain F residue 226 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 93 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 39 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 52 optimal weight: 0.0470 chunk 70 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 overall best weight: 0.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN B 203 ASN D 131 ASN D 242 ASN D 303 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.114318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.093663 restraints weight = 18009.656| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.69 r_work: 0.3159 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2181 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 : 0.475 6.254 14562 Z= 0.253 Chirality : 0.041 0.157 1536 Planarity : 0.003 0.033 1818 Dihedral : 11.267 146.917 1464 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.01 % Allowed : 7.42 % Favored : 90.57 % 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: 1.40 (0.24), residues: 1230 helix: 1.76 (0.23), residues: 504 sheet: 0.46 (0.38), residues: 174 loop : 0.43 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 224 TYR 0.011 0.001 TYR A 241 PHE 0.011 0.001 PHE F 194 TRP 0.026 0.001 TRP F 273 Details of bonding type rmsd covalent geometry : bond 0.00264 (10758) covalent geometry : angle 0.47479 (14562) hydrogen bonds : bond 0.04047 ( 419) hydrogen bonds : angle 5.10969 ( 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 197 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 175 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: B 297 ASP cc_start: 0.8307 (m-30) cc_final: 0.8012 (t0) REVERT: C 275 ASN cc_start: 0.6939 (t0) cc_final: 0.6725 (t0) REVERT: D 131 ASN cc_start: 0.9172 (m-40) cc_final: 0.8858 (m-40) REVERT: D 166 LYS cc_start: 0.9016 (mmtp) cc_final: 0.8552 (mmmt) REVERT: D 248 LYS cc_start: 0.8539 (ttmt) cc_final: 0.8273 (ttpp) REVERT: D 269 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8032 (mm-30) REVERT: D 319 ARG cc_start: 0.7481 (mtp85) cc_final: 0.7221 (mtm-85) REVERT: D 321 TYR cc_start: 0.8879 (t80) cc_final: 0.8615 (t80) REVERT: E 133 ASN cc_start: 0.8118 (t0) cc_final: 0.7458 (t0) REVERT: E 136 GLU cc_start: 0.8789 (mp0) cc_final: 0.8354 (mp0) REVERT: E 221 ASP cc_start: 0.8679 (OUTLIER) cc_final: 0.8454 (m-30) REVERT: F 290 THR cc_start: 0.8901 (m) cc_final: 0.8511 (p) REVERT: F 297 ASP cc_start: 0.8548 (m-30) cc_final: 0.8268 (t0) outliers start: 22 outliers final: 14 residues processed: 183 average time/residue: 0.0780 time to fit residues: 21.7163 Evaluate side-chains 183 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 168 time to evaluate : 0.441 ------------------------------------------------------------------------------- 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 202 SER Chi-restraints excluded: chain B residue 203 ASN 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 C residue 274 VAL Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain E residue 221 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: 0.9980 chunk 102 optimal weight: 0.6980 chunk 73 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 56 optimal weight: 0.1980 chunk 34 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN B 203 ASN D 242 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.113560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.093321 restraints weight = 18155.014| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.66 r_work: 0.3173 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2358 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= 0.100 Angle : 0.451 5.825 14562 Z= 0.241 Chirality : 0.040 0.155 1536 Planarity : 0.003 0.036 1818 Dihedral : 11.130 147.112 1464 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.74 % Allowed : 8.70 % Favored : 89.56 % 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: 1.50 (0.24), residues: 1230 helix: 1.94 (0.23), residues: 504 sheet: 0.41 (0.37), residues: 174 loop : 0.42 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 224 TYR 0.010 0.001 TYR D 295 PHE 0.010 0.001 PHE F 194 TRP 0.022 0.001 TRP F 273 Details of bonding type rmsd covalent geometry : bond 0.00218 (10758) covalent geometry : angle 0.45060 (14562) hydrogen bonds : bond 0.03685 ( 419) hydrogen bonds : angle 4.92757 ( 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: 19 poor density : 172 time to evaluate : 0.387 Fit side-chains REVERT: B 297 ASP cc_start: 0.8302 (m-30) cc_final: 0.8003 (t0) REVERT: C 246 GLN cc_start: 0.8820 (tt0) cc_final: 0.8602 (tt0) REVERT: D 166 LYS cc_start: 0.9019 (mmtp) cc_final: 0.8546 (mmmt) REVERT: D 248 LYS cc_start: 0.8534 (ttmt) cc_final: 0.8182 (ttpp) REVERT: D 269 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8041 (mm-30) REVERT: D 273 TRP cc_start: 0.5646 (p-90) cc_final: 0.5388 (p-90) REVERT: D 321 TYR cc_start: 0.8891 (t80) cc_final: 0.8600 (t80) REVERT: E 133 ASN cc_start: 0.8252 (t0) cc_final: 0.7441 (t0) REVERT: E 136 GLU cc_start: 0.8813 (mp0) cc_final: 0.8349 (mp0) REVERT: E 221 ASP cc_start: 0.8676 (OUTLIER) cc_final: 0.8472 (m-30) REVERT: E 282 GLU cc_start: 0.8154 (pp20) cc_final: 0.7819 (pp20) REVERT: E 290 THR cc_start: 0.8931 (m) cc_final: 0.8718 (p) REVERT: F 290 THR cc_start: 0.8899 (m) cc_final: 0.8511 (p) REVERT: F 297 ASP cc_start: 0.8549 (m-30) cc_final: 0.8275 (t0) outliers start: 19 outliers final: 13 residues processed: 180 average time/residue: 0.0720 time to fit residues: 19.6499 Evaluate side-chains 179 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 165 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 202 SER Chi-restraints excluded: chain B residue 203 ASN 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 239 ASP Chi-restraints excluded: chain E residue 221 ASP Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain F residue 225 LYS Chi-restraints excluded: chain F residue 226 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 119 optimal weight: 0.7980 chunk 101 optimal weight: 0.9980 chunk 109 optimal weight: 5.9990 chunk 80 optimal weight: 0.0770 chunk 7 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 108 optimal weight: 4.9990 chunk 106 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 131 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.115163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.094778 restraints weight = 18153.362| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.69 r_work: 0.3173 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2515 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= 0.096 Angle : 0.438 5.934 14562 Z= 0.234 Chirality : 0.040 0.156 1536 Planarity : 0.003 0.034 1818 Dihedral : 11.044 147.251 1464 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.83 % Allowed : 8.61 % Favored : 89.56 % 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: 2.07 (0.23), residues: 504 sheet: 0.40 (0.38), residues: 174 loop : 0.43 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 224 TYR 0.008 0.001 TYR A 241 PHE 0.010 0.001 PHE F 194 TRP 0.023 0.001 TRP F 273 Details of bonding type rmsd covalent geometry : bond 0.00210 (10758) covalent geometry : angle 0.43762 (14562) hydrogen bonds : bond 0.03486 ( 419) hydrogen bonds : angle 4.80788 ( 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 190 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 170 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: B 297 ASP cc_start: 0.8317 (m-30) cc_final: 0.8002 (t0) REVERT: C 246 GLN cc_start: 0.8811 (tt0) cc_final: 0.8605 (tt0) REVERT: D 131 ASN cc_start: 0.9166 (m-40) cc_final: 0.8825 (m-40) REVERT: D 166 LYS cc_start: 0.9028 (mmtp) cc_final: 0.8567 (mmmt) REVERT: D 248 LYS cc_start: 0.8477 (ttmt) cc_final: 0.8214 (ttpp) REVERT: D 269 GLU cc_start: 0.8462 (mt-10) cc_final: 0.8084 (mm-30) REVERT: D 273 TRP cc_start: 0.5564 (p-90) cc_final: 0.5282 (p-90) REVERT: D 321 TYR cc_start: 0.8879 (t80) cc_final: 0.8607 (t80) REVERT: E 133 ASN cc_start: 0.8375 (t0) cc_final: 0.7380 (t0) REVERT: E 136 GLU cc_start: 0.8848 (mp0) cc_final: 0.8350 (mp0) REVERT: E 282 GLU cc_start: 0.8193 (pp20) cc_final: 0.7771 (pp20) REVERT: F 290 THR cc_start: 0.8922 (m) cc_final: 0.8532 (p) REVERT: F 297 ASP cc_start: 0.8543 (m-30) cc_final: 0.8321 (t0) outliers start: 20 outliers final: 14 residues processed: 178 average time/residue: 0.0771 time to fit residues: 20.9671 Evaluate side-chains 176 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 162 time to evaluate : 0.317 ------------------------------------------------------------------------------- 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 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 C residue 232 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 E residue 314 LEU Chi-restraints excluded: chain F residue 165 ASP 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: 0.6980 chunk 94 optimal weight: 0.0470 chunk 99 optimal weight: 7.9990 chunk 93 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 106 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 246 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.115816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.095550 restraints weight = 18187.986| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.66 r_work: 0.3188 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10758 Z= 0.089 Angle : 0.424 6.401 14562 Z= 0.228 Chirality : 0.040 0.156 1536 Planarity : 0.003 0.034 1818 Dihedral : 10.938 146.925 1464 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.37 % Allowed : 9.71 % Favored : 88.92 % 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: 1.70 (0.24), residues: 1230 helix: 2.19 (0.23), residues: 504 sheet: 0.41 (0.38), residues: 174 loop : 0.47 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 224 TYR 0.008 0.001 TYR F 241 PHE 0.010 0.001 PHE F 194 TRP 0.026 0.001 TRP F 273 Details of bonding type rmsd covalent geometry : bond 0.00192 (10758) covalent geometry : angle 0.42371 (14562) hydrogen bonds : bond 0.03257 ( 419) hydrogen bonds : angle 4.68430 ( 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 181 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 166 time to evaluate : 0.398 Fit side-chains REVERT: B 297 ASP cc_start: 0.8317 (m-30) cc_final: 0.8009 (t0) REVERT: D 166 LYS cc_start: 0.9030 (mmtp) cc_final: 0.8563 (mmmt) REVERT: D 248 LYS cc_start: 0.8513 (ttmt) cc_final: 0.8207 (ttpp) REVERT: D 269 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8043 (mm-30) REVERT: D 273 TRP cc_start: 0.5621 (p-90) cc_final: 0.5364 (p-90) REVERT: D 321 TYR cc_start: 0.8863 (t80) cc_final: 0.8577 (t80) REVERT: E 282 GLU cc_start: 0.8189 (pp20) cc_final: 0.7702 (pp20) REVERT: F 297 ASP cc_start: 0.8540 (m-30) cc_final: 0.8308 (t0) outliers start: 15 outliers final: 10 residues processed: 171 average time/residue: 0.0778 time to fit residues: 20.0947 Evaluate side-chains 170 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 160 time to evaluate : 0.314 ------------------------------------------------------------------------------- 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 C residue 232 SER Chi-restraints excluded: chain D residue 239 ASP 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 84 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 54 optimal weight: 0.4980 chunk 95 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 131 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.114914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.094702 restraints weight = 18023.203| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.67 r_work: 0.3176 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2732 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= 0.102 Angle : 0.439 7.658 14562 Z= 0.234 Chirality : 0.040 0.156 1536 Planarity : 0.003 0.034 1818 Dihedral : 10.903 146.978 1464 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.19 % Allowed : 10.44 % Favored : 88.37 % 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: 1.84 (0.24), residues: 1230 helix: 2.23 (0.23), residues: 504 sheet: 1.49 (0.49), residues: 114 loop : 0.39 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 319 TYR 0.008 0.001 TYR B 241 PHE 0.009 0.001 PHE F 194 TRP 0.036 0.001 TRP F 273 Details of bonding type rmsd covalent geometry : bond 0.00232 (10758) covalent geometry : angle 0.43878 (14562) hydrogen bonds : bond 0.03315 ( 419) hydrogen bonds : angle 4.64520 ( 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 178 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 165 time to evaluate : 0.360 Fit side-chains REVERT: B 297 ASP cc_start: 0.8299 (m-30) cc_final: 0.7979 (t0) REVERT: C 275 ASN cc_start: 0.7003 (t0) cc_final: 0.6713 (t0) REVERT: D 166 LYS cc_start: 0.9054 (mmtp) cc_final: 0.8549 (mmmt) REVERT: D 248 LYS cc_start: 0.8488 (ttmt) cc_final: 0.8141 (ttpp) REVERT: D 269 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8032 (mm-30) REVERT: D 273 TRP cc_start: 0.5674 (p-90) cc_final: 0.5425 (p-90) REVERT: D 321 TYR cc_start: 0.8863 (t80) cc_final: 0.8572 (t80) REVERT: F 297 ASP cc_start: 0.8534 (m-30) cc_final: 0.8303 (t0) outliers start: 13 outliers final: 11 residues processed: 170 average time/residue: 0.0757 time to fit residues: 19.4237 Evaluate side-chains 174 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 163 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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 C residue 232 SER Chi-restraints excluded: chain D residue 239 ASP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 7 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 chunk 101 optimal weight: 6.9990 chunk 78 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 92 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 119 optimal weight: 0.6980 chunk 57 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 246 GLN D 131 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.114899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.095010 restraints weight = 18115.738| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.64 r_work: 0.3184 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10758 Z= 0.103 Angle : 0.438 6.965 14562 Z= 0.235 Chirality : 0.040 0.156 1536 Planarity : 0.003 0.034 1818 Dihedral : 10.902 146.704 1464 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.37 % Allowed : 10.53 % Favored : 88.10 % 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: 2.26 (0.23), residues: 504 sheet: 1.48 (0.49), residues: 114 loop : 0.38 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 150 TYR 0.008 0.001 TYR A 241 PHE 0.008 0.001 PHE F 194 TRP 0.036 0.001 TRP F 273 Details of bonding type rmsd covalent geometry : bond 0.00233 (10758) covalent geometry : angle 0.43835 (14562) hydrogen bonds : bond 0.03309 ( 419) hydrogen bonds : angle 4.58835 ( 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 180 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 165 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: B 297 ASP cc_start: 0.8303 (m-30) cc_final: 0.7982 (t0) REVERT: D 166 LYS cc_start: 0.9034 (mmtp) cc_final: 0.8573 (mmmt) REVERT: D 248 LYS cc_start: 0.8472 (ttmt) cc_final: 0.8190 (ttpp) REVERT: D 269 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8042 (mm-30) REVERT: D 273 TRP cc_start: 0.5677 (p-90) cc_final: 0.5443 (p-90) REVERT: D 321 TYR cc_start: 0.8864 (t80) cc_final: 0.8573 (t80) REVERT: F 297 ASP cc_start: 0.8535 (m-30) cc_final: 0.8301 (t0) outliers start: 15 outliers final: 13 residues processed: 170 average time/residue: 0.0777 time to fit residues: 20.2669 Evaluate side-chains 173 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 160 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 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 C residue 232 SER Chi-restraints excluded: chain D residue 239 ASP 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 Chi-restraints excluded: chain F residue 290 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 20 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 117 optimal weight: 5.9990 chunk 44 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 ASN C 246 GLN D 131 ASN D 159 GLN E 275 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.112362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.091878 restraints weight = 18388.070| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.70 r_work: 0.3129 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2712 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= 0.175 Angle : 0.493 7.066 14562 Z= 0.262 Chirality : 0.042 0.153 1536 Planarity : 0.003 0.033 1818 Dihedral : 11.084 146.631 1464 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.56 % Allowed : 10.07 % Favored : 88.37 % 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: 1.67 (0.24), residues: 1230 helix: 2.09 (0.23), residues: 504 sheet: 1.36 (0.48), residues: 114 loop : 0.31 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 123 TYR 0.010 0.001 TYR A 241 PHE 0.009 0.001 PHE B 271 TRP 0.034 0.001 TRP F 273 Details of bonding type rmsd covalent geometry : bond 0.00421 (10758) covalent geometry : angle 0.49284 (14562) hydrogen bonds : bond 0.03884 ( 419) hydrogen bonds : angle 4.71461 ( 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 179 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 162 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: B 297 ASP cc_start: 0.8361 (m-30) cc_final: 0.7989 (t0) REVERT: C 275 ASN cc_start: 0.7045 (t0) cc_final: 0.6782 (t0) REVERT: D 166 LYS cc_start: 0.9058 (mmtp) cc_final: 0.8560 (mmmt) REVERT: D 248 LYS cc_start: 0.8471 (ttmt) cc_final: 0.8176 (ttpp) REVERT: D 269 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8086 (mm-30) REVERT: D 321 TYR cc_start: 0.8910 (t80) cc_final: 0.8625 (t80) REVERT: F 297 ASP cc_start: 0.8572 (m-30) cc_final: 0.8330 (t0) outliers start: 17 outliers final: 13 residues processed: 170 average time/residue: 0.0774 time to fit residues: 19.7315 Evaluate side-chains 171 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 158 time to evaluate : 0.422 ------------------------------------------------------------------------------- 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 179 THR Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain D residue 239 ASP Chi-restraints excluded: chain D residue 268 SER 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 Chi-restraints excluded: chain F residue 290 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 45 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 47 optimal weight: 0.5980 chunk 109 optimal weight: 0.8980 chunk 102 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 ASN C 246 GLN D 131 ASN D 159 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.114339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.093936 restraints weight = 18037.748| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.69 r_work: 0.3166 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10758 Z= 0.101 Angle : 0.448 7.503 14562 Z= 0.240 Chirality : 0.040 0.155 1536 Planarity : 0.003 0.035 1818 Dihedral : 10.959 146.082 1464 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.28 % Allowed : 10.99 % 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: 1.78 (0.24), residues: 1230 helix: 2.20 (0.23), residues: 504 sheet: 1.35 (0.49), residues: 114 loop : 0.36 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 123 TYR 0.010 0.001 TYR A 241 PHE 0.009 0.001 PHE F 194 TRP 0.039 0.001 TRP F 273 Details of bonding type rmsd covalent geometry : bond 0.00227 (10758) covalent geometry : angle 0.44783 (14562) hydrogen bonds : bond 0.03365 ( 419) hydrogen bonds : angle 4.60125 ( 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 180 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 166 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: B 297 ASP cc_start: 0.8316 (m-30) cc_final: 0.7984 (t0) REVERT: C 275 ASN cc_start: 0.7184 (t0) cc_final: 0.6950 (t0) REVERT: D 166 LYS cc_start: 0.9063 (mmtp) cc_final: 0.8620 (mmmt) REVERT: D 248 LYS cc_start: 0.8476 (ttmt) cc_final: 0.8222 (ttpp) REVERT: D 269 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8036 (mm-30) REVERT: D 273 TRP cc_start: 0.5640 (p-90) cc_final: 0.5379 (p-90) REVERT: D 321 TYR cc_start: 0.8878 (t80) cc_final: 0.8603 (t80) REVERT: F 297 ASP cc_start: 0.8545 (m-30) cc_final: 0.8300 (t0) outliers start: 14 outliers final: 12 residues processed: 171 average time/residue: 0.0768 time to fit residues: 19.9507 Evaluate side-chains 173 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 161 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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 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 C residue 232 SER 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 Chi-restraints excluded: chain F residue 290 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 118 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 69 optimal weight: 0.0670 chunk 2 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 74 optimal weight: 5.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 ASN C 246 GLN D 131 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.114927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.094654 restraints weight = 18143.158| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.65 r_work: 0.3179 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10758 Z= 0.097 Angle : 0.444 7.424 14562 Z= 0.238 Chirality : 0.040 0.154 1536 Planarity : 0.003 0.043 1818 Dihedral : 10.900 145.757 1464 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.01 % Allowed : 11.36 % Favored : 87.64 % 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: 1.83 (0.24), residues: 1230 helix: 2.27 (0.23), residues: 504 sheet: 1.39 (0.49), residues: 114 loop : 0.36 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 123 TYR 0.009 0.001 TYR A 241 PHE 0.009 0.001 PHE F 194 TRP 0.037 0.001 TRP F 273 Details of bonding type rmsd covalent geometry : bond 0.00216 (10758) covalent geometry : angle 0.44395 (14562) hydrogen bonds : bond 0.03233 ( 419) hydrogen bonds : angle 4.56132 ( 1191) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2064.24 seconds wall clock time: 36 minutes 6.53 seconds (2166.53 seconds total)