Starting phenix.real_space_refine on Thu Jul 2 16:36:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pqo_71787/07_2026/9pqo_71787.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pqo_71787/07_2026/9pqo_71787.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9pqo_71787/07_2026/9pqo_71787.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pqo_71787/07_2026/9pqo_71787.map" model { file = "/net/cci-nas-00/data/ceres_data/9pqo_71787/07_2026/9pqo_71787.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pqo_71787/07_2026/9pqo_71787.cif" } resolution = 3.1 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 12 5.49 5 Mg 4 5.21 5 S 31 5.16 5 C 5826 2.51 5 N 1519 2.21 5 O 1661 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 9053 Number of models: 1 Model: "" Number of chains: 10 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: 325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 325 Classifications: {'peptide': 40} Link IDs: {'TRANS': 39} 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" 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: "D" 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} Time building chain proxies: 2.07, per 1000 atoms: 0.23 Number of scatterers: 9053 At special positions: 0 Unit cell: (105.84, 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 31 16.00 P 12 15.00 Mg 4 11.99 O 1661 8.00 N 1519 7.00 C 5826 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: 0.71 Conformation dependent library (CDL) restraints added in 415.5 milliseconds 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2004 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 17 sheets defined 48.8% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 121 through 132 removed outlier: 3.647A pdb=" N LYS A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 128 " --> pdb=" O GLU A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 141 Processing helix chain 'A' and resid 144 through 162 removed outlier: 3.731A pdb=" N ILE A 149 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N VAL A 160 " --> pdb=" O ASN A 156 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLN A 161 " --> pdb=" O ILE A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 195 Processing helix chain 'A' and resid 224 through 228 Processing helix chain 'A' and resid 232 through 239 removed outlier: 3.794A pdb=" N ARG A 236 " --> pdb=" O SER A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 271 removed outlier: 3.845A pdb=" N PHE A 271 " --> pdb=" O PRO A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 293 Processing helix chain 'A' and resid 307 through 323 Processing helix chain 'B' and resid 122 through 132 removed outlier: 3.507A pdb=" N LEU B 128 " --> pdb=" O GLU B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 140 Processing helix chain 'B' and resid 144 through 162 removed outlier: 3.669A pdb=" N ILE B 149 " --> pdb=" O ALA B 145 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL B 160 " --> pdb=" O ASN B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 196 removed outlier: 3.655A pdb=" N ASN B 196 " --> pdb=" O GLU B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 228 Processing helix chain 'B' and resid 231 through 238 removed outlier: 4.461A pdb=" N LEU B 235 " --> pdb=" O TRP B 231 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG B 236 " --> pdb=" O SER B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 271 removed outlier: 3.811A pdb=" N PHE B 271 " --> pdb=" O PRO B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 293 removed outlier: 3.746A pdb=" N ARG B 292 " --> pdb=" O GLN B 288 " (cutoff:3.500A) 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: 3.528A pdb=" N ILE C 148 " --> pdb=" O GLY C 144 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE C 149 " --> pdb=" O ALA C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 196 removed outlier: 3.666A pdb=" N ALA C 191 " --> pdb=" O ALA C 187 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN C 196 " --> pdb=" O GLU C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 228 Processing helix chain 'C' and resid 231 through 238 removed outlier: 4.304A pdb=" N LEU C 235 " --> pdb=" O TRP C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 294 removed outlier: 3.609A pdb=" N ARG C 292 " --> pdb=" O GLN C 288 " (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 removed outlier: 3.505A pdb=" N ILE D 149 " --> pdb=" O ALA D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 195 Processing helix chain 'D' and resid 224 through 228 removed outlier: 3.594A pdb=" N LEU D 228 " --> pdb=" O LYS D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 239 removed outlier: 4.156A pdb=" N LEU D 235 " --> pdb=" O TRP D 231 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP D 239 " --> pdb=" O LEU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 271 removed outlier: 3.772A pdb=" N PHE D 271 " --> pdb=" O PRO D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 294 removed outlier: 3.610A pdb=" N ARG D 291 " --> pdb=" O VAL D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 323 Processing helix chain 'E' and resid 122 through 132 removed outlier: 3.514A pdb=" N GLU E 127 " --> pdb=" O ARG E 123 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU E 128 " --> pdb=" O GLU E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 141 Processing helix chain 'E' and resid 144 through 162 removed outlier: 3.570A pdb=" N ILE E 149 " --> pdb=" O ALA E 145 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL E 160 " --> pdb=" O ASN E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 195 removed outlier: 3.577A pdb=" N ALA E 191 " --> pdb=" O ALA E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 228 removed outlier: 3.641A pdb=" N LEU E 228 " --> pdb=" O LYS E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 239 Processing helix chain 'E' and resid 266 through 271 removed outlier: 3.669A pdb=" N PHE E 271 " --> pdb=" O PRO E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 294 Processing helix chain 'E' and resid 307 through 323 Processing helix chain 'F' and resid 122 through 132 removed outlier: 3.699A pdb=" N MET F 129 " --> pdb=" O LYS F 125 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE F 130 " --> pdb=" O ALA F 126 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN F 131 " --> pdb=" O GLU F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 140 removed outlier: 3.766A pdb=" N MET F 139 " --> pdb=" O ARG F 135 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 160 removed outlier: 3.934A pdb=" N VAL F 160 " --> pdb=" O ASN F 156 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 199 through 201 removed outlier: 6.392A pdb=" N TRP A 200 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N ASP A 221 " --> pdb=" O TRP A 200 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N TYR A 302 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TRP A 174 " --> pdb=" O TYR A 302 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N PHE A 304 " --> pdb=" O TRP A 174 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LYS A 176 " --> pdb=" O PHE A 304 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 243 through 247 removed outlier: 4.261A pdb=" N LEU A 243 " --> pdb=" O TRP A 254 " (cutoff:3.500A) 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 200 through 201 removed outlier: 6.254A pdb=" N TRP B 200 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ALA B 218 " --> pdb=" O ILE B 260 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N THR B 262 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ILE B 220 " --> pdb=" O THR B 262 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY B 177 " --> pdb=" O SER B 263 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N TYR B 302 " --> pdb=" O ILE B 172 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N TRP B 174 " --> pdb=" O TYR B 302 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N PHE B 304 " --> pdb=" O TRP B 174 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LYS B 176 " --> pdb=" O PHE B 304 " (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: 3.570A 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 199 through 201 removed outlier: 6.189A pdb=" N TRP C 200 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ASP C 221 " --> pdb=" O TRP C 200 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LEU C 171 " --> pdb=" O ILE C 259 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N VAL C 261 " --> pdb=" O LEU C 171 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU C 173 " --> pdb=" O VAL C 261 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N TYR C 302 " --> pdb=" O ILE C 172 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N TRP C 174 " --> pdb=" O TYR C 302 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N PHE C 304 " --> pdb=" O TRP C 174 " (cutoff:3.500A) removed outlier: 6.710A 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: 3.731A pdb=" N GLY D 177 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N TYR D 302 " --> pdb=" O ILE D 172 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N TRP D 174 " --> pdb=" O TYR D 302 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N PHE D 304 " --> pdb=" O TRP D 174 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LYS D 176 " --> pdb=" O PHE D 304 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 244 through 247 removed outlier: 3.621A 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 removed outlier: 3.838A pdb=" N TRP D 273 " --> pdb=" O ILE D 281 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 200 through 201 removed outlier: 6.460A pdb=" N TRP E 200 " --> pdb=" O ILE E 219 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ALA E 218 " --> pdb=" O ILE E 260 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N THR E 262 " --> pdb=" O ALA E 218 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ILE E 220 " --> pdb=" O THR E 262 " (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 274 370 hydrogen bonds defined for protein. 1059 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: 1.12 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.34: 2880 1.34 - 1.49: 2437 1.49 - 1.64: 3883 1.64 - 1.80: 30 1.80 - 1.95: 28 Bond restraints: 9258 Sorted by residual: bond pdb=" O2G AGS C 401 " pdb=" PG AGS C 401 " ideal model delta sigma weight residual 1.604 1.488 0.116 2.00e-02 2.50e+03 3.39e+01 bond pdb=" O3B AGS D 401 " pdb=" PB AGS D 401 " ideal model delta sigma weight residual 1.673 1.581 0.092 2.00e-02 2.50e+03 2.10e+01 bond pdb=" O3B AGS A 401 " pdb=" PB AGS A 401 " ideal model delta sigma weight residual 1.673 1.583 0.090 2.00e-02 2.50e+03 2.04e+01 bond pdb=" O3B AGS D 402 " pdb=" PB AGS D 402 " ideal model delta sigma weight residual 1.673 1.584 0.089 2.00e-02 2.50e+03 1.97e+01 bond pdb=" O3A AGS D 402 " pdb=" PA AGS D 402 " ideal model delta sigma weight residual 1.664 1.579 0.085 2.00e-02 2.50e+03 1.80e+01 ... (remaining 9253 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 12255 1.86 - 3.73: 198 3.73 - 5.59: 37 5.59 - 7.46: 11 7.46 - 9.32: 14 Bond angle restraints: 12515 Sorted by residual: angle pdb=" O3A AGS D 401 " pdb=" PB AGS D 401 " pdb=" O3B AGS D 401 " ideal model delta sigma weight residual 100.38 109.70 -9.32 3.00e+00 1.11e-01 9.65e+00 angle pdb=" O1B AGS D 402 " pdb=" PB AGS D 402 " pdb=" O2B AGS D 402 " ideal model delta sigma weight residual 121.53 112.22 9.31 3.00e+00 1.11e-01 9.64e+00 angle pdb=" O3A AGS A 401 " pdb=" PB AGS A 401 " pdb=" O3B AGS A 401 " ideal model delta sigma weight residual 100.38 109.59 -9.21 3.00e+00 1.11e-01 9.43e+00 angle pdb=" O1A AGS A 401 " pdb=" PA AGS A 401 " pdb=" O2A AGS A 401 " ideal model delta sigma weight residual 122.09 113.47 8.62 3.00e+00 1.11e-01 8.27e+00 angle pdb=" O3G AGS A 401 " pdb=" PG AGS A 401 " pdb=" S1G AGS A 401 " ideal model delta sigma weight residual 117.10 108.59 8.51 3.00e+00 1.11e-01 8.04e+00 ... (remaining 12510 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.87: 5368 31.87 - 63.74: 183 63.74 - 95.61: 54 95.61 - 127.47: 0 127.47 - 159.34: 3 Dihedral angle restraints: 5608 sinusoidal: 2500 harmonic: 3108 Sorted by residual: dihedral pdb=" O1B AGS D 402 " pdb=" O3B AGS D 402 " pdb=" PB AGS D 402 " pdb=" PG AGS D 402 " ideal model delta sinusoidal sigma weight residual 138.55 -20.79 159.34 1 3.00e+01 1.11e-03 2.06e+01 dihedral pdb=" O2B AGS D 402 " pdb=" O3B AGS D 402 " pdb=" PB AGS D 402 " pdb=" PG AGS D 402 " ideal model delta sinusoidal sigma weight residual 7.37 -143.66 151.03 1 3.00e+01 1.11e-03 2.00e+01 dihedral pdb=" O3A AGS D 402 " pdb=" O3B AGS D 402 " pdb=" PB AGS D 402 " pdb=" PG AGS D 402 " ideal model delta sinusoidal sigma weight residual 252.61 101.63 150.98 1 3.00e+01 1.11e-03 2.00e+01 ... (remaining 5605 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1134 0.058 - 0.116: 161 0.116 - 0.175: 15 0.175 - 0.233: 1 0.233 - 0.291: 4 Chirality restraints: 1315 Sorted by residual: chirality pdb=" C3' AGS C 401 " pdb=" C2' AGS C 401 " pdb=" C4' AGS C 401 " pdb=" O3' AGS C 401 " both_signs ideal model delta sigma weight residual False -2.37 -2.66 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" C3' AGS D 402 " pdb=" C2' AGS D 402 " pdb=" C4' AGS D 402 " pdb=" O3' AGS D 402 " both_signs ideal model delta sigma weight residual False -2.37 -2.63 0.26 2.00e-01 2.50e+01 1.75e+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 -2.63 0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 1312 not shown) Planarity restraints: 1570 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 241 " 0.018 2.00e-02 2.50e+03 1.92e-02 7.38e+00 pdb=" CG TYR B 241 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR B 241 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR B 241 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR B 241 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR B 241 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR B 241 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 241 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B 255 " 0.043 5.00e-02 4.00e+02 6.39e-02 6.54e+00 pdb=" N PRO B 256 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO B 256 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 256 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 304 " 0.022 5.00e-02 4.00e+02 3.40e-02 1.85e+00 pdb=" N PRO C 305 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO C 305 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 305 " 0.017 5.00e-02 4.00e+02 ... (remaining 1567 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 56 2.51 - 3.11: 6407 3.11 - 3.70: 13391 3.70 - 4.30: 20474 4.30 - 4.90: 33781 Nonbonded interactions: 74109 Sorted by model distance: nonbonded pdb=" O3G AGS A 401 " pdb="MG MG A 402 " model vdw 1.911 2.170 nonbonded pdb=" OG1 THR A 184 " pdb="MG MG A 402 " model vdw 1.935 2.170 nonbonded pdb=" OG1 THR D 184 " pdb="MG MG D 403 " model vdw 1.990 2.170 nonbonded pdb=" O2B AGS A 401 " pdb="MG MG A 402 " model vdw 1.993 2.170 nonbonded pdb=" OG1 THR B 184 " pdb="MG MG B 401 " model vdw 2.065 2.170 ... (remaining 74104 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.910 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: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.560 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 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 : 0.005 0.116 9258 Z= 0.248 Angle : 0.701 9.322 12515 Z= 0.353 Chirality : 0.043 0.291 1315 Planarity : 0.004 0.064 1570 Dihedral : 17.438 159.343 3604 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.21 % Allowed : 0.42 % 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: 0.31 (0.25), residues: 1063 helix: 0.28 (0.24), residues: 442 sheet: 0.00 (0.37), residues: 170 loop : 0.46 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 236 TYR 0.045 0.002 TYR B 241 PHE 0.020 0.002 PHE D 251 TRP 0.015 0.002 TRP B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.25 ( 9258) covalent geometry : angle 0.70052 / 0.35 (12515) hydrogen bonds : bond 0.26611 / 17.11 ( 370) hydrogen bonds : angle 8.46148 / 6.04 ( 1059) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 233 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: A 125 LYS cc_start: 0.8510 (tttt) cc_final: 0.8138 (mmtt) REVERT: A 136 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7358 (mp0) REVERT: A 189 ASP cc_start: 0.7742 (t70) cc_final: 0.7409 (t0) REVERT: C 147 ASP cc_start: 0.8433 (m-30) cc_final: 0.8213 (m-30) REVERT: C 194 PHE cc_start: 0.7711 (m-80) cc_final: 0.7489 (m-80) REVERT: C 196 ASN cc_start: 0.8034 (t0) cc_final: 0.7811 (t0) REVERT: C 248 LYS cc_start: 0.8120 (mttt) cc_final: 0.7491 (mptt) REVERT: D 285 LYS cc_start: 0.7018 (mttt) cc_final: 0.6366 (mptt) REVERT: D 297 ASP cc_start: 0.7782 (t0) cc_final: 0.7458 (t0) REVERT: F 125 LYS cc_start: 0.8780 (tmtt) cc_final: 0.8556 (tmtt) outliers start: 2 outliers final: 0 residues processed: 234 average time/residue: 0.1065 time to fit residues: 32.8272 Evaluate side-chains 167 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.0060 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 9.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 ASN B 168 GLN ** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 GLN C 131 ASN D 156 ASN ** D 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 161 GLN E 196 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.169125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.129493 restraints weight = 9784.838| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.36 r_work: 0.3396 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9258 Z= 0.124 Angle : 0.537 7.616 12515 Z= 0.286 Chirality : 0.043 0.180 1315 Planarity : 0.004 0.050 1570 Dihedral : 9.550 85.419 1315 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.38 % Allowed : 7.52 % Favored : 91.10 % 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: 0.86 (0.25), residues: 1063 helix: 1.06 (0.23), residues: 456 sheet: 0.09 (0.37), residues: 170 loop : 0.45 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 135 TYR 0.018 0.001 TYR D 295 PHE 0.014 0.001 PHE E 194 TRP 0.015 0.001 TRP B 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 9258) covalent geometry : angle 0.53726 / 0.29 (12515) hydrogen bonds : bond 0.05036 / 3.24 ( 370) hydrogen bonds : angle 5.74132 / 3.99 ( 1059) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 182 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 LYS cc_start: 0.8421 (tttt) cc_final: 0.7851 (mmtt) REVERT: A 136 GLU cc_start: 0.7141 (mt-10) cc_final: 0.6670 (mm-30) REVERT: A 189 ASP cc_start: 0.7634 (t70) cc_final: 0.7186 (t0) REVERT: B 241 TYR cc_start: 0.8179 (m-80) cc_final: 0.7935 (m-80) REVERT: C 196 ASN cc_start: 0.8151 (t0) cc_final: 0.7755 (t0) REVERT: C 248 LYS cc_start: 0.8074 (mttt) cc_final: 0.7227 (mptt) REVERT: C 262 THR cc_start: 0.8166 (p) cc_final: 0.7900 (p) REVERT: D 155 ARG cc_start: 0.8222 (mtt90) cc_final: 0.7959 (mtt90) REVERT: E 230 GLU cc_start: 0.6407 (pt0) cc_final: 0.6190 (pt0) REVERT: E 291 ARG cc_start: 0.7080 (ttp80) cc_final: 0.6872 (ttp80) REVERT: F 125 LYS cc_start: 0.8522 (tmtt) cc_final: 0.8130 (tmtt) outliers start: 13 outliers final: 9 residues processed: 186 average time/residue: 0.0996 time to fit residues: 25.2020 Evaluate side-chains 168 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 159 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 GLN Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 273 TRP Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 268 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 12 optimal weight: 0.3980 chunk 46 optimal weight: 0.7980 chunk 20 optimal weight: 0.0980 chunk 58 optimal weight: 0.4980 chunk 91 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 ASN ** D 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 196 ASN E 203 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.165202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.124761 restraints weight = 9798.086| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.55 r_work: 0.3351 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 9258 Z= 0.107 Angle : 0.482 6.109 12515 Z= 0.255 Chirality : 0.041 0.175 1315 Planarity : 0.003 0.044 1570 Dihedral : 6.867 51.120 1315 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.80 % Allowed : 9.43 % Favored : 88.77 % 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: 1.03 (0.25), residues: 1063 helix: 1.33 (0.24), residues: 457 sheet: 0.01 (0.38), residues: 170 loop : 0.46 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 135 TYR 0.020 0.001 TYR D 295 PHE 0.009 0.001 PHE E 175 TRP 0.014 0.001 TRP B 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 ( 9258) covalent geometry : angle 0.48171 / 0.26 (12515) hydrogen bonds : bond 0.03953 / 2.54 ( 370) hydrogen bonds : angle 5.21558 / 3.65 ( 1059) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 171 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LYS cc_start: 0.8452 (tttt) cc_final: 0.7989 (mmtt) REVERT: A 136 GLU cc_start: 0.7066 (mt-10) cc_final: 0.6659 (mm-30) REVERT: A 189 ASP cc_start: 0.7493 (t70) cc_final: 0.7063 (t0) REVERT: A 282 GLU cc_start: 0.8053 (mp0) cc_final: 0.7793 (mp0) REVERT: A 311 GLN cc_start: 0.7238 (tt0) cc_final: 0.6511 (tp-100) REVERT: A 327 MET cc_start: 0.8214 (tpt) cc_final: 0.8001 (tpp) REVERT: B 273 TRP cc_start: 0.6353 (p90) cc_final: 0.6125 (p-90) REVERT: C 196 ASN cc_start: 0.7904 (t0) cc_final: 0.7533 (t0) REVERT: C 248 LYS cc_start: 0.7967 (mttt) cc_final: 0.7133 (mptt) REVERT: C 262 THR cc_start: 0.8095 (p) cc_final: 0.7808 (p) REVERT: D 155 ARG cc_start: 0.8243 (mtt90) cc_final: 0.7948 (mtt90) REVERT: D 215 GLN cc_start: 0.7749 (OUTLIER) cc_final: 0.7041 (mt0) REVERT: D 321 TYR cc_start: 0.7580 (t80) cc_final: 0.7259 (t80) REVERT: E 201 MET cc_start: 0.8481 (tpp) cc_final: 0.8127 (tpp) REVERT: E 291 ARG cc_start: 0.7204 (ttp80) cc_final: 0.6922 (ttp80) REVERT: F 139 MET cc_start: 0.7705 (mmm) cc_final: 0.7454 (mmm) outliers start: 17 outliers final: 14 residues processed: 180 average time/residue: 0.0963 time to fit residues: 23.6429 Evaluate side-chains 166 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 151 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain D residue 215 GLN Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 273 TRP Chi-restraints excluded: chain E residue 203 ASN Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 268 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 0.1980 chunk 45 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 94 optimal weight: 0.2980 chunk 82 optimal weight: 0.9980 chunk 29 optimal weight: 0.4980 chunk 46 optimal weight: 0.5980 chunk 87 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 ASN D 196 ASN D 215 GLN E 156 ASN E 196 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.165488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.124737 restraints weight = 9894.177| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.54 r_work: 0.3350 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9258 Z= 0.102 Angle : 0.476 6.609 12515 Z= 0.252 Chirality : 0.041 0.173 1315 Planarity : 0.003 0.040 1570 Dihedral : 6.481 43.640 1315 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.69 % Allowed : 12.08 % Favored : 86.23 % 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: 1.14 (0.25), residues: 1063 helix: 1.43 (0.24), residues: 458 sheet: -0.01 (0.38), residues: 170 loop : 0.53 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 135 TYR 0.022 0.001 TYR D 295 PHE 0.009 0.001 PHE E 175 TRP 0.014 0.001 TRP C 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 ( 9258) covalent geometry : angle 0.47582 / 0.25 (12515) hydrogen bonds : bond 0.03697 / 2.36 ( 370) hydrogen bonds : angle 5.06278 / 3.54 ( 1059) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 162 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LYS cc_start: 0.8688 (tttt) cc_final: 0.7995 (mmtt) REVERT: A 129 MET cc_start: 0.7852 (ttm) cc_final: 0.7579 (mtp) REVERT: A 282 GLU cc_start: 0.7980 (mp0) cc_final: 0.7346 (mt-10) REVERT: A 311 GLN cc_start: 0.7244 (tt0) cc_final: 0.6538 (tp-100) REVERT: B 213 ARG cc_start: 0.7667 (ttp-110) cc_final: 0.7285 (mtm-85) REVERT: C 196 ASN cc_start: 0.7870 (t0) cc_final: 0.7260 (t0) REVERT: C 201 MET cc_start: 0.7711 (mmt) cc_final: 0.7506 (mmt) REVERT: C 248 LYS cc_start: 0.7974 (mttt) cc_final: 0.7109 (mptt) REVERT: C 262 THR cc_start: 0.8044 (p) cc_final: 0.7737 (p) REVERT: C 273 TRP cc_start: 0.6060 (p-90) cc_final: 0.5848 (p-90) REVERT: D 321 TYR cc_start: 0.7617 (t80) cc_final: 0.7309 (t80) REVERT: E 201 MET cc_start: 0.8441 (tpp) cc_final: 0.7700 (mmm) REVERT: E 291 ARG cc_start: 0.7301 (ttp80) cc_final: 0.6873 (ttp80) REVERT: F 135 ARG cc_start: 0.7514 (tpt-90) cc_final: 0.7283 (tpt-90) outliers start: 16 outliers final: 14 residues processed: 170 average time/residue: 0.0993 time to fit residues: 23.0577 Evaluate side-chains 165 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 151 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain B residue 168 GLN Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 273 TRP Chi-restraints excluded: chain E residue 203 ASN Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain E residue 268 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 86 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 GLN ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 196 ASN E 203 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.159320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.118281 restraints weight = 9938.299| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.46 r_work: 0.3281 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9258 Z= 0.174 Angle : 0.551 8.857 12515 Z= 0.285 Chirality : 0.044 0.195 1315 Planarity : 0.003 0.043 1570 Dihedral : 6.714 36.191 1315 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.54 % Allowed : 12.08 % Favored : 85.38 % 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: 0.87 (0.25), residues: 1063 helix: 1.26 (0.24), residues: 461 sheet: -0.26 (0.37), residues: 170 loop : 0.36 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 236 TYR 0.027 0.002 TYR D 295 PHE 0.020 0.002 PHE E 175 TRP 0.016 0.001 TRP B 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.17 ( 9258) covalent geometry : angle 0.55092 / 0.28 (12515) hydrogen bonds : bond 0.04195 / 2.72 ( 370) hydrogen bonds : angle 5.19554 / 3.64 ( 1059) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 152 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LYS cc_start: 0.8712 (tttt) cc_final: 0.8113 (mmtt) REVERT: A 189 ASP cc_start: 0.7469 (t70) cc_final: 0.7052 (t0) REVERT: A 319 ARG cc_start: 0.7767 (mtp85) cc_final: 0.7545 (mtt90) REVERT: B 166 LYS cc_start: 0.8683 (mmtp) cc_final: 0.8461 (mmtm) REVERT: B 320 LYS cc_start: 0.7615 (ttmm) cc_final: 0.7377 (ttpt) REVERT: C 196 ASN cc_start: 0.7957 (t0) cc_final: 0.7292 (t0) REVERT: C 201 MET cc_start: 0.7948 (mmt) cc_final: 0.7667 (mmt) REVERT: C 248 LYS cc_start: 0.7981 (mttt) cc_final: 0.7072 (mptt) REVERT: C 273 TRP cc_start: 0.6292 (p-90) cc_final: 0.6048 (p-90) REVERT: D 196 ASN cc_start: 0.7952 (t0) cc_final: 0.7715 (t0) REVERT: D 321 TYR cc_start: 0.7614 (t80) cc_final: 0.7290 (t80) REVERT: E 291 ARG cc_start: 0.7230 (ttp80) cc_final: 0.6871 (ttp80) outliers start: 24 outliers final: 20 residues processed: 165 average time/residue: 0.1042 time to fit residues: 23.3061 Evaluate side-chains 164 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 144 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 168 GLN Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 273 TRP Chi-restraints excluded: chain E residue 203 ASN Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain E residue 268 SER Chi-restraints excluded: chain E residue 287 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 0.3980 chunk 58 optimal weight: 6.9990 chunk 74 optimal weight: 0.0980 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 88 optimal weight: 0.2980 chunk 28 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 ASN E 196 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.164120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.123451 restraints weight = 9761.301| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.46 r_work: 0.3345 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9258 Z= 0.101 Angle : 0.473 6.334 12515 Z= 0.250 Chirality : 0.041 0.169 1315 Planarity : 0.003 0.039 1570 Dihedral : 6.145 28.190 1315 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.91 % Allowed : 12.50 % Favored : 85.59 % 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: 1.07 (0.25), residues: 1063 helix: 1.40 (0.24), residues: 461 sheet: -0.19 (0.37), residues: 170 loop : 0.53 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 213 TYR 0.025 0.001 TYR D 295 PHE 0.009 0.001 PHE E 175 TRP 0.016 0.001 TRP E 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 ( 9258) covalent geometry : angle 0.47294 / 0.25 (12515) hydrogen bonds : bond 0.03530 / 2.28 ( 370) hydrogen bonds : angle 5.01808 / 3.51 ( 1059) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 151 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LYS cc_start: 0.8746 (tttt) cc_final: 0.8030 (mmtt) REVERT: A 282 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7687 (mt-10) REVERT: A 298 GLU cc_start: 0.7350 (tp30) cc_final: 0.7133 (tp30) REVERT: C 196 ASN cc_start: 0.7897 (t0) cc_final: 0.7261 (t0) REVERT: C 248 LYS cc_start: 0.7956 (mttt) cc_final: 0.7059 (mptt) REVERT: C 262 THR cc_start: 0.8060 (p) cc_final: 0.7767 (p) REVERT: C 273 TRP cc_start: 0.6140 (p-90) cc_final: 0.5875 (p-90) REVERT: D 196 ASN cc_start: 0.7906 (t0) cc_final: 0.7655 (t0) REVERT: D 243 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8436 (tp) REVERT: D 321 TYR cc_start: 0.7572 (t80) cc_final: 0.7277 (t80) REVERT: E 291 ARG cc_start: 0.7206 (ttp80) cc_final: 0.6897 (ttp80) REVERT: F 139 MET cc_start: 0.7760 (mmm) cc_final: 0.7484 (mmm) outliers start: 18 outliers final: 15 residues processed: 162 average time/residue: 0.0956 time to fit residues: 21.1585 Evaluate side-chains 157 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 140 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 GLN Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain B residue 168 GLN Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 273 TRP Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain E residue 268 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 85 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 98 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 196 ASN E 255 GLN E 303 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.159838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.118695 restraints weight = 9957.692| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.45 r_work: 0.3273 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9258 Z= 0.163 Angle : 0.550 10.314 12515 Z= 0.282 Chirality : 0.044 0.212 1315 Planarity : 0.003 0.039 1570 Dihedral : 6.649 38.006 1315 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.12 % Allowed : 13.24 % Favored : 84.64 % 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: 0.89 (0.25), residues: 1063 helix: 1.29 (0.24), residues: 461 sheet: -0.37 (0.37), residues: 170 loop : 0.41 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 213 TYR 0.026 0.002 TYR D 295 PHE 0.018 0.002 PHE E 175 TRP 0.022 0.001 TRP B 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.16 ( 9258) covalent geometry : angle 0.54953 / 0.28 (12515) hydrogen bonds : bond 0.03976 / 2.58 ( 370) hydrogen bonds : angle 5.12647 / 3.58 ( 1059) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 147 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LYS cc_start: 0.8686 (tttt) cc_final: 0.8130 (mmtt) REVERT: A 189 ASP cc_start: 0.7475 (t70) cc_final: 0.7080 (t0) REVERT: A 298 GLU cc_start: 0.7305 (tp30) cc_final: 0.7081 (tp30) REVERT: B 320 LYS cc_start: 0.7622 (ttmm) cc_final: 0.7389 (ttpt) REVERT: C 196 ASN cc_start: 0.7979 (t0) cc_final: 0.7324 (t0) REVERT: C 201 MET cc_start: 0.7866 (mmt) cc_final: 0.7409 (mmt) REVERT: C 248 LYS cc_start: 0.8020 (mttt) cc_final: 0.7079 (mptt) REVERT: C 273 TRP cc_start: 0.6281 (p-90) cc_final: 0.6004 (p-90) REVERT: D 196 ASN cc_start: 0.7938 (t0) cc_final: 0.7463 (t0) REVERT: D 321 TYR cc_start: 0.7596 (t80) cc_final: 0.7290 (t80) REVERT: E 291 ARG cc_start: 0.7172 (ttp80) cc_final: 0.6907 (ttp80) REVERT: F 139 MET cc_start: 0.7832 (mmm) cc_final: 0.7630 (mmm) outliers start: 20 outliers final: 15 residues processed: 159 average time/residue: 0.0986 time to fit residues: 21.0261 Evaluate side-chains 155 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 140 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain B residue 168 GLN Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain E residue 287 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 71 optimal weight: 0.9980 chunk 15 optimal weight: 7.9990 chunk 76 optimal weight: 0.7980 chunk 8 optimal weight: 0.0070 chunk 16 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 196 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.160901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.117560 restraints weight = 9920.999| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.47 r_work: 0.3319 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9258 Z= 0.136 Angle : 0.518 8.717 12515 Z= 0.268 Chirality : 0.043 0.218 1315 Planarity : 0.003 0.039 1570 Dihedral : 6.552 37.505 1315 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.91 % Allowed : 13.45 % Favored : 84.64 % 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: 0.88 (0.25), residues: 1063 helix: 1.29 (0.24), residues: 461 sheet: -0.45 (0.36), residues: 170 loop : 0.44 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 213 TYR 0.026 0.002 TYR D 295 PHE 0.015 0.001 PHE E 175 TRP 0.019 0.001 TRP B 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 9258) covalent geometry : angle 0.51758 / 0.27 (12515) hydrogen bonds : bond 0.03773 / 2.45 ( 370) hydrogen bonds : angle 5.06135 / 3.54 ( 1059) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 142 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LYS cc_start: 0.8730 (tttt) cc_final: 0.8024 (mmtt) REVERT: A 129 MET cc_start: 0.7579 (ttm) cc_final: 0.7260 (mtp) REVERT: A 189 ASP cc_start: 0.7494 (t70) cc_final: 0.7101 (t0) REVERT: B 320 LYS cc_start: 0.7572 (ttmm) cc_final: 0.7339 (ttpt) REVERT: C 196 ASN cc_start: 0.8091 (t0) cc_final: 0.7438 (t0) REVERT: C 201 MET cc_start: 0.7854 (mmt) cc_final: 0.7329 (mmt) REVERT: C 248 LYS cc_start: 0.8012 (mttt) cc_final: 0.6998 (mptt) REVERT: C 273 TRP cc_start: 0.6337 (p-90) cc_final: 0.6034 (p-90) REVERT: D 196 ASN cc_start: 0.7962 (t0) cc_final: 0.7493 (t0) REVERT: D 321 TYR cc_start: 0.7565 (t80) cc_final: 0.7244 (t80) REVERT: F 139 MET cc_start: 0.7811 (mmm) cc_final: 0.7592 (mmm) outliers start: 18 outliers final: 12 residues processed: 153 average time/residue: 0.0936 time to fit residues: 19.7848 Evaluate side-chains 151 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 139 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain B residue 168 GLN Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain E residue 287 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 18 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 63 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 12 optimal weight: 8.9990 chunk 31 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 196 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.162159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.121284 restraints weight = 9819.750| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.44 r_work: 0.3317 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9258 Z= 0.115 Angle : 0.499 9.131 12515 Z= 0.259 Chirality : 0.042 0.176 1315 Planarity : 0.003 0.038 1570 Dihedral : 6.322 34.818 1315 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.48 % Allowed : 13.88 % Favored : 84.64 % 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: 0.96 (0.26), residues: 1063 helix: 1.36 (0.24), residues: 461 sheet: -0.41 (0.37), residues: 170 loop : 0.48 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 213 TYR 0.025 0.001 TYR D 295 PHE 0.012 0.001 PHE E 175 TRP 0.035 0.001 TRP C 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 9258) covalent geometry : angle 0.49878 / 0.26 (12515) hydrogen bonds : bond 0.03603 / 2.35 ( 370) hydrogen bonds : angle 5.00659 / 3.51 ( 1059) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 149 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 GLU cc_start: 0.8554 (pt0) cc_final: 0.7968 (pm20) REVERT: A 125 LYS cc_start: 0.8720 (tttt) cc_final: 0.8044 (mmtt) REVERT: A 129 MET cc_start: 0.7655 (ttm) cc_final: 0.7347 (mtp) REVERT: B 140 GLU cc_start: 0.7423 (mt-10) cc_final: 0.7119 (mm-30) REVERT: C 196 ASN cc_start: 0.7939 (t0) cc_final: 0.7296 (t0) REVERT: C 201 MET cc_start: 0.7714 (mmt) cc_final: 0.7059 (mmt) REVERT: C 248 LYS cc_start: 0.8002 (mttt) cc_final: 0.7022 (mptt) REVERT: C 273 TRP cc_start: 0.6300 (p-90) cc_final: 0.6002 (p-90) REVERT: D 196 ASN cc_start: 0.7884 (t0) cc_final: 0.7467 (t0) REVERT: D 321 TYR cc_start: 0.7559 (t80) cc_final: 0.7257 (t80) REVERT: E 230 GLU cc_start: 0.6939 (mm-30) cc_final: 0.6432 (pt0) outliers start: 14 outliers final: 13 residues processed: 159 average time/residue: 0.0901 time to fit residues: 19.7682 Evaluate side-chains 153 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 140 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain B residue 168 GLN Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 260 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 80 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 56 optimal weight: 0.2980 chunk 75 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 ASN E 196 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.161795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.120737 restraints weight = 9928.156| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.48 r_work: 0.3304 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9258 Z= 0.125 Angle : 0.523 9.416 12515 Z= 0.270 Chirality : 0.043 0.179 1315 Planarity : 0.003 0.038 1570 Dihedral : 6.382 36.258 1315 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.69 % Allowed : 14.30 % Favored : 84.00 % 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: 0.94 (0.26), residues: 1063 helix: 1.32 (0.24), residues: 461 sheet: -0.44 (0.37), residues: 170 loop : 0.50 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 213 TYR 0.030 0.001 TYR D 295 PHE 0.013 0.001 PHE A 209 TRP 0.039 0.001 TRP C 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.12 ( 9258) covalent geometry : angle 0.52336 / 0.27 (12515) hydrogen bonds : bond 0.03747 / 2.47 ( 370) hydrogen bonds : angle 5.05256 / 3.54 ( 1059) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 GLU cc_start: 0.8532 (pt0) cc_final: 0.7927 (pm20) REVERT: A 125 LYS cc_start: 0.8739 (tttt) cc_final: 0.8080 (mmtt) REVERT: A 129 MET cc_start: 0.7680 (ttm) cc_final: 0.7392 (mtp) REVERT: A 136 GLU cc_start: 0.7103 (mt-10) cc_final: 0.6767 (mm-30) REVERT: B 140 GLU cc_start: 0.7381 (mt-10) cc_final: 0.7075 (mm-30) REVERT: B 309 GLN cc_start: 0.7529 (pm20) cc_final: 0.7304 (pm20) REVERT: C 196 ASN cc_start: 0.7959 (t0) cc_final: 0.7317 (t0) REVERT: C 248 LYS cc_start: 0.8010 (mttt) cc_final: 0.7022 (mptt) REVERT: C 273 TRP cc_start: 0.6301 (p-90) cc_final: 0.5994 (p-90) REVERT: D 196 ASN cc_start: 0.7891 (t0) cc_final: 0.7489 (t0) REVERT: D 321 TYR cc_start: 0.7557 (t80) cc_final: 0.7272 (t80) REVERT: E 178 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7734 (tt0) REVERT: F 139 MET cc_start: 0.7751 (mmm) cc_final: 0.7459 (mmm) outliers start: 16 outliers final: 15 residues processed: 157 average time/residue: 0.1086 time to fit residues: 23.2355 Evaluate side-chains 158 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 143 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain B residue 168 GLN Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain E residue 287 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 25 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 196 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.161956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.121689 restraints weight = 9833.723| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.42 r_work: 0.3321 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9258 Z= 0.126 Angle : 0.530 9.378 12515 Z= 0.275 Chirality : 0.043 0.179 1315 Planarity : 0.003 0.038 1570 Dihedral : 6.379 36.438 1315 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.59 % Allowed : 14.30 % Favored : 84.11 % 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: 0.92 (0.26), residues: 1063 helix: 1.28 (0.24), residues: 461 sheet: -0.40 (0.37), residues: 170 loop : 0.51 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 213 TYR 0.031 0.001 TYR D 295 PHE 0.013 0.001 PHE A 209 TRP 0.056 0.001 TRP C 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 9258) covalent geometry : angle 0.52972 / 0.27 (12515) hydrogen bonds : bond 0.03734 / 2.46 ( 370) hydrogen bonds : angle 5.13236 / 3.59 ( 1059) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2486.47 seconds wall clock time: 43 minutes 8.40 seconds (2588.40 seconds total)