Starting phenix.real_space_refine on Tue Mar 3 23:37:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pqo_71787/03_2026/9pqo_71787.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pqo_71787/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/9pqo_71787/03_2026/9pqo_71787.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pqo_71787/03_2026/9pqo_71787.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pqo_71787/03_2026/9pqo_71787.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pqo_71787/03_2026/9pqo_71787.map" } 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): 0.00s 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: 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: 0.72 Conformation dependent library (CDL) restraints added in 240.9 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: 0.31 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: 1.31 Time building geometry restraints manager: 0.99 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=" CA TYR C 241 " pdb=" C TYR C 241 " ideal model delta sigma weight residual 1.528 1.477 0.051 1.39e-02 5.18e+03 1.37e+01 bond pdb=" O2G AGS C 401 " pdb=" PG AGS C 401 " ideal model delta sigma weight residual 1.557 1.488 0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C TYR C 241 " pdb=" O TYR C 241 " ideal model delta sigma weight residual 1.234 1.191 0.043 1.38e-02 5.25e+03 9.84e+00 bond pdb=" O2B AGS C 401 " pdb=" PB AGS C 401 " ideal model delta sigma weight residual 1.531 1.483 0.048 1.60e-02 3.91e+03 9.15e+00 bond pdb=" O2A AGS C 401 " pdb=" PA AGS C 401 " ideal model delta sigma weight residual 1.531 1.483 0.048 1.60e-02 3.91e+03 9.08e+00 ... (remaining 9253 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 12413 2.23 - 4.46: 91 4.46 - 6.68: 6 6.68 - 8.91: 3 8.91 - 11.14: 2 Bond angle restraints: 12515 Sorted by residual: angle pdb=" PB AGS C 401 " pdb=" O3B AGS C 401 " pdb=" PG AGS C 401 " ideal model delta sigma weight residual 120.12 131.26 -11.14 3.00e+00 1.11e-01 1.38e+01 angle pdb=" C2' AGS C 401 " pdb=" C1' AGS C 401 " pdb=" O4' AGS C 401 " ideal model delta sigma weight residual 106.47 103.17 3.30 1.15e+00 7.51e-01 8.17e+00 angle pdb=" PA AGS C 401 " pdb=" O3A AGS C 401 " pdb=" PB AGS C 401 " ideal model delta sigma weight residual 119.76 128.11 -8.35 3.00e+00 1.11e-01 7.75e+00 angle pdb=" O2G AGS C 401 " pdb=" PG AGS C 401 " pdb=" O3B AGS C 401 " ideal model delta sigma weight residual 109.53 101.32 8.21 3.00e+00 1.11e-01 7.49e+00 angle pdb=" C1' AGS C 401 " pdb=" C2' AGS C 401 " pdb=" C3' AGS C 401 " ideal model delta sigma weight residual 101.46 98.57 2.89 1.19e+00 7.12e-01 5.96e+00 ... (remaining 12510 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.61: 5270 27.61 - 55.21: 225 55.21 - 82.82: 35 82.82 - 110.43: 4 110.43 - 138.04: 2 Dihedral angle restraints: 5536 sinusoidal: 2428 harmonic: 3108 Sorted by residual: dihedral pdb=" O1A AGS D 401 " pdb=" O3A AGS D 401 " pdb=" PA AGS D 401 " pdb=" PB AGS D 401 " ideal model delta sinusoidal sigma weight residual -67.73 70.31 -138.04 1 3.00e+01 1.11e-03 1.86e+01 dihedral pdb=" O1A AGS C 401 " pdb=" O3A AGS C 401 " pdb=" PA AGS C 401 " pdb=" PB AGS C 401 " ideal model delta sinusoidal sigma weight residual -67.73 61.29 -129.02 1 3.00e+01 1.11e-03 1.74e+01 dihedral pdb=" CA GLN A 246 " pdb=" C GLN A 246 " pdb=" N VAL A 247 " pdb=" CA VAL A 247 " ideal model delta harmonic sigma weight residual 180.00 159.82 20.18 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 5533 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 965 0.037 - 0.073: 252 0.073 - 0.110: 79 0.110 - 0.146: 25 0.146 - 0.183: 2 Chirality restraints: 1323 Sorted by residual: chirality pdb=" CA TYR C 241 " pdb=" N TYR C 241 " pdb=" C TYR C 241 " pdb=" CB TYR C 241 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.34e-01 chirality pdb=" CA ILE E 301 " pdb=" N ILE E 301 " pdb=" C ILE E 301 " pdb=" CB ILE E 301 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.20e-01 chirality pdb=" CA ILE A 220 " pdb=" N ILE A 220 " pdb=" C ILE A 220 " pdb=" CB ILE A 220 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.16e-01 ... (remaining 1320 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: 1.470 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.220 Find NCS groups from input model: 0.130 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: 0.000 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: 12.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 9258 Z= 0.180 Angle : 0.598 11.141 12515 Z= 0.335 Chirality : 0.040 0.183 1323 Planarity : 0.004 0.064 1570 Dihedral : 14.946 138.036 3532 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 covalent geometry : bond 0.00377 ( 9258) covalent geometry : angle 0.59769 (12515) hydrogen bonds : bond 0.26611 ( 370) hydrogen bonds : angle 8.46148 ( 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 : 0.362 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: 0.1139 time to fit residues: 34.7907 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 : 0.296 ------------------------------------------------------------------------------- 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: 4.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 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... Flipped N/Q/H residues before XYZ refinement: ** 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** D 255 GLN E 156 ASN E 161 GLN E 196 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.168004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.125626 restraints weight = 9817.288| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.43 r_work: 0.3406 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9258 Z= 0.139 Angle : 0.576 5.970 12515 Z= 0.311 Chirality : 0.043 0.187 1323 Planarity : 0.004 0.051 1570 Dihedral : 10.332 129.810 1243 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.38 % Allowed : 7.94 % Favored : 90.68 % 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: 0.67 (0.24), residues: 1063 helix: 0.82 (0.23), residues: 459 sheet: 0.00 (0.37), residues: 170 loop : 0.44 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 135 TYR 0.020 0.001 TYR D 295 PHE 0.014 0.001 PHE E 175 TRP 0.016 0.001 TRP B 273 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 9258) covalent geometry : angle 0.57586 (12515) hydrogen bonds : bond 0.05612 ( 370) hydrogen bonds : angle 5.97967 ( 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 186 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 173 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LYS cc_start: 0.8398 (tttt) cc_final: 0.7829 (mmtt) REVERT: A 189 ASP cc_start: 0.7509 (t70) cc_final: 0.7141 (t0) REVERT: C 196 ASN cc_start: 0.8224 (t0) cc_final: 0.7600 (t0) REVERT: C 248 LYS cc_start: 0.8036 (mttt) cc_final: 0.7144 (mptt) REVERT: C 262 THR cc_start: 0.8157 (p) cc_final: 0.7931 (p) REVERT: D 155 ARG cc_start: 0.8144 (mtt90) cc_final: 0.7838 (mtt90) REVERT: D 196 ASN cc_start: 0.8181 (t0) cc_final: 0.7920 (t0) REVERT: E 127 GLU cc_start: 0.8017 (pp20) cc_final: 0.7807 (pp20) REVERT: E 156 ASN cc_start: 0.7622 (t160) cc_final: 0.7405 (t0) REVERT: E 166 LYS cc_start: 0.7450 (mmtt) cc_final: 0.7238 (mmtm) REVERT: F 125 LYS cc_start: 0.8478 (tmtt) cc_final: 0.8079 (tmtt) REVERT: F 139 MET cc_start: 0.7786 (mmm) cc_final: 0.7500 (mmm) outliers start: 13 outliers final: 10 residues processed: 178 average time/residue: 0.1026 time to fit residues: 24.2988 Evaluate side-chains 167 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 157 time to evaluate : 0.330 ------------------------------------------------------------------------------- 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 C residue 226 SER Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 273 TRP Chi-restraints excluded: chain E residue 229 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 12 optimal weight: 6.9990 chunk 46 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 4 optimal weight: 8.9990 chunk 88 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 215 GLN E 196 ASN E 203 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.159795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.118118 restraints weight = 9956.736| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.51 r_work: 0.3301 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9258 Z= 0.176 Angle : 0.563 6.070 12515 Z= 0.296 Chirality : 0.043 0.202 1323 Planarity : 0.004 0.046 1570 Dihedral : 10.364 135.531 1243 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.33 % Allowed : 8.79 % Favored : 88.88 % 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: 0.62 (0.25), residues: 1063 helix: 0.97 (0.24), residues: 457 sheet: -0.18 (0.37), residues: 170 loop : 0.26 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 236 TYR 0.022 0.002 TYR D 295 PHE 0.021 0.002 PHE E 175 TRP 0.016 0.001 TRP B 273 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 9258) covalent geometry : angle 0.56260 (12515) hydrogen bonds : bond 0.05151 ( 370) hydrogen bonds : angle 5.66218 ( 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 184 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LYS cc_start: 0.8420 (tttt) cc_final: 0.7875 (mmtt) REVERT: A 136 GLU cc_start: 0.7114 (mt-10) cc_final: 0.6658 (mm-30) REVERT: A 189 ASP cc_start: 0.7765 (t70) cc_final: 0.7385 (t0) REVERT: B 320 LYS cc_start: 0.7577 (ttmm) cc_final: 0.7369 (ttpt) REVERT: C 196 ASN cc_start: 0.8220 (t0) cc_final: 0.7585 (t0) REVERT: C 248 LYS cc_start: 0.8090 (mttt) cc_final: 0.7155 (mptt) REVERT: C 262 THR cc_start: 0.8184 (p) cc_final: 0.7928 (p) REVERT: C 307 TRP cc_start: 0.6763 (m100) cc_final: 0.6561 (m100) REVERT: D 196 ASN cc_start: 0.8190 (t0) cc_final: 0.7838 (t0) REVERT: D 321 TYR cc_start: 0.7591 (t80) cc_final: 0.7230 (t80) REVERT: E 129 MET cc_start: 0.8004 (ttm) cc_final: 0.7653 (mtp) REVERT: E 156 ASN cc_start: 0.7823 (t160) cc_final: 0.7563 (t0) REVERT: F 139 MET cc_start: 0.7812 (mmm) cc_final: 0.7573 (mmm) outliers start: 22 outliers final: 17 residues processed: 173 average time/residue: 0.1039 time to fit residues: 24.3274 Evaluate side-chains 167 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 150 time to evaluate : 0.301 ------------------------------------------------------------------------------- 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 142 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 287 VAL 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 258 VAL Chi-restraints excluded: chain E residue 287 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 94 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 87 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3966 r_free = 0.3966 target = 0.160884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.120685 restraints weight = 10005.691| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.45 r_work: 0.3313 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9258 Z= 0.129 Angle : 0.514 6.524 12515 Z= 0.272 Chirality : 0.041 0.188 1323 Planarity : 0.003 0.045 1570 Dihedral : 10.229 136.666 1243 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.12 % Allowed : 10.70 % Favored : 87.18 % 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: 0.68 (0.25), residues: 1063 helix: 1.07 (0.24), residues: 457 sheet: -0.26 (0.36), residues: 170 loop : 0.28 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 213 TYR 0.021 0.001 TYR D 295 PHE 0.014 0.001 PHE E 175 TRP 0.016 0.001 TRP B 273 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 9258) covalent geometry : angle 0.51362 (12515) hydrogen bonds : bond 0.04440 ( 370) hydrogen bonds : angle 5.46505 ( 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 176 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 156 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LYS cc_start: 0.8403 (tttt) cc_final: 0.7864 (mmtt) REVERT: A 136 GLU cc_start: 0.7093 (mt-10) cc_final: 0.6651 (mm-30) REVERT: A 189 ASP cc_start: 0.7713 (t70) cc_final: 0.7340 (t0) REVERT: B 320 LYS cc_start: 0.7550 (ttmm) cc_final: 0.7334 (ttpt) REVERT: C 196 ASN cc_start: 0.8073 (t0) cc_final: 0.7712 (t0) REVERT: C 201 MET cc_start: 0.7735 (mmt) cc_final: 0.7450 (mmt) REVERT: C 248 LYS cc_start: 0.7983 (mttt) cc_final: 0.7122 (mptt) REVERT: C 262 THR cc_start: 0.8089 (p) cc_final: 0.7848 (p) REVERT: D 196 ASN cc_start: 0.8113 (t0) cc_final: 0.7858 (t0) REVERT: D 302 TYR cc_start: 0.8018 (m-80) cc_final: 0.7792 (m-10) REVERT: D 321 TYR cc_start: 0.7571 (t80) cc_final: 0.7242 (t80) REVERT: E 129 MET cc_start: 0.7993 (ttm) cc_final: 0.7671 (mtp) REVERT: E 156 ASN cc_start: 0.7622 (t160) cc_final: 0.7384 (t0) REVERT: F 135 ARG cc_start: 0.7532 (tpt-90) cc_final: 0.7326 (tpt-90) REVERT: F 139 MET cc_start: 0.7799 (mmm) cc_final: 0.7518 (mmm) outliers start: 20 outliers final: 16 residues processed: 166 average time/residue: 0.0974 time to fit residues: 21.9762 Evaluate side-chains 165 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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 C residue 226 SER Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 229 THR 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 258 VAL 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: 0.9990 chunk 97 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 8 optimal weight: 4.9990 chunk 66 optimal weight: 0.5980 chunk 70 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 ASN E 196 ASN E 203 ASN E 255 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.161354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.120979 restraints weight = 9887.573| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.48 r_work: 0.3313 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9258 Z= 0.120 Angle : 0.486 6.355 12515 Z= 0.258 Chirality : 0.041 0.189 1323 Planarity : 0.003 0.040 1570 Dihedral : 10.125 138.252 1243 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.54 % Allowed : 10.70 % Favored : 86.76 % 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: 0.81 (0.25), residues: 1063 helix: 1.26 (0.24), residues: 458 sheet: -0.31 (0.36), residues: 170 loop : 0.30 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 291 TYR 0.024 0.001 TYR D 295 PHE 0.014 0.001 PHE E 175 TRP 0.015 0.001 TRP B 273 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 9258) covalent geometry : angle 0.48569 (12515) hydrogen bonds : bond 0.04010 ( 370) hydrogen bonds : angle 5.24797 ( 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 185 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 161 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LYS cc_start: 0.8439 (tttt) cc_final: 0.7850 (mmtt) REVERT: A 189 ASP cc_start: 0.7672 (t70) cc_final: 0.7325 (t0) REVERT: A 311 GLN cc_start: 0.7182 (tt0) cc_final: 0.6541 (tp-100) REVERT: A 319 ARG cc_start: 0.7657 (mtt90) cc_final: 0.7429 (tpp80) REVERT: A 327 MET cc_start: 0.8220 (tpt) cc_final: 0.8018 (tpp) REVERT: B 125 LYS cc_start: 0.7776 (tttp) cc_final: 0.7511 (tptm) REVERT: B 166 LYS cc_start: 0.8569 (mmtp) cc_final: 0.8356 (mmtm) REVERT: B 320 LYS cc_start: 0.7546 (ttmm) cc_final: 0.7309 (ttpt) REVERT: C 196 ASN cc_start: 0.8065 (t0) cc_final: 0.7445 (t0) REVERT: C 201 MET cc_start: 0.7814 (mmt) cc_final: 0.7436 (mmt) REVERT: C 248 LYS cc_start: 0.7979 (mttt) cc_final: 0.7125 (mptt) REVERT: D 196 ASN cc_start: 0.8021 (t0) cc_final: 0.7757 (t0) REVERT: D 302 TYR cc_start: 0.7981 (m-80) cc_final: 0.7767 (m-10) REVERT: D 321 TYR cc_start: 0.7562 (t80) cc_final: 0.7289 (t80) REVERT: E 129 MET cc_start: 0.7899 (ttm) cc_final: 0.7607 (mtp) REVERT: F 139 MET cc_start: 0.7869 (mmm) cc_final: 0.7587 (mmm) outliers start: 24 outliers final: 19 residues processed: 172 average time/residue: 0.1021 time to fit residues: 23.9298 Evaluate side-chains 169 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 150 time to evaluate : 0.349 ------------------------------------------------------------------------------- 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 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 C residue 287 VAL Chi-restraints excluded: chain D residue 127 GLU 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 258 VAL Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain E residue 268 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 0.0070 chunk 58 optimal weight: 0.6980 chunk 74 optimal weight: 0.0970 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 51 optimal weight: 0.0170 chunk 44 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 overall best weight: 0.3034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 255 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 = 0.3993 r_free = 0.3993 target = 0.163349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.123618 restraints weight = 9766.176| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.43 r_work: 0.3345 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9258 Z= 0.097 Angle : 0.471 6.667 12515 Z= 0.251 Chirality : 0.040 0.178 1323 Planarity : 0.003 0.038 1570 Dihedral : 9.990 138.107 1243 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.80 % Allowed : 11.65 % Favored : 86.55 % 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: 0.98 (0.25), residues: 1063 helix: 1.42 (0.24), residues: 458 sheet: -0.28 (0.37), residues: 170 loop : 0.37 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 213 TYR 0.024 0.001 TYR D 295 PHE 0.008 0.001 PHE E 175 TRP 0.014 0.001 TRP E 174 Details of bonding type rmsd covalent geometry : bond 0.00212 ( 9258) covalent geometry : angle 0.47132 (12515) hydrogen bonds : bond 0.03747 ( 370) hydrogen bonds : angle 5.15306 ( 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 172 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 155 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LYS cc_start: 0.8458 (tttt) cc_final: 0.7873 (mmtt) REVERT: A 136 GLU cc_start: 0.7049 (mt-10) cc_final: 0.6664 (mm-30) REVERT: A 189 ASP cc_start: 0.7704 (t70) cc_final: 0.7350 (t0) REVERT: A 311 GLN cc_start: 0.7240 (tt0) cc_final: 0.6567 (tp-100) REVERT: A 319 ARG cc_start: 0.7558 (mtt90) cc_final: 0.7333 (mmm-85) REVERT: A 327 MET cc_start: 0.8215 (tpt) cc_final: 0.7938 (tpp) REVERT: C 196 ASN cc_start: 0.8100 (t0) cc_final: 0.7465 (t0) REVERT: C 201 MET cc_start: 0.7835 (mmt) cc_final: 0.7371 (mmt) REVERT: C 248 LYS cc_start: 0.7990 (mttt) cc_final: 0.7102 (mptt) REVERT: D 196 ASN cc_start: 0.8069 (t0) cc_final: 0.7799 (t0) REVERT: D 321 TYR cc_start: 0.7614 (t80) cc_final: 0.7341 (t80) REVERT: E 129 MET cc_start: 0.7879 (ttm) cc_final: 0.7607 (mtp) REVERT: F 139 MET cc_start: 0.7850 (mmm) cc_final: 0.7619 (mmm) outliers start: 17 outliers final: 13 residues processed: 163 average time/residue: 0.1054 time to fit residues: 23.4062 Evaluate side-chains 161 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 148 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 GLN 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 D residue 127 GLU Chi-restraints excluded: chain D residue 229 THR 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 258 VAL Chi-restraints excluded: chain E residue 260 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 85 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 196 ASN E 203 ASN E 303 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.160813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.120183 restraints weight = 9911.551| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.46 r_work: 0.3302 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9258 Z= 0.139 Angle : 0.503 6.006 12515 Z= 0.265 Chirality : 0.042 0.198 1323 Planarity : 0.003 0.036 1570 Dihedral : 10.072 137.542 1243 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.91 % Allowed : 12.29 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.25), residues: 1063 helix: 1.40 (0.24), residues: 458 sheet: -0.37 (0.37), residues: 170 loop : 0.28 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 213 TYR 0.025 0.001 TYR D 295 PHE 0.016 0.001 PHE E 175 TRP 0.014 0.001 TRP E 174 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 9258) covalent geometry : angle 0.50350 (12515) hydrogen bonds : bond 0.03921 ( 370) hydrogen bonds : angle 5.15200 ( 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: 18 poor density : 149 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LYS cc_start: 0.8457 (tttt) cc_final: 0.7888 (mmtt) REVERT: A 189 ASP cc_start: 0.7652 (t70) cc_final: 0.7312 (t0) REVERT: A 311 GLN cc_start: 0.7284 (tt0) cc_final: 0.6639 (tp-100) REVERT: A 327 MET cc_start: 0.8191 (tpt) cc_final: 0.7940 (tpp) REVERT: B 166 LYS cc_start: 0.8610 (mmtp) cc_final: 0.8390 (mmtm) REVERT: B 320 LYS cc_start: 0.7598 (ttmm) cc_final: 0.7352 (ttpt) REVERT: C 196 ASN cc_start: 0.8037 (t0) cc_final: 0.7384 (t0) REVERT: C 201 MET cc_start: 0.7864 (mmt) cc_final: 0.7265 (mmt) REVERT: C 248 LYS cc_start: 0.7972 (mttt) cc_final: 0.7095 (mptt) REVERT: D 196 ASN cc_start: 0.8028 (t0) cc_final: 0.7753 (t0) REVERT: D 302 TYR cc_start: 0.7978 (m-80) cc_final: 0.7772 (m-10) REVERT: D 321 TYR cc_start: 0.7626 (t80) cc_final: 0.7387 (t80) REVERT: E 129 MET cc_start: 0.7948 (ttm) cc_final: 0.7645 (mtp) outliers start: 18 outliers final: 16 residues processed: 157 average time/residue: 0.1125 time to fit residues: 23.8055 Evaluate side-chains 162 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 GLN 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 C residue 287 VAL 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 258 VAL Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain E residue 268 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 71 optimal weight: 0.5980 chunk 15 optimal weight: 6.9990 chunk 76 optimal weight: 0.3980 chunk 8 optimal weight: 3.9990 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: 0.9990 chunk 82 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 196 ASN E 203 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.161078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.120496 restraints weight = 9870.623| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.47 r_work: 0.3310 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9258 Z= 0.125 Angle : 0.497 8.202 12515 Z= 0.261 Chirality : 0.041 0.202 1323 Planarity : 0.003 0.038 1570 Dihedral : 10.034 137.356 1243 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.01 % Allowed : 12.50 % Favored : 85.49 % 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: 1.40 (0.24), residues: 458 sheet: -0.40 (0.36), residues: 170 loop : 0.31 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 213 TYR 0.026 0.001 TYR D 295 PHE 0.014 0.001 PHE E 175 TRP 0.015 0.001 TRP E 174 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 9258) covalent geometry : angle 0.49691 (12515) hydrogen bonds : bond 0.03848 ( 370) hydrogen bonds : angle 5.13060 ( 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 167 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LYS cc_start: 0.8445 (tttt) cc_final: 0.7885 (mmtt) REVERT: A 189 ASP cc_start: 0.7625 (t70) cc_final: 0.7286 (t0) REVERT: A 311 GLN cc_start: 0.7291 (tt0) cc_final: 0.6634 (tp-100) REVERT: B 166 LYS cc_start: 0.8627 (mmtp) cc_final: 0.8401 (mmtm) REVERT: B 320 LYS cc_start: 0.7597 (ttmm) cc_final: 0.7350 (ttpt) REVERT: C 196 ASN cc_start: 0.8018 (t0) cc_final: 0.7371 (t0) REVERT: C 201 MET cc_start: 0.7811 (mmt) cc_final: 0.7297 (mmt) REVERT: C 248 LYS cc_start: 0.7968 (mttt) cc_final: 0.7086 (mptt) REVERT: D 196 ASN cc_start: 0.8034 (t0) cc_final: 0.7770 (t0) REVERT: D 321 TYR cc_start: 0.7614 (t80) cc_final: 0.7373 (t80) REVERT: E 129 MET cc_start: 0.7945 (ttm) cc_final: 0.7645 (mtp) outliers start: 19 outliers final: 17 residues processed: 155 average time/residue: 0.1046 time to fit residues: 21.8111 Evaluate side-chains 163 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 229 THR Chi-restraints excluded: chain D residue 273 TRP Chi-restraints excluded: chain E residue 196 ASN Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain E residue 268 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 18 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 79 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 255 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 = 0.3967 r_free = 0.3967 target = 0.160716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.120188 restraints weight = 9827.028| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.45 r_work: 0.3305 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9258 Z= 0.135 Angle : 0.517 10.289 12515 Z= 0.269 Chirality : 0.042 0.192 1323 Planarity : 0.003 0.036 1570 Dihedral : 10.061 137.440 1243 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.01 % Allowed : 12.29 % Favored : 85.70 % 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: 0.83 (0.25), residues: 1063 helix: 1.36 (0.24), residues: 458 sheet: -0.43 (0.36), residues: 170 loop : 0.26 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 319 TYR 0.027 0.001 TYR D 295 PHE 0.016 0.001 PHE E 175 TRP 0.015 0.001 TRP E 174 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 9258) covalent geometry : angle 0.51674 (12515) hydrogen bonds : bond 0.03845 ( 370) hydrogen bonds : angle 5.13371 ( 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 170 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 151 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LYS cc_start: 0.8421 (tttt) cc_final: 0.7886 (mmtt) REVERT: A 189 ASP cc_start: 0.7636 (t70) cc_final: 0.7291 (t0) REVERT: A 311 GLN cc_start: 0.7283 (tt0) cc_final: 0.6611 (tp-100) REVERT: B 166 LYS cc_start: 0.8622 (mmtp) cc_final: 0.8392 (mmtm) REVERT: B 320 LYS cc_start: 0.7605 (ttmm) cc_final: 0.7355 (ttpt) REVERT: C 196 ASN cc_start: 0.8013 (t0) cc_final: 0.7362 (t0) REVERT: C 201 MET cc_start: 0.7829 (mmt) cc_final: 0.7237 (mmt) REVERT: C 248 LYS cc_start: 0.8003 (mttt) cc_final: 0.7089 (mptt) REVERT: D 196 ASN cc_start: 0.8017 (t0) cc_final: 0.7764 (t0) REVERT: D 321 TYR cc_start: 0.7618 (t80) cc_final: 0.7374 (t80) REVERT: F 139 MET cc_start: 0.7776 (mmm) cc_final: 0.7454 (mmm) outliers start: 19 outliers final: 16 residues processed: 159 average time/residue: 0.1062 time to fit residues: 22.7820 Evaluate side-chains 164 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 148 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 229 THR 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 258 VAL Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain E residue 268 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 80 optimal weight: 6.9990 chunk 100 optimal weight: 7.9990 chunk 27 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 chunk 95 optimal weight: 8.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 255 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 = 0.3968 r_free = 0.3968 target = 0.160864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.120370 restraints weight = 9933.383| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.47 r_work: 0.3305 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9258 Z= 0.132 Angle : 0.518 8.858 12515 Z= 0.270 Chirality : 0.042 0.190 1323 Planarity : 0.003 0.038 1570 Dihedral : 10.056 137.471 1243 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.91 % Allowed : 12.82 % Favored : 85.28 % 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: 0.82 (0.25), residues: 1063 helix: 1.36 (0.24), residues: 458 sheet: -0.44 (0.36), residues: 170 loop : 0.26 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 213 TYR 0.031 0.001 TYR D 295 PHE 0.015 0.001 PHE E 175 TRP 0.015 0.001 TRP E 174 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 9258) covalent geometry : angle 0.51782 (12515) hydrogen bonds : bond 0.03795 ( 370) hydrogen bonds : angle 5.11868 ( 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 170 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 152 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LYS cc_start: 0.8489 (tttt) cc_final: 0.7958 (mmtt) REVERT: A 189 ASP cc_start: 0.7631 (t70) cc_final: 0.7291 (t0) REVERT: A 311 GLN cc_start: 0.7283 (tt0) cc_final: 0.6623 (tp-100) REVERT: B 166 LYS cc_start: 0.8632 (mmtp) cc_final: 0.8398 (mmtm) REVERT: B 320 LYS cc_start: 0.7599 (ttmm) cc_final: 0.7361 (ttpt) REVERT: C 196 ASN cc_start: 0.8039 (t0) cc_final: 0.7396 (t0) REVERT: C 201 MET cc_start: 0.7789 (mmt) cc_final: 0.7527 (mmt) REVERT: C 248 LYS cc_start: 0.8006 (mttt) cc_final: 0.7093 (mptt) REVERT: D 196 ASN cc_start: 0.8073 (t0) cc_final: 0.7823 (t0) REVERT: D 321 TYR cc_start: 0.7609 (t80) cc_final: 0.7375 (t80) REVERT: F 139 MET cc_start: 0.7803 (mmm) cc_final: 0.7507 (mmm) outliers start: 18 outliers final: 15 residues processed: 160 average time/residue: 0.1047 time to fit residues: 22.5845 Evaluate side-chains 167 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 152 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 VAL 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 229 THR 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 258 VAL Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain E residue 268 SER 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: 5.9990 chunk 68 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 51 optimal weight: 0.1980 chunk 45 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 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 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 255 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 = 0.3979 r_free = 0.3979 target = 0.161933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.122457 restraints weight = 9795.876| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.38 r_work: 0.3329 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.3313 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= 0.118 Angle : 0.509 9.396 12515 Z= 0.266 Chirality : 0.041 0.184 1323 Planarity : 0.003 0.037 1570 Dihedral : 10.002 137.716 1243 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.69 % Allowed : 12.50 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.25), residues: 1063 helix: 1.40 (0.24), residues: 458 sheet: -0.44 (0.37), residues: 170 loop : 0.29 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 319 TYR 0.032 0.001 TYR D 295 PHE 0.012 0.001 PHE E 175 TRP 0.016 0.001 TRP E 174 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 9258) covalent geometry : angle 0.50938 (12515) hydrogen bonds : bond 0.03681 ( 370) hydrogen bonds : angle 5.08588 ( 1059) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2748.74 seconds wall clock time: 47 minutes 27.77 seconds (2847.77 seconds total)