Starting phenix.real_space_refine on Thu Jul 2 04:53:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7sqg_25384/07_2026/7sqg_25384.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sqg_25384/07_2026/7sqg_25384.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7sqg_25384/07_2026/7sqg_25384.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7sqg_25384/07_2026/7sqg_25384.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sqg_25384/07_2026/7sqg_25384.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sqg_25384/07_2026/7sqg_25384.map" model { file = "/net/cci-nas-00/data/ceres_data/7sqg_25384/07_2026/7sqg_25384.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sqg_25384/07_2026/7sqg_25384.cif" } resolution = 2.6 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= 0.016 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: 4 Type Number sf(0) Gaussians S 27 5.16 5 C 4296 2.51 5 N 1083 2.21 5 O 1224 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 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: 6630 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2154 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 13, 'TRANS': 256} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 2154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2154 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 13, 'TRANS': 256} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 2154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2154 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 13, 'TRANS': 256} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 1.60, per 1000 atoms: 0.24 Number of scatterers: 6630 At special positions: 0 Unit cell: (83.426, 82.6, 125.552, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 27 16.00 O 1224 8.00 N 1083 7.00 C 4296 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 Links applied NAG-ASN " NAG A 401 " - " ASN A 148 " " NAG A 402 " - " ASN A 162 " " NAG A 403 " - " ASN A 190 " " NAG A 404 " - " ASN A 155 " " NAG B 401 " - " ASN B 148 " " NAG B 402 " - " ASN B 162 " " NAG B 403 " - " ASN B 190 " " NAG B 404 " - " ASN B 155 " " NAG C 401 " - " ASN C 148 " " NAG C 402 " - " ASN C 162 " " NAG C 403 " - " ASN C 190 " " NAG C 404 " - " ASN C 155 " Time building additional restraints: 0.55 Conformation dependent library (CDL) restraints added in 350.3 milliseconds 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1560 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 9 sheets defined 34.6% alpha, 43.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 65 through 98 removed outlier: 3.563A pdb=" N LEU A 69 " --> pdb=" O VAL A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 212 removed outlier: 3.516A pdb=" N PHE A 210 " --> pdb=" O SER A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 227 removed outlier: 3.691A pdb=" N SER A 225 " --> pdb=" O GLN A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 278 removed outlier: 3.810A pdb=" N SER A 277 " --> pdb=" O ALA A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 334 Processing helix chain 'B' and resid 66 through 98 Processing helix chain 'B' and resid 206 through 212 removed outlier: 3.516A pdb=" N PHE B 210 " --> pdb=" O SER B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 227 removed outlier: 3.691A pdb=" N SER B 225 " --> pdb=" O GLN B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 278 removed outlier: 3.810A pdb=" N SER B 277 " --> pdb=" O ALA B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 334 Processing helix chain 'C' and resid 66 through 98 Processing helix chain 'C' and resid 206 through 212 removed outlier: 3.516A pdb=" N PHE C 210 " --> pdb=" O SER C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 227 removed outlier: 3.691A pdb=" N SER C 225 " --> pdb=" O GLN C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 278 removed outlier: 3.810A pdb=" N SER C 277 " --> pdb=" O ALA C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 334 Processing sheet with id=AA1, first strand: chain 'A' and resid 100 through 107 removed outlier: 13.537A pdb=" N PHE A 291 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 9.278A pdb=" N MET A 242 " --> pdb=" O PHE A 291 " (cutoff:3.500A) removed outlier: 9.162A pdb=" N GLN A 293 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU A 244 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N VAL A 295 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LYS A 246 " --> pdb=" O VAL A 295 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ASP A 297 " --> pdb=" O LYS A 246 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N LYS A 248 " --> pdb=" O ASP A 297 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N PHE A 236 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N TRP A 287 " --> pdb=" O GLU A 181 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N GLU A 181 " --> pdb=" O TRP A 287 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ARG A 188 " --> pdb=" O LEU A 125 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N LEU A 125 " --> pdb=" O ARG A 188 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ASN A 148 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N CYS A 128 " --> pdb=" O ASN A 148 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 107 removed outlier: 13.537A pdb=" N PHE A 291 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 9.278A pdb=" N MET A 242 " --> pdb=" O PHE A 291 " (cutoff:3.500A) removed outlier: 9.162A pdb=" N GLN A 293 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU A 244 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N VAL A 295 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LYS A 246 " --> pdb=" O VAL A 295 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ASP A 297 " --> pdb=" O LYS A 246 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N LYS A 248 " --> pdb=" O ASP A 297 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 151 through 157 removed outlier: 3.743A pdb=" N ASP A 200 " --> pdb=" O TYR A 119 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 107 removed outlier: 13.537A pdb=" N PHE B 291 " --> pdb=" O VAL B 240 " (cutoff:3.500A) removed outlier: 9.278A pdb=" N MET B 242 " --> pdb=" O PHE B 291 " (cutoff:3.500A) removed outlier: 9.162A pdb=" N GLN B 293 " --> pdb=" O MET B 242 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU B 244 " --> pdb=" O GLN B 293 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N VAL B 295 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LYS B 246 " --> pdb=" O VAL B 295 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ASP B 297 " --> pdb=" O LYS B 246 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N LYS B 248 " --> pdb=" O ASP B 297 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N PHE B 236 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N TRP B 287 " --> pdb=" O GLU B 181 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N GLU B 181 " --> pdb=" O TRP B 287 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ARG B 188 " --> pdb=" O LEU B 125 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N LEU B 125 " --> pdb=" O ARG B 188 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ASN B 148 " --> pdb=" O LEU B 126 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N CYS B 128 " --> pdb=" O ASN B 148 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 107 removed outlier: 13.537A pdb=" N PHE B 291 " --> pdb=" O VAL B 240 " (cutoff:3.500A) removed outlier: 9.278A pdb=" N MET B 242 " --> pdb=" O PHE B 291 " (cutoff:3.500A) removed outlier: 9.162A pdb=" N GLN B 293 " --> pdb=" O MET B 242 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU B 244 " --> pdb=" O GLN B 293 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N VAL B 295 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LYS B 246 " --> pdb=" O VAL B 295 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ASP B 297 " --> pdb=" O LYS B 246 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N LYS B 248 " --> pdb=" O ASP B 297 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 151 through 157 removed outlier: 3.741A pdb=" N ASP B 200 " --> pdb=" O TYR B 119 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 100 through 107 removed outlier: 13.537A pdb=" N PHE C 291 " --> pdb=" O VAL C 240 " (cutoff:3.500A) removed outlier: 9.278A pdb=" N MET C 242 " --> pdb=" O PHE C 291 " (cutoff:3.500A) removed outlier: 9.162A pdb=" N GLN C 293 " --> pdb=" O MET C 242 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU C 244 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N VAL C 295 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LYS C 246 " --> pdb=" O VAL C 295 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ASP C 297 " --> pdb=" O LYS C 246 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N LYS C 248 " --> pdb=" O ASP C 297 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N PHE C 236 " --> pdb=" O LEU C 280 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N TRP C 287 " --> pdb=" O GLU C 181 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N GLU C 181 " --> pdb=" O TRP C 287 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ARG C 188 " --> pdb=" O LEU C 125 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N LEU C 125 " --> pdb=" O ARG C 188 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ASN C 148 " --> pdb=" O LEU C 126 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N CYS C 128 " --> pdb=" O ASN C 148 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 100 through 107 removed outlier: 13.537A pdb=" N PHE C 291 " --> pdb=" O VAL C 240 " (cutoff:3.500A) removed outlier: 9.278A pdb=" N MET C 242 " --> pdb=" O PHE C 291 " (cutoff:3.500A) removed outlier: 9.162A pdb=" N GLN C 293 " --> pdb=" O MET C 242 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU C 244 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N VAL C 295 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LYS C 246 " --> pdb=" O VAL C 295 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ASP C 297 " --> pdb=" O LYS C 246 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N LYS C 248 " --> pdb=" O ASP C 297 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 151 through 157 removed outlier: 3.733A pdb=" N ASP C 200 " --> pdb=" O TYR C 119 " (cutoff:3.500A) 414 hydrogen bonds defined for protein. 1179 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: 1.02 Time building geometry restraints manager: 0.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2049 1.34 - 1.46: 1202 1.46 - 1.57: 3505 1.57 - 1.69: 0 1.69 - 1.81: 42 Bond restraints: 6798 Sorted by residual: bond pdb=" N GLU A 224 " pdb=" CA GLU A 224 " ideal model delta sigma weight residual 1.459 1.490 -0.032 1.25e-02 6.40e+03 6.43e+00 bond pdb=" N ARG C 93 " pdb=" CA ARG C 93 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.19e-02 7.06e+03 6.36e+00 bond pdb=" N GLU C 224 " pdb=" CA GLU C 224 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.25e-02 6.40e+03 6.15e+00 bond pdb=" N ARG B 93 " pdb=" CA ARG B 93 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.19e-02 7.06e+03 6.15e+00 bond pdb=" N GLU B 224 " pdb=" CA GLU B 224 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.25e-02 6.40e+03 6.14e+00 ... (remaining 6793 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.97: 8460 0.97 - 1.94: 559 1.94 - 2.91: 161 2.91 - 3.88: 32 3.88 - 4.84: 10 Bond angle restraints: 9222 Sorted by residual: angle pdb=" C ARG A 259 " pdb=" N GLN A 260 " pdb=" CA GLN A 260 " ideal model delta sigma weight residual 122.99 118.15 4.84 1.41e+00 5.03e-01 1.18e+01 angle pdb=" C ARG C 259 " pdb=" N GLN C 260 " pdb=" CA GLN C 260 " ideal model delta sigma weight residual 122.99 118.15 4.84 1.41e+00 5.03e-01 1.18e+01 angle pdb=" C ARG B 259 " pdb=" N GLN B 260 " pdb=" CA GLN B 260 " ideal model delta sigma weight residual 122.99 118.23 4.76 1.41e+00 5.03e-01 1.14e+01 angle pdb=" CA ARG B 93 " pdb=" C ARG B 93 " pdb=" O ARG B 93 " ideal model delta sigma weight residual 120.82 117.99 2.83 1.05e+00 9.07e-01 7.29e+00 angle pdb=" CA ARG C 93 " pdb=" C ARG C 93 " pdb=" O ARG C 93 " ideal model delta sigma weight residual 120.82 118.00 2.82 1.05e+00 9.07e-01 7.22e+00 ... (remaining 9217 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.43: 3543 15.43 - 30.85: 292 30.85 - 46.27: 70 46.27 - 61.70: 36 61.70 - 77.12: 10 Dihedral angle restraints: 3951 sinusoidal: 1554 harmonic: 2397 Sorted by residual: dihedral pdb=" CA PHE A 236 " pdb=" C PHE A 236 " pdb=" N ARG A 237 " pdb=" CA ARG A 237 " ideal model delta harmonic sigma weight residual 180.00 155.89 24.11 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA PHE B 236 " pdb=" C PHE B 236 " pdb=" N ARG B 237 " pdb=" CA ARG B 237 " ideal model delta harmonic sigma weight residual 180.00 155.89 24.11 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA PHE C 236 " pdb=" C PHE C 236 " pdb=" N ARG C 237 " pdb=" CA ARG C 237 " ideal model delta harmonic sigma weight residual 180.00 155.94 24.06 0 5.00e+00 4.00e-02 2.31e+01 ... (remaining 3948 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 721 0.041 - 0.083: 231 0.083 - 0.124: 86 0.124 - 0.166: 8 0.166 - 0.207: 4 Chirality restraints: 1050 Sorted by residual: chirality pdb=" CA LEU A 169 " pdb=" N LEU A 169 " pdb=" C LEU A 169 " pdb=" CB LEU A 169 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA LEU B 169 " pdb=" N LEU B 169 " pdb=" C LEU B 169 " pdb=" CB LEU B 169 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA LEU C 169 " pdb=" N LEU C 169 " pdb=" C LEU C 169 " pdb=" CB LEU C 169 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.05e+00 ... (remaining 1047 not shown) Planarity restraints: 1170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 118 " -0.008 2.00e-02 2.50e+03 1.55e-02 2.41e+00 pdb=" C LEU C 118 " 0.027 2.00e-02 2.50e+03 pdb=" O LEU C 118 " -0.010 2.00e-02 2.50e+03 pdb=" N TYR C 119 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 118 " -0.007 2.00e-02 2.50e+03 1.51e-02 2.27e+00 pdb=" C LEU B 118 " 0.026 2.00e-02 2.50e+03 pdb=" O LEU B 118 " -0.010 2.00e-02 2.50e+03 pdb=" N TYR B 119 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 118 " -0.007 2.00e-02 2.50e+03 1.50e-02 2.26e+00 pdb=" C LEU A 118 " 0.026 2.00e-02 2.50e+03 pdb=" O LEU A 118 " -0.010 2.00e-02 2.50e+03 pdb=" N TYR A 119 " -0.009 2.00e-02 2.50e+03 ... (remaining 1167 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 2643 2.92 - 3.41: 5865 3.41 - 3.91: 11062 3.91 - 4.40: 11948 4.40 - 4.90: 20624 Nonbonded interactions: 52142 Sorted by model distance: nonbonded pdb=" OG1 THR A 150 " pdb=" OE1 GLN A 172 " model vdw 2.423 3.040 nonbonded pdb=" OG1 THR C 150 " pdb=" OE1 GLN C 172 " model vdw 2.423 3.040 nonbonded pdb=" OG1 THR B 150 " pdb=" OE1 GLN B 172 " model vdw 2.423 3.040 nonbonded pdb=" OG SER C 197 " pdb=" OE1 GLN C 279 " model vdw 2.439 3.040 nonbonded pdb=" OG SER A 197 " pdb=" OE1 GLN A 279 " model vdw 2.440 3.040 ... (remaining 52137 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 4.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.660 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:6.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 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 0.032 6810 Z= 0.223 Angle : 0.614 4.844 9258 Z= 0.342 Chirality : 0.047 0.207 1050 Planarity : 0.004 0.033 1158 Dihedral : 13.941 77.125 2391 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.39 (0.30), residues: 804 helix: 3.12 (0.28), residues: 273 sheet: 0.75 (0.29), residues: 318 loop : -1.86 (0.40), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 110 TYR 0.009 0.001 TYR A 201 PHE 0.020 0.002 PHE A 219 TRP 0.007 0.001 TRP B 304 HIS 0.001 0.001 HIS A 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.22 ( 6798) covalent geometry : angle 0.60470 / 0.34 ( 9222) hydrogen bonds : bond 0.09118 / 6.52 ( 390) hydrogen bonds : angle 4.91090 / 3.46 ( 1179) link_NAG-ASN : bond 0.00252 / 0.16 ( 12) link_NAG-ASN : angle 1.85381 / 1.27 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 261 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.7274 (ttt) cc_final: 0.6970 (ttt) REVERT: A 94 GLU cc_start: 0.7009 (tp30) cc_final: 0.6807 (tp30) REVERT: A 106 LYS cc_start: 0.7670 (tttp) cc_final: 0.7363 (tttp) REVERT: A 143 GLN cc_start: 0.7727 (mm110) cc_final: 0.7497 (mm110) REVERT: A 147 MET cc_start: 0.7523 (mtm) cc_final: 0.7285 (mtp) REVERT: A 166 LYS cc_start: 0.7903 (mtpt) cc_final: 0.7694 (mttm) REVERT: A 180 ARG cc_start: 0.7102 (mtp180) cc_final: 0.6806 (mtp180) REVERT: A 294 LYS cc_start: 0.7529 (mttt) cc_final: 0.7281 (mttt) REVERT: A 304 TRP cc_start: 0.7393 (m100) cc_final: 0.7012 (m100) REVERT: B 94 GLU cc_start: 0.7036 (tp30) cc_final: 0.6790 (tp30) REVERT: B 98 HIS cc_start: 0.8294 (m90) cc_final: 0.8075 (m-70) REVERT: B 180 ARG cc_start: 0.7003 (mtp180) cc_final: 0.6686 (mtp180) REVERT: B 197 SER cc_start: 0.8098 (p) cc_final: 0.7657 (p) REVERT: B 219 PHE cc_start: 0.7931 (t80) cc_final: 0.7657 (t80) REVERT: B 224 GLU cc_start: 0.7251 (mm-30) cc_final: 0.6878 (mm-30) REVERT: B 247 THR cc_start: 0.7494 (m) cc_final: 0.7187 (t) REVERT: B 275 LYS cc_start: 0.7412 (mmtt) cc_final: 0.6944 (mmmm) REVERT: C 92 PHE cc_start: 0.7508 (t80) cc_final: 0.6960 (t80) REVERT: C 124 GLN cc_start: 0.7490 (pt0) cc_final: 0.7262 (pt0) REVERT: C 148 ASN cc_start: 0.6303 (t0) cc_final: 0.6057 (p0) REVERT: C 176 GLU cc_start: 0.7333 (mp0) cc_final: 0.6829 (mp0) REVERT: C 179 LYS cc_start: 0.8267 (mtpp) cc_final: 0.8010 (mtmt) REVERT: C 188 ARG cc_start: 0.7500 (ttp-170) cc_final: 0.7048 (ttp-170) REVERT: C 194 GLU cc_start: 0.6927 (tm-30) cc_final: 0.6424 (tm-30) REVERT: C 197 SER cc_start: 0.8136 (p) cc_final: 0.7731 (p) REVERT: C 219 PHE cc_start: 0.7989 (t80) cc_final: 0.7659 (t80) REVERT: C 271 ARG cc_start: 0.7742 (mtm180) cc_final: 0.7444 (mtm-85) REVERT: C 304 TRP cc_start: 0.7634 (m100) cc_final: 0.7103 (m100) outliers start: 0 outliers final: 0 residues processed: 261 average time/residue: 0.6908 time to fit residues: 186.6280 Evaluate side-chains 236 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.1980 chunk 33 optimal weight: 0.0670 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.4980 chunk 61 optimal weight: 0.0030 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 overall best weight: 0.2728 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 152 GLN A 172 GLN A 208 GLN A 293 GLN A 296 GLN B 172 GLN ** B 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 GLN B 296 GLN C 98 HIS C 186 GLN ** C 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.141188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.122585 restraints weight = 9691.310| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.33 r_work: 0.3489 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 6810 Z= 0.136 Angle : 0.569 9.227 9258 Z= 0.287 Chirality : 0.043 0.142 1050 Planarity : 0.003 0.027 1158 Dihedral : 4.368 23.296 873 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.75 % Allowed : 14.35 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.47 (0.29), residues: 804 helix: 2.87 (0.29), residues: 279 sheet: 1.18 (0.29), residues: 291 loop : -1.82 (0.37), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 175 TYR 0.008 0.001 TYR B 119 PHE 0.021 0.002 PHE A 219 TRP 0.008 0.001 TRP A 304 HIS 0.009 0.002 HIS C 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 6798) covalent geometry : angle 0.55056 / 0.28 ( 9222) hydrogen bonds : bond 0.03198 / 2.21 ( 390) hydrogen bonds : angle 4.16112 / 2.89 ( 1179) link_NAG-ASN : bond 0.00361 / 0.25 ( 12) link_NAG-ASN : angle 2.38636 / 1.54 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 224 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: A 106 LYS cc_start: 0.8453 (tttp) cc_final: 0.8203 (ttmm) REVERT: A 147 MET cc_start: 0.7811 (mtm) cc_final: 0.7563 (mtp) REVERT: A 175 ARG cc_start: 0.7803 (mtp85) cc_final: 0.7554 (mtp85) REVERT: A 176 GLU cc_start: 0.8082 (mp0) cc_final: 0.7371 (mp0) REVERT: A 180 ARG cc_start: 0.7951 (mtp180) cc_final: 0.7706 (mtp180) REVERT: A 181 GLU cc_start: 0.8113 (tt0) cc_final: 0.7668 (tt0) REVERT: A 304 TRP cc_start: 0.8411 (m100) cc_final: 0.8196 (m100) REVERT: B 180 ARG cc_start: 0.7991 (mtp180) cc_final: 0.7753 (mtp180) REVERT: B 219 PHE cc_start: 0.8292 (t80) cc_final: 0.7812 (t80) REVERT: B 247 THR cc_start: 0.8148 (m) cc_final: 0.7946 (t) REVERT: C 92 PHE cc_start: 0.8640 (t80) cc_final: 0.8346 (t80) REVERT: C 106 LYS cc_start: 0.8412 (tttp) cc_final: 0.8203 (tttp) REVERT: C 148 ASN cc_start: 0.7071 (t0) cc_final: 0.6649 (p0) REVERT: C 176 GLU cc_start: 0.8183 (mp0) cc_final: 0.7353 (mp0) REVERT: C 181 GLU cc_start: 0.8088 (tt0) cc_final: 0.7697 (tt0) REVERT: C 188 ARG cc_start: 0.8293 (ttp-170) cc_final: 0.8004 (ttp-170) REVERT: C 194 GLU cc_start: 0.6971 (tm-30) cc_final: 0.6634 (tm-30) REVERT: C 219 PHE cc_start: 0.8389 (t80) cc_final: 0.8109 (t80) REVERT: C 271 ARG cc_start: 0.8672 (mtm180) cc_final: 0.8249 (mtm-85) REVERT: C 304 TRP cc_start: 0.8476 (m100) cc_final: 0.8189 (m100) outliers start: 19 outliers final: 10 residues processed: 227 average time/residue: 0.7065 time to fit residues: 166.3167 Evaluate side-chains 230 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 220 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain B residue 186 GLN Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 315 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 5 optimal weight: 0.0980 chunk 28 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 80 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 52 optimal weight: 0.2980 chunk 17 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 69 optimal weight: 0.4980 chunk 4 optimal weight: 0.8980 chunk 25 optimal weight: 0.2980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 208 GLN A 266 ASN A 293 GLN A 296 GLN B 98 HIS B 172 GLN B 266 ASN ** B 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 GLN C 98 HIS C 124 GLN C 266 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.140024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.121475 restraints weight = 9615.717| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.31 r_work: 0.3477 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6810 Z= 0.151 Angle : 0.536 7.775 9258 Z= 0.274 Chirality : 0.043 0.135 1050 Planarity : 0.003 0.028 1158 Dihedral : 4.381 24.211 873 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.90 % Allowed : 19.42 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.79 (0.29), residues: 804 helix: 3.28 (0.28), residues: 258 sheet: 1.09 (0.28), residues: 309 loop : -1.17 (0.39), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 175 TYR 0.010 0.001 TYR B 111 PHE 0.018 0.002 PHE B 204 TRP 0.006 0.001 TRP A 230 HIS 0.009 0.002 HIS C 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 ( 6798) covalent geometry : angle 0.52805 / 0.27 ( 9222) hydrogen bonds : bond 0.03197 / 2.20 ( 390) hydrogen bonds : angle 4.09091 / 2.84 ( 1179) link_NAG-ASN : bond 0.00419 / 0.30 ( 12) link_NAG-ASN : angle 1.58019 / 1.08 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 217 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: A 106 LYS cc_start: 0.8426 (tttp) cc_final: 0.8194 (tttp) REVERT: A 129 LYS cc_start: 0.8537 (mtpt) cc_final: 0.8269 (mttt) REVERT: A 147 MET cc_start: 0.7889 (mtm) cc_final: 0.7648 (mtp) REVERT: A 175 ARG cc_start: 0.7802 (mtp85) cc_final: 0.7454 (mtp85) REVERT: A 176 GLU cc_start: 0.8134 (mp0) cc_final: 0.7153 (mp0) REVERT: A 181 GLU cc_start: 0.8126 (tt0) cc_final: 0.7752 (tt0) REVERT: A 194 GLU cc_start: 0.6630 (tm-30) cc_final: 0.6269 (tm-30) REVERT: B 180 ARG cc_start: 0.8014 (mtp180) cc_final: 0.7728 (mtp180) REVERT: B 247 THR cc_start: 0.8232 (m) cc_final: 0.8018 (t) REVERT: C 89 ILE cc_start: 0.8856 (mm) cc_final: 0.8605 (mm) REVERT: C 93 ARG cc_start: 0.7713 (mtt180) cc_final: 0.7474 (mtm110) REVERT: C 148 ASN cc_start: 0.7088 (t0) cc_final: 0.6686 (p0) REVERT: C 176 GLU cc_start: 0.8160 (mp0) cc_final: 0.7303 (mp0) REVERT: C 181 GLU cc_start: 0.8072 (tt0) cc_final: 0.7696 (tt0) REVERT: C 188 ARG cc_start: 0.8356 (ttp-170) cc_final: 0.8107 (ttp-170) REVERT: C 194 GLU cc_start: 0.6955 (tm-30) cc_final: 0.6637 (tm-30) REVERT: C 212 GLN cc_start: 0.7173 (mp10) cc_final: 0.6722 (mp10) REVERT: C 248 LYS cc_start: 0.7462 (tppp) cc_final: 0.7251 (mmmm) REVERT: C 271 ARG cc_start: 0.8693 (mtm180) cc_final: 0.8251 (mtm-85) REVERT: C 304 TRP cc_start: 0.8468 (m100) cc_final: 0.8150 (m100) REVERT: C 314 PHE cc_start: 0.8332 (m-10) cc_final: 0.8124 (m-10) outliers start: 20 outliers final: 13 residues processed: 221 average time/residue: 0.7590 time to fit residues: 173.5924 Evaluate side-chains 226 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 213 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain B residue 186 GLN Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 315 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 43 optimal weight: 0.5980 chunk 5 optimal weight: 0.0470 chunk 36 optimal weight: 0.9990 chunk 79 optimal weight: 0.4980 chunk 26 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 0.3980 chunk 35 optimal weight: 1.9990 chunk 68 optimal weight: 0.0770 chunk 2 optimal weight: 0.3980 overall best weight: 0.2836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 172 GLN A 293 GLN B 186 GLN B 293 GLN C 186 GLN C 208 GLN C 212 GLN C 293 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.140064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.121629 restraints weight = 9618.459| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.31 r_work: 0.3480 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6810 Z= 0.131 Angle : 0.512 7.177 9258 Z= 0.265 Chirality : 0.042 0.135 1050 Planarity : 0.003 0.027 1158 Dihedral : 4.348 24.251 873 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.19 % Allowed : 20.29 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.91 (0.29), residues: 804 helix: 3.32 (0.28), residues: 258 sheet: 1.00 (0.27), residues: 324 loop : -0.89 (0.42), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 175 TYR 0.006 0.001 TYR B 119 PHE 0.016 0.002 PHE B 204 TRP 0.007 0.001 TRP C 239 HIS 0.002 0.001 HIS C 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 6798) covalent geometry : angle 0.50487 / 0.26 ( 9222) hydrogen bonds : bond 0.03040 / 2.09 ( 390) hydrogen bonds : angle 4.04664 / 2.79 ( 1179) link_NAG-ASN : bond 0.00312 / 0.21 ( 12) link_NAG-ASN : angle 1.45059 / 1.02 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 217 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: A 129 LYS cc_start: 0.8537 (mtpt) cc_final: 0.8309 (mttt) REVERT: A 147 MET cc_start: 0.7897 (mtm) cc_final: 0.7662 (mtp) REVERT: A 175 ARG cc_start: 0.7785 (mtp85) cc_final: 0.7467 (mtp85) REVERT: A 176 GLU cc_start: 0.8131 (mp0) cc_final: 0.7201 (mp0) REVERT: A 181 GLU cc_start: 0.8122 (tt0) cc_final: 0.7765 (tt0) REVERT: A 194 GLU cc_start: 0.6615 (tm-30) cc_final: 0.6366 (tm-30) REVERT: B 180 ARG cc_start: 0.8046 (mtp180) cc_final: 0.7779 (mtp180) REVERT: B 247 THR cc_start: 0.8250 (m) cc_final: 0.8042 (t) REVERT: C 93 ARG cc_start: 0.7722 (mtt180) cc_final: 0.7497 (mtm110) REVERT: C 148 ASN cc_start: 0.7120 (t0) cc_final: 0.6732 (p0) REVERT: C 176 GLU cc_start: 0.8155 (mp0) cc_final: 0.7305 (mp0) REVERT: C 181 GLU cc_start: 0.8057 (tt0) cc_final: 0.7662 (tt0) REVERT: C 188 ARG cc_start: 0.8371 (ttp-170) cc_final: 0.8097 (ttp-170) REVERT: C 194 GLU cc_start: 0.6988 (tm-30) cc_final: 0.6664 (tm-30) REVERT: C 271 ARG cc_start: 0.8711 (mtm180) cc_final: 0.8260 (mtm-85) REVERT: C 304 TRP cc_start: 0.8458 (m100) cc_final: 0.8099 (m100) REVERT: C 314 PHE cc_start: 0.8324 (m-10) cc_final: 0.8124 (m-10) REVERT: C 319 LYS cc_start: 0.8089 (tppt) cc_final: 0.7885 (ttmm) outliers start: 22 outliers final: 10 residues processed: 220 average time/residue: 0.7252 time to fit residues: 165.2846 Evaluate side-chains 224 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 214 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain C residue 212 GLN Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 294 LYS Chi-restraints excluded: chain C residue 315 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 68 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 24 optimal weight: 0.4980 chunk 41 optimal weight: 0.4980 chunk 21 optimal weight: 0.4980 chunk 7 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 5 optimal weight: 0.0980 chunk 46 optimal weight: 0.9980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 GLN B 293 GLN C 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.139364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.120668 restraints weight = 9696.976| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.34 r_work: 0.3463 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6810 Z= 0.171 Angle : 0.536 7.303 9258 Z= 0.276 Chirality : 0.043 0.130 1050 Planarity : 0.004 0.029 1158 Dihedral : 4.404 24.685 873 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.04 % Allowed : 20.43 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.88 (0.29), residues: 804 helix: 3.25 (0.28), residues: 258 sheet: 0.99 (0.27), residues: 327 loop : -0.87 (0.43), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 271 TYR 0.008 0.001 TYR B 119 PHE 0.018 0.002 PHE B 204 TRP 0.006 0.001 TRP C 239 HIS 0.002 0.001 HIS C 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 ( 6798) covalent geometry : angle 0.53027 / 0.28 ( 9222) hydrogen bonds : bond 0.03268 / 2.25 ( 390) hydrogen bonds : angle 4.10290 / 2.83 ( 1179) link_NAG-ASN : bond 0.00326 / 0.23 ( 12) link_NAG-ASN : angle 1.36445 / 0.96 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 229 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: A 129 LYS cc_start: 0.8548 (mtpt) cc_final: 0.8342 (mttt) REVERT: A 147 MET cc_start: 0.7937 (mtm) cc_final: 0.7697 (mtp) REVERT: A 194 GLU cc_start: 0.6668 (tm-30) cc_final: 0.6422 (tm-30) REVERT: B 247 THR cc_start: 0.8316 (m) cc_final: 0.8102 (t) REVERT: C 148 ASN cc_start: 0.7185 (t0) cc_final: 0.6796 (p0) REVERT: C 176 GLU cc_start: 0.8169 (mp0) cc_final: 0.7348 (mp0) REVERT: C 181 GLU cc_start: 0.8097 (tt0) cc_final: 0.7725 (tt0) REVERT: C 188 ARG cc_start: 0.8380 (ttp-170) cc_final: 0.8125 (ttp-170) REVERT: C 194 GLU cc_start: 0.6995 (tm-30) cc_final: 0.6682 (tm-30) REVERT: C 271 ARG cc_start: 0.8722 (mtm180) cc_final: 0.8245 (mtm-85) REVERT: C 304 TRP cc_start: 0.8464 (m100) cc_final: 0.8131 (m100) outliers start: 21 outliers final: 12 residues processed: 231 average time/residue: 0.6697 time to fit residues: 160.4871 Evaluate side-chains 238 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 226 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 294 LYS Chi-restraints excluded: chain C residue 315 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 44 optimal weight: 0.5980 chunk 27 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 47 optimal weight: 0.0870 chunk 75 optimal weight: 0.0980 chunk 8 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 172 GLN ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 GLN B 293 GLN C 186 GLN C 293 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.138892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.120254 restraints weight = 9573.532| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.32 r_work: 0.3457 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6810 Z= 0.181 Angle : 0.544 7.437 9258 Z= 0.283 Chirality : 0.044 0.189 1050 Planarity : 0.004 0.033 1158 Dihedral : 4.499 25.128 873 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.04 % Allowed : 21.45 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.87 (0.29), residues: 804 helix: 3.16 (0.28), residues: 258 sheet: 1.08 (0.27), residues: 324 loop : -0.92 (0.43), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 175 TYR 0.008 0.001 TYR B 111 PHE 0.019 0.002 PHE B 204 TRP 0.006 0.001 TRP B 230 HIS 0.002 0.001 HIS C 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.18 ( 6798) covalent geometry : angle 0.53833 / 0.28 ( 9222) hydrogen bonds : bond 0.03395 / 2.35 ( 390) hydrogen bonds : angle 4.15052 / 2.87 ( 1179) link_NAG-ASN : bond 0.00305 / 0.21 ( 12) link_NAG-ASN : angle 1.32336 / 0.94 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 230 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 LYS cc_start: 0.8462 (tttp) cc_final: 0.8228 (ttpp) REVERT: A 147 MET cc_start: 0.7969 (mtm) cc_final: 0.7717 (mtp) REVERT: A 194 GLU cc_start: 0.6753 (tm-30) cc_final: 0.6513 (tm-30) REVERT: A 219 PHE cc_start: 0.8234 (t80) cc_final: 0.7914 (t80) REVERT: A 268 ILE cc_start: 0.8094 (mm) cc_final: 0.7824 (mt) REVERT: B 206 SER cc_start: 0.8587 (m) cc_final: 0.8385 (t) REVERT: B 247 THR cc_start: 0.8337 (m) cc_final: 0.8124 (t) REVERT: C 75 LEU cc_start: 0.7919 (mt) cc_final: 0.7702 (mt) REVERT: C 93 ARG cc_start: 0.7727 (mtm110) cc_final: 0.7504 (mtm110) REVERT: C 148 ASN cc_start: 0.7192 (t0) cc_final: 0.6829 (p0) REVERT: C 176 GLU cc_start: 0.8205 (mp0) cc_final: 0.7360 (mp0) REVERT: C 181 GLU cc_start: 0.8103 (tt0) cc_final: 0.7715 (tt0) REVERT: C 188 ARG cc_start: 0.8373 (ttp-170) cc_final: 0.8109 (ttp-170) REVERT: C 194 GLU cc_start: 0.6998 (tm-30) cc_final: 0.6673 (tm-30) REVERT: C 248 LYS cc_start: 0.7565 (mmmm) cc_final: 0.7355 (ttmm) REVERT: C 271 ARG cc_start: 0.8689 (mtm180) cc_final: 0.8192 (mtm-85) REVERT: C 304 TRP cc_start: 0.8488 (m100) cc_final: 0.8157 (m100) outliers start: 21 outliers final: 13 residues processed: 233 average time/residue: 0.6949 time to fit residues: 168.0544 Evaluate side-chains 237 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 224 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 315 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 48 optimal weight: 0.0970 chunk 3 optimal weight: 0.8980 chunk 78 optimal weight: 0.5980 chunk 5 optimal weight: 0.0980 chunk 66 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 79 optimal weight: 0.7980 chunk 61 optimal weight: 0.4980 chunk 77 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 172 GLN ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 GLN B 172 GLN B 293 GLN C 186 GLN ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.139277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.120727 restraints weight = 9522.347| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.32 r_work: 0.3466 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6810 Z= 0.162 Angle : 0.534 7.180 9258 Z= 0.280 Chirality : 0.044 0.189 1050 Planarity : 0.004 0.033 1158 Dihedral : 4.497 25.258 873 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.17 % Allowed : 23.19 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.54 (0.30), residues: 804 helix: 2.77 (0.29), residues: 279 sheet: 0.97 (0.27), residues: 315 loop : -1.40 (0.43), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 175 TYR 0.008 0.001 TYR B 111 PHE 0.018 0.002 PHE B 204 TRP 0.006 0.001 TRP B 230 HIS 0.002 0.001 HIS C 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 ( 6798) covalent geometry : angle 0.52903 / 0.28 ( 9222) hydrogen bonds : bond 0.03257 / 2.25 ( 390) hydrogen bonds : angle 4.15064 / 2.87 ( 1179) link_NAG-ASN : bond 0.00300 / 0.21 ( 12) link_NAG-ASN : angle 1.25684 / 0.91 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 225 time to evaluate : 0.273 Fit side-chains revert: symmetry clash REVERT: A 106 LYS cc_start: 0.8465 (tttp) cc_final: 0.8228 (ttpp) REVERT: A 147 MET cc_start: 0.7951 (mtm) cc_final: 0.7690 (mtp) REVERT: A 180 ARG cc_start: 0.7971 (mtp180) cc_final: 0.7613 (mtp180) REVERT: A 194 GLU cc_start: 0.6723 (tm-30) cc_final: 0.6409 (tm-30) REVERT: A 197 SER cc_start: 0.8684 (p) cc_final: 0.8426 (m) REVERT: B 110 ARG cc_start: 0.7535 (ptm160) cc_final: 0.7191 (ptm160) REVERT: B 247 THR cc_start: 0.8375 (m) cc_final: 0.8143 (t) REVERT: C 148 ASN cc_start: 0.7182 (t0) cc_final: 0.6819 (p0) REVERT: C 176 GLU cc_start: 0.8180 (mp0) cc_final: 0.7324 (mp0) REVERT: C 180 ARG cc_start: 0.8059 (mtp180) cc_final: 0.7670 (mtp180) REVERT: C 181 GLU cc_start: 0.8069 (tt0) cc_final: 0.7698 (tt0) REVERT: C 188 ARG cc_start: 0.8353 (ttp-170) cc_final: 0.8092 (ttp-170) REVERT: C 194 GLU cc_start: 0.6994 (tm-30) cc_final: 0.6685 (tm-30) REVERT: C 248 LYS cc_start: 0.7605 (mmmm) cc_final: 0.7344 (mtpp) REVERT: C 271 ARG cc_start: 0.8684 (mtm180) cc_final: 0.8194 (mtm-85) REVERT: C 304 TRP cc_start: 0.8493 (m100) cc_final: 0.8165 (m100) outliers start: 15 outliers final: 8 residues processed: 227 average time/residue: 0.6874 time to fit residues: 161.9273 Evaluate side-chains 234 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 226 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain C residue 315 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 31 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 46 optimal weight: 0.0870 chunk 53 optimal weight: 0.9980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 172 GLN A 293 GLN B 293 GLN C 186 GLN C 293 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.137953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.119242 restraints weight = 9577.501| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.35 r_work: 0.3442 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 6810 Z= 0.240 Angle : 0.594 7.368 9258 Z= 0.306 Chirality : 0.046 0.205 1050 Planarity : 0.005 0.050 1158 Dihedral : 4.624 25.647 873 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.90 % Allowed : 23.04 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.47 (0.30), residues: 804 helix: 2.63 (0.29), residues: 279 sheet: 0.98 (0.27), residues: 315 loop : -1.40 (0.43), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 271 TYR 0.010 0.002 TYR B 119 PHE 0.023 0.002 PHE B 204 TRP 0.008 0.001 TRP B 230 HIS 0.003 0.001 HIS C 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00574 / 0.24 ( 6798) covalent geometry : angle 0.58956 / 0.31 ( 9222) hydrogen bonds : bond 0.03762 / 2.59 ( 390) hydrogen bonds : angle 4.27869 / 2.97 ( 1179) link_NAG-ASN : bond 0.00285 / 0.20 ( 12) link_NAG-ASN : angle 1.29887 / 0.94 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 223 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: A 106 LYS cc_start: 0.8469 (tttp) cc_final: 0.8229 (ttpp) REVERT: A 147 MET cc_start: 0.8005 (mtm) cc_final: 0.7762 (mtp) REVERT: A 176 GLU cc_start: 0.8078 (mp0) cc_final: 0.7227 (mp0) REVERT: A 194 GLU cc_start: 0.6833 (tm-30) cc_final: 0.6484 (tm-30) REVERT: A 197 SER cc_start: 0.8650 (p) cc_final: 0.8412 (m) REVERT: B 110 ARG cc_start: 0.7721 (ptm160) cc_final: 0.7401 (ptm160) REVERT: B 197 SER cc_start: 0.8660 (p) cc_final: 0.8457 (m) REVERT: C 148 ASN cc_start: 0.7262 (t0) cc_final: 0.6825 (p0) REVERT: C 176 GLU cc_start: 0.8229 (mp0) cc_final: 0.7444 (mp0) REVERT: C 181 GLU cc_start: 0.8172 (tt0) cc_final: 0.7802 (tt0) REVERT: C 188 ARG cc_start: 0.8380 (ttp-170) cc_final: 0.8123 (ttp-170) REVERT: C 194 GLU cc_start: 0.7016 (tm-30) cc_final: 0.6622 (tm-30) REVERT: C 248 LYS cc_start: 0.7625 (mmmm) cc_final: 0.7365 (mtpp) REVERT: C 271 ARG cc_start: 0.8685 (mtm180) cc_final: 0.8175 (mtm-85) REVERT: C 304 TRP cc_start: 0.8484 (m100) cc_final: 0.8154 (m100) REVERT: C 319 LYS cc_start: 0.8152 (tppt) cc_final: 0.7913 (ttmm) outliers start: 20 outliers final: 10 residues processed: 229 average time/residue: 0.5742 time to fit residues: 136.5023 Evaluate side-chains 223 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 213 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 315 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 56 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 71 optimal weight: 0.5980 chunk 77 optimal weight: 0.5980 chunk 68 optimal weight: 0.1980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 172 GLN A 293 GLN B 172 GLN B 186 GLN ** B 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 GLN C 186 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.138353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.119700 restraints weight = 9468.012| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.33 r_work: 0.3450 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 6810 Z= 0.197 Angle : 0.570 7.468 9258 Z= 0.296 Chirality : 0.045 0.204 1050 Planarity : 0.004 0.035 1158 Dihedral : 4.593 25.531 873 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.32 % Allowed : 23.33 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.47 (0.30), residues: 804 helix: 2.66 (0.29), residues: 279 sheet: 0.97 (0.28), residues: 315 loop : -1.42 (0.43), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 175 TYR 0.008 0.001 TYR B 119 PHE 0.020 0.002 PHE B 204 TRP 0.007 0.001 TRP B 230 HIS 0.004 0.001 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.20 ( 6798) covalent geometry : angle 0.56571 / 0.30 ( 9222) hydrogen bonds : bond 0.03571 / 2.46 ( 390) hydrogen bonds : angle 4.25461 / 2.95 ( 1179) link_NAG-ASN : bond 0.00263 / 0.19 ( 12) link_NAG-ASN : angle 1.28214 / 0.94 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 214 time to evaluate : 0.226 Fit side-chains revert: symmetry clash REVERT: A 106 LYS cc_start: 0.8464 (tttp) cc_final: 0.8222 (ttpp) REVERT: A 143 GLN cc_start: 0.8013 (mm110) cc_final: 0.7687 (mm110) REVERT: A 147 MET cc_start: 0.8009 (mtm) cc_final: 0.7775 (mtp) REVERT: A 176 GLU cc_start: 0.8032 (mp0) cc_final: 0.7169 (mp0) REVERT: A 180 ARG cc_start: 0.7958 (mtp180) cc_final: 0.7614 (mtp180) REVERT: A 194 GLU cc_start: 0.6855 (tm-30) cc_final: 0.6505 (tm-30) REVERT: A 197 SER cc_start: 0.8661 (p) cc_final: 0.8448 (m) REVERT: B 197 SER cc_start: 0.8652 (p) cc_final: 0.8452 (m) REVERT: B 279 GLN cc_start: 0.7746 (mt0) cc_final: 0.7496 (mt0) REVERT: C 148 ASN cc_start: 0.7228 (t0) cc_final: 0.6818 (p0) REVERT: C 176 GLU cc_start: 0.8218 (mp0) cc_final: 0.7380 (mp0) REVERT: C 181 GLU cc_start: 0.8156 (tt0) cc_final: 0.7757 (tt0) REVERT: C 188 ARG cc_start: 0.8386 (ttp-170) cc_final: 0.8112 (ttp-170) REVERT: C 194 GLU cc_start: 0.7041 (tm-30) cc_final: 0.6646 (tm-30) REVERT: C 248 LYS cc_start: 0.7614 (mmmm) cc_final: 0.7356 (mtpp) REVERT: C 304 TRP cc_start: 0.8485 (m100) cc_final: 0.8184 (m100) outliers start: 16 outliers final: 9 residues processed: 217 average time/residue: 0.5818 time to fit residues: 131.0027 Evaluate side-chains 219 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 210 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 315 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 69 optimal weight: 0.5980 chunk 50 optimal weight: 0.1980 chunk 28 optimal weight: 0.0980 chunk 5 optimal weight: 0.0870 chunk 27 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 overall best weight: 0.3358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 GLN ** B 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 GLN C 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.138988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.120450 restraints weight = 9485.884| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 2.33 r_work: 0.3463 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6810 Z= 0.149 Angle : 0.559 6.781 9258 Z= 0.290 Chirality : 0.045 0.206 1050 Planarity : 0.004 0.038 1158 Dihedral : 4.503 25.622 873 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.59 % Allowed : 24.49 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.49 (0.29), residues: 804 helix: 2.71 (0.29), residues: 279 sheet: 0.94 (0.27), residues: 315 loop : -1.42 (0.43), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 175 TYR 0.007 0.001 TYR B 111 PHE 0.020 0.002 PHE A 236 TRP 0.007 0.001 TRP A 304 HIS 0.004 0.001 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 ( 6798) covalent geometry : angle 0.55448 / 0.29 ( 9222) hydrogen bonds : bond 0.03360 / 2.32 ( 390) hydrogen bonds : angle 4.21122 / 2.91 ( 1179) link_NAG-ASN : bond 0.00263 / 0.18 ( 12) link_NAG-ASN : angle 1.24618 / 0.93 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 200 time to evaluate : 0.223 Fit side-chains revert: symmetry clash REVERT: A 106 LYS cc_start: 0.8479 (tttp) cc_final: 0.8210 (ttpp) REVERT: A 143 GLN cc_start: 0.8015 (mm110) cc_final: 0.7681 (mm110) REVERT: A 147 MET cc_start: 0.8008 (mtm) cc_final: 0.7782 (mtp) REVERT: A 180 ARG cc_start: 0.7946 (mtp180) cc_final: 0.7595 (mtp180) REVERT: A 194 GLU cc_start: 0.6799 (tm-30) cc_final: 0.6467 (tm-30) REVERT: B 110 ARG cc_start: 0.7671 (OUTLIER) cc_final: 0.7344 (ptm160) REVERT: C 148 ASN cc_start: 0.7184 (t0) cc_final: 0.6803 (p0) REVERT: C 176 GLU cc_start: 0.8170 (mp0) cc_final: 0.7283 (mp0) REVERT: C 181 GLU cc_start: 0.8104 (tt0) cc_final: 0.7682 (tt0) REVERT: C 188 ARG cc_start: 0.8377 (ttp-170) cc_final: 0.8108 (ttp-170) REVERT: C 194 GLU cc_start: 0.7061 (tm-30) cc_final: 0.6694 (tm-30) REVERT: C 248 LYS cc_start: 0.7600 (mmmm) cc_final: 0.7332 (mtpp) REVERT: C 271 ARG cc_start: 0.8686 (mtm180) cc_final: 0.8287 (mtm-85) REVERT: C 304 TRP cc_start: 0.8468 (m100) cc_final: 0.8163 (m100) REVERT: C 319 LYS cc_start: 0.8054 (tppt) cc_final: 0.7822 (ttmm) outliers start: 11 outliers final: 9 residues processed: 202 average time/residue: 0.6939 time to fit residues: 145.2453 Evaluate side-chains 209 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 199 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 110 ARG Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 315 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 15 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 chunk 52 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 GLN B 293 GLN C 186 GLN C 208 GLN C 212 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.137752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.119267 restraints weight = 9455.986| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.31 r_work: 0.3447 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 6810 Z= 0.235 Angle : 0.611 7.312 9258 Z= 0.314 Chirality : 0.046 0.214 1050 Planarity : 0.004 0.037 1158 Dihedral : 4.648 25.952 873 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.88 % Allowed : 24.20 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.42 (0.30), residues: 804 helix: 2.60 (0.30), residues: 279 sheet: 0.95 (0.28), residues: 315 loop : -1.44 (0.43), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 175 TYR 0.010 0.002 TYR B 119 PHE 0.025 0.002 PHE B 236 TRP 0.007 0.001 TRP B 230 HIS 0.003 0.001 HIS A 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00564 / 0.24 ( 6798) covalent geometry : angle 0.60690 / 0.31 ( 9222) hydrogen bonds : bond 0.03796 / 2.62 ( 390) hydrogen bonds : angle 4.31634 / 2.99 ( 1179) link_NAG-ASN : bond 0.00254 / 0.18 ( 12) link_NAG-ASN : angle 1.26075 / 0.93 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3644.81 seconds wall clock time: 62 minutes 41.78 seconds (3761.78 seconds total)