Starting phenix.real_space_refine on Thu Jul 24 23:15:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sqg_25384/07_2025/7sqg_25384.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sqg_25384/07_2025/7sqg_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7sqg_25384/07_2025/7sqg_25384.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sqg_25384/07_2025/7sqg_25384.map" model { file = "/net/cci-nas-00/data/ceres_data/7sqg_25384/07_2025/7sqg_25384.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sqg_25384/07_2025/7sqg_25384.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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 dihedrals: 12 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 dihedrals: 12 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 dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 5.63, per 1000 atoms: 0.85 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: 1.67 Conformation dependent library (CDL) restraints added in 974.9 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: 0.81 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: 2.02 Time building geometry restraints manager: 1.98 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 - 21.51: 3910 21.51 - 43.02: 199 43.02 - 64.53: 63 64.53 - 86.03: 7 86.03 - 107.54: 24 Dihedral angle restraints: 4203 sinusoidal: 1806 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 4200 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 5.060 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.890 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 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 : 17.267 107.543 2643 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.007 0.001 TRP B 304 HIS 0.001 0.001 HIS A 98 PHE 0.020 0.002 PHE A 219 TYR 0.009 0.001 TYR A 201 ARG 0.003 0.000 ARG A 110 Details of bonding type rmsd link_NAG-ASN : bond 0.00252 ( 12) link_NAG-ASN : angle 1.85381 ( 36) hydrogen bonds : bond 0.09118 ( 390) hydrogen bonds : angle 4.91090 ( 1179) covalent geometry : bond 0.00407 ( 6798) covalent geometry : angle 0.60470 ( 9222) *********************** 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 : 0.754 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: 0.6921 (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: 1.6059 time to fit residues: 433.7985 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 : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 68 optimal weight: 0.0670 chunk 61 optimal weight: 0.0000 chunk 34 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 41 optimal weight: 0.0970 chunk 32 optimal weight: 0.0470 chunk 63 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 overall best weight: 0.1818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3880 r_free = 0.3880 target = 0.139203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.121495 restraints weight = 9577.604| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.30 r_work: 0.3496 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 6810 Z= 0.119 Angle : 0.581 9.432 9258 Z= 0.286 Chirality : 0.044 0.188 1050 Planarity : 0.003 0.027 1158 Dihedral : 13.226 83.237 1125 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.46 % Allowed : 14.35 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.29), residues: 804 helix: 3.39 (0.28), residues: 258 sheet: 1.21 (0.29), residues: 297 loop : -1.27 (0.38), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 304 HIS 0.008 0.002 HIS C 98 PHE 0.021 0.002 PHE A 219 TYR 0.007 0.001 TYR C 111 ARG 0.004 0.001 ARG A 175 Details of bonding type rmsd link_NAG-ASN : bond 0.00367 ( 12) link_NAG-ASN : angle 2.40124 ( 36) hydrogen bonds : bond 0.03059 ( 390) hydrogen bonds : angle 4.14242 ( 1179) covalent geometry : bond 0.00269 ( 6798) covalent geometry : angle 0.56234 ( 9222) *********************** 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 245 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 228 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 LYS cc_start: 0.8411 (tttp) cc_final: 0.8175 (ttmm) REVERT: A 147 MET cc_start: 0.7761 (mtm) cc_final: 0.7511 (mtp) REVERT: A 175 ARG cc_start: 0.7758 (mtp85) cc_final: 0.7524 (mtp85) REVERT: A 176 GLU cc_start: 0.8032 (mp0) cc_final: 0.7302 (mp0) REVERT: A 180 ARG cc_start: 0.7901 (mtp180) cc_final: 0.7651 (mtp180) REVERT: A 181 GLU cc_start: 0.8073 (tt0) cc_final: 0.7607 (tt0) REVERT: A 206 SER cc_start: 0.8567 (m) cc_final: 0.8360 (t) REVERT: A 268 ILE cc_start: 0.8180 (mt) cc_final: 0.7927 (mt) REVERT: A 304 TRP cc_start: 0.8360 (m100) cc_final: 0.8138 (m100) REVERT: B 219 PHE cc_start: 0.8284 (t80) cc_final: 0.7796 (t80) REVERT: B 247 THR cc_start: 0.8141 (m) cc_final: 0.7941 (t) REVERT: B 271 ARG cc_start: 0.8715 (mtm180) cc_final: 0.8482 (mtm180) REVERT: C 92 PHE cc_start: 0.8645 (t80) cc_final: 0.8310 (t80) REVERT: C 148 ASN cc_start: 0.7022 (t0) cc_final: 0.6616 (p0) REVERT: C 176 GLU cc_start: 0.8118 (mp0) cc_final: 0.7226 (mp0) REVERT: C 181 GLU cc_start: 0.8045 (tt0) cc_final: 0.7607 (tt0) REVERT: C 188 ARG cc_start: 0.8264 (ttp-170) cc_final: 0.7988 (ttp-170) REVERT: C 194 GLU cc_start: 0.6937 (tm-30) cc_final: 0.6626 (tm-30) REVERT: C 219 PHE cc_start: 0.8379 (t80) cc_final: 0.8078 (t80) REVERT: C 271 ARG cc_start: 0.8658 (mtm180) cc_final: 0.8234 (mtm-85) REVERT: C 304 TRP cc_start: 0.8468 (m100) cc_final: 0.8172 (m100) outliers start: 17 outliers final: 9 residues processed: 230 average time/residue: 1.6450 time to fit residues: 391.5291 Evaluate side-chains 233 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 224 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 47 optimal weight: 0.0370 chunk 45 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 42 optimal weight: 0.3980 chunk 23 optimal weight: 0.4980 chunk 7 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN 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 B 296 GLN C 98 HIS C 124 GLN ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.139665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.121045 restraints weight = 9580.560| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.31 r_work: 0.3467 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6810 Z= 0.175 Angle : 0.599 8.379 9258 Z= 0.293 Chirality : 0.044 0.160 1050 Planarity : 0.004 0.029 1158 Dihedral : 9.667 58.091 1125 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.61 % Allowed : 20.72 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.29), residues: 804 helix: 3.24 (0.28), residues: 258 sheet: 0.89 (0.27), residues: 327 loop : -0.95 (0.42), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 230 HIS 0.009 0.002 HIS C 98 PHE 0.019 0.002 PHE B 204 TYR 0.010 0.001 TYR B 119 ARG 0.004 0.000 ARG C 93 Details of bonding type rmsd link_NAG-ASN : bond 0.00482 ( 12) link_NAG-ASN : angle 1.81483 ( 36) hydrogen bonds : bond 0.03383 ( 390) hydrogen bonds : angle 4.12607 ( 1179) covalent geometry : bond 0.00413 ( 6798) covalent geometry : angle 0.58939 ( 9222) *********************** 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 236 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 218 time to evaluate : 0.691 Fit side-chains revert: symmetry clash REVERT: A 129 LYS cc_start: 0.8533 (mtpt) cc_final: 0.8284 (mttt) REVERT: A 147 MET cc_start: 0.7897 (mtm) cc_final: 0.7658 (mtp) REVERT: A 175 ARG cc_start: 0.7841 (mtp85) cc_final: 0.7409 (mtp85) REVERT: A 176 GLU cc_start: 0.8156 (mp0) cc_final: 0.7179 (mp0) REVERT: A 181 GLU cc_start: 0.8131 (tt0) cc_final: 0.7790 (tt0) REVERT: A 194 GLU cc_start: 0.6583 (tm-30) cc_final: 0.6337 (tm-30) REVERT: B 180 ARG cc_start: 0.8053 (mtp180) cc_final: 0.7772 (mtp180) REVERT: B 247 THR cc_start: 0.8248 (m) cc_final: 0.8031 (t) REVERT: C 89 ILE cc_start: 0.8885 (mm) cc_final: 0.8612 (mt) REVERT: C 148 ASN cc_start: 0.7135 (t0) cc_final: 0.6722 (p0) REVERT: C 176 GLU cc_start: 0.8208 (mp0) cc_final: 0.7438 (mp0) REVERT: C 181 GLU cc_start: 0.8076 (tt0) cc_final: 0.7762 (tt0) REVERT: C 188 ARG cc_start: 0.8358 (ttp-170) cc_final: 0.8112 (ttp-170) REVERT: C 194 GLU cc_start: 0.6948 (tm-30) cc_final: 0.6628 (tm-30) REVERT: C 212 GLN cc_start: 0.7286 (mp10) cc_final: 0.7036 (mp10) REVERT: C 248 LYS cc_start: 0.7493 (tppp) cc_final: 0.7286 (mmmm) REVERT: C 271 ARG cc_start: 0.8708 (mtm180) cc_final: 0.8279 (mtm-85) REVERT: C 304 TRP cc_start: 0.8471 (m100) cc_final: 0.8124 (m100) REVERT: C 314 PHE cc_start: 0.8330 (m-10) cc_final: 0.8094 (m-10) outliers start: 18 outliers final: 9 residues processed: 222 average time/residue: 1.7432 time to fit residues: 402.9918 Evaluate side-chains 222 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 213 time to evaluate : 0.704 ------------------------------------------------------------------------------- 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 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 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 69 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 75 optimal weight: 0.2980 chunk 78 optimal weight: 0.3980 chunk 42 optimal weight: 0.8980 chunk 72 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN A 208 GLN A 266 ASN A 293 GLN B 172 GLN B 186 GLN B 293 GLN C 186 GLN C 266 ASN ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.138212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.119084 restraints weight = 9565.704| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 2.36 r_work: 0.3449 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6810 Z= 0.199 Angle : 0.596 7.441 9258 Z= 0.296 Chirality : 0.044 0.132 1050 Planarity : 0.004 0.028 1158 Dihedral : 7.788 59.630 1125 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.77 % Allowed : 20.87 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.29), residues: 804 helix: 3.16 (0.28), residues: 258 sheet: 1.04 (0.26), residues: 324 loop : -1.02 (0.42), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 239 HIS 0.003 0.001 HIS C 130 PHE 0.020 0.002 PHE B 204 TYR 0.010 0.001 TYR B 119 ARG 0.004 0.000 ARG A 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00430 ( 12) link_NAG-ASN : angle 1.88830 ( 36) hydrogen bonds : bond 0.03506 ( 390) hydrogen bonds : angle 4.19617 ( 1179) covalent geometry : bond 0.00473 ( 6798) covalent geometry : angle 0.58564 ( 9222) *********************** 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 249 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 223 time to evaluate : 0.791 Fit side-chains REVERT: A 129 LYS cc_start: 0.8559 (mtpt) cc_final: 0.8348 (mttt) REVERT: A 147 MET cc_start: 0.7940 (mtm) cc_final: 0.7684 (mtp) REVERT: A 180 ARG cc_start: 0.7973 (mtp180) cc_final: 0.7745 (mtp180) REVERT: A 194 GLU cc_start: 0.6683 (tm-30) cc_final: 0.6440 (tm-30) REVERT: B 181 GLU cc_start: 0.8266 (tt0) cc_final: 0.8040 (tt0) REVERT: B 247 THR cc_start: 0.8308 (m) cc_final: 0.8104 (t) REVERT: C 93 ARG cc_start: 0.7740 (mtm110) cc_final: 0.7532 (mtm110) REVERT: C 148 ASN cc_start: 0.7222 (t0) cc_final: 0.6800 (p0) REVERT: C 176 GLU cc_start: 0.8224 (mp0) cc_final: 0.7373 (mp0) REVERT: C 181 GLU cc_start: 0.8129 (tt0) cc_final: 0.7739 (tt0) REVERT: C 188 ARG cc_start: 0.8353 (ttp-170) cc_final: 0.8071 (ttp-170) REVERT: C 194 GLU cc_start: 0.6997 (tm-30) cc_final: 0.6649 (tm-30) REVERT: C 212 GLN cc_start: 0.7320 (mp10) cc_final: 0.7096 (mp10) REVERT: C 219 PHE cc_start: 0.8193 (t80) cc_final: 0.7949 (t80) REVERT: C 271 ARG cc_start: 0.8663 (mtm180) cc_final: 0.8196 (mtm-85) REVERT: C 304 TRP cc_start: 0.8488 (m100) cc_final: 0.8157 (m100) outliers start: 26 outliers final: 10 residues processed: 225 average time/residue: 1.6255 time to fit residues: 378.5958 Evaluate side-chains 232 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 222 time to evaluate : 0.776 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 47 optimal weight: 0.0570 chunk 69 optimal weight: 0.1980 chunk 28 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 52 optimal weight: 0.1980 chunk 18 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 74 optimal weight: 0.0040 chunk 29 optimal weight: 0.6980 overall best weight: 0.2110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 GLN B 186 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 = 0.3868 r_free = 0.3868 target = 0.140011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.121458 restraints weight = 9493.224| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.30 r_work: 0.3481 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6810 Z= 0.114 Angle : 0.540 7.353 9258 Z= 0.270 Chirality : 0.043 0.160 1050 Planarity : 0.004 0.029 1158 Dihedral : 6.404 44.475 1125 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.88 % Allowed : 22.75 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.29), residues: 804 helix: 3.30 (0.28), residues: 258 sheet: 1.08 (0.27), residues: 324 loop : -0.83 (0.42), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 304 HIS 0.002 0.001 HIS C 130 PHE 0.016 0.002 PHE C 204 TYR 0.007 0.001 TYR B 111 ARG 0.007 0.000 ARG A 175 Details of bonding type rmsd link_NAG-ASN : bond 0.00390 ( 12) link_NAG-ASN : angle 1.82020 ( 36) hydrogen bonds : bond 0.02951 ( 390) hydrogen bonds : angle 4.08205 ( 1179) covalent geometry : bond 0.00256 ( 6798) covalent geometry : angle 0.52863 ( 9222) *********************** 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 217 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 204 time to evaluate : 0.679 Fit side-chains revert: symmetry clash REVERT: A 106 LYS cc_start: 0.8439 (tttp) cc_final: 0.8208 (ttpp) REVERT: A 147 MET cc_start: 0.7925 (mtm) cc_final: 0.7680 (mtp) REVERT: A 194 GLU cc_start: 0.6645 (tm-30) cc_final: 0.6405 (tm-30) REVERT: B 206 SER cc_start: 0.8647 (m) cc_final: 0.8437 (t) REVERT: C 148 ASN cc_start: 0.7124 (t0) cc_final: 0.6776 (p0) REVERT: C 176 GLU cc_start: 0.8157 (mp0) cc_final: 0.7273 (mp0) REVERT: C 181 GLU cc_start: 0.8071 (tt0) cc_final: 0.7681 (tt0) REVERT: C 188 ARG cc_start: 0.8345 (ttp-170) cc_final: 0.8090 (ttp-170) REVERT: C 194 GLU cc_start: 0.7016 (tm-30) cc_final: 0.6698 (tm-30) REVERT: C 219 PHE cc_start: 0.8129 (t80) cc_final: 0.7905 (t80) REVERT: C 271 ARG cc_start: 0.8691 (mtm180) cc_final: 0.8233 (mtm-85) REVERT: C 304 TRP cc_start: 0.8458 (m100) cc_final: 0.8135 (m100) outliers start: 13 outliers final: 7 residues processed: 207 average time/residue: 1.6341 time to fit residues: 350.0933 Evaluate side-chains 209 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 202 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 322 GLU 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 59 optimal weight: 0.0980 chunk 28 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 41 optimal weight: 0.0870 chunk 79 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 GLN B 293 GLN C 186 GLN C 293 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.138572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.119745 restraints weight = 9471.938| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.31 r_work: 0.3452 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 6810 Z= 0.215 Angle : 0.586 7.483 9258 Z= 0.295 Chirality : 0.044 0.167 1050 Planarity : 0.004 0.032 1158 Dihedral : 5.816 34.223 1125 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.61 % Allowed : 22.32 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.29), residues: 804 helix: 2.79 (0.29), residues: 279 sheet: 1.01 (0.27), residues: 324 loop : -1.41 (0.44), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 230 HIS 0.003 0.001 HIS C 130 PHE 0.026 0.002 PHE A 219 TYR 0.009 0.002 TYR B 119 ARG 0.008 0.000 ARG A 175 Details of bonding type rmsd link_NAG-ASN : bond 0.00343 ( 12) link_NAG-ASN : angle 1.85086 ( 36) hydrogen bonds : bond 0.03478 ( 390) hydrogen bonds : angle 4.20078 ( 1179) covalent geometry : bond 0.00518 ( 6798) covalent geometry : angle 0.57597 ( 9222) *********************** 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 240 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 222 time to evaluate : 0.670 Fit side-chains revert: symmetry clash REVERT: A 106 LYS cc_start: 0.8475 (tttp) cc_final: 0.8239 (ttpp) REVERT: A 147 MET cc_start: 0.7992 (mtm) cc_final: 0.7754 (mtp) REVERT: A 176 GLU cc_start: 0.8097 (mp0) cc_final: 0.7189 (mp0) REVERT: A 180 ARG cc_start: 0.7952 (mtp180) cc_final: 0.7612 (mtp180) REVERT: A 181 GLU cc_start: 0.8162 (tt0) cc_final: 0.7509 (tt0) REVERT: A 194 GLU cc_start: 0.6722 (tm-30) cc_final: 0.6390 (tm-30) REVERT: A 197 SER cc_start: 0.8658 (p) cc_final: 0.8410 (m) REVERT: A 248 LYS cc_start: 0.7537 (tppp) cc_final: 0.7307 (mtpt) REVERT: B 247 THR cc_start: 0.8387 (m) cc_final: 0.8141 (t) REVERT: C 93 ARG cc_start: 0.7879 (mtt90) cc_final: 0.7619 (mtm110) REVERT: C 148 ASN cc_start: 0.7241 (t0) cc_final: 0.6828 (p0) REVERT: C 176 GLU cc_start: 0.8219 (mp0) cc_final: 0.7446 (mp0) REVERT: C 180 ARG cc_start: 0.8121 (mtp180) cc_final: 0.7748 (mtp180) REVERT: C 181 GLU cc_start: 0.8136 (tt0) cc_final: 0.7789 (tt0) REVERT: C 188 ARG cc_start: 0.8353 (ttp-170) cc_final: 0.8091 (ttp-170) REVERT: C 194 GLU cc_start: 0.7007 (tm-30) cc_final: 0.6676 (tm-30) REVERT: C 248 LYS cc_start: 0.7577 (mmmm) cc_final: 0.7285 (ttmm) REVERT: C 271 ARG cc_start: 0.8692 (mtm180) cc_final: 0.8190 (mtm-85) REVERT: C 304 TRP cc_start: 0.8476 (m100) cc_final: 0.8154 (m100) outliers start: 18 outliers final: 8 residues processed: 226 average time/residue: 1.5182 time to fit residues: 356.0989 Evaluate side-chains 222 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 214 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 315 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 45 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 50 optimal weight: 0.5980 chunk 58 optimal weight: 0.0970 chunk 34 optimal weight: 0.0050 chunk 2 optimal weight: 0.4980 chunk 46 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 overall best weight: 0.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3844 r_free = 0.3844 target = 0.139207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.120984 restraints weight = 9515.965| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.27 r_work: 0.3459 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6810 Z= 0.151 Angle : 0.550 7.519 9258 Z= 0.279 Chirality : 0.044 0.180 1050 Planarity : 0.004 0.032 1158 Dihedral : 5.167 31.493 1125 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.46 % Allowed : 23.04 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.29), residues: 804 helix: 2.83 (0.29), residues: 279 sheet: 0.93 (0.27), residues: 324 loop : -1.39 (0.43), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 304 HIS 0.002 0.001 HIS A 98 PHE 0.024 0.002 PHE A 219 TYR 0.006 0.001 TYR B 111 ARG 0.008 0.000 ARG A 175 Details of bonding type rmsd link_NAG-ASN : bond 0.00330 ( 12) link_NAG-ASN : angle 1.75287 ( 36) hydrogen bonds : bond 0.03205 ( 390) hydrogen bonds : angle 4.15805 ( 1179) covalent geometry : bond 0.00352 ( 6798) covalent geometry : angle 0.53978 ( 9222) *********************** 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 236 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 219 time to evaluate : 0.746 Fit side-chains revert: symmetry clash REVERT: A 106 LYS cc_start: 0.8444 (tttp) cc_final: 0.8210 (ttpp) REVERT: A 143 GLN cc_start: 0.8011 (mm110) cc_final: 0.7726 (mm110) REVERT: A 147 MET cc_start: 0.7921 (mtm) cc_final: 0.7691 (mtp) REVERT: A 180 ARG cc_start: 0.7962 (mtp180) cc_final: 0.7620 (mtp180) REVERT: A 194 GLU cc_start: 0.6720 (tm-30) cc_final: 0.6406 (tm-30) REVERT: A 197 SER cc_start: 0.8658 (p) cc_final: 0.8432 (m) REVERT: A 248 LYS cc_start: 0.7539 (tppp) cc_final: 0.7318 (mtpt) REVERT: A 268 ILE cc_start: 0.7942 (mm) cc_final: 0.7717 (mt) REVERT: B 110 ARG cc_start: 0.7549 (ptm160) cc_final: 0.7223 (ptm160) REVERT: B 247 THR cc_start: 0.8395 (m) cc_final: 0.8128 (t) REVERT: C 93 ARG cc_start: 0.7818 (mtt90) cc_final: 0.7587 (mtm110) REVERT: C 148 ASN cc_start: 0.7195 (t0) cc_final: 0.6856 (p0) REVERT: C 176 GLU cc_start: 0.8148 (mp0) cc_final: 0.7278 (mp0) REVERT: C 181 GLU cc_start: 0.8077 (tt0) cc_final: 0.7655 (tt0) REVERT: C 188 ARG cc_start: 0.8349 (ttp-170) cc_final: 0.8094 (ttp-170) REVERT: C 194 GLU cc_start: 0.7080 (tm-30) cc_final: 0.6741 (tm-30) REVERT: C 248 LYS cc_start: 0.7598 (mmmm) cc_final: 0.7357 (mtpp) REVERT: C 271 ARG cc_start: 0.8722 (mtm180) cc_final: 0.8231 (mtm-85) REVERT: C 304 TRP cc_start: 0.8448 (m100) cc_final: 0.8131 (m100) REVERT: C 319 LYS cc_start: 0.8106 (tppt) cc_final: 0.7858 (ttmm) outliers start: 17 outliers final: 4 residues processed: 222 average time/residue: 1.5577 time to fit residues: 358.9688 Evaluate side-chains 222 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 218 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain B residue 186 GLN 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 37 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 6 optimal weight: 0.0980 chunk 32 optimal weight: 0.2980 chunk 57 optimal weight: 0.9990 chunk 63 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 GLN B 172 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 = 0.3834 r_free = 0.3834 target = 0.138346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.119980 restraints weight = 9493.140| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.27 r_work: 0.3445 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 6810 Z= 0.191 Angle : 0.568 7.118 9258 Z= 0.290 Chirality : 0.045 0.183 1050 Planarity : 0.004 0.032 1158 Dihedral : 4.818 29.462 1125 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.88 % Allowed : 24.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.30), residues: 804 helix: 2.76 (0.29), residues: 279 sheet: 0.96 (0.27), residues: 324 loop : -1.42 (0.43), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 230 HIS 0.003 0.001 HIS C 130 PHE 0.026 0.002 PHE A 219 TYR 0.009 0.001 TYR C 201 ARG 0.007 0.001 ARG A 175 Details of bonding type rmsd link_NAG-ASN : bond 0.00312 ( 12) link_NAG-ASN : angle 1.68666 ( 36) hydrogen bonds : bond 0.03514 ( 390) hydrogen bonds : angle 4.22542 ( 1179) covalent geometry : bond 0.00453 ( 6798) covalent geometry : angle 0.55951 ( 9222) *********************** 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 230 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 217 time to evaluate : 0.709 Fit side-chains revert: symmetry clash REVERT: A 106 LYS cc_start: 0.8461 (tttp) cc_final: 0.8196 (ttpp) REVERT: A 143 GLN cc_start: 0.8013 (mm110) cc_final: 0.7695 (mm110) REVERT: A 147 MET cc_start: 0.7961 (mtm) cc_final: 0.7735 (mtp) REVERT: A 176 GLU cc_start: 0.8001 (mp0) cc_final: 0.7151 (mp0) REVERT: A 180 ARG cc_start: 0.7970 (mtp180) cc_final: 0.7635 (mtp180) REVERT: A 248 LYS cc_start: 0.7585 (tppp) cc_final: 0.7378 (mtpt) REVERT: A 268 ILE cc_start: 0.8241 (mm) cc_final: 0.8025 (mt) REVERT: B 110 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.7336 (ptm160) REVERT: B 129 LYS cc_start: 0.8607 (tttm) cc_final: 0.8403 (tttp) REVERT: B 247 THR cc_start: 0.8397 (m) cc_final: 0.8129 (t) REVERT: C 148 ASN cc_start: 0.7219 (t0) cc_final: 0.6864 (p0) REVERT: C 176 GLU cc_start: 0.8176 (mp0) cc_final: 0.7386 (mp0) REVERT: C 180 ARG cc_start: 0.7986 (mtp180) cc_final: 0.7762 (mtp180) REVERT: C 181 GLU cc_start: 0.8127 (tt0) cc_final: 0.7764 (tt0) REVERT: C 188 ARG cc_start: 0.8361 (ttp-170) cc_final: 0.8095 (ttp-170) REVERT: C 194 GLU cc_start: 0.7078 (tm-30) cc_final: 0.6740 (tm-30) REVERT: C 248 LYS cc_start: 0.7609 (mmmm) cc_final: 0.7398 (mtpp) REVERT: C 304 TRP cc_start: 0.8461 (m100) cc_final: 0.8172 (m100) outliers start: 13 outliers final: 8 residues processed: 220 average time/residue: 2.1558 time to fit residues: 491.7096 Evaluate side-chains 223 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 214 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain B residue 110 ARG Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 186 GLN Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 322 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 26 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 71 optimal weight: 0.0980 chunk 48 optimal weight: 0.2980 chunk 64 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 GLN B 172 GLN ** B 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 GLN C 186 GLN C 279 GLN C 293 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.137758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.119407 restraints weight = 9562.896| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.27 r_work: 0.3440 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 6810 Z= 0.214 Angle : 0.586 7.498 9258 Z= 0.300 Chirality : 0.045 0.220 1050 Planarity : 0.004 0.036 1158 Dihedral : 4.701 28.146 1125 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.61 % Allowed : 23.77 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.29), residues: 804 helix: 2.63 (0.29), residues: 279 sheet: 1.03 (0.27), residues: 321 loop : -1.55 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 230 HIS 0.003 0.001 HIS C 130 PHE 0.023 0.002 PHE A 219 TYR 0.009 0.001 TYR B 119 ARG 0.008 0.000 ARG A 175 Details of bonding type rmsd link_NAG-ASN : bond 0.00285 ( 12) link_NAG-ASN : angle 1.63679 ( 36) hydrogen bonds : bond 0.03642 ( 390) hydrogen bonds : angle 4.27978 ( 1179) covalent geometry : bond 0.00512 ( 6798) covalent geometry : angle 0.57864 ( 9222) *********************** 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 228 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 210 time to evaluate : 0.865 Fit side-chains revert: symmetry clash REVERT: A 106 LYS cc_start: 0.8454 (tttp) cc_final: 0.8200 (ttpp) REVERT: A 143 GLN cc_start: 0.8000 (mm110) cc_final: 0.7675 (mm110) REVERT: A 147 MET cc_start: 0.7971 (mtm) cc_final: 0.7746 (mtp) REVERT: A 176 GLU cc_start: 0.7999 (mp0) cc_final: 0.7149 (mp0) REVERT: A 180 ARG cc_start: 0.7973 (mtp180) cc_final: 0.7628 (mtp180) REVERT: B 110 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.7509 (ptm160) REVERT: B 129 LYS cc_start: 0.8611 (tttm) cc_final: 0.8397 (tttp) REVERT: C 148 ASN cc_start: 0.7226 (t0) cc_final: 0.6877 (p0) REVERT: C 176 GLU cc_start: 0.8168 (mp0) cc_final: 0.7361 (mp0) REVERT: C 180 ARG cc_start: 0.7991 (mtp180) cc_final: 0.7767 (mtp180) REVERT: C 181 GLU cc_start: 0.8133 (tt0) cc_final: 0.7741 (tt0) REVERT: C 188 ARG cc_start: 0.8371 (ttp-170) cc_final: 0.8111 (ttp-170) REVERT: C 194 GLU cc_start: 0.7081 (tm-30) cc_final: 0.6739 (tm-30) REVERT: C 248 LYS cc_start: 0.7614 (mmmm) cc_final: 0.7408 (mtpp) REVERT: C 271 ARG cc_start: 0.8731 (mtm180) cc_final: 0.8344 (mtm-85) REVERT: C 304 TRP cc_start: 0.8471 (m100) cc_final: 0.8177 (m100) outliers start: 18 outliers final: 10 residues processed: 216 average time/residue: 1.6299 time to fit residues: 365.2730 Evaluate side-chains 220 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 209 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 110 ARG Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 186 GLN 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 294 LYS 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 50 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 78 optimal weight: 0.7980 chunk 42 optimal weight: 0.0980 chunk 36 optimal weight: 0.8980 chunk 80 optimal weight: 0.4980 chunk 68 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 C 293 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.137701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.119422 restraints weight = 9647.090| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.28 r_work: 0.3442 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 6810 Z= 0.204 Angle : 0.585 7.228 9258 Z= 0.301 Chirality : 0.046 0.229 1050 Planarity : 0.004 0.035 1158 Dihedral : 4.586 27.167 1125 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.59 % Allowed : 24.64 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.30), residues: 804 helix: 2.59 (0.29), residues: 279 sheet: 1.04 (0.27), residues: 321 loop : -1.58 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 230 HIS 0.003 0.001 HIS B 98 PHE 0.022 0.002 PHE A 219 TYR 0.007 0.001 TYR B 119 ARG 0.010 0.001 ARG C 93 Details of bonding type rmsd link_NAG-ASN : bond 0.00274 ( 12) link_NAG-ASN : angle 1.55716 ( 36) hydrogen bonds : bond 0.03608 ( 390) hydrogen bonds : angle 4.30804 ( 1179) covalent geometry : bond 0.00485 ( 6798) covalent geometry : angle 0.57846 ( 9222) ********************** 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 219 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 208 time to evaluate : 0.727 Fit side-chains revert: symmetry clash REVERT: A 106 LYS cc_start: 0.8453 (tttp) cc_final: 0.8203 (ttpp) REVERT: A 122 GLN cc_start: 0.8172 (mm-40) cc_final: 0.7971 (mm-40) REVERT: A 143 GLN cc_start: 0.8002 (mm110) cc_final: 0.7657 (mm110) REVERT: A 147 MET cc_start: 0.7968 (mtm) cc_final: 0.7758 (mtp) REVERT: A 176 GLU cc_start: 0.7980 (mp0) cc_final: 0.7132 (mp0) REVERT: A 180 ARG cc_start: 0.7982 (mtp180) cc_final: 0.7699 (mtp180) REVERT: B 129 LYS cc_start: 0.8615 (tttm) cc_final: 0.8400 (tttp) REVERT: B 271 ARG cc_start: 0.8816 (mtm180) cc_final: 0.8583 (mtm-85) REVERT: C 148 ASN cc_start: 0.7223 (t0) cc_final: 0.6879 (p0) REVERT: C 176 GLU cc_start: 0.8192 (mp0) cc_final: 0.7378 (mp0) REVERT: C 180 ARG cc_start: 0.7978 (mtp180) cc_final: 0.7770 (mtp180) REVERT: C 181 GLU cc_start: 0.8141 (tt0) cc_final: 0.7750 (tt0) REVERT: C 188 ARG cc_start: 0.8370 (ttp-170) cc_final: 0.8107 (ttp-170) REVERT: C 194 GLU cc_start: 0.7090 (tm-30) cc_final: 0.6707 (tm-30) REVERT: C 248 LYS cc_start: 0.7600 (mmmm) cc_final: 0.7391 (mtpp) REVERT: C 271 ARG cc_start: 0.8734 (mtm180) cc_final: 0.8279 (mtm-85) REVERT: C 304 TRP cc_start: 0.8479 (m100) cc_final: 0.8185 (m100) outliers start: 11 outliers final: 10 residues processed: 210 average time/residue: 1.8773 time to fit residues: 408.7814 Evaluate side-chains 217 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 207 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain B residue 110 ARG Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 186 GLN 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 294 LYS 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 46 optimal weight: 0.4980 chunk 68 optimal weight: 0.0270 chunk 61 optimal weight: 0.0000 chunk 64 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 21 optimal weight: 0.0970 chunk 74 optimal weight: 0.7980 chunk 80 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 50 optimal weight: 0.0980 overall best weight: 0.1440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.139651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.121598 restraints weight = 9672.365| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.28 r_work: 0.3473 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6810 Z= 0.112 Angle : 0.542 6.993 9258 Z= 0.282 Chirality : 0.044 0.229 1050 Planarity : 0.004 0.035 1158 Dihedral : 4.314 25.673 1125 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.59 % Allowed : 25.07 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.29), residues: 804 helix: 2.71 (0.29), residues: 279 sheet: 1.04 (0.27), residues: 321 loop : -1.48 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 304 HIS 0.003 0.001 HIS B 98 PHE 0.023 0.002 PHE A 219 TYR 0.006 0.001 TYR B 111 ARG 0.009 0.001 ARG C 93 Details of bonding type rmsd link_NAG-ASN : bond 0.00278 ( 12) link_NAG-ASN : angle 1.48409 ( 36) hydrogen bonds : bond 0.03102 ( 390) hydrogen bonds : angle 4.17019 ( 1179) covalent geometry : bond 0.00251 ( 6798) covalent geometry : angle 0.53487 ( 9222) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8590.91 seconds wall clock time: 150 minutes 8.52 seconds (9008.52 seconds total)