Starting phenix.real_space_refine on Fri Dec 27 21:46:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sqg_25384/12_2024/7sqg_25384.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sqg_25384/12_2024/7sqg_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_25384/12_2024/7sqg_25384.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sqg_25384/12_2024/7sqg_25384.map" model { file = "/net/cci-nas-00/data/ceres_data/7sqg_25384/12_2024/7sqg_25384.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sqg_25384/12_2024/7sqg_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-5532/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: 4.82, per 1000 atoms: 0.73 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: 1.56 Conformation dependent library (CDL) restraints added in 987.8 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: 0.91 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: 2.14 Time building geometry restraints manager: 1.82 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: 0.00 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: 3.760 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: 19.900 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 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:14.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.810 ------------------------------------------------------------------------------- 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 6798 Z= 0.266 Angle : 0.605 4.844 9222 Z= 0.340 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 *********************** 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 : 0.771 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: 1.6535 time to fit residues: 446.7679 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 : 0.822 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 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 6798 Z= 0.174 Angle : 0.562 6.321 9222 Z= 0.282 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 *********************** 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 : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.7329 (ttt) cc_final: 0.7014 (ttt) REVERT: A 94 GLU cc_start: 0.6924 (tp30) cc_final: 0.6609 (tp30) REVERT: A 97 LYS cc_start: 0.7664 (OUTLIER) cc_final: 0.7389 (mtpm) REVERT: A 106 LYS cc_start: 0.7794 (tttp) cc_final: 0.7389 (ttmm) REVERT: A 147 MET cc_start: 0.7519 (mtm) cc_final: 0.7296 (mtp) REVERT: A 175 ARG cc_start: 0.7286 (mtp85) cc_final: 0.7021 (mtp85) REVERT: A 176 GLU cc_start: 0.7487 (mp0) cc_final: 0.6636 (mp0) REVERT: A 180 ARG cc_start: 0.7116 (mtp180) cc_final: 0.6842 (mtp180) REVERT: A 181 GLU cc_start: 0.7740 (tt0) cc_final: 0.7282 (tt0) REVERT: A 206 SER cc_start: 0.8025 (m) cc_final: 0.7693 (t) REVERT: A 257 GLU cc_start: 0.7451 (pt0) cc_final: 0.7228 (pt0) REVERT: A 268 ILE cc_start: 0.7863 (mt) cc_final: 0.7600 (mt) REVERT: A 294 LYS cc_start: 0.7549 (mttt) cc_final: 0.7348 (mttp) REVERT: A 304 TRP cc_start: 0.7424 (m100) cc_final: 0.7023 (m100) REVERT: B 94 GLU cc_start: 0.6949 (tp30) cc_final: 0.6727 (tp30) REVERT: B 219 PHE cc_start: 0.7921 (t80) cc_final: 0.7585 (t80) REVERT: B 247 THR cc_start: 0.7485 (m) cc_final: 0.7190 (t) REVERT: B 271 ARG cc_start: 0.8189 (mtm180) cc_final: 0.7976 (mtm180) REVERT: C 92 PHE cc_start: 0.7540 (t80) cc_final: 0.7242 (t80) REVERT: C 93 ARG cc_start: 0.6667 (mtt180) cc_final: 0.6352 (mtt180) REVERT: C 106 LYS cc_start: 0.7763 (tttp) cc_final: 0.7376 (tttp) REVERT: C 124 GLN cc_start: 0.7531 (pt0) cc_final: 0.7322 (pt0) REVERT: C 148 ASN cc_start: 0.6375 (t0) cc_final: 0.6174 (p0) REVERT: C 176 GLU cc_start: 0.7497 (mp0) cc_final: 0.6443 (mp0) REVERT: C 179 LYS cc_start: 0.8256 (mtpp) cc_final: 0.8035 (mtmt) REVERT: C 181 GLU cc_start: 0.7727 (tt0) cc_final: 0.7250 (tt0) REVERT: C 188 ARG cc_start: 0.7557 (ttp-170) cc_final: 0.7125 (ttp-170) REVERT: C 194 GLU cc_start: 0.6870 (tm-30) cc_final: 0.6453 (tm-30) REVERT: C 219 PHE cc_start: 0.7987 (t80) cc_final: 0.7660 (t80) REVERT: C 271 ARG cc_start: 0.8048 (mtm180) cc_final: 0.7626 (mtm-85) REVERT: C 294 LYS cc_start: 0.7807 (mttt) cc_final: 0.7527 (mttp) REVERT: C 299 VAL cc_start: 0.8434 (t) cc_final: 0.8127 (p) REVERT: C 304 TRP cc_start: 0.7671 (m100) cc_final: 0.7147 (m100) outliers start: 17 outliers final: 9 residues processed: 230 average time/residue: 1.6594 time to fit residues: 395.2393 Evaluate side-chains 234 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 224 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LYS 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 40 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 65 optimal weight: 0.3980 chunk 25 optimal weight: 0.2980 chunk 59 optimal weight: 0.0980 chunk 72 optimal weight: 0.5980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 B 296 GLN C 98 HIS C 172 GLN C 266 ASN ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6798 Z= 0.252 Angle : 0.578 8.277 9222 Z= 0.285 Chirality : 0.044 0.158 1050 Planarity : 0.003 0.028 1158 Dihedral : 9.389 54.965 1125 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.32 % Allowed : 20.29 % Favored : 77.39 % 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: 3.30 (0.28), residues: 258 sheet: 0.90 (0.27), residues: 327 loop : -0.93 (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 0.018 0.002 PHE B 204 TYR 0.009 0.001 TYR B 119 ARG 0.004 0.000 ARG A 175 *********************** 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 234 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 218 time to evaluate : 0.773 Fit side-chains revert: symmetry clash REVERT: A 78 MET cc_start: 0.7313 (ttt) cc_final: 0.7031 (ttt) REVERT: A 93 ARG cc_start: 0.6731 (mtt-85) cc_final: 0.6460 (mmt-90) REVERT: A 94 GLU cc_start: 0.6976 (tp30) cc_final: 0.6732 (tp30) REVERT: A 97 LYS cc_start: 0.7703 (mtpm) cc_final: 0.7488 (mtpp) REVERT: A 106 LYS cc_start: 0.7852 (tttp) cc_final: 0.7467 (tttp) REVERT: A 129 LYS cc_start: 0.8226 (mtpt) cc_final: 0.7911 (mttt) REVERT: A 147 MET cc_start: 0.7581 (mtm) cc_final: 0.7363 (mtp) REVERT: A 175 ARG cc_start: 0.7311 (mtp85) cc_final: 0.6974 (mtp85) REVERT: A 176 GLU cc_start: 0.7545 (mp0) cc_final: 0.6501 (mp0) REVERT: A 181 GLU cc_start: 0.7748 (tt0) cc_final: 0.7467 (tt0) REVERT: A 194 GLU cc_start: 0.6489 (tm-30) cc_final: 0.6202 (tm-30) REVERT: A 197 SER cc_start: 0.8372 (OUTLIER) cc_final: 0.8147 (p) REVERT: A 206 SER cc_start: 0.8082 (m) cc_final: 0.7744 (t) REVERT: A 294 LYS cc_start: 0.7631 (mttt) cc_final: 0.7380 (mttp) REVERT: B 94 GLU cc_start: 0.6939 (tp30) cc_final: 0.6699 (tp30) REVERT: B 106 LYS cc_start: 0.8017 (tttm) cc_final: 0.7810 (ttpp) REVERT: B 180 ARG cc_start: 0.7073 (mtp180) cc_final: 0.6720 (mtp180) REVERT: B 247 THR cc_start: 0.7582 (m) cc_final: 0.7259 (t) REVERT: C 93 ARG cc_start: 0.6802 (mtt180) cc_final: 0.6460 (mtt180) REVERT: C 106 LYS cc_start: 0.7876 (tttp) cc_final: 0.7631 (tttp) REVERT: C 124 GLN cc_start: 0.7586 (pt0) cc_final: 0.7252 (pt0) REVERT: C 176 GLU cc_start: 0.7503 (mp0) cc_final: 0.6481 (mp0) REVERT: C 181 GLU cc_start: 0.7714 (tt0) cc_final: 0.7341 (tt0) REVERT: C 188 ARG cc_start: 0.7517 (ttp-170) cc_final: 0.7049 (ttp-170) REVERT: C 194 GLU cc_start: 0.6877 (tm-30) cc_final: 0.6453 (tm-30) REVERT: C 212 GLN cc_start: 0.7139 (mp10) cc_final: 0.6638 (mp10) REVERT: C 248 LYS cc_start: 0.7145 (tppp) cc_final: 0.6909 (mmmm) REVERT: C 271 ARG cc_start: 0.8098 (mtm180) cc_final: 0.7666 (mtm-85) REVERT: C 299 VAL cc_start: 0.8536 (t) cc_final: 0.8266 (p) REVERT: C 304 TRP cc_start: 0.7623 (m100) cc_final: 0.7042 (m100) outliers start: 16 outliers final: 9 residues processed: 222 average time/residue: 1.6642 time to fit residues: 382.5385 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 : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 197 SER 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 55 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 35 optimal weight: 0.0370 chunk 49 optimal weight: 0.2980 chunk 73 optimal weight: 0.9980 chunk 78 optimal weight: 0.1980 chunk 70 optimal weight: 0.9990 chunk 21 optimal weight: 0.1980 chunk 65 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 overall best weight: 0.2658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN B 172 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6798 Z= 0.193 Angle : 0.555 7.213 9222 Z= 0.276 Chirality : 0.043 0.133 1050 Planarity : 0.003 0.027 1158 Dihedral : 8.062 58.874 1125 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.46 % Allowed : 21.30 % Favored : 76.23 % 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: 1.96 (0.29), residues: 804 helix: 3.37 (0.28), residues: 258 sheet: 1.03 (0.27), residues: 324 loop : -0.88 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 304 HIS 0.002 0.001 HIS A 130 PHE 0.015 0.001 PHE C 204 TYR 0.006 0.001 TYR B 111 ARG 0.003 0.000 ARG B 110 *********************** 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 234 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 217 time to evaluate : 0.761 Fit side-chains revert: symmetry clash REVERT: A 78 MET cc_start: 0.7352 (ttt) cc_final: 0.7147 (ttt) REVERT: A 93 ARG cc_start: 0.6757 (mtt-85) cc_final: 0.6479 (mmt-90) REVERT: A 94 GLU cc_start: 0.6944 (tp30) cc_final: 0.6726 (tp30) REVERT: A 97 LYS cc_start: 0.7706 (mtpm) cc_final: 0.7490 (mtpp) REVERT: A 129 LYS cc_start: 0.8232 (mtpt) cc_final: 0.7937 (mttt) REVERT: A 147 MET cc_start: 0.7598 (mtm) cc_final: 0.7352 (mtp) REVERT: A 175 ARG cc_start: 0.7251 (mtp85) cc_final: 0.6947 (mtp85) REVERT: A 176 GLU cc_start: 0.7510 (mp0) cc_final: 0.6482 (mp0) REVERT: A 180 ARG cc_start: 0.7217 (mtp180) cc_final: 0.7003 (mtp180) REVERT: A 181 GLU cc_start: 0.7722 (tt0) cc_final: 0.7427 (tt0) REVERT: A 194 GLU cc_start: 0.6477 (tm-30) cc_final: 0.6051 (tm-30) REVERT: A 206 SER cc_start: 0.8082 (m) cc_final: 0.7727 (t) REVERT: A 294 LYS cc_start: 0.7634 (mttt) cc_final: 0.7384 (mttp) REVERT: B 94 GLU cc_start: 0.6958 (tp30) cc_final: 0.6708 (tp30) REVERT: B 106 LYS cc_start: 0.8046 (tttm) cc_final: 0.7824 (ttpp) REVERT: B 180 ARG cc_start: 0.7065 (mtp180) cc_final: 0.6693 (mtp180) REVERT: B 247 THR cc_start: 0.7595 (m) cc_final: 0.7266 (t) REVERT: B 299 VAL cc_start: 0.8611 (t) cc_final: 0.8365 (p) REVERT: C 93 ARG cc_start: 0.6775 (mtt180) cc_final: 0.6488 (mtt180) REVERT: C 124 GLN cc_start: 0.7589 (pt0) cc_final: 0.7243 (pt0) REVERT: C 176 GLU cc_start: 0.7495 (mp0) cc_final: 0.6403 (mp0) REVERT: C 181 GLU cc_start: 0.7691 (tt0) cc_final: 0.7251 (tt0) REVERT: C 188 ARG cc_start: 0.7519 (ttp-170) cc_final: 0.7045 (ttp-170) REVERT: C 194 GLU cc_start: 0.6897 (tm-30) cc_final: 0.6475 (tm-30) REVERT: C 212 GLN cc_start: 0.7113 (mp10) cc_final: 0.6762 (mp10) REVERT: C 248 LYS cc_start: 0.7167 (tppp) cc_final: 0.6934 (mmmm) REVERT: C 271 ARG cc_start: 0.8094 (mtm180) cc_final: 0.7620 (mtm-85) REVERT: C 299 VAL cc_start: 0.8572 (t) cc_final: 0.8307 (p) REVERT: C 304 TRP cc_start: 0.7621 (m100) cc_final: 0.7034 (m100) outliers start: 17 outliers final: 7 residues processed: 219 average time/residue: 1.6801 time to fit residues: 380.8389 Evaluate side-chains 223 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 216 time to evaluate : 0.777 ------------------------------------------------------------------------------- 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 315 LEU 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 315 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 1 optimal weight: 0.7980 chunk 58 optimal weight: 0.0670 chunk 32 optimal weight: 0.0470 chunk 66 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 70 optimal weight: 0.4980 chunk 19 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 overall best weight: 0.3816 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6798 Z= 0.242 Angle : 0.552 7.152 9222 Z= 0.278 Chirality : 0.043 0.135 1050 Planarity : 0.004 0.034 1158 Dihedral : 6.525 43.738 1125 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.75 % Allowed : 20.72 % 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 (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: 1.96 (0.29), residues: 804 helix: 3.35 (0.28), residues: 258 sheet: 1.02 (0.27), residues: 327 loop : -0.85 (0.42), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 239 HIS 0.002 0.001 HIS C 130 PHE 0.018 0.002 PHE B 204 TYR 0.008 0.001 TYR B 111 ARG 0.003 0.000 ARG B 271 *********************** 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 234 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 215 time to evaluate : 0.754 Fit side-chains revert: symmetry clash REVERT: A 78 MET cc_start: 0.7308 (ttt) cc_final: 0.7097 (ttt) REVERT: A 129 LYS cc_start: 0.8238 (mtpt) cc_final: 0.7984 (mttt) REVERT: A 147 MET cc_start: 0.7626 (mtm) cc_final: 0.7395 (mtp) REVERT: A 194 GLU cc_start: 0.6488 (tm-30) cc_final: 0.6071 (tm-30) REVERT: A 206 SER cc_start: 0.8096 (m) cc_final: 0.7750 (t) REVERT: A 294 LYS cc_start: 0.7661 (mttt) cc_final: 0.7406 (mttp) REVERT: A 299 VAL cc_start: 0.8564 (t) cc_final: 0.8296 (p) REVERT: B 94 GLU cc_start: 0.6923 (tp30) cc_final: 0.6670 (tp30) REVERT: B 106 LYS cc_start: 0.8035 (tttm) cc_final: 0.7793 (ttpp) REVERT: B 181 GLU cc_start: 0.7877 (tt0) cc_final: 0.7564 (tt0) REVERT: B 299 VAL cc_start: 0.8644 (t) cc_final: 0.8403 (p) REVERT: C 93 ARG cc_start: 0.6813 (mtt180) cc_final: 0.6502 (mtt180) REVERT: C 124 GLN cc_start: 0.7563 (pt0) cc_final: 0.7178 (pt0) REVERT: C 176 GLU cc_start: 0.7494 (mp0) cc_final: 0.6462 (mp0) REVERT: C 181 GLU cc_start: 0.7721 (tt0) cc_final: 0.7340 (tt0) REVERT: C 188 ARG cc_start: 0.7529 (ttp-170) cc_final: 0.7011 (ttp-170) REVERT: C 194 GLU cc_start: 0.6908 (tm-30) cc_final: 0.6498 (tm-30) REVERT: C 212 GLN cc_start: 0.7167 (mp10) cc_final: 0.6893 (mp10) REVERT: C 248 LYS cc_start: 0.7203 (tppp) cc_final: 0.6993 (mmmm) REVERT: C 271 ARG cc_start: 0.8092 (mtm180) cc_final: 0.7601 (mtm-85) REVERT: C 299 VAL cc_start: 0.8593 (t) cc_final: 0.8355 (p) REVERT: C 304 TRP cc_start: 0.7611 (m100) cc_final: 0.7069 (m100) outliers start: 19 outliers final: 9 residues processed: 217 average time/residue: 1.6801 time to fit residues: 377.6631 Evaluate side-chains 220 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 211 time to evaluate : 0.798 ------------------------------------------------------------------------------- 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 150 THR 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 45 optimal weight: 0.0770 chunk 19 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 65 optimal weight: 0.3980 chunk 36 optimal weight: 0.9980 chunk 6 optimal weight: 0.2980 chunk 25 optimal weight: 1.9990 chunk 41 optimal weight: 0.4980 chunk 75 optimal weight: 0.0970 chunk 8 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 overall best weight: 0.2736 ------------------------------------------------------------------------------- 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 293 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6798 Z= 0.193 Angle : 0.530 6.953 9222 Z= 0.270 Chirality : 0.042 0.177 1050 Planarity : 0.003 0.028 1158 Dihedral : 5.825 35.275 1125 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.32 % Allowed : 21.59 % Favored : 76.09 % 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: 2.05 (0.29), residues: 804 helix: 3.41 (0.28), residues: 258 sheet: 1.06 (0.27), residues: 327 loop : -0.76 (0.43), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 304 HIS 0.002 0.001 HIS C 130 PHE 0.016 0.002 PHE B 204 TYR 0.007 0.001 TYR B 111 ARG 0.007 0.000 ARG A 175 *********************** 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 222 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 206 time to evaluate : 0.848 Fit side-chains revert: symmetry clash REVERT: A 78 MET cc_start: 0.7326 (ttt) cc_final: 0.7125 (ttt) REVERT: A 129 LYS cc_start: 0.8230 (mtpt) cc_final: 0.8004 (mttt) REVERT: A 147 MET cc_start: 0.7624 (mtm) cc_final: 0.7407 (mtp) REVERT: A 152 GLN cc_start: 0.8086 (tp40) cc_final: 0.7870 (tp40) REVERT: A 176 GLU cc_start: 0.7451 (mp0) cc_final: 0.6466 (mp0) REVERT: A 194 GLU cc_start: 0.6508 (tm-30) cc_final: 0.6283 (tm-30) REVERT: A 206 SER cc_start: 0.8089 (m) cc_final: 0.7743 (t) REVERT: A 294 LYS cc_start: 0.7653 (mttt) cc_final: 0.7390 (mttp) REVERT: A 299 VAL cc_start: 0.8560 (t) cc_final: 0.8307 (p) REVERT: B 94 GLU cc_start: 0.6932 (tp30) cc_final: 0.6683 (tp30) REVERT: B 106 LYS cc_start: 0.8026 (tttm) cc_final: 0.7788 (ttpp) REVERT: B 129 LYS cc_start: 0.8159 (ttmm) cc_final: 0.7891 (mttm) REVERT: B 181 GLU cc_start: 0.7871 (tt0) cc_final: 0.7561 (tt0) REVERT: B 206 SER cc_start: 0.8028 (m) cc_final: 0.7727 (t) REVERT: B 268 ILE cc_start: 0.7295 (mm) cc_final: 0.6921 (mt) REVERT: B 271 ARG cc_start: 0.8202 (mtm180) cc_final: 0.7953 (mtm-85) REVERT: B 299 VAL cc_start: 0.8648 (t) cc_final: 0.8408 (p) REVERT: C 75 LEU cc_start: 0.7739 (mt) cc_final: 0.7487 (mt) REVERT: C 93 ARG cc_start: 0.6811 (mtt180) cc_final: 0.6523 (mtt180) REVERT: C 124 GLN cc_start: 0.7554 (pt0) cc_final: 0.7143 (pt0) REVERT: C 176 GLU cc_start: 0.7494 (mp0) cc_final: 0.6454 (mp0) REVERT: C 181 GLU cc_start: 0.7711 (tt0) cc_final: 0.7333 (tt0) REVERT: C 188 ARG cc_start: 0.7527 (ttp-170) cc_final: 0.6997 (ttp-170) REVERT: C 194 GLU cc_start: 0.6917 (tm-30) cc_final: 0.6510 (tm-30) REVERT: C 212 GLN cc_start: 0.7141 (mp10) cc_final: 0.6875 (mp10) REVERT: C 248 LYS cc_start: 0.7209 (tppp) cc_final: 0.7002 (mmmm) REVERT: C 271 ARG cc_start: 0.8100 (mtm180) cc_final: 0.7603 (mtm-85) REVERT: C 299 VAL cc_start: 0.8591 (t) cc_final: 0.8350 (p) REVERT: C 304 TRP cc_start: 0.7637 (m100) cc_final: 0.7091 (m100) REVERT: C 319 LYS cc_start: 0.7213 (tppt) cc_final: 0.6985 (ttmm) outliers start: 16 outliers final: 9 residues processed: 210 average time/residue: 1.7081 time to fit residues: 371.7517 Evaluate side-chains 214 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 205 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 200 ASP 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 315 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 57 optimal weight: 0.0370 chunk 44 optimal weight: 0.6980 chunk 65 optimal weight: 0.1980 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 48 optimal weight: 0.2980 chunk 47 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 23 optimal weight: 0.3980 overall best weight: 0.3058 ------------------------------------------------------------------------------- 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** B 186 GLN B 293 GLN C 186 GLN C 279 GLN C 293 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 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 : 0.003 0.033 6798 Z= 0.207 Angle : 0.528 6.858 9222 Z= 0.271 Chirality : 0.043 0.182 1050 Planarity : 0.003 0.029 1158 Dihedral : 5.187 31.881 1125 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.88 % Allowed : 22.32 % Favored : 75.80 % 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: 2.11 (0.29), residues: 804 helix: 3.41 (0.28), residues: 258 sheet: 1.16 (0.27), residues: 324 loop : -0.76 (0.43), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 304 HIS 0.002 0.001 HIS A 130 PHE 0.016 0.002 PHE A 204 TYR 0.009 0.001 TYR B 111 ARG 0.008 0.000 ARG A 175 *********************** 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 231 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 218 time to evaluate : 0.716 Fit side-chains revert: symmetry clash REVERT: A 78 MET cc_start: 0.7341 (ttt) cc_final: 0.7139 (ttt) REVERT: A 129 LYS cc_start: 0.8221 (mttt) cc_final: 0.8020 (mttt) REVERT: A 147 MET cc_start: 0.7623 (mtm) cc_final: 0.7411 (mtp) REVERT: A 152 GLN cc_start: 0.8108 (tp40) cc_final: 0.7852 (tp40) REVERT: A 180 ARG cc_start: 0.7244 (mtp180) cc_final: 0.6917 (mtp180) REVERT: A 194 GLU cc_start: 0.6619 (tm-30) cc_final: 0.6359 (tm-30) REVERT: A 206 SER cc_start: 0.8097 (m) cc_final: 0.7758 (t) REVERT: A 248 LYS cc_start: 0.7154 (tppp) cc_final: 0.6801 (mtpt) REVERT: A 294 LYS cc_start: 0.7659 (mttt) cc_final: 0.7390 (mttp) REVERT: A 299 VAL cc_start: 0.8567 (t) cc_final: 0.8318 (p) REVERT: B 94 GLU cc_start: 0.6937 (tp30) cc_final: 0.6659 (tp30) REVERT: B 106 LYS cc_start: 0.8027 (tttm) cc_final: 0.7805 (ttpp) REVERT: B 181 GLU cc_start: 0.7868 (tt0) cc_final: 0.7548 (tt0) REVERT: B 206 SER cc_start: 0.8015 (m) cc_final: 0.7722 (t) REVERT: B 268 ILE cc_start: 0.6986 (mm) cc_final: 0.6756 (mt) REVERT: B 271 ARG cc_start: 0.8225 (mtm180) cc_final: 0.7965 (mtm-85) REVERT: B 299 VAL cc_start: 0.8650 (t) cc_final: 0.8409 (p) REVERT: B 319 LYS cc_start: 0.7372 (ttmt) cc_final: 0.7099 (ttmm) REVERT: C 75 LEU cc_start: 0.7745 (mt) cc_final: 0.7512 (mt) REVERT: C 93 ARG cc_start: 0.6822 (mtt180) cc_final: 0.6549 (mtt180) REVERT: C 124 GLN cc_start: 0.7555 (pt0) cc_final: 0.7133 (pt0) REVERT: C 176 GLU cc_start: 0.7498 (mp0) cc_final: 0.6459 (mp0) REVERT: C 181 GLU cc_start: 0.7727 (tt0) cc_final: 0.7341 (tt0) REVERT: C 188 ARG cc_start: 0.7499 (ttp-170) cc_final: 0.6968 (ttp-170) REVERT: C 194 GLU cc_start: 0.6932 (tm-30) cc_final: 0.6519 (tm-30) REVERT: C 212 GLN cc_start: 0.7180 (mp10) cc_final: 0.6939 (mp10) REVERT: C 248 LYS cc_start: 0.7209 (tppp) cc_final: 0.6996 (mmmm) REVERT: C 271 ARG cc_start: 0.8080 (mtm180) cc_final: 0.7627 (mtm-85) REVERT: C 299 VAL cc_start: 0.8612 (t) cc_final: 0.8370 (p) REVERT: C 304 TRP cc_start: 0.7620 (m100) cc_final: 0.7076 (m100) outliers start: 13 outliers final: 8 residues processed: 219 average time/residue: 1.7051 time to fit residues: 386.4923 Evaluate side-chains 216 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 208 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 150 THR 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 15 optimal weight: 0.0670 chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 74 optimal weight: 0.5980 chunk 68 optimal weight: 0.1980 chunk 72 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 overall best weight: 0.4318 ------------------------------------------------------------------------------- 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 293 GLN C 186 GLN C 293 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6798 Z= 0.257 Angle : 0.551 7.343 9222 Z= 0.284 Chirality : 0.043 0.196 1050 Planarity : 0.004 0.028 1158 Dihedral : 4.788 29.412 1125 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.46 % Allowed : 21.45 % Favored : 76.09 % 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: 1.68 (0.30), residues: 804 helix: 2.88 (0.29), residues: 279 sheet: 0.97 (0.28), residues: 318 loop : -1.21 (0.42), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 230 HIS 0.003 0.001 HIS C 130 PHE 0.033 0.002 PHE A 219 TYR 0.008 0.001 TYR A 201 ARG 0.008 0.000 ARG A 175 *********************** 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 235 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 218 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.8238 (mttt) cc_final: 0.8033 (mttt) REVERT: A 147 MET cc_start: 0.7640 (mtm) cc_final: 0.7435 (mtp) REVERT: A 180 ARG cc_start: 0.7231 (mtp180) cc_final: 0.6893 (mtp180) REVERT: A 194 GLU cc_start: 0.6648 (tm-30) cc_final: 0.6325 (tm-30) REVERT: A 206 SER cc_start: 0.8058 (m) cc_final: 0.7723 (t) REVERT: A 248 LYS cc_start: 0.7183 (tppp) cc_final: 0.6851 (mtpt) REVERT: A 279 GLN cc_start: 0.7163 (mt0) cc_final: 0.6883 (mt0) REVERT: A 294 LYS cc_start: 0.7694 (mttt) cc_final: 0.7407 (mttp) REVERT: A 299 VAL cc_start: 0.8582 (t) cc_final: 0.8338 (p) REVERT: B 94 GLU cc_start: 0.6917 (tp30) cc_final: 0.6650 (tp30) REVERT: B 110 ARG cc_start: 0.7124 (OUTLIER) cc_final: 0.6813 (ptm160) REVERT: B 181 GLU cc_start: 0.7898 (tt0) cc_final: 0.7570 (tt0) REVERT: B 206 SER cc_start: 0.8001 (m) cc_final: 0.7726 (t) REVERT: B 247 THR cc_start: 0.7704 (m) cc_final: 0.7310 (t) REVERT: B 268 ILE cc_start: 0.7753 (mm) cc_final: 0.7472 (mt) REVERT: B 299 VAL cc_start: 0.8646 (t) cc_final: 0.8419 (p) REVERT: C 75 LEU cc_start: 0.7749 (mt) cc_final: 0.7545 (mt) REVERT: C 93 ARG cc_start: 0.6818 (mtt180) cc_final: 0.6575 (mtt180) REVERT: C 124 GLN cc_start: 0.7564 (pt0) cc_final: 0.7090 (pt0) REVERT: C 148 ASN cc_start: 0.6244 (p0) cc_final: 0.5259 (t0) REVERT: C 176 GLU cc_start: 0.7499 (mp0) cc_final: 0.6467 (mp0) REVERT: C 181 GLU cc_start: 0.7763 (tt0) cc_final: 0.7354 (tt0) REVERT: C 188 ARG cc_start: 0.7546 (ttp-170) cc_final: 0.6966 (ttp-170) REVERT: C 194 GLU cc_start: 0.6950 (tm-30) cc_final: 0.6527 (tm-30) REVERT: C 248 LYS cc_start: 0.7231 (tppp) cc_final: 0.7026 (mmmm) REVERT: C 271 ARG cc_start: 0.8105 (mtm180) cc_final: 0.7659 (mtm-85) REVERT: C 299 VAL cc_start: 0.8599 (t) cc_final: 0.8376 (p) REVERT: C 304 TRP cc_start: 0.7604 (m100) cc_final: 0.7062 (m100) REVERT: C 319 LYS cc_start: 0.7212 (tppt) cc_final: 0.6890 (ttmm) outliers start: 17 outliers final: 10 residues processed: 223 average time/residue: 1.5386 time to fit residues: 356.1855 Evaluate side-chains 229 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 218 time to evaluate : 0.760 ------------------------------------------------------------------------------- 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 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 197 SER 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 31 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 chunk 68 optimal weight: 0.5980 chunk 72 optimal weight: 0.9980 chunk 47 optimal weight: 0.0060 chunk 76 optimal weight: 1.9990 chunk 46 optimal weight: 0.0370 chunk 36 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 overall best weight: 0.3674 ------------------------------------------------------------------------------- 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 279 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6798 Z= 0.229 Angle : 0.533 7.078 9222 Z= 0.277 Chirality : 0.043 0.200 1050 Planarity : 0.004 0.031 1158 Dihedral : 4.611 27.380 1125 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.03 % Allowed : 22.46 % 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 (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: 1.69 (0.30), residues: 804 helix: 2.88 (0.30), residues: 279 sheet: 1.00 (0.28), residues: 318 loop : -1.23 (0.43), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 230 HIS 0.002 0.001 HIS C 130 PHE 0.026 0.002 PHE A 219 TYR 0.007 0.001 TYR B 111 ARG 0.007 0.000 ARG A 175 *********************** 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 234 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 220 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 LYS cc_start: 0.7868 (tttp) cc_final: 0.7451 (ttpp) REVERT: A 129 LYS cc_start: 0.8227 (mttt) cc_final: 0.8017 (mttp) REVERT: A 143 GLN cc_start: 0.7828 (mm110) cc_final: 0.7477 (mm110) REVERT: A 180 ARG cc_start: 0.7235 (mtp180) cc_final: 0.6903 (mtp180) REVERT: A 194 GLU cc_start: 0.6666 (tm-30) cc_final: 0.6269 (tm-30) REVERT: A 197 SER cc_start: 0.8402 (p) cc_final: 0.8114 (m) REVERT: A 206 SER cc_start: 0.8056 (m) cc_final: 0.7713 (t) REVERT: A 248 LYS cc_start: 0.7191 (tppp) cc_final: 0.6875 (mtpt) REVERT: A 294 LYS cc_start: 0.7683 (mttt) cc_final: 0.7377 (mttp) REVERT: A 299 VAL cc_start: 0.8585 (t) cc_final: 0.8347 (p) REVERT: B 94 GLU cc_start: 0.6911 (tp30) cc_final: 0.6632 (tp30) REVERT: B 101 MET cc_start: 0.8285 (ttm) cc_final: 0.8051 (ttm) REVERT: B 180 ARG cc_start: 0.7104 (mtp180) cc_final: 0.6686 (mtp180) REVERT: B 181 GLU cc_start: 0.7879 (tt0) cc_final: 0.7553 (tt0) REVERT: B 206 SER cc_start: 0.8013 (m) cc_final: 0.7735 (t) REVERT: B 247 THR cc_start: 0.7721 (m) cc_final: 0.7316 (t) REVERT: B 268 ILE cc_start: 0.7806 (mm) cc_final: 0.7555 (mt) REVERT: B 299 VAL cc_start: 0.8651 (t) cc_final: 0.8423 (p) REVERT: C 93 ARG cc_start: 0.6825 (mtt180) cc_final: 0.6592 (mtt180) REVERT: C 124 GLN cc_start: 0.7553 (pt0) cc_final: 0.7123 (pt0) REVERT: C 148 ASN cc_start: 0.6248 (p0) cc_final: 0.5222 (OUTLIER) REVERT: C 176 GLU cc_start: 0.7494 (mp0) cc_final: 0.6459 (mp0) REVERT: C 181 GLU cc_start: 0.7757 (tt0) cc_final: 0.7353 (tt0) REVERT: C 188 ARG cc_start: 0.7555 (ttp-170) cc_final: 0.7009 (ttp-170) REVERT: C 194 GLU cc_start: 0.6961 (tm-30) cc_final: 0.6536 (tm-30) REVERT: C 271 ARG cc_start: 0.8103 (mtm180) cc_final: 0.7646 (mtm-85) REVERT: C 299 VAL cc_start: 0.8582 (t) cc_final: 0.8358 (p) REVERT: C 304 TRP cc_start: 0.7595 (m100) cc_final: 0.7100 (m100) outliers start: 14 outliers final: 12 residues processed: 223 average time/residue: 1.5551 time to fit residues: 359.7323 Evaluate side-chains 229 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 218 time to evaluate : 0.762 ------------------------------------------------------------------------------- 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 200 ASP Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain C residue 197 SER 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 80 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 59 optimal weight: 0.0770 chunk 9 optimal weight: 0.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6798 Z= 0.314 Angle : 0.577 7.293 9222 Z= 0.298 Chirality : 0.045 0.210 1050 Planarity : 0.004 0.033 1158 Dihedral : 4.595 26.365 1125 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.74 % Allowed : 23.04 % Favored : 75.22 % 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 (0.30), residues: 804 helix: 2.81 (0.30), residues: 279 sheet: 0.98 (0.28), residues: 318 loop : -1.32 (0.42), residues: 207 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 0.025 0.002 PHE A 219 TYR 0.009 0.001 TYR B 119 ARG 0.008 0.001 ARG B 271 ********************** 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 227 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 215 time to evaluate : 0.803 Fit side-chains revert: symmetry clash REVERT: A 106 LYS cc_start: 0.7865 (tttp) cc_final: 0.7448 (ttpp) REVERT: A 129 LYS cc_start: 0.8240 (mttt) cc_final: 0.8029 (mttp) REVERT: A 143 GLN cc_start: 0.7833 (mm110) cc_final: 0.7472 (mm110) REVERT: A 180 ARG cc_start: 0.7228 (mtp180) cc_final: 0.6898 (mtp180) REVERT: A 206 SER cc_start: 0.8034 (m) cc_final: 0.7706 (t) REVERT: A 248 LYS cc_start: 0.7170 (tppp) cc_final: 0.6871 (mtpt) REVERT: A 294 LYS cc_start: 0.7688 (mttt) cc_final: 0.7390 (mttp) REVERT: A 299 VAL cc_start: 0.8576 (t) cc_final: 0.8341 (p) REVERT: B 94 GLU cc_start: 0.6885 (tp30) cc_final: 0.6636 (tp30) REVERT: B 180 ARG cc_start: 0.7102 (mtp180) cc_final: 0.6678 (mtp180) REVERT: B 181 GLU cc_start: 0.7907 (tt0) cc_final: 0.7596 (tt0) REVERT: B 206 SER cc_start: 0.7987 (m) cc_final: 0.7716 (t) REVERT: B 268 ILE cc_start: 0.7969 (mm) cc_final: 0.7733 (mt) REVERT: B 299 VAL cc_start: 0.8667 (t) cc_final: 0.8443 (p) REVERT: C 93 ARG cc_start: 0.6844 (mtt180) cc_final: 0.6580 (mtt180) REVERT: C 124 GLN cc_start: 0.7550 (pt0) cc_final: 0.7064 (pt0) REVERT: C 148 ASN cc_start: 0.6416 (p0) cc_final: 0.5393 (OUTLIER) REVERT: C 176 GLU cc_start: 0.7546 (mp0) cc_final: 0.6522 (mp0) REVERT: C 180 ARG cc_start: 0.7225 (mtp180) cc_final: 0.6927 (mtp180) REVERT: C 181 GLU cc_start: 0.7797 (tt0) cc_final: 0.7390 (tt0) REVERT: C 188 ARG cc_start: 0.7576 (ttp-170) cc_final: 0.6984 (ttp-170) REVERT: C 194 GLU cc_start: 0.6952 (tm-30) cc_final: 0.6519 (tm-30) REVERT: C 271 ARG cc_start: 0.8084 (mtm180) cc_final: 0.7606 (mtm-85) REVERT: C 299 VAL cc_start: 0.8603 (t) cc_final: 0.8382 (p) REVERT: C 304 TRP cc_start: 0.7609 (m100) cc_final: 0.7107 (m100) REVERT: C 319 LYS cc_start: 0.7231 (tppt) cc_final: 0.6944 (ttmm) outliers start: 12 outliers final: 11 residues processed: 220 average time/residue: 1.5413 time to fit residues: 351.8841 Evaluate side-chains 229 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 219 time to evaluate : 0.781 ------------------------------------------------------------------------------- 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 197 SER 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 17 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 26 optimal weight: 0.4980 chunk 66 optimal weight: 0.9980 chunk 8 optimal weight: 0.0570 chunk 11 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.5098 ------------------------------------------------------------------------------- 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 = 0.3831 r_free = 0.3831 target = 0.137497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.119411 restraints weight = 9464.954| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.24 r_work: 0.3446 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 6798 Z= 0.297 Angle : 0.568 7.331 9222 Z= 0.294 Chirality : 0.045 0.209 1050 Planarity : 0.004 0.032 1158 Dihedral : 4.555 26.110 1125 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.74 % Allowed : 23.91 % 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 (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: 1.57 (0.30), residues: 804 helix: 2.77 (0.30), residues: 279 sheet: 1.02 (0.28), residues: 315 loop : -1.44 (0.43), residues: 210 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 0.025 0.002 PHE A 219 TYR 0.008 0.001 TYR C 201 ARG 0.007 0.000 ARG A 175 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5426.93 seconds wall clock time: 96 minutes 48.49 seconds (5808.49 seconds total)