Starting phenix.real_space_refine on Mon Mar 11 02:28:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sqg_25384/03_2024/7sqg_25384.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sqg_25384/03_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sqg_25384/03_2024/7sqg_25384.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sqg_25384/03_2024/7sqg_25384.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sqg_25384/03_2024/7sqg_25384.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sqg_25384/03_2024/7sqg_25384.pdb" } 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 Residue "A TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 4.01, per 1000 atoms: 0.60 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 - 3.50 Amino acid : False - 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: 2.43 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 65 through 98 removed outlier: 3.563A pdb=" N LEU A 69 " --> pdb=" O VAL A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 212 removed outlier: 3.516A pdb=" N PHE A 210 " --> pdb=" O SER A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 227 removed outlier: 3.691A pdb=" N SER A 225 " --> pdb=" O GLN A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 278 removed outlier: 3.810A pdb=" N SER A 277 " --> pdb=" O ALA A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 334 Processing helix chain 'B' and resid 66 through 98 Processing helix chain 'B' and resid 206 through 212 removed outlier: 3.516A pdb=" N PHE B 210 " --> pdb=" O SER B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 227 removed outlier: 3.691A pdb=" N SER B 225 " --> pdb=" O GLN B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 278 removed outlier: 3.810A pdb=" N SER B 277 " --> pdb=" O ALA B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 334 Processing helix chain 'C' and resid 66 through 98 Processing helix chain 'C' and resid 206 through 212 removed outlier: 3.516A pdb=" N PHE C 210 " --> pdb=" O SER C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 227 removed outlier: 3.691A pdb=" N SER C 225 " --> pdb=" O GLN C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 278 removed outlier: 3.810A pdb=" N SER C 277 " --> pdb=" O ALA C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 334 Processing sheet with id=AA1, first strand: chain 'A' and resid 100 through 107 removed outlier: 13.537A pdb=" N PHE A 291 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 9.278A pdb=" N MET A 242 " --> pdb=" O PHE A 291 " (cutoff:3.500A) removed outlier: 9.162A pdb=" N GLN A 293 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU A 244 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N VAL A 295 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LYS A 246 " --> pdb=" O VAL A 295 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ASP A 297 " --> pdb=" O LYS A 246 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N LYS A 248 " --> pdb=" O ASP A 297 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N PHE A 236 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N TRP A 287 " --> pdb=" O GLU A 181 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N GLU A 181 " --> pdb=" O TRP A 287 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ARG A 188 " --> pdb=" O LEU A 125 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N LEU A 125 " --> pdb=" O ARG A 188 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ASN A 148 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N CYS A 128 " --> pdb=" O ASN A 148 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 107 removed outlier: 13.537A pdb=" N PHE A 291 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 9.278A pdb=" N MET A 242 " --> pdb=" O PHE A 291 " (cutoff:3.500A) removed outlier: 9.162A pdb=" N GLN A 293 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU A 244 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N VAL A 295 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LYS A 246 " --> pdb=" O VAL A 295 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ASP A 297 " --> pdb=" O LYS A 246 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N LYS A 248 " --> pdb=" O ASP A 297 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 151 through 157 removed outlier: 3.743A pdb=" N ASP A 200 " --> pdb=" O TYR A 119 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 107 removed outlier: 13.537A pdb=" N PHE B 291 " --> pdb=" O VAL B 240 " (cutoff:3.500A) removed outlier: 9.278A pdb=" N MET B 242 " --> pdb=" O PHE B 291 " (cutoff:3.500A) removed outlier: 9.162A pdb=" N GLN B 293 " --> pdb=" O MET B 242 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU B 244 " --> pdb=" O GLN B 293 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N VAL B 295 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LYS B 246 " --> pdb=" O VAL B 295 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ASP B 297 " --> pdb=" O LYS B 246 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N LYS B 248 " --> pdb=" O ASP B 297 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N PHE B 236 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N TRP B 287 " --> pdb=" O GLU B 181 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N GLU B 181 " --> pdb=" O TRP B 287 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ARG B 188 " --> pdb=" O LEU B 125 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N LEU B 125 " --> pdb=" O ARG B 188 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ASN B 148 " --> pdb=" O LEU B 126 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N CYS B 128 " --> pdb=" O ASN B 148 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 107 removed outlier: 13.537A pdb=" N PHE B 291 " --> pdb=" O VAL B 240 " (cutoff:3.500A) removed outlier: 9.278A pdb=" N MET B 242 " --> pdb=" O PHE B 291 " (cutoff:3.500A) removed outlier: 9.162A pdb=" N GLN B 293 " --> pdb=" O MET B 242 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU B 244 " --> pdb=" O GLN B 293 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N VAL B 295 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LYS B 246 " --> pdb=" O VAL B 295 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ASP B 297 " --> pdb=" O LYS B 246 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N LYS B 248 " --> pdb=" O ASP B 297 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 151 through 157 removed outlier: 3.741A pdb=" N ASP B 200 " --> pdb=" O TYR B 119 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 100 through 107 removed outlier: 13.537A pdb=" N PHE C 291 " --> pdb=" O VAL C 240 " (cutoff:3.500A) removed outlier: 9.278A pdb=" N MET C 242 " --> pdb=" O PHE C 291 " (cutoff:3.500A) removed outlier: 9.162A pdb=" N GLN C 293 " --> pdb=" O MET C 242 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU C 244 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N VAL C 295 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LYS C 246 " --> pdb=" O VAL C 295 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ASP C 297 " --> pdb=" O LYS C 246 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N LYS C 248 " --> pdb=" O ASP C 297 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N PHE C 236 " --> pdb=" O LEU C 280 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N TRP C 287 " --> pdb=" O GLU C 181 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N GLU C 181 " --> pdb=" O TRP C 287 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ARG C 188 " --> pdb=" O LEU C 125 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N LEU C 125 " --> pdb=" O ARG C 188 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ASN C 148 " --> pdb=" O LEU C 126 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N CYS C 128 " --> pdb=" O ASN C 148 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 100 through 107 removed outlier: 13.537A pdb=" N PHE C 291 " --> pdb=" O VAL C 240 " (cutoff:3.500A) removed outlier: 9.278A pdb=" N MET C 242 " --> pdb=" O PHE C 291 " (cutoff:3.500A) removed outlier: 9.162A pdb=" N GLN C 293 " --> pdb=" O MET C 242 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU C 244 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N VAL C 295 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LYS C 246 " --> pdb=" O VAL C 295 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ASP C 297 " --> pdb=" O LYS C 246 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N LYS C 248 " --> pdb=" O ASP C 297 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 151 through 157 removed outlier: 3.733A pdb=" N ASP C 200 " --> pdb=" O TYR C 119 " (cutoff:3.500A) 414 hydrogen bonds defined for protein. 1179 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.88 Time building geometry restraints manager: 2.63 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: 100.78 - 107.46: 249 107.46 - 114.14: 3855 114.14 - 120.81: 2915 120.81 - 127.49: 2145 127.49 - 134.17: 58 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 2.440 nonbonded pdb=" OG1 THR C 150 " pdb=" OE1 GLN C 172 " model vdw 2.423 2.440 nonbonded pdb=" OG1 THR B 150 " pdb=" OE1 GLN B 172 " model vdw 2.423 2.440 nonbonded pdb=" OG SER C 197 " pdb=" OE1 GLN C 279 " model vdw 2.439 2.440 nonbonded pdb=" OG SER A 197 " pdb=" OE1 GLN A 279 " model vdw 2.440 2.440 ... (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 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: 3.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 11.470 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 21.710 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 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:12.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.880 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 261 time to evaluate : 0.756 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: 1.6132 time to fit residues: 435.5450 Evaluate side-chains 236 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 236 time to evaluate : 0.687 ------------------------------------------------------------------------------- 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: 0.0980 chunk 61 optimal weight: 0.0070 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 41 optimal weight: 0.0370 chunk 32 optimal weight: 0.2980 chunk 63 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 47 optimal weight: 0.0980 chunk 73 optimal weight: 1.9990 overall best weight: 0.1076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN A 208 GLN A 293 GLN A 296 GLN B 279 GLN 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 6798 Z= 0.149 Angle : 0.537 7.275 9222 Z= 0.270 Chirality : 0.044 0.197 1050 Planarity : 0.003 0.029 1158 Dihedral : 13.143 83.019 1125 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.17 % Allowed : 14.64 % 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: 1.81 (0.29), residues: 804 helix: 3.43 (0.28), residues: 258 sheet: 1.13 (0.29), residues: 300 loop : -1.28 (0.39), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 304 HIS 0.009 0.002 HIS C 98 PHE 0.021 0.002 PHE A 219 TYR 0.006 0.001 TYR C 201 ARG 0.005 0.000 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 240 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 225 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.7317 (ttt) cc_final: 0.7002 (ttt) REVERT: A 94 GLU cc_start: 0.6921 (tp30) cc_final: 0.6617 (tp30) REVERT: A 97 LYS cc_start: 0.7635 (OUTLIER) cc_final: 0.7359 (mtpm) REVERT: A 106 LYS cc_start: 0.7779 (tttp) cc_final: 0.7378 (ttmm) REVERT: A 143 GLN cc_start: 0.7713 (mm110) cc_final: 0.7483 (mm110) REVERT: A 147 MET cc_start: 0.7506 (mtm) cc_final: 0.7283 (mtp) REVERT: A 175 ARG cc_start: 0.7275 (mtp85) cc_final: 0.7010 (mtp85) REVERT: A 176 GLU cc_start: 0.7449 (mp0) cc_final: 0.6589 (mp0) REVERT: A 180 ARG cc_start: 0.7099 (mtp180) cc_final: 0.6815 (mtp180) REVERT: A 181 GLU cc_start: 0.7721 (tt0) cc_final: 0.7265 (tt0) REVERT: A 194 GLU cc_start: 0.6549 (tm-30) cc_final: 0.6148 (tm-30) REVERT: A 304 TRP cc_start: 0.7412 (m100) cc_final: 0.7044 (m100) REVERT: B 94 GLU cc_start: 0.6942 (tp30) cc_final: 0.6726 (tp30) REVERT: B 180 ARG cc_start: 0.7013 (mtp180) cc_final: 0.6705 (mtp180) REVERT: B 219 PHE cc_start: 0.7918 (t80) cc_final: 0.7581 (t80) REVERT: B 247 THR cc_start: 0.7459 (m) cc_final: 0.7171 (t) REVERT: C 92 PHE cc_start: 0.7530 (t80) cc_final: 0.7176 (t80) REVERT: C 93 ARG cc_start: 0.6647 (mtt180) cc_final: 0.6334 (mtt180) REVERT: C 106 LYS cc_start: 0.7762 (tttp) cc_final: 0.7375 (tttp) REVERT: C 124 GLN cc_start: 0.7541 (pt0) cc_final: 0.7334 (pt0) REVERT: C 176 GLU cc_start: 0.7480 (mp0) cc_final: 0.6721 (mp0) REVERT: C 179 LYS cc_start: 0.8252 (mtpp) cc_final: 0.8032 (mtmt) REVERT: C 188 ARG cc_start: 0.7527 (ttp-170) cc_final: 0.7116 (ttp-170) REVERT: C 194 GLU cc_start: 0.6895 (tm-30) cc_final: 0.6473 (tm-30) REVERT: C 219 PHE cc_start: 0.7989 (t80) cc_final: 0.7644 (t80) REVERT: C 271 ARG cc_start: 0.7831 (mtm180) cc_final: 0.7585 (mtm-85) REVERT: C 294 LYS cc_start: 0.7805 (mttt) cc_final: 0.7534 (mttp) REVERT: C 299 VAL cc_start: 0.8438 (t) cc_final: 0.8120 (p) REVERT: C 304 TRP cc_start: 0.7667 (m100) cc_final: 0.7179 (m100) outliers start: 15 outliers final: 6 residues processed: 226 average time/residue: 1.6026 time to fit residues: 374.6189 Evaluate side-chains 228 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 221 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 322 GLU 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 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: 0.1980 chunk 22 optimal weight: 0.7980 chunk 61 optimal weight: 0.0000 chunk 50 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 73 optimal weight: 0.8980 chunk 79 optimal weight: 0.3980 chunk 65 optimal weight: 0.6980 chunk 25 optimal weight: 0.0970 chunk 59 optimal weight: 0.2980 chunk 72 optimal weight: 0.6980 overall best weight: 0.1982 ------------------------------------------------------------------------------- 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 293 GLN B 296 GLN C 98 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6798 Z= 0.171 Angle : 0.549 7.692 9222 Z= 0.270 Chirality : 0.043 0.169 1050 Planarity : 0.003 0.026 1158 Dihedral : 10.448 63.035 1125 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.61 % Allowed : 19.57 % Favored : 77.83 % 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: 1.90 (0.29), residues: 804 helix: 3.54 (0.28), residues: 258 sheet: 1.15 (0.28), residues: 300 loop : -1.23 (0.38), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 304 HIS 0.008 0.001 HIS C 98 PHE 0.016 0.001 PHE A 281 TYR 0.007 0.001 TYR A 201 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 238 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 220 time to evaluate : 0.789 Fit side-chains revert: symmetry clash REVERT: A 78 MET cc_start: 0.7356 (ttt) cc_final: 0.7055 (ttt) REVERT: A 94 GLU cc_start: 0.6955 (tp30) cc_final: 0.6732 (tp30) REVERT: A 97 LYS cc_start: 0.7663 (OUTLIER) cc_final: 0.7408 (mtpp) REVERT: A 98 HIS cc_start: 0.8333 (m90) cc_final: 0.8014 (m170) REVERT: A 106 LYS cc_start: 0.7844 (tttp) cc_final: 0.7461 (tttp) REVERT: A 129 LYS cc_start: 0.8193 (mtpt) cc_final: 0.7853 (mttt) REVERT: A 143 GLN cc_start: 0.7732 (mm110) cc_final: 0.7502 (mm110) REVERT: A 147 MET cc_start: 0.7523 (mtm) cc_final: 0.7311 (mtp) REVERT: A 175 ARG cc_start: 0.7274 (mtp85) cc_final: 0.7055 (mtp85) REVERT: A 176 GLU cc_start: 0.7478 (mp0) cc_final: 0.6527 (mp0) REVERT: A 180 ARG cc_start: 0.7122 (mtp180) cc_final: 0.6856 (mtp180) REVERT: A 181 GLU cc_start: 0.7726 (tt0) cc_final: 0.7217 (tt0) REVERT: A 194 GLU cc_start: 0.6490 (tm-30) cc_final: 0.6250 (tm-30) REVERT: A 286 GLU cc_start: 0.8023 (pt0) cc_final: 0.7819 (pt0) REVERT: B 94 GLU cc_start: 0.6933 (tp30) cc_final: 0.6698 (tp30) REVERT: B 180 ARG cc_start: 0.7048 (mtp180) cc_final: 0.6700 (mtp180) REVERT: B 219 PHE cc_start: 0.7872 (t80) cc_final: 0.7604 (t80) REVERT: B 247 THR cc_start: 0.7499 (m) cc_final: 0.7214 (t) REVERT: C 92 PHE cc_start: 0.7556 (t80) cc_final: 0.7340 (t80) REVERT: C 93 ARG cc_start: 0.6718 (mtt180) cc_final: 0.6382 (mtt180) REVERT: C 106 LYS cc_start: 0.7813 (tttp) cc_final: 0.7526 (tttp) REVERT: C 124 GLN cc_start: 0.7554 (pt0) cc_final: 0.7231 (pt0) REVERT: C 176 GLU cc_start: 0.7481 (mp0) cc_final: 0.6430 (mp0) REVERT: C 181 GLU cc_start: 0.7690 (tt0) cc_final: 0.7277 (tt0) REVERT: C 188 ARG cc_start: 0.7524 (ttp-170) cc_final: 0.7057 (ttp-170) REVERT: C 194 GLU cc_start: 0.6879 (tm-30) cc_final: 0.6462 (tm-30) REVERT: C 219 PHE cc_start: 0.7998 (t80) cc_final: 0.7690 (t80) REVERT: C 271 ARG cc_start: 0.7880 (mtm180) cc_final: 0.7628 (mtm-85) REVERT: C 294 LYS cc_start: 0.7825 (mttt) cc_final: 0.7573 (mttp) REVERT: C 299 VAL cc_start: 0.8486 (t) cc_final: 0.8194 (p) REVERT: C 304 TRP cc_start: 0.7635 (m100) cc_final: 0.7132 (m100) outliers start: 18 outliers final: 7 residues processed: 227 average time/residue: 1.6015 time to fit residues: 376.4007 Evaluate side-chains 226 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 218 time to evaluate : 0.747 ------------------------------------------------------------------------------- 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 150 THR 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: 0.4980 chunk 8 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 chunk 21 optimal weight: 0.0570 chunk 65 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 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 266 ASN ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 GLN B 98 HIS B 186 GLN B 293 GLN C 186 GLN C 266 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6798 Z= 0.307 Angle : 0.582 7.948 9222 Z= 0.289 Chirality : 0.044 0.138 1050 Planarity : 0.003 0.028 1158 Dihedral : 7.824 49.875 1125 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.61 % Allowed : 21.16 % 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: 1.82 (0.29), residues: 804 helix: 3.42 (0.28), residues: 258 sheet: 1.06 (0.27), residues: 309 loop : -1.23 (0.39), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 239 HIS 0.009 0.001 HIS B 98 PHE 0.018 0.002 PHE B 204 TYR 0.011 0.002 TYR B 119 ARG 0.004 0.000 ARG A 175 *********************** 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 241 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 223 time to evaluate : 0.773 Fit side-chains revert: symmetry clash REVERT: A 78 MET cc_start: 0.7317 (ttt) cc_final: 0.7038 (ttt) REVERT: A 94 GLU cc_start: 0.6982 (tp30) cc_final: 0.6774 (tp30) REVERT: A 97 LYS cc_start: 0.7777 (mtpm) cc_final: 0.7563 (mtpp) REVERT: A 106 LYS cc_start: 0.7858 (tttp) cc_final: 0.7456 (ttpp) REVERT: A 129 LYS cc_start: 0.8237 (mtpt) cc_final: 0.7924 (mttt) REVERT: A 147 MET cc_start: 0.7606 (mtm) cc_final: 0.7379 (mtp) REVERT: A 175 ARG cc_start: 0.7332 (mtp85) cc_final: 0.6902 (mtp85) REVERT: A 176 GLU cc_start: 0.7529 (mp0) cc_final: 0.6467 (mp0) REVERT: A 180 ARG cc_start: 0.7156 (mtp180) cc_final: 0.6948 (mtp180) REVERT: A 181 GLU cc_start: 0.7783 (tt0) cc_final: 0.7506 (tt0) REVERT: A 194 GLU cc_start: 0.6551 (tm-30) cc_final: 0.6268 (tm-30) REVERT: B 94 GLU cc_start: 0.6928 (tp30) cc_final: 0.6695 (tp30) REVERT: B 106 LYS cc_start: 0.8010 (tttm) cc_final: 0.7798 (ttpp) REVERT: B 176 GLU cc_start: 0.7439 (mp0) cc_final: 0.6897 (mp0) REVERT: B 180 ARG cc_start: 0.7054 (mtp180) cc_final: 0.6688 (mtp180) REVERT: B 181 GLU cc_start: 0.7670 (tt0) cc_final: 0.7265 (tt0) REVERT: B 247 THR cc_start: 0.7570 (m) cc_final: 0.7272 (t) REVERT: B 299 VAL cc_start: 0.8617 (t) cc_final: 0.8360 (p) REVERT: C 93 ARG cc_start: 0.6822 (mtt180) cc_final: 0.6479 (mtt180) REVERT: C 106 LYS cc_start: 0.7878 (tttp) cc_final: 0.7665 (tttp) REVERT: C 124 GLN cc_start: 0.7582 (pt0) cc_final: 0.7135 (pt0) REVERT: C 148 ASN cc_start: 0.6190 (p0) cc_final: 0.5342 (t0) REVERT: C 176 GLU cc_start: 0.7480 (mp0) cc_final: 0.6470 (mp0) REVERT: C 181 GLU cc_start: 0.7745 (tt0) cc_final: 0.7326 (tt0) REVERT: C 188 ARG cc_start: 0.7500 (ttp-170) cc_final: 0.7007 (ttp-170) REVERT: C 194 GLU cc_start: 0.6891 (tm-30) cc_final: 0.6480 (tm-30) REVERT: C 212 GLN cc_start: 0.7155 (pp30) cc_final: 0.6627 (pp30) REVERT: C 248 LYS cc_start: 0.7166 (tppp) cc_final: 0.6948 (mmmm) REVERT: C 271 ARG cc_start: 0.7957 (mtm180) cc_final: 0.7569 (mtm-85) REVERT: C 299 VAL cc_start: 0.8563 (t) cc_final: 0.8299 (p) REVERT: C 304 TRP cc_start: 0.7621 (m100) cc_final: 0.7061 (m100) outliers start: 18 outliers final: 10 residues processed: 226 average time/residue: 1.6041 time to fit residues: 375.3123 Evaluate side-chains 230 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 220 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 200 ASP 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 1 optimal weight: 0.2980 chunk 58 optimal weight: 0.0970 chunk 32 optimal weight: 0.0870 chunk 66 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 chunk 0 optimal weight: 0.5980 chunk 39 optimal weight: 0.3980 chunk 70 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 overall best weight: 0.2956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 GLN B 186 GLN B 266 ASN B 293 GLN C 186 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6798 Z= 0.194 Angle : 0.522 7.206 9222 Z= 0.264 Chirality : 0.042 0.163 1050 Planarity : 0.003 0.026 1158 Dihedral : 6.516 45.281 1125 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.17 % Allowed : 22.03 % 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: 1.91 (0.29), residues: 804 helix: 3.48 (0.28), residues: 258 sheet: 1.08 (0.28), residues: 309 loop : -1.11 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 304 HIS 0.002 0.000 HIS C 130 PHE 0.015 0.002 PHE A 204 TYR 0.005 0.001 TYR A 201 ARG 0.003 0.000 ARG A 175 *********************** 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 233 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 218 time to evaluate : 0.693 Fit side-chains revert: symmetry clash REVERT: A 78 MET cc_start: 0.7299 (ttt) cc_final: 0.7093 (ttt) REVERT: A 97 LYS cc_start: 0.7707 (mtpm) cc_final: 0.7396 (mtpm) REVERT: A 106 LYS cc_start: 0.7874 (tttp) cc_final: 0.7452 (ttpp) REVERT: A 129 LYS cc_start: 0.8240 (mtpt) cc_final: 0.7968 (mttt) REVERT: A 147 MET cc_start: 0.7607 (mtm) cc_final: 0.7375 (mtp) REVERT: A 175 ARG cc_start: 0.7287 (mtp85) cc_final: 0.7072 (mtp85) REVERT: A 176 GLU cc_start: 0.7501 (mp0) cc_final: 0.6398 (mp0) REVERT: A 181 GLU cc_start: 0.7750 (tt0) cc_final: 0.7444 (tt0) REVERT: A 194 GLU cc_start: 0.6621 (tm-30) cc_final: 0.6369 (tm-30) REVERT: A 294 LYS cc_start: 0.7774 (mttp) cc_final: 0.7569 (mttp) REVERT: A 299 VAL cc_start: 0.8560 (t) cc_final: 0.8297 (p) REVERT: B 94 GLU cc_start: 0.6986 (tp30) cc_final: 0.6718 (tp30) REVERT: B 106 LYS cc_start: 0.8030 (tttm) cc_final: 0.7783 (ttpp) REVERT: B 247 THR cc_start: 0.7589 (m) cc_final: 0.7283 (t) REVERT: B 299 VAL cc_start: 0.8608 (t) cc_final: 0.8362 (p) REVERT: C 93 ARG cc_start: 0.6803 (mtt180) cc_final: 0.6500 (mtt180) REVERT: C 124 GLN cc_start: 0.7555 (pt0) cc_final: 0.6992 (pt0) REVERT: C 176 GLU cc_start: 0.7477 (mp0) cc_final: 0.6411 (mp0) REVERT: C 181 GLU cc_start: 0.7707 (tt0) cc_final: 0.7280 (tt0) REVERT: C 188 ARG cc_start: 0.7484 (ttp-170) cc_final: 0.6927 (ttp-170) REVERT: C 194 GLU cc_start: 0.6845 (tm-30) cc_final: 0.6459 (tm-30) REVERT: C 212 GLN cc_start: 0.7140 (pp30) cc_final: 0.6629 (pp30) REVERT: C 248 LYS cc_start: 0.7132 (tppp) cc_final: 0.6918 (mmmm) REVERT: C 271 ARG cc_start: 0.7987 (mtm180) cc_final: 0.7581 (mtm-85) REVERT: C 299 VAL cc_start: 0.8600 (t) cc_final: 0.8347 (p) REVERT: C 304 TRP cc_start: 0.7635 (m100) cc_final: 0.7065 (m100) outliers start: 15 outliers final: 7 residues processed: 219 average time/residue: 1.6978 time to fit residues: 384.5302 Evaluate side-chains 220 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 213 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 200 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 45 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 78 optimal weight: 0.0970 chunk 65 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 41 optimal weight: 0.4980 chunk 75 optimal weight: 0.1980 chunk 8 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 overall best weight: 0.4178 ------------------------------------------------------------------------------- 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 B 296 GLN C 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6798 Z= 0.261 Angle : 0.539 7.331 9222 Z= 0.273 Chirality : 0.043 0.176 1050 Planarity : 0.003 0.027 1158 Dihedral : 5.924 41.792 1125 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.17 % Allowed : 22.32 % 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: 1.89 (0.29), residues: 804 helix: 3.44 (0.29), residues: 258 sheet: 1.09 (0.28), residues: 309 loop : -1.14 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 230 HIS 0.002 0.001 HIS C 98 PHE 0.028 0.002 PHE A 219 TYR 0.007 0.001 TYR B 111 ARG 0.003 0.000 ARG A 180 *********************** 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 234 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 219 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.7342 (ttt) cc_final: 0.7135 (ttt) REVERT: A 97 LYS cc_start: 0.7768 (mtpm) cc_final: 0.7460 (mtpm) REVERT: A 106 LYS cc_start: 0.7877 (tttp) cc_final: 0.7453 (ttpp) REVERT: A 129 LYS cc_start: 0.8241 (mtpt) cc_final: 0.7989 (mttt) REVERT: A 147 MET cc_start: 0.7610 (mtm) cc_final: 0.7382 (mtp) REVERT: A 194 GLU cc_start: 0.6641 (tm-30) cc_final: 0.6358 (tm-30) REVERT: A 294 LYS cc_start: 0.7796 (mttp) cc_final: 0.7590 (mttp) REVERT: A 299 VAL cc_start: 0.8567 (t) cc_final: 0.8305 (p) REVERT: B 94 GLU cc_start: 0.6943 (tp30) cc_final: 0.6680 (tp30) REVERT: B 106 LYS cc_start: 0.8026 (tttm) cc_final: 0.7795 (ttpp) REVERT: B 180 ARG cc_start: 0.7061 (mtp180) cc_final: 0.6692 (mtp180) REVERT: B 299 VAL cc_start: 0.8614 (t) cc_final: 0.8364 (p) REVERT: C 75 LEU cc_start: 0.7729 (mt) cc_final: 0.7476 (mt) REVERT: C 93 ARG cc_start: 0.6804 (mtt180) cc_final: 0.6560 (mtt180) REVERT: C 124 GLN cc_start: 0.7524 (pt0) cc_final: 0.7003 (pt0) REVERT: C 148 ASN cc_start: 0.6115 (p0) cc_final: 0.5224 (t0) REVERT: C 176 GLU cc_start: 0.7472 (mp0) cc_final: 0.6495 (mp0) REVERT: C 181 GLU cc_start: 0.7734 (tt0) cc_final: 0.7378 (tt0) REVERT: C 188 ARG cc_start: 0.7460 (ttp-170) cc_final: 0.6930 (ttp-170) REVERT: C 194 GLU cc_start: 0.6852 (tm-30) cc_final: 0.6471 (tm-30) REVERT: C 212 GLN cc_start: 0.7188 (pp30) cc_final: 0.6677 (pp30) REVERT: C 248 LYS cc_start: 0.7197 (tppp) cc_final: 0.6985 (mmmm) REVERT: C 271 ARG cc_start: 0.7983 (mtm180) cc_final: 0.7564 (mtm-85) REVERT: C 299 VAL cc_start: 0.8593 (t) cc_final: 0.8355 (p) REVERT: C 304 TRP cc_start: 0.7612 (m100) cc_final: 0.7064 (m100) REVERT: C 319 LYS cc_start: 0.7273 (tppt) cc_final: 0.7009 (ttmm) outliers start: 15 outliers final: 10 residues processed: 220 average time/residue: 1.6326 time to fit residues: 371.8144 Evaluate side-chains 227 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 217 time to evaluate : 0.771 ------------------------------------------------------------------------------- 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 200 ASP Chi-restraints excluded: chain C residue 257 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 57 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 65 optimal weight: 0.3980 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 0.0980 chunk 48 optimal weight: 0.0980 chunk 47 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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 152 GLN C 186 GLN C 293 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.2556 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= 0.249 Angle : 0.529 7.495 9222 Z= 0.272 Chirality : 0.043 0.182 1050 Planarity : 0.004 0.029 1158 Dihedral : 5.298 38.178 1125 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.90 % Allowed : 22.03 % 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: 1.98 (0.29), residues: 804 helix: 3.43 (0.29), residues: 258 sheet: 1.00 (0.27), residues: 327 loop : -0.89 (0.43), 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 0.023 0.002 PHE A 219 TYR 0.007 0.001 TYR B 119 ARG 0.009 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 244 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 224 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.7743 (mtpm) cc_final: 0.7434 (mtpm) REVERT: A 106 LYS cc_start: 0.7884 (tttp) cc_final: 0.7457 (ttpp) REVERT: A 129 LYS cc_start: 0.8236 (mttt) cc_final: 0.8026 (mttt) REVERT: A 143 GLN cc_start: 0.7816 (mm110) cc_final: 0.7488 (mm110) REVERT: A 147 MET cc_start: 0.7611 (mtm) cc_final: 0.7385 (mtp) REVERT: A 194 GLU cc_start: 0.6670 (tm-30) cc_final: 0.6383 (tm-30) REVERT: A 248 LYS cc_start: 0.7178 (tppp) cc_final: 0.6818 (mtpt) REVERT: A 294 LYS cc_start: 0.7799 (mttp) cc_final: 0.7592 (mttp) REVERT: A 299 VAL cc_start: 0.8552 (t) cc_final: 0.8299 (p) REVERT: B 94 GLU cc_start: 0.6924 (tp30) cc_final: 0.6650 (tp30) REVERT: B 106 LYS cc_start: 0.8020 (tttm) cc_final: 0.7795 (ttpp) REVERT: B 180 ARG cc_start: 0.7074 (mtp180) cc_final: 0.6685 (mtp180) REVERT: B 247 THR cc_start: 0.7660 (m) cc_final: 0.7296 (t) REVERT: B 299 VAL cc_start: 0.8636 (t) cc_final: 0.8391 (p) REVERT: C 75 LEU cc_start: 0.7767 (mt) cc_final: 0.7550 (mt) REVERT: C 93 ARG cc_start: 0.6823 (mtt180) cc_final: 0.6567 (mtt180) REVERT: C 124 GLN cc_start: 0.7477 (pt0) cc_final: 0.6921 (pt0) REVERT: C 148 ASN cc_start: 0.6171 (p0) cc_final: 0.5265 (t0) REVERT: C 176 GLU cc_start: 0.7478 (mp0) cc_final: 0.6474 (mp0) REVERT: C 181 GLU cc_start: 0.7746 (tt0) cc_final: 0.7360 (tt0) REVERT: C 188 ARG cc_start: 0.7426 (ttp-170) cc_final: 0.6870 (ttp-170) REVERT: C 194 GLU cc_start: 0.6867 (tm-30) cc_final: 0.6424 (tm-30) REVERT: C 212 GLN cc_start: 0.7174 (pp30) cc_final: 0.6678 (pp30) REVERT: C 248 LYS cc_start: 0.7217 (tppp) cc_final: 0.7011 (mmmm) REVERT: C 271 ARG cc_start: 0.7992 (mtm180) cc_final: 0.7566 (mtm-85) REVERT: C 299 VAL cc_start: 0.8601 (t) cc_final: 0.8363 (p) REVERT: C 304 TRP cc_start: 0.7595 (m100) cc_final: 0.7054 (m100) outliers start: 20 outliers final: 12 residues processed: 226 average time/residue: 1.5689 time to fit residues: 367.4631 Evaluate side-chains 235 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 223 time to evaluate : 0.812 ------------------------------------------------------------------------------- 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 211 LEU Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain C residue 106 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 15 optimal weight: 0.0770 chunk 49 optimal weight: 0.4980 chunk 53 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 74 optimal weight: 0.7980 chunk 68 optimal weight: 0.1980 chunk 72 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 overall best weight: 0.3938 ------------------------------------------------------------------------------- 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 B 296 GLN C 186 GLN C 293 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6798 Z= 0.241 Angle : 0.524 7.150 9222 Z= 0.272 Chirality : 0.043 0.192 1050 Planarity : 0.004 0.030 1158 Dihedral : 4.992 35.689 1125 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.75 % Allowed : 22.03 % 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: 1.96 (0.29), residues: 804 helix: 3.40 (0.29), residues: 258 sheet: 1.01 (0.27), residues: 327 loop : -0.91 (0.43), residues: 219 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 0.025 0.002 PHE A 219 TYR 0.007 0.001 TYR B 111 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 239 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 220 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.7762 (mtpm) cc_final: 0.7469 (mtpm) REVERT: A 106 LYS cc_start: 0.7883 (tttp) cc_final: 0.7454 (ttpp) REVERT: A 143 GLN cc_start: 0.7823 (mm110) cc_final: 0.7474 (mm110) REVERT: A 147 MET cc_start: 0.7616 (mtm) cc_final: 0.7391 (mtp) REVERT: A 194 GLU cc_start: 0.6685 (tm-30) cc_final: 0.6394 (tm-30) REVERT: A 248 LYS cc_start: 0.7173 (tppp) cc_final: 0.6836 (mtpt) REVERT: A 294 LYS cc_start: 0.7802 (mttp) cc_final: 0.7595 (mttp) REVERT: A 299 VAL cc_start: 0.8567 (t) cc_final: 0.8317 (p) REVERT: B 94 GLU cc_start: 0.6907 (tp30) cc_final: 0.6648 (tp30) REVERT: B 106 LYS cc_start: 0.8021 (tttm) cc_final: 0.7797 (ttpp) REVERT: B 110 ARG cc_start: 0.7221 (ptm160) cc_final: 0.6996 (ptm160) REVERT: B 247 THR cc_start: 0.7665 (m) cc_final: 0.7283 (t) REVERT: B 299 VAL cc_start: 0.8645 (t) cc_final: 0.8402 (p) REVERT: C 93 ARG cc_start: 0.6817 (mtt180) cc_final: 0.6570 (mtt180) REVERT: C 124 GLN cc_start: 0.7407 (pt0) cc_final: 0.6793 (pt0) REVERT: C 176 GLU cc_start: 0.7476 (mp0) cc_final: 0.6473 (mp0) REVERT: C 181 GLU cc_start: 0.7746 (tt0) cc_final: 0.7363 (tt0) REVERT: C 188 ARG cc_start: 0.7410 (ttp-170) cc_final: 0.6856 (ttp-170) REVERT: C 194 GLU cc_start: 0.6865 (tm-30) cc_final: 0.6429 (tm-30) REVERT: C 212 GLN cc_start: 0.7192 (pp30) cc_final: 0.6720 (pp30) REVERT: C 248 LYS cc_start: 0.7213 (tppp) cc_final: 0.7012 (mmmm) REVERT: C 271 ARG cc_start: 0.7998 (mtm180) cc_final: 0.7567 (mtm-85) REVERT: C 299 VAL cc_start: 0.8577 (t) cc_final: 0.8348 (p) REVERT: C 304 TRP cc_start: 0.7601 (m100) cc_final: 0.7062 (m100) REVERT: C 319 LYS cc_start: 0.7207 (tppt) cc_final: 0.6853 (ttmm) outliers start: 19 outliers final: 12 residues processed: 222 average time/residue: 1.6046 time to fit residues: 368.8860 Evaluate side-chains 225 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 213 time to evaluate : 0.743 ------------------------------------------------------------------------------- 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 211 LEU Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain C residue 106 LYS Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 200 ASP 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: 0.9990 chunk 57 optimal weight: 0.0980 chunk 22 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 chunk 68 optimal weight: 0.3980 chunk 72 optimal weight: 0.0370 chunk 47 optimal weight: 0.5980 chunk 76 optimal weight: 0.5980 chunk 46 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 overall best weight: 0.3458 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6798 Z= 0.220 Angle : 0.519 7.068 9222 Z= 0.269 Chirality : 0.043 0.194 1050 Planarity : 0.004 0.031 1158 Dihedral : 4.774 33.776 1125 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.17 % Allowed : 23.48 % 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: 1.98 (0.30), residues: 804 helix: 3.42 (0.29), residues: 258 sheet: 1.01 (0.27), residues: 327 loop : -0.89 (0.43), residues: 219 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 0.023 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 236 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 221 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.7721 (mtpm) cc_final: 0.7426 (mtpm) REVERT: A 106 LYS cc_start: 0.7884 (tttp) cc_final: 0.7395 (ttpp) REVERT: A 143 GLN cc_start: 0.7827 (mm110) cc_final: 0.7475 (mm110) REVERT: A 147 MET cc_start: 0.7609 (mtm) cc_final: 0.7396 (mtp) REVERT: A 194 GLU cc_start: 0.6709 (tm-30) cc_final: 0.6416 (tm-30) REVERT: A 248 LYS cc_start: 0.7183 (tppp) cc_final: 0.6844 (mtpt) REVERT: A 294 LYS cc_start: 0.7804 (mttp) cc_final: 0.7595 (mttp) REVERT: A 299 VAL cc_start: 0.8534 (t) cc_final: 0.8302 (p) REVERT: B 94 GLU cc_start: 0.6909 (tp30) cc_final: 0.6642 (tp30) REVERT: B 101 MET cc_start: 0.8313 (ttm) cc_final: 0.8080 (ttm) REVERT: B 247 THR cc_start: 0.7700 (m) cc_final: 0.7303 (t) REVERT: B 299 VAL cc_start: 0.8649 (t) cc_final: 0.8409 (p) REVERT: C 93 ARG cc_start: 0.6821 (mtt180) cc_final: 0.6569 (mtt180) REVERT: C 176 GLU cc_start: 0.7469 (mp0) cc_final: 0.6428 (mp0) REVERT: C 181 GLU cc_start: 0.7745 (tt0) cc_final: 0.7330 (tt0) REVERT: C 194 GLU cc_start: 0.6870 (tm-30) cc_final: 0.6435 (tm-30) REVERT: C 212 GLN cc_start: 0.7199 (pp30) cc_final: 0.6734 (pp30) REVERT: C 271 ARG cc_start: 0.7994 (mtm180) cc_final: 0.7559 (mtm-85) REVERT: C 299 VAL cc_start: 0.8579 (t) cc_final: 0.8351 (p) REVERT: C 304 TRP cc_start: 0.7600 (m100) cc_final: 0.7101 (m100) REVERT: C 319 LYS cc_start: 0.7188 (tppt) cc_final: 0.6853 (ttmm) outliers start: 15 outliers final: 12 residues processed: 223 average time/residue: 1.5543 time to fit residues: 359.1383 Evaluate side-chains 228 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 216 time to evaluate : 0.822 ------------------------------------------------------------------------------- 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 211 LEU Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain C residue 106 LYS Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 200 ASP 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: 0.5980 chunk 64 optimal weight: 0.2980 chunk 6 optimal weight: 0.0010 chunk 49 optimal weight: 0.0670 chunk 39 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 overall best weight: 0.3124 ------------------------------------------------------------------------------- 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 ** B 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 GLN C 293 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6798 Z= 0.206 Angle : 0.515 7.136 9222 Z= 0.269 Chirality : 0.043 0.200 1050 Planarity : 0.004 0.030 1158 Dihedral : 4.591 31.678 1125 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.88 % Allowed : 24.20 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.98 (0.29), residues: 804 helix: 3.43 (0.29), residues: 258 sheet: 1.01 (0.27), residues: 327 loop : -0.90 (0.43), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 304 HIS 0.003 0.001 HIS C 98 PHE 0.022 0.002 PHE A 219 TYR 0.007 0.001 TYR B 111 ARG 0.007 0.000 ARG A 175 ********************** 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 225 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 212 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.7739 (mtpm) cc_final: 0.7449 (mtpm) REVERT: A 106 LYS cc_start: 0.7888 (tttp) cc_final: 0.7396 (ttpp) REVERT: A 143 GLN cc_start: 0.7827 (mm110) cc_final: 0.7468 (mm110) REVERT: A 147 MET cc_start: 0.7588 (mtm) cc_final: 0.7382 (mtp) REVERT: A 180 ARG cc_start: 0.7218 (mtp180) cc_final: 0.6899 (mtp180) REVERT: A 194 GLU cc_start: 0.6721 (tm-30) cc_final: 0.6421 (tm-30) REVERT: A 248 LYS cc_start: 0.7133 (tppp) cc_final: 0.6807 (mtpt) REVERT: A 294 LYS cc_start: 0.7809 (mttp) cc_final: 0.7598 (mttp) REVERT: A 299 VAL cc_start: 0.8541 (t) cc_final: 0.8303 (p) REVERT: B 94 GLU cc_start: 0.6903 (tp30) cc_final: 0.6627 (tp30) REVERT: B 101 MET cc_start: 0.8310 (ttm) cc_final: 0.8077 (ttm) REVERT: B 299 VAL cc_start: 0.8649 (t) cc_final: 0.8409 (p) REVERT: C 93 ARG cc_start: 0.6819 (mtt180) cc_final: 0.6564 (mtt180) REVERT: C 176 GLU cc_start: 0.7467 (mp0) cc_final: 0.6423 (mp0) REVERT: C 181 GLU cc_start: 0.7740 (tt0) cc_final: 0.7325 (tt0) REVERT: C 188 ARG cc_start: 0.7405 (ttp-170) cc_final: 0.7003 (ttp-170) REVERT: C 194 GLU cc_start: 0.6870 (tm-30) cc_final: 0.6442 (tm-30) REVERT: C 212 GLN cc_start: 0.7204 (pp30) cc_final: 0.6747 (pp30) REVERT: C 248 LYS cc_start: 0.7244 (mmmm) cc_final: 0.7018 (ttmm) REVERT: C 271 ARG cc_start: 0.8004 (mtm180) cc_final: 0.7574 (mtm-85) REVERT: C 299 VAL cc_start: 0.8583 (t) cc_final: 0.8364 (p) REVERT: C 304 TRP cc_start: 0.7599 (m100) cc_final: 0.7097 (m100) REVERT: C 319 LYS cc_start: 0.7166 (tppt) cc_final: 0.6837 (ttmm) outliers start: 13 outliers final: 10 residues processed: 214 average time/residue: 1.5555 time to fit residues: 345.0848 Evaluate side-chains 226 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 216 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 200 ASP 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: 0.7980 chunk 64 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 66 optimal weight: 0.0570 chunk 8 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 46 optimal weight: 0.0270 chunk 73 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.4556 ------------------------------------------------------------------------------- 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 ** B 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3841 r_free = 0.3841 target = 0.138430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.120483 restraints weight = 9462.087| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.25 r_work: 0.3461 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6798 Z= 0.275 Angle : 0.541 7.472 9222 Z= 0.281 Chirality : 0.044 0.205 1050 Planarity : 0.004 0.035 1158 Dihedral : 4.552 29.411 1125 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.74 % Allowed : 24.78 % Favored : 73.48 % 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: 1.90 (0.30), residues: 804 helix: 3.36 (0.29), residues: 258 sheet: 0.94 (0.27), residues: 330 loop : -0.92 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 230 HIS 0.002 0.001 HIS C 130 PHE 0.024 0.002 PHE A 236 TYR 0.008 0.001 TYR B 111 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: 5476.59 seconds wall clock time: 96 minutes 32.14 seconds (5792.14 seconds total)