Starting phenix.real_space_refine (version: 1.21rc1) on Thu Aug 10 03:17:49 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sqg_25384/08_2023/7sqg_25384.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sqg_25384/08_2023/7sqg_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_25384/08_2023/7sqg_25384.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sqg_25384/08_2023/7sqg_25384.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sqg_25384/08_2023/7sqg_25384.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sqg_25384/08_2023/7sqg_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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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 chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 3.95, 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: 2.52 Conformation dependent library (CDL) restraints added in 1.0 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: 0.66 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: 1.91 Time building geometry restraints manager: 2.77 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 - 15.43: 3543 15.43 - 30.85: 292 30.85 - 46.27: 70 46.27 - 61.70: 36 61.70 - 77.12: 10 Dihedral angle restraints: 3951 sinusoidal: 1554 harmonic: 2397 Sorted by residual: dihedral pdb=" CA PHE A 236 " pdb=" C PHE A 236 " pdb=" N ARG A 237 " pdb=" CA ARG A 237 " ideal model delta harmonic sigma weight residual 180.00 155.89 24.11 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA PHE B 236 " pdb=" C PHE B 236 " pdb=" N ARG B 237 " pdb=" CA ARG B 237 " ideal model delta harmonic sigma weight residual 180.00 155.89 24.11 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA PHE C 236 " pdb=" C PHE C 236 " pdb=" N ARG C 237 " pdb=" CA ARG C 237 " ideal model delta harmonic sigma weight residual 180.00 155.94 24.06 0 5.00e+00 4.00e-02 2.31e+01 ... (remaining 3948 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 721 0.041 - 0.083: 231 0.083 - 0.124: 86 0.124 - 0.166: 8 0.166 - 0.207: 4 Chirality restraints: 1050 Sorted by residual: chirality pdb=" CA LEU A 169 " pdb=" N LEU A 169 " pdb=" C LEU A 169 " pdb=" CB LEU A 169 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA LEU B 169 " pdb=" N LEU B 169 " pdb=" C LEU B 169 " pdb=" CB LEU B 169 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA LEU C 169 " pdb=" N LEU C 169 " pdb=" C LEU C 169 " pdb=" CB LEU C 169 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.05e+00 ... (remaining 1047 not shown) Planarity restraints: 1170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 118 " -0.008 2.00e-02 2.50e+03 1.55e-02 2.41e+00 pdb=" C LEU C 118 " 0.027 2.00e-02 2.50e+03 pdb=" O LEU C 118 " -0.010 2.00e-02 2.50e+03 pdb=" N TYR C 119 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 118 " -0.007 2.00e-02 2.50e+03 1.51e-02 2.27e+00 pdb=" C LEU B 118 " 0.026 2.00e-02 2.50e+03 pdb=" O LEU B 118 " -0.010 2.00e-02 2.50e+03 pdb=" N TYR B 119 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 118 " -0.007 2.00e-02 2.50e+03 1.50e-02 2.26e+00 pdb=" C LEU A 118 " 0.026 2.00e-02 2.50e+03 pdb=" O LEU A 118 " -0.010 2.00e-02 2.50e+03 pdb=" N TYR A 119 " -0.009 2.00e-02 2.50e+03 ... (remaining 1167 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 2643 2.92 - 3.41: 5865 3.41 - 3.91: 11062 3.91 - 4.40: 11948 4.40 - 4.90: 20624 Nonbonded interactions: 52142 Sorted by model distance: nonbonded pdb=" OG1 THR A 150 " pdb=" OE1 GLN A 172 " model vdw 2.423 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: 2.330 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: 11.750 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 21.390 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 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:13.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.750 ------------------------------------------------------------------------------- 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 : 13.941 77.125 2391 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer Outliers : 0.00 % 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 *********************** 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 : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 261 average time/residue: 1.6159 time to fit residues: 436.5326 Evaluate side-chains 236 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 236 time to evaluate : 0.706 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9837 ------------------------------------------------------------------------------- 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: 0.5980 chunk 61 optimal weight: 0.0020 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 32 optimal weight: 0.3980 chunk 63 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 47 optimal weight: 0.2980 chunk 73 optimal weight: 0.9980 overall best weight: 0.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 152 GLN A 208 GLN A 266 ASN A 293 GLN A 296 GLN B 266 ASN B 293 GLN B 296 GLN C 98 HIS C 186 GLN C 266 ASN ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 GLN ** C 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 6798 Z= 0.259 Angle : 0.572 7.297 9222 Z= 0.292 Chirality : 0.044 0.148 1050 Planarity : 0.003 0.030 1158 Dihedral : 4.408 23.701 873 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer Outliers : 2.61 % 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: 1.47 (0.30), residues: 804 helix: 2.87 (0.29), residues: 279 sheet: 0.90 (0.28), residues: 318 loop : -1.68 (0.40), residues: 207 *********************** 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 253 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 235 time to evaluate : 0.800 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 13 residues processed: 237 average time/residue: 1.5567 time to fit residues: 382.2445 Evaluate side-chains 242 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 229 time to evaluate : 0.742 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 1 residues processed: 12 average time/residue: 0.6009 time to fit residues: 8.9207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 40 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 25 optimal weight: 0.1980 chunk 59 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN A 208 GLN A 293 GLN B 293 GLN C 98 HIS C 186 GLN ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.044 6798 Z= 0.365 Angle : 0.589 7.931 9222 Z= 0.307 Chirality : 0.045 0.189 1050 Planarity : 0.004 0.030 1158 Dihedral : 4.589 24.771 873 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer Outliers : 3.48 % 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: 1.36 (0.29), residues: 804 helix: 2.73 (0.29), residues: 279 sheet: 0.90 (0.27), residues: 315 loop : -1.72 (0.41), residues: 210 *********************** 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 248 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 224 time to evaluate : 0.749 Fit side-chains outliers start: 24 outliers final: 11 residues processed: 232 average time/residue: 1.5671 time to fit residues: 376.9971 Evaluate side-chains 233 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 222 time to evaluate : 0.763 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 3 residues processed: 8 average time/residue: 0.7120 time to fit residues: 7.1620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 55 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 78 optimal weight: 0.3980 chunk 70 optimal weight: 0.5980 chunk 21 optimal weight: 0.1980 chunk 65 optimal weight: 0.4980 chunk 44 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 98 HIS ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 6798 Z= 0.284 Angle : 0.567 7.867 9222 Z= 0.296 Chirality : 0.044 0.188 1050 Planarity : 0.004 0.029 1158 Dihedral : 4.528 24.731 873 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer Outliers : 4.20 % 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: 1.36 (0.29), residues: 804 helix: 2.75 (0.29), residues: 279 sheet: 0.86 (0.27), residues: 315 loop : -1.68 (0.42), residues: 210 *********************** 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 245 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 216 time to evaluate : 0.778 Fit side-chains revert: symmetry clash outliers start: 29 outliers final: 17 residues processed: 224 average time/residue: 1.6316 time to fit residues: 378.8372 Evaluate side-chains 230 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 213 time to evaluate : 0.778 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 5 residues processed: 12 average time/residue: 0.6796 time to fit residues: 9.8391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 1 optimal weight: 0.3980 chunk 58 optimal weight: 0.6980 chunk 32 optimal weight: 0.1980 chunk 66 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 chunk 0 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 GLN B 293 GLN ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 6798 Z= 0.291 Angle : 0.566 7.323 9222 Z= 0.296 Chirality : 0.044 0.186 1050 Planarity : 0.004 0.030 1158 Dihedral : 4.536 25.009 873 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer Outliers : 4.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.65 (0.29), residues: 804 helix: 3.24 (0.29), residues: 258 sheet: 0.81 (0.26), residues: 324 loop : -1.14 (0.43), residues: 222 *********************** 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 258 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 226 time to evaluate : 0.766 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 15 residues processed: 234 average time/residue: 1.5406 time to fit residues: 373.9625 Evaluate side-chains 236 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 221 time to evaluate : 0.749 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 5 residues processed: 10 average time/residue: 0.7338 time to fit residues: 8.8391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 45 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 78 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 36 optimal weight: 0.3980 chunk 6 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 41 optimal weight: 0.0770 chunk 75 optimal weight: 0.1980 chunk 8 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 overall best weight: 0.3738 ------------------------------------------------------------------------------- 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 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.026 6798 Z= 0.233 Angle : 0.551 8.245 9222 Z= 0.289 Chirality : 0.044 0.184 1050 Planarity : 0.004 0.032 1158 Dihedral : 4.476 24.937 873 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer Outliers : 3.48 % 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: 1.64 (0.29), residues: 804 helix: 3.23 (0.28), residues: 258 sheet: 0.80 (0.26), residues: 324 loop : -1.12 (0.43), residues: 222 *********************** 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 242 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 218 time to evaluate : 0.797 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 15 residues processed: 227 average time/residue: 1.5917 time to fit residues: 374.3546 Evaluate side-chains 231 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 216 time to evaluate : 0.772 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 7 residues processed: 8 average time/residue: 0.8445 time to fit residues: 8.2445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 57 optimal weight: 0.0040 chunk 44 optimal weight: 0.4980 chunk 65 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 78 optimal weight: 0.2980 chunk 48 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 36 optimal weight: 0.4980 chunk 31 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 overall best weight: 0.3992 ------------------------------------------------------------------------------- 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 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 GLN ** C 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.2749 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= 0.248 Angle : 0.551 7.135 9222 Z= 0.288 Chirality : 0.044 0.192 1050 Planarity : 0.004 0.043 1158 Dihedral : 4.478 25.029 873 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer Outliers : 3.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.29), residues: 804 helix: 3.21 (0.29), residues: 258 sheet: 0.81 (0.26), residues: 324 loop : -1.12 (0.43), residues: 222 *********************** 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 242 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 219 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 16 residues processed: 229 average time/residue: 1.6036 time to fit residues: 380.4693 Evaluate side-chains 233 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 217 time to evaluate : 0.760 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 9 residues processed: 7 average time/residue: 0.9917 time to fit residues: 8.3421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 15 optimal weight: 0.5980 chunk 49 optimal weight: 0.4980 chunk 53 optimal weight: 1.9990 chunk 38 optimal weight: 0.4980 chunk 7 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 71 optimal weight: 0.4980 chunk 74 optimal weight: 0.2980 chunk 68 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 293 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.2864 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= 0.283 Angle : 0.567 7.442 9222 Z= 0.296 Chirality : 0.045 0.199 1050 Planarity : 0.004 0.040 1158 Dihedral : 4.542 25.196 873 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer Outliers : 3.04 % 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: 1.64 (0.29), residues: 804 helix: 3.19 (0.29), residues: 258 sheet: 0.82 (0.26), residues: 324 loop : -1.13 (0.43), residues: 222 *********************** 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 234 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 213 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 10 residues processed: 222 average time/residue: 1.5773 time to fit residues: 362.9704 Evaluate side-chains 223 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 213 time to evaluate : 0.834 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 6 residues processed: 4 average time/residue: 1.0106 time to fit residues: 5.3581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.5980 chunk 22 optimal weight: 0.5980 chunk 65 optimal weight: 0.2980 chunk 68 optimal weight: 0.5980 chunk 72 optimal weight: 0.4980 chunk 47 optimal weight: 1.9990 chunk 76 optimal weight: 0.2980 chunk 46 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 GLN ** B 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 GLN C 293 GLN ** C 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.2960 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= 0.275 Angle : 0.574 7.358 9222 Z= 0.300 Chirality : 0.045 0.204 1050 Planarity : 0.004 0.036 1158 Dihedral : 4.582 25.386 873 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer Outliers : 2.75 % 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: 1.60 (0.29), residues: 804 helix: 3.18 (0.29), residues: 258 sheet: 0.79 (0.26), residues: 324 loop : -1.15 (0.43), residues: 222 *********************** 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 235 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 216 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 11 residues processed: 224 average time/residue: 1.5933 time to fit residues: 369.8037 Evaluate side-chains 224 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 213 time to evaluate : 0.788 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 8 residues processed: 3 average time/residue: 1.2150 time to fit residues: 4.8427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 80 optimal weight: 0.0170 chunk 74 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 6 optimal weight: 0.0170 chunk 49 optimal weight: 0.9990 chunk 39 optimal weight: 0.4980 chunk 51 optimal weight: 0.9980 chunk 68 optimal weight: 0.1980 chunk 19 optimal weight: 0.9990 chunk 59 optimal weight: 0.0670 chunk 9 optimal weight: 0.6980 overall best weight: 0.1594 ------------------------------------------------------------------------------- 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 ** B 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 GLN ** C 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 6798 Z= 0.169 Angle : 0.537 6.626 9222 Z= 0.284 Chirality : 0.044 0.194 1050 Planarity : 0.004 0.036 1158 Dihedral : 4.467 25.465 873 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer Outliers : 2.03 % 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: 1.70 (0.30), residues: 804 helix: 3.34 (0.29), residues: 258 sheet: 0.69 (0.26), residues: 327 loop : -0.94 (0.44), residues: 219 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 205 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 10 residues processed: 212 average time/residue: 1.5856 time to fit residues: 348.2760 Evaluate side-chains 214 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 204 time to evaluate : 0.761 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 7 residues processed: 3 average time/residue: 0.6735 time to fit residues: 3.2630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 17 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 GLN ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 GLN B 293 GLN B 296 GLN C 293 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.137258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.119320 restraints weight = 9423.228| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.26 r_work: 0.3452 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.047 6798 Z= 0.393 Angle : 0.623 7.603 9222 Z= 0.321 Chirality : 0.046 0.215 1050 Planarity : 0.004 0.037 1158 Dihedral : 4.707 25.893 873 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer Outliers : 1.88 % 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: 1.31 (0.30), residues: 804 helix: 2.72 (0.30), residues: 279 sheet: 0.72 (0.27), residues: 318 loop : -1.56 (0.43), residues: 207 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5430.25 seconds wall clock time: 95 minutes 35.33 seconds (5735.33 seconds total)