Starting phenix.real_space_refine on Wed Feb 12 11:01:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7c99_30309/02_2025/7c99_30309.cif Found real_map, /net/cci-nas-00/data/ceres_data/7c99_30309/02_2025/7c99_30309.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7c99_30309/02_2025/7c99_30309.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7c99_30309/02_2025/7c99_30309.map" model { file = "/net/cci-nas-00/data/ceres_data/7c99_30309/02_2025/7c99_30309.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7c99_30309/02_2025/7c99_30309.cif" } resolution = 3.36 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= 0.002 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: 6 Type Number sf(0) Gaussians Ca 3 9.91 5 P 27 5.49 5 S 33 5.16 5 C 4755 2.51 5 N 1341 2.21 5 O 1497 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 7656 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2397 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "B" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2397 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "C" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2397 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "D" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 180 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "E" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 189 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.30, per 1000 atoms: 0.82 Number of scatterers: 7656 At special positions: 0 Unit cell: (107.52, 78.12, 115.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 3 19.99 S 33 16.00 P 27 15.00 O 1497 8.00 N 1341 7.00 C 4755 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.12 Conformation dependent library (CDL) restraints added in 1.1 seconds 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1692 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 9 sheets defined 40.2% alpha, 11.9% beta 8 base pairs and 12 stacking pairs defined. Time for finding SS restraints: 2.63 Creating SS restraints... Processing helix chain 'A' and resid 27 through 31 removed outlier: 4.269A pdb=" N GLY A 31 " --> pdb=" O GLN A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 41 Processing helix chain 'A' and resid 47 through 53 removed outlier: 3.503A pdb=" N ILE A 51 " --> pdb=" O THR A 47 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN A 52 " --> pdb=" O ILE A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 79 removed outlier: 3.660A pdb=" N LYS A 74 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA A 76 " --> pdb=" O LYS A 72 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 95 removed outlier: 3.697A pdb=" N GLU A 93 " --> pdb=" O PHE A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 113 removed outlier: 3.814A pdb=" N LEU A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 143 removed outlier: 3.500A pdb=" N LEU A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL A 141 " --> pdb=" O HIS A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 151 removed outlier: 4.023A pdb=" N GLY A 150 " --> pdb=" O GLY A 147 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR A 151 " --> pdb=" O ALA A 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 147 through 151' Processing helix chain 'A' and resid 166 through 168 No H-bonds generated for 'chain 'A' and resid 166 through 168' Processing helix chain 'A' and resid 169 through 174 Processing helix chain 'A' and resid 195 through 202 Processing helix chain 'A' and resid 202 through 213 removed outlier: 3.564A pdb=" N VAL A 206 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 260 removed outlier: 3.560A pdb=" N ARG A 242 " --> pdb=" O GLU A 238 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLN A 248 " --> pdb=" O GLN A 244 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET A 249 " --> pdb=" O LYS A 245 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG A 252 " --> pdb=" O GLN A 248 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU A 258 " --> pdb=" O GLN A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 297 removed outlier: 3.934A pdb=" N LEU A 293 " --> pdb=" O GLY A 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 31 removed outlier: 4.269A pdb=" N GLY B 31 " --> pdb=" O GLN B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 41 Processing helix chain 'B' and resid 47 through 53 removed outlier: 3.502A pdb=" N ILE B 51 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN B 52 " --> pdb=" O ILE B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 79 removed outlier: 3.660A pdb=" N LYS B 74 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA B 76 " --> pdb=" O LYS B 72 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS B 79 " --> pdb=" O GLU B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 95 removed outlier: 3.697A pdb=" N GLU B 93 " --> pdb=" O PHE B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 113 removed outlier: 3.814A pdb=" N LEU B 111 " --> pdb=" O GLU B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 143 removed outlier: 3.500A pdb=" N LEU B 139 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL B 141 " --> pdb=" O HIS B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 151 removed outlier: 4.024A pdb=" N GLY B 150 " --> pdb=" O GLY B 147 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR B 151 " --> pdb=" O ALA B 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 147 through 151' Processing helix chain 'B' and resid 166 through 168 No H-bonds generated for 'chain 'B' and resid 166 through 168' Processing helix chain 'B' and resid 169 through 174 Processing helix chain 'B' and resid 195 through 202 Processing helix chain 'B' and resid 202 through 213 removed outlier: 3.564A pdb=" N VAL B 206 " --> pdb=" O LEU B 202 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU B 213 " --> pdb=" O LYS B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 260 removed outlier: 3.562A pdb=" N ARG B 242 " --> pdb=" O GLU B 238 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLN B 248 " --> pdb=" O GLN B 244 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET B 249 " --> pdb=" O LYS B 245 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG B 252 " --> pdb=" O GLN B 248 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU B 258 " --> pdb=" O GLN B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 297 removed outlier: 3.934A pdb=" N LEU B 293 " --> pdb=" O GLY B 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 31 removed outlier: 4.270A pdb=" N GLY C 31 " --> pdb=" O GLN C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 41 Processing helix chain 'C' and resid 47 through 53 removed outlier: 3.503A pdb=" N ILE C 51 " --> pdb=" O THR C 47 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN C 52 " --> pdb=" O ILE C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 79 removed outlier: 3.660A pdb=" N LYS C 74 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA C 76 " --> pdb=" O LYS C 72 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS C 79 " --> pdb=" O GLU C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 95 removed outlier: 3.698A pdb=" N GLU C 93 " --> pdb=" O PHE C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 113 removed outlier: 3.814A pdb=" N LEU C 111 " --> pdb=" O GLU C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 143 removed outlier: 3.501A pdb=" N LEU C 139 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL C 141 " --> pdb=" O HIS C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 151 removed outlier: 4.023A pdb=" N GLY C 150 " --> pdb=" O GLY C 147 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR C 151 " --> pdb=" O ALA C 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 147 through 151' Processing helix chain 'C' and resid 166 through 168 No H-bonds generated for 'chain 'C' and resid 166 through 168' Processing helix chain 'C' and resid 169 through 174 Processing helix chain 'C' and resid 195 through 202 Processing helix chain 'C' and resid 202 through 213 removed outlier: 3.564A pdb=" N VAL C 206 " --> pdb=" O LEU C 202 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU C 213 " --> pdb=" O LYS C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 260 removed outlier: 3.561A pdb=" N ARG C 242 " --> pdb=" O GLU C 238 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLN C 248 " --> pdb=" O GLN C 244 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET C 249 " --> pdb=" O LYS C 245 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG C 252 " --> pdb=" O GLN C 248 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU C 258 " --> pdb=" O GLN C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 297 removed outlier: 3.933A pdb=" N LEU C 293 " --> pdb=" O GLY C 289 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 326 through 327 removed outlier: 3.835A pdb=" N ALA A 313 " --> pdb=" O ALA A 326 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N THR A 122 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ASN A 268 " --> pdb=" O THR A 122 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ALA A 124 " --> pdb=" O ASN A 268 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LYS A 218 " --> pdb=" O ALA A 263 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N PHE A 265 " --> pdb=" O LYS A 218 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU A 220 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N THR A 267 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ILE A 222 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N LYS A 155 " --> pdb=" O PHE A 217 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU A 219 " --> pdb=" O LYS A 155 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE A 156 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N ALA A 191 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N PHE A 158 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 270 through 271 Processing sheet with id=AA3, first strand: chain 'A' and resid 330 through 331 Processing sheet with id=AA4, first strand: chain 'B' and resid 326 through 327 removed outlier: 3.835A pdb=" N ALA B 313 " --> pdb=" O ALA B 326 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N THR B 122 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ASN B 268 " --> pdb=" O THR B 122 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ALA B 124 " --> pdb=" O ASN B 268 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LYS B 218 " --> pdb=" O ALA B 263 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N PHE B 265 " --> pdb=" O LYS B 218 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU B 220 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N THR B 267 " --> pdb=" O LEU B 220 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ILE B 222 " --> pdb=" O THR B 267 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N LYS B 155 " --> pdb=" O PHE B 217 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU B 219 " --> pdb=" O LYS B 155 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N ALA B 191 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N PHE B 158 " --> pdb=" O ALA B 191 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 270 through 271 Processing sheet with id=AA6, first strand: chain 'B' and resid 330 through 331 Processing sheet with id=AA7, first strand: chain 'C' and resid 188 through 192 removed outlier: 6.372A pdb=" N ILE C 156 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N ALA C 191 " --> pdb=" O ILE C 156 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N PHE C 158 " --> pdb=" O ALA C 191 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N LYS C 155 " --> pdb=" O PHE C 217 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU C 219 " --> pdb=" O LYS C 155 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LYS C 218 " --> pdb=" O ALA C 263 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N PHE C 265 " --> pdb=" O LYS C 218 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU C 220 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N THR C 267 " --> pdb=" O LEU C 220 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ILE C 222 " --> pdb=" O THR C 267 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N THR C 122 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N ASN C 268 " --> pdb=" O THR C 122 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ALA C 124 " --> pdb=" O ASN C 268 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA C 313 " --> pdb=" O ALA C 326 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 270 through 271 Processing sheet with id=AA9, first strand: chain 'C' and resid 330 through 331 203 hydrogen bonds defined for protein. 558 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 16 hydrogen bonds 32 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 12 stacking parallelities Total time for adding SS restraints: 2.62 Time building geometry restraints manager: 2.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2021 1.33 - 1.45: 1371 1.45 - 1.57: 4313 1.57 - 1.69: 51 1.69 - 1.81: 57 Bond restraints: 7813 Sorted by residual: bond pdb=" O3A ANP C 401 " pdb=" PB ANP C 401 " ideal model delta sigma weight residual 1.700 1.551 0.149 2.00e-02 2.50e+03 5.57e+01 bond pdb=" O3A ANP A 402 " pdb=" PB ANP A 402 " ideal model delta sigma weight residual 1.700 1.553 0.147 2.00e-02 2.50e+03 5.39e+01 bond pdb=" O3A ANP B 402 " pdb=" PB ANP B 402 " ideal model delta sigma weight residual 1.700 1.553 0.147 2.00e-02 2.50e+03 5.37e+01 bond pdb=" N3B ANP C 401 " pdb=" PG ANP C 401 " ideal model delta sigma weight residual 1.795 1.680 0.115 2.00e-02 2.50e+03 3.33e+01 bond pdb=" N3B ANP A 402 " pdb=" PG ANP A 402 " ideal model delta sigma weight residual 1.795 1.684 0.111 2.00e-02 2.50e+03 3.09e+01 ... (remaining 7808 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.51: 10525 4.51 - 9.02: 67 9.02 - 13.53: 5 13.53 - 18.04: 0 18.04 - 22.55: 3 Bond angle restraints: 10600 Sorted by residual: angle pdb=" PB ANP A 402 " pdb=" N3B ANP A 402 " pdb=" PG ANP A 402 " ideal model delta sigma weight residual 126.95 104.40 22.55 3.00e+00 1.11e-01 5.65e+01 angle pdb=" PB ANP B 402 " pdb=" N3B ANP B 402 " pdb=" PG ANP B 402 " ideal model delta sigma weight residual 126.95 104.41 22.54 3.00e+00 1.11e-01 5.65e+01 angle pdb=" PB ANP C 401 " pdb=" N3B ANP C 401 " pdb=" PG ANP C 401 " ideal model delta sigma weight residual 126.95 105.31 21.64 3.00e+00 1.11e-01 5.20e+01 angle pdb=" N VAL A 184 " pdb=" CA VAL A 184 " pdb=" C VAL A 184 " ideal model delta sigma weight residual 113.71 107.64 6.07 9.50e-01 1.11e+00 4.09e+01 angle pdb=" N VAL B 184 " pdb=" CA VAL B 184 " pdb=" C VAL B 184 " ideal model delta sigma weight residual 113.71 107.66 6.05 9.50e-01 1.11e+00 4.06e+01 ... (remaining 10595 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.94: 4363 25.94 - 51.89: 301 51.89 - 77.83: 64 77.83 - 103.78: 18 103.78 - 129.72: 3 Dihedral angle restraints: 4749 sinusoidal: 2115 harmonic: 2634 Sorted by residual: dihedral pdb=" CA ASN A 163 " pdb=" C ASN A 163 " pdb=" N THR A 164 " pdb=" CA THR A 164 " ideal model delta harmonic sigma weight residual -180.00 -151.55 -28.45 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CA ASN B 163 " pdb=" C ASN B 163 " pdb=" N THR B 164 " pdb=" CA THR B 164 " ideal model delta harmonic sigma weight residual -180.00 -151.57 -28.43 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA ASN C 163 " pdb=" C ASN C 163 " pdb=" N THR C 164 " pdb=" CA THR C 164 " ideal model delta harmonic sigma weight residual -180.00 -151.62 -28.38 0 5.00e+00 4.00e-02 3.22e+01 ... (remaining 4746 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 928 0.060 - 0.120: 231 0.120 - 0.180: 31 0.180 - 0.241: 1 0.241 - 0.301: 3 Chirality restraints: 1194 Sorted by residual: chirality pdb=" C3' ANP C 401 " pdb=" C2' ANP C 401 " pdb=" C4' ANP C 401 " pdb=" O3' ANP C 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.66 0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" C3' ANP A 402 " pdb=" C2' ANP A 402 " pdb=" C4' ANP A 402 " pdb=" O3' ANP A 402 " both_signs ideal model delta sigma weight residual False -2.36 -2.66 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" C3' ANP B 402 " pdb=" C2' ANP B 402 " pdb=" C4' ANP B 402 " pdb=" O3' ANP B 402 " both_signs ideal model delta sigma weight residual False -2.36 -2.65 0.30 2.00e-01 2.50e+01 2.21e+00 ... (remaining 1191 not shown) Planarity restraints: 1290 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 317 " -0.012 2.00e-02 2.50e+03 2.48e-02 6.17e+00 pdb=" C ASP B 317 " 0.043 2.00e-02 2.50e+03 pdb=" O ASP B 317 " -0.017 2.00e-02 2.50e+03 pdb=" N SER B 318 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 317 " -0.012 2.00e-02 2.50e+03 2.46e-02 6.03e+00 pdb=" C ASP C 317 " 0.042 2.00e-02 2.50e+03 pdb=" O ASP C 317 " -0.016 2.00e-02 2.50e+03 pdb=" N SER C 318 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 317 " -0.012 2.00e-02 2.50e+03 2.44e-02 5.94e+00 pdb=" C ASP A 317 " 0.042 2.00e-02 2.50e+03 pdb=" O ASP A 317 " -0.016 2.00e-02 2.50e+03 pdb=" N SER A 318 " -0.014 2.00e-02 2.50e+03 ... (remaining 1287 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 29 2.40 - 3.03: 3868 3.03 - 3.65: 10308 3.65 - 4.28: 16421 4.28 - 4.90: 27920 Nonbonded interactions: 58546 Sorted by model distance: nonbonded pdb=" OD1 ASP A 168 " pdb=" NH2 ARG A 171 " model vdw 1.776 3.120 nonbonded pdb=" OD1 ASP B 168 " pdb=" NH2 ARG B 171 " model vdw 1.777 3.120 nonbonded pdb="CA CA B 401 " pdb=" O2G ANP B 402 " model vdw 2.084 2.510 nonbonded pdb="CA CA A 401 " pdb=" O2G ANP A 402 " model vdw 2.084 2.510 nonbonded pdb=" O2G ANP C 401 " pdb="CA CA C 402 " model vdw 2.099 2.510 ... (remaining 58541 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 22 through 337) selection = (chain 'B' and resid 22 through 337) selection = (chain 'C' and resid 22 through 337) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.830 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 24.270 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 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 : 0.008 0.149 7813 Z= 0.471 Angle : 1.051 22.547 10600 Z= 0.544 Chirality : 0.053 0.301 1194 Planarity : 0.004 0.028 1290 Dihedral : 18.459 129.722 3057 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % 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: -5.91 (0.18), residues: 915 helix: -4.79 (0.09), residues: 384 sheet: -1.97 (0.34), residues: 162 loop : -3.63 (0.23), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS C 30 PHE 0.028 0.003 PHE C 128 TYR 0.008 0.002 TYR B 260 ARG 0.010 0.001 ARG C 192 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 THR cc_start: 0.8734 (m) cc_final: 0.8488 (t) REVERT: A 244 GLN cc_start: 0.8190 (mt0) cc_final: 0.7940 (mt0) REVERT: A 273 ASP cc_start: 0.7985 (t0) cc_final: 0.7750 (t70) REVERT: A 331 THR cc_start: 0.9030 (p) cc_final: 0.8781 (t) REVERT: B 94 LYS cc_start: 0.8341 (mmtt) cc_final: 0.7989 (mmtp) REVERT: B 119 MET cc_start: 0.8617 (mtt) cc_final: 0.8339 (mtm) REVERT: B 202 LEU cc_start: 0.9131 (tp) cc_final: 0.8626 (tt) REVERT: B 314 LYS cc_start: 0.8819 (ttmm) cc_final: 0.8579 (tttt) REVERT: C 123 GLU cc_start: 0.7564 (tt0) cc_final: 0.7353 (tt0) REVERT: C 155 LYS cc_start: 0.8567 (mttt) cc_final: 0.8237 (mtpt) REVERT: C 335 ILE cc_start: 0.8921 (mm) cc_final: 0.8559 (mm) outliers start: 0 outliers final: 0 residues processed: 249 average time/residue: 0.2588 time to fit residues: 81.0894 Evaluate side-chains 154 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 0.0370 chunk 68 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN A 30 HIS A 243 GLN A 261 ASN B 22 GLN B 30 HIS B 199 GLN B 243 GLN C 22 GLN C 30 HIS C 199 GLN C 243 GLN C 244 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.157506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.124901 restraints weight = 10436.357| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.09 r_work: 0.3143 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7813 Z= 0.171 Angle : 0.568 6.416 10600 Z= 0.308 Chirality : 0.044 0.155 1194 Planarity : 0.003 0.024 1290 Dihedral : 17.835 153.812 1299 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.58 % Allowed : 10.67 % Favored : 87.75 % 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: -4.72 (0.20), residues: 915 helix: -3.44 (0.17), residues: 399 sheet: -1.54 (0.36), residues: 153 loop : -3.30 (0.24), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 30 PHE 0.017 0.001 PHE B 128 TYR 0.007 0.001 TYR B 194 ARG 0.006 0.000 ARG B 252 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 181 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 THR cc_start: 0.8723 (m) cc_final: 0.8495 (m) REVERT: A 93 GLU cc_start: 0.8276 (mp0) cc_final: 0.7671 (mm-30) REVERT: A 194 TYR cc_start: 0.9046 (m-80) cc_final: 0.8643 (m-80) REVERT: A 252 ARG cc_start: 0.8480 (ttt90) cc_final: 0.8273 (ttm-80) REVERT: A 331 THR cc_start: 0.8971 (p) cc_final: 0.8741 (t) REVERT: B 119 MET cc_start: 0.9026 (mtt) cc_final: 0.8802 (mtm) REVERT: B 180 ASP cc_start: 0.8075 (m-30) cc_final: 0.7519 (t0) REVERT: B 210 PHE cc_start: 0.8819 (m-10) cc_final: 0.8507 (m-80) REVERT: C 49 LYS cc_start: 0.7130 (OUTLIER) cc_final: 0.6838 (tttt) REVERT: C 90 GLU cc_start: 0.7858 (mp0) cc_final: 0.7625 (mp0) REVERT: C 155 LYS cc_start: 0.8698 (mttt) cc_final: 0.8252 (mtpt) outliers start: 12 outliers final: 6 residues processed: 189 average time/residue: 0.2224 time to fit residues: 54.7771 Evaluate side-chains 165 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 158 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 231 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 37 optimal weight: 6.9990 chunk 7 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 34 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 HIS C 244 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.152577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.120137 restraints weight = 10602.623| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.09 r_work: 0.3073 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7813 Z= 0.260 Angle : 0.568 5.843 10600 Z= 0.306 Chirality : 0.045 0.181 1194 Planarity : 0.003 0.030 1290 Dihedral : 16.901 149.408 1299 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 2.77 % Allowed : 13.44 % Favored : 83.79 % 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: -3.86 (0.23), residues: 915 helix: -2.45 (0.22), residues: 396 sheet: -1.50 (0.36), residues: 159 loop : -3.03 (0.26), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS A 211 PHE 0.021 0.002 PHE C 128 TYR 0.010 0.001 TYR A 194 ARG 0.006 0.001 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 0.823 Fit side-chains revert: symmetry clash REVERT: A 93 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7798 (mm-30) REVERT: A 194 TYR cc_start: 0.9238 (m-80) cc_final: 0.8839 (m-80) REVERT: A 258 GLU cc_start: 0.8889 (mt-10) cc_final: 0.8682 (mt-10) REVERT: A 309 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8262 (mt-10) REVERT: B 93 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.7585 (mp0) REVERT: C 117 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7780 (mt-10) REVERT: C 119 MET cc_start: 0.8942 (mtt) cc_final: 0.8739 (mtt) REVERT: C 155 LYS cc_start: 0.8737 (mttt) cc_final: 0.8311 (mtpt) REVERT: C 238 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8403 (mt-10) outliers start: 21 outliers final: 11 residues processed: 155 average time/residue: 0.2028 time to fit residues: 42.1233 Evaluate side-chains 139 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 323 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 21 optimal weight: 5.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 244 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.146980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.115355 restraints weight = 10565.176| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.03 r_work: 0.3096 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 7813 Z= 0.320 Angle : 0.587 6.440 10600 Z= 0.314 Chirality : 0.047 0.199 1194 Planarity : 0.004 0.037 1290 Dihedral : 16.731 149.612 1299 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 3.16 % Allowed : 14.89 % Favored : 81.95 % 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: -3.43 (0.24), residues: 915 helix: -1.92 (0.24), residues: 396 sheet: -1.28 (0.39), residues: 153 loop : -3.02 (0.26), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 295 PHE 0.024 0.002 PHE C 128 TYR 0.010 0.002 TYR A 260 ARG 0.005 0.001 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.890 Fit side-chains revert: symmetry clash REVERT: A 93 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7899 (mm-30) REVERT: A 252 ARG cc_start: 0.8578 (ttt90) cc_final: 0.8363 (ttm-80) REVERT: B 90 GLU cc_start: 0.8322 (tp30) cc_final: 0.8088 (tp30) REVERT: B 93 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.7633 (mp0) REVERT: B 175 ASP cc_start: 0.8537 (m-30) cc_final: 0.8334 (m-30) REVERT: B 180 ASP cc_start: 0.8091 (m-30) cc_final: 0.7643 (t0) REVERT: B 260 TYR cc_start: 0.8689 (m-10) cc_final: 0.8364 (m-10) REVERT: C 117 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7825 (mt-10) REVERT: C 155 LYS cc_start: 0.8701 (mttt) cc_final: 0.8367 (mtpt) REVERT: C 192 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.7564 (ttt180) REVERT: C 238 GLU cc_start: 0.8781 (mt-10) cc_final: 0.8444 (mt-10) outliers start: 24 outliers final: 10 residues processed: 138 average time/residue: 0.2152 time to fit residues: 39.7367 Evaluate side-chains 132 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 192 ARG Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 323 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 76 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 HIS C 100 HIS C 244 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.149710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.118058 restraints weight = 10515.935| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.02 r_work: 0.3067 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 7813 Z= 0.301 Angle : 0.568 6.622 10600 Z= 0.304 Chirality : 0.046 0.202 1194 Planarity : 0.003 0.031 1290 Dihedral : 16.615 149.486 1299 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 3.16 % Allowed : 16.07 % Favored : 80.76 % 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: -3.14 (0.25), residues: 915 helix: -1.60 (0.25), residues: 396 sheet: -1.26 (0.38), residues: 153 loop : -2.92 (0.26), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 295 PHE 0.023 0.002 PHE C 128 TYR 0.011 0.002 TYR B 260 ARG 0.004 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.908 Fit side-chains REVERT: A 252 ARG cc_start: 0.8500 (ttt90) cc_final: 0.8294 (ttm-80) REVERT: B 93 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.7611 (mp0) REVERT: B 110 LYS cc_start: 0.9051 (ttpp) cc_final: 0.8835 (ttmt) REVERT: B 172 ASP cc_start: 0.7709 (m-30) cc_final: 0.7503 (m-30) REVERT: B 175 ASP cc_start: 0.8566 (m-30) cc_final: 0.8364 (m-30) REVERT: B 180 ASP cc_start: 0.8037 (m-30) cc_final: 0.7590 (t0) REVERT: B 260 TYR cc_start: 0.8727 (m-10) cc_final: 0.8509 (m-10) REVERT: C 72 LYS cc_start: 0.8552 (mttp) cc_final: 0.7707 (tptt) REVERT: C 93 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.7940 (mp0) REVERT: C 106 GLN cc_start: 0.8470 (mt0) cc_final: 0.8252 (mm-40) REVERT: C 155 LYS cc_start: 0.8722 (mttt) cc_final: 0.8355 (mtpt) REVERT: C 192 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.7585 (ttt180) REVERT: C 238 GLU cc_start: 0.8790 (mt-10) cc_final: 0.8436 (mt-10) outliers start: 24 outliers final: 10 residues processed: 136 average time/residue: 0.2339 time to fit residues: 42.1199 Evaluate side-chains 134 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 192 ARG Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 323 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 0 optimal weight: 20.0000 chunk 6 optimal weight: 0.2980 chunk 2 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 63 optimal weight: 8.9990 chunk 22 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 HIS C 244 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.151077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.119484 restraints weight = 10510.694| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.04 r_work: 0.3097 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7813 Z= 0.171 Angle : 0.505 6.124 10600 Z= 0.273 Chirality : 0.044 0.176 1194 Planarity : 0.003 0.021 1290 Dihedral : 16.484 150.213 1299 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 2.11 % Allowed : 17.79 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.25), residues: 915 helix: -1.22 (0.26), residues: 396 sheet: -1.17 (0.38), residues: 153 loop : -2.79 (0.27), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 137 PHE 0.022 0.001 PHE C 128 TYR 0.009 0.001 TYR B 260 ARG 0.003 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 0.861 Fit side-chains revert: symmetry clash REVERT: A 252 ARG cc_start: 0.8447 (ttt90) cc_final: 0.8246 (ttm-80) REVERT: B 90 GLU cc_start: 0.8292 (tp30) cc_final: 0.8021 (tp30) REVERT: B 93 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.7572 (mp0) REVERT: B 110 LYS cc_start: 0.9064 (ttpp) cc_final: 0.8851 (ttmt) REVERT: B 172 ASP cc_start: 0.7738 (m-30) cc_final: 0.7530 (m-30) REVERT: B 180 ASP cc_start: 0.8009 (m-30) cc_final: 0.7515 (t0) REVERT: B 260 TYR cc_start: 0.8646 (m-10) cc_final: 0.8216 (m-10) REVERT: B 261 ASN cc_start: 0.9076 (t0) cc_final: 0.8841 (t0) REVERT: C 72 LYS cc_start: 0.8603 (mttp) cc_final: 0.7739 (tptt) REVERT: C 93 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.7943 (mp0) REVERT: C 192 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.7509 (ttt180) REVERT: C 238 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8574 (mt-10) outliers start: 16 outliers final: 10 residues processed: 146 average time/residue: 0.2168 time to fit residues: 41.9742 Evaluate side-chains 142 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 129 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 192 ARG Chi-restraints excluded: chain C residue 323 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 58 optimal weight: 3.9990 chunk 61 optimal weight: 9.9990 chunk 48 optimal weight: 0.3980 chunk 6 optimal weight: 0.0060 chunk 67 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 chunk 64 optimal weight: 7.9990 chunk 66 optimal weight: 0.0030 chunk 73 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 overall best weight: 1.6810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 HIS ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 244 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.150544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.119067 restraints weight = 10582.479| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.04 r_work: 0.3076 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7813 Z= 0.244 Angle : 0.535 6.463 10600 Z= 0.287 Chirality : 0.045 0.192 1194 Planarity : 0.003 0.029 1290 Dihedral : 16.426 150.049 1299 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 2.37 % Allowed : 18.05 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.26), residues: 915 helix: -1.10 (0.26), residues: 396 sheet: -1.11 (0.38), residues: 153 loop : -2.71 (0.28), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS A 211 PHE 0.023 0.002 PHE B 108 TYR 0.012 0.001 TYR B 205 ARG 0.003 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.779 Fit side-chains REVERT: A 252 ARG cc_start: 0.8486 (ttt90) cc_final: 0.8283 (ttm-80) REVERT: B 90 GLU cc_start: 0.8390 (tp30) cc_final: 0.8100 (tp30) REVERT: B 93 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.7562 (mp0) REVERT: B 168 ASP cc_start: 0.8159 (m-30) cc_final: 0.7887 (m-30) REVERT: B 172 ASP cc_start: 0.7814 (m-30) cc_final: 0.7601 (m-30) REVERT: B 180 ASP cc_start: 0.7990 (m-30) cc_final: 0.7576 (t0) REVERT: B 261 ASN cc_start: 0.9089 (t0) cc_final: 0.8869 (t0) REVERT: C 38 LYS cc_start: 0.7410 (pttm) cc_final: 0.6413 (ptmm) REVERT: C 72 LYS cc_start: 0.8557 (mttp) cc_final: 0.7724 (tptt) REVERT: C 192 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.7528 (ttt180) REVERT: C 238 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8496 (mt-10) outliers start: 18 outliers final: 10 residues processed: 135 average time/residue: 0.2231 time to fit residues: 39.6510 Evaluate side-chains 133 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 192 ARG Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 323 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 52 optimal weight: 0.6980 chunk 37 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 2 optimal weight: 8.9990 chunk 51 optimal weight: 0.7980 chunk 59 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 244 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.149140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.117660 restraints weight = 10694.675| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.08 r_work: 0.3087 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.3943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7813 Z= 0.239 Angle : 0.535 6.418 10600 Z= 0.286 Chirality : 0.045 0.191 1194 Planarity : 0.003 0.027 1290 Dihedral : 16.401 150.155 1299 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.37 % Allowed : 18.97 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.26), residues: 915 helix: -1.00 (0.26), residues: 396 sheet: -1.10 (0.38), residues: 153 loop : -2.64 (0.28), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 211 PHE 0.023 0.002 PHE C 128 TYR 0.026 0.002 TYR B 260 ARG 0.003 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.824 Fit side-chains revert: symmetry clash REVERT: A 252 ARG cc_start: 0.8468 (ttt90) cc_final: 0.8230 (ttm-80) REVERT: B 90 GLU cc_start: 0.8378 (tp30) cc_final: 0.8113 (tp30) REVERT: B 93 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.7519 (mp0) REVERT: B 168 ASP cc_start: 0.8177 (m-30) cc_final: 0.7906 (m-30) REVERT: B 172 ASP cc_start: 0.7906 (m-30) cc_final: 0.7672 (m-30) REVERT: B 180 ASP cc_start: 0.7952 (m-30) cc_final: 0.7530 (t0) REVERT: B 261 ASN cc_start: 0.9056 (t0) cc_final: 0.8845 (t0) REVERT: C 38 LYS cc_start: 0.7335 (pttm) cc_final: 0.6380 (ptmm) REVERT: C 72 LYS cc_start: 0.8545 (mttp) cc_final: 0.7675 (tptt) REVERT: C 93 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.7919 (mp0) REVERT: C 192 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.7573 (ttt180) REVERT: C 238 GLU cc_start: 0.8872 (mt-10) cc_final: 0.8568 (mt-10) outliers start: 18 outliers final: 11 residues processed: 136 average time/residue: 0.2240 time to fit residues: 40.5738 Evaluate side-chains 137 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 192 ARG Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 323 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 30 optimal weight: 20.0000 chunk 71 optimal weight: 0.5980 chunk 84 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 67 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 244 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.149522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.118282 restraints weight = 10749.332| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.07 r_work: 0.3081 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7813 Z= 0.198 Angle : 0.515 6.495 10600 Z= 0.277 Chirality : 0.044 0.183 1194 Planarity : 0.003 0.021 1290 Dihedral : 16.356 150.429 1299 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.24 % Allowed : 18.84 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.26), residues: 915 helix: -0.81 (0.27), residues: 396 sheet: -1.07 (0.38), residues: 153 loop : -2.52 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 211 PHE 0.023 0.002 PHE C 128 TYR 0.031 0.002 TYR B 260 ARG 0.003 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.837 Fit side-chains REVERT: A 252 ARG cc_start: 0.8464 (ttt90) cc_final: 0.8228 (ttm-80) REVERT: B 90 GLU cc_start: 0.8380 (tp30) cc_final: 0.8124 (tp30) REVERT: B 93 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.7418 (mp0) REVERT: B 168 ASP cc_start: 0.8192 (m-30) cc_final: 0.7917 (m-30) REVERT: B 172 ASP cc_start: 0.7925 (m-30) cc_final: 0.7692 (m-30) REVERT: B 180 ASP cc_start: 0.7921 (m-30) cc_final: 0.7521 (t0) REVERT: C 38 LYS cc_start: 0.7322 (pttm) cc_final: 0.6411 (ptmm) REVERT: C 72 LYS cc_start: 0.8504 (mttp) cc_final: 0.7607 (tptt) REVERT: C 90 GLU cc_start: 0.8155 (mp0) cc_final: 0.7925 (mp0) REVERT: C 93 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.7977 (mp0) REVERT: C 192 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.7538 (ttt180) REVERT: C 238 GLU cc_start: 0.8873 (mt-10) cc_final: 0.8578 (mt-10) outliers start: 17 outliers final: 12 residues processed: 135 average time/residue: 0.2198 time to fit residues: 39.8178 Evaluate side-chains 139 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 192 ARG Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 323 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 82 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 85 optimal weight: 0.0980 chunk 38 optimal weight: 5.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 244 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.150932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.119769 restraints weight = 10622.776| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.06 r_work: 0.3082 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7813 Z= 0.219 Angle : 0.534 6.460 10600 Z= 0.284 Chirality : 0.045 0.187 1194 Planarity : 0.003 0.025 1290 Dihedral : 16.334 150.246 1299 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 1.98 % Allowed : 19.10 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.26), residues: 915 helix: -0.79 (0.26), residues: 399 sheet: -1.16 (0.37), residues: 159 loop : -2.37 (0.29), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 211 PHE 0.022 0.002 PHE C 128 TYR 0.025 0.002 TYR B 260 ARG 0.003 0.000 ARG A 252 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.833 Fit side-chains REVERT: A 90 GLU cc_start: 0.8025 (mp0) cc_final: 0.7801 (mp0) REVERT: A 252 ARG cc_start: 0.8504 (ttt90) cc_final: 0.8282 (ttm-80) REVERT: B 90 GLU cc_start: 0.8379 (tp30) cc_final: 0.8130 (tp30) REVERT: B 93 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.7493 (mp0) REVERT: B 168 ASP cc_start: 0.8192 (m-30) cc_final: 0.7924 (m-30) REVERT: B 180 ASP cc_start: 0.7899 (m-30) cc_final: 0.7498 (t0) REVERT: C 72 LYS cc_start: 0.8515 (mttp) cc_final: 0.7622 (tptt) REVERT: C 90 GLU cc_start: 0.8177 (mp0) cc_final: 0.7974 (mp0) REVERT: C 93 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.7985 (mp0) REVERT: C 192 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.7556 (ttt180) REVERT: C 238 GLU cc_start: 0.8886 (mt-10) cc_final: 0.8584 (mt-10) outliers start: 15 outliers final: 12 residues processed: 133 average time/residue: 0.2036 time to fit residues: 36.5857 Evaluate side-chains 141 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 192 ARG Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 323 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 6 optimal weight: 5.9990 chunk 62 optimal weight: 0.0670 chunk 65 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 overall best weight: 2.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 ASN C 244 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.145453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.114402 restraints weight = 10728.388| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.05 r_work: 0.3099 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.4070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 7813 Z= 0.379 Angle : 0.628 6.724 10600 Z= 0.330 Chirality : 0.048 0.214 1194 Planarity : 0.004 0.040 1290 Dihedral : 16.409 149.753 1299 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 1.98 % Allowed : 19.24 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.26), residues: 915 helix: -1.10 (0.25), residues: 414 sheet: -1.03 (0.39), residues: 153 loop : -2.55 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 211 PHE 0.024 0.002 PHE C 128 TYR 0.028 0.002 TYR B 260 ARG 0.003 0.000 ARG C 176 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4132.98 seconds wall clock time: 73 minutes 58.01 seconds (4438.01 seconds total)