Starting phenix.real_space_refine on Fri Jul 25 15:34:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7c99_30309/07_2025/7c99_30309.cif Found real_map, /net/cci-nas-00/data/ceres_data/7c99_30309/07_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_30309/07_2025/7c99_30309.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7c99_30309/07_2025/7c99_30309.map" model { file = "/net/cci-nas-00/data/ceres_data/7c99_30309/07_2025/7c99_30309.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7c99_30309/07_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 6.55, per 1000 atoms: 0.86 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: 1.85 Conformation dependent library (CDL) restraints added in 984.1 milliseconds 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: 2.33 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: 2.07 Time building geometry restraints manager: 2.21 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: 6.270 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: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 24.100 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.150 ------------------------------------------------------------------------------- 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= 0.371 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 Details of bonding type rmsd hydrogen bonds : bond 0.32240 ( 219) hydrogen bonds : angle 9.96492 ( 590) covalent geometry : bond 0.00791 ( 7813) covalent geometry : angle 1.05148 (10600) *********************** 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 : 0.731 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: 0.7938 (mt0) REVERT: A 273 ASP cc_start: 0.7985 (t0) cc_final: 0.7749 (t70) REVERT: A 331 THR cc_start: 0.9030 (p) cc_final: 0.8796 (t) REVERT: B 94 LYS cc_start: 0.8341 (mmtt) cc_final: 0.7988 (mmtp) REVERT: B 119 MET cc_start: 0.8617 (mtt) cc_final: 0.8336 (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: 0.8576 (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: 0.2573 time to fit residues: 80.4315 Evaluate side-chains 153 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.824 ------------------------------------------------------------------------------- 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 = 0.3731 r_free = 0.3731 target = 0.156324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.123680 restraints weight = 10441.625| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.09 r_work: 0.3139 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 7813 Z= 0.120 Angle : 0.563 6.281 10600 Z= 0.305 Chirality : 0.044 0.153 1194 Planarity : 0.003 0.023 1290 Dihedral : 17.882 154.416 1299 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.58 % Allowed : 11.33 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.68 (0.20), residues: 915 helix: -3.43 (0.17), residues: 393 sheet: -1.73 (0.35), residues: 159 loop : -3.17 (0.24), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 30 PHE 0.018 0.001 PHE B 128 TYR 0.007 0.001 TYR B 194 ARG 0.005 0.000 ARG B 252 Details of bonding type rmsd hydrogen bonds : bond 0.04955 ( 219) hydrogen bonds : angle 4.88740 ( 590) covalent geometry : bond 0.00258 ( 7813) covalent geometry : angle 0.56257 (10600) *********************** 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 : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 THR cc_start: 0.8721 (m) cc_final: 0.8488 (m) REVERT: A 93 GLU cc_start: 0.8280 (mp0) cc_final: 0.7674 (mm-30) REVERT: A 194 TYR cc_start: 0.9041 (m-80) cc_final: 0.8688 (m-80) REVERT: A 252 ARG cc_start: 0.8478 (ttt90) cc_final: 0.8261 (ttm-80) REVERT: A 268 ASN cc_start: 0.9117 (p0) cc_final: 0.8868 (p0) REVERT: A 331 THR cc_start: 0.8982 (p) cc_final: 0.8758 (t) REVERT: B 180 ASP cc_start: 0.8075 (m-30) cc_final: 0.7483 (t0) REVERT: B 210 PHE cc_start: 0.8824 (m-10) cc_final: 0.8516 (m-80) REVERT: C 49 LYS cc_start: 0.7086 (OUTLIER) cc_final: 0.6797 (tttt) REVERT: C 90 GLU cc_start: 0.7866 (mp0) cc_final: 0.7632 (mp0) REVERT: C 108 PHE cc_start: 0.8950 (t80) cc_final: 0.8681 (t80) REVERT: C 155 LYS cc_start: 0.8681 (mttt) cc_final: 0.8223 (mtpt) outliers start: 12 outliers final: 6 residues processed: 189 average time/residue: 0.2471 time to fit residues: 61.6638 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 : 0.838 ------------------------------------------------------------------------------- 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: 5.9990 chunk 7 optimal weight: 8.9990 chunk 47 optimal weight: 0.9980 chunk 85 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 = 0.3692 r_free = 0.3692 target = 0.153215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.120795 restraints weight = 10587.018| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.08 r_work: 0.3151 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7813 Z= 0.155 Angle : 0.552 5.740 10600 Z= 0.297 Chirality : 0.045 0.175 1194 Planarity : 0.003 0.028 1290 Dihedral : 16.886 148.883 1299 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.64 % Allowed : 13.70 % Favored : 83.66 % 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: -3.82 (0.23), residues: 915 helix: -2.42 (0.22), residues: 396 sheet: -1.30 (0.35), residues: 165 loop : -3.14 (0.26), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS A 211 PHE 0.020 0.002 PHE C 128 TYR 0.010 0.001 TYR A 194 ARG 0.005 0.000 ARG A 129 Details of bonding type rmsd hydrogen bonds : bond 0.04187 ( 219) hydrogen bonds : angle 4.16158 ( 590) covalent geometry : bond 0.00362 ( 7813) covalent geometry : angle 0.55201 (10600) *********************** 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 169 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 1.694 Fit side-chains revert: symmetry clash REVERT: A 93 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7763 (mm-30) REVERT: A 194 TYR cc_start: 0.9238 (m-80) cc_final: 0.8838 (m-80) REVERT: A 252 ARG cc_start: 0.8487 (ttt90) cc_final: 0.8266 (ttm-80) REVERT: A 258 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8653 (mt-10) REVERT: A 309 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8174 (mt-10) REVERT: A 331 THR cc_start: 0.9004 (p) cc_final: 0.8790 (t) REVERT: B 93 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.7579 (mp0) REVERT: B 180 ASP cc_start: 0.8069 (m-30) cc_final: 0.7576 (t0) REVERT: B 210 PHE cc_start: 0.8768 (m-10) cc_final: 0.8335 (m-80) REVERT: C 117 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7734 (mt-10) REVERT: C 155 LYS cc_start: 0.8750 (mttt) cc_final: 0.8323 (mtpt) REVERT: C 238 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8408 (mt-10) outliers start: 20 outliers final: 8 residues processed: 160 average time/residue: 0.3114 time to fit residues: 66.3775 Evaluate side-chains 143 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 133 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLU 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 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: 5.9990 chunk 5 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 34 optimal weight: 0.1980 chunk 88 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 overall best weight: 4.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 HIS B 244 GLN C 100 HIS C 244 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.143030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.111294 restraints weight = 10636.868| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.01 r_work: 0.3000 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.078 7813 Z= 0.384 Angle : 0.764 8.054 10600 Z= 0.402 Chirality : 0.053 0.244 1194 Planarity : 0.005 0.061 1290 Dihedral : 16.928 148.779 1299 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 3.29 % Allowed : 15.81 % Favored : 80.90 % 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: -3.75 (0.24), residues: 915 helix: -2.27 (0.23), residues: 393 sheet: -1.38 (0.39), residues: 153 loop : -3.11 (0.26), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 30 PHE 0.027 0.003 PHE C 128 TYR 0.013 0.002 TYR A 260 ARG 0.007 0.001 ARG A 129 Details of bonding type rmsd hydrogen bonds : bond 0.05670 ( 219) hydrogen bonds : angle 4.65844 ( 590) covalent geometry : bond 0.00911 ( 7813) covalent geometry : angle 0.76445 (10600) *********************** 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 153 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 0.830 Fit side-chains revert: symmetry clash REVERT: A 194 TYR cc_start: 0.9322 (m-80) cc_final: 0.9104 (m-80) REVERT: B 93 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.7662 (mp0) REVERT: B 172 ASP cc_start: 0.7758 (m-30) cc_final: 0.7542 (m-30) REVERT: B 180 ASP cc_start: 0.8086 (m-30) cc_final: 0.7613 (t0) REVERT: B 260 TYR cc_start: 0.8893 (m-10) cc_final: 0.8481 (m-10) REVERT: C 72 LYS cc_start: 0.8471 (mttt) cc_final: 0.8044 (tttt) REVERT: C 117 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7888 (mt-10) REVERT: C 155 LYS cc_start: 0.8717 (mttt) cc_final: 0.8402 (mtpt) REVERT: C 192 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.7742 (ttt180) REVERT: C 238 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8425 (mt-10) REVERT: C 335 ILE cc_start: 0.9166 (mm) cc_final: 0.8947 (mm) outliers start: 25 outliers final: 14 residues processed: 145 average time/residue: 0.2060 time to fit residues: 39.7775 Evaluate side-chains 138 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.792 ------------------------------------------------------------------------------- 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 96 LYS Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 192 ARG Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 219 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: 0.1980 chunk 70 optimal weight: 0.7980 chunk 64 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 chunk 82 optimal weight: 0.5980 chunk 61 optimal weight: 10.0000 chunk 80 optimal weight: 0.6980 chunk 65 optimal weight: 0.0870 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN B 244 GLN C 244 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.153356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.121752 restraints weight = 10393.561| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.05 r_work: 0.3109 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 7813 Z= 0.096 Angle : 0.500 7.391 10600 Z= 0.271 Chirality : 0.043 0.161 1194 Planarity : 0.003 0.020 1290 Dihedral : 16.720 150.268 1299 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.71 % Allowed : 17.00 % Favored : 81.29 % 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: -3.08 (0.25), residues: 915 helix: -1.49 (0.25), residues: 396 sheet: -1.26 (0.37), residues: 165 loop : -2.98 (0.27), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 211 PHE 0.022 0.001 PHE C 128 TYR 0.012 0.001 TYR B 260 ARG 0.004 0.000 ARG A 252 Details of bonding type rmsd hydrogen bonds : bond 0.03203 ( 219) hydrogen bonds : angle 3.83574 ( 590) covalent geometry : bond 0.00209 ( 7813) covalent geometry : angle 0.50009 (10600) *********************** 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 155 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 142 time to evaluate : 0.802 Fit side-chains revert: symmetry clash REVERT: A 252 ARG cc_start: 0.8406 (ttt90) cc_final: 0.8176 (ttm-80) REVERT: B 93 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.7586 (mp0) REVERT: B 180 ASP cc_start: 0.8013 (m-30) cc_final: 0.7501 (t0) REVERT: C 38 LYS cc_start: 0.7399 (pttm) cc_final: 0.6340 (ptmm) REVERT: C 93 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.7914 (mp0) REVERT: C 117 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7768 (mt-10) outliers start: 13 outliers final: 5 residues processed: 149 average time/residue: 0.2279 time to fit residues: 45.0681 Evaluate side-chains 131 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 124 time to evaluate : 0.808 ------------------------------------------------------------------------------- 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 93 GLU Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 97 MET 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: 7.9990 chunk 2 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 12 optimal weight: 7.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 = 0.3574 r_free = 0.3574 target = 0.143376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.111865 restraints weight = 10707.246| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.02 r_work: 0.3021 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 7813 Z= 0.287 Angle : 0.660 7.501 10600 Z= 0.348 Chirality : 0.050 0.228 1194 Planarity : 0.004 0.028 1290 Dihedral : 16.608 149.847 1299 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 2.50 % Allowed : 18.45 % Favored : 79.05 % 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: -1.63 (0.25), residues: 396 sheet: -1.20 (0.39), residues: 153 loop : -2.90 (0.27), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 295 PHE 0.026 0.003 PHE C 128 TYR 0.030 0.002 TYR B 260 ARG 0.003 0.000 ARG C 176 Details of bonding type rmsd hydrogen bonds : bond 0.04795 ( 219) hydrogen bonds : angle 4.22541 ( 590) covalent geometry : bond 0.00683 ( 7813) covalent geometry : angle 0.65955 (10600) *********************** 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 143 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 0.779 Fit side-chains revert: symmetry clash REVERT: B 90 GLU cc_start: 0.8330 (tp30) cc_final: 0.8058 (tp30) REVERT: B 93 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.7644 (mp0) REVERT: B 180 ASP cc_start: 0.8039 (m-30) cc_final: 0.7589 (t0) REVERT: C 72 LYS cc_start: 0.8534 (mttp) cc_final: 0.7684 (tptt) REVERT: C 93 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.7954 (mp0) REVERT: C 117 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7897 (mt-10) outliers start: 19 outliers final: 13 residues processed: 137 average time/residue: 0.2168 time to fit residues: 40.1557 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 : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 PHE 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 C residue 93 GLU Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 225 ILE 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: 4.9990 chunk 61 optimal weight: 8.9990 chunk 48 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.3631 r_free = 0.3631 target = 0.148354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.116665 restraints weight = 10591.246| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.05 r_work: 0.3074 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.3906 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= 0.131 Angle : 0.532 7.255 10600 Z= 0.284 Chirality : 0.044 0.188 1194 Planarity : 0.003 0.030 1290 Dihedral : 16.483 150.230 1299 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.64 % Allowed : 18.31 % Favored : 79.05 % 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: -2.77 (0.26), residues: 915 helix: -1.22 (0.26), residues: 396 sheet: -1.24 (0.37), residues: 159 loop : -2.73 (0.28), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 211 PHE 0.023 0.002 PHE C 128 TYR 0.010 0.001 TYR C 190 ARG 0.006 0.000 ARG A 252 Details of bonding type rmsd hydrogen bonds : bond 0.03531 ( 219) hydrogen bonds : angle 3.88753 ( 590) covalent geometry : bond 0.00307 ( 7813) covalent geometry : angle 0.53223 (10600) *********************** 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 151 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 252 ARG cc_start: 0.8438 (ttt90) cc_final: 0.8225 (ttm-80) REVERT: B 90 GLU cc_start: 0.8357 (tp30) cc_final: 0.8065 (tp30) REVERT: B 93 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.7589 (mp0) REVERT: B 180 ASP cc_start: 0.7969 (m-30) cc_final: 0.7522 (t0) REVERT: C 38 LYS cc_start: 0.7426 (pttm) cc_final: 0.6472 (ptmm) REVERT: C 72 LYS cc_start: 0.8591 (mttp) cc_final: 0.7732 (tptt) REVERT: C 93 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.7960 (mp0) REVERT: C 117 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7883 (mt-10) outliers start: 20 outliers final: 13 residues processed: 142 average time/residue: 0.2745 time to fit residues: 51.1796 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 : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR 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 C residue 93 GLU Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 225 ILE 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: 2.9990 chunk 37 optimal weight: 0.0370 chunk 13 optimal weight: 6.9990 chunk 73 optimal weight: 0.7980 chunk 2 optimal weight: 8.9990 chunk 51 optimal weight: 0.6980 chunk 59 optimal weight: 20.0000 chunk 26 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.7062 ------------------------------------------------------------------------------- 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 = 0.3661 r_free = 0.3661 target = 0.150889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.119820 restraints weight = 10655.136| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.04 r_work: 0.3104 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7813 Z= 0.104 Angle : 0.502 7.093 10600 Z= 0.269 Chirality : 0.043 0.172 1194 Planarity : 0.003 0.028 1290 Dihedral : 16.372 150.790 1299 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 2.11 % Allowed : 19.10 % 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: -2.58 (0.26), residues: 915 helix: -1.07 (0.26), residues: 414 sheet: -1.12 (0.36), residues: 165 loop : -2.71 (0.30), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 137 PHE 0.023 0.001 PHE C 128 TYR 0.024 0.001 TYR B 260 ARG 0.006 0.000 ARG A 252 Details of bonding type rmsd hydrogen bonds : bond 0.03099 ( 219) hydrogen bonds : angle 3.76561 ( 590) covalent geometry : bond 0.00234 ( 7813) covalent geometry : angle 0.50171 (10600) *********************** 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 153 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 PHE cc_start: 0.8772 (m-80) cc_final: 0.8555 (m-80) REVERT: A 252 ARG cc_start: 0.8396 (ttt90) cc_final: 0.8184 (ttm-80) REVERT: B 90 GLU cc_start: 0.8418 (tp30) cc_final: 0.8156 (tp30) REVERT: B 93 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.7513 (mp0) REVERT: B 180 ASP cc_start: 0.7921 (m-30) cc_final: 0.7492 (t0) REVERT: B 210 PHE cc_start: 0.8803 (m-10) cc_final: 0.8454 (m-10) REVERT: B 293 LEU cc_start: 0.8948 (tp) cc_final: 0.8748 (tp) REVERT: C 38 LYS cc_start: 0.7320 (pttm) cc_final: 0.6363 (ptmm) REVERT: C 72 LYS cc_start: 0.8574 (mttp) cc_final: 0.7706 (tptt) REVERT: C 93 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.7990 (mp0) REVERT: C 117 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7868 (mt-10) REVERT: C 119 MET cc_start: 0.8847 (mtt) cc_final: 0.8521 (mtt) REVERT: C 192 ARG cc_start: 0.8494 (ttt90) cc_final: 0.8105 (tpt-90) outliers start: 16 outliers final: 8 residues processed: 147 average time/residue: 0.2050 time to fit residues: 40.3358 Evaluate side-chains 144 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 134 time to evaluate : 0.852 ------------------------------------------------------------------------------- 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 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 C residue 93 GLU Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 225 ILE 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: 0.6980 chunk 84 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 67 optimal weight: 0.2980 chunk 80 optimal weight: 0.0020 chunk 7 optimal weight: 8.9990 chunk 6 optimal weight: 3.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- 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 = 0.3696 r_free = 0.3696 target = 0.154135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.122936 restraints weight = 10663.361| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.07 r_work: 0.3138 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7813 Z= 0.096 Angle : 0.499 6.971 10600 Z= 0.266 Chirality : 0.043 0.168 1194 Planarity : 0.003 0.027 1290 Dihedral : 16.269 150.608 1299 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.58 % Allowed : 19.76 % 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: -2.32 (0.27), residues: 915 helix: -0.85 (0.26), residues: 414 sheet: -1.23 (0.35), residues: 174 loop : -2.48 (0.31), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 211 PHE 0.023 0.001 PHE C 128 TYR 0.024 0.001 TYR B 260 ARG 0.006 0.000 ARG A 252 Details of bonding type rmsd hydrogen bonds : bond 0.02838 ( 219) hydrogen bonds : angle 3.67790 ( 590) covalent geometry : bond 0.00217 ( 7813) covalent geometry : angle 0.49931 (10600) *********************** 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 149 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 137 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 GLN cc_start: 0.9010 (mp10) cc_final: 0.8634 (mp10) REVERT: A 252 ARG cc_start: 0.8398 (ttt90) cc_final: 0.8188 (ttm-80) REVERT: A 269 GLN cc_start: 0.8852 (mt0) cc_final: 0.8618 (mt0) REVERT: B 90 GLU cc_start: 0.8386 (tp30) cc_final: 0.8155 (tp30) REVERT: B 93 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.7509 (mp0) REVERT: B 180 ASP cc_start: 0.7898 (m-30) cc_final: 0.7465 (t0) REVERT: B 210 PHE cc_start: 0.8665 (m-10) cc_final: 0.8400 (m-10) REVERT: C 38 LYS cc_start: 0.7247 (pttm) cc_final: 0.6320 (ptmm) REVERT: C 72 LYS cc_start: 0.8561 (mttp) cc_final: 0.7702 (tptt) REVERT: C 117 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7869 (mt-10) REVERT: C 192 ARG cc_start: 0.8460 (ttt90) cc_final: 0.8202 (tpt-90) outliers start: 12 outliers final: 7 residues processed: 144 average time/residue: 0.2307 time to fit residues: 44.9152 Evaluate side-chains 134 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 126 time to evaluate : 0.868 ------------------------------------------------------------------------------- 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 93 GLU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain C residue 225 ILE 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: 0.8980 chunk 72 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 134 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.150709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.119562 restraints weight = 10638.763| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.04 r_work: 0.3141 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7813 Z= 0.114 Angle : 0.522 7.913 10600 Z= 0.276 Chirality : 0.044 0.173 1194 Planarity : 0.003 0.028 1290 Dihedral : 16.229 150.360 1299 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 1.19 % Allowed : 20.82 % Favored : 78.00 % 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: -2.22 (0.27), residues: 915 helix: -0.84 (0.26), residues: 417 sheet: -1.08 (0.36), residues: 171 loop : -2.37 (0.32), residues: 327 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 0.033 0.002 TYR B 260 ARG 0.007 0.000 ARG A 129 Details of bonding type rmsd hydrogen bonds : bond 0.03103 ( 219) hydrogen bonds : angle 3.74680 ( 590) covalent geometry : bond 0.00266 ( 7813) covalent geometry : angle 0.52236 (10600) ********************** 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 137 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 128 time to evaluate : 1.092 Fit side-chains revert: symmetry clash REVERT: A 252 ARG cc_start: 0.8412 (ttt90) cc_final: 0.8206 (ttm-80) REVERT: B 90 GLU cc_start: 0.8367 (tp30) cc_final: 0.8163 (tp30) REVERT: B 93 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.7497 (mp0) REVERT: B 180 ASP cc_start: 0.7887 (m-30) cc_final: 0.7491 (t0) REVERT: C 72 LYS cc_start: 0.8526 (mttp) cc_final: 0.7639 (tptt) REVERT: C 117 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7933 (mt-10) REVERT: C 192 ARG cc_start: 0.8428 (ttt90) cc_final: 0.8158 (tpt-90) outliers start: 9 outliers final: 7 residues processed: 133 average time/residue: 0.2826 time to fit residues: 50.5522 Evaluate side-chains 136 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 128 time to evaluate : 0.877 ------------------------------------------------------------------------------- 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 219 LEU Chi-restraints excluded: chain B residue 323 GLU 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: 0.9980 chunk 62 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 1 optimal weight: 8.9990 chunk 44 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- 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 = 0.3591 r_free = 0.3591 target = 0.144944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.113337 restraints weight = 10699.855| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.08 r_work: 0.3029 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.4134 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= 0.197 Angle : 0.599 9.110 10600 Z= 0.314 Chirality : 0.047 0.203 1194 Planarity : 0.003 0.031 1290 Dihedral : 16.321 149.606 1299 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 1.58 % Allowed : 20.82 % Favored : 77.60 % 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: -2.30 (0.27), residues: 915 helix: -0.94 (0.26), residues: 414 sheet: -1.06 (0.36), residues: 171 loop : -2.39 (0.31), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 211 PHE 0.024 0.002 PHE C 128 TYR 0.028 0.002 TYR B 260 ARG 0.010 0.001 ARG A 129 Details of bonding type rmsd hydrogen bonds : bond 0.03902 ( 219) hydrogen bonds : angle 3.92182 ( 590) covalent geometry : bond 0.00469 ( 7813) covalent geometry : angle 0.59868 (10600) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4937.43 seconds wall clock time: 89 minutes 41.30 seconds (5381.30 seconds total)