Starting phenix.real_space_refine on Tue Mar 3 17:58:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7c98_30308/03_2026/7c98_30308.cif Found real_map, /net/cci-nas-00/data/ceres_data/7c98_30308/03_2026/7c98_30308.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7c98_30308/03_2026/7c98_30308.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7c98_30308/03_2026/7c98_30308.map" model { file = "/net/cci-nas-00/data/ceres_data/7c98_30308/03_2026/7c98_30308.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7c98_30308/03_2026/7c98_30308.cif" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 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 21 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 1.76, per 1000 atoms: 0.23 Number of scatterers: 7656 At special positions: 0 Unit cell: (81.48, 102.48, 114.24, 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 268.1 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: 45 helices and 6 sheets defined 43.8% alpha, 11.9% beta 7 base pairs and 12 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 27 through 31 removed outlier: 3.837A pdb=" N GLY A 31 " --> pdb=" O GLN A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 44 removed outlier: 3.500A pdb=" N LEU A 40 " --> pdb=" O ASP A 36 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS A 41 " --> pdb=" O ILE A 37 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL A 43 " --> pdb=" O LYS A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 61 Processing helix chain 'A' and resid 70 through 79 removed outlier: 3.613A pdb=" N LYS A 74 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA A 76 " --> pdb=" O LYS A 72 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASN A 78 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LYS A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 95 removed outlier: 3.513A pdb=" N GLU A 93 " --> pdb=" O PHE A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 106 through 111 Processing helix chain 'A' and resid 131 through 143 removed outlier: 3.597A pdb=" N LEU A 135 " --> pdb=" O GLY A 131 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL A 141 " --> pdb=" O HIS A 137 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 151 removed outlier: 3.868A pdb=" N GLY A 150 " --> pdb=" O GLY A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 177 removed outlier: 3.919A pdb=" N ARG A 171 " --> pdb=" O PRO A 167 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASP A 172 " --> pdb=" O ASP A 168 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE A 173 " --> pdb=" O ARG A 169 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP A 175 " --> pdb=" O ARG A 171 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG A 176 " --> pdb=" O ASP A 172 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE A 177 " --> pdb=" O ILE A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 202 removed outlier: 3.572A pdb=" N MET A 200 " --> pdb=" O SER A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 212 removed outlier: 3.618A pdb=" N VAL A 206 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU A 212 " --> pdb=" O ALA A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 233 removed outlier: 4.139A pdb=" N PHE A 229 " --> pdb=" O ILE A 225 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG A 230 " --> pdb=" O MET A 226 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N VAL A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE A 233 " --> pdb=" O PHE A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 260 removed outlier: 3.574A pdb=" N GLN A 248 " --> pdb=" O GLN A 244 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N MET A 249 " --> pdb=" O LYS A 245 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU A 258 " --> pdb=" O GLN A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 297 removed outlier: 3.851A pdb=" N LEU A 293 " --> pdb=" O GLY A 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 31 removed outlier: 3.837A pdb=" N GLY B 31 " --> pdb=" O GLN B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 44 removed outlier: 3.672A pdb=" N LYS B 41 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL B 43 " --> pdb=" O LYS B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 61 Processing helix chain 'B' and resid 70 through 79 removed outlier: 3.614A pdb=" N LYS B 74 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA B 76 " --> pdb=" O LYS B 72 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASN B 78 " --> pdb=" O LYS B 74 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LYS B 79 " --> pdb=" O GLU B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 95 removed outlier: 3.514A pdb=" N GLU B 93 " --> pdb=" O PHE B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 98 No H-bonds generated for 'chain 'B' and resid 96 through 98' Processing helix chain 'B' and resid 106 through 111 Processing helix chain 'B' and resid 131 through 143 removed outlier: 3.596A pdb=" N LEU B 135 " --> pdb=" O GLY B 131 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N VAL B 141 " --> pdb=" O HIS B 137 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA B 143 " --> pdb=" O LEU B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 151 removed outlier: 3.868A pdb=" N GLY B 150 " --> pdb=" O GLY B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 177 removed outlier: 3.920A pdb=" N ARG B 171 " --> pdb=" O PRO B 167 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASP B 172 " --> pdb=" O ASP B 168 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE B 173 " --> pdb=" O ARG B 169 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP B 175 " --> pdb=" O ARG B 171 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG B 176 " --> pdb=" O ASP B 172 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE B 177 " --> pdb=" O ILE B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 202 removed outlier: 3.571A pdb=" N MET B 200 " --> pdb=" O SER B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 212 removed outlier: 3.618A pdb=" N VAL B 206 " --> pdb=" O LEU B 202 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU B 212 " --> pdb=" O ALA B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 233 removed outlier: 4.139A pdb=" N PHE B 229 " --> pdb=" O ILE B 225 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG B 230 " --> pdb=" O MET B 226 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N VAL B 231 " --> pdb=" O ALA B 227 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE B 233 " --> pdb=" O PHE B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 260 removed outlier: 3.574A pdb=" N GLN B 248 " --> pdb=" O GLN B 244 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N MET B 249 " --> pdb=" O LYS B 245 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU B 258 " --> pdb=" O GLN B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 297 removed outlier: 3.851A pdb=" N LEU B 293 " --> pdb=" O GLY B 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 31 removed outlier: 3.837A pdb=" N GLY C 31 " --> pdb=" O GLN C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 44 removed outlier: 3.500A pdb=" N LEU C 40 " --> pdb=" O ASP C 36 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS C 41 " --> pdb=" O ILE C 37 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL C 43 " --> pdb=" O LYS C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 61 Processing helix chain 'C' and resid 70 through 79 removed outlier: 3.614A pdb=" N LYS C 74 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA C 76 " --> pdb=" O LYS C 72 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASN C 78 " --> pdb=" O LYS C 74 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LYS C 79 " --> pdb=" O GLU C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 95 removed outlier: 3.513A pdb=" N GLU C 93 " --> pdb=" O PHE C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 98 No H-bonds generated for 'chain 'C' and resid 96 through 98' Processing helix chain 'C' and resid 106 through 111 Processing helix chain 'C' and resid 131 through 143 removed outlier: 3.596A pdb=" N LEU C 135 " --> pdb=" O GLY C 131 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N VAL C 141 " --> pdb=" O HIS C 137 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA C 143 " --> pdb=" O LEU C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 151 removed outlier: 3.868A pdb=" N GLY C 150 " --> pdb=" O GLY C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 177 removed outlier: 3.920A pdb=" N ARG C 171 " --> pdb=" O PRO C 167 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP C 172 " --> pdb=" O ASP C 168 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE C 173 " --> pdb=" O ARG C 169 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP C 175 " --> pdb=" O ARG C 171 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG C 176 " --> pdb=" O ASP C 172 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE C 177 " --> pdb=" O ILE C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 202 removed outlier: 3.571A pdb=" N MET C 200 " --> pdb=" O SER C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 212 removed outlier: 3.618A pdb=" N VAL C 206 " --> pdb=" O LEU C 202 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU C 212 " --> pdb=" O ALA C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 233 removed outlier: 4.140A pdb=" N PHE C 229 " --> pdb=" O ILE C 225 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG C 230 " --> pdb=" O MET C 226 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N VAL C 231 " --> pdb=" O ALA C 227 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE C 233 " --> pdb=" O PHE C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 260 removed outlier: 3.575A pdb=" N GLN C 248 " --> pdb=" O GLN C 244 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N MET C 249 " --> pdb=" O LYS C 245 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU C 258 " --> pdb=" O GLN C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 297 removed outlier: 3.851A 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: 3.763A pdb=" N ALA A 313 " --> pdb=" O ALA A 326 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N THR A 122 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ASN A 268 " --> pdb=" O THR A 122 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ALA A 124 " --> pdb=" O ASN A 268 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR A 267 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N SER A 224 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N LYS A 155 " --> pdb=" O PHE A 217 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU A 219 " --> pdb=" O LYS A 155 " (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 'B' and resid 326 through 327 removed outlier: 3.762A pdb=" N ALA B 313 " --> pdb=" O ALA B 326 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N THR B 122 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ASN B 268 " --> pdb=" O THR B 122 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ALA B 124 " --> pdb=" O ASN B 268 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR B 267 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N SER B 224 " --> pdb=" O THR B 267 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N LYS B 155 " --> pdb=" O PHE B 217 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU B 219 " --> pdb=" O LYS B 155 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 270 through 271 Processing sheet with id=AA5, first strand: chain 'C' and resid 188 through 192 removed outlier: 5.403A pdb=" N LYS C 155 " --> pdb=" O PHE C 217 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU C 219 " --> pdb=" O LYS C 155 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR C 267 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N SER C 224 " --> pdb=" O THR C 267 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N THR C 122 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N ASN C 268 " --> pdb=" O THR C 122 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ALA C 124 " --> pdb=" O ASN C 268 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA C 313 " --> pdb=" O ALA C 326 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 270 through 271 219 hydrogen bonds defined for protein. 579 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 14 hydrogen bonds 28 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 12 stacking parallelities Total time for adding SS restraints: 1.13 Time building geometry restraints manager: 0.98 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: 1747 1.33 - 1.45: 1584 1.45 - 1.57: 4376 1.57 - 1.68: 47 1.68 - 1.80: 59 Bond restraints: 7813 Sorted by residual: bond pdb=" O3A ANP B 402 " pdb=" PB ANP B 402 " ideal model delta sigma weight residual 1.700 1.541 0.159 2.00e-02 2.50e+03 6.32e+01 bond pdb=" O3A ANP C 401 " pdb=" PB ANP C 401 " ideal model delta sigma weight residual 1.700 1.549 0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" N3B ANP C 401 " pdb=" PG ANP C 401 " ideal model delta sigma weight residual 1.795 1.683 0.112 2.00e-02 2.50e+03 3.16e+01 bond pdb=" N3B ANP B 402 " pdb=" PG ANP B 402 " ideal model delta sigma weight residual 1.795 1.684 0.111 2.00e-02 2.50e+03 3.08e+01 bond pdb=" O3A ANP A 402 " pdb=" PB ANP A 402 " ideal model delta sigma weight residual 1.700 1.608 0.092 2.00e-02 2.50e+03 2.14e+01 ... (remaining 7808 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.23: 10523 4.23 - 8.47: 65 8.47 - 12.70: 10 12.70 - 16.94: 0 16.94 - 21.17: 2 Bond angle restraints: 10600 Sorted by residual: angle pdb=" PB ANP B 402 " pdb=" N3B ANP B 402 " pdb=" PG ANP B 402 " ideal model delta sigma weight residual 126.95 105.78 21.17 3.00e+00 1.11e-01 4.98e+01 angle pdb=" PB ANP C 401 " pdb=" N3B ANP C 401 " pdb=" PG ANP C 401 " ideal model delta sigma weight residual 126.95 107.30 19.65 3.00e+00 1.11e-01 4.29e+01 angle pdb=" O1B ANP C 401 " pdb=" PB ANP C 401 " pdb=" O2B ANP C 401 " ideal model delta sigma weight residual 120.08 109.23 10.85 3.00e+00 1.11e-01 1.31e+01 angle pdb=" C PHE C 328 " pdb=" CA PHE C 328 " pdb=" CB PHE C 328 " ideal model delta sigma weight residual 113.33 105.31 8.02 2.26e+00 1.96e-01 1.26e+01 angle pdb=" C PHE B 328 " pdb=" CA PHE B 328 " pdb=" CB PHE B 328 " ideal model delta sigma weight residual 113.33 105.33 8.00 2.26e+00 1.96e-01 1.25e+01 ... (remaining 10595 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.83: 4427 30.83 - 61.66: 289 61.66 - 92.48: 28 92.48 - 123.31: 2 123.31 - 154.14: 3 Dihedral angle restraints: 4749 sinusoidal: 2115 harmonic: 2634 Sorted by residual: dihedral pdb=" CA THR B 331 " pdb=" C THR B 331 " pdb=" N ALA B 332 " pdb=" CA ALA B 332 " ideal model delta harmonic sigma weight residual 180.00 144.78 35.22 0 5.00e+00 4.00e-02 4.96e+01 dihedral pdb=" CA THR C 331 " pdb=" C THR C 331 " pdb=" N ALA C 332 " pdb=" CA ALA C 332 " ideal model delta harmonic sigma weight residual 180.00 144.80 35.20 0 5.00e+00 4.00e-02 4.96e+01 dihedral pdb=" CA THR A 331 " pdb=" C THR A 331 " pdb=" N ALA A 332 " pdb=" CA ALA A 332 " ideal model delta harmonic sigma weight residual 180.00 144.82 35.18 0 5.00e+00 4.00e-02 4.95e+01 ... (remaining 4746 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 977 0.068 - 0.136: 185 0.136 - 0.204: 26 0.204 - 0.272: 5 0.272 - 0.340: 1 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 -2.70 0.34 2.00e-01 2.50e+01 2.89e+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 -2.61 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CB VAL A 62 " pdb=" CA VAL A 62 " pdb=" CG1 VAL A 62 " pdb=" CG2 VAL A 62 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 1191 not shown) Planarity restraints: 1290 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ANP B 402 " -0.046 2.00e-02 2.50e+03 4.05e-02 4.50e+01 pdb=" C2 ANP B 402 " 0.012 2.00e-02 2.50e+03 pdb=" C4 ANP B 402 " -0.000 2.00e-02 2.50e+03 pdb=" C5 ANP B 402 " 0.078 2.00e-02 2.50e+03 pdb=" C6 ANP B 402 " -0.006 2.00e-02 2.50e+03 pdb=" C8 ANP B 402 " 0.053 2.00e-02 2.50e+03 pdb=" N1 ANP B 402 " -0.018 2.00e-02 2.50e+03 pdb=" N3 ANP B 402 " -0.005 2.00e-02 2.50e+03 pdb=" N6 ANP B 402 " -0.014 2.00e-02 2.50e+03 pdb=" N7 ANP B 402 " -0.076 2.00e-02 2.50e+03 pdb=" N9 ANP B 402 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 320 " 0.022 2.00e-02 2.50e+03 4.48e-02 2.01e+01 pdb=" C GLU C 320 " -0.078 2.00e-02 2.50e+03 pdb=" O GLU C 320 " 0.028 2.00e-02 2.50e+03 pdb=" N MET C 321 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 320 " 0.022 2.00e-02 2.50e+03 4.46e-02 1.99e+01 pdb=" C GLU A 320 " -0.077 2.00e-02 2.50e+03 pdb=" O GLU A 320 " 0.028 2.00e-02 2.50e+03 pdb=" N MET A 321 " 0.027 2.00e-02 2.50e+03 ... (remaining 1287 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.50: 49 2.50 - 3.10: 4915 3.10 - 3.70: 11303 3.70 - 4.30: 16402 4.30 - 4.90: 26743 Nonbonded interactions: 59412 Sorted by model distance: nonbonded pdb="CA CA B 401 " pdb=" O3G ANP B 402 " model vdw 1.906 2.510 nonbonded pdb=" NZ LYS A 245 " pdb=" NH2 ARG B 57 " model vdw 1.966 3.200 nonbonded pdb=" O1B ANP C 401 " pdb="CA CA C 402 " model vdw 2.097 2.510 nonbonded pdb=" NZ LYS B 245 " pdb=" NH2 ARG C 57 " model vdw 2.142 3.200 nonbonded pdb="CA CA A 401 " pdb=" O1B ANP A 402 " model vdw 2.230 2.510 ... (remaining 59407 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: 4.140 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: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 9.810 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.010 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 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 : 0.013 0.728 7816 Z= 1.167 Angle : 1.015 21.173 10600 Z= 0.512 Chirality : 0.054 0.340 1194 Planarity : 0.005 0.060 1290 Dihedral : 18.649 154.140 3057 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 0.00 % Allowed : 11.46 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.67 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.56 (0.22), residues: 915 helix: -4.21 (0.14), residues: 315 sheet: -1.90 (0.40), residues: 150 loop : -2.44 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 169 TYR 0.014 0.001 TYR C 91 PHE 0.027 0.002 PHE A 128 HIS 0.004 0.001 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00762 ( 7813) covalent geometry : angle 1.01483 (10600) hydrogen bonds : bond 0.29936 ( 233) hydrogen bonds : angle 8.98611 ( 607) Misc. bond : bond 0.56600 ( 3) *********************** 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 263 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 PHE cc_start: 0.7512 (m-80) cc_final: 0.6664 (t80) REVERT: A 118 SER cc_start: 0.7951 (p) cc_final: 0.7641 (m) REVERT: A 209 LYS cc_start: 0.9276 (tppt) cc_final: 0.8979 (tptt) REVERT: A 213 GLU cc_start: 0.8223 (mp0) cc_final: 0.7879 (mp0) REVERT: A 258 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7562 (mm-30) REVERT: A 301 ILE cc_start: 0.9181 (mt) cc_final: 0.8899 (tp) REVERT: A 335 ILE cc_start: 0.8698 (mm) cc_final: 0.8437 (mm) REVERT: B 335 ILE cc_start: 0.8995 (mm) cc_final: 0.8599 (mm) REVERT: C 101 ILE cc_start: 0.9064 (mm) cc_final: 0.8755 (mt) REVERT: C 194 TYR cc_start: 0.8195 (m-80) cc_final: 0.7990 (m-80) REVERT: C 244 GLN cc_start: 0.8237 (mt0) cc_final: 0.7979 (mt0) REVERT: C 245 LYS cc_start: 0.8839 (mttp) cc_final: 0.8615 (mtpp) REVERT: C 248 GLN cc_start: 0.8750 (mm-40) cc_final: 0.8492 (mp10) REVERT: C 249 MET cc_start: 0.8595 (ttm) cc_final: 0.8369 (ttm) REVERT: C 285 LYS cc_start: 0.8723 (mtmm) cc_final: 0.8423 (mttm) REVERT: C 304 ARG cc_start: 0.7606 (ptt90) cc_final: 0.7259 (ptt90) outliers start: 0 outliers final: 0 residues processed: 263 average time/residue: 0.0989 time to fit residues: 33.6382 Evaluate side-chains 158 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.0570 chunk 45 optimal weight: 0.0000 chunk 74 optimal weight: 8.9990 overall best weight: 1.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 61 ASN A 144 GLN A 178 ASN A 254 GLN B 30 HIS B 61 ASN B 198 HIS C 30 HIS C 61 ASN C 211 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.153641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.122092 restraints weight = 13385.483| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.58 r_work: 0.3327 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7816 Z= 0.128 Angle : 0.613 9.556 10600 Z= 0.324 Chirality : 0.043 0.154 1194 Planarity : 0.004 0.050 1290 Dihedral : 18.110 158.035 1299 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.90 % Allowed : 18.58 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.68 (0.23), residues: 915 helix: -2.31 (0.23), residues: 345 sheet: -2.04 (0.38), residues: 153 loop : -2.62 (0.25), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 307 TYR 0.021 0.002 TYR B 190 PHE 0.018 0.002 PHE C 128 HIS 0.002 0.001 HIS C 295 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 7813) covalent geometry : angle 0.61301 (10600) hydrogen bonds : bond 0.04648 ( 233) hydrogen bonds : angle 4.82627 ( 607) Misc. bond : bond 0.00251 ( 3) *********************** 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 200 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 178 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 PHE cc_start: 0.7566 (m-80) cc_final: 0.6691 (t80) REVERT: A 95 ARG cc_start: 0.8647 (ttt90) cc_final: 0.7974 (mtm180) REVERT: A 118 SER cc_start: 0.8080 (p) cc_final: 0.7694 (p) REVERT: A 119 MET cc_start: 0.8083 (mmm) cc_final: 0.7828 (mmm) REVERT: A 321 MET cc_start: 0.7611 (mmm) cc_final: 0.7310 (mmm) REVERT: A 335 ILE cc_start: 0.8708 (mm) cc_final: 0.8462 (mm) REVERT: B 220 LEU cc_start: 0.9347 (tp) cc_final: 0.9120 (tt) REVERT: B 254 GLN cc_start: 0.9273 (tp-100) cc_final: 0.8996 (tp-100) REVERT: B 273 ASP cc_start: 0.8711 (t0) cc_final: 0.8453 (t0) REVERT: B 335 ILE cc_start: 0.8998 (mm) cc_final: 0.8532 (mm) REVERT: C 130 THR cc_start: 0.9215 (OUTLIER) cc_final: 0.8916 (m) REVERT: C 155 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7915 (mtpp) REVERT: C 244 GLN cc_start: 0.8846 (mt0) cc_final: 0.8566 (mt0) REVERT: C 245 LYS cc_start: 0.9150 (mttp) cc_final: 0.8821 (mtpp) REVERT: C 285 LYS cc_start: 0.8883 (mtmm) cc_final: 0.8372 (mttm) outliers start: 22 outliers final: 9 residues processed: 193 average time/residue: 0.0880 time to fit residues: 22.9870 Evaluate side-chains 166 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 155 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 211 HIS Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 224 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 68 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 178 ASN A 198 HIS B 163 ASN B 244 GLN C 106 GLN C 199 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.149832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.116730 restraints weight = 13396.608| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.59 r_work: 0.3293 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7816 Z= 0.142 Angle : 0.578 8.676 10600 Z= 0.307 Chirality : 0.043 0.150 1194 Planarity : 0.004 0.042 1290 Dihedral : 17.253 153.598 1299 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 3.69 % Allowed : 20.69 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.85 (0.25), residues: 915 helix: -1.38 (0.27), residues: 348 sheet: -2.06 (0.36), residues: 156 loop : -2.17 (0.27), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 252 TYR 0.017 0.001 TYR C 190 PHE 0.020 0.002 PHE C 128 HIS 0.002 0.001 HIS C 198 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 7813) covalent geometry : angle 0.57773 (10600) hydrogen bonds : bond 0.04037 ( 233) hydrogen bonds : angle 4.53123 ( 607) Misc. bond : bond 0.00207 ( 3) *********************** 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 193 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 165 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 PHE cc_start: 0.7687 (m-80) cc_final: 0.6698 (t80) REVERT: A 95 ARG cc_start: 0.8703 (ttt90) cc_final: 0.8068 (mtm180) REVERT: A 119 MET cc_start: 0.8012 (mmm) cc_final: 0.7648 (mmm) REVERT: A 335 ILE cc_start: 0.8857 (mm) cc_final: 0.8631 (mm) REVERT: B 101 ILE cc_start: 0.9105 (OUTLIER) cc_final: 0.8853 (mt) REVERT: B 254 GLN cc_start: 0.9322 (tp-100) cc_final: 0.9076 (tp-100) REVERT: B 335 ILE cc_start: 0.9167 (mm) cc_final: 0.8676 (mm) REVERT: C 101 ILE cc_start: 0.9105 (OUTLIER) cc_final: 0.8842 (mt) REVERT: C 155 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7795 (mtpp) REVERT: C 245 LYS cc_start: 0.9094 (mttp) cc_final: 0.8775 (mtpp) REVERT: C 249 MET cc_start: 0.9084 (ttm) cc_final: 0.8881 (ttm) REVERT: C 273 ASP cc_start: 0.8592 (t0) cc_final: 0.8333 (t0) REVERT: C 285 LYS cc_start: 0.8865 (mtmm) cc_final: 0.8301 (mttm) REVERT: C 317 ASP cc_start: 0.7310 (t0) cc_final: 0.6883 (t0) outliers start: 28 outliers final: 14 residues processed: 186 average time/residue: 0.0887 time to fit residues: 22.0794 Evaluate side-chains 155 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 211 HIS Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 163 ASN Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 224 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 34 optimal weight: 0.0030 chunk 2 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 83 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 45 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 overall best weight: 1.2794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN A 254 GLN A 261 ASN B 178 ASN B 244 GLN C 244 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.151436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.120704 restraints weight = 13567.352| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.52 r_work: 0.3313 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7816 Z= 0.118 Angle : 0.550 8.221 10600 Z= 0.291 Chirality : 0.042 0.143 1194 Planarity : 0.004 0.044 1290 Dihedral : 17.209 159.537 1299 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 3.82 % Allowed : 23.45 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.38 (0.26), residues: 915 helix: -0.87 (0.29), residues: 348 sheet: -1.98 (0.35), residues: 156 loop : -1.95 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 307 TYR 0.021 0.001 TYR B 260 PHE 0.017 0.001 PHE A 128 HIS 0.002 0.000 HIS C 198 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 7813) covalent geometry : angle 0.55001 (10600) hydrogen bonds : bond 0.03501 ( 233) hydrogen bonds : angle 4.27867 ( 607) Misc. bond : bond 0.00170 ( 3) *********************** 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 187 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 158 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 ARG cc_start: 0.8744 (ttt90) cc_final: 0.8174 (mtm180) REVERT: A 139 LEU cc_start: 0.9420 (mt) cc_final: 0.9147 (mm) REVERT: A 335 ILE cc_start: 0.8833 (mm) cc_final: 0.8615 (mm) REVERT: B 101 ILE cc_start: 0.9091 (OUTLIER) cc_final: 0.8840 (mt) REVERT: B 254 GLN cc_start: 0.9327 (tp-100) cc_final: 0.8903 (tp-100) REVERT: B 335 ILE cc_start: 0.9201 (mm) cc_final: 0.8789 (mm) REVERT: C 130 THR cc_start: 0.9178 (m) cc_final: 0.8942 (m) REVERT: C 245 LYS cc_start: 0.9035 (mttp) cc_final: 0.8699 (mtpp) REVERT: C 249 MET cc_start: 0.9091 (ttm) cc_final: 0.8875 (ttm) REVERT: C 273 ASP cc_start: 0.8536 (t0) cc_final: 0.8267 (t0) REVERT: C 285 LYS cc_start: 0.8845 (mtmm) cc_final: 0.8256 (mttm) REVERT: C 317 ASP cc_start: 0.7300 (t0) cc_final: 0.6845 (t0) outliers start: 29 outliers final: 17 residues processed: 179 average time/residue: 0.0838 time to fit residues: 20.5012 Evaluate side-chains 160 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 142 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 211 HIS Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 264 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 48 optimal weight: 5.9990 chunk 30 optimal weight: 20.0000 chunk 28 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 43 optimal weight: 8.9990 chunk 13 optimal weight: 9.9990 chunk 60 optimal weight: 20.0000 chunk 68 optimal weight: 0.7980 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN A 199 GLN B 244 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.144261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.112937 restraints weight = 13889.225| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.52 r_work: 0.3235 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 7816 Z= 0.251 Angle : 0.679 10.350 10600 Z= 0.356 Chirality : 0.047 0.194 1194 Planarity : 0.004 0.045 1290 Dihedral : 17.412 160.069 1299 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 5.01 % Allowed : 23.72 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.62 (0.26), residues: 915 helix: -0.95 (0.27), residues: 372 sheet: -1.80 (0.36), residues: 153 loop : -2.41 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 307 TYR 0.020 0.002 TYR B 260 PHE 0.025 0.002 PHE C 128 HIS 0.004 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00577 ( 7813) covalent geometry : angle 0.67944 (10600) hydrogen bonds : bond 0.04646 ( 233) hydrogen bonds : angle 4.61234 ( 607) Misc. bond : bond 0.00215 ( 3) *********************** 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 190 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 152 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.6649 (OUTLIER) cc_final: 0.6378 (mtt) REVERT: A 95 ARG cc_start: 0.8884 (ttt90) cc_final: 0.8201 (mtm180) REVERT: A 190 TYR cc_start: 0.8918 (t80) cc_final: 0.8659 (t80) REVERT: A 224 SER cc_start: 0.8849 (m) cc_final: 0.8377 (p) REVERT: A 254 GLN cc_start: 0.9428 (tp-100) cc_final: 0.9177 (tp-100) REVERT: A 317 ASP cc_start: 0.5333 (t70) cc_final: 0.5131 (m-30) REVERT: B 101 ILE cc_start: 0.9084 (OUTLIER) cc_final: 0.8773 (mt) REVERT: C 101 ILE cc_start: 0.9098 (OUTLIER) cc_final: 0.8807 (mt) REVERT: C 245 LYS cc_start: 0.9143 (mttp) cc_final: 0.8839 (mtpp) REVERT: C 273 ASP cc_start: 0.8769 (t0) cc_final: 0.8484 (t0) REVERT: C 317 ASP cc_start: 0.7252 (t0) cc_final: 0.6819 (t0) REVERT: C 321 MET cc_start: 0.8453 (mpp) cc_final: 0.8023 (mpp) outliers start: 38 outliers final: 22 residues processed: 177 average time/residue: 0.0776 time to fit residues: 19.0096 Evaluate side-chains 168 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 211 HIS Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 144 GLN Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 293 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 52 optimal weight: 0.9980 chunk 61 optimal weight: 7.9990 chunk 78 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN B 244 GLN B 254 GLN ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.148373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.116452 restraints weight = 13700.055| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.58 r_work: 0.3268 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7816 Z= 0.122 Angle : 0.575 10.215 10600 Z= 0.305 Chirality : 0.043 0.146 1194 Planarity : 0.004 0.043 1290 Dihedral : 17.154 164.192 1299 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 4.22 % Allowed : 25.30 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.27), residues: 915 helix: -0.42 (0.29), residues: 354 sheet: -1.78 (0.36), residues: 153 loop : -1.96 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 307 TYR 0.017 0.001 TYR A 194 PHE 0.018 0.001 PHE C 128 HIS 0.002 0.000 HIS A 211 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 7813) covalent geometry : angle 0.57462 (10600) hydrogen bonds : bond 0.03510 ( 233) hydrogen bonds : angle 4.23758 ( 607) Misc. bond : bond 0.00173 ( 3) *********************** 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 185 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 153 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 ARG cc_start: 0.8805 (ttt90) cc_final: 0.8118 (mtm180) REVERT: A 101 ILE cc_start: 0.8862 (OUTLIER) cc_final: 0.8655 (mm) REVERT: A 190 TYR cc_start: 0.8847 (t80) cc_final: 0.8396 (t80) REVERT: A 224 SER cc_start: 0.8876 (m) cc_final: 0.8405 (p) REVERT: A 254 GLN cc_start: 0.9415 (tp-100) cc_final: 0.9162 (tp-100) REVERT: A 273 ASP cc_start: 0.8885 (t0) cc_final: 0.8594 (t0) REVERT: A 335 ILE cc_start: 0.9021 (mm) cc_final: 0.8780 (mm) REVERT: B 89 PHE cc_start: 0.8485 (t80) cc_final: 0.8265 (t80) REVERT: B 101 ILE cc_start: 0.9024 (OUTLIER) cc_final: 0.8754 (mt) REVERT: C 101 ILE cc_start: 0.9039 (OUTLIER) cc_final: 0.8758 (mt) REVERT: C 245 LYS cc_start: 0.9095 (mttp) cc_final: 0.8757 (mtpp) REVERT: C 273 ASP cc_start: 0.8629 (t0) cc_final: 0.8377 (t0) REVERT: C 317 ASP cc_start: 0.7119 (t0) cc_final: 0.6571 (t0) REVERT: C 321 MET cc_start: 0.8414 (mpp) cc_final: 0.7728 (mpp) outliers start: 32 outliers final: 22 residues processed: 176 average time/residue: 0.0807 time to fit residues: 19.6033 Evaluate side-chains 169 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 211 HIS Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 254 GLN Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 144 GLN Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 320 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 67 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 88 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 45 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 28 optimal weight: 7.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN ** B 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN ** C 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.148169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.115954 restraints weight = 13784.144| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.57 r_work: 0.3279 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7816 Z= 0.147 Angle : 0.592 9.777 10600 Z= 0.311 Chirality : 0.044 0.159 1194 Planarity : 0.004 0.046 1290 Dihedral : 17.065 165.012 1299 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 4.74 % Allowed : 24.77 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.27), residues: 915 helix: -0.20 (0.30), residues: 348 sheet: -1.75 (0.37), residues: 153 loop : -1.95 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 307 TYR 0.016 0.002 TYR A 194 PHE 0.024 0.002 PHE C 89 HIS 0.002 0.001 HIS A 211 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 7813) covalent geometry : angle 0.59162 (10600) hydrogen bonds : bond 0.03650 ( 233) hydrogen bonds : angle 4.24265 ( 607) Misc. bond : bond 0.00180 ( 3) *********************** 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 196 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 160 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.6617 (OUTLIER) cc_final: 0.6377 (mtt) REVERT: A 95 ARG cc_start: 0.8802 (ttt90) cc_final: 0.8117 (mtm180) REVERT: A 101 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8676 (mm) REVERT: A 134 GLN cc_start: 0.8649 (mp10) cc_final: 0.8411 (mp10) REVERT: A 190 TYR cc_start: 0.8878 (t80) cc_final: 0.8418 (t80) REVERT: A 224 SER cc_start: 0.8831 (m) cc_final: 0.8368 (p) REVERT: A 254 GLN cc_start: 0.9406 (tp-100) cc_final: 0.9153 (tp-100) REVERT: A 273 ASP cc_start: 0.8876 (t0) cc_final: 0.8596 (t0) REVERT: B 89 PHE cc_start: 0.8498 (t80) cc_final: 0.8254 (t80) REVERT: B 101 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8768 (mt) REVERT: C 101 ILE cc_start: 0.9022 (OUTLIER) cc_final: 0.8734 (mt) REVERT: C 245 LYS cc_start: 0.9081 (mttp) cc_final: 0.8736 (mtpp) REVERT: C 273 ASP cc_start: 0.8607 (t0) cc_final: 0.8348 (t0) REVERT: C 317 ASP cc_start: 0.7079 (t0) cc_final: 0.6533 (t0) REVERT: C 321 MET cc_start: 0.8411 (mpp) cc_final: 0.8012 (mpp) outliers start: 36 outliers final: 25 residues processed: 185 average time/residue: 0.0767 time to fit residues: 19.6265 Evaluate side-chains 177 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 148 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 211 HIS Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 254 GLN Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 144 GLN Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 320 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 37 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 47 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN ** B 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.148162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.115080 restraints weight = 13679.110| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.61 r_work: 0.3272 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.4350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7816 Z= 0.158 Angle : 0.608 9.663 10600 Z= 0.319 Chirality : 0.044 0.156 1194 Planarity : 0.004 0.052 1290 Dihedral : 17.054 165.575 1299 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 4.74 % Allowed : 25.56 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.28), residues: 915 helix: -0.06 (0.30), residues: 345 sheet: -1.71 (0.37), residues: 153 loop : -1.90 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 307 TYR 0.017 0.002 TYR A 194 PHE 0.022 0.002 PHE C 128 HIS 0.002 0.001 HIS A 211 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 7813) covalent geometry : angle 0.60806 (10600) hydrogen bonds : bond 0.03674 ( 233) hydrogen bonds : angle 4.26045 ( 607) Misc. bond : bond 0.00183 ( 3) *********************** 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 192 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 156 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7956 (mp10) cc_final: 0.7666 (mp10) REVERT: A 53 MET cc_start: 0.6698 (OUTLIER) cc_final: 0.6433 (mtt) REVERT: A 95 ARG cc_start: 0.8834 (ttt90) cc_final: 0.8129 (mtm180) REVERT: A 101 ILE cc_start: 0.8891 (OUTLIER) cc_final: 0.8687 (mm) REVERT: A 134 GLN cc_start: 0.8683 (mp10) cc_final: 0.8433 (mp10) REVERT: A 190 TYR cc_start: 0.8915 (t80) cc_final: 0.8450 (t80) REVERT: A 224 SER cc_start: 0.8834 (m) cc_final: 0.8377 (p) REVERT: A 254 GLN cc_start: 0.9414 (tp-100) cc_final: 0.9158 (tp-100) REVERT: A 273 ASP cc_start: 0.8854 (t0) cc_final: 0.8549 (t0) REVERT: B 89 PHE cc_start: 0.8506 (t80) cc_final: 0.8276 (t80) REVERT: B 101 ILE cc_start: 0.8977 (OUTLIER) cc_final: 0.8716 (mt) REVERT: B 130 THR cc_start: 0.9264 (OUTLIER) cc_final: 0.9062 (m) REVERT: C 101 ILE cc_start: 0.8999 (OUTLIER) cc_final: 0.8693 (mt) REVERT: C 245 LYS cc_start: 0.9084 (mttp) cc_final: 0.8738 (mtpp) REVERT: C 273 ASP cc_start: 0.8683 (t0) cc_final: 0.8398 (t0) REVERT: C 317 ASP cc_start: 0.7062 (t0) cc_final: 0.6490 (t0) REVERT: C 321 MET cc_start: 0.8390 (mpp) cc_final: 0.7923 (mpp) outliers start: 36 outliers final: 26 residues processed: 178 average time/residue: 0.0780 time to fit residues: 19.2475 Evaluate side-chains 177 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 146 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 211 HIS Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 181 HIS Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 254 GLN Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 144 GLN Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 320 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 16 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 23 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 chunk 3 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN ** B 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.149448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.117019 restraints weight = 13513.801| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.57 r_work: 0.3294 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.4443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7816 Z= 0.115 Angle : 0.570 9.289 10600 Z= 0.300 Chirality : 0.043 0.158 1194 Planarity : 0.004 0.056 1290 Dihedral : 16.941 167.566 1299 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 4.61 % Allowed : 25.56 % Favored : 69.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.28), residues: 915 helix: 0.08 (0.30), residues: 348 sheet: -1.49 (0.38), residues: 147 loop : -1.84 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 307 TYR 0.017 0.001 TYR A 194 PHE 0.023 0.001 PHE C 89 HIS 0.002 0.000 HIS A 211 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 7813) covalent geometry : angle 0.56982 (10600) hydrogen bonds : bond 0.03273 ( 233) hydrogen bonds : angle 4.12790 ( 607) Misc. bond : bond 0.00171 ( 3) *********************** 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 193 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 158 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7927 (mp10) cc_final: 0.7681 (mp10) REVERT: A 53 MET cc_start: 0.6632 (OUTLIER) cc_final: 0.6389 (mtt) REVERT: A 95 ARG cc_start: 0.8818 (ttt90) cc_final: 0.8043 (mtm180) REVERT: A 134 GLN cc_start: 0.8686 (mp10) cc_final: 0.8410 (mp10) REVERT: A 190 TYR cc_start: 0.8884 (t80) cc_final: 0.8419 (t80) REVERT: A 224 SER cc_start: 0.8847 (m) cc_final: 0.8410 (p) REVERT: A 254 GLN cc_start: 0.9402 (tp-100) cc_final: 0.9150 (tp-100) REVERT: A 273 ASP cc_start: 0.8784 (t0) cc_final: 0.8480 (t0) REVERT: A 335 ILE cc_start: 0.9000 (mm) cc_final: 0.8797 (mm) REVERT: B 89 PHE cc_start: 0.8493 (t80) cc_final: 0.8276 (t80) REVERT: B 101 ILE cc_start: 0.9021 (OUTLIER) cc_final: 0.8757 (mt) REVERT: C 101 ILE cc_start: 0.8957 (OUTLIER) cc_final: 0.8672 (mt) REVERT: C 245 LYS cc_start: 0.9060 (mttp) cc_final: 0.8702 (mtpp) REVERT: C 273 ASP cc_start: 0.8637 (t0) cc_final: 0.8339 (t0) REVERT: C 285 LYS cc_start: 0.8870 (mtmm) cc_final: 0.8205 (mttm) REVERT: C 317 ASP cc_start: 0.7034 (t0) cc_final: 0.6488 (t0) outliers start: 35 outliers final: 24 residues processed: 177 average time/residue: 0.0789 time to fit residues: 19.3356 Evaluate side-chains 177 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 150 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 211 HIS Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 181 HIS Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 144 GLN Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 320 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 14 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 199 GLN ** B 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.148297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.115636 restraints weight = 13675.300| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.58 r_work: 0.3230 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.4489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7816 Z= 0.157 Angle : 0.607 9.493 10600 Z= 0.320 Chirality : 0.044 0.156 1194 Planarity : 0.004 0.064 1290 Dihedral : 16.957 167.161 1299 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 3.95 % Allowed : 26.61 % Favored : 69.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.28), residues: 915 helix: 0.06 (0.30), residues: 348 sheet: -1.48 (0.38), residues: 147 loop : -1.82 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 307 TYR 0.018 0.002 TYR A 194 PHE 0.021 0.002 PHE C 128 HIS 0.002 0.001 HIS A 211 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 7813) covalent geometry : angle 0.60717 (10600) hydrogen bonds : bond 0.03595 ( 233) hydrogen bonds : angle 4.22560 ( 607) Misc. bond : bond 0.00178 ( 3) ********************** 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 183 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 153 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7989 (mp10) cc_final: 0.7671 (mp10) REVERT: A 53 MET cc_start: 0.6679 (OUTLIER) cc_final: 0.6430 (mtt) REVERT: A 95 ARG cc_start: 0.8836 (ttt90) cc_final: 0.8091 (mtm180) REVERT: A 134 GLN cc_start: 0.8723 (mp10) cc_final: 0.8474 (mp10) REVERT: A 190 TYR cc_start: 0.8919 (t80) cc_final: 0.8431 (t80) REVERT: A 224 SER cc_start: 0.8856 (m) cc_final: 0.8420 (p) REVERT: A 254 GLN cc_start: 0.9408 (tp-100) cc_final: 0.9159 (tp-100) REVERT: A 273 ASP cc_start: 0.8846 (t0) cc_final: 0.8555 (t0) REVERT: B 89 PHE cc_start: 0.8493 (t80) cc_final: 0.8277 (t80) REVERT: B 101 ILE cc_start: 0.8970 (OUTLIER) cc_final: 0.8717 (mt) REVERT: B 130 THR cc_start: 0.9278 (OUTLIER) cc_final: 0.9068 (m) REVERT: C 101 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8663 (mt) REVERT: C 245 LYS cc_start: 0.9082 (mttp) cc_final: 0.8737 (mtpp) REVERT: C 273 ASP cc_start: 0.8692 (t0) cc_final: 0.8397 (t0) REVERT: C 317 ASP cc_start: 0.7031 (t0) cc_final: 0.6484 (t0) outliers start: 30 outliers final: 24 residues processed: 170 average time/residue: 0.0820 time to fit residues: 19.3115 Evaluate side-chains 175 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 147 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 211 HIS Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 181 HIS Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 254 GLN Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 144 GLN Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 320 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 37 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 30 optimal weight: 10.0000 chunk 62 optimal weight: 0.4980 chunk 46 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 13 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 199 GLN ** B 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.149178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.118626 restraints weight = 13581.585| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.50 r_work: 0.3250 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.4499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.205 7816 Z= 0.209 Angle : 0.964 59.156 10600 Z= 0.555 Chirality : 0.045 0.387 1194 Planarity : 0.004 0.062 1290 Dihedral : 16.962 167.232 1299 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 4.22 % Allowed : 26.48 % Favored : 69.30 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.28), residues: 915 helix: 0.01 (0.30), residues: 348 sheet: -1.48 (0.38), residues: 147 loop : -1.82 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 307 TYR 0.016 0.001 TYR A 194 PHE 0.020 0.002 PHE C 128 HIS 0.002 0.001 HIS A 211 Details of bonding type rmsd covalent geometry : bond 0.00464 ( 7813) covalent geometry : angle 0.96390 (10600) hydrogen bonds : bond 0.03541 ( 233) hydrogen bonds : angle 4.23842 ( 607) Misc. bond : bond 0.00173 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1744.75 seconds wall clock time: 30 minutes 36.15 seconds (1836.15 seconds total)