Starting phenix.real_space_refine on Fri Sep 11 05:00:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7c98_30308/09_2026/7c98_30308.cif Found real_map, /net/cci-nas-00/data/ceres_data/7c98_30308/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7c98_30308/09_2026/7c98_30308.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7c98_30308/09_2026/7c98_30308.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7c98_30308/09_2026/7c98_30308.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7c98_30308/09_2026/7c98_30308.map" model { file = "/net/cci-nas-00/data/ceres_data/7c98_30308/09_2026/7c98_30308.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7c98_30308/09_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 1.69, per 1000 atoms: 0.22 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: 0.48 Conformation dependent library (CDL) restraints added in 430.1 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: 0.84 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: 1.09 Time building geometry restraints manager: 0.63 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=" O4' DA E 8 " pdb=" C4' DA E 8 " pdb=" C3' DA E 8 " ideal model delta sigma weight residual 106.00 103.42 2.58 6.00e-01 2.78e+00 1.85e+01 angle pdb=" N3 DT D 8 " pdb=" C4 DT D 8 " pdb=" O4 DT D 8 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" N3 DT D 3 " pdb=" C4 DT D 3 " pdb=" O4 DT D 3 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.69e+01 ... (remaining 10595 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.83: 4389 30.83 - 61.66: 257 61.66 - 92.48: 14 92.48 - 123.31: 2 123.31 - 154.14: 3 Dihedral angle restraints: 4665 sinusoidal: 2031 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 4662 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 957 0.068 - 0.136: 205 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: 3.920 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: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.260 Find NCS groups from input model: 0.150 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: 0.010 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 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 : 0.014 0.728 7816 Z= 1.183 Angle : 1.030 21.173 10600 Z= 0.562 Chirality : 0.055 0.340 1194 Planarity : 0.005 0.060 1290 Dihedral : 17.545 154.140 2973 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/Z covalent geometry : bond 0.00771 / 0.41 ( 7813) covalent geometry : angle 1.02961 / 0.56 (10600) hydrogen bonds : bond 0.29936 / 19.76 ( 233) hydrogen bonds : angle 8.98611 / 5.82 ( 607) Misc. bond : bond 0.56600 / 28.91 ( 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 : 0.325 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: 0.0921 time to fit residues: 31.8591 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 : 0.270 ------------------------------------------------------------------------------- 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... A 30 HIS A 61 ASN A 144 GLN A 178 ASN A 254 GLN B 30 HIS B 61 ASN B 144 GLN B 163 ASN B 198 HIS B 254 GLN C 30 HIS C 61 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.151874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.118849 restraints weight = 13407.163| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.56 r_work: 0.3309 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7816 Z= 0.151 Angle : 0.698 9.896 10600 Z= 0.372 Chirality : 0.045 0.167 1194 Planarity : 0.005 0.046 1290 Dihedral : 17.190 155.971 1215 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 3.82 % Allowed : 18.97 % Favored : 77.21 % 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: -3.62 (0.23), residues: 915 helix: -2.31 (0.23), residues: 342 sheet: -1.81 (0.39), residues: 153 loop : -2.64 (0.25), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 307 TYR 0.024 0.002 TYR B 190 PHE 0.020 0.002 PHE B 328 HIS 0.003 0.001 HIS C 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.15 ( 7813) covalent geometry : angle 0.69773 / 0.37 (10600) hydrogen bonds : bond 0.06297 / 4.18 ( 233) hydrogen bonds : angle 5.44498 / 3.59 ( 607) Misc. bond : bond 0.00863 / 0.44 ( 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 199 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 170 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 PHE cc_start: 0.7599 (m-80) cc_final: 0.6638 (t80) REVERT: A 95 ARG cc_start: 0.8617 (ttt90) cc_final: 0.7985 (mtm180) REVERT: A 118 SER cc_start: 0.8073 (p) cc_final: 0.7490 (m) REVERT: A 119 MET cc_start: 0.8132 (mmm) cc_final: 0.7635 (mmm) REVERT: A 321 MET cc_start: 0.7446 (mmm) cc_final: 0.7177 (mmm) REVERT: A 335 ILE cc_start: 0.8691 (mm) cc_final: 0.7913 (tp) REVERT: B 273 ASP cc_start: 0.8719 (t0) cc_final: 0.8451 (t0) REVERT: B 335 ILE cc_start: 0.9088 (mm) cc_final: 0.8568 (mm) REVERT: C 101 ILE cc_start: 0.9137 (OUTLIER) cc_final: 0.8847 (mt) REVERT: C 244 GLN cc_start: 0.8808 (mt0) cc_final: 0.8584 (mt0) REVERT: C 245 LYS cc_start: 0.9167 (mttp) cc_final: 0.8863 (mtpp) REVERT: C 285 LYS cc_start: 0.8838 (mtmm) cc_final: 0.8399 (mttm) outliers start: 29 outliers final: 11 residues processed: 190 average time/residue: 0.0840 time to fit residues: 21.7199 Evaluate side-chains 158 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 146 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain B residue 163 ASN Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 101 ILE 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 264 VAL Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 330 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 68 optimal weight: 0.6980 chunk 1 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 overall best weight: 1.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 178 ASN C 211 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.150978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.118242 restraints weight = 13427.380| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.57 r_work: 0.3274 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7816 Z= 0.150 Angle : 0.623 9.172 10600 Z= 0.333 Chirality : 0.044 0.177 1194 Planarity : 0.004 0.041 1290 Dihedral : 17.128 157.059 1215 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 3.29 % Allowed : 21.87 % Favored : 74.84 % 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: -3.12 (0.25), residues: 915 helix: -1.56 (0.26), residues: 348 sheet: -1.83 (0.38), residues: 153 loop : -2.56 (0.26), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 307 TYR 0.024 0.002 TYR B 190 PHE 0.021 0.002 PHE C 128 HIS 0.003 0.001 HIS C 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 ( 7813) covalent geometry : angle 0.62327 / 0.33 (10600) hydrogen bonds : bond 0.05041 / 3.33 ( 233) hydrogen bonds : angle 4.95781 / 3.29 ( 607) Misc. bond : bond 0.00253 / 0.13 ( 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 177 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 152 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 PHE cc_start: 0.7744 (m-80) cc_final: 0.6697 (t80) REVERT: A 95 ARG cc_start: 0.8643 (ttt90) cc_final: 0.8041 (mtm180) REVERT: A 118 SER cc_start: 0.8005 (p) cc_final: 0.7610 (p) REVERT: A 258 GLU cc_start: 0.8664 (mm-30) cc_final: 0.8418 (mm-30) REVERT: A 321 MET cc_start: 0.7546 (mmm) cc_final: 0.7322 (mmm) REVERT: A 335 ILE cc_start: 0.8689 (mm) cc_final: 0.8392 (mm) REVERT: B 101 ILE cc_start: 0.9059 (OUTLIER) cc_final: 0.8818 (mt) REVERT: B 163 ASN cc_start: 0.8244 (t0) cc_final: 0.7865 (m-40) REVERT: B 254 GLN cc_start: 0.9290 (tp40) cc_final: 0.8940 (tp-100) REVERT: B 273 ASP cc_start: 0.8688 (t0) cc_final: 0.8443 (t0) REVERT: B 335 ILE cc_start: 0.9106 (mm) cc_final: 0.8638 (mm) REVERT: C 245 LYS cc_start: 0.9146 (mttp) cc_final: 0.8819 (mtpp) REVERT: C 285 LYS cc_start: 0.8849 (mtmm) cc_final: 0.8352 (mttm) REVERT: C 304 ARG cc_start: 0.8309 (ptt90) cc_final: 0.8036 (ptt90) REVERT: C 317 ASP cc_start: 0.7346 (t0) cc_final: 0.6925 (t0) outliers start: 25 outliers final: 15 residues processed: 168 average time/residue: 0.0803 time to fit residues: 18.3635 Evaluate side-chains 159 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 143 time to evaluate : 0.177 ------------------------------------------------------------------------------- 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 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 211 HIS Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain C residue 45 ILE 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 266 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 34 optimal weight: 20.0000 chunk 2 optimal weight: 0.4980 chunk 51 optimal weight: 9.9990 chunk 15 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 66 optimal weight: 7.9990 chunk 50 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 56 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 ASN A 178 ASN A 254 GLN B 244 GLN C 144 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 = 0.3868 r_free = 0.3868 target = 0.151807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.118976 restraints weight = 13632.757| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.60 r_work: 0.3282 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2964 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= 0.121 Angle : 0.580 8.669 10600 Z= 0.312 Chirality : 0.043 0.154 1194 Planarity : 0.004 0.040 1290 Dihedral : 17.080 157.094 1215 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 3.95 % Allowed : 22.79 % Favored : 73.25 % 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: -2.83 (0.25), residues: 915 helix: -1.18 (0.28), residues: 348 sheet: -1.90 (0.36), residues: 153 loop : -2.44 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 307 TYR 0.029 0.002 TYR B 260 PHE 0.019 0.001 PHE C 128 HIS 0.001 0.000 HIS A 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 ( 7813) covalent geometry : angle 0.57996 / 0.31 (10600) hydrogen bonds : bond 0.04215 / 2.78 ( 233) hydrogen bonds : angle 4.63421 / 3.06 ( 607) Misc. bond : bond 0.00215 / 0.10 ( 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 182 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 152 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 PHE cc_start: 0.7682 (m-80) cc_final: 0.6675 (t80) REVERT: A 95 ARG cc_start: 0.8656 (ttt90) cc_final: 0.8028 (mtm180) REVERT: A 139 LEU cc_start: 0.9471 (mt) cc_final: 0.9117 (mp) REVERT: A 335 ILE cc_start: 0.8660 (mm) cc_final: 0.8344 (mm) REVERT: B 101 ILE cc_start: 0.9079 (OUTLIER) cc_final: 0.8840 (mt) REVERT: B 163 ASN cc_start: 0.8221 (t0) cc_final: 0.7916 (m-40) REVERT: B 273 ASP cc_start: 0.8680 (t0) cc_final: 0.8451 (t0) REVERT: B 317 ASP cc_start: 0.6997 (t0) cc_final: 0.6781 (t0) REVERT: B 335 ILE cc_start: 0.9132 (mm) cc_final: 0.8657 (mm) REVERT: C 101 ILE cc_start: 0.9114 (OUTLIER) cc_final: 0.8825 (mt) REVERT: C 245 LYS cc_start: 0.9132 (mttp) cc_final: 0.8800 (mtpp) REVERT: C 273 ASP cc_start: 0.8536 (t0) cc_final: 0.8223 (t0) REVERT: C 285 LYS cc_start: 0.8874 (mtmm) cc_final: 0.8322 (mttm) REVERT: C 317 ASP cc_start: 0.7308 (t0) cc_final: 0.6825 (t0) outliers start: 30 outliers final: 16 residues processed: 171 average time/residue: 0.0820 time to fit residues: 19.2697 Evaluate side-chains 161 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 0.298 ------------------------------------------------------------------------------- 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 256 ILE Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 264 VAL 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 220 LEU Chi-restraints excluded: chain C residue 224 SER 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: 0.9980 chunk 30 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 9 optimal weight: 8.9990 chunk 8 optimal weight: 1.9990 chunk 10 optimal weight: 8.9990 chunk 43 optimal weight: 7.9990 chunk 13 optimal weight: 10.0000 chunk 60 optimal weight: 20.0000 chunk 68 optimal weight: 1.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 ASN C 199 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.150458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.118132 restraints weight = 13720.524| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.59 r_work: 0.3253 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7816 Z= 0.198 Angle : 0.627 8.364 10600 Z= 0.333 Chirality : 0.045 0.191 1194 Planarity : 0.004 0.045 1290 Dihedral : 17.079 158.363 1215 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 4.22 % Allowed : 23.45 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.65 (0.26), residues: 915 helix: -1.08 (0.27), residues: 357 sheet: -1.75 (0.37), residues: 153 loop : -2.32 (0.28), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 307 TYR 0.037 0.003 TYR C 260 PHE 0.027 0.002 PHE C 128 HIS 0.004 0.001 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.20 ( 7813) covalent geometry : angle 0.62662 / 0.33 (10600) hydrogen bonds : bond 0.04387 / 2.87 ( 233) hydrogen bonds : angle 4.63296 / 3.09 ( 607) Misc. bond : bond 0.00204 / 0.10 ( 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 176 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 144 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: A 95 ARG cc_start: 0.8760 (ttt90) cc_final: 0.8077 (mtm180) REVERT: A 258 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8482 (mm-30) REVERT: A 317 ASP cc_start: 0.5450 (t70) cc_final: 0.5156 (m-30) REVERT: A 321 MET cc_start: 0.8039 (mpp) cc_final: 0.7221 (mpp) REVERT: A 335 ILE cc_start: 0.8761 (mm) cc_final: 0.8501 (mm) REVERT: B 101 ILE cc_start: 0.9117 (OUTLIER) cc_final: 0.8867 (mt) REVERT: B 163 ASN cc_start: 0.8246 (t0) cc_final: 0.7962 (m-40) REVERT: B 335 ILE cc_start: 0.9216 (mm) cc_final: 0.8760 (mm) REVERT: C 101 ILE cc_start: 0.9128 (OUTLIER) cc_final: 0.8900 (mt) REVERT: C 245 LYS cc_start: 0.9155 (mttp) cc_final: 0.8789 (mtpp) REVERT: C 273 ASP cc_start: 0.8613 (t0) cc_final: 0.8323 (t0) REVERT: C 317 ASP cc_start: 0.7259 (t0) cc_final: 0.6780 (t0) outliers start: 32 outliers final: 16 residues processed: 168 average time/residue: 0.0827 time to fit residues: 19.2497 Evaluate side-chains 152 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.287 ------------------------------------------------------------------------------- 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 B residue 101 ILE Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain B residue 219 LEU 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 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 201 GLU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain C residue 264 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 52 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 78 optimal weight: 0.9990 chunk 12 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 ASN A 198 HIS B 244 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.149047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.115715 restraints weight = 13554.049| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.57 r_work: 0.3252 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7816 Z= 0.173 Angle : 0.604 8.304 10600 Z= 0.322 Chirality : 0.044 0.179 1194 Planarity : 0.004 0.047 1290 Dihedral : 17.079 159.525 1215 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 4.08 % Allowed : 23.45 % Favored : 72.46 % 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: -2.37 (0.26), residues: 915 helix: -0.82 (0.28), residues: 357 sheet: -1.70 (0.37), residues: 153 loop : -2.14 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 307 TYR 0.038 0.002 TYR C 260 PHE 0.024 0.002 PHE C 128 HIS 0.003 0.001 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 ( 7813) covalent geometry : angle 0.60418 / 0.32 (10600) hydrogen bonds : bond 0.04039 / 2.65 ( 233) hydrogen bonds : angle 4.47691 / 2.99 ( 607) Misc. bond : bond 0.00167 / 0.08 ( 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 179 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 148 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.2131 (OUTLIER) cc_final: 0.1627 (mt-10) REVERT: A 95 ARG cc_start: 0.8779 (ttt90) cc_final: 0.8062 (mtm180) REVERT: A 317 ASP cc_start: 0.5382 (t70) cc_final: 0.5105 (m-30) REVERT: A 335 ILE cc_start: 0.8787 (mm) cc_final: 0.8506 (mm) REVERT: B 101 ILE cc_start: 0.9099 (OUTLIER) cc_final: 0.8833 (mt) REVERT: B 163 ASN cc_start: 0.8038 (t0) cc_final: 0.7777 (m-40) REVERT: B 335 ILE cc_start: 0.9244 (mm) cc_final: 0.8863 (mm) REVERT: C 49 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.8103 (tttp) REVERT: C 101 ILE cc_start: 0.9065 (OUTLIER) cc_final: 0.8820 (mt) REVERT: C 245 LYS cc_start: 0.9153 (mttp) cc_final: 0.8825 (mtpp) REVERT: C 273 ASP cc_start: 0.8612 (t0) cc_final: 0.8341 (t0) REVERT: C 317 ASP cc_start: 0.7187 (t0) cc_final: 0.6682 (t0) REVERT: C 321 MET cc_start: 0.8314 (mpp) cc_final: 0.8102 (mpp) outliers start: 31 outliers final: 19 residues processed: 173 average time/residue: 0.0830 time to fit residues: 19.6012 Evaluate side-chains 161 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 0.260 ------------------------------------------------------------------------------- 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 67 GLU 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 238 GLU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain B residue 219 LEU 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 C residue 45 ILE Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 101 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 67 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 35 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 ASN A 254 GLN A 261 ASN ** B 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 GLN B 254 GLN ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.149325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.116209 restraints weight = 13529.696| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.56 r_work: 0.3265 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.3578 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= 0.143 Angle : 0.590 8.112 10600 Z= 0.311 Chirality : 0.044 0.165 1194 Planarity : 0.004 0.048 1290 Dihedral : 17.017 157.887 1215 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 3.69 % Allowed : 24.64 % Favored : 71.67 % 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: -2.15 (0.27), residues: 915 helix: -0.58 (0.28), residues: 357 sheet: -1.69 (0.36), residues: 153 loop : -2.03 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 307 TYR 0.025 0.002 TYR B 190 PHE 0.023 0.002 PHE C 128 HIS 0.002 0.001 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 7813) covalent geometry : angle 0.58970 / 0.31 (10600) hydrogen bonds : bond 0.03802 / 2.50 ( 233) hydrogen bonds : angle 4.35251 / 2.90 ( 607) Misc. bond : bond 0.00168 / 0.08 ( 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 174 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 0.283 Fit side-chains revert: symmetry clash REVERT: A 95 ARG cc_start: 0.8831 (ttt90) cc_final: 0.8091 (mtm180) REVERT: A 317 ASP cc_start: 0.5347 (t70) cc_final: 0.5094 (m-30) REVERT: A 321 MET cc_start: 0.7910 (mpp) cc_final: 0.6898 (mpp) REVERT: A 335 ILE cc_start: 0.8823 (mm) cc_final: 0.8565 (mm) REVERT: B 101 ILE cc_start: 0.9082 (OUTLIER) cc_final: 0.8805 (mt) REVERT: B 130 THR cc_start: 0.9144 (OUTLIER) cc_final: 0.8941 (m) REVERT: B 335 ILE cc_start: 0.9264 (mm) cc_final: 0.8893 (mm) REVERT: C 101 ILE cc_start: 0.9048 (OUTLIER) cc_final: 0.8777 (mt) REVERT: C 245 LYS cc_start: 0.9146 (mttp) cc_final: 0.8802 (mtpp) REVERT: C 273 ASP cc_start: 0.8606 (t0) cc_final: 0.8339 (t0) REVERT: C 317 ASP cc_start: 0.7122 (t0) cc_final: 0.6582 (t0) REVERT: C 321 MET cc_start: 0.8345 (mpp) cc_final: 0.7786 (mpp) outliers start: 28 outliers final: 21 residues processed: 168 average time/residue: 0.0842 time to fit residues: 19.5669 Evaluate side-chains 161 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 0.296 ------------------------------------------------------------------------------- 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 163 ASN 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 130 THR Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain B residue 219 LEU 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 254 GLN Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 101 ILE 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 325 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 37 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 68 optimal weight: 0.2980 chunk 55 optimal weight: 0.7980 chunk 47 optimal weight: 7.9990 chunk 4 optimal weight: 20.0000 chunk 50 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 ASN A 199 GLN ** B 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 ASN B 244 GLN B 254 GLN ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.148644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.115994 restraints weight = 13621.315| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.54 r_work: 0.3260 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7816 Z= 0.141 Angle : 0.594 9.666 10600 Z= 0.314 Chirality : 0.044 0.170 1194 Planarity : 0.004 0.058 1290 Dihedral : 16.999 157.611 1215 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 3.82 % Allowed : 25.30 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.85 (0.27), residues: 915 helix: -0.41 (0.29), residues: 348 sheet: -1.68 (0.36), residues: 153 loop : -1.68 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 307 TYR 0.026 0.002 TYR B 190 PHE 0.023 0.002 PHE C 128 HIS 0.002 0.001 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 7813) covalent geometry : angle 0.59358 / 0.31 (10600) hydrogen bonds : bond 0.03750 / 2.45 ( 233) hydrogen bonds : angle 4.31509 / 2.87 ( 607) Misc. bond : bond 0.00166 / 0.08 ( 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 174 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 145 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.2193 (OUTLIER) cc_final: 0.1767 (mt-10) REVERT: A 95 ARG cc_start: 0.8826 (ttt90) cc_final: 0.8098 (mtm180) REVERT: A 224 SER cc_start: 0.8967 (m) cc_final: 0.8518 (p) REVERT: A 317 ASP cc_start: 0.5360 (t70) cc_final: 0.5101 (m-30) REVERT: A 321 MET cc_start: 0.7976 (mpp) cc_final: 0.6946 (mpp) REVERT: A 335 ILE cc_start: 0.8810 (mm) cc_final: 0.8550 (mm) REVERT: B 101 ILE cc_start: 0.9088 (OUTLIER) cc_final: 0.8819 (mt) REVERT: B 335 ILE cc_start: 0.9272 (mm) cc_final: 0.8934 (mm) REVERT: C 101 ILE cc_start: 0.9061 (OUTLIER) cc_final: 0.8771 (mt) REVERT: C 245 LYS cc_start: 0.9133 (mttp) cc_final: 0.8786 (mtpp) REVERT: C 273 ASP cc_start: 0.8587 (t0) cc_final: 0.8326 (t0) REVERT: C 317 ASP cc_start: 0.7125 (t0) cc_final: 0.6599 (t0) outliers start: 29 outliers final: 23 residues processed: 165 average time/residue: 0.0809 time to fit residues: 18.5825 Evaluate side-chains 165 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 0.294 ------------------------------------------------------------------------------- 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 67 GLU Chi-restraints excluded: chain A residue 163 ASN 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 130 THR 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 219 LEU 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 254 GLN Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain C residue 101 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 16 optimal weight: 8.9990 chunk 75 optimal weight: 10.0000 chunk 34 optimal weight: 20.0000 chunk 23 optimal weight: 4.9990 chunk 83 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 9 optimal weight: 8.9990 chunk 3 optimal weight: 0.0070 chunk 21 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 overall best weight: 0.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 ASN A 199 GLN A 254 GLN ** B 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 ASN ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.149907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.117780 restraints weight = 13475.089| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.51 r_work: 0.3291 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7816 Z= 0.113 Angle : 0.582 9.579 10600 Z= 0.308 Chirality : 0.043 0.164 1194 Planarity : 0.004 0.060 1290 Dihedral : 16.967 156.762 1215 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 3.95 % Allowed : 25.16 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.77 (0.28), residues: 915 helix: -0.32 (0.29), residues: 348 sheet: -1.67 (0.36), residues: 153 loop : -1.64 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 307 TYR 0.028 0.002 TYR B 190 PHE 0.020 0.002 PHE C 128 HIS 0.001 0.000 HIS B 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 ( 7813) covalent geometry : angle 0.58153 / 0.31 (10600) hydrogen bonds : bond 0.03548 / 2.32 ( 233) hydrogen bonds : angle 4.24983 / 2.82 ( 607) Misc. bond : bond 0.00157 / 0.07 ( 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 184 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 154 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.2079 (OUTLIER) cc_final: 0.1792 (mt-10) REVERT: A 95 ARG cc_start: 0.8769 (ttt90) cc_final: 0.8060 (mtm180) REVERT: A 224 SER cc_start: 0.8961 (m) cc_final: 0.8525 (p) REVERT: A 317 ASP cc_start: 0.5235 (t70) cc_final: 0.4976 (m-30) REVERT: A 321 MET cc_start: 0.7835 (mpp) cc_final: 0.6812 (mpp) REVERT: A 335 ILE cc_start: 0.8791 (mm) cc_final: 0.8533 (mm) REVERT: B 89 PHE cc_start: 0.8522 (t80) cc_final: 0.8305 (t80) REVERT: B 101 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8819 (mt) REVERT: B 335 ILE cc_start: 0.9273 (mm) cc_final: 0.8943 (mm) REVERT: C 101 ILE cc_start: 0.9029 (OUTLIER) cc_final: 0.8729 (mt) REVERT: C 245 LYS cc_start: 0.9109 (mttp) cc_final: 0.8760 (mtpp) REVERT: C 273 ASP cc_start: 0.8556 (t0) cc_final: 0.8284 (t0) REVERT: C 317 ASP cc_start: 0.7073 (t0) cc_final: 0.6542 (t0) outliers start: 30 outliers final: 23 residues processed: 174 average time/residue: 0.0846 time to fit residues: 20.3088 Evaluate side-chains 171 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 0.297 ------------------------------------------------------------------------------- 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 67 GLU Chi-restraints excluded: chain A residue 163 ASN 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 179 VAL Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain B residue 219 LEU 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 C residue 101 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 14 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 36 optimal weight: 9.9990 chunk 75 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 ASN A 199 GLN ** B 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 ASN ** 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 = 0.3826 r_free = 0.3826 target = 0.148933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.116334 restraints weight = 13521.566| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.50 r_work: 0.3268 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 7816 Z= 0.168 Angle : 0.613 9.496 10600 Z= 0.325 Chirality : 0.044 0.165 1194 Planarity : 0.004 0.068 1290 Dihedral : 16.951 156.671 1215 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 3.43 % Allowed : 25.56 % Favored : 71.01 % 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: -1.65 (0.28), residues: 915 helix: -0.25 (0.29), residues: 348 sheet: -1.58 (0.37), residues: 153 loop : -1.57 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 307 TYR 0.029 0.002 TYR B 190 PHE 0.025 0.002 PHE C 128 HIS 0.002 0.001 HIS C 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 ( 7813) covalent geometry : angle 0.61341 / 0.32 (10600) hydrogen bonds : bond 0.03764 / 2.46 ( 233) hydrogen bonds : angle 4.32167 / 2.87 ( 607) Misc. bond : bond 0.00166 / 0.08 ( 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 174 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 0.237 Fit side-chains REVERT: A 53 MET cc_start: 0.6784 (OUTLIER) cc_final: 0.6509 (mtt) REVERT: A 67 GLU cc_start: 0.2127 (OUTLIER) cc_final: 0.1846 (mt-10) REVERT: A 95 ARG cc_start: 0.8783 (ttt90) cc_final: 0.8104 (mtm180) REVERT: A 190 TYR cc_start: 0.8875 (t80) cc_final: 0.8522 (t80) REVERT: A 224 SER cc_start: 0.8971 (m) cc_final: 0.8547 (p) REVERT: A 317 ASP cc_start: 0.5308 (t70) cc_final: 0.5078 (m-30) REVERT: A 321 MET cc_start: 0.7806 (mpp) cc_final: 0.6853 (mpp) REVERT: A 335 ILE cc_start: 0.8838 (mm) cc_final: 0.8563 (mm) REVERT: B 101 ILE cc_start: 0.9087 (OUTLIER) cc_final: 0.8827 (mt) REVERT: B 335 ILE cc_start: 0.9287 (mm) cc_final: 0.8973 (mm) REVERT: C 97 MET cc_start: 0.8087 (pmm) cc_final: 0.7873 (pmm) REVERT: C 101 ILE cc_start: 0.9035 (OUTLIER) cc_final: 0.8730 (mt) REVERT: C 245 LYS cc_start: 0.9128 (mttp) cc_final: 0.8788 (mtpp) REVERT: C 273 ASP cc_start: 0.8564 (t0) cc_final: 0.8291 (t0) REVERT: C 317 ASP cc_start: 0.7123 (t0) cc_final: 0.6606 (t0) outliers start: 26 outliers final: 19 residues processed: 164 average time/residue: 0.0833 time to fit residues: 18.9577 Evaluate side-chains 167 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 144 time to evaluate : 0.294 ------------------------------------------------------------------------------- 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 67 GLU 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 179 VAL Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain C residue 101 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 37 optimal weight: 8.9990 chunk 35 optimal weight: 7.9990 chunk 58 optimal weight: 0.9980 chunk 30 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 chunk 46 optimal weight: 9.9990 chunk 82 optimal weight: 0.6980 chunk 13 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 199 GLN ** B 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 ASN 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 = 0.3811 r_free = 0.3811 target = 0.147453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.115075 restraints weight = 13590.143| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.54 r_work: 0.3260 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 7816 Z= 0.204 Angle : 0.654 9.742 10600 Z= 0.344 Chirality : 0.046 0.189 1194 Planarity : 0.005 0.080 1290 Dihedral : 17.014 157.607 1215 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 3.82 % Allowed : 25.16 % Favored : 71.01 % 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: -1.58 (0.28), residues: 915 helix: -0.17 (0.29), residues: 345 sheet: -1.49 (0.38), residues: 153 loop : -1.54 (0.32), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 307 TYR 0.047 0.003 TYR B 260 PHE 0.028 0.002 PHE C 128 HIS 0.004 0.001 HIS C 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.20 ( 7813) covalent geometry : angle 0.65401 / 0.34 (10600) hydrogen bonds : bond 0.04137 / 2.68 ( 233) hydrogen bonds : angle 4.46996 / 2.98 ( 607) Misc. bond : bond 0.00209 / 0.10 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1789.87 seconds wall clock time: 31 minutes 25.88 seconds (1885.88 seconds total)