Starting phenix.real_space_refine on Fri Jul 25 15:46:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7c98_30308/07_2025/7c98_30308.cif Found real_map, /net/cci-nas-00/data/ceres_data/7c98_30308/07_2025/7c98_30308.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7c98_30308/07_2025/7c98_30308.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7c98_30308/07_2025/7c98_30308.map" model { file = "/net/cci-nas-00/data/ceres_data/7c98_30308/07_2025/7c98_30308.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7c98_30308/07_2025/7c98_30308.cif" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 7656 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2397 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "B" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2397 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "C" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2397 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "D" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 180 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "E" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 189 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.93, per 1000 atoms: 0.77 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: 2.04 Conformation dependent library (CDL) restraints added in 839.4 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: 3.71 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: 2.03 Time building geometry restraints manager: 2.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1747 1.33 - 1.45: 1584 1.45 - 1.57: 4376 1.57 - 1.68: 47 1.68 - 1.80: 59 Bond restraints: 7813 Sorted by residual: bond pdb=" O3A ANP B 402 " pdb=" PB ANP B 402 " ideal model delta sigma weight residual 1.700 1.541 0.159 2.00e-02 2.50e+03 6.32e+01 bond pdb=" O3A ANP C 401 " pdb=" PB ANP C 401 " ideal model delta sigma weight residual 1.700 1.549 0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" N3B ANP C 401 " pdb=" PG ANP C 401 " ideal model delta sigma weight residual 1.795 1.683 0.112 2.00e-02 2.50e+03 3.16e+01 bond pdb=" N3B ANP B 402 " pdb=" PG ANP B 402 " ideal model delta sigma weight residual 1.795 1.684 0.111 2.00e-02 2.50e+03 3.08e+01 bond pdb=" O3A ANP A 402 " pdb=" PB ANP A 402 " ideal model delta sigma weight residual 1.700 1.608 0.092 2.00e-02 2.50e+03 2.14e+01 ... (remaining 7808 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.23: 10523 4.23 - 8.47: 65 8.47 - 12.70: 10 12.70 - 16.94: 0 16.94 - 21.17: 2 Bond angle restraints: 10600 Sorted by residual: angle pdb=" PB ANP B 402 " pdb=" N3B ANP B 402 " pdb=" PG ANP B 402 " ideal model delta sigma weight residual 126.95 105.78 21.17 3.00e+00 1.11e-01 4.98e+01 angle pdb=" PB ANP C 401 " pdb=" N3B ANP C 401 " pdb=" PG ANP C 401 " ideal model delta sigma weight residual 126.95 107.30 19.65 3.00e+00 1.11e-01 4.29e+01 angle pdb=" O1B ANP C 401 " pdb=" PB ANP C 401 " pdb=" O2B ANP C 401 " ideal model delta sigma weight residual 120.08 109.23 10.85 3.00e+00 1.11e-01 1.31e+01 angle pdb=" C PHE C 328 " pdb=" CA PHE C 328 " pdb=" CB PHE C 328 " ideal model delta sigma weight residual 113.33 105.31 8.02 2.26e+00 1.96e-01 1.26e+01 angle pdb=" C PHE B 328 " pdb=" CA PHE B 328 " pdb=" CB PHE B 328 " ideal model delta sigma weight residual 113.33 105.33 8.00 2.26e+00 1.96e-01 1.25e+01 ... (remaining 10595 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.83: 4427 30.83 - 61.66: 289 61.66 - 92.48: 28 92.48 - 123.31: 2 123.31 - 154.14: 3 Dihedral angle restraints: 4749 sinusoidal: 2115 harmonic: 2634 Sorted by residual: dihedral pdb=" CA THR B 331 " pdb=" C THR B 331 " pdb=" N ALA B 332 " pdb=" CA ALA B 332 " ideal model delta harmonic sigma weight residual 180.00 144.78 35.22 0 5.00e+00 4.00e-02 4.96e+01 dihedral pdb=" CA THR C 331 " pdb=" C THR C 331 " pdb=" N ALA C 332 " pdb=" CA ALA C 332 " ideal model delta harmonic sigma weight residual 180.00 144.80 35.20 0 5.00e+00 4.00e-02 4.96e+01 dihedral pdb=" CA THR A 331 " pdb=" C THR A 331 " pdb=" N ALA A 332 " pdb=" CA ALA A 332 " ideal model delta harmonic sigma weight residual 180.00 144.82 35.18 0 5.00e+00 4.00e-02 4.95e+01 ... (remaining 4746 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 977 0.068 - 0.136: 185 0.136 - 0.204: 26 0.204 - 0.272: 5 0.272 - 0.340: 1 Chirality restraints: 1194 Sorted by residual: chirality pdb=" C3' ANP C 401 " pdb=" C2' ANP C 401 " pdb=" C4' ANP C 401 " pdb=" O3' ANP C 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.70 0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" C3' ANP B 402 " pdb=" C2' ANP B 402 " pdb=" C4' ANP B 402 " pdb=" O3' ANP B 402 " both_signs ideal model delta sigma weight residual False -2.36 -2.61 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CB VAL A 62 " pdb=" CA VAL A 62 " pdb=" CG1 VAL A 62 " pdb=" CG2 VAL A 62 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 1191 not shown) Planarity restraints: 1290 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ANP B 402 " -0.046 2.00e-02 2.50e+03 4.05e-02 4.50e+01 pdb=" C2 ANP B 402 " 0.012 2.00e-02 2.50e+03 pdb=" C4 ANP B 402 " -0.000 2.00e-02 2.50e+03 pdb=" C5 ANP B 402 " 0.078 2.00e-02 2.50e+03 pdb=" C6 ANP B 402 " -0.006 2.00e-02 2.50e+03 pdb=" C8 ANP B 402 " 0.053 2.00e-02 2.50e+03 pdb=" N1 ANP B 402 " -0.018 2.00e-02 2.50e+03 pdb=" N3 ANP B 402 " -0.005 2.00e-02 2.50e+03 pdb=" N6 ANP B 402 " -0.014 2.00e-02 2.50e+03 pdb=" N7 ANP B 402 " -0.076 2.00e-02 2.50e+03 pdb=" N9 ANP B 402 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 320 " 0.022 2.00e-02 2.50e+03 4.48e-02 2.01e+01 pdb=" C GLU C 320 " -0.078 2.00e-02 2.50e+03 pdb=" O GLU C 320 " 0.028 2.00e-02 2.50e+03 pdb=" N MET C 321 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 320 " 0.022 2.00e-02 2.50e+03 4.46e-02 1.99e+01 pdb=" C GLU A 320 " -0.077 2.00e-02 2.50e+03 pdb=" O GLU A 320 " 0.028 2.00e-02 2.50e+03 pdb=" N MET A 321 " 0.027 2.00e-02 2.50e+03 ... (remaining 1287 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.50: 49 2.50 - 3.10: 4915 3.10 - 3.70: 11303 3.70 - 4.30: 16402 4.30 - 4.90: 26743 Nonbonded interactions: 59412 Sorted by model distance: nonbonded pdb="CA CA B 401 " pdb=" O3G ANP B 402 " model vdw 1.906 2.510 nonbonded pdb=" NZ LYS A 245 " pdb=" NH2 ARG B 57 " model vdw 1.966 3.200 nonbonded pdb=" O1B ANP C 401 " pdb="CA CA C 402 " model vdw 2.097 2.510 nonbonded pdb=" NZ LYS B 245 " pdb=" NH2 ARG C 57 " model vdw 2.142 3.200 nonbonded pdb="CA CA A 401 " pdb=" O1B ANP A 402 " model vdw 2.230 2.510 ... (remaining 59407 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 22 through 337) selection = (chain 'B' and resid 22 through 337) selection = (chain 'C' and resid 22 through 337) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 34.260 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.310 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.728 7816 Z= 1.167 Angle : 1.015 21.173 10600 Z= 0.512 Chirality : 0.054 0.340 1194 Planarity : 0.005 0.060 1290 Dihedral : 18.649 154.140 3057 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 9.01 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.56 (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 HIS 0.004 0.001 HIS A 198 PHE 0.027 0.002 PHE A 128 TYR 0.014 0.001 TYR C 91 ARG 0.011 0.001 ARG B 169 Details of bonding type rmsd hydrogen bonds : bond 0.29936 ( 233) hydrogen bonds : angle 8.98611 ( 607) covalent geometry : bond 0.00762 ( 7813) covalent geometry : angle 1.01483 (10600) Misc. bond : bond 0.56600 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 0.800 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: 0.7991 (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: 0.8616 (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: 0.8370 (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: 0.2237 time to fit residues: 75.8384 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 : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 9.9990 chunk 68 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 chunk 36 optimal weight: 20.0000 chunk 70 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 42 optimal weight: 9.9990 chunk 52 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 61 ASN A 144 GLN A 178 ASN A 254 GLN B 30 HIS B 61 ASN B 163 ASN B 198 HIS C 30 HIS C 61 ASN C 211 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.152628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.121609 restraints weight = 13374.949| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.48 r_work: 0.3317 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7816 Z= 0.139 Angle : 0.623 9.642 10600 Z= 0.330 Chirality : 0.044 0.157 1194 Planarity : 0.004 0.050 1290 Dihedral : 18.183 158.670 1299 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.90 % Allowed : 18.84 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.62 (0.23), residues: 915 helix: -2.23 (0.23), residues: 345 sheet: -2.00 (0.38), residues: 153 loop : -2.62 (0.25), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 295 PHE 0.019 0.002 PHE C 128 TYR 0.022 0.002 TYR B 190 ARG 0.007 0.001 ARG B 307 Details of bonding type rmsd hydrogen bonds : bond 0.04649 ( 233) hydrogen bonds : angle 4.83448 ( 607) covalent geometry : bond 0.00308 ( 7813) covalent geometry : angle 0.62333 (10600) Misc. bond : bond 0.00234 ( 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 202 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 180 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 PHE cc_start: 0.7691 (m-80) cc_final: 0.6736 (t80) REVERT: A 95 ARG cc_start: 0.8647 (ttt90) cc_final: 0.8001 (mtm180) REVERT: A 118 SER cc_start: 0.8068 (p) cc_final: 0.7717 (p) REVERT: A 119 MET cc_start: 0.8095 (mmm) cc_final: 0.7831 (mmm) REVERT: A 321 MET cc_start: 0.7605 (mmm) cc_final: 0.7314 (mmm) REVERT: A 335 ILE cc_start: 0.8728 (mm) cc_final: 0.8460 (mm) REVERT: B 254 GLN cc_start: 0.9290 (tp-100) cc_final: 0.9035 (tp-100) REVERT: B 273 ASP cc_start: 0.8695 (t0) cc_final: 0.8449 (t0) REVERT: C 130 THR cc_start: 0.9204 (OUTLIER) cc_final: 0.8914 (m) REVERT: C 155 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.8014 (mtpp) REVERT: C 244 GLN cc_start: 0.8826 (mt0) cc_final: 0.8569 (mt0) REVERT: C 245 LYS cc_start: 0.9133 (mttp) cc_final: 0.8811 (mtpp) REVERT: C 285 LYS cc_start: 0.8875 (mtmm) cc_final: 0.8379 (mttm) REVERT: C 304 ARG cc_start: 0.8308 (ptt90) cc_final: 0.8078 (ptt90) outliers start: 22 outliers final: 9 residues processed: 194 average time/residue: 0.1976 time to fit residues: 51.0120 Evaluate side-chains 166 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 155 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 211 HIS Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain B residue 163 ASN Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 224 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 37 optimal weight: 0.0870 chunk 7 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 85 optimal weight: 0.5980 chunk 23 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 chunk 63 optimal weight: 8.9990 chunk 79 optimal weight: 7.9990 chunk 40 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 overall best weight: 1.7364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN ** A 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 198 HIS B 244 GLN C 199 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.150523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.119368 restraints weight = 13549.445| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.58 r_work: 0.3273 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.3195 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= 0.145 Angle : 0.580 8.743 10600 Z= 0.308 Chirality : 0.043 0.150 1194 Planarity : 0.004 0.043 1290 Dihedral : 17.287 153.892 1299 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 3.29 % Allowed : 20.55 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.25), residues: 915 helix: -1.37 (0.27), residues: 348 sheet: -2.03 (0.36), residues: 156 loop : -2.17 (0.28), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 198 PHE 0.020 0.002 PHE C 128 TYR 0.019 0.002 TYR B 190 ARG 0.008 0.001 ARG C 252 Details of bonding type rmsd hydrogen bonds : bond 0.04011 ( 233) hydrogen bonds : angle 4.52678 ( 607) covalent geometry : bond 0.00321 ( 7813) covalent geometry : angle 0.57970 (10600) Misc. bond : bond 0.00198 ( 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 183 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 PHE cc_start: 0.7725 (m-80) cc_final: 0.6684 (t80) REVERT: A 95 ARG cc_start: 0.8720 (ttt90) cc_final: 0.8061 (mtm180) REVERT: A 119 MET cc_start: 0.8045 (mmm) cc_final: 0.7717 (mmm) REVERT: A 335 ILE cc_start: 0.8856 (mm) cc_final: 0.8634 (mm) REVERT: B 101 ILE cc_start: 0.9107 (OUTLIER) cc_final: 0.8837 (mt) REVERT: B 220 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9096 (tt) REVERT: B 254 GLN cc_start: 0.9338 (tp-100) cc_final: 0.9082 (tp-100) REVERT: B 335 ILE cc_start: 0.9247 (mm) cc_final: 0.8790 (mm) REVERT: C 101 ILE cc_start: 0.9118 (OUTLIER) cc_final: 0.8855 (mt) REVERT: C 155 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7982 (mtpp) REVERT: C 245 LYS cc_start: 0.9104 (mttp) cc_final: 0.8780 (mtpp) REVERT: C 249 MET cc_start: 0.9115 (ttm) cc_final: 0.8914 (ttm) REVERT: C 273 ASP cc_start: 0.8595 (t0) cc_final: 0.8336 (t0) REVERT: C 285 LYS cc_start: 0.8871 (mtmm) cc_final: 0.8294 (mttm) outliers start: 25 outliers final: 11 residues processed: 179 average time/residue: 0.2041 time to fit residues: 48.8526 Evaluate side-chains 153 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 138 time to evaluate : 0.899 ------------------------------------------------------------------------------- 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 309 GLU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 224 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 21 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 9 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 88 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN A 254 GLN B 244 GLN C 244 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.145962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.114127 restraints weight = 13569.877| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.53 r_work: 0.3217 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 7816 Z= 0.245 Angle : 0.678 9.018 10600 Z= 0.355 Chirality : 0.046 0.192 1194 Planarity : 0.005 0.048 1290 Dihedral : 17.472 158.282 1299 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 4.48 % Allowed : 23.58 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.26), residues: 915 helix: -1.16 (0.27), residues: 369 sheet: -1.84 (0.36), residues: 153 loop : -2.21 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 198 PHE 0.024 0.002 PHE C 128 TYR 0.021 0.002 TYR B 190 ARG 0.008 0.001 ARG C 307 Details of bonding type rmsd hydrogen bonds : bond 0.04673 ( 233) hydrogen bonds : angle 4.61619 ( 607) covalent geometry : bond 0.00566 ( 7813) covalent geometry : angle 0.67776 (10600) Misc. bond : bond 0.00196 ( 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 191 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 157 time to evaluate : 1.776 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.2087 (OUTLIER) cc_final: 0.1842 (mt-10) REVERT: A 95 ARG cc_start: 0.8869 (ttt90) cc_final: 0.8188 (mtm180) REVERT: A 224 SER cc_start: 0.8819 (m) cc_final: 0.8298 (p) REVERT: A 254 GLN cc_start: 0.9464 (tp40) cc_final: 0.9195 (tp-100) REVERT: A 317 ASP cc_start: 0.5435 (t70) cc_final: 0.5198 (m-30) REVERT: A 335 ILE cc_start: 0.8968 (mm) cc_final: 0.8714 (mm) REVERT: B 101 ILE cc_start: 0.9077 (OUTLIER) cc_final: 0.8804 (mt) REVERT: B 254 GLN cc_start: 0.9372 (tp-100) cc_final: 0.9108 (tp-100) REVERT: C 101 ILE cc_start: 0.9103 (OUTLIER) cc_final: 0.8806 (mt) REVERT: C 106 GLN cc_start: 0.8096 (tp-100) cc_final: 0.7795 (tp-100) REVERT: C 192 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.7611 (ttt-90) REVERT: C 245 LYS cc_start: 0.9135 (mttp) cc_final: 0.8825 (mtpp) REVERT: C 273 ASP cc_start: 0.8777 (t0) cc_final: 0.8521 (t0) REVERT: C 317 ASP cc_start: 0.7278 (t0) cc_final: 0.6847 (t0) REVERT: C 321 MET cc_start: 0.8354 (mpp) cc_final: 0.7836 (mpp) outliers start: 34 outliers final: 19 residues processed: 181 average time/residue: 0.2683 time to fit residues: 66.0346 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 : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 331 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 192 ARG Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 264 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 76 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 163 ASN B 244 GLN ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.149165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.116650 restraints weight = 13483.948| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.55 r_work: 0.3261 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7816 Z= 0.126 Angle : 0.560 8.493 10600 Z= 0.298 Chirality : 0.043 0.146 1194 Planarity : 0.004 0.044 1290 Dihedral : 17.215 161.979 1299 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 4.08 % Allowed : 24.77 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.27), residues: 915 helix: -0.58 (0.29), residues: 348 sheet: -1.78 (0.36), residues: 153 loop : -1.92 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 211 PHE 0.018 0.002 PHE C 128 TYR 0.022 0.002 TYR B 190 ARG 0.007 0.001 ARG C 307 Details of bonding type rmsd hydrogen bonds : bond 0.03537 ( 233) hydrogen bonds : angle 4.23208 ( 607) covalent geometry : bond 0.00286 ( 7813) covalent geometry : angle 0.56033 (10600) Misc. bond : bond 0.00181 ( 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 192 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 161 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 ARG cc_start: 0.8810 (ttt90) cc_final: 0.8091 (mtm180) REVERT: A 134 GLN cc_start: 0.8538 (mp10) cc_final: 0.8265 (mp10) REVERT: A 190 TYR cc_start: 0.8843 (t80) cc_final: 0.8480 (t80) REVERT: A 224 SER cc_start: 0.8858 (m) cc_final: 0.8376 (p) REVERT: A 317 ASP cc_start: 0.5314 (t70) cc_final: 0.5080 (m-30) REVERT: A 335 ILE cc_start: 0.8970 (mm) cc_final: 0.8748 (mm) REVERT: B 101 ILE cc_start: 0.9087 (OUTLIER) cc_final: 0.8810 (mt) REVERT: B 254 GLN cc_start: 0.9349 (tp-100) cc_final: 0.9101 (tp-100) REVERT: B 335 ILE cc_start: 0.9398 (mm) cc_final: 0.9184 (mm) REVERT: C 101 ILE cc_start: 0.9058 (OUTLIER) cc_final: 0.8757 (mt) REVERT: C 106 GLN cc_start: 0.8062 (tp-100) cc_final: 0.7720 (tp-100) REVERT: C 245 LYS cc_start: 0.9087 (mttp) cc_final: 0.8748 (mtpp) REVERT: C 273 ASP cc_start: 0.8613 (t0) cc_final: 0.8350 (t0) REVERT: C 317 ASP cc_start: 0.7170 (t0) cc_final: 0.6639 (t0) REVERT: C 321 MET cc_start: 0.8316 (mpp) cc_final: 0.8057 (mpp) outliers start: 31 outliers final: 20 residues processed: 182 average time/residue: 0.2165 time to fit residues: 53.4442 Evaluate side-chains 165 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 2.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 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 163 ASN Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 264 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 0 optimal weight: 20.0000 chunk 6 optimal weight: 4.9990 chunk 2 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN A 199 GLN A 248 GLN A 254 GLN ** B 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 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 = 0.3810 r_free = 0.3810 target = 0.148577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.116250 restraints weight = 13542.754| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.56 r_work: 0.3284 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7816 Z= 0.126 Angle : 0.557 9.778 10600 Z= 0.296 Chirality : 0.043 0.158 1194 Planarity : 0.004 0.042 1290 Dihedral : 17.097 163.219 1299 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 4.35 % Allowed : 25.96 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.28), residues: 915 helix: -0.33 (0.30), residues: 348 sheet: -1.76 (0.36), residues: 153 loop : -1.83 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 211 PHE 0.020 0.001 PHE C 128 TYR 0.024 0.002 TYR B 190 ARG 0.009 0.001 ARG C 307 Details of bonding type rmsd hydrogen bonds : bond 0.03443 ( 233) hydrogen bonds : angle 4.15766 ( 607) covalent geometry : bond 0.00287 ( 7813) covalent geometry : angle 0.55730 (10600) Misc. bond : bond 0.00171 ( 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 187 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 154 time to evaluate : 1.138 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.6783 (OUTLIER) cc_final: 0.6544 (mtt) REVERT: A 95 ARG cc_start: 0.8791 (ttt90) cc_final: 0.8125 (mtm180) REVERT: A 139 LEU cc_start: 0.9508 (OUTLIER) cc_final: 0.9247 (mp) REVERT: A 190 TYR cc_start: 0.8866 (t80) cc_final: 0.8404 (t80) REVERT: A 224 SER cc_start: 0.8885 (m) cc_final: 0.8380 (p) REVERT: A 335 ILE cc_start: 0.8962 (mm) cc_final: 0.8734 (mm) REVERT: B 89 PHE cc_start: 0.8477 (t80) cc_final: 0.8228 (t80) REVERT: B 101 ILE cc_start: 0.9027 (OUTLIER) cc_final: 0.8776 (mt) REVERT: B 254 GLN cc_start: 0.9353 (tp-100) cc_final: 0.9127 (tp-100) REVERT: B 260 TYR cc_start: 0.8659 (m-10) cc_final: 0.8411 (m-10) REVERT: C 101 ILE cc_start: 0.9030 (OUTLIER) cc_final: 0.8741 (mt) REVERT: C 106 GLN cc_start: 0.8009 (tp-100) cc_final: 0.7644 (tp-100) REVERT: C 245 LYS cc_start: 0.9087 (mttp) cc_final: 0.8746 (mtpp) REVERT: C 273 ASP cc_start: 0.8585 (t0) cc_final: 0.8318 (t0) REVERT: C 285 LYS cc_start: 0.8893 (mtmm) cc_final: 0.8227 (mttm) REVERT: C 317 ASP cc_start: 0.7185 (t0) cc_final: 0.6645 (t0) outliers start: 33 outliers final: 20 residues processed: 176 average time/residue: 0.2066 time to fit residues: 49.1660 Evaluate side-chains 171 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 147 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 139 LEU 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 55 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 144 GLN Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 320 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 58 optimal weight: 0.6980 chunk 61 optimal weight: 9.9990 chunk 48 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 chunk 67 optimal weight: 0.9990 chunk 75 optimal weight: 0.4980 chunk 64 optimal weight: 6.9990 chunk 66 optimal weight: 0.4980 chunk 73 optimal weight: 3.9990 chunk 81 optimal weight: 8.9990 chunk 62 optimal weight: 10.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN A 254 GLN ** B 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.149843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.117217 restraints weight = 13618.150| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.57 r_work: 0.3300 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.4197 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= 0.119 Angle : 0.561 9.151 10600 Z= 0.296 Chirality : 0.043 0.157 1194 Planarity : 0.003 0.042 1290 Dihedral : 16.976 164.456 1299 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 4.08 % Allowed : 26.09 % Favored : 69.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.28), residues: 915 helix: -0.23 (0.30), residues: 351 sheet: -1.73 (0.37), residues: 153 loop : -1.83 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 211 PHE 0.020 0.001 PHE C 128 TYR 0.026 0.002 TYR B 190 ARG 0.010 0.001 ARG C 307 Details of bonding type rmsd hydrogen bonds : bond 0.03317 ( 233) hydrogen bonds : angle 4.10080 ( 607) covalent geometry : bond 0.00272 ( 7813) covalent geometry : angle 0.56115 (10600) Misc. bond : bond 0.00166 ( 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 190 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 159 time to evaluate : 1.571 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.6840 (OUTLIER) cc_final: 0.6606 (mtt) REVERT: A 95 ARG cc_start: 0.8823 (ttt90) cc_final: 0.8172 (mtt180) REVERT: A 190 TYR cc_start: 0.8857 (t80) cc_final: 0.8393 (t80) REVERT: A 224 SER cc_start: 0.8863 (m) cc_final: 0.8375 (p) REVERT: A 273 ASP cc_start: 0.8787 (t0) cc_final: 0.8497 (t0) REVERT: A 335 ILE cc_start: 0.8955 (mm) cc_final: 0.8723 (mm) REVERT: B 89 PHE cc_start: 0.8486 (t80) cc_final: 0.8264 (t80) REVERT: B 254 GLN cc_start: 0.9348 (tp-100) cc_final: 0.9121 (tp-100) REVERT: C 101 ILE cc_start: 0.8998 (OUTLIER) cc_final: 0.8691 (mt) REVERT: C 106 GLN cc_start: 0.8069 (tp-100) cc_final: 0.7693 (tp-100) REVERT: C 130 THR cc_start: 0.9263 (m) cc_final: 0.9034 (m) REVERT: C 200 MET cc_start: 0.8996 (tpt) cc_final: 0.8689 (tpt) REVERT: C 245 LYS cc_start: 0.9058 (mttp) cc_final: 0.8710 (mtpp) REVERT: C 273 ASP cc_start: 0.8599 (t0) cc_final: 0.8315 (t0) REVERT: C 285 LYS cc_start: 0.8868 (mtmm) cc_final: 0.8155 (mttm) REVERT: C 317 ASP cc_start: 0.7102 (t0) cc_final: 0.6549 (t0) outliers start: 31 outliers final: 21 residues processed: 181 average time/residue: 0.2722 time to fit residues: 66.7660 Evaluate side-chains 174 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 151 time to evaluate : 1.426 ------------------------------------------------------------------------------- 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 202 LEU Chi-restraints excluded: chain A residue 211 HIS Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 67 GLU 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 225 ILE Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 144 GLN Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 320 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 52 optimal weight: 0.6980 chunk 37 optimal weight: 7.9990 chunk 13 optimal weight: 7.9990 chunk 73 optimal weight: 8.9990 chunk 2 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 59 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN ** B 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.146040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.113458 restraints weight = 13871.813| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.59 r_work: 0.3192 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 7816 Z= 0.194 Angle : 0.640 12.982 10600 Z= 0.333 Chirality : 0.045 0.177 1194 Planarity : 0.004 0.053 1290 Dihedral : 17.078 164.264 1299 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 4.08 % Allowed : 25.96 % Favored : 69.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.28), residues: 915 helix: -0.23 (0.29), residues: 348 sheet: -1.51 (0.38), residues: 147 loop : -1.88 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 211 PHE 0.023 0.002 PHE C 128 TYR 0.028 0.002 TYR B 190 ARG 0.011 0.001 ARG C 307 Details of bonding type rmsd hydrogen bonds : bond 0.03937 ( 233) hydrogen bonds : angle 4.36035 ( 607) covalent geometry : bond 0.00451 ( 7813) covalent geometry : angle 0.64014 (10600) Misc. bond : bond 0.00178 ( 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 182 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 151 time to evaluate : 0.833 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.6830 (OUTLIER) cc_final: 0.6614 (mtt) REVERT: A 95 ARG cc_start: 0.8799 (ttt90) cc_final: 0.8124 (mtm180) REVERT: A 190 TYR cc_start: 0.8928 (t80) cc_final: 0.8519 (t80) REVERT: A 224 SER cc_start: 0.8865 (m) cc_final: 0.8385 (p) REVERT: A 254 GLN cc_start: 0.9422 (tp40) cc_final: 0.9200 (tp-100) REVERT: A 273 ASP cc_start: 0.8887 (t0) cc_final: 0.8604 (t0) REVERT: B 89 PHE cc_start: 0.8482 (t80) cc_final: 0.8255 (t80) REVERT: B 254 GLN cc_start: 0.9366 (tp-100) cc_final: 0.9094 (tp-100) REVERT: C 101 ILE cc_start: 0.9022 (OUTLIER) cc_final: 0.8702 (mt) REVERT: C 200 MET cc_start: 0.8974 (tpt) cc_final: 0.8574 (tpt) REVERT: C 245 LYS cc_start: 0.9132 (mttp) cc_final: 0.8792 (mtpp) REVERT: C 252 ARG cc_start: 0.8642 (ttp80) cc_final: 0.8423 (ttp-110) REVERT: C 273 ASP cc_start: 0.8708 (t0) cc_final: 0.8416 (t0) REVERT: C 317 ASP cc_start: 0.7062 (t0) cc_final: 0.6501 (t0) outliers start: 31 outliers final: 24 residues processed: 169 average time/residue: 0.1945 time to fit residues: 44.4913 Evaluate side-chains 172 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 146 time to evaluate : 0.809 ------------------------------------------------------------------------------- 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 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 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 264 VAL Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 144 GLN Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 320 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 30 optimal weight: 20.0000 chunk 71 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 6 optimal weight: 7.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN A 261 ASN ** B 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.148493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.116526 restraints weight = 13864.928| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.60 r_work: 0.3290 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.4408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7816 Z= 0.133 Angle : 0.603 11.073 10600 Z= 0.314 Chirality : 0.043 0.157 1194 Planarity : 0.004 0.056 1290 Dihedral : 16.961 167.444 1299 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 3.69 % Allowed : 26.75 % Favored : 69.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.28), residues: 915 helix: -0.05 (0.30), residues: 348 sheet: -1.49 (0.38), residues: 147 loop : -1.77 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 211 PHE 0.021 0.002 PHE C 89 TYR 0.028 0.002 TYR B 190 ARG 0.012 0.001 ARG C 307 Details of bonding type rmsd hydrogen bonds : bond 0.03438 ( 233) hydrogen bonds : angle 4.23976 ( 607) covalent geometry : bond 0.00311 ( 7813) covalent geometry : angle 0.60346 (10600) Misc. bond : bond 0.00169 ( 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 183 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 155 time to evaluate : 0.773 Fit side-chains REVERT: A 53 MET cc_start: 0.6822 (OUTLIER) cc_final: 0.6604 (mtt) REVERT: A 95 ARG cc_start: 0.8810 (ttt90) cc_final: 0.8124 (mtm180) REVERT: A 190 TYR cc_start: 0.8876 (t80) cc_final: 0.8446 (t80) REVERT: A 224 SER cc_start: 0.8870 (m) cc_final: 0.8432 (p) REVERT: A 254 GLN cc_start: 0.9366 (tp40) cc_final: 0.9136 (tp-100) REVERT: A 273 ASP cc_start: 0.8777 (t0) cc_final: 0.8481 (t0) REVERT: B 89 PHE cc_start: 0.8466 (t80) cc_final: 0.8238 (t80) REVERT: B 254 GLN cc_start: 0.9357 (tp-100) cc_final: 0.9111 (tp-100) REVERT: C 101 ILE cc_start: 0.9018 (OUTLIER) cc_final: 0.8687 (mt) REVERT: C 130 THR cc_start: 0.9308 (m) cc_final: 0.9064 (m) REVERT: C 200 MET cc_start: 0.8919 (tpt) cc_final: 0.8622 (tpt) REVERT: C 245 LYS cc_start: 0.9070 (mttp) cc_final: 0.8719 (mtpp) REVERT: C 273 ASP cc_start: 0.8644 (t0) cc_final: 0.8343 (t0) REVERT: C 285 LYS cc_start: 0.8888 (mtmm) cc_final: 0.8136 (mttm) REVERT: C 317 ASP cc_start: 0.7005 (t0) cc_final: 0.6510 (t0) REVERT: C 321 MET cc_start: 0.7854 (mpp) cc_final: 0.7603 (mpp) outliers start: 28 outliers final: 22 residues processed: 172 average time/residue: 0.2100 time to fit residues: 49.2295 Evaluate side-chains 172 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 148 time to evaluate : 0.867 ------------------------------------------------------------------------------- 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 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 179 VAL Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 144 GLN Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 320 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 82 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN ** B 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.148017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.116173 restraints weight = 13779.945| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.56 r_work: 0.3277 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.4482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7816 Z= 0.159 Angle : 0.632 12.376 10600 Z= 0.327 Chirality : 0.044 0.161 1194 Planarity : 0.004 0.063 1290 Dihedral : 16.965 167.601 1299 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 3.82 % Allowed : 26.61 % Favored : 69.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.28), residues: 915 helix: -0.06 (0.30), residues: 348 sheet: -1.49 (0.39), residues: 147 loop : -1.76 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 211 PHE 0.022 0.002 PHE C 128 TYR 0.029 0.002 TYR B 190 ARG 0.014 0.001 ARG C 307 Details of bonding type rmsd hydrogen bonds : bond 0.03629 ( 233) hydrogen bonds : angle 4.30153 ( 607) covalent geometry : bond 0.00370 ( 7813) covalent geometry : angle 0.63166 (10600) Misc. bond : bond 0.00173 ( 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 176 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 147 time to evaluate : 0.833 Fit side-chains revert: symmetry clash REVERT: A 95 ARG cc_start: 0.8839 (ttt90) cc_final: 0.8079 (mtm180) REVERT: A 190 TYR cc_start: 0.8913 (t80) cc_final: 0.8476 (t80) REVERT: A 224 SER cc_start: 0.8851 (m) cc_final: 0.8438 (p) REVERT: A 254 GLN cc_start: 0.9344 (tp40) cc_final: 0.9118 (tp-100) REVERT: A 273 ASP cc_start: 0.8826 (t0) cc_final: 0.8520 (t0) REVERT: B 254 GLN cc_start: 0.9357 (tp-100) cc_final: 0.9116 (tp-100) REVERT: C 101 ILE cc_start: 0.9015 (OUTLIER) cc_final: 0.8676 (mt) REVERT: C 130 THR cc_start: 0.9305 (OUTLIER) cc_final: 0.9034 (m) REVERT: C 200 MET cc_start: 0.8941 (tpt) cc_final: 0.8333 (tpt) REVERT: C 245 LYS cc_start: 0.9059 (mttp) cc_final: 0.8709 (mtpp) REVERT: C 252 ARG cc_start: 0.8607 (ttp80) cc_final: 0.8387 (ttp-110) REVERT: C 273 ASP cc_start: 0.8695 (t0) cc_final: 0.8389 (t0) REVERT: C 317 ASP cc_start: 0.7014 (t0) cc_final: 0.6510 (t0) REVERT: C 321 MET cc_start: 0.7817 (mpp) cc_final: 0.7528 (mpp) outliers start: 29 outliers final: 24 residues processed: 165 average time/residue: 0.2010 time to fit residues: 45.2053 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 : 0.930 ------------------------------------------------------------------------------- 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 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 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 B residue 318 SER Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 144 GLN Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 320 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 6 optimal weight: 8.9990 chunk 62 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 9 optimal weight: 8.9990 chunk 34 optimal weight: 0.0670 chunk 45 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.4122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 199 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.148676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.116637 restraints weight = 13699.581| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.57 r_work: 0.3296 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.4559 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= 0.125 Angle : 0.606 15.575 10600 Z= 0.312 Chirality : 0.043 0.154 1194 Planarity : 0.004 0.062 1290 Dihedral : 16.847 170.061 1299 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 3.43 % Allowed : 27.01 % Favored : 69.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.28), residues: 915 helix: 0.02 (0.30), residues: 348 sheet: -1.50 (0.38), residues: 147 loop : -1.72 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 211 PHE 0.020 0.002 PHE C 128 TYR 0.027 0.002 TYR B 190 ARG 0.014 0.001 ARG C 307 Details of bonding type rmsd hydrogen bonds : bond 0.03294 ( 233) hydrogen bonds : angle 4.21016 ( 607) covalent geometry : bond 0.00288 ( 7813) covalent geometry : angle 0.60645 (10600) Misc. bond : bond 0.00167 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5063.82 seconds wall clock time: 92 minutes 2.26 seconds (5522.26 seconds total)