Starting phenix.real_space_refine on Wed Feb 12 11:04:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7c98_30308/02_2025/7c98_30308.cif Found real_map, /net/cci-nas-00/data/ceres_data/7c98_30308/02_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_30308/02_2025/7c98_30308.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7c98_30308/02_2025/7c98_30308.map" model { file = "/net/cci-nas-00/data/ceres_data/7c98_30308/02_2025/7c98_30308.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7c98_30308/02_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-5592/modules/chem_data/mon_lib" Total number of atoms: 7656 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2397 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "B" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2397 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "C" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2397 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "D" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 180 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "E" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 189 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.53, per 1000 atoms: 0.85 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: 2.11 Conformation dependent library (CDL) restraints added in 1.0 seconds 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1692 Finding SS restraints... Secondary structure from input PDB file: 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: 2.54 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: 2.28 Time building geometry restraints manager: 2.43 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: 8.950 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 23.470 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.590 ------------------------------------------------------------------------------- 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 : 0.008 0.159 7813 Z= 0.459 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 *********************** 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 : 0.796 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: 0.2521 time to fit residues: 84.5902 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 : 0.975 ------------------------------------------------------------------------------- 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 = 0.121610 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 7813 Z= 0.198 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 *********************** 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 : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 PHE cc_start: 0.7695 (m-80) cc_final: 0.6738 (t80) REVERT: A 95 ARG cc_start: 0.8648 (ttt90) cc_final: 0.8000 (mtm180) REVERT: A 118 SER cc_start: 0.8069 (p) cc_final: 0.7718 (p) REVERT: A 119 MET cc_start: 0.8095 (mmm) cc_final: 0.7831 (mmm) REVERT: A 321 MET cc_start: 0.7607 (mmm) cc_final: 0.7316 (mmm) REVERT: A 335 ILE cc_start: 0.8728 (mm) cc_final: 0.8461 (mm) REVERT: B 254 GLN cc_start: 0.9289 (tp-100) cc_final: 0.9035 (tp-100) REVERT: B 273 ASP cc_start: 0.8694 (t0) cc_final: 0.8448 (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: 0.8013 (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: 0.8812 (mtpp) REVERT: C 285 LYS cc_start: 0.8874 (mtmm) cc_final: 0.8378 (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: 0.2087 time to fit residues: 53.7217 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 : 0.855 ------------------------------------------------------------------------------- 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: 2.9990 chunk 47 optimal weight: 5.9990 chunk 85 optimal weight: 0.0070 chunk 23 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 79 optimal weight: 7.9990 chunk 40 optimal weight: 7.9990 chunk 1 optimal weight: 0.0170 overall best weight: 1.0218 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.151378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.118472 restraints weight = 13475.773| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.61 r_work: 0.3307 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7813 Z= 0.165 Angle : 0.558 8.644 10600 Z= 0.296 Chirality : 0.042 0.151 1194 Planarity : 0.003 0.041 1290 Dihedral : 17.294 153.539 1299 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 3.43 % Allowed : 20.69 % Favored : 75.89 % 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: -2.87 (0.25), residues: 915 helix: -1.40 (0.27), residues: 348 sheet: -2.08 (0.36), residues: 156 loop : -2.19 (0.27), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 198 PHE 0.019 0.001 PHE B 89 TYR 0.019 0.002 TYR B 190 ARG 0.008 0.001 ARG C 307 *********************** 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 192 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 166 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 PHE cc_start: 0.7655 (m-80) cc_final: 0.6731 (t80) REVERT: A 95 ARG cc_start: 0.8668 (ttt90) cc_final: 0.8056 (mtm180) REVERT: A 119 MET cc_start: 0.8103 (mmm) cc_final: 0.7888 (mmm) REVERT: A 134 GLN cc_start: 0.8342 (mm110) cc_final: 0.8142 (mp10) REVERT: A 335 ILE cc_start: 0.8800 (mm) cc_final: 0.8586 (mm) REVERT: B 101 ILE cc_start: 0.9083 (OUTLIER) cc_final: 0.8838 (mt) REVERT: B 118 SER cc_start: 0.8287 (p) cc_final: 0.8028 (m) REVERT: B 254 GLN cc_start: 0.9319 (tp-100) cc_final: 0.9049 (tp-100) REVERT: B 273 ASP cc_start: 0.8666 (t0) cc_final: 0.8463 (t0) REVERT: B 335 ILE cc_start: 0.9201 (mm) cc_final: 0.8715 (mm) REVERT: C 101 ILE cc_start: 0.9083 (OUTLIER) cc_final: 0.8817 (mt) REVERT: C 130 THR cc_start: 0.9187 (OUTLIER) cc_final: 0.8883 (m) REVERT: C 155 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7985 (mtpp) REVERT: C 245 LYS cc_start: 0.9095 (mttp) cc_final: 0.8764 (mtpp) REVERT: C 273 ASP cc_start: 0.8564 (t0) cc_final: 0.8289 (t0) REVERT: C 285 LYS cc_start: 0.8841 (mtmm) cc_final: 0.8259 (mttm) REVERT: C 304 ARG cc_start: 0.8292 (ptt90) cc_final: 0.8000 (ptt90) REVERT: C 317 ASP cc_start: 0.7345 (t0) cc_final: 0.6916 (t0) outliers start: 26 outliers final: 15 residues processed: 186 average time/residue: 0.2052 time to fit residues: 50.5323 Evaluate side-chains 165 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 146 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 211 HIS Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 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 103 THR 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 220 LEU Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain C residue 225 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 21 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 34 optimal weight: 9.9990 chunk 88 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 69 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 163 ASN A 199 GLN A 254 GLN 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 = 0.148562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.116939 restraints weight = 13461.610| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.57 r_work: 0.3253 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7813 Z= 0.263 Angle : 0.605 8.560 10600 Z= 0.319 Chirality : 0.044 0.170 1194 Planarity : 0.004 0.043 1290 Dihedral : 17.216 158.912 1299 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 3.95 % Allowed : 23.32 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.41 (0.26), residues: 915 helix: -0.95 (0.28), residues: 348 sheet: -1.94 (0.35), residues: 156 loop : -1.95 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 198 PHE 0.024 0.002 PHE C 128 TYR 0.021 0.002 TYR B 190 ARG 0.007 0.001 ARG C 307 *********************** 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 189 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 159 time to evaluate : 0.835 Fit side-chains revert: symmetry clash REVERT: A 95 ARG cc_start: 0.8738 (ttt90) cc_final: 0.8127 (mtm180) REVERT: A 254 GLN cc_start: 0.9446 (tp40) cc_final: 0.9181 (tp-100) REVERT: A 317 ASP cc_start: 0.5356 (t70) cc_final: 0.5080 (m-30) REVERT: A 335 ILE cc_start: 0.8913 (mm) cc_final: 0.8672 (mm) REVERT: B 101 ILE cc_start: 0.9105 (OUTLIER) cc_final: 0.8844 (mt) REVERT: B 220 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.9147 (tt) REVERT: B 254 GLN cc_start: 0.9331 (tp-100) cc_final: 0.9078 (tp-100) REVERT: B 335 ILE cc_start: 0.9338 (mm) cc_final: 0.9011 (mm) REVERT: C 200 MET cc_start: 0.8647 (tpt) cc_final: 0.8429 (tpt) REVERT: C 245 LYS cc_start: 0.9116 (mttp) cc_final: 0.8791 (mtpp) REVERT: C 252 ARG cc_start: 0.8739 (tpp80) cc_final: 0.8286 (ttm-80) REVERT: C 273 ASP cc_start: 0.8677 (t0) cc_final: 0.8415 (t0) REVERT: C 317 ASP cc_start: 0.7238 (t0) cc_final: 0.6802 (t0) outliers start: 30 outliers final: 16 residues processed: 181 average time/residue: 0.2018 time to fit residues: 49.1867 Evaluate side-chains 162 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 211 HIS Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 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 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: 9.9990 chunk 70 optimal weight: 0.9990 chunk 64 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN 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 = 0.3785 r_free = 0.3785 target = 0.145620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.113613 restraints weight = 13639.116| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.55 r_work: 0.3226 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 7813 Z= 0.329 Angle : 0.647 9.109 10600 Z= 0.341 Chirality : 0.046 0.170 1194 Planarity : 0.004 0.048 1290 Dihedral : 17.339 159.917 1299 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 4.61 % Allowed : 23.85 % Favored : 71.54 % 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: -2.14 (0.27), residues: 915 helix: -0.62 (0.29), residues: 345 sheet: -1.74 (0.36), residues: 153 loop : -1.92 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 198 PHE 0.023 0.002 PHE C 128 TYR 0.023 0.002 TYR B 190 ARG 0.009 0.001 ARG C 307 *********************** 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 191 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 156 time to evaluate : 0.845 Fit side-chains REVERT: A 95 ARG cc_start: 0.8843 (ttt90) cc_final: 0.8217 (mtm180) REVERT: A 134 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.8388 (mp10) REVERT: A 190 TYR cc_start: 0.8919 (t80) cc_final: 0.8633 (t80) REVERT: A 224 SER cc_start: 0.8841 (m) cc_final: 0.8336 (p) REVERT: A 317 ASP cc_start: 0.5331 (t70) cc_final: 0.5126 (m-30) REVERT: B 101 ILE cc_start: 0.9069 (OUTLIER) cc_final: 0.8797 (mt) REVERT: B 254 GLN cc_start: 0.9373 (tp-100) cc_final: 0.9147 (tp-100) REVERT: C 101 ILE cc_start: 0.9105 (OUTLIER) cc_final: 0.8829 (mt) REVERT: C 245 LYS cc_start: 0.9099 (mttp) cc_final: 0.8779 (mtpp) REVERT: C 252 ARG cc_start: 0.8762 (tpp80) cc_final: 0.8456 (ttm-80) REVERT: C 273 ASP cc_start: 0.8754 (t0) cc_final: 0.8456 (t0) REVERT: C 317 ASP cc_start: 0.7237 (t0) cc_final: 0.6777 (t0) REVERT: C 321 MET cc_start: 0.8465 (mpp) cc_final: 0.8028 (mpp) outliers start: 35 outliers final: 23 residues processed: 181 average time/residue: 0.2013 time to fit residues: 49.1130 Evaluate side-chains 167 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 211 HIS Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 184 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 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 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 293 LEU 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: 10.0000 chunk 2 optimal weight: 0.4980 chunk 27 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 12 optimal weight: 9.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 A 261 ASN ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.150751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.118483 restraints weight = 13498.476| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.56 r_work: 0.3301 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.4147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7813 Z= 0.150 Angle : 0.553 8.119 10600 Z= 0.292 Chirality : 0.043 0.148 1194 Planarity : 0.003 0.042 1290 Dihedral : 17.086 164.956 1299 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 3.69 % Allowed : 25.43 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.85 (0.28), residues: 915 helix: -0.26 (0.30), residues: 342 sheet: -1.72 (0.36), residues: 153 loop : -1.79 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 211 PHE 0.016 0.001 PHE B 128 TYR 0.025 0.001 TYR B 190 ARG 0.008 0.001 ARG C 307 *********************** 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 190 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 162 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 ARG cc_start: 0.8827 (ttt90) cc_final: 0.8075 (mtm180) REVERT: A 139 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.9273 (mp) REVERT: A 190 TYR cc_start: 0.8794 (t80) cc_final: 0.8296 (t80) REVERT: A 224 SER cc_start: 0.8874 (m) cc_final: 0.8369 (p) REVERT: A 273 ASP cc_start: 0.8806 (t0) cc_final: 0.8516 (t0) REVERT: A 335 ILE cc_start: 0.8970 (mm) cc_final: 0.8733 (mm) REVERT: B 89 PHE cc_start: 0.8475 (t80) cc_final: 0.8244 (t80) REVERT: B 101 ILE cc_start: 0.9045 (OUTLIER) cc_final: 0.8773 (mt) REVERT: B 254 GLN cc_start: 0.9343 (tp-100) cc_final: 0.9091 (tp-100) REVERT: C 101 ILE cc_start: 0.9022 (OUTLIER) cc_final: 0.8745 (mt) REVERT: C 106 GLN cc_start: 0.8043 (tp-100) cc_final: 0.7707 (tp-100) REVERT: C 245 LYS cc_start: 0.9075 (mttp) cc_final: 0.8724 (mtpp) REVERT: C 273 ASP cc_start: 0.8611 (t0) cc_final: 0.8332 (t0) REVERT: C 285 LYS cc_start: 0.8899 (mtmm) cc_final: 0.8198 (mttm) REVERT: C 317 ASP cc_start: 0.7094 (t0) cc_final: 0.6551 (t0) REVERT: C 321 MET cc_start: 0.8404 (mpp) cc_final: 0.8036 (mpp) outliers start: 28 outliers final: 20 residues processed: 181 average time/residue: 0.1971 time to fit residues: 48.4848 Evaluate side-chains 178 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 103 THR 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 101 ILE Chi-restraints excluded: chain B residue 168 ASP 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 58 optimal weight: 2.9990 chunk 61 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 67 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 64 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 73 optimal weight: 0.9980 chunk 81 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 ASN A 199 GLN A 254 GLN ** B 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.147761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.115260 restraints weight = 13681.934| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.58 r_work: 0.3239 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.4252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7813 Z= 0.281 Angle : 0.624 10.918 10600 Z= 0.327 Chirality : 0.045 0.167 1194 Planarity : 0.004 0.046 1290 Dihedral : 17.116 163.686 1299 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 4.61 % Allowed : 25.69 % 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: -1.88 (0.28), residues: 915 helix: -0.27 (0.29), residues: 351 sheet: -1.69 (0.37), residues: 153 loop : -1.88 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 137 PHE 0.023 0.002 PHE C 128 TYR 0.026 0.002 TYR B 190 ARG 0.010 0.001 ARG C 307 *********************** 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 184 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 149 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 ARG cc_start: 0.8804 (ttt90) cc_final: 0.8110 (mtm180) REVERT: A 101 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8778 (mm) REVERT: A 139 LEU cc_start: 0.9511 (OUTLIER) cc_final: 0.9236 (mp) REVERT: A 190 TYR cc_start: 0.8927 (t80) cc_final: 0.8550 (t80) REVERT: A 224 SER cc_start: 0.8864 (m) cc_final: 0.8385 (p) REVERT: A 254 GLN cc_start: 0.9453 (tp40) cc_final: 0.9222 (tp-100) REVERT: A 273 ASP cc_start: 0.8921 (t0) cc_final: 0.8629 (t0) REVERT: B 53 MET cc_start: 0.8396 (mtp) cc_final: 0.8182 (mtt) REVERT: B 101 ILE cc_start: 0.9050 (OUTLIER) cc_final: 0.8811 (mt) REVERT: B 254 GLN cc_start: 0.9343 (tp-100) cc_final: 0.9108 (tp-100) REVERT: C 101 ILE cc_start: 0.9035 (OUTLIER) cc_final: 0.8732 (mt) REVERT: C 245 LYS cc_start: 0.9120 (mttp) cc_final: 0.8784 (mtpp) REVERT: C 273 ASP cc_start: 0.8698 (t0) cc_final: 0.8418 (t0) REVERT: C 317 ASP cc_start: 0.7060 (t0) cc_final: 0.6531 (t0) REVERT: C 321 MET cc_start: 0.8387 (mpp) cc_final: 0.7969 (mpp) outliers start: 35 outliers final: 24 residues processed: 175 average time/residue: 0.2036 time to fit residues: 47.9791 Evaluate side-chains 166 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 138 time to evaluate : 0.794 ------------------------------------------------------------------------------- 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 101 ILE Chi-restraints excluded: chain A residue 103 THR 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 101 ILE Chi-restraints excluded: chain B residue 168 ASP 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 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 138 THR Chi-restraints excluded: chain C residue 144 GLN Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 320 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 52 optimal weight: 0.6980 chunk 37 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 2 optimal weight: 20.0000 chunk 51 optimal weight: 3.9990 chunk 59 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3797 r_free = 0.3797 target = 0.146652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.114416 restraints weight = 13832.639| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.61 r_work: 0.3259 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7813 Z= 0.260 Angle : 0.623 10.944 10600 Z= 0.325 Chirality : 0.045 0.156 1194 Planarity : 0.004 0.050 1290 Dihedral : 17.081 165.732 1299 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 3.82 % Allowed : 27.54 % Favored : 68.64 % 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: -1.74 (0.28), residues: 915 helix: -0.20 (0.29), residues: 351 sheet: -1.45 (0.38), residues: 147 loop : -1.85 (0.30), residues: 417 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 0.028 0.002 TYR B 190 ARG 0.010 0.001 ARG C 307 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 145 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 ARG cc_start: 0.8819 (ttt90) cc_final: 0.8114 (mtm180) REVERT: A 139 LEU cc_start: 0.9487 (OUTLIER) cc_final: 0.9274 (mp) REVERT: A 190 TYR cc_start: 0.8914 (t80) cc_final: 0.8493 (t80) REVERT: A 224 SER cc_start: 0.8853 (m) cc_final: 0.8418 (p) REVERT: A 254 GLN cc_start: 0.9382 (tp40) cc_final: 0.9177 (tp-100) REVERT: A 273 ASP cc_start: 0.8883 (t0) cc_final: 0.8569 (t0) REVERT: B 89 PHE cc_start: 0.8530 (t80) cc_final: 0.8300 (t80) REVERT: B 101 ILE cc_start: 0.8990 (OUTLIER) cc_final: 0.8720 (mt) REVERT: B 254 GLN cc_start: 0.9381 (tp-100) cc_final: 0.9132 (tp-100) REVERT: C 101 ILE cc_start: 0.9017 (OUTLIER) cc_final: 0.8704 (mt) REVERT: C 106 GLN cc_start: 0.8048 (tp-100) cc_final: 0.7732 (tp-100) REVERT: C 245 LYS cc_start: 0.9088 (mttp) cc_final: 0.8758 (mtpp) REVERT: C 273 ASP cc_start: 0.8716 (t0) cc_final: 0.8423 (t0) REVERT: C 317 ASP cc_start: 0.7044 (t0) cc_final: 0.6520 (t0) REVERT: C 321 MET cc_start: 0.8396 (mpp) cc_final: 0.7926 (mpp) outliers start: 29 outliers final: 23 residues processed: 163 average time/residue: 0.1988 time to fit residues: 43.6390 Evaluate side-chains 168 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 0.858 ------------------------------------------------------------------------------- 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 103 THR 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 101 ILE Chi-restraints excluded: chain B residue 168 ASP 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 253 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 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: 9.9990 chunk 71 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 7 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 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 30 HIS 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.148752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.116462 restraints weight = 13766.114| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.59 r_work: 0.3281 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.4478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7813 Z= 0.191 Angle : 0.585 10.577 10600 Z= 0.306 Chirality : 0.044 0.156 1194 Planarity : 0.004 0.054 1290 Dihedral : 16.961 168.199 1299 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 4.48 % Allowed : 26.22 % Favored : 69.30 % 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: -1.61 (0.28), residues: 915 helix: -0.03 (0.30), residues: 351 sheet: -1.45 (0.38), residues: 147 loop : -1.79 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 211 PHE 0.023 0.002 PHE C 89 TYR 0.028 0.002 TYR B 190 ARG 0.012 0.001 ARG C 307 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 150 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 ARG cc_start: 0.8826 (ttt90) cc_final: 0.8037 (mtm180) REVERT: A 139 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9133 (mm) REVERT: A 190 TYR cc_start: 0.8876 (t80) cc_final: 0.8428 (t80) REVERT: A 224 SER cc_start: 0.8869 (m) cc_final: 0.8427 (p) REVERT: A 254 GLN cc_start: 0.9365 (tp40) cc_final: 0.9154 (tp-100) REVERT: A 273 ASP cc_start: 0.8783 (t0) cc_final: 0.8477 (t0) REVERT: B 89 PHE cc_start: 0.8480 (t80) cc_final: 0.8269 (t80) REVERT: B 254 GLN cc_start: 0.9379 (tp-100) cc_final: 0.9135 (tp-100) REVERT: C 101 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8703 (mt) REVERT: C 106 GLN cc_start: 0.8017 (tp-100) cc_final: 0.7629 (tp-100) REVERT: C 107 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8145 (pm20) REVERT: C 245 LYS cc_start: 0.9060 (mttp) cc_final: 0.8706 (mtpp) REVERT: C 273 ASP cc_start: 0.8688 (t0) cc_final: 0.8387 (t0) REVERT: C 317 ASP cc_start: 0.7052 (t0) cc_final: 0.6486 (t0) REVERT: C 321 MET cc_start: 0.8378 (mpp) cc_final: 0.7876 (mpp) outliers start: 34 outliers final: 22 residues processed: 170 average time/residue: 0.1947 time to fit residues: 44.7448 Evaluate side-chains 168 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 0.883 ------------------------------------------------------------------------------- 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 103 THR 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 A residue 331 THR Chi-restraints excluded: chain B residue 168 ASP 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 264 VAL Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 107 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 82 optimal weight: 1.9990 chunk 72 optimal weight: 0.0770 chunk 58 optimal weight: 2.9990 chunk 75 optimal weight: 9.9990 chunk 8 optimal weight: 0.9990 chunk 63 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.7740 ------------------------------------------------------------------------------- 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** C 254 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.151186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.118359 restraints weight = 13628.475| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.63 r_work: 0.3315 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.4667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7813 Z= 0.153 Angle : 0.565 10.174 10600 Z= 0.295 Chirality : 0.043 0.155 1194 Planarity : 0.004 0.058 1290 Dihedral : 16.770 170.095 1299 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 3.56 % Allowed : 27.40 % Favored : 69.04 % 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: -1.49 (0.28), residues: 915 helix: 0.09 (0.30), residues: 354 sheet: -1.49 (0.38), residues: 147 loop : -1.70 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 100 PHE 0.017 0.001 PHE C 128 TYR 0.026 0.001 TYR B 190 ARG 0.014 0.001 ARG C 307 ********************** 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 182 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 ARG cc_start: 0.8783 (ttt90) cc_final: 0.8100 (mtt180) REVERT: A 224 SER cc_start: 0.8872 (m) cc_final: 0.8435 (p) REVERT: A 273 ASP cc_start: 0.8714 (t0) cc_final: 0.8432 (t0) REVERT: B 254 GLN cc_start: 0.9369 (tp-100) cc_final: 0.9115 (tp-100) REVERT: C 101 ILE cc_start: 0.8947 (OUTLIER) cc_final: 0.8607 (mt) REVERT: C 273 ASP cc_start: 0.8675 (t0) cc_final: 0.8375 (t0) REVERT: C 285 LYS cc_start: 0.8840 (mtmm) cc_final: 0.8115 (mttm) REVERT: C 317 ASP cc_start: 0.6989 (t0) cc_final: 0.6416 (t0) outliers start: 27 outliers final: 22 residues processed: 171 average time/residue: 0.1800 time to fit residues: 42.2014 Evaluate side-chains 175 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 152 time to evaluate : 0.927 ------------------------------------------------------------------------------- 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 103 THR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 211 HIS Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 168 ASP 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 264 VAL Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 144 GLN Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain C residue 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: 10.0000 chunk 62 optimal weight: 20.0000 chunk 65 optimal weight: 0.5980 chunk 17 optimal weight: 10.0000 chunk 1 optimal weight: 20.0000 chunk 44 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- 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** C 254 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.147987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.115046 restraints weight = 13774.042| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.60 r_work: 0.3254 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.4641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 7813 Z= 0.262 Angle : 0.645 10.741 10600 Z= 0.333 Chirality : 0.046 0.291 1194 Planarity : 0.004 0.065 1290 Dihedral : 16.893 168.551 1299 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 3.29 % Allowed : 28.59 % Favored : 68.12 % 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: -1.51 (0.28), residues: 915 helix: 0.08 (0.30), residues: 345 sheet: -1.48 (0.38), residues: 147 loop : -1.71 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 100 PHE 0.025 0.002 PHE C 89 TYR 0.029 0.002 TYR B 190 ARG 0.014 0.001 ARG C 307 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3710.51 seconds wall clock time: 66 minutes 52.78 seconds (4012.78 seconds total)