Starting phenix.real_space_refine on Fri Jul 3 06:00:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ype_73295/07_2026/9ype_73295.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ype_73295/07_2026/9ype_73295.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ype_73295/07_2026/9ype_73295.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ype_73295/07_2026/9ype_73295.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ype_73295/07_2026/9ype_73295.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ype_73295/07_2026/9ype_73295.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.012 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 P 28 5.49 5 Mg 12 5.21 5 S 50 5.16 5 C 7716 2.51 5 N 2099 2.21 5 O 2381 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12286 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2515 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "B" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1687 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 7, 'TRANS': 201} Chain: "C" Number of atoms: 2515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2515 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "D" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1687 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 7, 'TRANS': 201} Chain: "E" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1687 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 7, 'TRANS': 201} Chain: "F" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1687 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 7, 'TRANS': 201} Chain: "G" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 466 Classifications: {'RNA': 22} Modifications used: {'rna3p_pur': 10, 'rna3p_pyr': 12} Link IDs: {'rna3p': 21} Chain breaks: 1 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 7 Unusual residues: {' MG': 2, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 7 Unusual residues: {' MG': 2, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 7 Unusual residues: {' MG': 2, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 7 Unusual residues: {' MG': 2, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 7 Unusual residues: {' MG': 2, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 7 Unusual residues: {' MG': 2, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.01, per 1000 atoms: 0.24 Number of scatterers: 12286 At special positions: 0 Unit cell: (116.8, 116.07, 106.58, 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) S 50 16.00 P 28 15.00 Mg 12 11.99 O 2381 8.00 N 2099 7.00 C 7716 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.07 Conformation dependent library (CDL) restraints added in 524.2 milliseconds 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2764 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 4 sheets defined 60.7% alpha, 6.0% beta 10 base pairs and 13 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 3 through 7 Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 90 through 94 Processing helix chain 'A' and resid 96 through 101 removed outlier: 3.597A pdb=" N VAL A 101 " --> pdb=" O GLU A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 120 removed outlier: 3.822A pdb=" N TYR A 118 " --> pdb=" O GLU A 114 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU A 120 " --> pdb=" O SER A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 138 Processing helix chain 'A' and resid 157 through 177 removed outlier: 3.687A pdb=" N SER A 172 " --> pdb=" O ARG A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 192 Processing helix chain 'A' and resid 195 through 200 Processing helix chain 'A' and resid 209 through 215 Processing helix chain 'A' and resid 216 through 233 removed outlier: 3.535A pdb=" N VAL A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL A 226 " --> pdb=" O SER A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 248 removed outlier: 4.395A pdb=" N MET A 240 " --> pdb=" O GLY A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 256 Processing helix chain 'A' and resid 263 through 288 removed outlier: 3.707A pdb=" N ILE A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N MET A 281 " --> pdb=" O ALA A 277 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LYS A 288 " --> pdb=" O LYS A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 302 removed outlier: 3.706A pdb=" N GLU A 302 " --> pdb=" O PHE A 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 120 removed outlier: 3.679A pdb=" N HIS B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TYR B 118 " --> pdb=" O GLU B 114 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU B 120 " --> pdb=" O SER B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 138 Processing helix chain 'B' and resid 157 through 177 removed outlier: 3.616A pdb=" N SER B 172 " --> pdb=" O ARG B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 192 Processing helix chain 'B' and resid 194 through 200 removed outlier: 4.437A pdb=" N ARG B 198 " --> pdb=" O ILE B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 215 Processing helix chain 'B' and resid 216 through 233 Processing helix chain 'B' and resid 237 through 248 Processing helix chain 'B' and resid 252 through 256 Processing helix chain 'B' and resid 263 through 283 Processing helix chain 'B' and resid 298 through 302 removed outlier: 3.733A pdb=" N GLU B 302 " --> pdb=" O PHE B 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 60 Processing helix chain 'C' and resid 90 through 94 removed outlier: 3.708A pdb=" N GLN C 94 " --> pdb=" O THR C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 100 Processing helix chain 'C' and resid 107 through 120 removed outlier: 3.615A pdb=" N TYR C 118 " --> pdb=" O GLU C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 138 Processing helix chain 'C' and resid 138 through 143 removed outlier: 3.994A pdb=" N TYR C 143 " --> pdb=" O GLN C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 177 removed outlier: 3.549A pdb=" N SER C 172 " --> pdb=" O ARG C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 192 Processing helix chain 'C' and resid 193 through 200 removed outlier: 3.516A pdb=" N VAL C 197 " --> pdb=" O ALA C 193 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ARG C 198 " --> pdb=" O ILE C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 215 Processing helix chain 'C' and resid 215 through 232 removed outlier: 4.136A pdb=" N SER C 219 " --> pdb=" O LEU C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 248 removed outlier: 3.537A pdb=" N ILE C 246 " --> pdb=" O LEU C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 289 removed outlier: 4.101A pdb=" N LYS C 288 " --> pdb=" O LYS C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 302 Processing helix chain 'D' and resid 107 through 120 removed outlier: 3.750A pdb=" N TYR D 118 " --> pdb=" O GLU D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 138 Processing helix chain 'D' and resid 159 through 177 removed outlier: 5.264A pdb=" N THR D 165 " --> pdb=" O TYR D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 192 Processing helix chain 'D' and resid 195 through 199 Processing helix chain 'D' and resid 209 through 215 Processing helix chain 'D' and resid 215 through 233 removed outlier: 4.350A pdb=" N SER D 219 " --> pdb=" O LEU D 215 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL D 226 " --> pdb=" O SER D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 248 Processing helix chain 'D' and resid 263 through 288 removed outlier: 3.734A pdb=" N LYS D 287 " --> pdb=" O GLU D 283 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LYS D 288 " --> pdb=" O LYS D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 302 Processing helix chain 'E' and resid 107 through 120 removed outlier: 3.851A pdb=" N TYR E 118 " --> pdb=" O GLU E 114 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU E 120 " --> pdb=" O SER E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 138 Processing helix chain 'E' and resid 138 through 143 removed outlier: 3.839A pdb=" N TYR E 143 " --> pdb=" O GLN E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 177 removed outlier: 3.547A pdb=" N SER E 172 " --> pdb=" O ARG E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 193 removed outlier: 4.363A pdb=" N ALA E 193 " --> pdb=" O ILE E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 197 removed outlier: 3.656A pdb=" N VAL E 197 " --> pdb=" O ILE E 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 194 through 197' Processing helix chain 'E' and resid 209 through 233 removed outlier: 7.775A pdb=" N HIS E 217 " --> pdb=" O ASN E 213 " (cutoff:3.500A) removed outlier: 9.452A pdb=" N ILE E 218 " --> pdb=" O LEU E 214 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N SER E 219 " --> pdb=" O LEU E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 248 Processing helix chain 'E' and resid 252 through 256 Processing helix chain 'E' and resid 263 through 288 removed outlier: 3.617A pdb=" N LYS E 287 " --> pdb=" O GLU E 283 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LYS E 288 " --> pdb=" O LYS E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 302 removed outlier: 3.512A pdb=" N GLU E 302 " --> pdb=" O PHE E 299 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 120 removed outlier: 3.875A pdb=" N TYR F 118 " --> pdb=" O GLU F 114 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU F 120 " --> pdb=" O SER F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 138 Processing helix chain 'F' and resid 138 through 143 removed outlier: 3.919A pdb=" N TYR F 143 " --> pdb=" O GLN F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 177 Processing helix chain 'F' and resid 181 through 193 removed outlier: 4.595A pdb=" N ALA F 193 " --> pdb=" O ILE F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 199 Processing helix chain 'F' and resid 209 through 215 Processing helix chain 'F' and resid 215 through 232 removed outlier: 4.231A pdb=" N SER F 219 " --> pdb=" O LEU F 215 " (cutoff:3.500A) Processing helix chain 'F' and resid 236 through 248 removed outlier: 4.419A pdb=" N MET F 240 " --> pdb=" O GLY F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 256 Processing helix chain 'F' and resid 263 through 287 Processing helix chain 'F' and resid 298 through 302 removed outlier: 3.903A pdb=" N GLU F 302 " --> pdb=" O PHE F 299 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 22 removed outlier: 6.913A pdb=" N HIS A 37 " --> pdb=" O HIS A 20 " (cutoff:3.500A) removed outlier: 10.084A pdb=" N GLU A 44 " --> pdb=" O LYS A 79 " (cutoff:3.500A) removed outlier: 9.350A pdb=" N MET A 81 " --> pdb=" O GLU A 44 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLU A 46 " --> pdb=" O MET A 81 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N VAL A 83 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LYS A 48 " --> pdb=" O VAL A 83 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N GLN A 85 " --> pdb=" O LYS A 48 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N LYS A 79 " --> pdb=" O TYR A 75 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N TYR A 75 " --> pdb=" O LYS A 79 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N MET A 81 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE A 73 " --> pdb=" O MET A 81 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N VAL A 83 " --> pdb=" O ASP A 71 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ASP A 71 " --> pdb=" O VAL A 83 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N HIS A 15 " --> pdb=" O VAL A 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 17 through 23 removed outlier: 5.282A pdb=" N VAL C 19 " --> pdb=" O GLN C 39 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N GLN C 39 " --> pdb=" O VAL C 19 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS C 21 " --> pdb=" O HIS C 37 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N HIS C 37 " --> pdb=" O LYS C 21 " (cutoff:3.500A) removed outlier: 8.813A pdb=" N MET C 81 " --> pdb=" O GLU C 44 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N GLU C 46 " --> pdb=" O MET C 81 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL C 83 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LYS C 48 " --> pdb=" O VAL C 83 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N GLN C 85 " --> pdb=" O LYS C 48 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N LYS C 69 " --> pdb=" O ASN C 84 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ILE C 86 " --> pdb=" O HIS C 67 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N HIS C 67 " --> pdb=" O ILE C 86 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N LEU C 88 " --> pdb=" O ILE C 65 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N ILE C 65 " --> pdb=" O LEU C 88 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU C 64 " --> pdb=" O VAL C 19 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 200 through 201 removed outlier: 4.201A pdb=" N SER D 207 " --> pdb=" O SER D 201 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 200 through 201 removed outlier: 4.243A pdb=" N SER F 207 " --> pdb=" O SER F 201 " (cutoff:3.500A) 595 hydrogen bonds defined for protein. 1689 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 25 hydrogen bonds 46 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 13 stacking parallelities Total time for adding SS restraints: 1.95 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2233 1.32 - 1.45: 3204 1.45 - 1.57: 7003 1.57 - 1.69: 42 1.69 - 1.81: 88 Bond restraints: 12570 Sorted by residual: bond pdb=" C ALA C 47 " pdb=" N LYS C 48 " ideal model delta sigma weight residual 1.332 1.431 -0.100 1.35e-02 5.49e+03 5.44e+01 bond pdb=" CA THR C 35 " pdb=" C THR C 35 " ideal model delta sigma weight residual 1.523 1.480 0.043 1.23e-02 6.61e+03 1.23e+01 bond pdb=" CA LYS A 48 " pdb=" C LYS A 48 " ideal model delta sigma weight residual 1.522 1.480 0.042 1.22e-02 6.72e+03 1.20e+01 bond pdb=" CA TYR C 33 " pdb=" C TYR C 33 " ideal model delta sigma weight residual 1.522 1.481 0.041 1.24e-02 6.50e+03 1.07e+01 bond pdb=" CA PHE C 49 " pdb=" C PHE C 49 " ideal model delta sigma weight residual 1.525 1.484 0.041 1.29e-02 6.01e+03 1.01e+01 ... (remaining 12565 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 16721 1.43 - 2.86: 282 2.86 - 4.29: 50 4.29 - 5.72: 17 5.72 - 7.15: 2 Bond angle restraints: 17072 Sorted by residual: angle pdb=" N LYS C 48 " pdb=" CA LYS C 48 " pdb=" C LYS C 48 " ideal model delta sigma weight residual 108.02 115.17 -7.15 1.78e+00 3.16e-01 1.61e+01 angle pdb=" O ALA C 47 " pdb=" C ALA C 47 " pdb=" N LYS C 48 " ideal model delta sigma weight residual 123.24 127.85 -4.61 1.23e+00 6.61e-01 1.40e+01 angle pdb=" N LYS A 48 " pdb=" CA LYS A 48 " pdb=" C LYS A 48 " ideal model delta sigma weight residual 109.40 114.76 -5.36 1.63e+00 3.76e-01 1.08e+01 angle pdb=" C ALA C 47 " pdb=" N LYS C 48 " pdb=" CA LYS C 48 " ideal model delta sigma weight residual 122.86 118.22 4.64 1.42e+00 4.96e-01 1.07e+01 angle pdb=" CA ALA C 47 " pdb=" C ALA C 47 " pdb=" N LYS C 48 " ideal model delta sigma weight residual 115.58 110.91 4.67 1.48e+00 4.57e-01 9.98e+00 ... (remaining 17067 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 6654 17.47 - 34.94: 771 34.94 - 52.41: 135 52.41 - 69.88: 60 69.88 - 87.35: 20 Dihedral angle restraints: 7640 sinusoidal: 3338 harmonic: 4302 Sorted by residual: dihedral pdb=" O4' U G 26 " pdb=" C1' U G 26 " pdb=" N1 U G 26 " pdb=" C2 U G 26 " ideal model delta sinusoidal sigma weight residual -160.00 -89.86 -70.14 1 1.50e+01 4.44e-03 2.82e+01 dihedral pdb=" CA ALA F 156 " pdb=" C ALA F 156 " pdb=" N SER F 157 " pdb=" CA SER F 157 " ideal model delta harmonic sigma weight residual -180.00 -157.78 -22.22 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA ASP C 14 " pdb=" C ASP C 14 " pdb=" N HIS C 15 " pdb=" CA HIS C 15 " ideal model delta harmonic sigma weight residual 180.00 162.32 17.68 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 7637 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1534 0.044 - 0.087: 303 0.087 - 0.131: 58 0.131 - 0.174: 5 0.174 - 0.218: 4 Chirality restraints: 1904 Sorted by residual: chirality pdb=" C3' G G 16 " pdb=" C4' G G 16 " pdb=" O3' G G 16 " pdb=" C2' G G 16 " both_signs ideal model delta sigma weight residual False -2.48 -2.70 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" C2' G G 16 " pdb=" C3' G G 16 " pdb=" O2' G G 16 " pdb=" C1' G G 16 " both_signs ideal model delta sigma weight residual False -2.75 -2.56 -0.20 2.00e-01 2.50e+01 9.54e-01 chirality pdb=" C3' U G 26 " pdb=" C4' U G 26 " pdb=" O3' U G 26 " pdb=" C2' U G 26 " both_signs ideal model delta sigma weight residual False -2.48 -2.66 0.18 2.00e-01 2.50e+01 8.28e-01 ... (remaining 1901 not shown) Planarity restraints: 2098 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 202 " 0.036 5.00e-02 4.00e+02 5.50e-02 4.85e+00 pdb=" N PRO D 203 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO D 203 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 203 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 72 " -0.009 2.00e-02 2.50e+03 1.90e-02 3.62e+00 pdb=" C ILE C 72 " 0.033 2.00e-02 2.50e+03 pdb=" O ILE C 72 " -0.013 2.00e-02 2.50e+03 pdb=" N ILE C 73 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 33 " 0.015 2.00e-02 2.50e+03 1.12e-02 2.50e+00 pdb=" CG TYR C 33 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR C 33 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR C 33 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR C 33 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR C 33 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR C 33 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR C 33 " 0.000 2.00e-02 2.50e+03 ... (remaining 2095 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 134 2.57 - 3.16: 9662 3.16 - 3.74: 19279 3.74 - 4.32: 27562 4.32 - 4.90: 45181 Nonbonded interactions: 101818 Sorted by model distance: nonbonded pdb=" O1 PO4 D 401 " pdb="MG MG D 402 " model vdw 1.992 2.170 nonbonded pdb="MG MG E 402 " pdb=" O1 PO4 E 403 " model vdw 1.993 2.170 nonbonded pdb=" O3 PO4 D 401 " pdb="MG MG D 403 " model vdw 2.010 2.170 nonbonded pdb=" O1 PO4 B 402 " pdb="MG MG B 403 " model vdw 2.021 2.170 nonbonded pdb="MG MG A1002 " pdb=" O3 PO4 A1003 " model vdw 2.023 2.170 ... (remaining 101813 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 1 through 313 or resid 1002)) selection = (chain 'C' and (resid 1 through 313 or resid 402)) } ncs_group { reference = (chain 'B' and resid 105 through 313) selection = (chain 'D' and resid 105 through 313) selection = (chain 'E' and resid 105 through 313) selection = (chain 'F' and resid 105 through 313) } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.900 Find NCS groups from input model: 0.370 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 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 : 0.004 0.100 12570 Z= 0.221 Angle : 0.480 7.149 17072 Z= 0.284 Chirality : 0.037 0.218 1904 Planarity : 0.003 0.055 2098 Dihedral : 15.906 87.347 4876 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.10 % Favored : 94.62 % Rotamer: Outliers : 0.62 % Allowed : 0.39 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.21), residues: 1450 helix: 0.92 (0.18), residues: 740 sheet: -1.60 (0.59), residues: 74 loop : -0.57 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 278 TYR 0.027 0.001 TYR C 33 PHE 0.008 0.001 PHE C 49 TRP 0.008 0.002 TRP C 50 HIS 0.004 0.001 HIS D 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.22 (12570) covalent geometry : angle 0.47970 / 0.28 (17072) hydrogen bonds : bond 0.23159 / 16.05 ( 620) hydrogen bonds : angle 6.43286 / 4.53 ( 1735) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 162 time to evaluate : 0.480 Fit side-chains REVERT: A 139 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.8324 (tm-30) REVERT: B 279 MET cc_start: 0.8905 (mmm) cc_final: 0.8677 (mmm) REVERT: F 139 GLN cc_start: 0.8075 (tm-30) cc_final: 0.7699 (tm-30) outliers start: 8 outliers final: 3 residues processed: 169 average time/residue: 0.1044 time to fit residues: 26.4957 Evaluate side-chains 134 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 130 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 139 GLN Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 73 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.0470 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.0010 chunk 55 optimal weight: 9.9990 overall best weight: 0.7886 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 GLN A 112 GLN A 139 GLN A 181 ASN C 24 GLN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN ** C 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 293 GLN F 151 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.132825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.099546 restraints weight = 16910.295| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.77 r_work: 0.3064 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12570 Z= 0.130 Angle : 0.508 7.371 17072 Z= 0.273 Chirality : 0.038 0.144 1904 Planarity : 0.004 0.046 2098 Dihedral : 10.711 74.249 1956 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.24 % Favored : 94.55 % Rotamer: Outliers : 1.01 % Allowed : 6.23 % Favored : 92.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.22), residues: 1450 helix: 1.64 (0.18), residues: 746 sheet: -1.92 (0.54), residues: 89 loop : -0.56 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 243 TYR 0.014 0.001 TYR E 208 PHE 0.010 0.001 PHE C 299 TRP 0.006 0.001 TRP A 50 HIS 0.005 0.001 HIS C 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (12570) covalent geometry : angle 0.50802 / 0.27 (17072) hydrogen bonds : bond 0.06290 / 4.40 ( 620) hydrogen bonds : angle 4.34938 / 3.10 ( 1735) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 146 time to evaluate : 0.476 Fit side-chains REVERT: A 64 GLU cc_start: 0.7118 (pm20) cc_final: 0.6896 (pm20) REVERT: A 271 TYR cc_start: 0.8789 (m-80) cc_final: 0.8216 (m-10) REVERT: F 139 GLN cc_start: 0.8072 (tm-30) cc_final: 0.7581 (tm-30) outliers start: 13 outliers final: 6 residues processed: 155 average time/residue: 0.0952 time to fit residues: 22.9087 Evaluate side-chains 141 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 135 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 6 ASN Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain F residue 240 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 43 optimal weight: 0.3980 chunk 71 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 4 optimal weight: 0.0030 chunk 121 optimal weight: 7.9990 overall best weight: 1.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 HIS E 154 ASN E 280 ASN E 293 GLN ** F 250 HIS ** 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 = 0.3618 r_free = 0.3618 target = 0.130478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.097364 restraints weight = 17197.482| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.78 r_work: 0.3019 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12570 Z= 0.159 Angle : 0.479 6.426 17072 Z= 0.257 Chirality : 0.038 0.157 1904 Planarity : 0.004 0.041 2098 Dihedral : 10.298 73.633 1947 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.97 % Favored : 94.83 % Rotamer: Outliers : 1.25 % Allowed : 8.80 % Favored : 89.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.22), residues: 1450 helix: 1.81 (0.18), residues: 746 sheet: -2.10 (0.50), residues: 93 loop : -0.64 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 304 TYR 0.012 0.001 TYR F 138 PHE 0.020 0.001 PHE B 299 TRP 0.004 0.001 TRP A 50 HIS 0.007 0.001 HIS F 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 (12570) covalent geometry : angle 0.47916 / 0.26 (17072) hydrogen bonds : bond 0.05568 / 3.87 ( 620) hydrogen bonds : angle 4.15224 / 2.95 ( 1735) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 0.498 Fit side-chains REVERT: A 64 GLU cc_start: 0.7173 (pm20) cc_final: 0.6901 (pm20) REVERT: F 139 GLN cc_start: 0.8032 (tm-30) cc_final: 0.7585 (tm-30) outliers start: 16 outliers final: 12 residues processed: 151 average time/residue: 0.0973 time to fit residues: 22.6103 Evaluate side-chains 146 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain C residue 6 ASN Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain F residue 121 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 75 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 9 optimal weight: 0.0060 chunk 6 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 106 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 overall best weight: 1.4800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 HIS A 94 GLN ** C 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 ASN E 280 ASN E 293 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.131283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.098413 restraints weight = 17127.359| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 1.76 r_work: 0.2992 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12570 Z= 0.133 Angle : 0.451 6.754 17072 Z= 0.243 Chirality : 0.037 0.142 1904 Planarity : 0.003 0.035 2098 Dihedral : 10.170 73.743 1947 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.59 % Favored : 94.28 % Rotamer: Outliers : 1.32 % Allowed : 10.44 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.22), residues: 1450 helix: 1.99 (0.18), residues: 740 sheet: -1.92 (0.52), residues: 87 loop : -0.72 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 304 TYR 0.014 0.001 TYR F 138 PHE 0.011 0.001 PHE A 299 TRP 0.005 0.001 TRP A 50 HIS 0.006 0.001 HIS D 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 (12570) covalent geometry : angle 0.45105 / 0.24 (17072) hydrogen bonds : bond 0.04766 / 3.32 ( 620) hydrogen bonds : angle 3.96606 / 2.80 ( 1735) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 0.541 Fit side-chains REVERT: F 139 GLN cc_start: 0.8030 (tm-30) cc_final: 0.7605 (tm-30) outliers start: 17 outliers final: 11 residues processed: 150 average time/residue: 0.0993 time to fit residues: 22.9173 Evaluate side-chains 141 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain C residue 6 ASN Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 240 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 23 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 chunk 49 optimal weight: 7.9990 chunk 61 optimal weight: 10.0000 chunk 88 optimal weight: 3.9990 chunk 115 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 129 optimal weight: 5.9990 chunk 48 optimal weight: 0.6980 chunk 57 optimal weight: 10.0000 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 GLN B 154 ASN ** C 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 ASN E 280 ASN E 293 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.128708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.096084 restraints weight = 17177.456| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.73 r_work: 0.3013 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 12570 Z= 0.198 Angle : 0.491 7.139 17072 Z= 0.263 Chirality : 0.038 0.140 1904 Planarity : 0.004 0.040 2098 Dihedral : 10.090 73.706 1946 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.59 % Favored : 94.28 % Rotamer: Outliers : 1.95 % Allowed : 10.59 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.22), residues: 1450 helix: 1.88 (0.18), residues: 744 sheet: -2.17 (0.52), residues: 85 loop : -0.74 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 304 TYR 0.012 0.001 TYR F 138 PHE 0.017 0.002 PHE B 299 TRP 0.004 0.001 TRP A 50 HIS 0.008 0.001 HIS F 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.20 (12570) covalent geometry : angle 0.49143 / 0.26 (17072) hydrogen bonds : bond 0.05045 / 3.49 ( 620) hydrogen bonds : angle 4.01965 / 2.83 ( 1735) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 0.491 Fit side-chains REVERT: B 134 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8494 (mm) REVERT: E 175 ASP cc_start: 0.9017 (OUTLIER) cc_final: 0.8796 (m-30) REVERT: F 139 GLN cc_start: 0.8076 (tm-30) cc_final: 0.7635 (tm-30) REVERT: F 276 ASP cc_start: 0.8646 (t0) cc_final: 0.8430 (t0) outliers start: 25 outliers final: 16 residues processed: 149 average time/residue: 0.0933 time to fit residues: 21.5854 Evaluate side-chains 144 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain E residue 175 ASP Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain F residue 240 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 33 optimal weight: 3.9990 chunk 137 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 106 optimal weight: 7.9990 chunk 64 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 chunk 120 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 154 ASN ** C 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 ASN E 280 ASN E 293 GLN F 181 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.130852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.098192 restraints weight = 17112.813| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 1.74 r_work: 0.3010 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12570 Z= 0.128 Angle : 0.449 6.774 17072 Z= 0.242 Chirality : 0.037 0.140 1904 Planarity : 0.003 0.044 2098 Dihedral : 10.000 73.878 1946 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.31 % Favored : 94.55 % Rotamer: Outliers : 1.95 % Allowed : 11.84 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.22), residues: 1450 helix: 2.05 (0.18), residues: 744 sheet: -2.12 (0.53), residues: 80 loop : -0.72 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 243 TYR 0.011 0.001 TYR F 138 PHE 0.015 0.001 PHE A 16 TRP 0.003 0.001 TRP A 50 HIS 0.004 0.001 HIS C 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (12570) covalent geometry : angle 0.44943 / 0.24 (17072) hydrogen bonds : bond 0.04443 / 3.08 ( 620) hydrogen bonds : angle 3.86942 / 2.72 ( 1735) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 0.482 Fit side-chains REVERT: F 139 GLN cc_start: 0.8016 (tm-30) cc_final: 0.7640 (tm-30) REVERT: F 276 ASP cc_start: 0.8604 (t0) cc_final: 0.8386 (t0) outliers start: 25 outliers final: 15 residues processed: 150 average time/residue: 0.0906 time to fit residues: 21.4213 Evaluate side-chains 146 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain C residue 6 ASN Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain F residue 240 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 140 optimal weight: 8.9990 chunk 93 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 chunk 106 optimal weight: 0.0010 chunk 51 optimal weight: 20.0000 chunk 83 optimal weight: 5.9990 chunk 138 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 136 optimal weight: 0.9990 overall best weight: 1.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 154 ASN ** C 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 ASN E 280 ASN E 293 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.130468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.097816 restraints weight = 17070.310| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.73 r_work: 0.3018 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12570 Z= 0.140 Angle : 0.464 7.138 17072 Z= 0.247 Chirality : 0.037 0.138 1904 Planarity : 0.003 0.040 2098 Dihedral : 9.948 73.896 1946 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.45 % Favored : 94.41 % Rotamer: Outliers : 1.71 % Allowed : 12.77 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.22), residues: 1450 helix: 2.06 (0.18), residues: 744 sheet: -2.26 (0.51), residues: 85 loop : -0.69 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 243 TYR 0.010 0.001 TYR F 138 PHE 0.017 0.001 PHE B 299 TRP 0.003 0.001 TRP A 50 HIS 0.009 0.001 HIS F 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 (12570) covalent geometry : angle 0.46436 / 0.25 (17072) hydrogen bonds : bond 0.04461 / 3.09 ( 620) hydrogen bonds : angle 3.87333 / 2.72 ( 1735) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 0.501 Fit side-chains REVERT: F 139 GLN cc_start: 0.8041 (tm-30) cc_final: 0.7654 (tm-30) REVERT: F 276 ASP cc_start: 0.8655 (t0) cc_final: 0.8411 (t0) outliers start: 22 outliers final: 17 residues processed: 147 average time/residue: 0.0947 time to fit residues: 21.6412 Evaluate side-chains 142 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain C residue 6 ASN Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain F residue 240 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 1 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 53 optimal weight: 8.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 20 HIS B 154 ASN ** C 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 ASN E 280 ASN E 293 GLN ** F 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.130520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.097780 restraints weight = 17018.285| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 1.74 r_work: 0.3030 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12570 Z= 0.138 Angle : 0.459 6.738 17072 Z= 0.245 Chirality : 0.037 0.149 1904 Planarity : 0.003 0.041 2098 Dihedral : 9.853 73.917 1946 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.66 % Favored : 94.28 % Rotamer: Outliers : 1.71 % Allowed : 13.55 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.22), residues: 1450 helix: 2.06 (0.18), residues: 750 sheet: -2.19 (0.52), residues: 80 loop : -0.65 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 230 TYR 0.010 0.001 TYR F 138 PHE 0.020 0.001 PHE B 299 TRP 0.003 0.001 TRP C 50 HIS 0.005 0.001 HIS C 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (12570) covalent geometry : angle 0.45921 / 0.25 (17072) hydrogen bonds : bond 0.04392 / 3.04 ( 620) hydrogen bonds : angle 3.85089 / 2.70 ( 1735) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.484 Fit side-chains REVERT: F 139 GLN cc_start: 0.8027 (tm-30) cc_final: 0.7639 (tm-30) REVERT: F 166 MET cc_start: 0.8847 (mmm) cc_final: 0.8617 (mtt) REVERT: F 276 ASP cc_start: 0.8630 (t0) cc_final: 0.8422 (t0) outliers start: 22 outliers final: 17 residues processed: 147 average time/residue: 0.0896 time to fit residues: 20.6276 Evaluate side-chains 143 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain C residue 6 ASN Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain F residue 240 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 38 optimal weight: 3.9990 chunk 133 optimal weight: 0.7980 chunk 142 optimal weight: 50.0000 chunk 57 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 115 optimal weight: 0.9980 chunk 136 optimal weight: 0.8980 chunk 65 optimal weight: 6.9990 chunk 58 optimal weight: 0.4980 chunk 42 optimal weight: 7.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 20 HIS ** A 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 ASN ** C 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 ASN E 280 ASN E 293 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.131527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.099014 restraints weight = 16965.498| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.73 r_work: 0.3045 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12570 Z= 0.112 Angle : 0.446 6.825 17072 Z= 0.237 Chirality : 0.036 0.140 1904 Planarity : 0.003 0.031 2098 Dihedral : 9.765 73.969 1946 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.17 % Favored : 94.76 % Rotamer: Outliers : 1.87 % Allowed : 13.55 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.22), residues: 1450 helix: 2.16 (0.18), residues: 750 sheet: -2.13 (0.52), residues: 80 loop : -0.61 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 230 TYR 0.010 0.001 TYR F 138 PHE 0.021 0.001 PHE B 299 TRP 0.004 0.001 TRP C 50 HIS 0.005 0.001 HIS E 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (12570) covalent geometry : angle 0.44614 / 0.24 (17072) hydrogen bonds : bond 0.04093 / 2.85 ( 620) hydrogen bonds : angle 3.76311 / 2.64 ( 1735) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 0.486 Fit side-chains REVERT: C 39 GLN cc_start: 0.8370 (tt0) cc_final: 0.7864 (tm-30) REVERT: D 302 GLU cc_start: 0.8101 (mp0) cc_final: 0.7858 (mp0) REVERT: F 139 GLN cc_start: 0.7996 (tm-30) cc_final: 0.7616 (tm-30) REVERT: F 166 MET cc_start: 0.8823 (mmm) cc_final: 0.8537 (mtt) outliers start: 24 outliers final: 20 residues processed: 150 average time/residue: 0.0916 time to fit residues: 21.4920 Evaluate side-chains 149 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain C residue 6 ASN Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain F residue 240 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 33 optimal weight: 0.9990 chunk 127 optimal weight: 8.9990 chunk 114 optimal weight: 6.9990 chunk 96 optimal weight: 0.0970 chunk 52 optimal weight: 0.0270 chunk 74 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 8 optimal weight: 0.0060 chunk 65 optimal weight: 6.9990 chunk 91 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 overall best weight: 0.3654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 ASN E 293 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.131693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.099033 restraints weight = 17088.365| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.74 r_work: 0.3050 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.155 12570 Z= 0.156 Angle : 0.726 59.158 17072 Z= 0.431 Chirality : 0.037 0.377 1904 Planarity : 0.003 0.039 2098 Dihedral : 9.781 73.995 1946 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.24 % Favored : 94.69 % Rotamer: Outliers : 1.79 % Allowed : 13.47 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.22), residues: 1450 helix: 2.17 (0.18), residues: 750 sheet: -2.13 (0.53), residues: 80 loop : -0.62 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 230 TYR 0.009 0.001 TYR A 33 PHE 0.017 0.001 PHE B 299 TRP 0.003 0.001 TRP C 50 HIS 0.006 0.001 HIS B 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.16 (12570) covalent geometry : angle 0.72564 / 0.43 (17072) hydrogen bonds : bond 0.04060 / 2.83 ( 620) hydrogen bonds : angle 3.76415 / 2.64 ( 1735) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 0.562 Fit side-chains REVERT: C 39 GLN cc_start: 0.8377 (tt0) cc_final: 0.7869 (tm-30) REVERT: D 302 GLU cc_start: 0.8122 (mp0) cc_final: 0.7875 (mp0) REVERT: F 139 GLN cc_start: 0.7987 (tm-30) cc_final: 0.7602 (tm-30) REVERT: F 166 MET cc_start: 0.8817 (mmm) cc_final: 0.8615 (mtt) outliers start: 23 outliers final: 19 residues processed: 146 average time/residue: 0.0928 time to fit residues: 21.1831 Evaluate side-chains 146 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain C residue 6 ASN Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain F residue 240 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 111 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 17 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 50 optimal weight: 0.5980 chunk 31 optimal weight: 6.9990 chunk 110 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 ASN E 293 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.131673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.099052 restraints weight = 16939.810| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.73 r_work: 0.3024 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.154 12570 Z= 0.155 Angle : 0.725 59.199 17072 Z= 0.431 Chirality : 0.037 0.371 1904 Planarity : 0.003 0.039 2098 Dihedral : 9.781 73.995 1946 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.24 % Favored : 94.69 % Rotamer: Outliers : 1.56 % Allowed : 13.63 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.22), residues: 1450 helix: 2.17 (0.18), residues: 750 sheet: -2.13 (0.53), residues: 80 loop : -0.62 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 230 TYR 0.009 0.001 TYR F 138 PHE 0.017 0.001 PHE B 299 TRP 0.003 0.001 TRP A 50 HIS 0.006 0.001 HIS B 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 (12570) covalent geometry : angle 0.72550 / 0.43 (17072) hydrogen bonds : bond 0.04060 / 2.83 ( 620) hydrogen bonds : angle 3.76413 / 2.64 ( 1735) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3138.23 seconds wall clock time: 54 minutes 43.76 seconds (3283.76 seconds total)