Starting phenix.real_space_refine on Thu Aug 6 00:10:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ype_73295/08_2026/9ype_73295.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ype_73295/08_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_73295/08_2026/9ype_73295.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ype_73295/08_2026/9ype_73295.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ype_73295/08_2026/9ype_73295.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ype_73295/08_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-2.2rc3-6140/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: 3.07, per 1000 atoms: 0.25 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: 0.99 Conformation dependent library (CDL) restraints added in 535.1 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: 1.22 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: 2.02 Time building geometry restraints manager: 1.34 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: 16667 1.43 - 2.86: 336 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: 1515 0.044 - 0.087: 305 0.087 - 0.131: 68 0.131 - 0.174: 13 0.174 - 0.218: 3 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=" 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 chirality pdb=" CA ILE C 73 " pdb=" N ILE C 73 " pdb=" C ILE C 73 " pdb=" CB ILE C 73 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.95e-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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.210 Find NCS groups from input model: 0.210 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:0.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.390 ------------------------------------------------------------------------------- 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= 0.223 Angle : 0.496 7.149 17072 Z= 0.297 Chirality : 0.039 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 0.00383 / 0.22 (12570) covalent geometry : angle 0.49600 / 0.30 (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 : 0.527 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: 0.1026 time to fit residues: 26.1314 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 : 0.498 ------------------------------------------------------------------------------- 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 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.132365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.099168 restraints weight = 16884.795| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.75 r_work: 0.3062 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12570 Z= 0.133 Angle : 0.504 6.863 17072 Z= 0.273 Chirality : 0.038 0.145 1904 Planarity : 0.004 0.048 2098 Dihedral : 10.704 73.624 1956 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.17 % Favored : 94.62 % Rotamer: Outliers : 0.86 % Allowed : 6.23 % Favored : 92.91 % 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: 1.69 (0.18), residues: 746 sheet: -1.44 (0.60), residues: 77 loop : -0.62 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 243 TYR 0.013 0.001 TYR E 208 PHE 0.011 0.001 PHE A 49 TRP 0.005 0.001 TRP A 50 HIS 0.004 0.001 HIS C 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (12570) covalent geometry : angle 0.50423 / 0.27 (17072) hydrogen bonds : bond 0.06453 / 4.51 ( 620) hydrogen bonds : angle 4.38685 / 3.12 ( 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 154 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 143 time to evaluate : 0.400 Fit side-chains REVERT: F 139 GLN cc_start: 0.8089 (tm-30) cc_final: 0.7601 (tm-30) outliers start: 11 outliers final: 5 residues processed: 150 average time/residue: 0.0927 time to fit residues: 21.6519 Evaluate side-chains 140 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 135 time to evaluate : 0.469 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 43 optimal weight: 0.0770 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: 1.9990 chunk 105 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 4 optimal weight: 0.0670 chunk 121 optimal weight: 0.9990 overall best weight: 1.0282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3641 r_free = 0.3641 target = 0.132253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.099471 restraints weight = 17136.962| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.77 r_work: 0.3055 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12570 Z= 0.116 Angle : 0.452 6.743 17072 Z= 0.243 Chirality : 0.037 0.151 1904 Planarity : 0.003 0.035 2098 Dihedral : 10.243 73.793 1947 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.76 % Favored : 95.03 % Rotamer: Outliers : 1.32 % Allowed : 8.26 % Favored : 90.42 % 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: 0.93 (0.22), residues: 1450 helix: 1.94 (0.18), residues: 746 sheet: -1.99 (0.52), residues: 88 loop : -0.62 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 243 TYR 0.012 0.001 TYR F 138 PHE 0.021 0.001 PHE B 299 TRP 0.004 0.001 TRP A 50 HIS 0.006 0.001 HIS D 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (12570) covalent geometry : angle 0.45216 / 0.24 (17072) hydrogen bonds : bond 0.05066 / 3.55 ( 620) hydrogen bonds : angle 4.02661 / 2.85 ( 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 162 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 145 time to evaluate : 0.451 Fit side-chains REVERT: F 139 GLN cc_start: 0.8009 (tm-30) cc_final: 0.7606 (tm-30) outliers start: 17 outliers final: 13 residues processed: 157 average time/residue: 0.0988 time to fit residues: 23.8592 Evaluate side-chains 149 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 0.487 ------------------------------------------------------------------------------- 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 88 LEU 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: 2.9990 chunk 134 optimal weight: 8.9990 chunk 9 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 106 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 132 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 HIS B 154 ASN B 308 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 152 HIS ** C 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 293 GLN ** F 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 181 ASN ** F 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.125527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.092795 restraints weight = 17264.912| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 1.72 r_work: 0.2966 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 12570 Z= 0.324 Angle : 0.596 6.395 17072 Z= 0.317 Chirality : 0.043 0.147 1904 Planarity : 0.005 0.048 2098 Dihedral : 10.204 73.583 1947 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.00 % Favored : 93.86 % Rotamer: Outliers : 1.64 % Allowed : 10.12 % 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: 0.47 (0.22), residues: 1450 helix: 1.55 (0.18), residues: 744 sheet: -1.41 (0.47), residues: 121 loop : -0.91 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 304 TYR 0.013 0.002 TYR D 145 PHE 0.024 0.002 PHE A 155 TRP 0.004 0.001 TRP A 50 HIS 0.010 0.002 HIS F 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00801 / 0.32 (12570) covalent geometry : angle 0.59614 / 0.32 (17072) hydrogen bonds : bond 0.06191 / 4.24 ( 620) hydrogen bonds : angle 4.32064 / 3.06 ( 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 154 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 0.357 Fit side-chains REVERT: D 139 GLN cc_start: 0.8594 (tm-30) cc_final: 0.8371 (tm-30) REVERT: E 175 ASP cc_start: 0.9051 (OUTLIER) cc_final: 0.8848 (m-30) REVERT: F 139 GLN cc_start: 0.8199 (tm-30) cc_final: 0.7747 (tm-30) REVERT: F 255 TYR cc_start: 0.8587 (m-10) cc_final: 0.8381 (m-10) outliers start: 21 outliers final: 12 residues processed: 146 average time/residue: 0.0779 time to fit residues: 17.3799 Evaluate side-chains 137 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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 289 THR 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 210 VAL Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain E residue 175 ASP Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 210 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 23 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 49 optimal weight: 8.9990 chunk 61 optimal weight: 5.9990 chunk 88 optimal weight: 0.8980 chunk 115 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 129 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 57 optimal weight: 9.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 GLN B 308 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 151 HIS D 152 HIS E 154 ASN E 293 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.129961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.097567 restraints weight = 17148.771| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.73 r_work: 0.3030 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12570 Z= 0.117 Angle : 0.460 6.864 17072 Z= 0.248 Chirality : 0.037 0.145 1904 Planarity : 0.003 0.030 2098 Dihedral : 10.066 74.004 1947 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.24 % Favored : 94.62 % Rotamer: Outliers : 1.40 % Allowed : 11.60 % Favored : 86.99 % 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: 0.82 (0.22), residues: 1450 helix: 1.90 (0.18), residues: 744 sheet: -2.24 (0.52), residues: 85 loop : -0.72 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 243 TYR 0.011 0.001 TYR A 33 PHE 0.018 0.001 PHE B 299 TRP 0.004 0.001 TRP A 50 HIS 0.005 0.001 HIS F 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (12570) covalent geometry : angle 0.46020 / 0.25 (17072) hydrogen bonds : bond 0.04661 / 3.24 ( 620) hydrogen bonds : angle 3.96447 / 2.79 ( 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 154 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 136 time to evaluate : 0.475 Fit side-chains REVERT: F 139 GLN cc_start: 0.8042 (tm-30) cc_final: 0.7591 (tm-30) outliers start: 18 outliers final: 14 residues processed: 148 average time/residue: 0.0928 time to fit residues: 21.3816 Evaluate side-chains 142 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR 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 24 GLN Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 79 LYS 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 D residue 121 ASP Chi-restraints excluded: chain F residue 119 LEU 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: 4.9990 chunk 137 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 105 optimal weight: 0.7980 chunk 120 optimal weight: 7.9990 chunk 35 optimal weight: 9.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 20 HIS 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 293 GLN F 181 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.129863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.097147 restraints weight = 17148.694| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.75 r_work: 0.3027 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12570 Z= 0.142 Angle : 0.466 6.901 17072 Z= 0.249 Chirality : 0.038 0.186 1904 Planarity : 0.003 0.030 2098 Dihedral : 9.989 73.984 1946 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.45 % Favored : 94.41 % Rotamer: Outliers : 1.56 % Allowed : 12.23 % 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: 0.88 (0.22), residues: 1450 helix: 1.98 (0.18), residues: 744 sheet: -2.32 (0.50), residues: 89 loop : -0.70 (0.25), residues: 617 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 0.012 0.001 PHE A 155 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 0.00340 / 0.14 (12570) covalent geometry : angle 0.46554 / 0.25 (17072) hydrogen bonds : bond 0.04612 / 3.20 ( 620) hydrogen bonds : angle 3.93471 / 2.77 ( 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 152 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.484 Fit side-chains REVERT: E 175 ASP cc_start: 0.9009 (OUTLIER) cc_final: 0.8776 (m-30) REVERT: F 139 GLN cc_start: 0.8061 (tm-30) cc_final: 0.7604 (tm-30) REVERT: F 166 MET cc_start: 0.8831 (mmm) cc_final: 0.8540 (mtt) outliers start: 20 outliers final: 13 residues processed: 144 average time/residue: 0.0975 time to fit residues: 21.8318 Evaluate side-chains 143 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR 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 46 GLU Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 79 LYS 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 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 240 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 140 optimal weight: 9.9990 chunk 93 optimal weight: 0.8980 chunk 135 optimal weight: 0.3980 chunk 139 optimal weight: 0.7980 chunk 119 optimal weight: 4.9990 chunk 106 optimal weight: 0.5980 chunk 51 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 136 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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** ** D 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 ASN 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 = 0.131627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.099476 restraints weight = 16989.054| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.71 r_work: 0.3040 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12570 Z= 0.101 Angle : 0.441 7.035 17072 Z= 0.235 Chirality : 0.036 0.150 1904 Planarity : 0.003 0.032 2098 Dihedral : 9.841 74.108 1946 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.38 % Favored : 94.48 % Rotamer: Outliers : 1.71 % Allowed : 12.85 % Favored : 85.44 % 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: 1.14 (0.22), residues: 1450 helix: 2.21 (0.18), residues: 742 sheet: -1.76 (0.57), residues: 74 loop : -0.70 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 243 TYR 0.011 0.001 TYR F 255 PHE 0.020 0.001 PHE B 299 TRP 0.004 0.001 TRP A 50 HIS 0.006 0.001 HIS D 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (12570) covalent geometry : angle 0.44085 / 0.24 (17072) hydrogen bonds : bond 0.04025 / 2.80 ( 620) hydrogen bonds : angle 3.77005 / 2.64 ( 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 162 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 0.364 Fit side-chains REVERT: C 79 LYS cc_start: 0.7724 (OUTLIER) cc_final: 0.6331 (ttpp) REVERT: F 139 GLN cc_start: 0.8003 (tm-30) cc_final: 0.7637 (tm-30) REVERT: F 166 MET cc_start: 0.8765 (mmm) cc_final: 0.8562 (mtt) outliers start: 22 outliers final: 16 residues processed: 152 average time/residue: 0.0980 time to fit residues: 22.8948 Evaluate side-chains 147 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 PHE Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 51 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 46 GLU Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 197 VAL 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 121 ASP 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: 10.0000 chunk 62 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 17 optimal weight: 0.0980 chunk 72 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 53 optimal weight: 10.0000 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 154 ASN B 280 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 293 GLN ** F 154 ASN ** 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 = 0.3607 r_free = 0.3607 target = 0.130059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.097365 restraints weight = 17003.777| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.75 r_work: 0.3002 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12570 Z= 0.152 Angle : 0.460 6.935 17072 Z= 0.245 Chirality : 0.037 0.141 1904 Planarity : 0.003 0.030 2098 Dihedral : 9.767 74.020 1946 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.52 % Favored : 94.41 % Rotamer: Outliers : 1.71 % Allowed : 13.47 % 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: 1.03 (0.22), residues: 1450 helix: 2.08 (0.18), residues: 750 sheet: -2.27 (0.51), residues: 84 loop : -0.62 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 230 TYR 0.010 0.001 TYR F 138 PHE 0.019 0.001 PHE B 299 TRP 0.003 0.001 TRP A 50 HIS 0.006 0.001 HIS F 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.15 (12570) covalent geometry : angle 0.45971 / 0.24 (17072) hydrogen bonds : bond 0.04419 / 3.06 ( 620) hydrogen bonds : angle 3.82677 / 2.68 ( 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 : 0.470 Fit side-chains REVERT: F 139 GLN cc_start: 0.8080 (tm-30) cc_final: 0.7660 (tm-30) REVERT: F 166 MET cc_start: 0.8793 (mmm) cc_final: 0.8567 (mtt) outliers start: 22 outliers final: 16 residues processed: 145 average time/residue: 0.0875 time to fit residues: 19.9480 Evaluate side-chains 143 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 0.452 ------------------------------------------------------------------------------- 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 46 GLU Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain D residue 213 ASN 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: 3.9990 chunk 142 optimal weight: 50.0000 chunk 57 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 chunk 136 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 154 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 293 GLN ** F 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.127389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.094501 restraints weight = 17080.124| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.73 r_work: 0.2983 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 12570 Z= 0.226 Angle : 0.522 6.829 17072 Z= 0.278 Chirality : 0.040 0.141 1904 Planarity : 0.004 0.031 2098 Dihedral : 9.775 73.928 1946 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.21 % Favored : 93.72 % Rotamer: Outliers : 1.79 % Allowed : 13.63 % 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: 0.74 (0.22), residues: 1450 helix: 1.83 (0.18), residues: 750 sheet: -1.85 (0.45), residues: 125 loop : -0.73 (0.26), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 304 TYR 0.010 0.001 TYR E 271 PHE 0.023 0.002 PHE B 299 TRP 0.004 0.001 TRP C 50 HIS 0.010 0.002 HIS F 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.23 (12570) covalent geometry : angle 0.52247 / 0.28 (17072) hydrogen bonds : bond 0.05182 / 3.55 ( 620) hydrogen bonds : angle 4.02889 / 2.82 ( 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 148 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.482 Fit side-chains REVERT: C 79 LYS cc_start: 0.7736 (OUTLIER) cc_final: 0.6328 (ttpp) REVERT: F 139 GLN cc_start: 0.8137 (tm-30) cc_final: 0.7660 (tm-30) REVERT: F 166 MET cc_start: 0.8846 (mmm) cc_final: 0.8619 (mtt) outliers start: 23 outliers final: 18 residues processed: 138 average time/residue: 0.0911 time to fit residues: 19.5750 Evaluate side-chains 140 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.423 ------------------------------------------------------------------------------- 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 46 GLU Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 79 LYS 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 121 ASP Chi-restraints excluded: chain D residue 213 ASN Chi-restraints excluded: chain E residue 301 LEU 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: 3.9990 chunk 127 optimal weight: 1.9990 chunk 114 optimal weight: 7.9990 chunk 96 optimal weight: 0.0980 chunk 52 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 97 optimal weight: 0.6980 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 293 GLN ** F 154 ASN ** 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 = 0.3578 r_free = 0.3578 target = 0.127740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.094910 restraints weight = 17190.774| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 1.74 r_work: 0.2991 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.161 12570 Z= 0.212 Angle : 0.775 59.200 17072 Z= 0.454 Chirality : 0.040 0.458 1904 Planarity : 0.004 0.045 2098 Dihedral : 9.798 74.020 1946 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.07 % Favored : 93.86 % Rotamer: Outliers : 1.64 % Allowed : 13.94 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.74 (0.22), residues: 1450 helix: 1.85 (0.18), residues: 750 sheet: -1.86 (0.45), residues: 125 loop : -0.75 (0.26), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 304 TYR 0.010 0.001 TYR E 271 PHE 0.019 0.001 PHE B 299 TRP 0.004 0.001 TRP C 50 HIS 0.009 0.002 HIS F 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.21 (12570) covalent geometry : angle 0.77480 / 0.45 (17072) hydrogen bonds : bond 0.05030 / 3.46 ( 620) hydrogen bonds : angle 4.02877 / 2.82 ( 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 141 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.467 Fit side-chains revert: symmetry clash REVERT: B 154 ASN cc_start: 0.8598 (OUTLIER) cc_final: 0.8234 (p0) REVERT: C 79 LYS cc_start: 0.7740 (OUTLIER) cc_final: 0.6336 (ttpp) REVERT: F 139 GLN cc_start: 0.8121 (tm-30) cc_final: 0.7644 (tm-30) REVERT: F 166 MET cc_start: 0.8851 (mmm) cc_final: 0.8602 (mtt) outliers start: 21 outliers final: 17 residues processed: 134 average time/residue: 0.0952 time to fit residues: 19.9030 Evaluate side-chains 138 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.478 ------------------------------------------------------------------------------- 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 46 GLU Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 79 LYS 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 301 LEU 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: 1.9990 chunk 64 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 chunk 17 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 293 GLN ** F 154 ASN ** 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 = 0.3578 r_free = 0.3578 target = 0.127746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.094986 restraints weight = 17043.610| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 1.74 r_work: 0.2991 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.161 12570 Z= 0.212 Angle : 0.775 59.200 17072 Z= 0.454 Chirality : 0.040 0.458 1904 Planarity : 0.004 0.045 2098 Dihedral : 9.798 74.020 1946 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.07 % Favored : 93.86 % Rotamer: Outliers : 1.64 % Allowed : 13.94 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.74 (0.22), residues: 1450 helix: 1.85 (0.18), residues: 750 sheet: -1.86 (0.45), residues: 125 loop : -0.75 (0.26), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 304 TYR 0.010 0.001 TYR E 271 PHE 0.019 0.001 PHE B 299 TRP 0.004 0.001 TRP C 50 HIS 0.009 0.002 HIS F 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.21 (12570) covalent geometry : angle 0.77480 / 0.45 (17072) hydrogen bonds : bond 0.05030 / 3.46 ( 620) hydrogen bonds : angle 4.02877 / 2.82 ( 1735) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2857.94 seconds wall clock time: 49 minutes 49.34 seconds (2989.34 seconds total)