Starting phenix.real_space_refine on Tue Mar 3 18:18:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ej7_31154/03_2026/7ej7_31154_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ej7_31154/03_2026/7ej7_31154.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ej7_31154/03_2026/7ej7_31154.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ej7_31154/03_2026/7ej7_31154.map" model { file = "/net/cci-nas-00/data/ceres_data/7ej7_31154/03_2026/7ej7_31154_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ej7_31154/03_2026/7ej7_31154_trim.cif" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 27 5.49 5 Mg 3 5.21 5 S 39 5.16 5 C 4764 2.51 5 N 1371 2.21 5 O 1569 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7773 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2436 Classifications: {'peptide': 316} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 306} Chain: "A" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2436 Classifications: {'peptide': 316} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 306} Chain: "C" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2436 Classifications: {'peptide': 316} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 306} Chain: "D" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 180 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "E" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 189 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 1.65, per 1000 atoms: 0.21 Number of scatterers: 7773 At special positions: 0 Unit cell: (84.05, 96.35, 111.725, 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 39 16.00 P 27 15.00 Mg 3 11.99 O 1569 8.00 N 1371 7.00 C 4764 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=13, symmetry=0 Number of additional bonds: simple=13, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 284.3 milliseconds 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1716 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 3 sheets defined 46.5% alpha, 14.9% beta 7 base pairs and 10 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'B' and resid 20 through 25 removed outlier: 3.789A pdb=" N ASN B 24 " --> pdb=" O GLU B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 38 Processing helix chain 'B' and resid 43 through 48 Processing helix chain 'B' and resid 50 through 55 Processing helix chain 'B' and resid 62 through 76 removed outlier: 3.594A pdb=" N ILE B 76 " --> pdb=" O ALA B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 90 Processing helix chain 'B' and resid 100 through 107 Processing helix chain 'B' and resid 128 through 138 removed outlier: 3.836A pdb=" N HIS B 132 " --> pdb=" O THR B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 145 Processing helix chain 'B' and resid 161 through 172 removed outlier: 3.600A pdb=" N ILE B 165 " --> pdb=" O ARG B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 182 Processing helix chain 'B' and resid 190 through 205 removed outlier: 3.709A pdb=" N VAL B 198 " --> pdb=" O GLN B 194 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU B 199 " --> pdb=" O MET B 195 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU B 203 " --> pdb=" O GLU B 199 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU B 204 " --> pdb=" O GLN B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 226 Processing helix chain 'B' and resid 231 through 253 removed outlier: 3.597A pdb=" N LYS B 238 " --> pdb=" O GLU B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 291 removed outlier: 3.856A pdb=" N LEU B 287 " --> pdb=" O GLY B 283 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA B 288 " --> pdb=" O GLY B 284 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA B 290 " --> pdb=" O VAL B 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 25 removed outlier: 3.790A pdb=" N ASN A 24 " --> pdb=" O GLU A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 38 Processing helix chain 'A' and resid 43 through 48 Processing helix chain 'A' and resid 50 through 55 Processing helix chain 'A' and resid 62 through 76 removed outlier: 3.593A pdb=" N ILE A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 90 Processing helix chain 'A' and resid 100 through 107 Processing helix chain 'A' and resid 128 through 138 removed outlier: 4.076A pdb=" N HIS A 132 " --> pdb=" O THR A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 145 Processing helix chain 'A' and resid 161 through 172 removed outlier: 3.601A pdb=" N ILE A 165 " --> pdb=" O ARG A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 182 Processing helix chain 'A' and resid 190 through 205 removed outlier: 3.710A pdb=" N VAL A 198 " --> pdb=" O GLN A 194 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU A 199 " --> pdb=" O MET A 195 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN A 200 " --> pdb=" O GLU A 196 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU A 203 " --> pdb=" O GLU A 199 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU A 204 " --> pdb=" O GLN A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 226 Processing helix chain 'A' and resid 231 through 253 removed outlier: 3.597A pdb=" N LYS A 238 " --> pdb=" O GLU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 291 removed outlier: 3.855A pdb=" N LEU A 287 " --> pdb=" O GLY A 283 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA A 288 " --> pdb=" O GLY A 284 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA A 290 " --> pdb=" O VAL A 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 25 removed outlier: 3.789A pdb=" N ASN C 24 " --> pdb=" O GLU C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 38 Processing helix chain 'C' and resid 43 through 48 Processing helix chain 'C' and resid 50 through 55 Processing helix chain 'C' and resid 62 through 76 removed outlier: 3.594A pdb=" N ILE C 76 " --> pdb=" O ALA C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 90 Processing helix chain 'C' and resid 100 through 107 Processing helix chain 'C' and resid 128 through 138 removed outlier: 4.075A pdb=" N HIS C 132 " --> pdb=" O THR C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 145 Processing helix chain 'C' and resid 161 through 172 removed outlier: 3.601A pdb=" N ILE C 165 " --> pdb=" O ARG C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 182 Processing helix chain 'C' and resid 190 through 205 removed outlier: 3.710A pdb=" N VAL C 198 " --> pdb=" O GLN C 194 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU C 199 " --> pdb=" O MET C 195 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN C 200 " --> pdb=" O GLU C 196 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU C 203 " --> pdb=" O GLU C 199 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU C 204 " --> pdb=" O GLN C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 Processing helix chain 'C' and resid 231 through 253 removed outlier: 3.596A pdb=" N LYS C 238 " --> pdb=" O GLU C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 291 removed outlier: 3.855A pdb=" N LEU C 287 " --> pdb=" O GLY C 283 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA C 288 " --> pdb=" O GLY C 284 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA C 290 " --> pdb=" O VAL C 286 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 183 through 187 removed outlier: 7.596A pdb=" N LYS B 150 " --> pdb=" O ARG B 211 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE B 213 " --> pdb=" O LYS B 150 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ALA B 152 " --> pdb=" O ILE B 213 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N VAL B 215 " --> pdb=" O ALA B 152 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE B 154 " --> pdb=" O VAL B 215 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ARG B 211 " --> pdb=" O ALA B 256 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N PHE B 258 " --> pdb=" O ARG B 211 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE B 213 " --> pdb=" O PHE B 258 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N THR B 260 " --> pdb=" O ILE B 213 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL B 215 " --> pdb=" O THR B 260 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N SER B 115 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LEU B 259 " --> pdb=" O SER B 115 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N THR B 117 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ASN B 261 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL B 119 " --> pdb=" O ASN B 261 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ARG B 294 " --> pdb=" O GLN B 310 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N GLU B 304 " --> pdb=" O GLY B 300 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY B 328 " --> pdb=" O GLY B 325 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 183 through 187 removed outlier: 7.596A pdb=" N LYS A 150 " --> pdb=" O ARG A 211 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE A 213 " --> pdb=" O LYS A 150 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ALA A 152 " --> pdb=" O ILE A 213 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N VAL A 215 " --> pdb=" O ALA A 152 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE A 154 " --> pdb=" O VAL A 215 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ARG A 211 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N PHE A 258 " --> pdb=" O ARG A 211 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE A 213 " --> pdb=" O PHE A 258 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N THR A 260 " --> pdb=" O ILE A 213 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL A 215 " --> pdb=" O THR A 260 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N SER A 115 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N LEU A 259 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N THR A 117 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ASN A 261 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL A 119 " --> pdb=" O ASN A 261 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ARG A 294 " --> pdb=" O GLN A 310 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N GLU A 304 " --> pdb=" O GLY A 300 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLY A 328 " --> pdb=" O GLY A 325 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 183 through 187 removed outlier: 7.596A pdb=" N LYS C 150 " --> pdb=" O ARG C 211 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE C 213 " --> pdb=" O LYS C 150 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ALA C 152 " --> pdb=" O ILE C 213 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N VAL C 215 " --> pdb=" O ALA C 152 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ILE C 154 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ARG C 211 " --> pdb=" O ALA C 256 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N PHE C 258 " --> pdb=" O ARG C 211 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE C 213 " --> pdb=" O PHE C 258 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N THR C 260 " --> pdb=" O ILE C 213 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL C 215 " --> pdb=" O THR C 260 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N SER C 115 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N LEU C 259 " --> pdb=" O SER C 115 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N THR C 117 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ASN C 261 " --> pdb=" O THR C 117 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL C 119 " --> pdb=" O ASN C 261 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ARG C 294 " --> pdb=" O GLN C 310 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N GLU C 304 " --> pdb=" O GLY C 300 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY C 328 " --> pdb=" O GLY C 325 " (cutoff:3.500A) 294 hydrogen bonds defined for protein. 837 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 14 hydrogen bonds 28 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 10 stacking parallelities Total time for adding SS restraints: 1.07 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1293 1.30 - 1.42: 1934 1.42 - 1.55: 4576 1.55 - 1.68: 49 1.68 - 1.80: 60 Bond restraints: 7912 Sorted by residual: bond pdb=" C4 ATP C 402 " pdb=" C5 ATP C 402 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.44e+01 bond pdb=" C4 ATP C 401 " pdb=" C5 ATP C 401 " ideal model delta sigma weight residual 1.388 1.461 -0.073 1.00e-02 1.00e+04 5.35e+01 bond pdb=" C4 ATP B 602 " pdb=" C5 ATP B 602 " ideal model delta sigma weight residual 1.388 1.461 -0.073 1.00e-02 1.00e+04 5.34e+01 bond pdb=" C5 ATP C 402 " pdb=" C6 ATP C 402 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.30e+01 bond pdb=" C5 ATP B 602 " pdb=" C6 ATP B 602 " ideal model delta sigma weight residual 1.409 1.481 -0.072 1.00e-02 1.00e+04 5.18e+01 ... (remaining 7907 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.62: 10657 3.62 - 7.25: 72 7.25 - 10.87: 9 10.87 - 14.50: 0 14.50 - 18.12: 6 Bond angle restraints: 10744 Sorted by residual: angle pdb=" PA ATP C 402 " pdb=" O3A ATP C 402 " pdb=" PB ATP C 402 " ideal model delta sigma weight residual 136.83 118.71 18.12 1.00e+00 1.00e+00 3.28e+02 angle pdb=" PA ATP B 602 " pdb=" O3A ATP B 602 " pdb=" PB ATP B 602 " ideal model delta sigma weight residual 136.83 118.74 18.09 1.00e+00 1.00e+00 3.27e+02 angle pdb=" PA ATP C 401 " pdb=" O3A ATP C 401 " pdb=" PB ATP C 401 " ideal model delta sigma weight residual 136.83 118.74 18.09 1.00e+00 1.00e+00 3.27e+02 angle pdb=" PB ATP B 602 " pdb=" O3B ATP B 602 " pdb=" PG ATP B 602 " ideal model delta sigma weight residual 139.87 123.70 16.17 1.00e+00 1.00e+00 2.62e+02 angle pdb=" PB ATP C 401 " pdb=" O3B ATP C 401 " pdb=" PG ATP C 401 " ideal model delta sigma weight residual 139.87 123.74 16.13 1.00e+00 1.00e+00 2.60e+02 ... (remaining 10739 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.75: 4104 16.75 - 33.50: 516 33.50 - 50.25: 155 50.25 - 67.01: 40 67.01 - 83.76: 33 Dihedral angle restraints: 4848 sinusoidal: 2160 harmonic: 2688 Sorted by residual: dihedral pdb=" CA ASN B 28 " pdb=" C ASN B 28 " pdb=" N ALA B 29 " pdb=" CA ALA B 29 " ideal model delta harmonic sigma weight residual 180.00 -153.70 -26.30 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA ASN C 28 " pdb=" C ASN C 28 " pdb=" N ALA C 29 " pdb=" CA ALA C 29 " ideal model delta harmonic sigma weight residual -180.00 -153.71 -26.29 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA ASN A 28 " pdb=" C ASN A 28 " pdb=" N ALA A 29 " pdb=" CA ALA A 29 " ideal model delta harmonic sigma weight residual -180.00 -153.72 -26.28 0 5.00e+00 4.00e-02 2.76e+01 ... (remaining 4845 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 843 0.037 - 0.074: 267 0.074 - 0.111: 78 0.111 - 0.147: 24 0.147 - 0.184: 6 Chirality restraints: 1218 Sorted by residual: chirality pdb=" CA ASP A 216 " pdb=" N ASP A 216 " pdb=" C ASP A 216 " pdb=" CB ASP A 216 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.50e-01 chirality pdb=" CA ASP C 216 " pdb=" N ASP C 216 " pdb=" C ASP C 216 " pdb=" CB ASP C 216 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.73e-01 chirality pdb=" CA ASP B 216 " pdb=" N ASP B 216 " pdb=" C ASP B 216 " pdb=" CB ASP B 216 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.68e-01 ... (remaining 1215 not shown) Planarity restraints: 1323 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET C 315 " -0.014 2.00e-02 2.50e+03 2.86e-02 8.18e+00 pdb=" C MET C 315 " 0.049 2.00e-02 2.50e+03 pdb=" O MET C 315 " -0.019 2.00e-02 2.50e+03 pdb=" N PRO C 316 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 315 " 0.014 2.00e-02 2.50e+03 2.84e-02 8.05e+00 pdb=" C MET A 315 " -0.049 2.00e-02 2.50e+03 pdb=" O MET A 315 " 0.018 2.00e-02 2.50e+03 pdb=" N PRO A 316 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 315 " -0.014 2.00e-02 2.50e+03 2.83e-02 8.03e+00 pdb=" C MET B 315 " 0.049 2.00e-02 2.50e+03 pdb=" O MET B 315 " -0.018 2.00e-02 2.50e+03 pdb=" N PRO B 316 " -0.016 2.00e-02 2.50e+03 ... (remaining 1320 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 78 2.47 - 3.08: 6331 3.08 - 3.68: 11314 3.68 - 4.29: 17663 4.29 - 4.90: 29004 Nonbonded interactions: 64390 Sorted by model distance: nonbonded pdb=" O PRO B 316 " pdb=" O2' ATP B 602 " model vdw 1.860 3.040 nonbonded pdb=" O PRO C 316 " pdb=" O2' ATP C 401 " model vdw 1.901 3.040 nonbonded pdb=" O2G ATP C 402 " pdb="MG MG C 403 " model vdw 1.913 2.170 nonbonded pdb="MG MG B 601 " pdb=" O2G ATP C 401 " model vdw 1.913 2.170 nonbonded pdb=" O2G ATP B 602 " pdb="MG MG A 601 " model vdw 1.913 2.170 ... (remaining 64385 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 16 through 334) selection = (chain 'B' and resid 16 through 334) selection = (chain 'C' and resid 16 through 334) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.960 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 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 : 0.012 0.500 7925 Z= 1.056 Angle : 0.915 18.124 10744 Z= 0.680 Chirality : 0.043 0.184 1218 Planarity : 0.004 0.044 1323 Dihedral : 18.099 83.758 3132 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 43.44 Ramachandran Plot: Outliers : 0.96 % Allowed : 10.83 % Favored : 88.22 % Rotamer: Outliers : 1.75 % Allowed : 4.64 % Favored : 93.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: -4.75 (0.22), residues: 942 helix: -3.33 (0.19), residues: 381 sheet: -0.20 (0.45), residues: 150 loop : -4.17 (0.21), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 142 TYR 0.006 0.001 TYR B 41 PHE 0.007 0.001 PHE C 160 HIS 0.002 0.001 HIS B 193 Details of bonding type rmsd covalent geometry : bond 0.00618 ( 7912) covalent geometry : angle 0.91461 (10744) hydrogen bonds : bond 0.18053 ( 308) hydrogen bonds : angle 9.03162 ( 865) Misc. bond : bond 0.24084 ( 13) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: B 24 ASN cc_start: 0.8704 (p0) cc_final: 0.8486 (p0) REVERT: B 61 SER cc_start: 0.6819 (OUTLIER) cc_final: 0.6156 (m) REVERT: A 61 SER cc_start: 0.6980 (OUTLIER) cc_final: 0.6731 (m) REVERT: C 61 SER cc_start: 0.6506 (OUTLIER) cc_final: 0.6165 (m) outliers start: 14 outliers final: 2 residues processed: 111 average time/residue: 0.0990 time to fit residues: 14.4425 Evaluate side-chains 68 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 164 ARG Chi-restraints excluded: chain C residue 61 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 0.2980 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 ASN B 44 ASN B 182 ASN B 236 GLN A 28 ASN A 182 ASN A 236 GLN C 28 ASN C 44 ASN C 182 ASN C 236 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.098423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.073852 restraints weight = 14217.232| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 2.65 r_work: 0.2721 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 7925 Z= 0.209 Angle : 0.679 7.631 10744 Z= 0.359 Chirality : 0.048 0.148 1218 Planarity : 0.004 0.032 1323 Dihedral : 17.150 82.778 1349 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.64 % Allowed : 9.98 % Favored : 89.38 % Rotamer: Outliers : 2.63 % Allowed : 10.65 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.96 (0.25), residues: 942 helix: -1.44 (0.24), residues: 426 sheet: 1.01 (0.44), residues: 150 loop : -3.98 (0.24), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 229 TYR 0.015 0.001 TYR C 41 PHE 0.011 0.002 PHE B 120 HIS 0.003 0.001 HIS C 193 Details of bonding type rmsd covalent geometry : bond 0.00480 ( 7912) covalent geometry : angle 0.67925 (10744) hydrogen bonds : bond 0.03733 ( 308) hydrogen bonds : angle 5.70157 ( 865) Misc. bond : bond 0.00608 ( 13) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 76 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 89 ILE cc_start: 0.9065 (tt) cc_final: 0.8814 (mt) REVERT: B 272 LEU cc_start: 0.6846 (OUTLIER) cc_final: 0.6561 (mp) REVERT: A 41 TYR cc_start: 0.7746 (m-80) cc_final: 0.7463 (m-10) REVERT: A 89 ILE cc_start: 0.9076 (tt) cc_final: 0.8822 (mt) REVERT: A 144 MET cc_start: 0.8558 (mmm) cc_final: 0.8325 (mtt) REVERT: C 231 GLU cc_start: 0.8679 (pt0) cc_final: 0.8462 (pt0) outliers start: 21 outliers final: 10 residues processed: 96 average time/residue: 0.0776 time to fit residues: 10.2456 Evaluate side-chains 70 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 164 ARG Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 314 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 45 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 4 optimal weight: 9.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 HIS A 242 HIS C 242 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.099334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.074671 restraints weight = 14016.913| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 2.66 r_work: 0.2741 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7925 Z= 0.171 Angle : 0.616 8.084 10744 Z= 0.326 Chirality : 0.046 0.140 1218 Planarity : 0.004 0.031 1323 Dihedral : 16.754 82.909 1346 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.13 % Favored : 90.34 % Rotamer: Outliers : 2.63 % Allowed : 13.53 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.33 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.27), residues: 942 helix: -0.40 (0.25), residues: 426 sheet: 1.01 (0.43), residues: 165 loop : -3.81 (0.25), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 229 TYR 0.019 0.001 TYR B 41 PHE 0.009 0.001 PHE B 120 HIS 0.002 0.001 HIS C 193 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 7912) covalent geometry : angle 0.61635 (10744) hydrogen bonds : bond 0.03188 ( 308) hydrogen bonds : angle 4.97871 ( 865) Misc. bond : bond 0.00576 ( 13) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 72 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ILE cc_start: 0.9079 (tt) cc_final: 0.8849 (mt) REVERT: A 247 ASN cc_start: 0.9343 (t0) cc_final: 0.9039 (t0) REVERT: C 144 MET cc_start: 0.8534 (mtt) cc_final: 0.8165 (mtp) outliers start: 21 outliers final: 16 residues processed: 86 average time/residue: 0.0893 time to fit residues: 10.2927 Evaluate side-chains 76 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 164 ARG Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 314 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 63 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.099370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.074598 restraints weight = 14368.889| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 2.72 r_work: 0.2744 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7925 Z= 0.163 Angle : 0.585 4.901 10744 Z= 0.312 Chirality : 0.045 0.141 1218 Planarity : 0.004 0.032 1323 Dihedral : 16.576 83.969 1346 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.66 % Favored : 89.81 % Rotamer: Outliers : 3.76 % Allowed : 14.04 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: -1.59 (0.27), residues: 942 helix: 0.01 (0.26), residues: 426 sheet: 1.05 (0.42), residues: 168 loop : -3.64 (0.25), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 229 TYR 0.018 0.001 TYR A 41 PHE 0.008 0.001 PHE B 120 HIS 0.002 0.001 HIS C 242 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 7912) covalent geometry : angle 0.58517 (10744) hydrogen bonds : bond 0.03000 ( 308) hydrogen bonds : angle 4.74220 ( 865) Misc. bond : bond 0.00565 ( 13) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 69 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 LYS cc_start: 0.8475 (mmtm) cc_final: 0.8237 (mmtm) REVERT: B 296 LEU cc_start: 0.9421 (OUTLIER) cc_final: 0.9138 (tp) REVERT: B 318 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7904 (mptt) REVERT: A 89 ILE cc_start: 0.9091 (tt) cc_final: 0.8868 (mt) REVERT: A 144 MET cc_start: 0.8671 (mtt) cc_final: 0.8471 (mtt) REVERT: A 247 ASN cc_start: 0.9338 (t0) cc_final: 0.9021 (t0) outliers start: 30 outliers final: 21 residues processed: 91 average time/residue: 0.0996 time to fit residues: 11.9087 Evaluate side-chains 86 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 63 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 318 LYS Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 164 ARG Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 314 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 44 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 88 optimal weight: 0.4980 chunk 51 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 HIS A 242 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.101408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.076864 restraints weight = 14263.950| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 2.69 r_work: 0.2777 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7925 Z= 0.135 Angle : 0.560 4.746 10744 Z= 0.299 Chirality : 0.044 0.131 1218 Planarity : 0.004 0.032 1323 Dihedral : 16.290 83.629 1346 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.45 % Favored : 90.02 % Rotamer: Outliers : 3.01 % Allowed : 14.91 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: -1.26 (0.27), residues: 942 helix: 0.26 (0.26), residues: 423 sheet: 1.32 (0.42), residues: 168 loop : -3.46 (0.26), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 164 TYR 0.018 0.001 TYR A 41 PHE 0.007 0.001 PHE B 120 HIS 0.002 0.001 HIS A 289 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 7912) covalent geometry : angle 0.56011 (10744) hydrogen bonds : bond 0.02771 ( 308) hydrogen bonds : angle 4.57948 ( 865) Misc. bond : bond 0.00549 ( 13) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 78 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 LYS cc_start: 0.8491 (mmtm) cc_final: 0.8241 (mmtm) REVERT: B 144 MET cc_start: 0.8715 (mtt) cc_final: 0.8387 (mtm) REVERT: B 251 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8148 (mt-10) REVERT: B 296 LEU cc_start: 0.9415 (OUTLIER) cc_final: 0.9155 (tp) REVERT: B 318 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7859 (mptt) REVERT: A 89 ILE cc_start: 0.9079 (tt) cc_final: 0.8864 (mt) outliers start: 24 outliers final: 17 residues processed: 96 average time/residue: 0.1029 time to fit residues: 12.9774 Evaluate side-chains 84 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 65 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 318 LYS Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 314 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 89 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 71 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 77 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 chunk 56 optimal weight: 0.0670 chunk 79 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 overall best weight: 1.1320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.100714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.075836 restraints weight = 14091.811| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.70 r_work: 0.2762 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7925 Z= 0.139 Angle : 0.557 5.525 10744 Z= 0.296 Chirality : 0.044 0.131 1218 Planarity : 0.004 0.032 1323 Dihedral : 16.256 84.573 1342 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.45 % Favored : 90.02 % Rotamer: Outliers : 3.38 % Allowed : 15.91 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: -1.08 (0.28), residues: 942 helix: 0.32 (0.26), residues: 426 sheet: 1.44 (0.42), residues: 165 loop : -3.24 (0.27), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 124 TYR 0.013 0.001 TYR C 41 PHE 0.008 0.001 PHE B 120 HIS 0.002 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 7912) covalent geometry : angle 0.55724 (10744) hydrogen bonds : bond 0.02800 ( 308) hydrogen bonds : angle 4.49110 ( 865) Misc. bond : bond 0.00546 ( 13) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 73 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 LYS cc_start: 0.8525 (mmtm) cc_final: 0.8268 (mmtm) REVERT: B 104 ASP cc_start: 0.8386 (m-30) cc_final: 0.8065 (m-30) REVERT: B 251 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8116 (mt-10) REVERT: B 296 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.9146 (tp) REVERT: B 318 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7807 (mptt) REVERT: A 89 ILE cc_start: 0.9045 (tt) cc_final: 0.8824 (mt) REVERT: C 34 LYS cc_start: 0.8896 (mtmm) cc_final: 0.8602 (mtmm) outliers start: 27 outliers final: 19 residues processed: 90 average time/residue: 0.1015 time to fit residues: 12.1773 Evaluate side-chains 90 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 69 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 318 LYS Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 314 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 27 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 31 optimal weight: 9.9990 chunk 54 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 16 optimal weight: 7.9990 chunk 80 optimal weight: 0.0980 chunk 49 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.102560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.077746 restraints weight = 14062.230| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 2.65 r_work: 0.2803 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7925 Z= 0.129 Angle : 0.553 5.206 10744 Z= 0.293 Chirality : 0.044 0.129 1218 Planarity : 0.003 0.035 1323 Dihedral : 16.187 84.972 1342 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.13 % Favored : 90.34 % Rotamer: Outliers : 3.63 % Allowed : 15.79 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: -0.94 (0.28), residues: 942 helix: 0.41 (0.26), residues: 426 sheet: 1.45 (0.42), residues: 165 loop : -3.10 (0.28), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 124 TYR 0.007 0.001 TYR C 41 PHE 0.009 0.001 PHE B 253 HIS 0.002 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 7912) covalent geometry : angle 0.55252 (10744) hydrogen bonds : bond 0.02674 ( 308) hydrogen bonds : angle 4.42511 ( 865) Misc. bond : bond 0.00535 ( 13) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 73 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 LYS cc_start: 0.8568 (mmtm) cc_final: 0.8320 (mmtm) REVERT: B 104 ASP cc_start: 0.8342 (m-30) cc_final: 0.8003 (m-30) REVERT: B 251 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8075 (mt-10) REVERT: B 296 LEU cc_start: 0.9428 (OUTLIER) cc_final: 0.9152 (tp) REVERT: B 318 LYS cc_start: 0.8057 (OUTLIER) cc_final: 0.7825 (mptt) REVERT: A 89 ILE cc_start: 0.9052 (tt) cc_final: 0.8827 (mt) REVERT: A 144 MET cc_start: 0.8544 (mtm) cc_final: 0.8179 (mtm) REVERT: C 326 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8044 (tm-30) outliers start: 29 outliers final: 20 residues processed: 93 average time/residue: 0.1009 time to fit residues: 12.4363 Evaluate side-chains 91 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 68 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 318 LYS Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 148 GLU Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 326 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 41 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.102542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.078657 restraints weight = 14175.919| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 2.47 r_work: 0.2800 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7925 Z= 0.138 Angle : 0.552 6.550 10744 Z= 0.292 Chirality : 0.044 0.131 1218 Planarity : 0.003 0.032 1323 Dihedral : 16.173 85.732 1342 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.55 % Favored : 89.92 % Rotamer: Outliers : 3.63 % Allowed : 16.04 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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 (0.28), residues: 942 helix: 0.43 (0.26), residues: 429 sheet: 1.50 (0.42), residues: 165 loop : -3.07 (0.29), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 124 TYR 0.006 0.001 TYR C 41 PHE 0.010 0.001 PHE B 253 HIS 0.002 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 7912) covalent geometry : angle 0.55201 (10744) hydrogen bonds : bond 0.02700 ( 308) hydrogen bonds : angle 4.39320 ( 865) Misc. bond : bond 0.00545 ( 13) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 68 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 LYS cc_start: 0.8549 (mmtm) cc_final: 0.8318 (mmtm) REVERT: B 104 ASP cc_start: 0.8470 (m-30) cc_final: 0.8134 (m-30) REVERT: B 251 GLU cc_start: 0.8731 (mt-10) cc_final: 0.8282 (mt-10) REVERT: B 296 LEU cc_start: 0.9516 (OUTLIER) cc_final: 0.9262 (tp) REVERT: B 318 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7947 (mptt) REVERT: A 89 ILE cc_start: 0.9118 (tt) cc_final: 0.8856 (mt) REVERT: A 144 MET cc_start: 0.8638 (mtm) cc_final: 0.8184 (mtp) REVERT: C 34 LYS cc_start: 0.8732 (mtmm) cc_final: 0.8510 (mtmm) REVERT: C 326 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8158 (tm-30) outliers start: 29 outliers final: 20 residues processed: 89 average time/residue: 0.0961 time to fit residues: 11.3359 Evaluate side-chains 90 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 67 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 318 LYS Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 148 GLU Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 326 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 56 optimal weight: 0.1980 chunk 8 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 overall best weight: 1.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.102196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.078284 restraints weight = 14227.446| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.46 r_work: 0.2804 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7925 Z= 0.143 Angle : 0.557 7.053 10744 Z= 0.295 Chirality : 0.044 0.132 1218 Planarity : 0.003 0.031 1323 Dihedral : 16.183 86.721 1342 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.24 % Favored : 90.23 % Rotamer: Outliers : 3.51 % Allowed : 15.79 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: -0.85 (0.28), residues: 942 helix: 0.46 (0.26), residues: 429 sheet: 1.49 (0.42), residues: 165 loop : -3.04 (0.29), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 124 TYR 0.005 0.001 TYR B 41 PHE 0.009 0.001 PHE B 253 HIS 0.002 0.001 HIS C 242 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 7912) covalent geometry : angle 0.55670 (10744) hydrogen bonds : bond 0.02721 ( 308) hydrogen bonds : angle 4.39567 ( 865) Misc. bond : bond 0.00550 ( 13) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 65 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 LYS cc_start: 0.8596 (mmtm) cc_final: 0.8356 (mmtm) REVERT: B 104 ASP cc_start: 0.8497 (m-30) cc_final: 0.8176 (m-30) REVERT: B 251 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8256 (mt-10) REVERT: B 318 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7953 (mptt) REVERT: A 144 MET cc_start: 0.8582 (mtm) cc_final: 0.8178 (mtp) REVERT: C 34 LYS cc_start: 0.8721 (mtmm) cc_final: 0.8489 (mtmm) REVERT: C 144 MET cc_start: 0.8602 (mtm) cc_final: 0.8329 (mtm) REVERT: C 326 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8165 (tm-30) outliers start: 28 outliers final: 19 residues processed: 86 average time/residue: 0.0927 time to fit residues: 10.7976 Evaluate side-chains 86 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 65 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 318 LYS Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 326 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 34 optimal weight: 1.9990 chunk 81 optimal weight: 0.2980 chunk 33 optimal weight: 0.9980 chunk 19 optimal weight: 0.0970 chunk 46 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 chunk 79 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 2 optimal weight: 8.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.103910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.079389 restraints weight = 14122.328| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.67 r_work: 0.2829 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7925 Z= 0.114 Angle : 0.546 7.601 10744 Z= 0.287 Chirality : 0.043 0.130 1218 Planarity : 0.003 0.032 1323 Dihedral : 16.040 85.359 1342 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.53 % Allowed : 8.92 % Favored : 90.55 % Rotamer: Outliers : 2.51 % Allowed : 16.79 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: -0.69 (0.28), residues: 942 helix: 0.58 (0.26), residues: 429 sheet: 1.60 (0.42), residues: 159 loop : -2.88 (0.29), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 124 TYR 0.005 0.001 TYR B 41 PHE 0.009 0.001 PHE B 253 HIS 0.002 0.000 HIS A 289 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 7912) covalent geometry : angle 0.54637 (10744) hydrogen bonds : bond 0.02521 ( 308) hydrogen bonds : angle 4.27096 ( 865) Misc. bond : bond 0.00533 ( 13) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 LYS cc_start: 0.8618 (mmtm) cc_final: 0.8397 (mmtm) REVERT: B 104 ASP cc_start: 0.8395 (m-30) cc_final: 0.8037 (m-30) REVERT: A 56 LYS cc_start: 0.8650 (mmtm) cc_final: 0.8414 (mmtm) REVERT: A 144 MET cc_start: 0.8515 (mtm) cc_final: 0.8166 (mtp) REVERT: C 240 ASN cc_start: 0.9497 (t0) cc_final: 0.9200 (t0) outliers start: 20 outliers final: 15 residues processed: 90 average time/residue: 0.1031 time to fit residues: 12.2454 Evaluate side-chains 85 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 314 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 64 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 68 optimal weight: 9.9990 chunk 63 optimal weight: 9.9990 chunk 14 optimal weight: 0.6980 chunk 78 optimal weight: 0.3980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 HIS C 167 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.104123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.080234 restraints weight = 14183.327| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 2.48 r_work: 0.2840 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7925 Z= 0.124 Angle : 0.560 7.701 10744 Z= 0.295 Chirality : 0.043 0.130 1218 Planarity : 0.003 0.031 1323 Dihedral : 16.022 85.467 1342 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.53 % Allowed : 8.81 % Favored : 90.66 % Rotamer: Outliers : 2.26 % Allowed : 17.42 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: -0.70 (0.28), residues: 942 helix: 0.58 (0.26), residues: 429 sheet: 1.60 (0.42), residues: 159 loop : -2.90 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 124 TYR 0.005 0.001 TYR A 41 PHE 0.008 0.001 PHE B 253 HIS 0.002 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 7912) covalent geometry : angle 0.56025 (10744) hydrogen bonds : bond 0.02587 ( 308) hydrogen bonds : angle 4.23375 ( 865) Misc. bond : bond 0.00541 ( 13) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1618.58 seconds wall clock time: 28 minutes 28.93 seconds (1708.93 seconds total)