Starting phenix.real_space_refine on Fri Sep 11 05:21:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ej7_31154/09_2026/7ej7_31154_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ej7_31154/09_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_31154/09_2026/7ej7_31154.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ej7_31154/09_2026/7ej7_31154.map" model { file = "/net/cci-nas-00/data/ceres_data/7ej7_31154/09_2026/7ej7_31154_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ej7_31154/09_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-2.2.1-6174/lib/python3.11/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: 1.82, per 1000 atoms: 0.23 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: 0.84 Conformation dependent library (CDL) restraints added in 382.2 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: 0.75 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: 1.17 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: 833 0.037 - 0.074: 262 0.074 - 0.111: 91 0.111 - 0.147: 26 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: 3.330 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.190 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 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= 1.072 Angle : 0.930 18.124 10744 Z= 0.714 Chirality : 0.044 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/Z covalent geometry : bond 0.00631 / 0.45 ( 7912) covalent geometry : angle 0.92959 / 0.71 (10744) hydrogen bonds : bond 0.18053 / 12.04 ( 308) hydrogen bonds : angle 9.03162 / 6.06 ( 865) Misc. bond : bond 0.24084 / 9.96 ( 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 : 0.287 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: 0.1044 time to fit residues: 15.4147 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 : 0.270 ------------------------------------------------------------------------------- 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... B 44 ASN B 182 ASN B 236 GLN 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.097928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.073479 restraints weight = 14226.554| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 2.62 r_work: 0.2720 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 7925 Z= 0.221 Angle : 0.725 7.271 10744 Z= 0.387 Chirality : 0.048 0.158 1218 Planarity : 0.005 0.037 1323 Dihedral : 17.772 84.549 1349 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.96 % Allowed : 9.66 % Favored : 89.38 % Rotamer: Outliers : 2.76 % Allowed : 10.03 % Favored : 87.22 % 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: -2.98 (0.25), residues: 942 helix: -1.47 (0.23), residues: 426 sheet: 1.17 (0.45), residues: 150 loop : -4.05 (0.24), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 164 TYR 0.015 0.001 TYR C 41 PHE 0.010 0.002 PHE A 160 HIS 0.003 0.001 HIS C 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.22 ( 7912) covalent geometry : angle 0.72462 / 0.39 (10744) hydrogen bonds : bond 0.04284 / 2.80 ( 308) hydrogen bonds : angle 5.85765 / 3.87 ( 865) Misc. bond : bond 0.00752 / 0.44 ( 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 95 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 73 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 61 SER cc_start: 0.6505 (OUTLIER) cc_final: 0.6266 (p) REVERT: B 144 MET cc_start: 0.8520 (mmt) cc_final: 0.8201 (mtt) REVERT: B 252 GLU cc_start: 0.8572 (pt0) cc_final: 0.8364 (tt0) REVERT: B 254 ASN cc_start: 0.9484 (t0) cc_final: 0.9155 (t0) REVERT: A 89 ILE cc_start: 0.9068 (tt) cc_final: 0.8810 (mt) REVERT: A 144 MET cc_start: 0.8543 (mmm) cc_final: 0.8335 (mtt) REVERT: C 89 ILE cc_start: 0.9114 (tt) cc_final: 0.8787 (mt) REVERT: C 112 MET cc_start: 0.9245 (mmm) cc_final: 0.8999 (mmm) REVERT: C 252 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8143 (tt0) outliers start: 22 outliers final: 10 residues processed: 93 average time/residue: 0.0899 time to fit residues: 11.6893 Evaluate side-chains 73 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 61 SER 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 252 GLU 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: 1.9990 chunk 9 optimal weight: 0.3980 chunk 91 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 62 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 78 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 84 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 28 ASN A 28 ASN C 241 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.099636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.075036 restraints weight = 14099.506| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 2.68 r_work: 0.2747 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7925 Z= 0.150 Angle : 0.611 5.592 10744 Z= 0.331 Chirality : 0.045 0.148 1218 Planarity : 0.004 0.030 1323 Dihedral : 16.941 83.357 1348 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.64 % Allowed : 9.45 % Favored : 89.92 % Rotamer: Outliers : 3.01 % Allowed : 11.15 % Favored : 85.84 % 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: -2.10 (0.26), residues: 942 helix: -0.55 (0.25), residues: 426 sheet: 1.18 (0.42), residues: 159 loop : -3.78 (0.25), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 229 TYR 0.027 0.001 TYR A 41 PHE 0.012 0.001 PHE B 160 HIS 0.003 0.001 HIS B 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.15 ( 7912) covalent geometry : angle 0.61069 / 0.33 (10744) hydrogen bonds : bond 0.03460 / 2.30 ( 308) hydrogen bonds : angle 5.17531 / 3.42 ( 865) Misc. bond : bond 0.00680 / 0.43 ( 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: 24 poor density : 69 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 144 MET cc_start: 0.8563 (mmt) cc_final: 0.8331 (mtt) REVERT: B 227 CYS cc_start: 0.8603 (p) cc_final: 0.8384 (m) REVERT: B 296 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.9190 (tp) REVERT: A 89 ILE cc_start: 0.9116 (tt) cc_final: 0.8881 (mt) REVERT: A 144 MET cc_start: 0.8520 (mmm) cc_final: 0.8296 (mtt) REVERT: C 89 ILE cc_start: 0.9111 (tt) cc_final: 0.8848 (mt) outliers start: 24 outliers final: 14 residues processed: 91 average time/residue: 0.0943 time to fit residues: 11.8872 Evaluate side-chains 78 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.309 ------------------------------------------------------------------------------- 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 296 LEU Chi-restraints excluded: chain A residue 50 THR 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 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: 3.9990 chunk 52 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3319 r_free = 0.3319 target = 0.099108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.074232 restraints weight = 14328.641| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 2.70 r_work: 0.2732 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7925 Z= 0.167 Angle : 0.598 5.506 10744 Z= 0.322 Chirality : 0.045 0.137 1218 Planarity : 0.004 0.030 1323 Dihedral : 16.790 82.684 1346 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.64 % Allowed : 10.08 % Favored : 89.28 % Rotamer: Outliers : 2.51 % Allowed : 13.53 % Favored : 83.96 % 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: -1.73 (0.27), residues: 942 helix: -0.16 (0.25), residues: 426 sheet: 1.36 (0.42), residues: 165 loop : -3.80 (0.24), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 229 TYR 0.018 0.001 TYR B 185 PHE 0.011 0.001 PHE C 253 HIS 0.002 0.001 HIS A 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 ( 7912) covalent geometry : angle 0.59778 / 0.32 (10744) hydrogen bonds : bond 0.03310 / 2.21 ( 308) hydrogen bonds : angle 4.91605 / 3.25 ( 865) Misc. bond : bond 0.00587 / 0.39 ( 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 85 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 65 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 196 GLU cc_start: 0.8906 (mm-30) cc_final: 0.8453 (tp30) REVERT: B 296 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.9177 (tp) REVERT: A 41 TYR cc_start: 0.7628 (m-10) cc_final: 0.7172 (m-10) REVERT: A 144 MET cc_start: 0.8542 (mmm) cc_final: 0.8331 (mtt) REVERT: C 89 ILE cc_start: 0.9140 (tt) cc_final: 0.8874 (mt) REVERT: C 144 MET cc_start: 0.8442 (mtt) cc_final: 0.7959 (mtp) outliers start: 20 outliers final: 16 residues processed: 81 average time/residue: 0.1031 time to fit residues: 11.3743 Evaluate side-chains 75 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 58 time to evaluate : 0.255 ------------------------------------------------------------------------------- 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 296 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 212 LEU 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 44 optimal weight: 7.9990 chunk 52 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 35 optimal weight: 10.0000 chunk 37 optimal weight: 0.0270 chunk 60 optimal weight: 7.9990 chunk 73 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 overall best weight: 0.7438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 242 HIS A 242 HIS C 241 GLN C 242 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.100471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.075556 restraints weight = 14120.171| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 2.68 r_work: 0.2755 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7925 Z= 0.130 Angle : 0.579 5.578 10744 Z= 0.312 Chirality : 0.044 0.146 1218 Planarity : 0.004 0.030 1323 Dihedral : 16.512 81.466 1346 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.02 % Favored : 90.45 % Rotamer: Outliers : 3.01 % Allowed : 14.16 % Favored : 82.83 % 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: -1.46 (0.27), residues: 942 helix: 0.05 (0.25), residues: 426 sheet: 1.45 (0.42), residues: 165 loop : -3.61 (0.25), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 229 TYR 0.013 0.001 TYR B 41 PHE 0.007 0.001 PHE B 160 HIS 0.002 0.001 HIS A 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 ( 7912) covalent geometry : angle 0.57912 / 0.31 (10744) hydrogen bonds : bond 0.03035 / 2.07 ( 308) hydrogen bonds : angle 4.73889 / 3.12 ( 865) Misc. bond : bond 0.00548 / 0.37 ( 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 89 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 65 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 196 GLU cc_start: 0.8887 (mm-30) cc_final: 0.8358 (tp30) REVERT: B 296 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.9152 (tp) REVERT: A 41 TYR cc_start: 0.7594 (m-80) cc_final: 0.7093 (m-10) REVERT: C 144 MET cc_start: 0.8428 (mtt) cc_final: 0.7972 (mtp) outliers start: 24 outliers final: 20 residues processed: 83 average time/residue: 0.1008 time to fit residues: 11.3924 Evaluate side-chains 77 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 56 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 212 LEU Chi-restraints excluded: chain B residue 296 LEU 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 216 ASP 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 A residue 324 ILE Chi-restraints excluded: chain C residue 50 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 89 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 57 optimal weight: 0.0270 chunk 71 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 overall best weight: 1.6044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3319 r_free = 0.3319 target = 0.099151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.074268 restraints weight = 14199.746| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 2.69 r_work: 0.2734 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7925 Z= 0.168 Angle : 0.582 5.270 10744 Z= 0.312 Chirality : 0.045 0.138 1218 Planarity : 0.004 0.030 1323 Dihedral : 16.549 81.175 1346 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.77 % Favored : 89.70 % Rotamer: Outliers : 3.38 % Allowed : 14.29 % Favored : 82.33 % 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: -1.32 (0.27), residues: 942 helix: 0.17 (0.25), residues: 426 sheet: 1.42 (0.43), residues: 165 loop : -3.50 (0.25), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 229 TYR 0.011 0.001 TYR B 185 PHE 0.008 0.001 PHE B 120 HIS 0.002 0.001 HIS A 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 ( 7912) covalent geometry : angle 0.58181 / 0.31 (10744) hydrogen bonds : bond 0.03043 / 2.05 ( 308) hydrogen bonds : angle 4.68005 / 3.10 ( 865) Misc. bond : bond 0.00570 / 0.38 ( 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 87 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 60 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 196 GLU cc_start: 0.8884 (mm-30) cc_final: 0.8356 (tp30) REVERT: B 296 LEU cc_start: 0.9422 (OUTLIER) cc_final: 0.9159 (tp) REVERT: C 144 MET cc_start: 0.8497 (mtt) cc_final: 0.8090 (mtp) outliers start: 27 outliers final: 24 residues processed: 83 average time/residue: 0.0950 time to fit residues: 11.0141 Evaluate side-chains 81 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 56 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 93 VAL 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 231 GLU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain A residue 50 THR 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 216 ASP 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 A residue 324 ILE Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 106 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 27 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3319 r_free = 0.3319 target = 0.099521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.074724 restraints weight = 14138.227| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 2.68 r_work: 0.2720 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7925 Z= 0.176 Angle : 0.581 5.307 10744 Z= 0.312 Chirality : 0.045 0.137 1218 Planarity : 0.004 0.030 1323 Dihedral : 16.544 81.673 1346 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.66 % Favored : 89.81 % Rotamer: Outliers : 3.88 % Allowed : 15.54 % 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: -1.17 (0.27), residues: 942 helix: 0.27 (0.26), residues: 426 sheet: 1.37 (0.43), residues: 165 loop : -3.33 (0.27), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 229 TYR 0.019 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/Z covalent geometry : bond 0.00390 / 0.17 ( 7912) covalent geometry : angle 0.58100 / 0.31 (10744) hydrogen bonds : bond 0.03094 / 2.08 ( 308) hydrogen bonds : angle 4.64820 / 3.08 ( 865) Misc. bond : bond 0.00572 / 0.39 ( 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 85 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 54 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 196 GLU cc_start: 0.8870 (mm-30) cc_final: 0.8341 (tp30) REVERT: B 296 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.9117 (tp) REVERT: A 144 MET cc_start: 0.8544 (mtt) cc_final: 0.8327 (mtm) REVERT: C 104 ASP cc_start: 0.8156 (m-30) cc_final: 0.7446 (m-30) REVERT: C 231 GLU cc_start: 0.8865 (pt0) cc_final: 0.8552 (pt0) outliers start: 31 outliers final: 25 residues processed: 78 average time/residue: 0.0924 time to fit residues: 10.0920 Evaluate side-chains 81 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 55 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 93 VAL 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 231 GLU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 324 ILE 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 216 ASP 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 A residue 324 ILE Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 106 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 41 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 17 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 242 HIS A 167 GLN A 242 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.097642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.072688 restraints weight = 14306.964| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 2.66 r_work: 0.2704 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 7925 Z= 0.228 Angle : 0.610 4.787 10744 Z= 0.325 Chirality : 0.046 0.138 1218 Planarity : 0.004 0.033 1323 Dihedral : 16.690 81.983 1346 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.98 % Favored : 89.49 % Rotamer: Outliers : 4.01 % Allowed : 15.41 % 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: -1.15 (0.28), residues: 942 helix: 0.32 (0.26), residues: 426 sheet: 1.09 (0.43), residues: 168 loop : -3.22 (0.28), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 229 TYR 0.018 0.001 TYR A 41 PHE 0.009 0.001 PHE B 120 HIS 0.002 0.001 HIS A 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.23 ( 7912) covalent geometry : angle 0.60971 / 0.33 (10744) hydrogen bonds : bond 0.03284 / 2.19 ( 308) hydrogen bonds : angle 4.70492 / 3.13 ( 865) Misc. bond : bond 0.00593 / 0.40 ( 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 85 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 53 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 196 GLU cc_start: 0.8910 (mm-30) cc_final: 0.8389 (tp30) REVERT: A 144 MET cc_start: 0.8582 (mtt) cc_final: 0.8335 (mpp) REVERT: C 231 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8472 (pt0) outliers start: 32 outliers final: 26 residues processed: 79 average time/residue: 0.0896 time to fit residues: 9.9755 Evaluate side-chains 80 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 53 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 93 VAL 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 231 GLU Chi-restraints excluded: chain B residue 314 ASP 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 216 ASP 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 A residue 324 ILE Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 231 GLU Chi-restraints excluded: chain C residue 314 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 56 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 76 optimal weight: 0.0970 chunk 53 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 242 HIS A 242 HIS C 167 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.099587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.074669 restraints weight = 14239.963| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 2.70 r_work: 0.2733 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7925 Z= 0.135 Angle : 0.569 7.562 10744 Z= 0.305 Chirality : 0.044 0.143 1218 Planarity : 0.004 0.031 1323 Dihedral : 16.449 82.154 1346 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.55 % Favored : 89.92 % Rotamer: Outliers : 3.26 % Allowed : 16.42 % 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: -1.00 (0.28), residues: 942 helix: 0.37 (0.26), residues: 429 sheet: 1.15 (0.42), residues: 168 loop : -3.05 (0.29), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 164 TYR 0.018 0.001 TYR B 41 PHE 0.007 0.001 PHE B 120 HIS 0.002 0.001 HIS B 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 ( 7912) covalent geometry : angle 0.56920 / 0.30 (10744) hydrogen bonds : bond 0.02953 / 2.00 ( 308) hydrogen bonds : angle 4.58398 / 3.04 ( 865) Misc. bond : bond 0.00573 / 0.38 ( 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 82 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 56 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 231 GLU cc_start: 0.8821 (pt0) cc_final: 0.8484 (pt0) outliers start: 26 outliers final: 23 residues processed: 75 average time/residue: 0.0880 time to fit residues: 9.2378 Evaluate side-chains 75 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 52 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 212 LEU Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 314 ASP 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 312 SER Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 144 MET 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 34 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 19 optimal weight: 0.2980 chunk 46 optimal weight: 0.9990 chunk 91 optimal weight: 0.0870 chunk 79 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 2 optimal weight: 0.0270 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3357 r_free = 0.3357 target = 0.101882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.077385 restraints weight = 14087.663| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 2.67 r_work: 0.2774 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7925 Z= 0.118 Angle : 0.568 7.679 10744 Z= 0.301 Chirality : 0.044 0.173 1218 Planarity : 0.003 0.032 1323 Dihedral : 16.245 80.822 1346 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.66 % Favored : 89.81 % Rotamer: Outliers : 2.88 % Allowed : 16.79 % 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: -0.84 (0.28), residues: 942 helix: 0.49 (0.26), residues: 426 sheet: 1.27 (0.42), residues: 165 loop : -2.92 (0.29), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 164 TYR 0.010 0.001 TYR B 185 PHE 0.006 0.001 PHE A 120 HIS 0.002 0.001 HIS C 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.12 ( 7912) covalent geometry : angle 0.56818 / 0.30 (10744) hydrogen bonds : bond 0.02754 / 1.88 ( 308) hydrogen bonds : angle 4.47094 / 2.97 ( 865) Misc. bond : bond 0.00551 / 0.37 ( 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 86 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 63 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 MET cc_start: 0.8593 (mtm) cc_final: 0.8275 (mtm) REVERT: C 231 GLU cc_start: 0.8743 (pt0) cc_final: 0.8405 (pt0) outliers start: 23 outliers final: 20 residues processed: 80 average time/residue: 0.1051 time to fit residues: 11.4358 Evaluate side-chains 73 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 53 time to evaluate : 0.307 ------------------------------------------------------------------------------- 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 231 GLU Chi-restraints excluded: chain B residue 314 ASP 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 312 SER Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 106 ILE 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: 7.9990 chunk 33 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 79 optimal weight: 5.9990 chunk 68 optimal weight: 0.4980 chunk 63 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 242 HIS A 242 HIS C 241 GLN C 242 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.100293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.075440 restraints weight = 14155.380| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 2.68 r_work: 0.2754 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7925 Z= 0.145 Angle : 0.571 7.566 10744 Z= 0.303 Chirality : 0.044 0.257 1218 Planarity : 0.004 0.032 1323 Dihedral : 16.246 80.566 1346 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.55 % Favored : 89.92 % Rotamer: Outliers : 2.63 % Allowed : 16.92 % Favored : 80.45 % 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: -0.86 (0.28), residues: 942 helix: 0.50 (0.26), residues: 429 sheet: 1.28 (0.42), residues: 168 loop : -3.03 (0.29), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 124 TYR 0.015 0.001 TYR B 41 PHE 0.010 0.001 PHE B 123 HIS 0.002 0.001 HIS C 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 7912) covalent geometry : angle 0.57117 / 0.30 (10744) hydrogen bonds : bond 0.02820 / 1.92 ( 308) hydrogen bonds : angle 4.45804 / 2.96 ( 865) Misc. bond : bond 0.00549 / 0.37 ( 13) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1633.33 seconds wall clock time: 28 minutes 57.18 seconds (1737.18 seconds total)