Starting phenix.real_space_refine on Thu Jul 2 08:37:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ej7_31154/07_2026/7ej7_31154_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ej7_31154/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/7ej7_31154/07_2026/7ej7_31154_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ej7_31154/07_2026/7ej7_31154_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ej7_31154/07_2026/7ej7_31154.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ej7_31154/07_2026/7ej7_31154.map" } 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-6108/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: 1.49, per 1000 atoms: 0.19 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: 0.70 Conformation dependent library (CDL) restraints added in 322.6 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: 0.96 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: 1.25 Time building geometry restraints manager: 0.84 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: 3.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.830 Find NCS groups from input model: 0.160 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.510 ------------------------------------------------------------------------------- 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 : 0.929 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 0.92944 / 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 : 0.260 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: 0.0882 time to fit residues: 13.1701 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 : 0.273 ------------------------------------------------------------------------------- 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 = 0.3303 r_free = 0.3303 target = 0.098097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.073481 restraints weight = 14114.799| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 2.64 r_work: 0.2718 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 7925 Z= 0.219 Angle : 0.720 7.067 10744 Z= 0.385 Chirality : 0.048 0.163 1218 Planarity : 0.005 0.036 1323 Dihedral : 17.864 85.427 1349 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.96 % Allowed : 9.55 % Favored : 89.49 % Rotamer: Outliers : 2.76 % Allowed : 9.52 % Favored : 87.72 % 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: -3.08 (0.25), residues: 942 helix: -1.55 (0.23), residues: 426 sheet: 1.10 (0.45), residues: 150 loop : -4.11 (0.24), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 164 TYR 0.014 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 0.72012 / 0.39 (10744) hydrogen bonds : bond 0.04492 / 2.94 ( 308) hydrogen bonds : angle 5.95020 / 3.93 ( 865) Misc. bond : bond 0.00610 / 0.40 ( 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 : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 61 SER cc_start: 0.6511 (OUTLIER) cc_final: 0.6278 (p) REVERT: B 89 ILE cc_start: 0.9110 (tt) cc_final: 0.8900 (mt) REVERT: B 144 MET cc_start: 0.8559 (mmt) cc_final: 0.8221 (mtt) REVERT: B 254 ASN cc_start: 0.9488 (t0) cc_final: 0.9151 (t0) REVERT: A 89 ILE cc_start: 0.9143 (tt) cc_final: 0.8870 (mt) REVERT: A 144 MET cc_start: 0.8551 (mmm) cc_final: 0.8327 (mtt) REVERT: C 89 ILE cc_start: 0.9126 (tt) cc_final: 0.8806 (mt) REVERT: C 112 MET cc_start: 0.9264 (mmm) cc_final: 0.9027 (mmm) REVERT: C 252 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8159 (tt0) outliers start: 22 outliers final: 9 residues processed: 93 average time/residue: 0.0729 time to fit residues: 9.4324 Evaluate side-chains 74 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.224 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 9 optimal weight: 0.8980 chunk 91 optimal weight: 7.9990 chunk 45 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 78 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 84 optimal weight: 0.9980 chunk 4 optimal weight: 9.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 28 ASN A 28 ASN 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 = 0.3301 r_free = 0.3301 target = 0.098144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.073473 restraints weight = 14142.725| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 2.63 r_work: 0.2712 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 7925 Z= 0.204 Angle : 0.636 5.337 10744 Z= 0.344 Chirality : 0.046 0.148 1218 Planarity : 0.004 0.031 1323 Dihedral : 17.143 84.235 1347 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.64 % Allowed : 9.87 % Favored : 89.49 % Rotamer: Outliers : 2.88 % Allowed : 11.78 % Favored : 85.34 % 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: -2.27 (0.26), residues: 942 helix: -0.71 (0.24), residues: 426 sheet: 1.07 (0.43), residues: 159 loop : -3.83 (0.25), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 229 TYR 0.014 0.001 TYR C 41 PHE 0.011 0.001 PHE B 160 HIS 0.003 0.001 HIS C 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.20 ( 7912) covalent geometry : angle 0.63629 / 0.34 (10744) hydrogen bonds : bond 0.03759 / 2.49 ( 308) hydrogen bonds : angle 5.33263 / 3.52 ( 865) Misc. bond : bond 0.00612 / 0.41 ( 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 87 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 64 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 227 CYS cc_start: 0.8666 (p) cc_final: 0.8414 (m) REVERT: B 296 LEU cc_start: 0.9422 (OUTLIER) cc_final: 0.9186 (tp) REVERT: A 89 ILE cc_start: 0.9068 (tt) cc_final: 0.8854 (mt) REVERT: A 144 MET cc_start: 0.8541 (mmm) cc_final: 0.8310 (mtt) REVERT: C 89 ILE cc_start: 0.9114 (tt) cc_final: 0.8853 (mt) outliers start: 23 outliers final: 15 residues processed: 85 average time/residue: 0.0866 time to fit residues: 10.1777 Evaluate side-chains 74 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 0.218 ------------------------------------------------------------------------------- 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 B residue 314 ASP 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: 0.8980 chunk 52 optimal weight: 0.6980 chunk 14 optimal weight: 0.0770 chunk 53 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 chunk 91 optimal weight: 8.9990 overall best weight: 0.8540 ------------------------------------------------------------------------------- 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 = 0.3331 r_free = 0.3331 target = 0.099880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.075202 restraints weight = 14238.192| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 2.67 r_work: 0.2749 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7925 Z= 0.138 Angle : 0.591 5.474 10744 Z= 0.319 Chirality : 0.044 0.148 1218 Planarity : 0.004 0.030 1323 Dihedral : 16.735 83.615 1346 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.66 % Favored : 89.81 % Rotamer: Outliers : 3.26 % Allowed : 12.91 % Favored : 83.83 % 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: -1.70 (0.27), residues: 942 helix: -0.15 (0.25), residues: 426 sheet: 1.32 (0.42), residues: 165 loop : -3.73 (0.25), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 294 TYR 0.014 0.001 TYR A 41 PHE 0.013 0.001 PHE C 253 HIS 0.002 0.001 HIS B 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.14 ( 7912) covalent geometry : angle 0.59126 / 0.32 (10744) hydrogen bonds : bond 0.03202 / 2.14 ( 308) hydrogen bonds : angle 4.91904 / 3.25 ( 865) Misc. bond : bond 0.00572 / 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 99 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 73 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 296 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9156 (tp) REVERT: A 41 TYR cc_start: 0.7603 (m-10) cc_final: 0.7184 (m-10) REVERT: A 144 MET cc_start: 0.8553 (mmm) cc_final: 0.8337 (mtt) REVERT: C 89 ILE cc_start: 0.9104 (tt) cc_final: 0.8838 (mt) REVERT: C 144 MET cc_start: 0.8447 (mtt) cc_final: 0.7976 (mtp) REVERT: C 318 LYS cc_start: 0.8657 (mttt) cc_final: 0.8448 (mttp) outliers start: 26 outliers final: 17 residues processed: 93 average time/residue: 0.0961 time to fit residues: 12.0673 Evaluate side-chains 77 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 0.311 ------------------------------------------------------------------------------- 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 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 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: 0.0980 chunk 52 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 35 optimal weight: 10.0000 chunk 37 optimal weight: 7.9990 chunk 60 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 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 = 0.3327 r_free = 0.3327 target = 0.099584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.074620 restraints weight = 14216.470| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 2.68 r_work: 0.2738 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7925 Z= 0.148 Angle : 0.578 5.575 10744 Z= 0.312 Chirality : 0.044 0.152 1218 Planarity : 0.004 0.031 1323 Dihedral : 16.616 82.714 1346 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.55 % Favored : 89.92 % Rotamer: Outliers : 3.38 % Allowed : 14.16 % Favored : 82.46 % 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: -1.44 (0.27), residues: 942 helix: 0.05 (0.25), residues: 426 sheet: 1.42 (0.43), residues: 165 loop : -3.57 (0.25), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 229 TYR 0.019 0.001 TYR B 185 PHE 0.010 0.001 PHE B 160 HIS 0.002 0.001 HIS A 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 ( 7912) covalent geometry : angle 0.57822 / 0.31 (10744) hydrogen bonds : bond 0.03125 / 2.11 ( 308) hydrogen bonds : angle 4.76929 / 3.15 ( 865) Misc. bond : bond 0.00570 / 0.38 ( 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 88 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 61 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 296 LEU cc_start: 0.9404 (OUTLIER) cc_final: 0.9166 (tp) REVERT: C 106 ILE cc_start: 0.9087 (OUTLIER) cc_final: 0.8827 (pt) REVERT: C 144 MET cc_start: 0.8479 (mtt) cc_final: 0.8069 (mtp) outliers start: 27 outliers final: 21 residues processed: 81 average time/residue: 0.0902 time to fit residues: 10.0648 Evaluate side-chains 79 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 56 time to evaluate : 0.291 ------------------------------------------------------------------------------- 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 89 optimal weight: 0.0000 chunk 30 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 77 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 overall best weight: 0.7184 ------------------------------------------------------------------------------- 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 = 0.3341 r_free = 0.3341 target = 0.100521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.075610 restraints weight = 14072.625| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 2.68 r_work: 0.2767 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.2770 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= 0.125 Angle : 0.560 5.340 10744 Z= 0.302 Chirality : 0.044 0.134 1218 Planarity : 0.004 0.030 1323 Dihedral : 16.423 81.528 1346 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.45 % Favored : 90.02 % Rotamer: Outliers : 3.26 % Allowed : 14.41 % 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: -1.23 (0.27), residues: 942 helix: 0.23 (0.26), residues: 426 sheet: 1.51 (0.43), residues: 165 loop : -3.45 (0.25), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 92 TYR 0.019 0.001 TYR A 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 0.00253 / 0.12 ( 7912) covalent geometry : angle 0.56021 / 0.30 (10744) hydrogen bonds : bond 0.02880 / 1.95 ( 308) hydrogen bonds : angle 4.61790 / 3.04 ( 865) Misc. bond : bond 0.00542 / 0.37 ( 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 92 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 66 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 296 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.9168 (tp) REVERT: C 144 MET cc_start: 0.8455 (mtt) cc_final: 0.8056 (mtp) outliers start: 26 outliers final: 21 residues processed: 85 average time/residue: 0.0971 time to fit residues: 11.2095 Evaluate side-chains 77 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 55 time to evaluate : 0.295 ------------------------------------------------------------------------------- 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 296 LEU Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 324 ILE 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 A residue 324 ILE 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=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: 5.9990 chunk 31 optimal weight: 10.0000 chunk 54 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3339 r_free = 0.3339 target = 0.100309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.075356 restraints weight = 14041.130| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 2.67 r_work: 0.2764 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7925 Z= 0.140 Angle : 0.563 6.200 10744 Z= 0.302 Chirality : 0.044 0.132 1218 Planarity : 0.004 0.030 1323 Dihedral : 16.430 81.019 1346 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.66 % Favored : 89.81 % Rotamer: Outliers : 3.01 % Allowed : 15.41 % Favored : 81.58 % 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: -1.13 (0.27), residues: 942 helix: 0.31 (0.26), residues: 426 sheet: 1.47 (0.43), residues: 165 loop : -3.36 (0.26), residues: 351 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 0.009 0.001 PHE A 123 HIS 0.002 0.001 HIS A 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 ( 7912) covalent geometry : angle 0.56252 / 0.30 (10744) hydrogen bonds : bond 0.02911 / 1.96 ( 308) hydrogen bonds : angle 4.58368 / 3.02 ( 865) Misc. bond : bond 0.00548 / 0.37 ( 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 80 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 56 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 296 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.9162 (tp) REVERT: C 104 ASP cc_start: 0.8069 (m-30) cc_final: 0.7343 (m-30) REVERT: C 231 GLU cc_start: 0.8802 (pt0) cc_final: 0.8512 (pt0) outliers start: 24 outliers final: 20 residues processed: 76 average time/residue: 0.0879 time to fit residues: 9.3941 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 : 0.291 ------------------------------------------------------------------------------- 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 296 LEU Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 324 ILE 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 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 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: 1.9990 chunk 61 optimal weight: 2.9990 chunk 38 optimal weight: 0.0670 chunk 26 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 54 optimal weight: 0.9990 chunk 85 optimal weight: 0.0980 chunk 2 optimal weight: 0.3980 chunk 17 optimal weight: 3.9990 overall best weight: 0.7122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 242 HIS A 167 GLN A 242 HIS C 241 GLN C 242 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.101059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.076102 restraints weight = 14103.041| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 2.69 r_work: 0.2771 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7925 Z= 0.122 Angle : 0.553 6.818 10744 Z= 0.296 Chirality : 0.043 0.132 1218 Planarity : 0.003 0.030 1323 Dihedral : 16.295 80.491 1346 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.45 % Favored : 90.02 % Rotamer: Outliers : 3.13 % Allowed : 15.66 % Favored : 81.20 % 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: -0.98 (0.28), residues: 942 helix: 0.40 (0.26), residues: 426 sheet: 1.50 (0.43), residues: 165 loop : -3.20 (0.27), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 142 TYR 0.019 0.001 TYR B 41 PHE 0.007 0.001 PHE B 253 HIS 0.002 0.001 HIS A 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 ( 7912) covalent geometry : angle 0.55334 / 0.30 (10744) hydrogen bonds : bond 0.02809 / 1.91 ( 308) hydrogen bonds : angle 4.49566 / 2.97 ( 865) Misc. bond : bond 0.00543 / 0.37 ( 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 88 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 63 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 296 LEU cc_start: 0.9405 (OUTLIER) cc_final: 0.9170 (tp) REVERT: A 144 MET cc_start: 0.8598 (mtm) cc_final: 0.8160 (mtm) REVERT: C 104 ASP cc_start: 0.8097 (m-30) cc_final: 0.7362 (m-30) REVERT: C 231 GLU cc_start: 0.8751 (pt0) cc_final: 0.8444 (pt0) outliers start: 25 outliers final: 21 residues processed: 82 average time/residue: 0.0870 time to fit residues: 10.0231 Evaluate side-chains 80 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 58 time to evaluate : 0.306 ------------------------------------------------------------------------------- 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 296 LEU Chi-restraints excluded: chain B residue 314 ASP 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 56 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 76 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 242 HIS A 242 HIS C 167 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 = 0.3302 r_free = 0.3302 target = 0.098245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.073149 restraints weight = 14331.499| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 2.67 r_work: 0.2707 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 7925 Z= 0.228 Angle : 0.605 6.783 10744 Z= 0.322 Chirality : 0.046 0.148 1218 Planarity : 0.004 0.033 1323 Dihedral : 16.502 81.856 1346 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.98 % Favored : 89.49 % Rotamer: Outliers : 3.63 % Allowed : 15.29 % Favored : 81.08 % 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: -0.98 (0.28), residues: 942 helix: 0.44 (0.26), residues: 426 sheet: 1.17 (0.42), residues: 168 loop : -3.10 (0.29), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 229 TYR 0.016 0.001 TYR A 41 PHE 0.009 0.001 PHE B 120 HIS 0.003 0.001 HIS C 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.23 ( 7912) covalent geometry : angle 0.60533 / 0.32 (10744) hydrogen bonds : bond 0.03226 / 2.14 ( 308) hydrogen bonds : angle 4.58533 / 3.04 ( 865) Misc. bond : bond 0.00567 / 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 88 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 59 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.8328 (mtm) REVERT: C 104 ASP cc_start: 0.8316 (m-30) cc_final: 0.7518 (m-30) REVERT: C 231 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.8515 (pt0) outliers start: 29 outliers final: 24 residues processed: 79 average time/residue: 0.0927 time to fit residues: 10.2028 Evaluate side-chains 84 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 58 time to evaluate : 0.218 ------------------------------------------------------------------------------- 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 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 144 MET 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 34 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.3327 r_free = 0.3327 target = 0.099677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.074611 restraints weight = 14125.958| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 2.70 r_work: 0.2737 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7925 Z= 0.142 Angle : 0.569 7.834 10744 Z= 0.303 Chirality : 0.044 0.137 1218 Planarity : 0.003 0.030 1323 Dihedral : 16.254 82.192 1346 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.87 % Favored : 89.60 % Rotamer: Outliers : 3.26 % Allowed : 15.79 % Favored : 80.95 % 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: -0.92 (0.28), residues: 942 helix: 0.47 (0.26), residues: 426 sheet: 1.37 (0.42), residues: 165 loop : -3.08 (0.29), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 124 TYR 0.018 0.001 TYR A 41 PHE 0.007 0.001 PHE B 120 HIS 0.002 0.001 HIS C 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 ( 7912) covalent geometry : angle 0.56919 / 0.30 (10744) hydrogen bonds : bond 0.02895 / 1.95 ( 308) hydrogen bonds : angle 4.49958 / 2.97 ( 865) Misc. bond : bond 0.00556 / 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 84 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 58 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.7906 (mtm) REVERT: C 231 GLU cc_start: 0.8784 (pt0) cc_final: 0.8428 (pt0) outliers start: 26 outliers final: 23 residues processed: 76 average time/residue: 0.0835 time to fit residues: 8.8856 Evaluate side-chains 81 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 57 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 231 GLU Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 144 MET 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 128 THR Chi-restraints excluded: chain C residue 148 GLU Chi-restraints excluded: chain C residue 174 LEU 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: 10.0000 chunk 9 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 15 optimal weight: 0.3980 chunk 20 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 14 optimal weight: 0.0770 chunk 78 optimal weight: 0.7980 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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 = 0.3348 r_free = 0.3348 target = 0.100982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.076135 restraints weight = 14158.996| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 2.69 r_work: 0.2779 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7925 Z= 0.120 Angle : 0.553 7.683 10744 Z= 0.295 Chirality : 0.043 0.130 1218 Planarity : 0.003 0.032 1323 Dihedral : 16.105 81.214 1342 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.45 % Favored : 90.02 % Rotamer: Outliers : 2.51 % Allowed : 16.42 % Favored : 81.08 % 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: -0.84 (0.28), residues: 942 helix: 0.53 (0.26), residues: 426 sheet: 1.41 (0.42), residues: 165 loop : -3.06 (0.29), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 164 TYR 0.011 0.001 TYR B 185 PHE 0.006 0.001 PHE B 253 HIS 0.002 0.001 HIS B 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.12 ( 7912) covalent geometry : angle 0.55271 / 0.29 (10744) hydrogen bonds : bond 0.02730 / 1.86 ( 308) hydrogen bonds : angle 4.42594 / 2.93 ( 865) Misc. bond : bond 0.00547 / 0.37 ( 13) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1574.00 seconds wall clock time: 27 minutes 51.92 seconds (1671.92 seconds total)