Starting phenix.real_space_refine on Sat Dec 28 06:16:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ej7_31154/12_2024/7ej7_31154_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ej7_31154/12_2024/7ej7_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_31154/12_2024/7ej7_31154.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ej7_31154/12_2024/7ej7_31154.map" model { file = "/net/cci-nas-00/data/ceres_data/7ej7_31154/12_2024/7ej7_31154_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ej7_31154/12_2024/7ej7_31154_trim.cif" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 6.37, per 1000 atoms: 0.82 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: 2.59 Conformation dependent library (CDL) restraints added in 883.1 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: 2.68 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: 2.30 Time building geometry restraints manager: 2.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1293 1.30 - 1.42: 1934 1.42 - 1.55: 4576 1.55 - 1.68: 49 1.68 - 1.80: 60 Bond restraints: 7912 Sorted by residual: bond pdb=" C4 ATP C 402 " pdb=" C5 ATP C 402 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.44e+01 bond pdb=" C4 ATP C 401 " pdb=" C5 ATP C 401 " ideal model delta sigma weight residual 1.388 1.461 -0.073 1.00e-02 1.00e+04 5.35e+01 bond pdb=" C4 ATP B 602 " pdb=" C5 ATP B 602 " ideal model delta sigma weight residual 1.388 1.461 -0.073 1.00e-02 1.00e+04 5.34e+01 bond pdb=" C5 ATP C 402 " pdb=" C6 ATP C 402 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.30e+01 bond pdb=" C5 ATP B 602 " pdb=" C6 ATP B 602 " ideal model delta sigma weight residual 1.409 1.481 -0.072 1.00e-02 1.00e+04 5.18e+01 ... (remaining 7907 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.62: 10657 3.62 - 7.25: 72 7.25 - 10.87: 9 10.87 - 14.50: 0 14.50 - 18.12: 6 Bond angle restraints: 10744 Sorted by residual: angle pdb=" PA ATP C 402 " pdb=" O3A ATP C 402 " pdb=" PB ATP C 402 " ideal model delta sigma weight residual 136.83 118.71 18.12 1.00e+00 1.00e+00 3.28e+02 angle pdb=" PA ATP B 602 " pdb=" O3A ATP B 602 " pdb=" PB ATP B 602 " ideal model delta sigma weight residual 136.83 118.74 18.09 1.00e+00 1.00e+00 3.27e+02 angle pdb=" PA ATP C 401 " pdb=" O3A ATP C 401 " pdb=" PB ATP C 401 " ideal model delta sigma weight residual 136.83 118.74 18.09 1.00e+00 1.00e+00 3.27e+02 angle pdb=" PB ATP B 602 " pdb=" O3B ATP B 602 " pdb=" PG ATP B 602 " ideal model delta sigma weight residual 139.87 123.70 16.17 1.00e+00 1.00e+00 2.62e+02 angle pdb=" PB ATP C 401 " pdb=" O3B ATP C 401 " pdb=" PG ATP C 401 " ideal model delta sigma weight residual 139.87 123.74 16.13 1.00e+00 1.00e+00 2.60e+02 ... (remaining 10739 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.75: 4104 16.75 - 33.50: 516 33.50 - 50.25: 155 50.25 - 67.01: 40 67.01 - 83.76: 33 Dihedral angle restraints: 4848 sinusoidal: 2160 harmonic: 2688 Sorted by residual: dihedral pdb=" CA ASN B 28 " pdb=" C ASN B 28 " pdb=" N ALA B 29 " pdb=" CA ALA B 29 " ideal model delta harmonic sigma weight residual 180.00 -153.70 -26.30 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA ASN C 28 " pdb=" C ASN C 28 " pdb=" N ALA C 29 " pdb=" CA ALA C 29 " ideal model delta harmonic sigma weight residual -180.00 -153.71 -26.29 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA ASN A 28 " pdb=" C ASN A 28 " pdb=" N ALA A 29 " pdb=" CA ALA A 29 " ideal model delta harmonic sigma weight residual -180.00 -153.72 -26.28 0 5.00e+00 4.00e-02 2.76e+01 ... (remaining 4845 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 843 0.037 - 0.074: 267 0.074 - 0.111: 78 0.111 - 0.147: 24 0.147 - 0.184: 6 Chirality restraints: 1218 Sorted by residual: chirality pdb=" CA ASP A 216 " pdb=" N ASP A 216 " pdb=" C ASP A 216 " pdb=" CB ASP A 216 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.50e-01 chirality pdb=" CA ASP C 216 " pdb=" N ASP C 216 " pdb=" C ASP C 216 " pdb=" CB ASP C 216 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.73e-01 chirality pdb=" CA ASP B 216 " pdb=" N ASP B 216 " pdb=" C ASP B 216 " pdb=" CB ASP B 216 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.68e-01 ... (remaining 1215 not shown) Planarity restraints: 1323 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET C 315 " -0.014 2.00e-02 2.50e+03 2.86e-02 8.18e+00 pdb=" C MET C 315 " 0.049 2.00e-02 2.50e+03 pdb=" O MET C 315 " -0.019 2.00e-02 2.50e+03 pdb=" N PRO C 316 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 315 " 0.014 2.00e-02 2.50e+03 2.84e-02 8.05e+00 pdb=" C MET A 315 " -0.049 2.00e-02 2.50e+03 pdb=" O MET A 315 " 0.018 2.00e-02 2.50e+03 pdb=" N PRO A 316 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 315 " -0.014 2.00e-02 2.50e+03 2.83e-02 8.03e+00 pdb=" C MET B 315 " 0.049 2.00e-02 2.50e+03 pdb=" O MET B 315 " -0.018 2.00e-02 2.50e+03 pdb=" N PRO B 316 " -0.016 2.00e-02 2.50e+03 ... (remaining 1320 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 78 2.47 - 3.08: 6331 3.08 - 3.68: 11314 3.68 - 4.29: 17663 4.29 - 4.90: 29004 Nonbonded interactions: 64390 Sorted by model distance: nonbonded pdb=" O PRO B 316 " pdb=" O2' ATP B 602 " model vdw 1.860 3.040 nonbonded pdb=" O PRO C 316 " pdb=" O2' ATP C 401 " model vdw 1.901 3.040 nonbonded pdb=" O2G ATP C 402 " pdb="MG MG C 403 " model vdw 1.913 2.170 nonbonded pdb="MG MG B 601 " pdb=" O2G ATP C 401 " model vdw 1.913 2.170 nonbonded pdb=" O2G ATP B 602 " pdb="MG MG A 601 " model vdw 1.913 2.170 ... (remaining 64385 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 16 through 334) selection = (chain 'B' and resid 16 through 334) selection = (chain 'C' and resid 16 through 334) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.380 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: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.090 Process input model: 24.390 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 7912 Z= 0.382 Angle : 0.915 18.124 10744 Z= 0.680 Chirality : 0.043 0.184 1218 Planarity : 0.004 0.044 1323 Dihedral : 18.099 83.758 3132 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 43.57 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.002 0.001 HIS B 193 PHE 0.007 0.001 PHE C 160 TYR 0.006 0.001 TYR B 41 ARG 0.003 0.000 ARG A 142 *********************** 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 : 0.883 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: 0.6729 (m) REVERT: C 61 SER cc_start: 0.6506 (OUTLIER) cc_final: 0.6167 (m) outliers start: 14 outliers final: 2 residues processed: 111 average time/residue: 0.2334 time to fit residues: 34.1832 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 : 0.843 ------------------------------------------------------------------------------- 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 78 optimal weight: 0.9980 chunk 70 optimal weight: 0.4980 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 37 optimal weight: 0.0070 chunk 72 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 ASN B 44 ASN B 182 ASN B 236 GLN A 182 ASN A 236 GLN C 44 ASN C 182 ASN C 236 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7912 Z= 0.196 Angle : 0.658 8.614 10744 Z= 0.344 Chirality : 0.046 0.142 1218 Planarity : 0.004 0.030 1323 Dihedral : 16.828 78.714 1349 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.64 % Allowed : 9.24 % Favored : 90.13 % Rotamer: Outliers : 2.13 % Allowed : 10.65 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.25), residues: 942 helix: -1.34 (0.24), residues: 426 sheet: 0.79 (0.44), residues: 159 loop : -4.00 (0.24), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 193 PHE 0.011 0.001 PHE A 160 TYR 0.014 0.001 TYR C 41 ARG 0.004 0.001 ARG B 229 *********************** 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 109 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 254 ASN cc_start: 0.9267 (t0) cc_final: 0.8994 (t0) REVERT: B 272 LEU cc_start: 0.6583 (OUTLIER) cc_final: 0.6233 (mp) REVERT: A 89 ILE cc_start: 0.9124 (tt) cc_final: 0.8786 (mt) outliers start: 17 outliers final: 8 residues processed: 109 average time/residue: 0.2313 time to fit residues: 33.3120 Evaluate side-chains 77 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain A residue 164 ARG Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 314 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 46 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 chunk 75 optimal weight: 0.0020 chunk 83 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 overall best weight: 1.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 HIS C 242 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7912 Z= 0.272 Angle : 0.627 7.827 10744 Z= 0.331 Chirality : 0.046 0.140 1218 Planarity : 0.004 0.030 1323 Dihedral : 16.680 81.218 1346 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.13 % Favored : 90.34 % Rotamer: Outliers : 2.38 % Allowed : 14.54 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.27), residues: 942 helix: -0.38 (0.25), residues: 426 sheet: 1.07 (0.43), residues: 165 loop : -3.85 (0.25), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 285 PHE 0.009 0.001 PHE C 160 TYR 0.013 0.001 TYR C 41 ARG 0.004 0.000 ARG B 229 *********************** 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 89 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 70 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 272 LEU cc_start: 0.6454 (OUTLIER) cc_final: 0.6170 (mp) REVERT: A 89 ILE cc_start: 0.9196 (tt) cc_final: 0.8947 (mt) REVERT: A 247 ASN cc_start: 0.9163 (t0) cc_final: 0.8955 (t0) REVERT: C 144 MET cc_start: 0.7197 (mtt) cc_final: 0.6934 (mtp) outliers start: 19 outliers final: 15 residues processed: 84 average time/residue: 0.2227 time to fit residues: 25.2546 Evaluate side-chains 77 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 128 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 93 VAL Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 314 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 9 optimal weight: 0.0670 chunk 40 optimal weight: 7.9990 chunk 56 optimal weight: 7.9990 chunk 84 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.1922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 HIS C 242 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7912 Z= 0.208 Angle : 0.578 8.238 10744 Z= 0.306 Chirality : 0.044 0.132 1218 Planarity : 0.004 0.031 1323 Dihedral : 16.448 80.497 1346 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.66 % Favored : 89.81 % Rotamer: Outliers : 3.01 % Allowed : 14.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.27), residues: 942 helix: 0.04 (0.26), residues: 426 sheet: 1.29 (0.42), residues: 165 loop : -3.72 (0.25), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 289 PHE 0.008 0.001 PHE B 120 TYR 0.018 0.001 TYR A 41 ARG 0.003 0.000 ARG B 229 *********************** 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: 24 poor density : 75 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ILE cc_start: 0.9192 (tt) cc_final: 0.8942 (mt) REVERT: A 247 ASN cc_start: 0.9165 (t0) cc_final: 0.8943 (t0) outliers start: 24 outliers final: 16 residues processed: 94 average time/residue: 0.2383 time to fit residues: 29.7982 Evaluate side-chains 81 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 1.268 ------------------------------------------------------------------------------- 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 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 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 74 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 62 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 45 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 HIS A 242 HIS C 242 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7912 Z= 0.198 Angle : 0.563 4.910 10744 Z= 0.299 Chirality : 0.044 0.130 1218 Planarity : 0.003 0.031 1323 Dihedral : 16.202 79.942 1346 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.34 % Favored : 90.13 % Rotamer: Outliers : 3.26 % Allowed : 15.04 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.27), residues: 942 helix: 0.21 (0.26), residues: 426 sheet: 1.47 (0.42), residues: 165 loop : -3.45 (0.25), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 289 PHE 0.007 0.001 PHE B 120 TYR 0.013 0.001 TYR C 41 ARG 0.003 0.000 ARG A 164 *********************** 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 103 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 77 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 318 LYS cc_start: 0.7595 (OUTLIER) cc_final: 0.7261 (mtmt) REVERT: A 89 ILE cc_start: 0.9165 (tt) cc_final: 0.8933 (mt) outliers start: 26 outliers final: 16 residues processed: 97 average time/residue: 0.2580 time to fit residues: 32.8800 Evaluate side-chains 84 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.903 ------------------------------------------------------------------------------- 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 318 LYS Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 30 optimal weight: 2.9990 chunk 80 optimal weight: 0.0870 chunk 17 optimal weight: 8.9990 chunk 52 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 overall best weight: 1.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7912 Z= 0.251 Angle : 0.583 5.373 10744 Z= 0.308 Chirality : 0.045 0.133 1218 Planarity : 0.004 0.032 1323 Dihedral : 16.280 81.571 1342 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.66 % Favored : 89.81 % Rotamer: Outliers : 3.26 % Allowed : 16.04 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.27), residues: 942 helix: 0.25 (0.26), residues: 426 sheet: 1.51 (0.43), residues: 165 loop : -3.28 (0.27), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 242 PHE 0.008 0.001 PHE B 120 TYR 0.017 0.001 TYR B 41 ARG 0.002 0.000 ARG A 142 *********************** 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 93 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 67 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 231 GLU cc_start: 0.7586 (pt0) cc_final: 0.7310 (pt0) REVERT: B 318 LYS cc_start: 0.7727 (OUTLIER) cc_final: 0.7352 (mtmt) REVERT: A 144 MET cc_start: 0.7446 (mtm) cc_final: 0.7066 (mtm) outliers start: 26 outliers final: 20 residues processed: 85 average time/residue: 0.2381 time to fit residues: 26.9811 Evaluate side-chains 84 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 63 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 318 LYS Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 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 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 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 86 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 75 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 54 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 HIS A 242 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7912 Z= 0.243 Angle : 0.575 5.396 10744 Z= 0.304 Chirality : 0.044 0.150 1218 Planarity : 0.004 0.032 1323 Dihedral : 16.263 82.251 1342 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.55 % Favored : 89.92 % Rotamer: Outliers : 3.63 % Allowed : 16.04 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.28), residues: 942 helix: 0.30 (0.26), residues: 429 sheet: 1.47 (0.42), residues: 165 loop : -3.15 (0.28), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 285 PHE 0.008 0.001 PHE B 120 TYR 0.005 0.001 TYR A 41 ARG 0.002 0.000 ARG A 301 *********************** 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 97 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 68 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 318 LYS cc_start: 0.7617 (OUTLIER) cc_final: 0.7286 (mtmt) REVERT: A 144 MET cc_start: 0.7509 (mtm) cc_final: 0.7120 (mtm) outliers start: 29 outliers final: 22 residues processed: 86 average time/residue: 0.2312 time to fit residues: 26.5702 Evaluate side-chains 88 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 65 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 318 LYS Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 148 GLU 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 320 CYS 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 148 GLU Chi-restraints excluded: chain C residue 192 GLU 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 35 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 85 optimal weight: 0.8980 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 7912 Z= 0.426 Angle : 0.649 6.199 10744 Z= 0.343 Chirality : 0.048 0.163 1218 Planarity : 0.004 0.038 1323 Dihedral : 16.841 89.062 1342 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.64 % Allowed : 9.77 % Favored : 89.60 % Rotamer: Outliers : 4.01 % Allowed : 16.54 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.28), residues: 942 helix: 0.27 (0.26), residues: 426 sheet: 1.19 (0.43), residues: 168 loop : -3.12 (0.28), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 285 PHE 0.011 0.001 PHE B 120 TYR 0.009 0.001 TYR C 41 ARG 0.003 0.001 ARG B 142 *********************** 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 92 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 60 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 318 LYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7583 (mtmt) REVERT: A 144 MET cc_start: 0.7541 (mtm) cc_final: 0.7206 (mtp) REVERT: A 318 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.8016 (mptt) outliers start: 32 outliers final: 23 residues processed: 84 average time/residue: 0.2319 time to fit residues: 26.1527 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 : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 318 LYS Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 148 GLU 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 318 LYS 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 106 ILE Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain C residue 148 GLU Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 314 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 85 optimal weight: 0.3980 chunk 50 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 25 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 88 optimal weight: 0.0870 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 HIS A 242 HIS C 167 GLN C 242 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7912 Z= 0.169 Angle : 0.561 5.870 10744 Z= 0.298 Chirality : 0.043 0.132 1218 Planarity : 0.003 0.034 1323 Dihedral : 16.309 85.435 1342 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.02 % Favored : 90.45 % Rotamer: Outliers : 3.51 % Allowed : 17.17 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.28), residues: 942 helix: 0.40 (0.26), residues: 429 sheet: 1.51 (0.42), residues: 159 loop : -2.95 (0.29), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 289 PHE 0.006 0.001 PHE C 120 TYR 0.007 0.001 TYR C 41 ARG 0.003 0.000 ARG B 164 *********************** 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 102 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 74 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 251 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7290 (mt-10) REVERT: B 318 LYS cc_start: 0.7464 (OUTLIER) cc_final: 0.7218 (mtmt) REVERT: A 144 MET cc_start: 0.7543 (mtm) cc_final: 0.7215 (mtp) REVERT: A 318 LYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7762 (mptt) REVERT: C 104 ASP cc_start: 0.7199 (m-30) cc_final: 0.6871 (m-30) outliers start: 28 outliers final: 18 residues processed: 91 average time/residue: 0.2344 time to fit residues: 28.1578 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 : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 318 LYS Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 128 THR 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 318 LYS Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain C residue 148 GLU 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 53 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 92 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 56 optimal weight: 0.0570 chunk 45 optimal weight: 0.1980 chunk 58 optimal weight: 0.7980 chunk 78 optimal weight: 0.5980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7912 Z= 0.160 Angle : 0.553 7.393 10744 Z= 0.291 Chirality : 0.043 0.255 1218 Planarity : 0.003 0.034 1323 Dihedral : 16.100 82.705 1342 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.66 % Favored : 89.81 % Rotamer: Outliers : 2.38 % Allowed : 17.92 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.28), residues: 942 helix: 0.47 (0.26), residues: 432 sheet: 1.54 (0.42), residues: 159 loop : -2.81 (0.30), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 289 PHE 0.008 0.001 PHE B 253 TYR 0.007 0.001 TYR C 41 ARG 0.003 0.000 ARG B 164 ********************** 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 97 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 318 LYS cc_start: 0.7478 (OUTLIER) cc_final: 0.7258 (mtmt) REVERT: A 144 MET cc_start: 0.7507 (mtm) cc_final: 0.7248 (mtp) REVERT: C 104 ASP cc_start: 0.7124 (m-30) cc_final: 0.6906 (m-30) outliers start: 19 outliers final: 13 residues processed: 89 average time/residue: 0.2342 time to fit residues: 27.8382 Evaluate side-chains 83 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.905 ------------------------------------------------------------------------------- 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 314 ASP Chi-restraints excluded: chain B residue 318 LYS Chi-restraints excluded: chain A residue 128 THR 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 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 22 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 HIS C 241 GLN C 242 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.098692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.073202 restraints weight = 14114.149| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 2.72 r_work: 0.2721 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 7912 Z= 0.313 Angle : 0.621 7.374 10744 Z= 0.326 Chirality : 0.046 0.241 1218 Planarity : 0.004 0.031 1323 Dihedral : 16.406 87.410 1342 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.77 % Favored : 89.70 % Rotamer: Outliers : 2.51 % Allowed : 18.17 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.28), residues: 942 helix: 0.47 (0.26), residues: 429 sheet: 1.31 (0.42), residues: 165 loop : -2.98 (0.29), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 285 PHE 0.010 0.001 PHE B 253 TYR 0.017 0.001 TYR B 41 ARG 0.002 0.000 ARG C 294 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1750.73 seconds wall clock time: 32 minutes 42.69 seconds (1962.69 seconds total)