Starting phenix.real_space_refine on Mon Apr 6 09:04:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qhw_53181/04_2026/9qhw_53181_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qhw_53181/04_2026/9qhw_53181.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9qhw_53181/04_2026/9qhw_53181.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qhw_53181/04_2026/9qhw_53181.map" model { file = "/net/cci-nas-00/data/ceres_data/9qhw_53181/04_2026/9qhw_53181_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qhw_53181/04_2026/9qhw_53181_trim.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.049 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: 7 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 32 5.16 5 C 5440 2.51 5 N 1446 2.21 5 O 1468 1.98 5 H 8538 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16932 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 4441 Classifications: {'peptide': 265} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 252} Chain: "B" Number of atoms: 4441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 4441 Classifications: {'peptide': 265} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 252} Chain: "C" Number of atoms: 3993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 3993 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 6, 'TRANS': 252} Chain: "D" Number of atoms: 3993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 3993 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 6, 'TRANS': 252} Chain: "C" 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: "D" 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} Time building chain proxies: 3.10, per 1000 atoms: 0.18 Number of scatterers: 16932 At special positions: 0 Unit cell: (87.1, 87.1, 109.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 32 16.00 P 6 15.00 Mg 2 11.99 O 1468 8.00 N 1446 7.00 C 5440 6.00 H 8538 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.33 Conformation dependent library (CDL) restraints added in 682.6 milliseconds 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1932 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 4 sheets defined 67.4% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 32 through 45 Processing helix chain 'A' and resid 46 through 65 removed outlier: 3.718A pdb=" N TRP A 50 " --> pdb=" O HIS A 46 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN A 52 " --> pdb=" O GLN A 48 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 91 removed outlier: 4.043A pdb=" N ILE A 72 " --> pdb=" O GLY A 68 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N MET A 83 " --> pdb=" O THR A 79 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLN A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 121 Proline residue: A 100 - end of helix removed outlier: 4.140A pdb=" N LEU A 111 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE A 112 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP A 121 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 131 Processing helix chain 'A' and resid 137 through 166 removed outlier: 3.690A pdb=" N VAL A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE A 157 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ILE A 158 " --> pdb=" O HIS A 154 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE A 159 " --> pdb=" O ASN A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 202 removed outlier: 3.529A pdb=" N TRP A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 218 removed outlier: 3.521A pdb=" N GLN A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 231 Processing helix chain 'A' and resid 235 through 240 Processing helix chain 'A' and resid 241 through 243 No H-bonds generated for 'chain 'A' and resid 241 through 243' Processing helix chain 'A' and resid 244 through 258 removed outlier: 3.949A pdb=" N ILE A 252 " --> pdb=" O PHE A 248 " (cutoff:3.500A) Proline residue: A 255 - end of helix Processing helix chain 'A' and resid 262 through 288 removed outlier: 3.939A pdb=" N TRP A 266 " --> pdb=" O GLN A 262 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG A 288 " --> pdb=" O MET A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 295 Processing helix chain 'B' and resid 32 through 45 Processing helix chain 'B' and resid 46 through 65 removed outlier: 3.717A pdb=" N TRP B 50 " --> pdb=" O HIS B 46 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN B 52 " --> pdb=" O GLN B 48 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG B 61 " --> pdb=" O ASP B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 91 removed outlier: 4.043A pdb=" N ILE B 72 " --> pdb=" O GLY B 68 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N MET B 83 " --> pdb=" O THR B 79 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLN B 89 " --> pdb=" O ILE B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 121 Proline residue: B 100 - end of helix removed outlier: 4.139A pdb=" N LEU B 111 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE B 112 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP B 121 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 131 Processing helix chain 'B' and resid 137 through 166 removed outlier: 3.690A pdb=" N VAL B 141 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ILE B 158 " --> pdb=" O HIS B 154 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE B 159 " --> pdb=" O ASN B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 202 removed outlier: 3.529A pdb=" N TRP B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 218 removed outlier: 3.521A pdb=" N GLN B 214 " --> pdb=" O GLY B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 231 Processing helix chain 'B' and resid 235 through 240 Processing helix chain 'B' and resid 241 through 243 No H-bonds generated for 'chain 'B' and resid 241 through 243' Processing helix chain 'B' and resid 244 through 258 removed outlier: 3.948A pdb=" N ILE B 252 " --> pdb=" O PHE B 248 " (cutoff:3.500A) Proline residue: B 255 - end of helix Processing helix chain 'B' and resid 262 through 288 removed outlier: 3.939A pdb=" N TRP B 266 " --> pdb=" O GLN B 262 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG B 288 " --> pdb=" O MET B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 295 Processing helix chain 'C' and resid 70 through 79 Processing helix chain 'C' and resid 110 through 122 removed outlier: 3.660A pdb=" N ILE C 116 " --> pdb=" O TYR C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 132 Processing helix chain 'C' and resid 132 through 140 Processing helix chain 'C' and resid 142 through 148 Processing helix chain 'C' and resid 149 through 153 Processing helix chain 'C' and resid 154 through 169 removed outlier: 3.675A pdb=" N ILE C 169 " --> pdb=" O VAL C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 183 Processing helix chain 'C' and resid 184 through 202 removed outlier: 3.749A pdb=" N LYS C 190 " --> pdb=" O GLU C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 219 removed outlier: 3.570A pdb=" N LEU C 215 " --> pdb=" O SER C 211 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ARG C 217 " --> pdb=" O GLU C 213 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N CYS C 219 " --> pdb=" O LEU C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 245 Processing helix chain 'C' and resid 245 through 260 Processing helix chain 'D' and resid 70 through 79 Processing helix chain 'D' and resid 110 through 122 removed outlier: 3.659A pdb=" N ILE D 116 " --> pdb=" O TYR D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 132 Processing helix chain 'D' and resid 132 through 140 Processing helix chain 'D' and resid 142 through 148 Processing helix chain 'D' and resid 149 through 153 Processing helix chain 'D' and resid 154 through 169 removed outlier: 3.674A pdb=" N ILE D 169 " --> pdb=" O VAL D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 183 Processing helix chain 'D' and resid 184 through 202 removed outlier: 3.749A pdb=" N LYS D 190 " --> pdb=" O GLU D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 219 removed outlier: 3.569A pdb=" N LEU D 215 " --> pdb=" O SER D 211 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ARG D 217 " --> pdb=" O GLU D 213 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N CYS D 219 " --> pdb=" O LEU D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 245 Processing helix chain 'D' and resid 245 through 260 Processing sheet with id=AA1, first strand: chain 'C' and resid 34 through 37 removed outlier: 4.143A pdb=" N ALA C 34 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL C 43 " --> pdb=" O ILE C 15 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL C 11 " --> pdb=" O ALA C 47 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ARG C 49 " --> pdb=" O ALA C 9 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ALA C 9 " --> pdb=" O ARG C 49 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE C 51 " --> pdb=" O HIS C 7 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N HIS C 7 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N LEU C 53 " --> pdb=" O GLN C 5 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLN C 5 " --> pdb=" O LEU C 53 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU C 55 " --> pdb=" O SER C 3 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N SER C 3 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ALA C 9 " --> pdb=" O ARG C 86 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ARG C 86 " --> pdb=" O ALA C 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 95 through 98 removed outlier: 3.689A pdb=" N LEU C 175 " --> pdb=" O ALA C 96 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU C 174 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N ALA C 208 " --> pdb=" O LEU C 174 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU C 176 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ARG C 60 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N MET C 223 " --> pdb=" O ARG C 60 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLY C 62 " --> pdb=" O MET C 223 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ILE C 225 " --> pdb=" O GLY C 62 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL C 64 " --> pdb=" O ILE C 225 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ALA C 222 " --> pdb=" O SER C 233 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N SER C 233 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N TRP C 224 " --> pdb=" O LYS C 231 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 34 through 37 removed outlier: 4.143A pdb=" N ALA D 34 " --> pdb=" O GLU D 46 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL D 43 " --> pdb=" O ILE D 15 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL D 11 " --> pdb=" O ALA D 47 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ARG D 49 " --> pdb=" O ALA D 9 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ALA D 9 " --> pdb=" O ARG D 49 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE D 51 " --> pdb=" O HIS D 7 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N HIS D 7 " --> pdb=" O ILE D 51 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N LEU D 53 " --> pdb=" O GLN D 5 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLN D 5 " --> pdb=" O LEU D 53 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU D 55 " --> pdb=" O SER D 3 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N SER D 3 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ALA D 9 " --> pdb=" O ARG D 86 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ARG D 86 " --> pdb=" O ALA D 9 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 95 through 98 removed outlier: 3.689A pdb=" N LEU D 175 " --> pdb=" O ALA D 96 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU D 174 " --> pdb=" O VAL D 206 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ALA D 208 " --> pdb=" O LEU D 174 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU D 176 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ARG D 60 " --> pdb=" O THR D 221 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N MET D 223 " --> pdb=" O ARG D 60 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLY D 62 " --> pdb=" O MET D 223 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ILE D 225 " --> pdb=" O GLY D 62 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL D 64 " --> pdb=" O ILE D 225 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ALA D 222 " --> pdb=" O SER D 233 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N SER D 233 " --> pdb=" O ALA D 222 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N TRP D 224 " --> pdb=" O LYS D 231 " (cutoff:3.500A) 488 hydrogen bonds defined for protein. 1398 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.36 Time building geometry restraints manager: 1.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8534 1.03 - 1.23: 4 1.23 - 1.42: 3584 1.42 - 1.62: 4944 1.62 - 1.81: 60 Bond restraints: 17126 Sorted by residual: bond pdb=" CB ASN C 220 " pdb=" CG ASN C 220 " ideal model delta sigma weight residual 1.516 1.568 -0.052 2.50e-02 1.60e+03 4.27e+00 bond pdb=" CB ASN D 220 " pdb=" CG ASN D 220 " ideal model delta sigma weight residual 1.516 1.567 -0.051 2.50e-02 1.60e+03 4.22e+00 bond pdb=" CA ASN C 220 " pdb=" CB ASN C 220 " ideal model delta sigma weight residual 1.536 1.561 -0.025 1.42e-02 4.96e+03 3.14e+00 bond pdb=" CA ASN D 220 " pdb=" CB ASN D 220 " ideal model delta sigma weight residual 1.536 1.561 -0.025 1.42e-02 4.96e+03 3.14e+00 bond pdb=" CB GLU C 141 " pdb=" CG GLU C 141 " ideal model delta sigma weight residual 1.520 1.566 -0.046 3.00e-02 1.11e+03 2.37e+00 ... (remaining 17121 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 29599 1.31 - 2.63: 1259 2.63 - 3.94: 84 3.94 - 5.25: 44 5.25 - 6.57: 14 Bond angle restraints: 31000 Sorted by residual: angle pdb=" CA ASN C 220 " pdb=" CB ASN C 220 " pdb=" CG ASN C 220 " ideal model delta sigma weight residual 112.60 116.05 -3.45 1.00e+00 1.00e+00 1.19e+01 angle pdb=" CA ASN D 220 " pdb=" CB ASN D 220 " pdb=" CG ASN D 220 " ideal model delta sigma weight residual 112.60 116.01 -3.41 1.00e+00 1.00e+00 1.16e+01 angle pdb=" C3' ATP C 502 " pdb=" C4' ATP C 502 " pdb=" C5' ATP C 502 " ideal model delta sigma weight residual 115.19 110.18 5.01 1.76e+00 3.23e-01 8.11e+00 angle pdb=" C3' ATP D 502 " pdb=" C4' ATP D 502 " pdb=" C5' ATP D 502 " ideal model delta sigma weight residual 115.19 110.22 4.97 1.76e+00 3.23e-01 7.97e+00 angle pdb=" CA TYR D 112 " pdb=" CB TYR D 112 " pdb=" CG TYR D 112 " ideal model delta sigma weight residual 113.90 118.96 -5.06 1.80e+00 3.09e-01 7.91e+00 ... (remaining 30995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 7035 17.74 - 35.48: 625 35.48 - 53.22: 242 53.22 - 70.96: 66 70.96 - 88.70: 8 Dihedral angle restraints: 7976 sinusoidal: 4366 harmonic: 3610 Sorted by residual: dihedral pdb=" CA ALA C 26 " pdb=" C ALA C 26 " pdb=" N PHE C 27 " pdb=" CA PHE C 27 " ideal model delta harmonic sigma weight residual 180.00 -157.85 -22.15 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA ALA D 26 " pdb=" C ALA D 26 " pdb=" N PHE D 27 " pdb=" CA PHE D 27 " ideal model delta harmonic sigma weight residual -180.00 -157.87 -22.13 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA LEU B 86 " pdb=" C LEU B 86 " pdb=" N TYR B 87 " pdb=" CA TYR B 87 " ideal model delta harmonic sigma weight residual -180.00 -159.50 -20.50 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 7973 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1110 0.055 - 0.110: 196 0.110 - 0.166: 28 0.166 - 0.221: 0 0.221 - 0.276: 6 Chirality restraints: 1340 Sorted by residual: chirality pdb=" C2' ATP C 502 " pdb=" C1' ATP C 502 " pdb=" C3' ATP C 502 " pdb=" O2' ATP C 502 " both_signs ideal model delta sigma weight residual False -2.68 -2.96 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" C2' ATP D 502 " pdb=" C1' ATP D 502 " pdb=" C3' ATP D 502 " pdb=" O2' ATP D 502 " both_signs ideal model delta sigma weight residual False -2.68 -2.95 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" C3' ATP C 502 " pdb=" C2' ATP C 502 " pdb=" C4' ATP C 502 " pdb=" O3' ATP C 502 " both_signs ideal model delta sigma weight residual False -2.63 -2.88 0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 1337 not shown) Planarity restraints: 2456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 160 " 0.196 9.50e-02 1.11e+02 6.61e-02 6.65e+00 pdb=" NE ARG C 160 " -0.020 2.00e-02 2.50e+03 pdb=" CZ ARG C 160 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG C 160 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG C 160 " 0.017 2.00e-02 2.50e+03 pdb="HH11 ARG C 160 " -0.010 2.00e-02 2.50e+03 pdb="HH12 ARG C 160 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG C 160 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG C 160 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 160 " -0.195 9.50e-02 1.11e+02 6.59e-02 6.64e+00 pdb=" NE ARG D 160 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG D 160 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG D 160 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG D 160 " -0.018 2.00e-02 2.50e+03 pdb="HH11 ARG D 160 " 0.010 2.00e-02 2.50e+03 pdb="HH12 ARG D 160 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG D 160 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG D 160 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 84 " -0.012 2.00e-02 2.50e+03 2.34e-02 5.48e+00 pdb=" C GLY A 84 " 0.040 2.00e-02 2.50e+03 pdb=" O GLY A 84 " -0.015 2.00e-02 2.50e+03 pdb=" N ILE A 85 " -0.014 2.00e-02 2.50e+03 ... (remaining 2453 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.30: 2834 2.30 - 2.87: 39164 2.87 - 3.45: 44433 3.45 - 4.02: 60620 4.02 - 4.60: 93391 Nonbonded interactions: 240442 Sorted by model distance: nonbonded pdb="HH11 ARG C 160 " pdb=" HB2 PHE C 187 " model vdw 1.719 2.270 nonbonded pdb="HH11 ARG D 160 " pdb=" HB2 PHE D 187 " model vdw 1.720 2.270 nonbonded pdb="HH22 ARG C 160 " pdb=" HB3 ASP C 184 " model vdw 1.864 2.270 nonbonded pdb="HH22 ARG D 160 " pdb=" HB3 ASP D 184 " model vdw 1.865 2.270 nonbonded pdb=" HG SER D 211 " pdb=" HE1 PHE D 214 " model vdw 1.892 2.100 ... (remaining 240437 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 0.860 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: 0.100 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.490 Find NCS groups from input model: 0.090 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: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8588 Z= 0.193 Angle : 0.739 6.568 11680 Z= 0.409 Chirality : 0.045 0.276 1340 Planarity : 0.007 0.094 1448 Dihedral : 16.420 88.699 3138 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.00 % Allowed : 15.77 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.25), residues: 1040 helix: -0.98 (0.19), residues: 608 sheet: -1.03 (0.65), residues: 64 loop : -0.39 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 217 TYR 0.019 0.002 TYR A 166 PHE 0.020 0.001 PHE B 217 TRP 0.017 0.002 TRP B 71 HIS 0.013 0.002 HIS B 46 Details of bonding type rmsd covalent geometry : bond 0.00438 ( 8588) covalent geometry : angle 0.73852 (11680) hydrogen bonds : bond 0.18024 ( 488) hydrogen bonds : angle 7.29799 ( 1398) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 SER cc_start: 0.8177 (p) cc_final: 0.7924 (p) REVERT: B 41 SER cc_start: 0.8174 (p) cc_final: 0.7919 (p) REVERT: C 144 GLU cc_start: 0.8234 (tp30) cc_final: 0.7702 (tp30) REVERT: D 144 GLU cc_start: 0.8204 (tp30) cc_final: 0.7600 (tp30) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.1940 time to fit residues: 32.2293 Evaluate side-chains 105 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN C 114 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.169664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.145774 restraints weight = 28947.299| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.18 r_work: 0.3536 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8588 Z= 0.167 Angle : 0.521 4.660 11680 Z= 0.289 Chirality : 0.039 0.136 1340 Planarity : 0.004 0.038 1448 Dihedral : 9.040 86.166 1208 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.13 % Allowed : 15.43 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.25), residues: 1040 helix: 0.10 (0.20), residues: 612 sheet: -0.97 (0.64), residues: 64 loop : -0.21 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 160 TYR 0.009 0.001 TYR A 87 PHE 0.010 0.001 PHE A 177 TRP 0.013 0.001 TRP B 50 HIS 0.005 0.001 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 8588) covalent geometry : angle 0.52103 (11680) hydrogen bonds : bond 0.04420 ( 488) hydrogen bonds : angle 4.93339 ( 1398) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: A 261 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8214 (mt0) REVERT: B 35 ARG cc_start: 0.7413 (tpp80) cc_final: 0.7086 (tpp-160) REVERT: C 130 GLN cc_start: 0.8110 (tt0) cc_final: 0.7845 (tt0) REVERT: C 144 GLU cc_start: 0.8569 (tp30) cc_final: 0.8207 (tp30) REVERT: D 144 GLU cc_start: 0.8555 (tp30) cc_final: 0.8177 (tp30) REVERT: D 250 ASP cc_start: 0.7540 (m-30) cc_final: 0.6960 (m-30) outliers start: 10 outliers final: 9 residues processed: 113 average time/residue: 0.1718 time to fit residues: 28.2865 Evaluate side-chains 108 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain C residue 56 LYS Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain D residue 56 LYS Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 106 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 90 optimal weight: 0.0970 chunk 58 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 261 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.169027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.144903 restraints weight = 29321.929| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.20 r_work: 0.3514 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8588 Z= 0.155 Angle : 0.489 4.523 11680 Z= 0.270 Chirality : 0.039 0.136 1340 Planarity : 0.004 0.040 1448 Dihedral : 8.994 87.935 1208 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.13 % Allowed : 15.65 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.26), residues: 1040 helix: 0.36 (0.21), residues: 612 sheet: -0.73 (0.67), residues: 64 loop : -0.13 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 217 TYR 0.008 0.001 TYR B 87 PHE 0.011 0.001 PHE A 177 TRP 0.013 0.001 TRP B 50 HIS 0.004 0.001 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 8588) covalent geometry : angle 0.48866 (11680) hydrogen bonds : bond 0.04135 ( 488) hydrogen bonds : angle 4.63770 ( 1398) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 261 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.8206 (mt0) REVERT: C 144 GLU cc_start: 0.8566 (tp30) cc_final: 0.8232 (tp30) REVERT: D 144 GLU cc_start: 0.8545 (tp30) cc_final: 0.8196 (tp30) REVERT: D 250 ASP cc_start: 0.7619 (m-30) cc_final: 0.7053 (m-30) outliers start: 10 outliers final: 8 residues processed: 110 average time/residue: 0.1725 time to fit residues: 27.1322 Evaluate side-chains 104 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 261 GLN Chi-restraints excluded: chain C residue 56 LYS Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain D residue 56 LYS Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 106 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 4 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.167859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.143362 restraints weight = 29330.320| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.23 r_work: 0.3496 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8588 Z= 0.150 Angle : 0.479 4.426 11680 Z= 0.265 Chirality : 0.038 0.138 1340 Planarity : 0.004 0.040 1448 Dihedral : 8.859 85.755 1208 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.03 % Allowed : 14.64 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.26), residues: 1040 helix: 0.51 (0.21), residues: 612 sheet: -0.62 (0.70), residues: 64 loop : -0.04 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 253 TYR 0.008 0.001 TYR A 87 PHE 0.011 0.001 PHE B 177 TRP 0.013 0.001 TRP A 50 HIS 0.004 0.001 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 8588) covalent geometry : angle 0.47876 (11680) hydrogen bonds : bond 0.03856 ( 488) hydrogen bonds : angle 4.49479 ( 1398) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 TYR cc_start: 0.8699 (t80) cc_final: 0.8481 (t80) REVERT: B 101 TYR cc_start: 0.8709 (t80) cc_final: 0.8491 (t80) REVERT: C 144 GLU cc_start: 0.8566 (tp30) cc_final: 0.8229 (tp30) REVERT: C 250 ASP cc_start: 0.7581 (m-30) cc_final: 0.7032 (m-30) REVERT: D 144 GLU cc_start: 0.8552 (tp30) cc_final: 0.8217 (tp30) REVERT: D 250 ASP cc_start: 0.7614 (m-30) cc_final: 0.7032 (m-30) outliers start: 18 outliers final: 13 residues processed: 116 average time/residue: 0.1906 time to fit residues: 31.0614 Evaluate side-chains 117 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 56 LYS Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 56 LYS Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 106 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 45 optimal weight: 0.0980 chunk 16 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 43 optimal weight: 0.0970 chunk 18 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.169508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.145134 restraints weight = 29098.625| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.22 r_work: 0.3528 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8588 Z= 0.107 Angle : 0.450 4.283 11680 Z= 0.247 Chirality : 0.038 0.135 1340 Planarity : 0.004 0.037 1448 Dihedral : 8.286 80.267 1208 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.69 % Allowed : 15.09 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.27), residues: 1040 helix: 0.80 (0.21), residues: 610 sheet: -0.40 (0.72), residues: 64 loop : 0.11 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 217 TYR 0.017 0.001 TYR B 166 PHE 0.007 0.001 PHE B 177 TRP 0.013 0.001 TRP A 50 HIS 0.003 0.001 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 8588) covalent geometry : angle 0.44962 (11680) hydrogen bonds : bond 0.03480 ( 488) hydrogen bonds : angle 4.27016 ( 1398) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 TYR cc_start: 0.8665 (t80) cc_final: 0.8403 (t80) REVERT: B 101 TYR cc_start: 0.8668 (t80) cc_final: 0.8396 (t80) REVERT: C 144 GLU cc_start: 0.8505 (tp30) cc_final: 0.8173 (tp30) REVERT: C 250 ASP cc_start: 0.7592 (m-30) cc_final: 0.7080 (m-30) REVERT: D 59 ASP cc_start: 0.8331 (OUTLIER) cc_final: 0.7875 (t0) REVERT: D 144 GLU cc_start: 0.8490 (tp30) cc_final: 0.8140 (tp30) REVERT: D 250 ASP cc_start: 0.7597 (m-30) cc_final: 0.7068 (m-30) outliers start: 15 outliers final: 8 residues processed: 111 average time/residue: 0.1937 time to fit residues: 30.1725 Evaluate side-chains 112 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 56 LYS Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 106 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 62 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 40 optimal weight: 0.0050 chunk 63 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 72 optimal weight: 3.9990 chunk 37 optimal weight: 0.3980 chunk 56 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 41 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.170393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.145706 restraints weight = 29127.567| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.25 r_work: 0.3526 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8588 Z= 0.108 Angle : 0.447 4.245 11680 Z= 0.246 Chirality : 0.038 0.137 1340 Planarity : 0.003 0.036 1448 Dihedral : 8.067 75.194 1208 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.24 % Allowed : 15.20 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.27), residues: 1040 helix: 0.87 (0.21), residues: 614 sheet: -0.24 (0.74), residues: 64 loop : 0.17 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 64 TYR 0.016 0.001 TYR B 166 PHE 0.007 0.001 PHE A 177 TRP 0.018 0.001 TRP B 50 HIS 0.002 0.001 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 8588) covalent geometry : angle 0.44737 (11680) hydrogen bonds : bond 0.03361 ( 488) hydrogen bonds : angle 4.17939 ( 1398) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 TYR cc_start: 0.8699 (t80) cc_final: 0.8448 (t80) REVERT: B 101 TYR cc_start: 0.8711 (t80) cc_final: 0.8453 (t80) REVERT: C 59 ASP cc_start: 0.8215 (OUTLIER) cc_final: 0.7763 (t0) REVERT: C 144 GLU cc_start: 0.8637 (tp30) cc_final: 0.8265 (tp30) REVERT: C 250 ASP cc_start: 0.7512 (m-30) cc_final: 0.6946 (m-30) REVERT: D 59 ASP cc_start: 0.8285 (OUTLIER) cc_final: 0.7857 (t0) REVERT: D 144 GLU cc_start: 0.8633 (tp30) cc_final: 0.8262 (tp30) REVERT: D 250 ASP cc_start: 0.7521 (m-30) cc_final: 0.6975 (m-30) outliers start: 11 outliers final: 7 residues processed: 108 average time/residue: 0.1716 time to fit residues: 26.3734 Evaluate side-chains 112 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 56 LYS Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 106 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.165222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.140487 restraints weight = 29481.817| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.23 r_work: 0.3429 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8588 Z= 0.194 Angle : 0.507 4.450 11680 Z= 0.281 Chirality : 0.039 0.139 1340 Planarity : 0.004 0.040 1448 Dihedral : 8.799 77.785 1208 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.80 % Allowed : 15.43 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.26), residues: 1040 helix: 0.64 (0.21), residues: 614 sheet: -0.37 (0.75), residues: 64 loop : 0.26 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 253 TYR 0.017 0.001 TYR B 166 PHE 0.016 0.001 PHE B 177 TRP 0.013 0.001 TRP B 50 HIS 0.005 0.001 HIS B 98 Details of bonding type rmsd covalent geometry : bond 0.00458 ( 8588) covalent geometry : angle 0.50723 (11680) hydrogen bonds : bond 0.03735 ( 488) hydrogen bonds : angle 4.37922 ( 1398) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 TYR cc_start: 0.8794 (t80) cc_final: 0.8570 (t80) REVERT: B 35 ARG cc_start: 0.7530 (tpp80) cc_final: 0.7184 (tpp-160) REVERT: B 101 TYR cc_start: 0.8768 (t80) cc_final: 0.8545 (t80) REVERT: C 8 GLN cc_start: 0.8224 (mp10) cc_final: 0.7598 (mp10) REVERT: C 144 GLU cc_start: 0.8668 (tp30) cc_final: 0.8407 (tp30) REVERT: C 250 ASP cc_start: 0.7595 (m-30) cc_final: 0.6997 (m-30) REVERT: D 8 GLN cc_start: 0.8225 (mp10) cc_final: 0.7595 (mp10) REVERT: D 59 ASP cc_start: 0.8202 (OUTLIER) cc_final: 0.7746 (t0) REVERT: D 144 GLU cc_start: 0.8652 (tp30) cc_final: 0.8392 (tp30) REVERT: D 250 ASP cc_start: 0.7516 (m-30) cc_final: 0.6936 (m-30) outliers start: 16 outliers final: 12 residues processed: 118 average time/residue: 0.1916 time to fit residues: 31.6876 Evaluate side-chains 117 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 177 PHE Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 106 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 94 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 197 GLN D 197 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.165529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.140809 restraints weight = 29563.114| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.22 r_work: 0.3481 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8588 Z= 0.172 Angle : 0.492 4.373 11680 Z= 0.272 Chirality : 0.038 0.137 1340 Planarity : 0.004 0.040 1448 Dihedral : 8.393 72.912 1208 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.69 % Allowed : 16.10 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.26), residues: 1040 helix: 0.64 (0.21), residues: 614 sheet: -0.52 (0.74), residues: 64 loop : 0.26 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 253 TYR 0.016 0.001 TYR B 166 PHE 0.013 0.001 PHE B 177 TRP 0.015 0.001 TRP A 50 HIS 0.003 0.001 HIS B 98 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 8588) covalent geometry : angle 0.49232 (11680) hydrogen bonds : bond 0.03577 ( 488) hydrogen bonds : angle 4.34666 ( 1398) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 35 ARG cc_start: 0.7555 (tpp80) cc_final: 0.7184 (tpp-160) REVERT: B 101 TYR cc_start: 0.8769 (t80) cc_final: 0.8569 (t80) REVERT: C 8 GLN cc_start: 0.8205 (mp10) cc_final: 0.7590 (mp10) REVERT: C 59 ASP cc_start: 0.8122 (OUTLIER) cc_final: 0.7660 (t0) REVERT: C 144 GLU cc_start: 0.8608 (tp30) cc_final: 0.8399 (tp30) REVERT: C 250 ASP cc_start: 0.7574 (m-30) cc_final: 0.6993 (m-30) REVERT: D 8 GLN cc_start: 0.8191 (mp10) cc_final: 0.7576 (mp10) REVERT: D 59 ASP cc_start: 0.8121 (OUTLIER) cc_final: 0.7660 (t0) REVERT: D 144 GLU cc_start: 0.8602 (tp30) cc_final: 0.8368 (tp30) REVERT: D 250 ASP cc_start: 0.7571 (m-30) cc_final: 0.6997 (m-30) outliers start: 15 outliers final: 13 residues processed: 110 average time/residue: 0.1776 time to fit residues: 27.8717 Evaluate side-chains 116 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 177 PHE Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 197 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 79 optimal weight: 7.9990 chunk 84 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 72 optimal weight: 0.6980 chunk 73 optimal weight: 0.7980 chunk 87 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.166927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.142307 restraints weight = 29325.773| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.22 r_work: 0.3498 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8588 Z= 0.128 Angle : 0.482 6.674 11680 Z= 0.266 Chirality : 0.038 0.137 1340 Planarity : 0.004 0.039 1448 Dihedral : 7.993 70.506 1208 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.46 % Allowed : 16.67 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.27), residues: 1040 helix: 0.74 (0.21), residues: 618 sheet: -0.53 (0.74), residues: 64 loop : 0.26 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 160 TYR 0.015 0.001 TYR B 166 PHE 0.012 0.001 PHE A 177 TRP 0.016 0.001 TRP A 50 HIS 0.003 0.001 HIS B 98 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 8588) covalent geometry : angle 0.48176 (11680) hydrogen bonds : bond 0.03476 ( 488) hydrogen bonds : angle 4.26470 ( 1398) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 35 ARG cc_start: 0.7486 (tpp80) cc_final: 0.7105 (tpp-160) REVERT: C 8 GLN cc_start: 0.8174 (mp10) cc_final: 0.7556 (mp10) REVERT: C 59 ASP cc_start: 0.8122 (OUTLIER) cc_final: 0.7670 (t0) REVERT: C 144 GLU cc_start: 0.8588 (tp30) cc_final: 0.8343 (tp30) REVERT: C 250 ASP cc_start: 0.7593 (m-30) cc_final: 0.7001 (m-30) REVERT: D 8 GLN cc_start: 0.8161 (mp10) cc_final: 0.7546 (mp10) REVERT: D 59 ASP cc_start: 0.8117 (OUTLIER) cc_final: 0.7671 (t0) REVERT: D 144 GLU cc_start: 0.8583 (tp30) cc_final: 0.8338 (tp30) REVERT: D 250 ASP cc_start: 0.7523 (m-30) cc_final: 0.6910 (m-30) outliers start: 13 outliers final: 8 residues processed: 108 average time/residue: 0.1925 time to fit residues: 29.3775 Evaluate side-chains 108 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 106 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 67 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 19 optimal weight: 0.0770 chunk 68 optimal weight: 0.7980 chunk 14 optimal weight: 0.2980 chunk 34 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 197 GLN D 197 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.168615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.143943 restraints weight = 29179.260| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.23 r_work: 0.3518 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8588 Z= 0.108 Angle : 0.458 4.786 11680 Z= 0.252 Chirality : 0.038 0.136 1340 Planarity : 0.003 0.038 1448 Dihedral : 7.372 68.230 1208 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.24 % Allowed : 16.89 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.27), residues: 1040 helix: 0.94 (0.21), residues: 618 sheet: -0.51 (0.74), residues: 64 loop : 0.36 (0.35), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 160 TYR 0.018 0.001 TYR A 166 PHE 0.008 0.001 PHE A 177 TRP 0.017 0.001 TRP B 50 HIS 0.002 0.001 HIS B 264 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 8588) covalent geometry : angle 0.45811 (11680) hydrogen bonds : bond 0.03230 ( 488) hydrogen bonds : angle 4.14563 ( 1398) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 8 GLN cc_start: 0.8083 (mp10) cc_final: 0.7450 (mp10) REVERT: C 59 ASP cc_start: 0.8124 (OUTLIER) cc_final: 0.7703 (t0) REVERT: C 144 GLU cc_start: 0.8561 (tp30) cc_final: 0.8315 (tp30) REVERT: C 250 ASP cc_start: 0.7456 (m-30) cc_final: 0.6881 (m-30) REVERT: D 8 GLN cc_start: 0.8076 (mp10) cc_final: 0.7445 (mp10) REVERT: D 59 ASP cc_start: 0.8138 (OUTLIER) cc_final: 0.7705 (t0) REVERT: D 144 GLU cc_start: 0.8553 (tp30) cc_final: 0.8304 (tp30) REVERT: D 250 ASP cc_start: 0.7456 (m-30) cc_final: 0.6882 (m-30) outliers start: 11 outliers final: 9 residues processed: 109 average time/residue: 0.1729 time to fit residues: 27.2500 Evaluate side-chains 112 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain B residue 177 PHE Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 197 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 11 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 61 optimal weight: 0.2980 chunk 65 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 197 GLN D 197 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.168362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.143705 restraints weight = 29330.488| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.22 r_work: 0.3506 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.113 8588 Z= 0.174 Angle : 1.091 59.200 11680 Z= 0.655 Chirality : 0.039 0.191 1340 Planarity : 0.004 0.038 1448 Dihedral : 7.386 68.185 1208 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.24 % Allowed : 17.12 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.27), residues: 1040 helix: 0.93 (0.21), residues: 618 sheet: -0.49 (0.74), residues: 64 loop : 0.35 (0.35), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 64 TYR 0.015 0.001 TYR A 166 PHE 0.009 0.001 PHE A 177 TRP 0.016 0.001 TRP A 50 HIS 0.002 0.001 HIS B 264 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 8588) covalent geometry : angle 1.09136 (11680) hydrogen bonds : bond 0.03331 ( 488) hydrogen bonds : angle 4.16064 ( 1398) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3647.13 seconds wall clock time: 62 minutes 25.78 seconds (3745.78 seconds total)