Starting phenix.real_space_refine on Wed Feb 4 02:21:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xjj_33229/02_2026/7xjj_33229.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xjj_33229/02_2026/7xjj_33229.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/7xjj_33229/02_2026/7xjj_33229.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xjj_33229/02_2026/7xjj_33229.map" model { file = "/net/cci-nas-00/data/ceres_data/7xjj_33229/02_2026/7xjj_33229.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xjj_33229/02_2026/7xjj_33229.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= 0.102 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: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 5559 2.51 5 N 1473 2.21 5 O 1621 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8710 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1691 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 210} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "B" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2597 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 121 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 1, 'TRANS': 15} Chain: "E" Number of atoms: 2095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2095 Classifications: {'peptide': 269} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 11, 'TRANS': 257} Chain breaks: 3 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "S" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1777 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Time building chain proxies: 1.95, per 1000 atoms: 0.22 Number of scatterers: 8710 At special positions: 0 Unit cell: (88.047, 119.57, 125.005, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 1621 8.00 N 1473 7.00 C 5559 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 108 " - pdb=" SG CYS E 187 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.03 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: 0.70 Conformation dependent library (CDL) restraints added in 394.9 milliseconds 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2102 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 14 sheets defined 36.9% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 Processing helix chain 'A' and resid 243 through 256 Processing helix chain 'A' and resid 271 through 282 removed outlier: 3.505A pdb=" N PHE A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LYS A 280 " --> pdb=" O GLY A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 310 Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.955A pdb=" N ILE A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'C' and resid 3 through 12 Processing helix chain 'C' and resid 12 through 17 Processing helix chain 'E' and resid 34 through 59 Processing helix chain 'E' and resid 69 through 98 Proline residue: E 90 - end of helix Processing helix chain 'E' and resid 103 through 139 removed outlier: 4.141A pdb=" N ILE E 107 " --> pdb=" O LEU E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 173 removed outlier: 3.613A pdb=" N ALA E 165 " --> pdb=" O ALA E 161 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET E 166 " --> pdb=" O LEU E 162 " (cutoff:3.500A) Proline residue: E 169 - end of helix Processing helix chain 'E' and resid 193 through 231 removed outlier: 3.714A pdb=" N LYS E 197 " --> pdb=" O ASP E 193 " (cutoff:3.500A) Proline residue: E 212 - end of helix Processing helix chain 'E' and resid 235 through 272 Proline residue: E 262 - end of helix Processing helix chain 'E' and resid 278 through 304 Proline residue: E 300 - end of helix Processing helix chain 'E' and resid 307 through 317 Processing helix chain 'G' and resid 8 through 24 removed outlier: 3.710A pdb=" N ALA G 12 " --> pdb=" O SER G 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.625A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 87 through 91 removed outlier: 4.083A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 188 removed outlier: 5.915A pdb=" N LEU A 37 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N CYS A 225 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU A 39 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N ASP A 227 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 191 through 192 Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.612A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.881A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 103 removed outlier: 6.959A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.869A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.003A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.713A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.676A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER B 277 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA B 287 " --> pdb=" O ASN B 295 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 174 through 177 Processing sheet with id=AB2, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.689A pdb=" N GLY S 10 " --> pdb=" O THR S 116 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.247A pdb=" N VAL S 135 " --> pdb=" O GLU S 234 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 143 through 148 447 hydrogen bonds defined for protein. 1272 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: 1.45 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1405 1.27 - 1.41: 2326 1.41 - 1.55: 5090 1.55 - 1.69: 3 1.69 - 1.83: 80 Bond restraints: 8904 Sorted by residual: bond pdb=" C LEU A 23 " pdb=" O LEU A 23 " ideal model delta sigma weight residual 1.237 1.131 0.106 1.17e-02 7.31e+03 8.14e+01 bond pdb=" CA LEU A 23 " pdb=" C LEU A 23 " ideal model delta sigma weight residual 1.523 1.409 0.114 1.30e-02 5.92e+03 7.68e+01 bond pdb=" C ASN A 22 " pdb=" O ASN A 22 " ideal model delta sigma weight residual 1.237 1.138 0.098 1.16e-02 7.43e+03 7.19e+01 bond pdb=" CA ASP A 26 " pdb=" C ASP A 26 " ideal model delta sigma weight residual 1.524 1.433 0.090 1.29e-02 6.01e+03 4.89e+01 bond pdb=" C ASP A 26 " pdb=" O ASP A 26 " ideal model delta sigma weight residual 1.237 1.155 0.081 1.19e-02 7.06e+03 4.67e+01 ... (remaining 8899 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.22: 11986 4.22 - 8.43: 93 8.43 - 12.65: 7 12.65 - 16.86: 2 16.86 - 21.08: 2 Bond angle restraints: 12090 Sorted by residual: angle pdb=" N LYS A 35 " pdb=" CA LYS A 35 " pdb=" C LYS A 35 " ideal model delta sigma weight residual 110.36 131.10 -20.74 1.55e+00 4.16e-01 1.79e+02 angle pdb=" N GLY E 157 " pdb=" CA GLY E 157 " pdb=" C GLY E 157 " ideal model delta sigma weight residual 112.83 101.71 11.12 1.22e+00 6.72e-01 8.31e+01 angle pdb=" CA PRO E 169 " pdb=" N PRO E 169 " pdb=" CD PRO E 169 " ideal model delta sigma weight residual 112.00 101.15 10.85 1.40e+00 5.10e-01 6.00e+01 angle pdb=" CA LYS A 32 " pdb=" C LYS A 32 " pdb=" N ASP A 33 " ideal model delta sigma weight residual 117.30 125.75 -8.45 1.16e+00 7.43e-01 5.31e+01 angle pdb=" CA CYS E 158 " pdb=" CB CYS E 158 " pdb=" SG CYS E 158 " ideal model delta sigma weight residual 114.40 98.13 16.27 2.30e+00 1.89e-01 5.01e+01 ... (remaining 12085 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 4708 18.00 - 36.00: 425 36.00 - 54.00: 72 54.00 - 72.00: 14 72.00 - 90.00: 4 Dihedral angle restraints: 5223 sinusoidal: 1965 harmonic: 3258 Sorted by residual: dihedral pdb=" C MET E 166 " pdb=" N MET E 166 " pdb=" CA MET E 166 " pdb=" CB MET E 166 " ideal model delta harmonic sigma weight residual -122.60 -149.39 26.79 0 2.50e+00 1.60e-01 1.15e+02 dihedral pdb=" N MET E 166 " pdb=" C MET E 166 " pdb=" CA MET E 166 " pdb=" CB MET E 166 " ideal model delta harmonic sigma weight residual 122.80 146.38 -23.58 0 2.50e+00 1.60e-01 8.90e+01 dihedral pdb=" C ILE A 28 " pdb=" N ILE A 28 " pdb=" CA ILE A 28 " pdb=" CB ILE A 28 " ideal model delta harmonic sigma weight residual -122.00 -137.24 15.24 0 2.50e+00 1.60e-01 3.72e+01 ... (remaining 5220 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.219: 1366 0.219 - 0.439: 8 0.439 - 0.658: 3 0.658 - 0.877: 2 0.877 - 1.097: 1 Chirality restraints: 1380 Sorted by residual: chirality pdb=" CA MET E 166 " pdb=" N MET E 166 " pdb=" C MET E 166 " pdb=" CB MET E 166 " both_signs ideal model delta sigma weight residual False 2.51 1.41 1.10 2.00e-01 2.50e+01 3.01e+01 chirality pdb=" CA PRO E 169 " pdb=" N PRO E 169 " pdb=" C PRO E 169 " pdb=" CB PRO E 169 " both_signs ideal model delta sigma weight residual False 2.72 1.95 0.77 2.00e-01 2.50e+01 1.47e+01 chirality pdb=" CA LYS A 35 " pdb=" N LYS A 35 " pdb=" C LYS A 35 " pdb=" CB LYS A 35 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.09e+01 ... (remaining 1377 not shown) Planarity restraints: 1531 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER E 168 " -0.157 5.00e-02 4.00e+02 2.38e-01 9.05e+01 pdb=" N PRO E 169 " 0.411 5.00e-02 4.00e+02 pdb=" CA PRO E 169 " -0.135 5.00e-02 4.00e+02 pdb=" CD PRO E 169 " -0.119 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 156 " -0.025 2.00e-02 2.50e+03 5.16e-02 2.66e+01 pdb=" C VAL E 156 " 0.089 2.00e-02 2.50e+03 pdb=" O VAL E 156 " -0.034 2.00e-02 2.50e+03 pdb=" N GLY E 157 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 188 " 0.033 2.00e-02 2.50e+03 3.00e-02 2.24e+01 pdb=" CG TRP E 188 " -0.080 2.00e-02 2.50e+03 pdb=" CD1 TRP E 188 " 0.038 2.00e-02 2.50e+03 pdb=" CD2 TRP E 188 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 188 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP E 188 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP E 188 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 188 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 188 " 0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP E 188 " 0.001 2.00e-02 2.50e+03 ... (remaining 1528 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.40: 47 2.40 - 3.02: 5273 3.02 - 3.65: 13354 3.65 - 4.27: 19467 4.27 - 4.90: 33595 Nonbonded interactions: 71736 Sorted by model distance: nonbonded pdb=" O LYS A 35 " pdb=" CG LEU A 36 " model vdw 1.771 3.470 nonbonded pdb=" O LYS A 35 " pdb=" CD2 LEU A 36 " model vdw 1.950 3.460 nonbonded pdb=" CE1 TYR E 113 " pdb=" CB ALA E 167 " model vdw 1.990 3.760 nonbonded pdb=" O ASN E 33 " pdb=" OG1 THR E 36 " model vdw 2.139 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.149 3.040 ... (remaining 71731 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.560 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.340 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 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 : 0.007 0.114 8906 Z= 0.448 Angle : 0.880 21.081 12094 Z= 0.529 Chirality : 0.070 1.097 1380 Planarity : 0.008 0.238 1531 Dihedral : 14.108 89.998 3115 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.96 % Allowed : 1.49 % Favored : 97.55 % Cbeta Deviations : 0.48 % Peptide Plane: Cis-proline : 2.86 % 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: 0.40 (0.26), residues: 1104 helix: 2.09 (0.25), residues: 383 sheet: -0.58 (0.31), residues: 255 loop : -0.74 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 129 TYR 0.017 0.001 TYR S 101 PHE 0.018 0.001 PHE E 114 TRP 0.080 0.003 TRP E 188 HIS 0.006 0.001 HIS E 289 Details of bonding type rmsd covalent geometry : bond 0.00696 ( 8904) covalent geometry : angle 0.87949 (12090) SS BOND : bond 0.00160 ( 2) SS BOND : angle 2.44344 ( 4) hydrogen bonds : bond 0.12563 ( 447) hydrogen bonds : angle 5.89124 ( 1272) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 173 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: A 28 ILE cc_start: 0.8497 (OUTLIER) cc_final: 0.8114 (tp) REVERT: B 297 TRP cc_start: 0.7247 (m100) cc_final: 0.6894 (m100) REVERT: S 128 MET cc_start: 0.8094 (mmm) cc_final: 0.7627 (mmm) REVERT: S 217 CYS cc_start: 0.5906 (p) cc_final: 0.5491 (p) outliers start: 9 outliers final: 4 residues processed: 180 average time/residue: 0.0920 time to fit residues: 23.2549 Evaluate side-chains 146 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 141 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 169 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 0.0980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 30.0000 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN A 307 GLN A 347 ASN E 76 ASN ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 196 HIS S 174 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.193564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.146522 restraints weight = 11662.616| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 3.25 r_work: 0.3659 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 8906 Z= 0.240 Angle : 0.667 7.485 12094 Z= 0.351 Chirality : 0.046 0.180 1380 Planarity : 0.005 0.077 1531 Dihedral : 5.294 70.523 1216 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.92 % Allowed : 11.71 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.02 (0.25), residues: 1104 helix: 1.71 (0.25), residues: 386 sheet: -0.67 (0.30), residues: 283 loop : -1.08 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 133 TYR 0.032 0.002 TYR S 101 PHE 0.020 0.002 PHE E 177 TRP 0.043 0.002 TRP E 188 HIS 0.008 0.001 HIS E 289 Details of bonding type rmsd covalent geometry : bond 0.00559 ( 8904) covalent geometry : angle 0.66595 (12090) SS BOND : bond 0.00243 ( 2) SS BOND : angle 1.69431 ( 4) hydrogen bonds : bond 0.04799 ( 447) hydrogen bonds : angle 5.01476 ( 1272) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 155 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8246 (mtm-85) cc_final: 0.7962 (mtm-85) REVERT: A 25 GLU cc_start: 0.7751 (tm-30) cc_final: 0.7273 (tm-30) REVERT: A 244 MET cc_start: 0.9138 (tpp) cc_final: 0.8685 (tpt) REVERT: E 195 ARG cc_start: 0.7185 (tmt170) cc_final: 0.6923 (ttp80) REVERT: E 200 TYR cc_start: 0.8059 (t80) cc_final: 0.7658 (t80) REVERT: E 250 LEU cc_start: 0.8361 (tp) cc_final: 0.8088 (tp) REVERT: S 128 MET cc_start: 0.8242 (mmm) cc_final: 0.8005 (mmm) REVERT: S 180 MET cc_start: 0.7189 (ptt) cc_final: 0.6748 (ptt) REVERT: S 217 CYS cc_start: 0.6830 (p) cc_final: 0.6597 (p) REVERT: S 232 LYS cc_start: 0.8747 (tptp) cc_final: 0.8368 (tptt) outliers start: 18 outliers final: 13 residues processed: 164 average time/residue: 0.0785 time to fit residues: 17.7931 Evaluate side-chains 153 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 140 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 278 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 50 optimal weight: 0.9980 chunk 40 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 21 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN A 347 ASN E 190 GLN E 196 HIS S 159 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.193577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.151468 restraints weight = 11042.814| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 2.97 r_work: 0.3640 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8906 Z= 0.140 Angle : 0.568 6.437 12094 Z= 0.297 Chirality : 0.042 0.181 1380 Planarity : 0.004 0.064 1531 Dihedral : 4.598 67.084 1207 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.92 % Allowed : 15.76 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.18 (0.25), residues: 1104 helix: 1.96 (0.25), residues: 388 sheet: -0.67 (0.31), residues: 272 loop : -0.99 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 251 TYR 0.023 0.001 TYR S 101 PHE 0.019 0.001 PHE E 177 TRP 0.030 0.002 TRP E 188 HIS 0.006 0.001 HIS E 289 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 8904) covalent geometry : angle 0.56753 (12090) SS BOND : bond 0.00149 ( 2) SS BOND : angle 1.37277 ( 4) hydrogen bonds : bond 0.04104 ( 447) hydrogen bonds : angle 4.76346 ( 1272) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 158 time to evaluate : 0.275 Fit side-chains REVERT: A 10 ARG cc_start: 0.8179 (mtm-85) cc_final: 0.7802 (mtm-85) REVERT: A 225 CYS cc_start: 0.8599 (m) cc_final: 0.8316 (p) REVERT: A 244 MET cc_start: 0.9113 (tpp) cc_final: 0.8676 (tpt) REVERT: B 298 ASP cc_start: 0.7573 (t70) cc_final: 0.7323 (t70) REVERT: E 158 CYS cc_start: 0.7226 (t) cc_final: 0.6949 (t) REVERT: E 195 ARG cc_start: 0.7181 (tmt170) cc_final: 0.6885 (ttp80) REVERT: E 197 LYS cc_start: 0.7385 (tppt) cc_final: 0.6629 (tptm) REVERT: E 200 TYR cc_start: 0.7867 (t80) cc_final: 0.7659 (t80) REVERT: E 250 LEU cc_start: 0.8316 (tp) cc_final: 0.8060 (tp) REVERT: G 38 MET cc_start: 0.6026 (OUTLIER) cc_final: 0.5574 (pmm) REVERT: S 34 MET cc_start: 0.8669 (mmm) cc_final: 0.8270 (mmm) REVERT: S 180 MET cc_start: 0.7348 (ptt) cc_final: 0.6905 (ptt) REVERT: S 217 CYS cc_start: 0.6629 (p) cc_final: 0.6184 (p) REVERT: S 219 GLN cc_start: 0.9244 (pp30) cc_final: 0.8944 (pp30) outliers start: 18 outliers final: 9 residues processed: 166 average time/residue: 0.0845 time to fit residues: 19.4646 Evaluate side-chains 144 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 134 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain G residue 38 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 16 optimal weight: 8.9990 chunk 4 optimal weight: 0.0980 chunk 90 optimal weight: 0.0980 chunk 23 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 chunk 92 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 61 optimal weight: 7.9990 chunk 43 optimal weight: 6.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN E 92 GLN E 174 GLN S 159 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.197003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.156199 restraints weight = 11178.513| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 3.13 r_work: 0.3675 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8906 Z= 0.111 Angle : 0.545 6.763 12094 Z= 0.283 Chirality : 0.041 0.175 1380 Planarity : 0.004 0.056 1531 Dihedral : 4.374 66.445 1205 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.13 % Allowed : 17.47 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.30 (0.26), residues: 1104 helix: 2.12 (0.25), residues: 387 sheet: -0.62 (0.31), residues: 273 loop : -0.96 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 219 TYR 0.019 0.001 TYR S 101 PHE 0.020 0.001 PHE E 177 TRP 0.022 0.001 TRP E 188 HIS 0.004 0.001 HIS E 289 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 8904) covalent geometry : angle 0.54416 (12090) SS BOND : bond 0.00373 ( 2) SS BOND : angle 1.28231 ( 4) hydrogen bonds : bond 0.03725 ( 447) hydrogen bonds : angle 4.62475 ( 1272) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 154 time to evaluate : 0.225 Fit side-chains REVERT: A 244 MET cc_start: 0.9094 (tpp) cc_final: 0.8638 (tpt) REVERT: B 298 ASP cc_start: 0.7604 (t70) cc_final: 0.7300 (t70) REVERT: E 158 CYS cc_start: 0.7106 (t) cc_final: 0.6823 (t) REVERT: E 195 ARG cc_start: 0.7107 (tmt170) cc_final: 0.6785 (ttp80) REVERT: E 197 LYS cc_start: 0.7374 (tppt) cc_final: 0.6631 (tptm) REVERT: E 250 LEU cc_start: 0.8303 (tp) cc_final: 0.8078 (tp) REVERT: G 21 MET cc_start: 0.5440 (mpp) cc_final: 0.5165 (mpp) REVERT: G 38 MET cc_start: 0.6011 (OUTLIER) cc_final: 0.5559 (pmm) REVERT: S 34 MET cc_start: 0.8560 (mmm) cc_final: 0.8310 (mmm) REVERT: S 36 TRP cc_start: 0.8035 (m100) cc_final: 0.7465 (m100) REVERT: S 128 MET cc_start: 0.8482 (mmm) cc_final: 0.7112 (mmm) REVERT: S 180 MET cc_start: 0.7400 (ptt) cc_final: 0.7043 (ptt) REVERT: S 217 CYS cc_start: 0.6363 (p) cc_final: 0.5745 (p) REVERT: S 219 GLN cc_start: 0.9220 (pp30) cc_final: 0.8786 (pp30) REVERT: S 221 LEU cc_start: 0.8679 (tp) cc_final: 0.8188 (tp) outliers start: 20 outliers final: 13 residues processed: 165 average time/residue: 0.0834 time to fit residues: 19.0612 Evaluate side-chains 162 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 148 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain G residue 38 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 0.5980 chunk 92 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN A 347 ASN S 159 ASN S 174 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.194374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.149696 restraints weight = 11176.672| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 2.77 r_work: 0.3667 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8906 Z= 0.152 Angle : 0.563 6.894 12094 Z= 0.295 Chirality : 0.042 0.175 1380 Planarity : 0.004 0.054 1531 Dihedral : 4.517 70.056 1205 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.66 % Allowed : 18.74 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.30 (0.26), residues: 1104 helix: 2.13 (0.25), residues: 388 sheet: -0.66 (0.31), residues: 268 loop : -0.94 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 10 TYR 0.023 0.001 TYR E 200 PHE 0.020 0.001 PHE E 177 TRP 0.020 0.002 TRP E 188 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 8904) covalent geometry : angle 0.56305 (12090) SS BOND : bond 0.00176 ( 2) SS BOND : angle 1.16415 ( 4) hydrogen bonds : bond 0.03896 ( 447) hydrogen bonds : angle 4.64310 ( 1272) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 0.241 Fit side-chains revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8073 (mtm-85) cc_final: 0.7786 (mtm-85) REVERT: A 244 MET cc_start: 0.9105 (tpp) cc_final: 0.8658 (tpt) REVERT: B 217 MET cc_start: 0.7790 (ptp) cc_final: 0.7428 (ptm) REVERT: B 298 ASP cc_start: 0.7597 (t70) cc_final: 0.7272 (t70) REVERT: E 92 GLN cc_start: 0.8122 (mp-120) cc_final: 0.7891 (mp10) REVERT: E 158 CYS cc_start: 0.7086 (t) cc_final: 0.6797 (t) REVERT: E 187 CYS cc_start: 0.7069 (OUTLIER) cc_final: 0.6681 (t) REVERT: E 197 LYS cc_start: 0.7291 (tppt) cc_final: 0.7052 (tptp) REVERT: E 250 LEU cc_start: 0.8278 (tp) cc_final: 0.8028 (tp) REVERT: G 38 MET cc_start: 0.6025 (OUTLIER) cc_final: 0.5604 (pmm) REVERT: S 34 MET cc_start: 0.8556 (mmm) cc_final: 0.8324 (mmm) REVERT: S 36 TRP cc_start: 0.8016 (m100) cc_final: 0.7483 (m100) REVERT: S 58 ILE cc_start: 0.9142 (mp) cc_final: 0.8929 (mp) REVERT: S 128 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.7560 (mmm) REVERT: S 180 MET cc_start: 0.7350 (ptt) cc_final: 0.7074 (ptt) REVERT: S 219 GLN cc_start: 0.9269 (pp30) cc_final: 0.8846 (pp30) REVERT: S 221 LEU cc_start: 0.8655 (tp) cc_final: 0.8064 (tp) outliers start: 25 outliers final: 17 residues processed: 164 average time/residue: 0.0733 time to fit residues: 16.8613 Evaluate side-chains 167 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 147 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 187 CYS Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 218 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 33 optimal weight: 0.8980 chunk 95 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 88 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 98 optimal weight: 7.9990 chunk 73 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN A 347 ASN S 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.191925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.142215 restraints weight = 11121.611| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 3.00 r_work: 0.3618 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8906 Z= 0.186 Angle : 0.598 8.073 12094 Z= 0.311 Chirality : 0.043 0.187 1380 Planarity : 0.004 0.052 1531 Dihedral : 4.678 71.584 1205 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.19 % Allowed : 19.38 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.15 (0.25), residues: 1104 helix: 2.00 (0.25), residues: 388 sheet: -0.81 (0.30), residues: 274 loop : -0.98 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 10 TYR 0.021 0.002 TYR E 200 PHE 0.022 0.002 PHE E 177 TRP 0.021 0.002 TRP E 188 HIS 0.005 0.001 HIS E 263 Details of bonding type rmsd covalent geometry : bond 0.00431 ( 8904) covalent geometry : angle 0.59696 (12090) SS BOND : bond 0.00123 ( 2) SS BOND : angle 1.70275 ( 4) hydrogen bonds : bond 0.04127 ( 447) hydrogen bonds : angle 4.72321 ( 1272) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 152 time to evaluate : 0.225 Fit side-chains revert: symmetry clash REVERT: A 28 ILE cc_start: 0.7879 (OUTLIER) cc_final: 0.7426 (tp) REVERT: A 244 MET cc_start: 0.9111 (tpp) cc_final: 0.8664 (tpt) REVERT: B 217 MET cc_start: 0.7797 (ptp) cc_final: 0.7115 (ptm) REVERT: B 219 ARG cc_start: 0.8007 (mmp80) cc_final: 0.7310 (mmp80) REVERT: B 220 GLN cc_start: 0.7312 (mt0) cc_final: 0.6919 (mt0) REVERT: E 158 CYS cc_start: 0.6994 (t) cc_final: 0.6704 (t) REVERT: E 197 LYS cc_start: 0.7375 (tppt) cc_final: 0.6762 (tptp) REVERT: E 200 TYR cc_start: 0.7256 (t80) cc_final: 0.7012 (t80) REVERT: G 38 MET cc_start: 0.6048 (OUTLIER) cc_final: 0.5620 (pmm) REVERT: S 34 MET cc_start: 0.8575 (mmm) cc_final: 0.8354 (mmm) REVERT: S 36 TRP cc_start: 0.8038 (m100) cc_final: 0.7554 (m100) REVERT: S 128 MET cc_start: 0.8204 (mmm) cc_final: 0.7932 (mtp) REVERT: S 180 MET cc_start: 0.7385 (ptt) cc_final: 0.7120 (ptt) REVERT: S 219 GLN cc_start: 0.9272 (pp30) cc_final: 0.8845 (pp30) outliers start: 30 outliers final: 21 residues processed: 165 average time/residue: 0.0728 time to fit residues: 16.9203 Evaluate side-chains 168 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 218 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 26 optimal weight: 3.9990 chunk 23 optimal weight: 0.4980 chunk 104 optimal weight: 0.0030 chunk 54 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 19 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN A 347 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.197312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.151076 restraints weight = 11165.402| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 3.10 r_work: 0.3673 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8906 Z= 0.115 Angle : 0.565 8.905 12094 Z= 0.290 Chirality : 0.042 0.181 1380 Planarity : 0.004 0.050 1531 Dihedral : 4.471 68.473 1205 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.98 % Allowed : 19.70 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.37 (0.26), residues: 1104 helix: 2.22 (0.25), residues: 383 sheet: -0.60 (0.30), residues: 281 loop : -0.92 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 10 TYR 0.016 0.001 TYR E 200 PHE 0.024 0.001 PHE E 177 TRP 0.020 0.001 TRP B 82 HIS 0.004 0.001 HIS E 289 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 8904) covalent geometry : angle 0.56377 (12090) SS BOND : bond 0.00348 ( 2) SS BOND : angle 1.92500 ( 4) hydrogen bonds : bond 0.03717 ( 447) hydrogen bonds : angle 4.60441 ( 1272) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 157 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.7951 (mtm-85) cc_final: 0.7549 (mtm-85) REVERT: A 28 ILE cc_start: 0.7779 (OUTLIER) cc_final: 0.7369 (tp) REVERT: A 244 MET cc_start: 0.9095 (tpp) cc_final: 0.8645 (tpt) REVERT: B 217 MET cc_start: 0.7803 (ptp) cc_final: 0.7052 (ptm) REVERT: B 219 ARG cc_start: 0.7990 (mmp80) cc_final: 0.7344 (mmp80) REVERT: B 220 GLN cc_start: 0.7264 (mt0) cc_final: 0.7003 (mt0) REVERT: B 277 SER cc_start: 0.8729 (p) cc_final: 0.8451 (m) REVERT: B 298 ASP cc_start: 0.7525 (t70) cc_final: 0.7277 (t70) REVERT: E 92 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.7385 (mp10) REVERT: E 158 CYS cc_start: 0.7051 (t) cc_final: 0.6768 (t) REVERT: E 197 LYS cc_start: 0.7246 (tppt) cc_final: 0.6623 (tptp) REVERT: E 200 TYR cc_start: 0.7198 (t80) cc_final: 0.6950 (t80) REVERT: E 250 LEU cc_start: 0.8300 (tp) cc_final: 0.8081 (tp) REVERT: G 38 MET cc_start: 0.5945 (OUTLIER) cc_final: 0.5495 (pmm) REVERT: S 36 TRP cc_start: 0.7977 (m100) cc_final: 0.7522 (m100) REVERT: S 180 MET cc_start: 0.7311 (ptt) cc_final: 0.7070 (ptt) REVERT: S 219 GLN cc_start: 0.9181 (pp30) cc_final: 0.8853 (pp30) REVERT: S 221 LEU cc_start: 0.8676 (tp) cc_final: 0.8105 (tp) REVERT: S 232 LYS cc_start: 0.8606 (tptp) cc_final: 0.8307 (tptt) outliers start: 28 outliers final: 18 residues processed: 173 average time/residue: 0.0810 time to fit residues: 19.6916 Evaluate side-chains 168 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 305 GLN Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain E residue 92 GLN Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 218 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 0.3980 chunk 41 optimal weight: 7.9990 chunk 1 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 87 optimal weight: 0.0970 chunk 65 optimal weight: 8.9990 chunk 95 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.198790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.157080 restraints weight = 11023.553| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 3.03 r_work: 0.3692 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8906 Z= 0.116 Angle : 0.565 10.451 12094 Z= 0.291 Chirality : 0.042 0.173 1380 Planarity : 0.004 0.049 1531 Dihedral : 4.421 68.906 1205 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.77 % Allowed : 20.34 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.41 (0.26), residues: 1104 helix: 2.20 (0.25), residues: 386 sheet: -0.55 (0.31), residues: 276 loop : -0.88 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 10 TYR 0.015 0.001 TYR E 200 PHE 0.024 0.001 PHE E 177 TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS E 228 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 8904) covalent geometry : angle 0.56385 (12090) SS BOND : bond 0.00176 ( 2) SS BOND : angle 2.03554 ( 4) hydrogen bonds : bond 0.03659 ( 447) hydrogen bonds : angle 4.55967 ( 1272) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 ILE cc_start: 0.7799 (OUTLIER) cc_final: 0.7401 (tp) REVERT: A 244 MET cc_start: 0.9091 (tpp) cc_final: 0.8632 (tpt) REVERT: B 217 MET cc_start: 0.7781 (ptp) cc_final: 0.7018 (ptm) REVERT: B 219 ARG cc_start: 0.7966 (mmp80) cc_final: 0.7404 (mmp80) REVERT: B 220 GLN cc_start: 0.7111 (mt0) cc_final: 0.6878 (mt0) REVERT: B 298 ASP cc_start: 0.7460 (t70) cc_final: 0.7204 (t70) REVERT: E 158 CYS cc_start: 0.7051 (t) cc_final: 0.6787 (t) REVERT: E 197 LYS cc_start: 0.7207 (tppt) cc_final: 0.6727 (tptp) REVERT: E 250 LEU cc_start: 0.8321 (tp) cc_final: 0.8086 (tp) REVERT: G 38 MET cc_start: 0.5949 (OUTLIER) cc_final: 0.5691 (pmm) REVERT: S 36 TRP cc_start: 0.8041 (m100) cc_final: 0.7625 (m100) REVERT: S 65 LYS cc_start: 0.8278 (mtmm) cc_final: 0.8006 (mppt) REVERT: S 128 MET cc_start: 0.8086 (mtp) cc_final: 0.7805 (mmm) REVERT: S 180 MET cc_start: 0.7357 (ptt) cc_final: 0.7132 (ptt) REVERT: S 219 GLN cc_start: 0.9090 (pp30) cc_final: 0.8643 (pp30) REVERT: S 221 LEU cc_start: 0.8690 (tp) cc_final: 0.8173 (tp) outliers start: 26 outliers final: 17 residues processed: 159 average time/residue: 0.0811 time to fit residues: 18.0658 Evaluate side-chains 162 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 305 GLN Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 175 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 65 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 14 optimal weight: 0.0870 chunk 73 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 37 optimal weight: 8.9990 chunk 84 optimal weight: 6.9990 chunk 87 optimal weight: 10.0000 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN A 347 ASN S 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.193097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.151605 restraints weight = 11516.595| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 3.32 r_work: 0.3672 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 8906 Z= 0.231 Angle : 0.661 8.743 12094 Z= 0.345 Chirality : 0.044 0.149 1380 Planarity : 0.004 0.049 1531 Dihedral : 4.916 74.322 1205 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.66 % Allowed : 20.13 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.19 (0.26), residues: 1104 helix: 1.97 (0.25), residues: 386 sheet: -0.70 (0.31), residues: 276 loop : -0.94 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 314 TYR 0.019 0.002 TYR E 200 PHE 0.024 0.002 PHE E 177 TRP 0.022 0.002 TRP E 188 HIS 0.006 0.001 HIS E 263 Details of bonding type rmsd covalent geometry : bond 0.00536 ( 8904) covalent geometry : angle 0.66050 (12090) SS BOND : bond 0.00274 ( 2) SS BOND : angle 1.92056 ( 4) hydrogen bonds : bond 0.04427 ( 447) hydrogen bonds : angle 4.79362 ( 1272) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 141 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: A 28 ILE cc_start: 0.7938 (OUTLIER) cc_final: 0.7565 (tp) REVERT: A 244 MET cc_start: 0.9065 (tpp) cc_final: 0.8583 (tpt) REVERT: B 59 TYR cc_start: 0.9016 (m-80) cc_final: 0.8509 (m-80) REVERT: B 199 PHE cc_start: 0.6777 (p90) cc_final: 0.6568 (p90) REVERT: B 217 MET cc_start: 0.7866 (ptp) cc_final: 0.7133 (ptm) REVERT: B 219 ARG cc_start: 0.8097 (mmp80) cc_final: 0.7448 (mmp80) REVERT: B 220 GLN cc_start: 0.7341 (mt0) cc_final: 0.7008 (mt0) REVERT: B 298 ASP cc_start: 0.7622 (t70) cc_final: 0.7403 (t70) REVERT: E 92 GLN cc_start: 0.8160 (mp10) cc_final: 0.7604 (mp10) REVERT: E 129 MET cc_start: 0.7874 (tpp) cc_final: 0.7637 (ttm) REVERT: E 158 CYS cc_start: 0.7241 (t) cc_final: 0.6962 (t) REVERT: E 197 LYS cc_start: 0.7500 (tppt) cc_final: 0.7000 (tptp) REVERT: G 38 MET cc_start: 0.6283 (OUTLIER) cc_final: 0.5726 (pmm) REVERT: S 36 TRP cc_start: 0.8184 (m100) cc_final: 0.7790 (m100) REVERT: S 180 MET cc_start: 0.7616 (ptt) cc_final: 0.7303 (ptt) REVERT: S 219 GLN cc_start: 0.9210 (pp30) cc_final: 0.8853 (pp30) REVERT: S 232 LYS cc_start: 0.8726 (tptp) cc_final: 0.8377 (tptt) outliers start: 25 outliers final: 18 residues processed: 158 average time/residue: 0.0892 time to fit residues: 19.4342 Evaluate side-chains 155 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 174 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 93 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 77 optimal weight: 0.0980 chunk 104 optimal weight: 8.9990 chunk 16 optimal weight: 8.9990 chunk 74 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN A 347 ASN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.197799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.156801 restraints weight = 11470.070| |-----------------------------------------------------------------------------| r_work (start): 0.3984 rms_B_bonded: 3.16 r_work: 0.3739 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8906 Z= 0.135 Angle : 0.614 8.961 12094 Z= 0.318 Chirality : 0.043 0.169 1380 Planarity : 0.004 0.049 1531 Dihedral : 4.646 69.144 1205 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.13 % Allowed : 20.55 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.28 (0.26), residues: 1104 helix: 2.09 (0.26), residues: 380 sheet: -0.62 (0.31), residues: 276 loop : -0.92 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 10 TYR 0.015 0.001 TYR S 178 PHE 0.014 0.001 PHE S 80 TRP 0.016 0.002 TRP B 82 HIS 0.004 0.001 HIS E 289 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 8904) covalent geometry : angle 0.61289 (12090) SS BOND : bond 0.00207 ( 2) SS BOND : angle 1.64147 ( 4) hydrogen bonds : bond 0.03969 ( 447) hydrogen bonds : angle 4.66807 ( 1272) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 147 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 ILE cc_start: 0.7831 (OUTLIER) cc_final: 0.7467 (tp) REVERT: A 244 MET cc_start: 0.9066 (tpp) cc_final: 0.8575 (tpt) REVERT: A 313 ARG cc_start: 0.8471 (ttp-110) cc_final: 0.7964 (ptt-90) REVERT: B 217 MET cc_start: 0.7845 (ptp) cc_final: 0.7137 (ptm) REVERT: B 219 ARG cc_start: 0.8010 (mmp80) cc_final: 0.7479 (mmp80) REVERT: B 220 GLN cc_start: 0.7274 (mt0) cc_final: 0.7043 (mt0) REVERT: B 298 ASP cc_start: 0.7532 (t70) cc_final: 0.7300 (t70) REVERT: B 316 SER cc_start: 0.6935 (OUTLIER) cc_final: 0.6512 (m) REVERT: E 81 ASP cc_start: 0.7295 (t70) cc_final: 0.6820 (t70) REVERT: E 129 MET cc_start: 0.7826 (tpp) cc_final: 0.7415 (ttm) REVERT: E 158 CYS cc_start: 0.7144 (t) cc_final: 0.6878 (t) REVERT: E 197 LYS cc_start: 0.7473 (tppt) cc_final: 0.6970 (tptp) REVERT: G 38 MET cc_start: 0.6184 (OUTLIER) cc_final: 0.5639 (pmm) REVERT: S 36 TRP cc_start: 0.8161 (m100) cc_final: 0.7803 (m100) REVERT: S 65 LYS cc_start: 0.8318 (mtmm) cc_final: 0.8113 (mppt) REVERT: S 180 MET cc_start: 0.7561 (ptt) cc_final: 0.7273 (ptt) REVERT: S 219 GLN cc_start: 0.9124 (pp30) cc_final: 0.8865 (pp30) REVERT: S 232 LYS cc_start: 0.8760 (tptp) cc_final: 0.8399 (tptt) outliers start: 20 outliers final: 12 residues processed: 160 average time/residue: 0.0902 time to fit residues: 19.9878 Evaluate side-chains 156 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 141 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 143 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 73 optimal weight: 0.9980 chunk 101 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 chunk 96 optimal weight: 0.0070 chunk 32 optimal weight: 0.6980 chunk 51 optimal weight: 6.9990 chunk 104 optimal weight: 20.0000 chunk 6 optimal weight: 0.4980 chunk 18 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN A 347 ASN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.200500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.159403 restraints weight = 11489.409| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 3.10 r_work: 0.3785 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8906 Z= 0.119 Angle : 0.582 8.413 12094 Z= 0.302 Chirality : 0.042 0.150 1380 Planarity : 0.004 0.048 1531 Dihedral : 4.475 68.480 1205 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.81 % Allowed : 20.77 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.35 (0.26), residues: 1104 helix: 2.18 (0.26), residues: 379 sheet: -0.57 (0.31), residues: 280 loop : -0.91 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 10 TYR 0.014 0.001 TYR S 178 PHE 0.027 0.001 PHE E 177 TRP 0.016 0.001 TRP B 82 HIS 0.006 0.001 HIS E 289 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 8904) covalent geometry : angle 0.58114 (12090) SS BOND : bond 0.00344 ( 2) SS BOND : angle 2.20053 ( 4) hydrogen bonds : bond 0.03696 ( 447) hydrogen bonds : angle 4.59450 ( 1272) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1982.02 seconds wall clock time: 34 minutes 46.84 seconds (2086.84 seconds total)