Starting phenix.real_space_refine on Wed Jun 3 21:09:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7td3_25822/06_2026/7td3_25822.cif Found real_map, /net/cci-nas-00/data/ceres_data/7td3_25822/06_2026/7td3_25822.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7td3_25822/06_2026/7td3_25822.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7td3_25822/06_2026/7td3_25822.map" model { file = "/net/cci-nas-00/data/ceres_data/7td3_25822/06_2026/7td3_25822.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7td3_25822/06_2026/7td3_25822.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.975 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2072 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 53 5.16 5 C 4503 2.51 5 N 1193 2.21 5 O 1285 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7035 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 2556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2556 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 2, 'ARG:plan': 2, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 36 Chain: "A" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1759 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "G" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 405 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "R" Number of atoms: 2276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2276 Classifications: {'peptide': 292} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 6, 'TRANS': 285} Chain breaks: 2 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'NAG': 1, 'S1P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.94, per 1000 atoms: 0.28 Number of scatterers: 7035 At special positions: 0 Unit cell: (93.138, 95.304, 132.126, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 53 16.00 P 1 15.00 O 1285 8.00 N 1193 7.00 C 4503 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 184 " - pdb=" SG CYS R 191 " distance=2.03 Simple disulfide: pdb=" SG CYS R 282 " - pdb=" SG CYS R 287 " distance=2.01 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 Links applied NAG-ASN " NAG R 402 " - " ASN R 30 " Time building additional restraints: 0.62 Conformation dependent library (CDL) restraints added in 382.1 milliseconds 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1724 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 8 sheets defined 46.8% alpha, 18.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'B' and resid 3 through 24 removed outlier: 4.257A pdb=" N ALA B 11 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'A' and resid 8 through 31 Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.603A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 removed outlier: 4.053A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.721A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 352 Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.623A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.941A 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 'G' and resid 55 through 59 removed outlier: 3.506A pdb=" N ASN G 59 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 21 through 32 removed outlier: 4.277A pdb=" N ILE R 25 " --> pdb=" O ASN R 21 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL R 26 " --> pdb=" O TYR R 22 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 72 Processing helix chain 'R' and resid 73 through 77 Processing helix chain 'R' and resid 78 through 104 removed outlier: 3.612A pdb=" N TYR R 82 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing helix chain 'R' and resid 105 through 112 removed outlier: 3.508A pdb=" N THR R 108 " --> pdb=" O SER R 105 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR R 109 " --> pdb=" O GLY R 106 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N TYR R 110 " --> pdb=" O ALA R 107 " (cutoff:3.500A) Processing helix chain 'R' and resid 113 through 149 removed outlier: 3.786A pdb=" N MET R 124 " --> pdb=" O ARG R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 156 through 176 removed outlier: 3.623A pdb=" N LEU R 160 " --> pdb=" O ASN R 156 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE R 164 " --> pdb=" O LEU R 160 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA R 166 " --> pdb=" O LEU R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 199 through 234 removed outlier: 3.772A pdb=" N ARG R 234 " --> pdb=" O THR R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 249 through 282 removed outlier: 3.511A pdb=" N LEU R 255 " --> pdb=" O SER R 251 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N CYS R 268 " --> pdb=" O VAL R 264 " (cutoff:3.500A) Proline residue: R 271 - end of helix Processing helix chain 'R' and resid 288 through 292 Processing helix chain 'R' and resid 293 through 314 removed outlier: 3.638A pdb=" N VAL R 298 " --> pdb=" O GLU R 294 " (cutoff:3.500A) Proline residue: R 308 - end of helix removed outlier: 3.572A pdb=" N THR R 314 " --> pdb=" O ILE R 310 " (cutoff:3.500A) Processing helix chain 'R' and resid 317 through 323 removed outlier: 3.888A pdb=" N ILE R 323 " --> pdb=" O ARG R 319 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.522A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.702A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.655A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.503A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.978A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.475A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.476A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.375A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) 377 hydrogen bonds defined for protein. 1074 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: 1.14 Time building geometry restraints manager: 0.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 1124 1.30 - 1.43: 1871 1.43 - 1.56: 4096 1.56 - 1.69: 1 1.69 - 1.83: 75 Bond restraints: 7167 Sorted by residual: bond pdb=" O1 S1P R 401 " pdb=" P22 S1P R 401 " ideal model delta sigma weight residual 1.677 1.811 -0.134 2.00e-02 2.50e+03 4.49e+01 bond pdb=" C THR R 145 " pdb=" O THR R 145 " ideal model delta sigma weight residual 1.236 1.164 0.072 1.15e-02 7.56e+03 3.93e+01 bond pdb=" C MET R 146 " pdb=" O MET R 146 " ideal model delta sigma weight residual 1.237 1.164 0.073 1.17e-02 7.31e+03 3.84e+01 bond pdb=" CA SER R 192 " pdb=" CB SER R 192 " ideal model delta sigma weight residual 1.530 1.451 0.078 1.48e-02 4.57e+03 2.81e+01 bond pdb=" C PRO R 79 " pdb=" O PRO R 79 " ideal model delta sigma weight residual 1.237 1.171 0.066 1.26e-02 6.30e+03 2.75e+01 ... (remaining 7162 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 9472 2.22 - 4.43: 193 4.43 - 6.65: 41 6.65 - 8.86: 6 8.86 - 11.08: 5 Bond angle restraints: 9717 Sorted by residual: angle pdb=" C PHE R 65 " pdb=" CA PHE R 65 " pdb=" CB PHE R 65 " ideal model delta sigma weight residual 110.88 100.63 10.25 1.57e+00 4.06e-01 4.26e+01 angle pdb=" C THR R 145 " pdb=" CA THR R 145 " pdb=" CB THR R 145 " ideal model delta sigma weight residual 110.88 101.56 9.32 1.57e+00 4.06e-01 3.53e+01 angle pdb=" CA THR R 193 " pdb=" CB THR R 193 " pdb=" OG1 THR R 193 " ideal model delta sigma weight residual 109.60 100.98 8.62 1.50e+00 4.44e-01 3.30e+01 angle pdb=" CA THR R 145 " pdb=" CB THR R 145 " pdb=" OG1 THR R 145 " ideal model delta sigma weight residual 109.60 101.33 8.27 1.50e+00 4.44e-01 3.04e+01 angle pdb=" O VAL R 284 " pdb=" C VAL R 284 " pdb=" N LYS R 285 " ideal model delta sigma weight residual 122.67 127.83 -5.16 1.09e+00 8.42e-01 2.24e+01 ... (remaining 9712 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.01: 4191 31.01 - 62.02: 78 62.02 - 93.03: 2 93.03 - 124.04: 4 124.04 - 155.04: 2 Dihedral angle restraints: 4277 sinusoidal: 1621 harmonic: 2656 Sorted by residual: dihedral pdb=" CB CYS R 282 " pdb=" SG CYS R 282 " pdb=" SG CYS R 287 " pdb=" CB CYS R 287 " ideal model delta sinusoidal sigma weight residual -86.00 -147.71 61.71 1 1.00e+01 1.00e-02 5.05e+01 dihedral pdb=" C PHE R 65 " pdb=" N PHE R 65 " pdb=" CA PHE R 65 " pdb=" CB PHE R 65 " ideal model delta harmonic sigma weight residual -122.60 -110.13 -12.47 0 2.50e+00 1.60e-01 2.49e+01 dihedral pdb=" C CYS A 351 " pdb=" N CYS A 351 " pdb=" CA CYS A 351 " pdb=" CB CYS A 351 " ideal model delta harmonic sigma weight residual -122.60 -110.75 -11.85 0 2.50e+00 1.60e-01 2.25e+01 ... (remaining 4274 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1040 0.077 - 0.153: 83 0.153 - 0.230: 14 0.230 - 0.306: 7 0.306 - 0.383: 5 Chirality restraints: 1149 Sorted by residual: chirality pdb=" CA MET R 149 " pdb=" N MET R 149 " pdb=" C MET R 149 " pdb=" CB MET R 149 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.66e+00 chirality pdb=" CA ASN R 157 " pdb=" N ASN R 157 " pdb=" C ASN R 157 " pdb=" CB ASN R 157 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CA LYS R 150 " pdb=" N LYS R 150 " pdb=" C LYS R 150 " pdb=" CB LYS R 150 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.61e+00 ... (remaining 1146 not shown) Planarity restraints: 1209 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR R 73 " 0.018 2.00e-02 2.50e+03 3.77e-02 1.42e+01 pdb=" C THR R 73 " -0.065 2.00e-02 2.50e+03 pdb=" O THR R 73 " 0.024 2.00e-02 2.50e+03 pdb=" N LYS R 74 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG R 159 " -0.018 2.00e-02 2.50e+03 3.62e-02 1.31e+01 pdb=" C ARG R 159 " 0.063 2.00e-02 2.50e+03 pdb=" O ARG R 159 " -0.023 2.00e-02 2.50e+03 pdb=" N LEU R 160 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG R 402 " -0.040 2.00e-02 2.50e+03 3.20e-02 1.28e+01 pdb=" C7 NAG R 402 " 0.010 2.00e-02 2.50e+03 pdb=" C8 NAG R 402 " -0.030 2.00e-02 2.50e+03 pdb=" N2 NAG R 402 " 0.049 2.00e-02 2.50e+03 pdb=" O7 NAG R 402 " 0.011 2.00e-02 2.50e+03 ... (remaining 1206 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 66 2.63 - 3.20: 6307 3.20 - 3.76: 10456 3.76 - 4.33: 15362 4.33 - 4.90: 25349 Nonbonded interactions: 57540 Sorted by model distance: nonbonded pdb=" O ASP B 333 " pdb=" OG SER B 334 " model vdw 2.059 3.040 nonbonded pdb=" O THR B 86 " pdb=" OG1 THR B 87 " model vdw 2.193 3.040 nonbonded pdb=" O VAL R 96 " pdb=" OG1 THR R 99 " model vdw 2.334 3.040 nonbonded pdb=" O CYS A 254 " pdb=" NZ LYS A 317 " model vdw 2.336 3.120 nonbonded pdb=" OD1 ASP A 251 " pdb=" ND2 ASN A 255 " model vdw 2.337 3.120 ... (remaining 57535 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: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.770 Find NCS groups from input model: 0.030 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:7.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 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 0.134 7170 Z= 0.393 Angle : 0.793 11.079 9724 Z= 0.497 Chirality : 0.056 0.383 1149 Planarity : 0.005 0.041 1208 Dihedral : 13.047 155.044 2547 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.81 % Allowed : 6.10 % Favored : 93.09 % Cbeta Deviations : 0.35 % 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: -0.45 (0.27), residues: 895 helix: 1.02 (0.27), residues: 386 sheet: -0.51 (0.37), residues: 168 loop : -1.71 (0.29), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 159 TYR 0.009 0.001 TYR R 81 PHE 0.013 0.002 PHE R 65 TRP 0.013 0.002 TRP R 71 HIS 0.004 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00673 / 0.39 ( 7167) covalent geometry : angle 0.79110 / 0.50 ( 9717) SS BOND : bond 0.01294 / 0.62 ( 2) SS BOND : angle 1.92548 / 1.10 ( 4) hydrogen bonds : bond 0.14623 / 10.22 ( 377) hydrogen bonds : angle 5.25930 / 3.62 ( 1074) link_NAG-ASN : bond 0.00167 / 0.09 ( 1) link_NAG-ASN : angle 2.13528 / 1.07 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 197 time to evaluate : 0.349 Fit side-chains REVERT: B 22 ARG cc_start: 0.6830 (mtt180) cc_final: 0.6267 (mpt-90) REVERT: B 175 GLN cc_start: 0.7942 (mm-40) cc_final: 0.7696 (mm110) REVERT: B 197 ARG cc_start: 0.7890 (mtp85) cc_final: 0.7556 (mmm-85) REVERT: B 234 PHE cc_start: 0.9383 (OUTLIER) cc_final: 0.8798 (m-80) REVERT: B 251 ARG cc_start: 0.8553 (mtt-85) cc_final: 0.8232 (mtt-85) REVERT: B 325 MET cc_start: 0.8307 (mmt) cc_final: 0.8032 (mmt) REVERT: B 333 ASP cc_start: 0.8959 (p0) cc_final: 0.8633 (p0) REVERT: A 25 GLU cc_start: 0.7029 (mt-10) cc_final: 0.6818 (mt-10) REVERT: A 29 LYS cc_start: 0.8410 (ttpp) cc_final: 0.8141 (tttp) REVERT: A 32 ARG cc_start: 0.8189 (mtm-85) cc_final: 0.7908 (mtm-85) REVERT: A 242 ARG cc_start: 0.7583 (ttm170) cc_final: 0.7336 (ttm-80) REVERT: A 298 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7201 (tt0) REVERT: A 345 LYS cc_start: 0.8145 (tttt) cc_final: 0.7231 (mttp) REVERT: A 349 LYS cc_start: 0.8464 (mtpt) cc_final: 0.8002 (mtmm) REVERT: G 52 THR cc_start: 0.7643 (m) cc_final: 0.7102 (p) outliers start: 6 outliers final: 2 residues processed: 200 average time/residue: 0.6024 time to fit residues: 126.6008 Evaluate side-chains 153 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 149 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain R residue 148 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.4980 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 266 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 199 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.133825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.102386 restraints weight = 8608.414| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 2.05 r_work: 0.2868 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7170 Z= 0.147 Angle : 0.522 5.778 9724 Z= 0.284 Chirality : 0.043 0.139 1149 Planarity : 0.004 0.048 1208 Dihedral : 10.482 144.937 1032 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.39 % Allowed : 13.41 % Favored : 83.20 % 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: 0.48 (0.28), residues: 895 helix: 2.11 (0.27), residues: 379 sheet: -0.19 (0.38), residues: 170 loop : -1.50 (0.30), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 214 TYR 0.010 0.001 TYR A 287 PHE 0.014 0.002 PHE R 273 TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 ( 7167) covalent geometry : angle 0.52085 / 0.28 ( 9717) SS BOND : bond 0.00433 / 0.21 ( 2) SS BOND : angle 1.28755 / 0.70 ( 4) hydrogen bonds : bond 0.04565 / 3.13 ( 377) hydrogen bonds : angle 4.02379 / 2.77 ( 1074) link_NAG-ASN : bond 0.00143 / 0.08 ( 1) link_NAG-ASN : angle 1.70829 / 0.95 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 165 time to evaluate : 0.272 Fit side-chains REVERT: B 234 PHE cc_start: 0.9437 (OUTLIER) cc_final: 0.8935 (m-80) REVERT: B 268 ASN cc_start: 0.8102 (t0) cc_final: 0.7848 (t0) REVERT: B 303 ASP cc_start: 0.7907 (m-30) cc_final: 0.7674 (m-30) REVERT: A 29 LYS cc_start: 0.8409 (ttpp) cc_final: 0.8119 (tttp) REVERT: A 32 ARG cc_start: 0.8574 (mtm-85) cc_final: 0.8276 (mtm-85) REVERT: A 248 LYS cc_start: 0.8165 (mtpp) cc_final: 0.7674 (mtpt) REVERT: A 298 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7539 (tt0) REVERT: A 345 LYS cc_start: 0.8711 (tttt) cc_final: 0.7693 (tppt) REVERT: A 349 LYS cc_start: 0.8813 (mtpt) cc_final: 0.8471 (mtmm) REVERT: G 38 MET cc_start: 0.7983 (ttp) cc_final: 0.7646 (ttp) outliers start: 25 outliers final: 10 residues processed: 177 average time/residue: 0.5945 time to fit residues: 110.5471 Evaluate side-chains 165 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 153 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 211 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 40 optimal weight: 0.3980 chunk 43 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 54 optimal weight: 0.5980 chunk 82 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.134030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.102551 restraints weight = 8560.636| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.09 r_work: 0.2863 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7170 Z= 0.143 Angle : 0.496 6.000 9724 Z= 0.271 Chirality : 0.042 0.171 1149 Planarity : 0.004 0.051 1208 Dihedral : 9.780 137.357 1028 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 5.56 % Allowed : 14.23 % Favored : 80.22 % 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: 0.62 (0.28), residues: 895 helix: 2.25 (0.27), residues: 391 sheet: -0.24 (0.38), residues: 174 loop : -1.54 (0.31), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 314 TYR 0.011 0.001 TYR R 225 PHE 0.014 0.001 PHE R 58 TRP 0.011 0.001 TRP B 82 HIS 0.002 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 7167) covalent geometry : angle 0.49483 / 0.27 ( 9717) SS BOND : bond 0.00323 / 0.16 ( 2) SS BOND : angle 1.13947 / 0.61 ( 4) hydrogen bonds : bond 0.04419 / 3.05 ( 377) hydrogen bonds : angle 3.90220 / 2.68 ( 1074) link_NAG-ASN : bond 0.00072 / 0.04 ( 1) link_NAG-ASN : angle 1.55091 / 0.87 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 157 time to evaluate : 0.259 Fit side-chains REVERT: B 146 LEU cc_start: 0.9157 (tp) cc_final: 0.8836 (tp) REVERT: B 234 PHE cc_start: 0.9432 (OUTLIER) cc_final: 0.8883 (m-80) REVERT: B 268 ASN cc_start: 0.8230 (t0) cc_final: 0.7887 (t0) REVERT: B 281 SER cc_start: 0.9426 (OUTLIER) cc_final: 0.9217 (p) REVERT: A 29 LYS cc_start: 0.8343 (ttpp) cc_final: 0.8121 (tttp) REVERT: A 32 ARG cc_start: 0.8568 (mtm-85) cc_final: 0.8267 (mtm-85) REVERT: A 232 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7582 (mm) REVERT: A 248 LYS cc_start: 0.8161 (mtpp) cc_final: 0.7670 (mtpt) REVERT: A 276 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7807 (tm-30) REVERT: A 345 LYS cc_start: 0.8663 (tttt) cc_final: 0.7631 (mptt) REVERT: A 349 LYS cc_start: 0.8804 (mtpt) cc_final: 0.8454 (mtmm) REVERT: G 38 MET cc_start: 0.7907 (ttp) cc_final: 0.7531 (ttp) REVERT: R 233 ARG cc_start: 0.7635 (OUTLIER) cc_final: 0.6775 (mtt-85) outliers start: 41 outliers final: 19 residues processed: 175 average time/residue: 0.5634 time to fit residues: 103.8454 Evaluate side-chains 169 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 186 SER Chi-restraints excluded: chain R residue 211 THR Chi-restraints excluded: chain R residue 233 ARG Chi-restraints excluded: chain R residue 252 LEU Chi-restraints excluded: chain R residue 284 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 79 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 36 optimal weight: 0.2980 chunk 80 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 2 optimal weight: 0.0670 chunk 39 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 ASN B 239 ASN ** B 340 ASN ** 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 = 0.3422 r_free = 0.3422 target = 0.134137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.102875 restraints weight = 8647.781| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.03 r_work: 0.2883 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7170 Z= 0.127 Angle : 0.476 5.706 9724 Z= 0.259 Chirality : 0.042 0.159 1149 Planarity : 0.004 0.048 1208 Dihedral : 8.936 124.063 1025 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 4.88 % Allowed : 16.26 % Favored : 78.86 % 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: 0.88 (0.28), residues: 895 helix: 2.48 (0.27), residues: 391 sheet: -0.04 (0.38), residues: 171 loop : -1.46 (0.31), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 256 TYR 0.018 0.001 TYR A 287 PHE 0.016 0.001 PHE R 58 TRP 0.011 0.001 TRP B 82 HIS 0.002 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 7167) covalent geometry : angle 0.47485 / 0.26 ( 9717) SS BOND : bond 0.00235 / 0.12 ( 2) SS BOND : angle 1.11791 / 0.60 ( 4) hydrogen bonds : bond 0.04145 / 2.86 ( 377) hydrogen bonds : angle 3.80697 / 2.61 ( 1074) link_NAG-ASN : bond 0.00036 / 0.02 ( 1) link_NAG-ASN : angle 1.39309 / 0.79 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 159 time to evaluate : 0.277 Fit side-chains REVERT: B 127 LYS cc_start: 0.8490 (mmtt) cc_final: 0.8274 (mmtp) REVERT: B 146 LEU cc_start: 0.9181 (tp) cc_final: 0.8872 (tp) REVERT: B 234 PHE cc_start: 0.9446 (OUTLIER) cc_final: 0.8974 (m-80) REVERT: B 268 ASN cc_start: 0.8286 (t0) cc_final: 0.7923 (t0) REVERT: B 281 SER cc_start: 0.9397 (OUTLIER) cc_final: 0.9167 (p) REVERT: A 29 LYS cc_start: 0.8408 (ttpp) cc_final: 0.8170 (tttp) REVERT: A 32 ARG cc_start: 0.8590 (mtm-85) cc_final: 0.8278 (mtm-85) REVERT: A 248 LYS cc_start: 0.8252 (mtpp) cc_final: 0.7791 (mtpt) REVERT: A 272 ASP cc_start: 0.7961 (m-30) cc_final: 0.7632 (m-30) REVERT: A 298 GLU cc_start: 0.7786 (tt0) cc_final: 0.6958 (tt0) REVERT: A 345 LYS cc_start: 0.8693 (tttt) cc_final: 0.7703 (mptt) REVERT: A 349 LYS cc_start: 0.8808 (mtpt) cc_final: 0.8452 (mtmm) REVERT: G 51 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7995 (mp) REVERT: R 233 ARG cc_start: 0.7635 (OUTLIER) cc_final: 0.6800 (mtt-85) outliers start: 36 outliers final: 16 residues processed: 178 average time/residue: 0.5762 time to fit residues: 107.9014 Evaluate side-chains 173 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 153 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 211 THR Chi-restraints excluded: chain R residue 233 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 29 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 66 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 40 optimal weight: 0.0970 chunk 13 optimal weight: 2.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 237 ASN ** B 340 ASN ** 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 = 0.3429 r_free = 0.3429 target = 0.134684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.103181 restraints weight = 8721.331| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.15 r_work: 0.2867 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7170 Z= 0.130 Angle : 0.474 5.745 9724 Z= 0.257 Chirality : 0.042 0.158 1149 Planarity : 0.004 0.047 1208 Dihedral : 7.666 93.578 1025 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.34 % Allowed : 18.02 % Favored : 77.64 % 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: 0.96 (0.29), residues: 895 helix: 2.56 (0.27), residues: 392 sheet: -0.09 (0.38), residues: 173 loop : -1.40 (0.31), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 314 TYR 0.013 0.001 TYR R 225 PHE 0.018 0.001 PHE R 58 TRP 0.011 0.001 TRP B 82 HIS 0.002 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 7167) covalent geometry : angle 0.47268 / 0.26 ( 9717) SS BOND : bond 0.00219 / 0.11 ( 2) SS BOND : angle 1.06635 / 0.57 ( 4) hydrogen bonds : bond 0.04169 / 2.87 ( 377) hydrogen bonds : angle 3.78150 / 2.60 ( 1074) link_NAG-ASN : bond 0.00041 / 0.02 ( 1) link_NAG-ASN : angle 1.33232 / 0.76 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 161 time to evaluate : 0.285 Fit side-chains REVERT: B 127 LYS cc_start: 0.8434 (mmtt) cc_final: 0.8189 (mmtp) REVERT: B 146 LEU cc_start: 0.9164 (tp) cc_final: 0.8854 (tp) REVERT: B 234 PHE cc_start: 0.9437 (OUTLIER) cc_final: 0.8958 (m-80) REVERT: B 268 ASN cc_start: 0.8275 (t0) cc_final: 0.7912 (t0) REVERT: B 281 SER cc_start: 0.9408 (OUTLIER) cc_final: 0.9160 (p) REVERT: A 29 LYS cc_start: 0.8329 (ttpp) cc_final: 0.8094 (tttp) REVERT: A 32 ARG cc_start: 0.8574 (mtm-85) cc_final: 0.8272 (mtm-85) REVERT: A 242 ARG cc_start: 0.7450 (ttm170) cc_final: 0.7036 (ttm-80) REVERT: A 248 LYS cc_start: 0.8107 (mtpp) cc_final: 0.7625 (mtpt) REVERT: A 298 GLU cc_start: 0.7811 (tt0) cc_final: 0.7003 (tt0) REVERT: A 345 LYS cc_start: 0.8604 (tttt) cc_final: 0.7606 (mptt) REVERT: A 349 LYS cc_start: 0.8733 (mtpt) cc_final: 0.8373 (mtmm) REVERT: G 51 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7859 (mp) REVERT: R 233 ARG cc_start: 0.7623 (OUTLIER) cc_final: 0.6787 (mtt-85) outliers start: 32 outliers final: 18 residues processed: 180 average time/residue: 0.5802 time to fit residues: 109.8962 Evaluate side-chains 177 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 155 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 211 THR Chi-restraints excluded: chain R residue 233 ARG Chi-restraints excluded: chain R residue 252 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 0.2980 chunk 36 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 2 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.134410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.102810 restraints weight = 8710.064| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 2.15 r_work: 0.2863 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7170 Z= 0.141 Angle : 0.479 5.606 9724 Z= 0.261 Chirality : 0.042 0.160 1149 Planarity : 0.004 0.046 1208 Dihedral : 6.831 100.938 1025 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.47 % Allowed : 18.02 % Favored : 77.51 % 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: 1.01 (0.29), residues: 895 helix: 2.56 (0.27), residues: 392 sheet: 0.09 (0.37), residues: 176 loop : -1.43 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 256 TYR 0.014 0.001 TYR R 225 PHE 0.020 0.001 PHE R 58 TRP 0.011 0.001 TRP B 82 HIS 0.002 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 ( 7167) covalent geometry : angle 0.47801 / 0.26 ( 9717) SS BOND : bond 0.00220 / 0.11 ( 2) SS BOND : angle 1.08520 / 0.58 ( 4) hydrogen bonds : bond 0.04271 / 2.94 ( 377) hydrogen bonds : angle 3.82241 / 2.62 ( 1074) link_NAG-ASN : bond 0.00034 / 0.02 ( 1) link_NAG-ASN : angle 1.34542 / 0.77 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 155 time to evaluate : 0.283 Fit side-chains REVERT: B 127 LYS cc_start: 0.8458 (mmtt) cc_final: 0.8228 (mmtp) REVERT: B 146 LEU cc_start: 0.9176 (tp) cc_final: 0.8872 (tp) REVERT: B 234 PHE cc_start: 0.9433 (OUTLIER) cc_final: 0.8985 (m-80) REVERT: B 268 ASN cc_start: 0.8322 (t0) cc_final: 0.7958 (t0) REVERT: A 29 LYS cc_start: 0.8372 (ttpp) cc_final: 0.8132 (tttp) REVERT: A 32 ARG cc_start: 0.8581 (mtm-85) cc_final: 0.8275 (mtm-85) REVERT: A 232 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7674 (mm) REVERT: A 242 ARG cc_start: 0.7437 (ttm170) cc_final: 0.7188 (mtm-85) REVERT: A 248 LYS cc_start: 0.8128 (mtpp) cc_final: 0.7655 (mtpt) REVERT: A 278 ILE cc_start: 0.8006 (tt) cc_final: 0.7754 (tt) REVERT: A 298 GLU cc_start: 0.7836 (tt0) cc_final: 0.7084 (tt0) REVERT: A 345 LYS cc_start: 0.8628 (tttt) cc_final: 0.7652 (mptt) REVERT: A 349 LYS cc_start: 0.8780 (mtpt) cc_final: 0.8422 (mtmm) REVERT: G 51 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7983 (mp) REVERT: R 104 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7718 (mt) REVERT: R 233 ARG cc_start: 0.7661 (OUTLIER) cc_final: 0.6810 (mtt-85) outliers start: 33 outliers final: 22 residues processed: 174 average time/residue: 0.5864 time to fit residues: 107.3128 Evaluate side-chains 177 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 150 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 186 SER Chi-restraints excluded: chain R residue 211 THR Chi-restraints excluded: chain R residue 233 ARG Chi-restraints excluded: chain R residue 252 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 53 optimal weight: 0.8980 chunk 88 optimal weight: 0.0070 chunk 7 optimal weight: 0.5980 chunk 82 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 86 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 27 optimal weight: 0.4980 chunk 13 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS R 77 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.136116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.104668 restraints weight = 8725.569| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.15 r_work: 0.2890 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7170 Z= 0.114 Angle : 0.453 5.732 9724 Z= 0.248 Chirality : 0.041 0.158 1149 Planarity : 0.003 0.045 1208 Dihedral : 6.560 94.801 1025 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 4.47 % Allowed : 18.43 % Favored : 77.10 % 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: 1.13 (0.29), residues: 895 helix: 2.66 (0.27), residues: 392 sheet: 0.20 (0.38), residues: 176 loop : -1.42 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 256 TYR 0.018 0.001 TYR A 287 PHE 0.019 0.001 PHE R 58 TRP 0.011 0.001 TRP B 82 HIS 0.002 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 ( 7167) covalent geometry : angle 0.45243 / 0.25 ( 9717) SS BOND : bond 0.00202 / 0.10 ( 2) SS BOND : angle 1.04182 / 0.55 ( 4) hydrogen bonds : bond 0.03920 / 2.70 ( 377) hydrogen bonds : angle 3.71010 / 2.54 ( 1074) link_NAG-ASN : bond 0.00015 / 0.01 ( 1) link_NAG-ASN : angle 1.29315 / 0.75 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 157 time to evaluate : 0.268 Fit side-chains REVERT: B 127 LYS cc_start: 0.8412 (mmtt) cc_final: 0.8166 (mmtp) REVERT: B 146 LEU cc_start: 0.9162 (tp) cc_final: 0.8863 (tp) REVERT: B 175 GLN cc_start: 0.7692 (mm110) cc_final: 0.7248 (mm110) REVERT: B 234 PHE cc_start: 0.9412 (OUTLIER) cc_final: 0.8968 (m-80) REVERT: B 268 ASN cc_start: 0.8343 (t0) cc_final: 0.7981 (t0) REVERT: A 29 LYS cc_start: 0.8298 (ttpp) cc_final: 0.8069 (tttp) REVERT: A 32 ARG cc_start: 0.8587 (mtm-85) cc_final: 0.8284 (mtm-85) REVERT: A 232 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7695 (mm) REVERT: A 242 ARG cc_start: 0.7354 (ttm170) cc_final: 0.7104 (mtm-85) REVERT: A 248 LYS cc_start: 0.8116 (mtpp) cc_final: 0.7665 (mtpt) REVERT: A 278 ILE cc_start: 0.7942 (tt) cc_final: 0.7693 (tt) REVERT: A 298 GLU cc_start: 0.7794 (tt0) cc_final: 0.6993 (tt0) REVERT: A 345 LYS cc_start: 0.8598 (tttt) cc_final: 0.7617 (mptt) REVERT: A 349 LYS cc_start: 0.8740 (mtpt) cc_final: 0.8380 (mtmm) REVERT: G 51 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7951 (mp) REVERT: R 104 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7744 (mt) REVERT: R 233 ARG cc_start: 0.7596 (OUTLIER) cc_final: 0.6755 (mtt-85) outliers start: 33 outliers final: 21 residues processed: 178 average time/residue: 0.6028 time to fit residues: 112.7439 Evaluate side-chains 186 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 160 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 186 SER Chi-restraints excluded: chain R residue 233 ARG Chi-restraints excluded: chain R residue 252 LEU Chi-restraints excluded: chain R residue 266 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 27 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 73 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 26 optimal weight: 0.3980 chunk 60 optimal weight: 0.0370 chunk 13 optimal weight: 0.0980 chunk 46 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 overall best weight: 0.3858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN B 75 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.137152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.105500 restraints weight = 8680.451| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.17 r_work: 0.2910 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7170 Z= 0.104 Angle : 0.445 5.770 9724 Z= 0.242 Chirality : 0.041 0.157 1149 Planarity : 0.003 0.045 1208 Dihedral : 6.473 94.760 1025 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.93 % Allowed : 19.38 % Favored : 76.69 % 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: 1.16 (0.29), residues: 895 helix: 2.71 (0.27), residues: 394 sheet: 0.20 (0.38), residues: 178 loop : -1.45 (0.32), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 256 TYR 0.013 0.001 TYR R 225 PHE 0.018 0.001 PHE R 58 TRP 0.011 0.001 TRP B 82 HIS 0.002 0.000 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 ( 7167) covalent geometry : angle 0.44376 / 0.24 ( 9717) SS BOND : bond 0.00196 / 0.10 ( 2) SS BOND : angle 1.08394 / 0.58 ( 4) hydrogen bonds : bond 0.03730 / 2.58 ( 377) hydrogen bonds : angle 3.62408 / 2.49 ( 1074) link_NAG-ASN : bond 0.00015 / 0.01 ( 1) link_NAG-ASN : angle 1.19401 / 0.69 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 160 time to evaluate : 0.270 Fit side-chains REVERT: B 127 LYS cc_start: 0.8417 (mmtt) cc_final: 0.8178 (mmtp) REVERT: B 146 LEU cc_start: 0.9164 (tp) cc_final: 0.8863 (tp) REVERT: B 175 GLN cc_start: 0.7712 (mm110) cc_final: 0.7283 (mm110) REVERT: B 234 PHE cc_start: 0.9419 (OUTLIER) cc_final: 0.8930 (m-80) REVERT: B 268 ASN cc_start: 0.8339 (t0) cc_final: 0.7979 (t0) REVERT: B 333 ASP cc_start: 0.9113 (p0) cc_final: 0.8860 (p0) REVERT: A 32 ARG cc_start: 0.8594 (mtm-85) cc_final: 0.8242 (mtm-85) REVERT: A 232 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7653 (mm) REVERT: A 242 ARG cc_start: 0.7337 (ttm170) cc_final: 0.6877 (mtt90) REVERT: A 248 LYS cc_start: 0.8137 (mtpp) cc_final: 0.7692 (mtpt) REVERT: A 298 GLU cc_start: 0.7783 (tt0) cc_final: 0.7001 (tt0) REVERT: A 345 LYS cc_start: 0.8608 (tttt) cc_final: 0.7637 (mptt) REVERT: A 349 LYS cc_start: 0.8735 (mtpt) cc_final: 0.8291 (mtmm) REVERT: G 51 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.8000 (mp) REVERT: R 104 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7754 (mt) REVERT: R 233 ARG cc_start: 0.7570 (OUTLIER) cc_final: 0.6760 (mtt-85) outliers start: 29 outliers final: 19 residues processed: 175 average time/residue: 0.5982 time to fit residues: 109.9517 Evaluate side-chains 176 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 152 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 186 SER Chi-restraints excluded: chain R residue 233 ARG Chi-restraints excluded: chain R residue 252 LEU Chi-restraints excluded: chain R residue 266 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 9 optimal weight: 0.5980 chunk 88 optimal weight: 0.0000 chunk 67 optimal weight: 0.8980 chunk 2 optimal weight: 0.0870 chunk 39 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 81 optimal weight: 0.0370 chunk 63 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 48 optimal weight: 0.4980 overall best weight: 0.2440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.138769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.107924 restraints weight = 8682.950| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.06 r_work: 0.2952 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7170 Z= 0.092 Angle : 0.435 5.774 9724 Z= 0.237 Chirality : 0.041 0.155 1149 Planarity : 0.003 0.045 1208 Dihedral : 6.242 91.271 1025 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.12 % Allowed : 20.33 % Favored : 76.56 % 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: 1.26 (0.29), residues: 895 helix: 2.75 (0.26), residues: 394 sheet: 0.37 (0.39), residues: 178 loop : -1.42 (0.32), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 219 TYR 0.013 0.001 TYR R 225 PHE 0.018 0.001 PHE R 58 TRP 0.011 0.001 TRP B 99 HIS 0.002 0.000 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00192 / 0.09 ( 7167) covalent geometry : angle 0.43444 / 0.24 ( 9717) SS BOND : bond 0.00201 / 0.10 ( 2) SS BOND : angle 1.03801 / 0.55 ( 4) hydrogen bonds : bond 0.03414 / 2.35 ( 377) hydrogen bonds : angle 3.52252 / 2.42 ( 1074) link_NAG-ASN : bond 0.00044 / 0.02 ( 1) link_NAG-ASN : angle 1.13291 / 0.65 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 0.406 Fit side-chains REVERT: B 146 LEU cc_start: 0.9168 (tp) cc_final: 0.8880 (tp) REVERT: B 234 PHE cc_start: 0.9435 (OUTLIER) cc_final: 0.8990 (m-80) REVERT: B 268 ASN cc_start: 0.8326 (t0) cc_final: 0.7979 (t0) REVERT: B 333 ASP cc_start: 0.9106 (p0) cc_final: 0.8851 (p0) REVERT: A 20 ASP cc_start: 0.8192 (m-30) cc_final: 0.7797 (m-30) REVERT: A 232 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7619 (mm) REVERT: A 242 ARG cc_start: 0.7334 (ttm170) cc_final: 0.6906 (mtt90) REVERT: A 248 LYS cc_start: 0.8171 (mtpp) cc_final: 0.7740 (mtpt) REVERT: A 270 LYS cc_start: 0.8564 (mmtt) cc_final: 0.8284 (mmtm) REVERT: A 298 GLU cc_start: 0.7754 (tt0) cc_final: 0.6986 (tt0) REVERT: A 309 ASP cc_start: 0.8021 (m-30) cc_final: 0.7491 (p0) REVERT: A 345 LYS cc_start: 0.8604 (tttt) cc_final: 0.7693 (mptt) REVERT: A 349 LYS cc_start: 0.8708 (mtpt) cc_final: 0.8251 (mtmm) REVERT: R 104 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7726 (mt) REVERT: R 233 ARG cc_start: 0.7526 (OUTLIER) cc_final: 0.6734 (mtt-85) outliers start: 23 outliers final: 14 residues processed: 174 average time/residue: 0.5467 time to fit residues: 100.3227 Evaluate side-chains 167 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 149 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 186 SER Chi-restraints excluded: chain R residue 233 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 63 optimal weight: 5.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.133941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.102853 restraints weight = 8712.578| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.05 r_work: 0.2881 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7170 Z= 0.161 Angle : 0.501 5.648 9724 Z= 0.274 Chirality : 0.043 0.159 1149 Planarity : 0.004 0.046 1208 Dihedral : 6.934 99.100 1025 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.39 % Allowed : 20.73 % Favored : 75.88 % 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: 1.20 (0.29), residues: 895 helix: 2.69 (0.27), residues: 386 sheet: 0.31 (0.39), residues: 178 loop : -1.31 (0.32), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 219 TYR 0.016 0.002 TYR R 225 PHE 0.019 0.002 PHE R 58 TRP 0.014 0.001 TRP B 211 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 ( 7167) covalent geometry : angle 0.50015 / 0.27 ( 9717) SS BOND : bond 0.00216 / 0.11 ( 2) SS BOND : angle 1.12981 / 0.60 ( 4) hydrogen bonds : bond 0.04379 / 3.02 ( 377) hydrogen bonds : angle 3.80565 / 2.62 ( 1074) link_NAG-ASN : bond 0.00031 / 0.02 ( 1) link_NAG-ASN : angle 1.19774 / 0.68 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 0.259 Fit side-chains REVERT: B 127 LYS cc_start: 0.8512 (mmtt) cc_final: 0.8261 (mmtp) REVERT: B 146 LEU cc_start: 0.9185 (tp) cc_final: 0.8902 (tp) REVERT: B 175 GLN cc_start: 0.7684 (mm110) cc_final: 0.7252 (mm110) REVERT: B 234 PHE cc_start: 0.9455 (OUTLIER) cc_final: 0.8963 (m-80) REVERT: B 268 ASN cc_start: 0.8345 (t0) cc_final: 0.7990 (t0) REVERT: A 32 ARG cc_start: 0.8564 (mtm-85) cc_final: 0.8262 (mtm-85) REVERT: A 242 ARG cc_start: 0.7412 (ttm170) cc_final: 0.7100 (mtm-85) REVERT: A 248 LYS cc_start: 0.8198 (mtpp) cc_final: 0.7782 (mtpt) REVERT: A 272 ASP cc_start: 0.7993 (m-30) cc_final: 0.7723 (m-30) REVERT: A 298 GLU cc_start: 0.7827 (tt0) cc_final: 0.7041 (tt0) REVERT: A 309 ASP cc_start: 0.7978 (m-30) cc_final: 0.7454 (p0) REVERT: A 345 LYS cc_start: 0.8604 (tttt) cc_final: 0.7693 (mptt) REVERT: A 349 LYS cc_start: 0.8779 (mtpt) cc_final: 0.8417 (mtmm) REVERT: R 233 ARG cc_start: 0.7554 (OUTLIER) cc_final: 0.6715 (mtt-85) outliers start: 25 outliers final: 19 residues processed: 171 average time/residue: 0.5916 time to fit residues: 106.3234 Evaluate side-chains 171 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 150 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 186 SER Chi-restraints excluded: chain R residue 233 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 85 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 43 optimal weight: 6.9990 chunk 23 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 chunk 69 optimal weight: 0.5980 chunk 77 optimal weight: 0.1980 chunk 62 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 51 optimal weight: 0.4980 chunk 68 optimal weight: 3.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.135792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.105009 restraints weight = 8604.528| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.03 r_work: 0.2913 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7170 Z= 0.118 Angle : 0.474 5.800 9724 Z= 0.259 Chirality : 0.042 0.191 1149 Planarity : 0.004 0.045 1208 Dihedral : 6.708 96.634 1025 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.39 % Allowed : 21.41 % Favored : 75.20 % 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: 1.26 (0.29), residues: 895 helix: 2.74 (0.26), residues: 386 sheet: 0.41 (0.39), residues: 176 loop : -1.30 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 219 TYR 0.016 0.001 TYR R 225 PHE 0.020 0.001 PHE R 58 TRP 0.011 0.001 TRP B 82 HIS 0.002 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 7167) covalent geometry : angle 0.47352 / 0.26 ( 9717) SS BOND : bond 0.00219 / 0.11 ( 2) SS BOND : angle 1.06171 / 0.56 ( 4) hydrogen bonds : bond 0.03940 / 2.72 ( 377) hydrogen bonds : angle 3.71664 / 2.57 ( 1074) link_NAG-ASN : bond 0.00030 / 0.02 ( 1) link_NAG-ASN : angle 1.23409 / 0.71 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3195.42 seconds wall clock time: 55 minutes 6.39 seconds (3306.39 seconds total)