Starting phenix.real_space_refine on Sat Oct 11 19:36:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8irs_35684/10_2025/8irs_35684_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8irs_35684/10_2025/8irs_35684.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/8irs_35684/10_2025/8irs_35684.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8irs_35684/10_2025/8irs_35684.map" model { file = "/net/cci-nas-00/data/ceres_data/8irs_35684/10_2025/8irs_35684_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8irs_35684/10_2025/8irs_35684_neut_trim.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= 0.010 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: 5 Type Number sf(0) Gaussians S 65 5.16 5 C 5603 2.51 5 N 1479 2.21 5 O 1646 1.98 5 H 8717 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17510 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 3607 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 221} Chain breaks: 1 Chain: "B" Number of atoms: 5118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 5118 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "E" Number of atoms: 3516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 3516 Classifications: {'peptide': 233} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Chain: "G" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 900 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "R" Number of atoms: 4347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 4347 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 9, 'TRANS': 254} Chain breaks: 1 Chain: "R" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'R5F': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.67, per 1000 atoms: 0.15 Number of scatterers: 17510 At special positions: 0 Unit cell: (99.275, 125.4, 119.13, 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 65 16.00 O 1646 8.00 N 1479 7.00 C 5603 6.00 H 8717 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 107 " - pdb=" SG CYS R 182 " distance=2.03 Simple disulfide: pdb=" SG CYS R 399 " - pdb=" SG CYS R 401 " 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: 1.40 Conformation dependent library (CDL) restraints added in 548.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2106 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 14 sheets defined 40.5% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 removed outlier: 3.518A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 207 through 218 removed outlier: 5.374A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N GLY A 217 " --> pdb=" O CYS A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 231 removed outlier: 3.830A 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 256 through 260 removed outlier: 3.733A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 4.416A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 327 through 351 removed outlier: 3.538A pdb=" N ASN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 220 through 224 Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'R' and resid 35 through 62 removed outlier: 3.539A pdb=" N ILE R 45 " --> pdb=" O LEU R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 63 through 66 Processing helix chain 'R' and resid 67 through 87 removed outlier: 3.517A pdb=" N LEU R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL R 87 " --> pdb=" O VAL R 83 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 98 Processing helix chain 'R' and resid 103 through 138 removed outlier: 3.558A pdb=" N VAL R 136 " --> pdb=" O ARG R 132 " (cutoff:3.500A) Processing helix chain 'R' and resid 138 through 144 Processing helix chain 'R' and resid 144 through 172 removed outlier: 3.638A pdb=" N LYS R 149 " --> pdb=" O ARG R 145 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG R 150 " --> pdb=" O TYR R 146 " (cutoff:3.500A) Proline residue: R 169 - end of helix Processing helix chain 'R' and resid 186 through 198 Processing helix chain 'R' and resid 198 through 212 Processing helix chain 'R' and resid 368 through 399 removed outlier: 3.883A pdb=" N THR R 372 " --> pdb=" O GLU R 368 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TRP R 386 " --> pdb=" O PHE R 382 " (cutoff:3.500A) Proline residue: R 388 - end of helix removed outlier: 3.573A pdb=" N ILE R 394 " --> pdb=" O PHE R 390 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ILE R 397 " --> pdb=" O HIS R 393 " (cutoff:3.500A) Processing helix chain 'R' and resid 404 through 429 removed outlier: 3.655A pdb=" N ASN R 418 " --> pdb=" O LEU R 414 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N SER R 419 " --> pdb=" O GLY R 415 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA R 420 " --> pdb=" O TYR R 416 " (cutoff:3.500A) Proline residue: R 423 - end of helix removed outlier: 4.110A pdb=" N PHE R 429 " --> pdb=" O ILE R 425 " (cutoff:3.500A) Processing helix chain 'R' and resid 430 through 441 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 189 removed outlier: 6.067A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.707A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.766A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 105 removed outlier: 5.969A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.600A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.607A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.249A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.754A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 5 Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.669A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 11 through 12 removed outlier: 4.406A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 142 Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.599A pdb=" N VAL E 147 " --> pdb=" O GLU E 246 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.599A pdb=" N VAL E 147 " --> pdb=" O GLU E 246 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N THR E 238 " --> pdb=" O GLN E 231 " (cutoff:3.500A) 454 hydrogen bonds defined for protein. 1242 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: 3.76 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 1979 1.02 - 1.22: 6746 1.22 - 1.42: 3839 1.42 - 1.62: 5030 1.62 - 1.82: 95 Bond restraints: 17689 Sorted by residual: bond pdb=" CD2 PHE A 250 " pdb=" HD2 PHE A 250 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N ASP G 26 " pdb=" H ASP G 26 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" CD1 TRP B 332 " pdb=" HD1 TRP B 332 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N VAL R 406 " pdb=" H VAL R 406 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" NH1 ARG E 38 " pdb="HH11 ARG E 38 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 ... (remaining 17684 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.81: 27471 2.81 - 5.62: 3451 5.62 - 8.43: 888 8.43 - 11.24: 24 11.24 - 14.04: 25 Bond angle restraints: 31859 Sorted by residual: angle pdb=" CA ARG E 191 " pdb=" C ARG E 191 " pdb=" N MET E 192 " ideal model delta sigma weight residual 116.34 123.70 -7.36 1.04e+00 9.25e-01 5.01e+01 angle pdb=" C ARG E 191 " pdb=" CA ARG E 191 " pdb=" CB ARG E 191 " ideal model delta sigma weight residual 113.37 123.31 -9.94 1.61e+00 3.86e-01 3.81e+01 angle pdb=" CA ASN E 171 " pdb=" CB ASN E 171 " pdb=" CG ASN E 171 " ideal model delta sigma weight residual 112.60 118.25 -5.65 1.00e+00 1.00e+00 3.19e+01 angle pdb=" N SER B 161 " pdb=" CA SER B 161 " pdb=" C SER B 161 " ideal model delta sigma weight residual 109.07 117.45 -8.38 1.52e+00 4.33e-01 3.04e+01 angle pdb=" CA CYS B 250 " pdb=" C CYS B 250 " pdb=" N ARG B 251 " ideal model delta sigma weight residual 115.27 121.76 -6.49 1.24e+00 6.50e-01 2.74e+01 ... (remaining 31854 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 7578 17.46 - 34.92: 517 34.92 - 52.38: 117 52.38 - 69.83: 136 69.83 - 87.29: 13 Dihedral angle restraints: 8361 sinusoidal: 4485 harmonic: 3876 Sorted by residual: dihedral pdb=" CA ILE R 214 " pdb=" C ILE R 214 " pdb=" N VAL R 215 " pdb=" CA VAL R 215 " ideal model delta harmonic sigma weight residual 180.00 150.90 29.10 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA LEU B 284 " pdb=" C LEU B 284 " pdb=" N LEU B 285 " pdb=" CA LEU B 285 " ideal model delta harmonic sigma weight residual 180.00 150.97 29.03 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA LEU B 117 " pdb=" C LEU B 117 " pdb=" N ASP B 118 " pdb=" CA ASP B 118 " ideal model delta harmonic sigma weight residual 180.00 150.99 29.01 0 5.00e+00 4.00e-02 3.37e+01 ... (remaining 8358 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 957 0.095 - 0.191: 363 0.191 - 0.286: 54 0.286 - 0.382: 12 0.382 - 0.477: 7 Chirality restraints: 1393 Sorted by residual: chirality pdb=" CA GLU A 238 " pdb=" N GLU A 238 " pdb=" C GLU A 238 " pdb=" CB GLU A 238 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.69e+00 chirality pdb=" CA SER B 334 " pdb=" N SER B 334 " pdb=" C SER B 334 " pdb=" CB SER B 334 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.08e+00 chirality pdb=" CA ASP B 186 " pdb=" N ASP B 186 " pdb=" C ASP B 186 " pdb=" CB ASP B 186 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.64e+00 ... (remaining 1390 not shown) Planarity restraints: 2609 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 175 " -0.292 2.00e-02 2.50e+03 1.25e-01 4.71e+02 pdb=" CG TYR E 175 " 0.007 2.00e-02 2.50e+03 pdb=" CD1 TYR E 175 " 0.090 2.00e-02 2.50e+03 pdb=" CD2 TYR E 175 " 0.090 2.00e-02 2.50e+03 pdb=" CE1 TYR E 175 " 0.073 2.00e-02 2.50e+03 pdb=" CE2 TYR E 175 " 0.074 2.00e-02 2.50e+03 pdb=" CZ TYR E 175 " -0.015 2.00e-02 2.50e+03 pdb=" OH TYR E 175 " -0.248 2.00e-02 2.50e+03 pdb=" HD1 TYR E 175 " 0.081 2.00e-02 2.50e+03 pdb=" HD2 TYR E 175 " 0.073 2.00e-02 2.50e+03 pdb=" HE1 TYR E 175 " 0.028 2.00e-02 2.50e+03 pdb=" HE2 TYR E 175 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 413 " 0.242 2.00e-02 2.50e+03 8.72e-02 3.04e+02 pdb=" CG TRP R 413 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP R 413 " -0.046 2.00e-02 2.50e+03 pdb=" CD2 TRP R 413 " -0.032 2.00e-02 2.50e+03 pdb=" NE1 TRP R 413 " -0.076 2.00e-02 2.50e+03 pdb=" CE2 TRP R 413 " -0.018 2.00e-02 2.50e+03 pdb=" CE3 TRP R 413 " -0.069 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 413 " 0.041 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 413 " -0.033 2.00e-02 2.50e+03 pdb=" CH2 TRP R 413 " 0.045 2.00e-02 2.50e+03 pdb=" HD1 TRP R 413 " -0.014 2.00e-02 2.50e+03 pdb=" HE1 TRP R 413 " -0.092 2.00e-02 2.50e+03 pdb=" HE3 TRP R 413 " -0.120 2.00e-02 2.50e+03 pdb=" HZ2 TRP R 413 " 0.090 2.00e-02 2.50e+03 pdb=" HZ3 TRP R 413 " -0.050 2.00e-02 2.50e+03 pdb=" HH2 TRP R 413 " 0.095 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 22 " 0.003 9.50e-02 1.11e+02 1.14e-01 2.90e+02 pdb=" NE ARG B 22 " -0.056 2.00e-02 2.50e+03 pdb=" CZ ARG B 22 " -0.039 2.00e-02 2.50e+03 pdb=" NH1 ARG B 22 " -0.036 2.00e-02 2.50e+03 pdb=" NH2 ARG B 22 " -0.028 2.00e-02 2.50e+03 pdb="HH11 ARG B 22 " -0.002 2.00e-02 2.50e+03 pdb="HH12 ARG B 22 " 0.165 2.00e-02 2.50e+03 pdb="HH21 ARG B 22 " 0.200 2.00e-02 2.50e+03 pdb="HH22 ARG B 22 " -0.205 2.00e-02 2.50e+03 ... (remaining 2606 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 1345 2.20 - 2.80: 33347 2.80 - 3.40: 51108 3.40 - 4.00: 68443 4.00 - 4.60: 100108 Nonbonded interactions: 254351 Sorted by model distance: nonbonded pdb=" OD1 ASP R 80 " pdb=" HG SER R 419 " model vdw 1.600 2.450 nonbonded pdb=" OD2 ASP B 170 " pdb=" HG1 THR B 173 " model vdw 1.605 2.450 nonbonded pdb=" OD1 ASP B 205 " pdb=" HG SER B 207 " model vdw 1.610 2.450 nonbonded pdb=" OD1 ASP B 163 " pdb=" HG1 THR B 165 " model vdw 1.613 2.450 nonbonded pdb=" HH TYR A 320 " pdb=" OD2 ASP A 341 " model vdw 1.620 2.450 ... (remaining 254346 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: 0.410 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: 0.070 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 16.110 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.088 8976 Z= 0.742 Angle : 1.846 9.941 12166 Z= 1.230 Chirality : 0.100 0.477 1393 Planarity : 0.017 0.198 1529 Dihedral : 13.010 87.292 3237 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 0.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.76 % Peptide Plane: Cis-proline : 3.33 % 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 aren not related in a simple way. whole: -1.14 (0.24), residues: 1102 helix: -0.92 (0.22), residues: 395 sheet: -0.34 (0.31), residues: 262 loop : -0.63 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 46 TYR 0.251 0.027 TYR E 175 PHE 0.090 0.016 PHE A 259 TRP 0.164 0.026 TRP B 99 HIS 0.014 0.004 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.01220 ( 8972) covalent geometry : angle 1.84648 (12158) SS BOND : bond 0.00177 ( 4) SS BOND : angle 1.61605 ( 8) hydrogen bonds : bond 0.14784 ( 445) hydrogen bonds : angle 7.18117 ( 1242) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 318 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7573 (tt0) cc_final: 0.7351 (tt0) REVERT: A 32 ARG cc_start: 0.8120 (mtm180) cc_final: 0.7841 (mtp85) REVERT: A 251 ASP cc_start: 0.7884 (t0) cc_final: 0.7554 (t0) REVERT: A 252 SER cc_start: 0.8126 (t) cc_final: 0.7904 (t) REVERT: B 46 ARG cc_start: 0.7556 (mtp-110) cc_final: 0.7211 (ttm-80) REVERT: B 181 THR cc_start: 0.7631 (p) cc_final: 0.7375 (m) REVERT: B 188 MET cc_start: 0.8204 (mmm) cc_final: 0.7957 (mmm) REVERT: R 50 PHE cc_start: 0.8239 (t80) cc_final: 0.8001 (t80) REVERT: R 63 LYS cc_start: 0.7756 (tttt) cc_final: 0.7541 (tttp) REVERT: R 164 PHE cc_start: 0.8294 (t80) cc_final: 0.8087 (t80) outliers start: 0 outliers final: 0 residues processed: 318 average time/residue: 1.1511 time to fit residues: 392.3777 Evaluate side-chains 223 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 5.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN A 306 GLN A 346 ASN G 24 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.174677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.130071 restraints weight = 28746.338| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.46 r_work: 0.3456 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8976 Z= 0.167 Angle : 0.658 7.690 12166 Z= 0.358 Chirality : 0.043 0.165 1393 Planarity : 0.004 0.050 1529 Dihedral : 7.981 68.227 1231 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 4.14 % Allowed : 13.66 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 aren not related in a simple way. whole: -0.29 (0.24), residues: 1102 helix: 0.57 (0.24), residues: 406 sheet: -0.51 (0.30), residues: 270 loop : -0.54 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 160 TYR 0.034 0.002 TYR B 105 PHE 0.019 0.002 PHE R 189 TRP 0.023 0.002 TRP B 82 HIS 0.005 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 8972) covalent geometry : angle 0.65807 (12158) SS BOND : bond 0.00332 ( 4) SS BOND : angle 1.05827 ( 8) hydrogen bonds : bond 0.05030 ( 445) hydrogen bonds : angle 5.42649 ( 1242) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 247 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7837 (mtm180) cc_final: 0.7402 (mtp85) REVERT: A 252 SER cc_start: 0.8551 (t) cc_final: 0.8199 (p) REVERT: B 46 ARG cc_start: 0.7701 (mtp-110) cc_final: 0.6985 (mtp85) REVERT: B 181 THR cc_start: 0.7680 (p) cc_final: 0.7361 (m) REVERT: B 217 MET cc_start: 0.7842 (ptm) cc_final: 0.7372 (pp-130) REVERT: B 258 ASP cc_start: 0.7807 (t0) cc_final: 0.7600 (t0) REVERT: B 280 LYS cc_start: 0.8012 (tttm) cc_final: 0.7704 (ttmm) REVERT: B 303 ASP cc_start: 0.7572 (m-30) cc_final: 0.7119 (p0) REVERT: E 140 MET cc_start: 0.8576 (mmm) cc_final: 0.7849 (mmt) REVERT: E 234 GLU cc_start: 0.8651 (mt-10) cc_final: 0.8405 (mt-10) REVERT: R 50 PHE cc_start: 0.8187 (t80) cc_final: 0.7978 (t80) REVERT: R 63 LYS cc_start: 0.7836 (tttt) cc_final: 0.7623 (tttp) REVERT: R 78 VAL cc_start: 0.7676 (OUTLIER) cc_final: 0.7388 (t) REVERT: R 138 MET cc_start: 0.7534 (mtp) cc_final: 0.7229 (mtt) outliers start: 40 outliers final: 13 residues processed: 265 average time/residue: 1.2232 time to fit residues: 347.5747 Evaluate side-chains 225 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 211 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 214 ILE Chi-restraints excluded: chain R residue 393 HIS Chi-restraints excluded: chain R residue 409 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 23 optimal weight: 9.9990 chunk 100 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN B 13 GLN B 62 HIS E 171 ASN R 66 GLN ** R 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.171828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.125714 restraints weight = 29282.295| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.53 r_work: 0.3407 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.4549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8976 Z= 0.186 Angle : 0.599 6.259 12166 Z= 0.326 Chirality : 0.042 0.156 1393 Planarity : 0.004 0.055 1529 Dihedral : 7.164 64.359 1231 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.93 % Allowed : 17.18 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 aren not related in a simple way. whole: -0.14 (0.24), residues: 1102 helix: 1.04 (0.25), residues: 400 sheet: -0.80 (0.29), residues: 274 loop : -0.55 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 160 TYR 0.028 0.002 TYR B 105 PHE 0.019 0.002 PHE B 235 TRP 0.013 0.002 TRP B 82 HIS 0.006 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00416 ( 8972) covalent geometry : angle 0.59886 (12158) SS BOND : bond 0.00428 ( 4) SS BOND : angle 0.95605 ( 8) hydrogen bonds : bond 0.04245 ( 445) hydrogen bonds : angle 5.11138 ( 1242) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 227 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7985 (mtm180) cc_final: 0.7531 (mtp85) REVERT: A 186 GLU cc_start: 0.7637 (tt0) cc_final: 0.7150 (mt-10) REVERT: A 252 SER cc_start: 0.8446 (t) cc_final: 0.8090 (p) REVERT: B 42 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.8280 (mmm160) REVERT: B 46 ARG cc_start: 0.7763 (mtp-110) cc_final: 0.7083 (mtp85) REVERT: B 96 ARG cc_start: 0.7037 (OUTLIER) cc_final: 0.6375 (mmt180) REVERT: B 181 THR cc_start: 0.7785 (p) cc_final: 0.7548 (m) REVERT: B 212 ASP cc_start: 0.6434 (t70) cc_final: 0.6160 (t70) REVERT: B 217 MET cc_start: 0.7983 (ptm) cc_final: 0.7470 (ppp) REVERT: B 258 ASP cc_start: 0.7951 (t0) cc_final: 0.7741 (t0) REVERT: B 303 ASP cc_start: 0.7723 (m-30) cc_final: 0.7231 (p0) REVERT: E 43 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.8182 (mtmm) REVERT: E 119 VAL cc_start: 0.7432 (t) cc_final: 0.7186 (t) REVERT: E 140 MET cc_start: 0.8510 (mmm) cc_final: 0.7964 (mmt) REVERT: R 63 LYS cc_start: 0.7985 (tttt) cc_final: 0.7753 (tttp) REVERT: R 78 VAL cc_start: 0.7871 (OUTLIER) cc_final: 0.7596 (t) REVERT: R 116 MET cc_start: 0.7339 (ttt) cc_final: 0.6687 (tpt) REVERT: R 138 MET cc_start: 0.7720 (mtp) cc_final: 0.7508 (mtt) outliers start: 38 outliers final: 19 residues processed: 246 average time/residue: 1.1517 time to fit residues: 304.4279 Evaluate side-chains 229 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 206 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 134 THR Chi-restraints excluded: chain R residue 158 ILE Chi-restraints excluded: chain R residue 175 ASN Chi-restraints excluded: chain R residue 393 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 10 optimal weight: 3.9990 chunk 93 optimal weight: 0.1980 chunk 88 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 100 optimal weight: 0.4980 chunk 71 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN A 294 ASN B 13 GLN ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.172224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.126483 restraints weight = 28956.893| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.52 r_work: 0.3422 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.4982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8976 Z= 0.153 Angle : 0.564 6.369 12166 Z= 0.304 Chirality : 0.041 0.153 1393 Planarity : 0.004 0.054 1529 Dihedral : 6.844 59.620 1231 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.73 % Allowed : 20.08 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 aren not related in a simple way. whole: -0.05 (0.24), residues: 1102 helix: 1.33 (0.25), residues: 400 sheet: -0.96 (0.29), residues: 275 loop : -0.57 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 160 TYR 0.015 0.001 TYR E 190 PHE 0.016 0.002 PHE R 50 TRP 0.012 0.001 TRP B 82 HIS 0.006 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 8972) covalent geometry : angle 0.56337 (12158) SS BOND : bond 0.00364 ( 4) SS BOND : angle 0.79137 ( 8) hydrogen bonds : bond 0.03795 ( 445) hydrogen bonds : angle 4.93790 ( 1242) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 222 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8054 (mtm180) cc_final: 0.7560 (mtp85) REVERT: A 186 GLU cc_start: 0.7637 (tt0) cc_final: 0.7160 (mt-10) REVERT: A 252 SER cc_start: 0.8354 (t) cc_final: 0.7995 (p) REVERT: B 46 ARG cc_start: 0.7819 (mtp-110) cc_final: 0.7105 (mtp85) REVERT: B 181 THR cc_start: 0.7888 (p) cc_final: 0.7639 (m) REVERT: B 212 ASP cc_start: 0.6723 (t70) cc_final: 0.6471 (t70) REVERT: B 217 MET cc_start: 0.7947 (ptm) cc_final: 0.7440 (ppp) REVERT: B 280 LYS cc_start: 0.7947 (tttm) cc_final: 0.7692 (ttpp) REVERT: B 303 ASP cc_start: 0.7713 (m-30) cc_final: 0.7240 (p0) REVERT: E 43 LYS cc_start: 0.8526 (mtmt) cc_final: 0.8198 (mtmm) REVERT: E 119 VAL cc_start: 0.7480 (t) cc_final: 0.7231 (t) REVERT: E 140 MET cc_start: 0.8516 (mmm) cc_final: 0.8098 (mmt) REVERT: R 149 LYS cc_start: 0.8494 (tppp) cc_final: 0.8258 (tppp) REVERT: R 374 MET cc_start: 0.7495 (mmp) cc_final: 0.7235 (mmm) outliers start: 36 outliers final: 19 residues processed: 244 average time/residue: 1.1197 time to fit residues: 293.7347 Evaluate side-chains 228 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 209 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 131 ASP Chi-restraints excluded: chain R residue 214 ILE Chi-restraints excluded: chain R residue 393 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 74 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 105 optimal weight: 8.9990 chunk 5 optimal weight: 0.7980 chunk 83 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN B 13 GLN ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 ASN R 66 GLN ** R 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.169096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.123095 restraints weight = 29090.638| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.51 r_work: 0.3377 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.5260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 8976 Z= 0.216 Angle : 0.590 7.224 12166 Z= 0.318 Chirality : 0.042 0.149 1393 Planarity : 0.004 0.063 1529 Dihedral : 6.894 59.641 1231 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 4.35 % Allowed : 20.39 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 aren not related in a simple way. whole: -0.14 (0.25), residues: 1102 helix: 1.37 (0.25), residues: 399 sheet: -1.09 (0.30), residues: 270 loop : -0.69 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 160 TYR 0.017 0.002 TYR B 105 PHE 0.016 0.002 PHE B 235 TRP 0.011 0.002 TRP B 99 HIS 0.006 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00489 ( 8972) covalent geometry : angle 0.59025 (12158) SS BOND : bond 0.00378 ( 4) SS BOND : angle 0.85066 ( 8) hydrogen bonds : bond 0.03791 ( 445) hydrogen bonds : angle 4.98430 ( 1242) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 220 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8040 (mtm180) cc_final: 0.7623 (mtp85) REVERT: A 186 GLU cc_start: 0.7676 (tt0) cc_final: 0.7447 (mt-10) REVERT: A 197 LYS cc_start: 0.7963 (mttp) cc_final: 0.7473 (mtpt) REVERT: A 252 SER cc_start: 0.8354 (t) cc_final: 0.7982 (p) REVERT: B 42 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.7618 (tpm-80) REVERT: B 46 ARG cc_start: 0.7886 (mtp-110) cc_final: 0.7146 (mtp85) REVERT: B 181 THR cc_start: 0.7859 (p) cc_final: 0.7567 (m) REVERT: B 212 ASP cc_start: 0.6960 (t70) cc_final: 0.6670 (t70) REVERT: B 217 MET cc_start: 0.8082 (ptm) cc_final: 0.7521 (ppp) REVERT: B 280 LYS cc_start: 0.7938 (tttm) cc_final: 0.7713 (ttpp) REVERT: B 303 ASP cc_start: 0.7695 (m-30) cc_final: 0.7262 (p0) REVERT: E 43 LYS cc_start: 0.8570 (mtmt) cc_final: 0.8255 (mtmm) REVERT: E 140 MET cc_start: 0.8569 (mmm) cc_final: 0.8185 (mmt) REVERT: R 78 VAL cc_start: 0.7775 (OUTLIER) cc_final: 0.7471 (t) REVERT: R 149 LYS cc_start: 0.8479 (tppp) cc_final: 0.8158 (tppp) REVERT: R 374 MET cc_start: 0.7459 (mmp) cc_final: 0.7166 (mmm) outliers start: 42 outliers final: 28 residues processed: 247 average time/residue: 1.1004 time to fit residues: 292.8075 Evaluate side-chains 240 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 210 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 131 ASP Chi-restraints excluded: chain R residue 134 THR Chi-restraints excluded: chain R residue 158 ILE Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 393 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 63 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 5 optimal weight: 0.0070 chunk 6 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 78 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 92 optimal weight: 0.2980 chunk 51 optimal weight: 0.6980 overall best weight: 0.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN B 13 GLN ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 ASN ** R 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.173554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.128536 restraints weight = 28762.473| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 2.46 r_work: 0.3456 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.5425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8976 Z= 0.134 Angle : 0.554 5.835 12166 Z= 0.295 Chirality : 0.040 0.150 1393 Planarity : 0.004 0.071 1529 Dihedral : 6.636 57.625 1231 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.52 % Allowed : 21.95 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 aren not related in a simple way. whole: 0.04 (0.25), residues: 1102 helix: 1.59 (0.25), residues: 400 sheet: -1.11 (0.30), residues: 273 loop : -0.58 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 160 TYR 0.013 0.001 TYR E 190 PHE 0.013 0.001 PHE R 189 TRP 0.011 0.001 TRP B 82 HIS 0.006 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 8972) covalent geometry : angle 0.55393 (12158) SS BOND : bond 0.00335 ( 4) SS BOND : angle 0.69892 ( 8) hydrogen bonds : bond 0.03489 ( 445) hydrogen bonds : angle 4.81763 ( 1242) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 220 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8070 (mtm180) cc_final: 0.7637 (mtp85) REVERT: A 197 LYS cc_start: 0.7950 (mttp) cc_final: 0.7434 (mptt) REVERT: A 252 SER cc_start: 0.8369 (t) cc_final: 0.7982 (p) REVERT: A 306 GLN cc_start: 0.7997 (OUTLIER) cc_final: 0.7781 (tp40) REVERT: B 42 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.7601 (tpm-80) REVERT: B 46 ARG cc_start: 0.7914 (mtp-110) cc_final: 0.7258 (mtp85) REVERT: B 181 THR cc_start: 0.7885 (p) cc_final: 0.7608 (m) REVERT: B 212 ASP cc_start: 0.6954 (t70) cc_final: 0.6677 (t70) REVERT: B 217 MET cc_start: 0.8018 (ptm) cc_final: 0.7513 (ppp) REVERT: B 280 LYS cc_start: 0.7785 (tttm) cc_final: 0.7543 (ttpp) REVERT: B 303 ASP cc_start: 0.7704 (m-30) cc_final: 0.7309 (p0) REVERT: E 43 LYS cc_start: 0.8600 (mtmt) cc_final: 0.8280 (mtmm) REVERT: E 140 MET cc_start: 0.8543 (mmm) cc_final: 0.8072 (mmt) REVERT: E 220 GLU cc_start: 0.7188 (mp0) cc_final: 0.6920 (mp0) REVERT: R 116 MET cc_start: 0.7394 (ttt) cc_final: 0.6503 (tpp) REVERT: R 149 LYS cc_start: 0.8430 (tppp) cc_final: 0.8168 (tppp) outliers start: 34 outliers final: 22 residues processed: 241 average time/residue: 1.1122 time to fit residues: 288.7229 Evaluate side-chains 233 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 209 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 131 ASP Chi-restraints excluded: chain R residue 134 THR Chi-restraints excluded: chain R residue 158 ILE Chi-restraints excluded: chain R residue 393 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 88 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 14 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 ASN ** R 70 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 = 0.4086 r_free = 0.4086 target = 0.172536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.126780 restraints weight = 29135.378| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.49 r_work: 0.3436 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.5555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8976 Z= 0.168 Angle : 0.559 5.479 12166 Z= 0.300 Chirality : 0.041 0.147 1393 Planarity : 0.004 0.066 1529 Dihedral : 6.672 56.399 1231 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.73 % Allowed : 22.26 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 aren not related in a simple way. whole: -0.07 (0.25), residues: 1102 helix: 1.54 (0.25), residues: 400 sheet: -1.16 (0.30), residues: 275 loop : -0.68 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 160 TYR 0.014 0.001 TYR E 190 PHE 0.013 0.001 PHE B 235 TRP 0.009 0.001 TRP B 82 HIS 0.005 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 8972) covalent geometry : angle 0.55882 (12158) SS BOND : bond 0.00328 ( 4) SS BOND : angle 0.72752 ( 8) hydrogen bonds : bond 0.03469 ( 445) hydrogen bonds : angle 4.80732 ( 1242) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 215 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8135 (mtm180) cc_final: 0.7686 (mtp85) REVERT: A 186 GLU cc_start: 0.7627 (tt0) cc_final: 0.6954 (mt-10) REVERT: A 197 LYS cc_start: 0.7957 (mttp) cc_final: 0.7373 (mptt) REVERT: A 252 SER cc_start: 0.8377 (t) cc_final: 0.7967 (p) REVERT: B 46 ARG cc_start: 0.7964 (mtp-110) cc_final: 0.7311 (mtp85) REVERT: B 181 THR cc_start: 0.7886 (p) cc_final: 0.7599 (m) REVERT: B 212 ASP cc_start: 0.7093 (t70) cc_final: 0.6834 (t70) REVERT: B 217 MET cc_start: 0.8029 (ptm) cc_final: 0.7509 (ppp) REVERT: B 280 LYS cc_start: 0.7854 (tttm) cc_final: 0.7613 (ttpp) REVERT: B 303 ASP cc_start: 0.7724 (m-30) cc_final: 0.7344 (p0) REVERT: B 318 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7895 (mp) REVERT: E 43 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8314 (mtmm) REVERT: R 116 MET cc_start: 0.7390 (ttt) cc_final: 0.6456 (tpp) REVERT: R 149 LYS cc_start: 0.8400 (tppp) cc_final: 0.8148 (tppp) outliers start: 36 outliers final: 26 residues processed: 236 average time/residue: 1.0661 time to fit residues: 271.9415 Evaluate side-chains 237 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 209 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 131 ASP Chi-restraints excluded: chain R residue 134 THR Chi-restraints excluded: chain R residue 158 ILE Chi-restraints excluded: chain R residue 393 HIS Chi-restraints excluded: chain R residue 417 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 80 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 106 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN B 13 GLN ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 ASN ** R 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.171736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.125772 restraints weight = 28987.444| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.48 r_work: 0.3419 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.5678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8976 Z= 0.197 Angle : 0.581 5.733 12166 Z= 0.312 Chirality : 0.041 0.148 1393 Planarity : 0.004 0.074 1529 Dihedral : 6.726 56.167 1231 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.73 % Allowed : 22.98 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 aren not related in a simple way. whole: -0.14 (0.25), residues: 1102 helix: 1.53 (0.26), residues: 401 sheet: -1.22 (0.30), residues: 276 loop : -0.78 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 160 TYR 0.015 0.001 TYR E 190 PHE 0.014 0.002 PHE B 235 TRP 0.010 0.001 TRP B 99 HIS 0.005 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00445 ( 8972) covalent geometry : angle 0.58098 (12158) SS BOND : bond 0.00334 ( 4) SS BOND : angle 0.74991 ( 8) hydrogen bonds : bond 0.03482 ( 445) hydrogen bonds : angle 4.83203 ( 1242) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 203 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8171 (mtm180) cc_final: 0.7691 (mtp85) REVERT: A 197 LYS cc_start: 0.7975 (mttp) cc_final: 0.7420 (mptt) REVERT: A 252 SER cc_start: 0.8382 (t) cc_final: 0.7961 (p) REVERT: B 15 LYS cc_start: 0.8817 (mtpp) cc_final: 0.8592 (tptt) REVERT: B 42 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.7554 (tpm-80) REVERT: B 46 ARG cc_start: 0.7967 (mtp-110) cc_final: 0.7364 (mtp85) REVERT: B 120 ILE cc_start: 0.8463 (mt) cc_final: 0.8224 (mp) REVERT: B 181 THR cc_start: 0.7796 (p) cc_final: 0.7475 (m) REVERT: B 212 ASP cc_start: 0.7128 (t70) cc_final: 0.6832 (t70) REVERT: B 214 ARG cc_start: 0.7427 (mmp80) cc_final: 0.7179 (mmp80) REVERT: B 217 MET cc_start: 0.8054 (ptm) cc_final: 0.7506 (ppp) REVERT: B 280 LYS cc_start: 0.7824 (tttm) cc_final: 0.7582 (ttpp) REVERT: B 303 ASP cc_start: 0.7735 (m-30) cc_final: 0.7410 (p0) REVERT: B 318 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7891 (mp) REVERT: E 43 LYS cc_start: 0.8662 (mtmt) cc_final: 0.8354 (mtmm) REVERT: E 222 GLU cc_start: 0.6766 (pm20) cc_final: 0.6539 (pm20) REVERT: R 116 MET cc_start: 0.7346 (ttt) cc_final: 0.6555 (tpp) REVERT: R 149 LYS cc_start: 0.8386 (tppp) cc_final: 0.8140 (tppp) outliers start: 36 outliers final: 26 residues processed: 228 average time/residue: 1.0871 time to fit residues: 267.5106 Evaluate side-chains 224 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 196 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 131 ASP Chi-restraints excluded: chain R residue 134 THR Chi-restraints excluded: chain R residue 393 HIS Chi-restraints excluded: chain R residue 417 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 89 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN B 13 GLN E 13 GLN ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 ASN ** R 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.172864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.127076 restraints weight = 29075.122| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.49 r_work: 0.3441 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.5783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8976 Z= 0.155 Angle : 0.570 7.832 12166 Z= 0.303 Chirality : 0.040 0.154 1393 Planarity : 0.004 0.080 1529 Dihedral : 6.579 54.789 1231 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.73 % Allowed : 23.60 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 aren not related in a simple way. whole: -0.04 (0.25), residues: 1102 helix: 1.65 (0.26), residues: 400 sheet: -1.15 (0.30), residues: 276 loop : -0.77 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 160 TYR 0.013 0.001 TYR E 190 PHE 0.012 0.001 PHE R 189 TRP 0.011 0.001 TRP R 413 HIS 0.005 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 8972) covalent geometry : angle 0.57019 (12158) SS BOND : bond 0.00316 ( 4) SS BOND : angle 0.71927 ( 8) hydrogen bonds : bond 0.03370 ( 445) hydrogen bonds : angle 4.74457 ( 1242) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 201 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8190 (mtm180) cc_final: 0.7763 (mtp85) REVERT: A 186 GLU cc_start: 0.7652 (tt0) cc_final: 0.7142 (mt-10) REVERT: A 197 LYS cc_start: 0.7987 (mttp) cc_final: 0.7388 (mptt) REVERT: A 252 SER cc_start: 0.8304 (t) cc_final: 0.7891 (p) REVERT: B 15 LYS cc_start: 0.8827 (mtpp) cc_final: 0.8607 (tptt) REVERT: B 42 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.7543 (tpm-80) REVERT: B 46 ARG cc_start: 0.8010 (mtp-110) cc_final: 0.7391 (mtp85) REVERT: B 181 THR cc_start: 0.7879 (p) cc_final: 0.7562 (m) REVERT: B 212 ASP cc_start: 0.7171 (t70) cc_final: 0.6883 (t70) REVERT: B 214 ARG cc_start: 0.7465 (mmp80) cc_final: 0.7166 (mmp80) REVERT: B 217 MET cc_start: 0.8008 (ptm) cc_final: 0.7469 (ppp) REVERT: B 303 ASP cc_start: 0.7728 (m-30) cc_final: 0.7408 (p0) REVERT: B 318 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7858 (mp) REVERT: E 222 GLU cc_start: 0.6591 (OUTLIER) cc_final: 0.6357 (pm20) REVERT: R 116 MET cc_start: 0.7327 (ttt) cc_final: 0.6432 (tpp) REVERT: R 149 LYS cc_start: 0.8384 (tppp) cc_final: 0.8164 (tppp) REVERT: R 393 HIS cc_start: 0.8159 (OUTLIER) cc_final: 0.7951 (t70) outliers start: 36 outliers final: 22 residues processed: 222 average time/residue: 1.1424 time to fit residues: 272.2651 Evaluate side-chains 223 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 197 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain E residue 222 GLU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 131 ASP Chi-restraints excluded: chain R residue 134 THR Chi-restraints excluded: chain R residue 393 HIS Chi-restraints excluded: chain R residue 417 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 99 optimal weight: 0.9980 chunk 56 optimal weight: 8.9990 chunk 83 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 15 optimal weight: 0.0170 chunk 72 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN E 142 GLN ** R 70 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 = 0.4115 r_free = 0.4115 target = 0.175389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.129592 restraints weight = 29078.728| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.49 r_work: 0.3464 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.5846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8976 Z= 0.127 Angle : 0.566 7.562 12166 Z= 0.300 Chirality : 0.040 0.152 1393 Planarity : 0.004 0.086 1529 Dihedral : 6.447 54.985 1231 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.69 % Allowed : 24.84 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 aren not related in a simple way. whole: 0.06 (0.25), residues: 1102 helix: 1.73 (0.26), residues: 400 sheet: -1.07 (0.30), residues: 276 loop : -0.73 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG E 160 TYR 0.018 0.001 TYR A 230 PHE 0.013 0.001 PHE R 189 TRP 0.012 0.001 TRP B 82 HIS 0.005 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 8972) covalent geometry : angle 0.56608 (12158) SS BOND : bond 0.00320 ( 4) SS BOND : angle 0.65912 ( 8) hydrogen bonds : bond 0.03224 ( 445) hydrogen bonds : angle 4.65046 ( 1242) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 204 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.7686 (p0) cc_final: 0.7474 (m-40) REVERT: A 32 ARG cc_start: 0.8160 (mtm180) cc_final: 0.7681 (mtp85) REVERT: A 197 LYS cc_start: 0.7944 (mttp) cc_final: 0.7433 (mptt) REVERT: A 252 SER cc_start: 0.8257 (t) cc_final: 0.7872 (p) REVERT: B 15 LYS cc_start: 0.8812 (mtpp) cc_final: 0.8582 (tptt) REVERT: B 42 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.7508 (tpm-80) REVERT: B 46 ARG cc_start: 0.7987 (mtp-110) cc_final: 0.7363 (mtp85) REVERT: B 181 THR cc_start: 0.7933 (p) cc_final: 0.7648 (m) REVERT: B 212 ASP cc_start: 0.7093 (t70) cc_final: 0.6777 (t0) REVERT: B 214 ARG cc_start: 0.7480 (mmp80) cc_final: 0.7171 (mmp80) REVERT: B 217 MET cc_start: 0.7972 (ptm) cc_final: 0.7433 (ppp) REVERT: B 303 ASP cc_start: 0.7730 (m-30) cc_final: 0.7335 (p0) REVERT: B 318 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7841 (mp) REVERT: E 13 GLN cc_start: 0.7477 (pm20) cc_final: 0.7243 (pm20) REVERT: E 43 LYS cc_start: 0.8683 (mtmm) cc_final: 0.8368 (mtmt) REVERT: G 58 GLU cc_start: 0.8415 (mt-10) cc_final: 0.7872 (mp0) REVERT: R 116 MET cc_start: 0.7220 (ttt) cc_final: 0.6437 (tpp) REVERT: R 149 LYS cc_start: 0.8353 (tppp) cc_final: 0.7862 (tmmt) outliers start: 26 outliers final: 17 residues processed: 222 average time/residue: 1.0961 time to fit residues: 262.2358 Evaluate side-chains 217 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 198 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 131 ASP Chi-restraints excluded: chain R residue 134 THR Chi-restraints excluded: chain R residue 417 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 57 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 101 optimal weight: 0.0370 chunk 46 optimal weight: 2.9990 chunk 15 optimal weight: 0.0970 chunk 74 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 105 optimal weight: 0.0670 chunk 62 optimal weight: 0.5980 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN R 70 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.176483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.131958 restraints weight = 29007.898| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.48 r_work: 0.3499 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.6018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8976 Z= 0.110 Angle : 0.542 7.086 12166 Z= 0.286 Chirality : 0.040 0.143 1393 Planarity : 0.004 0.082 1529 Dihedral : 6.212 55.635 1231 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.97 % Allowed : 26.19 % Favored : 71.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 aren not related in a simple way. whole: 0.26 (0.25), residues: 1102 helix: 1.98 (0.26), residues: 400 sheet: -0.98 (0.30), residues: 278 loop : -0.69 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG E 160 TYR 0.014 0.001 TYR A 230 PHE 0.013 0.001 PHE R 189 TRP 0.013 0.001 TRP R 413 HIS 0.004 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 8972) covalent geometry : angle 0.54192 (12158) SS BOND : bond 0.00326 ( 4) SS BOND : angle 0.60508 ( 8) hydrogen bonds : bond 0.03080 ( 445) hydrogen bonds : angle 4.48893 ( 1242) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8154.23 seconds wall clock time: 138 minutes 31.13 seconds (8311.13 seconds total)