Starting phenix.real_space_refine on Sun May 18 16:12:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8irs_35684/05_2025/8irs_35684_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8irs_35684/05_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_35684/05_2025/8irs_35684.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8irs_35684/05_2025/8irs_35684.map" model { file = "/net/cci-nas-00/data/ceres_data/8irs_35684/05_2025/8irs_35684_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8irs_35684/05_2025/8irs_35684_neut_trim.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.010 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 8.07, per 1000 atoms: 0.46 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: 3.88 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.37 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: 6.36 Time building geometry restraints manager: 4.75 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: 0.400 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: 0.300 Extract box with map and model: 0.660 Check model and map are aligned: 0.140 Set scattering table: 0.160 Process input model: 36.220 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 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:12.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.080 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (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 TRP 0.164 0.026 TRP B 99 HIS 0.014 0.004 HIS B 54 PHE 0.090 0.016 PHE A 259 TYR 0.251 0.027 TYR E 175 ARG 0.010 0.001 ARG B 46 Details of bonding type rmsd hydrogen bonds : bond 0.14784 ( 445) hydrogen bonds : angle 7.18117 ( 1242) SS BOND : bond 0.00177 ( 4) SS BOND : angle 1.61605 ( 8) covalent geometry : bond 0.01220 ( 8972) covalent geometry : angle 1.84648 (12158) *********************** 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 : 1.282 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: symmetry clash REVERT: A 28 GLU cc_start: 0.7573 (tt0) cc_final: 0.7355 (tt0) REVERT: A 32 ARG cc_start: 0.8120 (mtm180) cc_final: 0.7840 (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: 0.7908 (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: 0.8002 (t80) REVERT: R 63 LYS cc_start: 0.7756 (tttt) cc_final: 0.7539 (tttp) REVERT: R 164 PHE cc_start: 0.8294 (t80) cc_final: 0.8089 (t80) outliers start: 0 outliers final: 0 residues processed: 318 average time/residue: 2.1979 time to fit residues: 752.7485 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 : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 85 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN A 346 ASN G 24 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 = 0.4088 r_free = 0.4088 target = 0.174577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.129628 restraints weight = 28608.068| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.47 r_work: 0.3458 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8976 Z= 0.164 Angle : 0.653 7.746 12166 Z= 0.355 Chirality : 0.043 0.168 1393 Planarity : 0.004 0.050 1529 Dihedral : 7.901 68.247 1231 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 4.24 % Allowed : 13.25 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.24), residues: 1102 helix: 0.57 (0.24), residues: 406 sheet: -0.51 (0.30), residues: 270 loop : -0.53 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 82 HIS 0.004 0.001 HIS G 44 PHE 0.018 0.002 PHE R 189 TYR 0.033 0.002 TYR B 105 ARG 0.006 0.001 ARG E 160 Details of bonding type rmsd hydrogen bonds : bond 0.04955 ( 445) hydrogen bonds : angle 5.40670 ( 1242) SS BOND : bond 0.00326 ( 4) SS BOND : angle 1.04098 ( 8) covalent geometry : bond 0.00359 ( 8972) covalent geometry : angle 0.65300 (12158) *********************** 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 291 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 250 time to evaluate : 1.355 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: A 32 ARG cc_start: 0.7815 (mtm180) cc_final: 0.7386 (mtp85) REVERT: A 252 SER cc_start: 0.8425 (t) cc_final: 0.8089 (p) REVERT: B 46 ARG cc_start: 0.7704 (mtp-110) cc_final: 0.6981 (mtp85) REVERT: B 181 THR cc_start: 0.7680 (p) cc_final: 0.7375 (m) REVERT: B 258 ASP cc_start: 0.7839 (t0) cc_final: 0.7622 (t0) REVERT: B 280 LYS cc_start: 0.8008 (tttm) cc_final: 0.7706 (ttmm) REVERT: B 303 ASP cc_start: 0.7559 (m-30) cc_final: 0.7115 (p0) REVERT: E 140 MET cc_start: 0.8581 (mmm) cc_final: 0.7849 (mmt) REVERT: R 50 PHE cc_start: 0.8161 (t80) cc_final: 0.7957 (t80) REVERT: R 63 LYS cc_start: 0.7820 (tttt) cc_final: 0.7611 (tttp) REVERT: R 78 VAL cc_start: 0.7655 (OUTLIER) cc_final: 0.7389 (t) REVERT: R 134 THR cc_start: 0.8440 (OUTLIER) cc_final: 0.8163 (t) REVERT: R 138 MET cc_start: 0.7469 (mtp) cc_final: 0.7168 (mtt) outliers start: 41 outliers final: 14 residues processed: 268 average time/residue: 2.1922 time to fit residues: 632.2201 Evaluate side-chains 231 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 215 time to evaluate : 1.230 ------------------------------------------------------------------------------- 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 42 ARG 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 134 THR 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 11 optimal weight: 8.9990 chunk 89 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 101 optimal weight: 0.0980 chunk 85 optimal weight: 0.9990 chunk 15 optimal weight: 9.9990 chunk 67 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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** B 6 GLN B 62 HIS B 237 ASN B 239 ASN E 39 GLN E 179 GLN ** R 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.172218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.126614 restraints weight = 29026.645| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.49 r_work: 0.3416 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.4562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8976 Z= 0.171 Angle : 0.590 6.504 12166 Z= 0.321 Chirality : 0.042 0.156 1393 Planarity : 0.004 0.058 1529 Dihedral : 7.063 63.009 1231 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.52 % Allowed : 17.70 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.24), residues: 1102 helix: 0.93 (0.25), residues: 407 sheet: -0.80 (0.29), residues: 283 loop : -0.49 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 82 HIS 0.006 0.001 HIS G 44 PHE 0.019 0.002 PHE B 235 TYR 0.025 0.002 TYR B 105 ARG 0.008 0.001 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.04194 ( 445) hydrogen bonds : angle 5.10121 ( 1242) SS BOND : bond 0.00402 ( 4) SS BOND : angle 0.93684 ( 8) covalent geometry : bond 0.00382 ( 8972) covalent geometry : angle 0.59014 (12158) *********************** 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 260 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 226 time to evaluate : 1.454 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: A 32 ARG cc_start: 0.7917 (mtm180) cc_final: 0.7459 (mtp85) REVERT: A 186 GLU cc_start: 0.7684 (tt0) cc_final: 0.6983 (mt-10) REVERT: A 197 LYS cc_start: 0.7982 (mttp) cc_final: 0.7432 (mptt) REVERT: A 252 SER cc_start: 0.8304 (t) cc_final: 0.7974 (p) REVERT: A 306 GLN cc_start: 0.8408 (mm110) cc_final: 0.8206 (tp-100) REVERT: B 46 ARG cc_start: 0.7772 (mtp-110) cc_final: 0.7247 (ttm-80) REVERT: B 96 ARG cc_start: 0.7044 (OUTLIER) cc_final: 0.6823 (mpt-90) REVERT: B 181 THR cc_start: 0.7801 (p) cc_final: 0.7577 (m) REVERT: B 212 ASP cc_start: 0.6244 (t70) cc_final: 0.6011 (t70) REVERT: B 217 MET cc_start: 0.7939 (ptm) cc_final: 0.7449 (ppp) REVERT: B 303 ASP cc_start: 0.7697 (m-30) cc_final: 0.7216 (p0) REVERT: E 43 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.8094 (mtmm) REVERT: E 119 VAL cc_start: 0.7427 (t) cc_final: 0.7178 (t) REVERT: R 50 PHE cc_start: 0.8152 (t80) cc_final: 0.7950 (t80) REVERT: R 134 THR cc_start: 0.8415 (OUTLIER) cc_final: 0.8113 (t) REVERT: R 138 MET cc_start: 0.7653 (mtp) cc_final: 0.7453 (mtt) REVERT: R 149 LYS cc_start: 0.8398 (tppp) cc_final: 0.8122 (tppp) REVERT: R 440 ILE cc_start: 0.8639 (mm) cc_final: 0.8427 (tp) outliers start: 34 outliers final: 13 residues processed: 243 average time/residue: 2.1359 time to fit residues: 560.7494 Evaluate side-chains 227 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 211 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 96 ARG Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain E residue 22 CYS 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 134 THR 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 34 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 39 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 83 optimal weight: 7.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4056 r_free = 0.4056 target = 0.170950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.125078 restraints weight = 28984.672| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.51 r_work: 0.3398 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.4989 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= 0.182 Angle : 0.572 6.259 12166 Z= 0.310 Chirality : 0.041 0.153 1393 Planarity : 0.004 0.057 1529 Dihedral : 6.883 59.834 1231 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.52 % Allowed : 19.88 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.25), residues: 1102 helix: 1.23 (0.25), residues: 401 sheet: -0.97 (0.29), residues: 276 loop : -0.57 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 82 HIS 0.006 0.001 HIS B 183 PHE 0.014 0.002 PHE B 235 TYR 0.018 0.002 TYR B 105 ARG 0.009 0.000 ARG E 160 Details of bonding type rmsd hydrogen bonds : bond 0.03846 ( 445) hydrogen bonds : angle 4.99591 ( 1242) SS BOND : bond 0.00361 ( 4) SS BOND : angle 0.79137 ( 8) covalent geometry : bond 0.00408 ( 8972) covalent geometry : angle 0.57154 (12158) *********************** 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 256 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 222 time to evaluate : 1.359 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 32 ARG cc_start: 0.8061 (mtm180) cc_final: 0.7574 (mtp85) REVERT: A 53 MET cc_start: 0.6956 (mtp) cc_final: 0.6722 (mtp) REVERT: A 186 GLU cc_start: 0.7678 (tt0) cc_final: 0.7234 (mt-10) REVERT: A 252 SER cc_start: 0.8298 (t) cc_final: 0.7940 (p) REVERT: B 46 ARG cc_start: 0.7787 (mtp-110) cc_final: 0.7085 (mtp85) REVERT: B 96 ARG cc_start: 0.6994 (OUTLIER) cc_final: 0.6791 (mpt-90) REVERT: B 181 THR cc_start: 0.7812 (p) cc_final: 0.7530 (m) REVERT: B 212 ASP cc_start: 0.6775 (t70) cc_final: 0.6515 (t70) REVERT: B 217 MET cc_start: 0.7991 (ptm) cc_final: 0.7462 (ppp) REVERT: B 280 LYS cc_start: 0.7950 (tttm) cc_final: 0.7698 (ttpp) REVERT: B 303 ASP cc_start: 0.7680 (m-30) cc_final: 0.7211 (p0) REVERT: E 43 LYS cc_start: 0.8428 (mtmt) cc_final: 0.8108 (mtmm) REVERT: E 119 VAL cc_start: 0.7499 (t) cc_final: 0.7252 (t) REVERT: E 140 MET cc_start: 0.8535 (mmm) cc_final: 0.8009 (mmt) REVERT: R 116 MET cc_start: 0.7294 (ttt) cc_final: 0.6659 (tpp) REVERT: R 134 THR cc_start: 0.8417 (OUTLIER) cc_final: 0.8116 (t) REVERT: R 374 MET cc_start: 0.7456 (mmp) cc_final: 0.7176 (mmm) outliers start: 34 outliers final: 20 residues processed: 244 average time/residue: 2.0149 time to fit residues: 532.9624 Evaluate side-chains 230 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 208 time to evaluate : 1.194 ------------------------------------------------------------------------------- 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 343 ILE Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 178 THR 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 117 LEU 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 134 THR 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 66 optimal weight: 0.9980 chunk 77 optimal weight: 0.0870 chunk 6 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 94 optimal weight: 0.8980 chunk 78 optimal weight: 10.0000 chunk 86 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- 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** ** 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 = 0.4079 r_free = 0.4079 target = 0.173202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.127699 restraints weight = 29146.345| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.52 r_work: 0.3436 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.5270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8976 Z= 0.124 Angle : 0.542 6.783 12166 Z= 0.289 Chirality : 0.041 0.149 1393 Planarity : 0.004 0.064 1529 Dihedral : 6.582 59.331 1231 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.11 % Allowed : 21.33 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.25), residues: 1102 helix: 1.55 (0.25), residues: 399 sheet: -1.01 (0.29), residues: 276 loop : -0.51 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.006 0.001 HIS B 183 PHE 0.019 0.001 PHE R 50 TYR 0.013 0.001 TYR E 190 ARG 0.011 0.000 ARG E 160 Details of bonding type rmsd hydrogen bonds : bond 0.03512 ( 445) hydrogen bonds : angle 4.80889 ( 1242) SS BOND : bond 0.00341 ( 4) SS BOND : angle 0.71223 ( 8) covalent geometry : bond 0.00275 ( 8972) covalent geometry : angle 0.54205 (12158) *********************** 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 253 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 223 time to evaluate : 1.427 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 29 LYS cc_start: 0.7857 (ttmt) cc_final: 0.7550 (mppt) REVERT: A 32 ARG cc_start: 0.8085 (mtm180) cc_final: 0.7601 (mtp85) REVERT: A 186 GLU cc_start: 0.7654 (tt0) cc_final: 0.7197 (mt-10) REVERT: A 252 SER cc_start: 0.8193 (t) cc_final: 0.7846 (p) REVERT: A 306 GLN cc_start: 0.8145 (tp40) cc_final: 0.7893 (tp40) REVERT: B 46 ARG cc_start: 0.7812 (mtp-110) cc_final: 0.7106 (mtp85) REVERT: B 181 THR cc_start: 0.7873 (p) cc_final: 0.7629 (m) REVERT: B 212 ASP cc_start: 0.6849 (t70) cc_final: 0.6604 (t70) REVERT: B 217 MET cc_start: 0.7952 (ptm) cc_final: 0.7460 (ppp) REVERT: B 280 LYS cc_start: 0.7784 (tttm) cc_final: 0.7540 (ttpp) REVERT: B 303 ASP cc_start: 0.7665 (m-30) cc_final: 0.7278 (p0) REVERT: E 43 LYS cc_start: 0.8474 (mtmt) cc_final: 0.8163 (mtmm) REVERT: E 119 VAL cc_start: 0.7370 (t) cc_final: 0.7152 (t) REVERT: E 140 MET cc_start: 0.8536 (mmm) cc_final: 0.7950 (mmt) REVERT: R 134 THR cc_start: 0.8472 (OUTLIER) cc_final: 0.8191 (t) REVERT: R 149 LYS cc_start: 0.8444 (tppp) cc_final: 0.7887 (tmmt) outliers start: 30 outliers final: 17 residues processed: 241 average time/residue: 2.0741 time to fit residues: 541.0402 Evaluate side-chains 231 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 213 time to evaluate : 1.405 ------------------------------------------------------------------------------- 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 343 ILE Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 165 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 23 SER 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 134 THR Chi-restraints excluded: chain R residue 214 ILE 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 17 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 15 optimal weight: 0.9980 chunk 74 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 68 optimal weight: 0.3980 chunk 52 optimal weight: 4.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN B 13 GLN ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4064 r_free = 0.4064 target = 0.170428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.124880 restraints weight = 29380.996| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.47 r_work: 0.3409 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.5499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8976 Z= 0.225 Angle : 0.595 6.694 12166 Z= 0.322 Chirality : 0.042 0.147 1393 Planarity : 0.004 0.073 1529 Dihedral : 6.866 59.134 1231 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.42 % Allowed : 22.26 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.25), residues: 1102 helix: 1.39 (0.25), residues: 401 sheet: -1.12 (0.29), residues: 272 loop : -0.74 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 36 HIS 0.006 0.001 HIS G 44 PHE 0.018 0.002 PHE B 235 TYR 0.018 0.002 TYR B 105 ARG 0.011 0.001 ARG E 160 Details of bonding type rmsd hydrogen bonds : bond 0.03726 ( 445) hydrogen bonds : angle 4.93835 ( 1242) SS BOND : bond 0.00353 ( 4) SS BOND : angle 0.81429 ( 8) covalent geometry : bond 0.00511 ( 8972) covalent geometry : angle 0.59481 (12158) *********************** 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 250 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 217 time to evaluate : 1.458 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: 0.8146 (mtm180) cc_final: 0.7692 (mtp85) REVERT: A 186 GLU cc_start: 0.7704 (tt0) cc_final: 0.7336 (mt-10) REVERT: A 197 LYS cc_start: 0.7994 (mttp) cc_final: 0.7623 (mtpt) REVERT: A 248 LYS cc_start: 0.7203 (mptt) cc_final: 0.6978 (mptt) REVERT: A 252 SER cc_start: 0.8255 (t) cc_final: 0.7883 (p) REVERT: B 15 LYS cc_start: 0.8803 (mtpp) cc_final: 0.8578 (tptt) REVERT: B 46 ARG cc_start: 0.7871 (mtp-110) cc_final: 0.7222 (mtp85) REVERT: B 120 ILE cc_start: 0.8452 (mt) cc_final: 0.8229 (mp) REVERT: B 181 THR cc_start: 0.7868 (p) cc_final: 0.7576 (m) REVERT: B 212 ASP cc_start: 0.7025 (t70) cc_final: 0.6797 (t70) REVERT: B 214 ARG cc_start: 0.7426 (mmp80) cc_final: 0.7166 (mmp80) REVERT: B 217 MET cc_start: 0.8089 (ptm) cc_final: 0.7525 (ppp) REVERT: B 303 ASP cc_start: 0.7715 (m-30) cc_final: 0.7361 (p0) REVERT: B 318 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7894 (mp) REVERT: E 43 LYS cc_start: 0.8572 (mtmt) cc_final: 0.8258 (mtmm) REVERT: E 222 GLU cc_start: 0.6937 (pm20) cc_final: 0.6683 (pm20) REVERT: R 116 MET cc_start: 0.7331 (ttt) cc_final: 0.6542 (tpp) REVERT: R 134 THR cc_start: 0.8498 (OUTLIER) cc_final: 0.8211 (t) REVERT: R 149 LYS cc_start: 0.8489 (tppp) cc_final: 0.8182 (tppp) outliers start: 33 outliers final: 24 residues processed: 238 average time/residue: 2.0505 time to fit residues: 529.2807 Evaluate side-chains 239 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 213 time to evaluate : 1.215 ------------------------------------------------------------------------------- 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 306 GLN Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 165 THR 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 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 134 THR Chi-restraints excluded: chain R residue 190 VAL 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 45 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 73 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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** B 13 GLN ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.172940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.128163 restraints weight = 29026.669| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.45 r_work: 0.3453 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.5622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8976 Z= 0.134 Angle : 0.550 5.156 12166 Z= 0.293 Chirality : 0.041 0.150 1393 Planarity : 0.004 0.079 1529 Dihedral : 6.530 57.199 1231 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.00 % Allowed : 22.88 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.25), residues: 1102 helix: 1.57 (0.25), residues: 398 sheet: -1.09 (0.30), residues: 274 loop : -0.77 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.005 0.001 HIS B 183 PHE 0.012 0.001 PHE R 189 TYR 0.013 0.001 TYR E 190 ARG 0.014 0.000 ARG E 160 Details of bonding type rmsd hydrogen bonds : bond 0.03364 ( 445) hydrogen bonds : angle 4.78574 ( 1242) SS BOND : bond 0.00324 ( 4) SS BOND : angle 0.65772 ( 8) covalent geometry : bond 0.00301 ( 8972) covalent geometry : angle 0.54983 (12158) *********************** 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 248 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 219 time to evaluate : 1.505 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: 0.8150 (mtm180) cc_final: 0.7749 (mtp85) REVERT: A 186 GLU cc_start: 0.7677 (tt0) cc_final: 0.7109 (mt-10) REVERT: A 252 SER cc_start: 0.8201 (t) cc_final: 0.7826 (p) REVERT: B 15 LYS cc_start: 0.8815 (mtpp) cc_final: 0.8588 (tptt) REVERT: B 46 ARG cc_start: 0.7846 (mtp-110) cc_final: 0.7210 (mtp85) REVERT: B 181 THR cc_start: 0.7935 (p) cc_final: 0.7664 (m) REVERT: B 196 THR cc_start: 0.8444 (t) cc_final: 0.8135 (m) REVERT: B 212 ASP cc_start: 0.7097 (t70) cc_final: 0.6858 (t70) REVERT: B 217 MET cc_start: 0.8027 (ptm) cc_final: 0.7499 (ppp) REVERT: B 280 LYS cc_start: 0.7829 (tttm) cc_final: 0.7601 (ttpp) REVERT: B 303 ASP cc_start: 0.7720 (m-30) cc_final: 0.7397 (p0) REVERT: E 43 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.8233 (mtmm) REVERT: E 220 GLU cc_start: 0.7325 (mp0) cc_final: 0.7078 (mp0) REVERT: R 134 THR cc_start: 0.8469 (OUTLIER) cc_final: 0.8190 (t) REVERT: R 149 LYS cc_start: 0.8365 (tppp) cc_final: 0.8096 (tppp) outliers start: 29 outliers final: 22 residues processed: 238 average time/residue: 1.9895 time to fit residues: 514.0393 Evaluate side-chains 237 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 213 time to evaluate : 1.198 ------------------------------------------------------------------------------- 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 13 GLN Chi-restraints excluded: chain B residue 165 THR 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 43 LYS Chi-restraints excluded: chain E residue 117 LEU 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 134 THR Chi-restraints excluded: chain R residue 393 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 39 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.171051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.125627 restraints weight = 29172.079| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.47 r_work: 0.3416 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: 0.7244 moved from start: 0.5717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8976 Z= 0.203 Angle : 0.585 6.834 12166 Z= 0.315 Chirality : 0.041 0.148 1393 Planarity : 0.004 0.073 1529 Dihedral : 6.672 55.779 1231 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.31 % Allowed : 23.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.25), residues: 1102 helix: 1.40 (0.25), residues: 401 sheet: -1.13 (0.30), residues: 275 loop : -0.82 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 99 HIS 0.005 0.001 HIS B 183 PHE 0.015 0.002 PHE B 235 TYR 0.015 0.002 TYR A 230 ARG 0.012 0.001 ARG E 160 Details of bonding type rmsd hydrogen bonds : bond 0.03500 ( 445) hydrogen bonds : angle 4.85363 ( 1242) SS BOND : bond 0.00330 ( 4) SS BOND : angle 0.72829 ( 8) covalent geometry : bond 0.00457 ( 8972) covalent geometry : angle 0.58537 (12158) *********************** 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: 32 poor density : 207 time to evaluate : 1.368 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: A 32 ARG cc_start: 0.8200 (mtm180) cc_final: 0.7762 (mtp85) REVERT: A 186 GLU cc_start: 0.7658 (tt0) cc_final: 0.7281 (mt-10) REVERT: A 252 SER cc_start: 0.8207 (t) cc_final: 0.7813 (p) REVERT: B 46 ARG cc_start: 0.7870 (mtp-110) cc_final: 0.7264 (mtp85) REVERT: B 120 ILE cc_start: 0.8472 (mt) cc_final: 0.8231 (mp) REVERT: B 181 THR cc_start: 0.7961 (p) cc_final: 0.7673 (m) REVERT: B 196 THR cc_start: 0.8441 (t) cc_final: 0.8138 (m) REVERT: B 212 ASP cc_start: 0.7103 (t70) cc_final: 0.6848 (t70) REVERT: B 214 ARG cc_start: 0.7404 (mmp80) cc_final: 0.7169 (mmp80) REVERT: B 217 MET cc_start: 0.8063 (ptm) cc_final: 0.7489 (ppp) REVERT: B 280 LYS cc_start: 0.7865 (tttm) cc_final: 0.7632 (ttpp) REVERT: B 303 ASP cc_start: 0.7696 (m-30) cc_final: 0.7366 (p0) REVERT: E 43 LYS cc_start: 0.8583 (mtmt) cc_final: 0.8289 (mtmm) REVERT: E 220 GLU cc_start: 0.7174 (mp0) cc_final: 0.6946 (mp0) REVERT: R 134 THR cc_start: 0.8489 (OUTLIER) cc_final: 0.8215 (t) REVERT: R 149 LYS cc_start: 0.8391 (tppp) cc_final: 0.8118 (tppp) outliers start: 32 outliers final: 23 residues processed: 229 average time/residue: 2.1041 time to fit residues: 520.8641 Evaluate side-chains 229 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 205 time to evaluate : 1.290 ------------------------------------------------------------------------------- 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 B residue 32 GLN Chi-restraints excluded: chain B residue 165 THR 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 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 134 THR Chi-restraints excluded: chain R residue 158 ILE Chi-restraints excluded: chain R residue 393 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 73 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 72 optimal weight: 0.3980 chunk 55 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN E 13 GLN ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4100 r_free = 0.4100 target = 0.174186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.129173 restraints weight = 29125.028| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.47 r_work: 0.3464 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.5837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8976 Z= 0.128 Angle : 0.545 5.557 12166 Z= 0.291 Chirality : 0.040 0.152 1393 Planarity : 0.004 0.079 1529 Dihedral : 6.358 56.952 1231 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.90 % Allowed : 23.91 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.25), residues: 1102 helix: 1.63 (0.26), residues: 402 sheet: -1.06 (0.30), residues: 275 loop : -0.78 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS B 183 PHE 0.012 0.001 PHE R 189 TYR 0.015 0.001 TYR A 230 ARG 0.014 0.000 ARG E 160 Details of bonding type rmsd hydrogen bonds : bond 0.03235 ( 445) hydrogen bonds : angle 4.67425 ( 1242) SS BOND : bond 0.00358 ( 4) SS BOND : angle 0.63413 ( 8) covalent geometry : bond 0.00286 ( 8972) covalent geometry : angle 0.54510 (12158) *********************** 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 238 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 210 time to evaluate : 1.393 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 22 ASN cc_start: 0.7638 (p0) cc_final: 0.7367 (m-40) REVERT: A 29 LYS cc_start: 0.8026 (ttmt) cc_final: 0.7778 (mppt) REVERT: A 32 ARG cc_start: 0.8194 (mtm180) cc_final: 0.7743 (mtp85) REVERT: A 197 LYS cc_start: 0.7909 (mttp) cc_final: 0.7484 (mptt) REVERT: A 252 SER cc_start: 0.8100 (t) cc_final: 0.7726 (p) REVERT: B 15 LYS cc_start: 0.8826 (mtpp) cc_final: 0.8606 (tptt) REVERT: B 46 ARG cc_start: 0.7913 (mtp-110) cc_final: 0.7268 (mtp85) REVERT: B 181 THR cc_start: 0.7935 (p) cc_final: 0.7669 (m) REVERT: B 196 THR cc_start: 0.8432 (t) cc_final: 0.8153 (m) REVERT: B 212 ASP cc_start: 0.7049 (t70) cc_final: 0.6786 (t0) REVERT: B 214 ARG cc_start: 0.7460 (mmp80) cc_final: 0.7191 (mmp80) REVERT: B 217 MET cc_start: 0.7967 (ptm) cc_final: 0.7410 (ppp) REVERT: B 258 ASP cc_start: 0.8027 (t0) cc_final: 0.7823 (t0) REVERT: E 43 LYS cc_start: 0.8559 (mtmt) cc_final: 0.8273 (mtmm) REVERT: G 58 GLU cc_start: 0.8364 (mt-10) cc_final: 0.7840 (mp0) REVERT: R 116 MET cc_start: 0.7338 (ttt) cc_final: 0.6353 (tpp) REVERT: R 134 THR cc_start: 0.8437 (OUTLIER) cc_final: 0.8162 (t) REVERT: R 149 LYS cc_start: 0.8326 (tppp) cc_final: 0.7853 (tmmt) REVERT: R 393 HIS cc_start: 0.8032 (OUTLIER) cc_final: 0.7768 (t70) outliers start: 28 outliers final: 16 residues processed: 229 average time/residue: 1.9982 time to fit residues: 496.0231 Evaluate side-chains 223 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 205 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 165 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 41 CYS Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 134 THR Chi-restraints excluded: chain R residue 393 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 61 optimal weight: 0.0770 chunk 89 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 96 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 106 optimal weight: 7.9990 chunk 59 optimal weight: 0.7980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.175065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.130440 restraints weight = 28958.156| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.47 r_work: 0.3483 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.5924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8976 Z= 0.121 Angle : 0.549 5.950 12166 Z= 0.293 Chirality : 0.040 0.146 1393 Planarity : 0.004 0.083 1529 Dihedral : 6.196 57.116 1231 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.07 % Allowed : 25.16 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.25), residues: 1102 helix: 1.78 (0.26), residues: 402 sheet: -1.12 (0.29), residues: 282 loop : -0.71 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 413 HIS 0.004 0.001 HIS B 183 PHE 0.012 0.001 PHE R 189 TYR 0.011 0.001 TYR A 230 ARG 0.014 0.000 ARG E 160 Details of bonding type rmsd hydrogen bonds : bond 0.03186 ( 445) hydrogen bonds : angle 4.57292 ( 1242) SS BOND : bond 0.00347 ( 4) SS BOND : angle 0.62426 ( 8) covalent geometry : bond 0.00273 ( 8972) covalent geometry : angle 0.54915 (12158) ********************** 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 235 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 215 time to evaluate : 1.346 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 29 LYS cc_start: 0.7944 (ttmt) cc_final: 0.7693 (mppt) REVERT: A 32 ARG cc_start: 0.8169 (mtm180) cc_final: 0.7701 (mtp85) REVERT: A 186 GLU cc_start: 0.7720 (tt0) cc_final: 0.7290 (mt-10) REVERT: A 248 LYS cc_start: 0.7586 (mptt) cc_final: 0.7348 (mptt) REVERT: A 252 SER cc_start: 0.8000 (t) cc_final: 0.7686 (p) REVERT: B 15 LYS cc_start: 0.8823 (mtpp) cc_final: 0.8606 (tptt) REVERT: B 46 ARG cc_start: 0.7898 (mtp-110) cc_final: 0.7379 (ttm-80) REVERT: B 196 THR cc_start: 0.8394 (t) cc_final: 0.8137 (m) REVERT: B 212 ASP cc_start: 0.6934 (t70) cc_final: 0.6694 (t0) REVERT: B 214 ARG cc_start: 0.7464 (mmp80) cc_final: 0.7186 (mmp80) REVERT: B 217 MET cc_start: 0.7910 (ptm) cc_final: 0.7329 (ppp) REVERT: B 258 ASP cc_start: 0.8025 (t0) cc_final: 0.7785 (t0) REVERT: B 325 MET cc_start: 0.8374 (tpp) cc_final: 0.7967 (tpt) REVERT: E 234 GLU cc_start: 0.8596 (pt0) cc_final: 0.8313 (pt0) REVERT: G 58 GLU cc_start: 0.8428 (mt-10) cc_final: 0.7882 (mp0) REVERT: R 116 MET cc_start: 0.7348 (ttt) cc_final: 0.6370 (tpp) REVERT: R 134 THR cc_start: 0.8391 (OUTLIER) cc_final: 0.8116 (t) REVERT: R 149 LYS cc_start: 0.8226 (tppp) cc_final: 0.7742 (tmmt) REVERT: R 393 HIS cc_start: 0.8212 (OUTLIER) cc_final: 0.7926 (t70) outliers start: 20 outliers final: 16 residues processed: 230 average time/residue: 2.0006 time to fit residues: 499.1620 Evaluate side-chains 221 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 203 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 165 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 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 134 THR Chi-restraints excluded: chain R residue 393 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 85 optimal weight: 0.9990 chunk 38 optimal weight: 0.1980 chunk 35 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 67 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 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 = 0.4101 r_free = 0.4101 target = 0.174558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.129355 restraints weight = 29187.812| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.49 r_work: 0.3458 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.5972 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= 0.155 Angle : 0.565 7.715 12166 Z= 0.301 Chirality : 0.040 0.145 1393 Planarity : 0.004 0.083 1529 Dihedral : 6.237 57.372 1231 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.38 % Allowed : 25.47 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.25), residues: 1102 helix: 1.80 (0.25), residues: 401 sheet: -1.17 (0.29), residues: 282 loop : -0.77 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 413 HIS 0.004 0.001 HIS B 183 PHE 0.012 0.001 PHE A 189 TYR 0.015 0.001 TYR E 103 ARG 0.014 0.000 ARG E 160 Details of bonding type rmsd hydrogen bonds : bond 0.03261 ( 445) hydrogen bonds : angle 4.61526 ( 1242) SS BOND : bond 0.00323 ( 4) SS BOND : angle 0.64678 ( 8) covalent geometry : bond 0.00355 ( 8972) covalent geometry : angle 0.56508 (12158) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14528.57 seconds wall clock time: 248 minutes 38.23 seconds (14918.23 seconds total)