Starting phenix.real_space_refine on Sun May 18 13:56:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8irt_35685/05_2025/8irt_35685_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8irt_35685/05_2025/8irt_35685.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8irt_35685/05_2025/8irt_35685.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8irt_35685/05_2025/8irt_35685.map" model { file = "/net/cci-nas-00/data/ceres_data/8irt_35685/05_2025/8irt_35685_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8irt_35685/05_2025/8irt_35685_neut_trim.cif" } resolution = 2.7 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= 0.009 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 69 5.16 5 C 5571 2.51 5 N 1485 2.21 5 O 1643 1.98 5 H 8669 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: 17437 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 3572 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 219} Chain breaks: 2 Chain: "B" Number of atoms: 5108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5108 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "E" Number of atoms: 3503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 3503 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "G" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 885 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "R" Number of atoms: 4341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 4341 Classifications: {'peptide': 273} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 262} Chain breaks: 1 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Unusual residues: {'R5F': 1} Classifications: {'undetermined': 1, 'water': 2} Link IDs: {None: 2} Time building chain proxies: 8.96, per 1000 atoms: 0.51 Number of scatterers: 17437 At special positions: 0 Unit cell: (112.86, 132.715, 108.68, 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 69 16.00 O 1643 8.00 N 1485 7.00 C 5571 6.00 H 8669 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=2.04 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 103 " - pdb=" SG CYS R 181 " distance=2.04 Simple disulfide: pdb=" SG CYS R 355 " - pdb=" SG CYS R 358 " distance=2.02 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: 4.72 Conformation dependent library (CDL) restraints added in 1.5 seconds 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2100 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 13 sheets defined 40.6% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.766A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 232 removed outlier: 3.863A pdb=" N TYR A 230 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU A 232 " --> pdb=" O ASP A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.875A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (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 329 through 351 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 4.211A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' 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 removed outlier: 3.560A pdb=" N VAL E 224 " --> pdb=" O ALA E 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'R' and resid 32 through 57 Processing helix chain 'R' and resid 58 through 61 Processing helix chain 'R' and resid 62 through 81 removed outlier: 3.627A pdb=" N LEU R 67 " --> pdb=" O THR R 63 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL R 68 " --> pdb=" O THR R 64 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 92 removed outlier: 4.522A pdb=" N TRP R 85 " --> pdb=" O LEU R 81 " (cutoff:3.500A) Processing helix chain 'R' and resid 99 through 134 removed outlier: 3.694A pdb=" N VAL R 132 " --> pdb=" O ARG R 128 " (cutoff:3.500A) Processing helix chain 'R' and resid 134 through 139 Processing helix chain 'R' and resid 143 through 166 Processing helix chain 'R' and resid 167 through 170 Processing helix chain 'R' and resid 185 through 197 removed outlier: 4.827A pdb=" N TYR R 191 " --> pdb=" O ASP R 187 " (cutoff:3.500A) Processing helix chain 'R' and resid 197 through 223 Processing helix chain 'R' and resid 322 through 354 Proline residue: R 344 - end of helix Processing helix chain 'R' and resid 361 through 384 removed outlier: 3.800A pdb=" N ASN R 375 " --> pdb=" O LEU R 371 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N SER R 376 " --> pdb=" O GLY R 372 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA R 377 " --> pdb=" O TYR R 373 " (cutoff:3.500A) Proline residue: R 380 - end of helix Processing helix chain 'R' and resid 387 through 400 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.706A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.500A 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: 6.532A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.747A 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: 6.836A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.940A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.568A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.508A 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: 6.743A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.133A 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: 6.451A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.625A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.210A 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 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.694A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AB3, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.525A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 4.043A pdb=" N THR E 238 " --> pdb=" O GLN E 231 " (cutoff:3.500A) 478 hydrogen bonds defined for protein. 1326 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: 6.62 Time building geometry restraints manager: 5.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.13: 8637 1.13 - 1.30: 1520 1.30 - 1.47: 3462 1.47 - 1.65: 3898 1.65 - 1.82: 98 Bond restraints: 17615 Sorted by residual: bond pdb=" NE2 GLN R 356 " pdb="HE22 GLN R 356 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" CE3 TRP E 36 " pdb=" HE3 TRP E 36 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N ASN R 97 " pdb=" H ASN R 97 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N ILE B 58 " pdb=" H ILE B 58 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" NH1 ARG B 283 " pdb="HH11 ARG B 283 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 ... (remaining 17610 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 27020 2.76 - 5.51: 3647 5.51 - 8.27: 960 8.27 - 11.02: 37 11.02 - 13.78: 28 Bond angle restraints: 31692 Sorted by residual: angle pdb=" C TYR B 105 " pdb=" CA TYR B 105 " pdb=" CB TYR B 105 " ideal model delta sigma weight residual 109.71 122.47 -12.76 1.83e+00 2.99e-01 4.86e+01 angle pdb=" N ASN A 269 " pdb=" CA ASN A 269 " pdb=" C ASN A 269 " ideal model delta sigma weight residual 113.18 121.46 -8.28 1.21e+00 6.83e-01 4.68e+01 angle pdb=" N ARG B 52 " pdb=" CA ARG B 52 " pdb=" C ARG B 52 " ideal model delta sigma weight residual 112.90 121.78 -8.88 1.31e+00 5.83e-01 4.59e+01 angle pdb=" C LEU B 51 " pdb=" CA LEU B 51 " pdb=" CB LEU B 51 " ideal model delta sigma weight residual 111.77 121.44 -9.67 1.52e+00 4.33e-01 4.05e+01 angle pdb=" CA ASP B 228 " pdb=" CB ASP B 228 " pdb=" CG ASP B 228 " ideal model delta sigma weight residual 112.60 118.66 -6.06 1.00e+00 1.00e+00 3.67e+01 ... (remaining 31687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 7617 17.95 - 35.91: 447 35.91 - 53.86: 145 53.86 - 71.81: 126 71.81 - 89.77: 8 Dihedral angle restraints: 8343 sinusoidal: 4468 harmonic: 3875 Sorted by residual: dihedral pdb=" CA ASN A 311 " pdb=" C ASN A 311 " pdb=" N LYS A 312 " pdb=" CA LYS A 312 " ideal model delta harmonic sigma weight residual 180.00 150.13 29.87 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CA TYR R 138 " pdb=" C TYR R 138 " pdb=" N GLN R 139 " pdb=" CA GLN R 139 " ideal model delta harmonic sigma weight residual -180.00 -150.27 -29.73 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA TYR B 289 " pdb=" C TYR B 289 " pdb=" N ASP B 290 " pdb=" CA ASP B 290 " ideal model delta harmonic sigma weight residual 180.00 150.95 29.05 0 5.00e+00 4.00e-02 3.37e+01 ... (remaining 8340 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 889 0.086 - 0.173: 379 0.173 - 0.259: 90 0.259 - 0.345: 26 0.345 - 0.431: 5 Chirality restraints: 1389 Sorted by residual: 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 2.08 0.43 2.00e-01 2.50e+01 4.65e+00 chirality pdb=" CA THR R 357 " pdb=" N THR R 357 " pdb=" C THR R 357 " pdb=" CB THR R 357 " both_signs ideal model delta sigma weight residual False 2.53 2.14 0.39 2.00e-01 2.50e+01 3.80e+00 chirality pdb=" CA ASP B 228 " pdb=" N ASP B 228 " pdb=" C ASP B 228 " pdb=" CB ASP B 228 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.42e+00 ... (remaining 1386 not shown) Planarity restraints: 2610 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 105 " 0.404 2.00e-02 2.50e+03 1.59e-01 7.54e+02 pdb=" CG TYR B 105 " -0.228 2.00e-02 2.50e+03 pdb=" CD1 TYR B 105 " -0.085 2.00e-02 2.50e+03 pdb=" CD2 TYR B 105 " -0.169 2.00e-02 2.50e+03 pdb=" CE1 TYR B 105 " -0.062 2.00e-02 2.50e+03 pdb=" CE2 TYR B 105 " -0.025 2.00e-02 2.50e+03 pdb=" CZ TYR B 105 " 0.014 2.00e-02 2.50e+03 pdb=" OH TYR B 105 " 0.176 2.00e-02 2.50e+03 pdb=" HD1 TYR B 105 " 0.005 2.00e-02 2.50e+03 pdb=" HD2 TYR B 105 " -0.090 2.00e-02 2.50e+03 pdb=" HE1 TYR B 105 " -0.021 2.00e-02 2.50e+03 pdb=" HE2 TYR B 105 " 0.082 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 175 " -0.293 2.00e-02 2.50e+03 1.22e-01 4.45e+02 pdb=" CG TYR E 175 " -0.003 2.00e-02 2.50e+03 pdb=" CD1 TYR E 175 " 0.089 2.00e-02 2.50e+03 pdb=" CD2 TYR E 175 " 0.067 2.00e-02 2.50e+03 pdb=" CE1 TYR E 175 " 0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR E 175 " 0.060 2.00e-02 2.50e+03 pdb=" CZ TYR E 175 " -0.038 2.00e-02 2.50e+03 pdb=" OH TYR E 175 " -0.202 2.00e-02 2.50e+03 pdb=" HD1 TYR E 175 " 0.149 2.00e-02 2.50e+03 pdb=" HD2 TYR E 175 " 0.079 2.00e-02 2.50e+03 pdb=" HE1 TYR E 175 " 0.004 2.00e-02 2.50e+03 pdb=" HE2 TYR E 175 " 0.070 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 47 " 0.026 2.00e-02 2.50e+03 1.05e-01 4.38e+02 pdb=" CG TRP E 47 " -0.098 2.00e-02 2.50e+03 pdb=" CD1 TRP E 47 " -0.079 2.00e-02 2.50e+03 pdb=" CD2 TRP E 47 " -0.086 2.00e-02 2.50e+03 pdb=" NE1 TRP E 47 " -0.029 2.00e-02 2.50e+03 pdb=" CE2 TRP E 47 " -0.098 2.00e-02 2.50e+03 pdb=" CE3 TRP E 47 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 47 " -0.074 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 47 " 0.025 2.00e-02 2.50e+03 pdb=" CH2 TRP E 47 " -0.036 2.00e-02 2.50e+03 pdb=" HD1 TRP E 47 " 0.008 2.00e-02 2.50e+03 pdb=" HE1 TRP E 47 " 0.328 2.00e-02 2.50e+03 pdb=" HE3 TRP E 47 " 0.069 2.00e-02 2.50e+03 pdb=" HZ2 TRP E 47 " -0.063 2.00e-02 2.50e+03 pdb=" HZ3 TRP E 47 " 0.130 2.00e-02 2.50e+03 pdb=" HH2 TRP E 47 " -0.019 2.00e-02 2.50e+03 ... (remaining 2607 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 1074 2.16 - 2.77: 30730 2.77 - 3.38: 52633 3.38 - 3.99: 71035 3.99 - 4.60: 103637 Nonbonded interactions: 259109 Sorted by model distance: nonbonded pdb=" HG SER B 108 " pdb=" OD1 ASP B 154 " model vdw 1.550 2.450 nonbonded pdb=" HG1 THR B 274 " pdb=" O VAL B 315 " model vdw 1.557 2.450 nonbonded pdb=" HG SER B 147 " pdb=" O VAL B 187 " model vdw 1.560 2.450 nonbonded pdb=" OE2 GLU A 8 " pdb=" HH TYR E 175 " model vdw 1.577 2.450 nonbonded pdb=" OD2 ASP B 170 " pdb=" HG1 THR B 173 " model vdw 1.596 2.450 ... (remaining 259104 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: 3.160 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: 0.000 Extract box with map and model: 2.420 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 38.390 Find NCS groups from input model: 0.110 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:10.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 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 0.082 8950 Z= 0.748 Angle : 1.886 12.762 12134 Z= 1.252 Chirality : 0.103 0.431 1389 Planarity : 0.019 0.274 1527 Dihedral : 13.032 89.767 3208 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 0.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.67 % 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: -0.67 (0.24), residues: 1104 helix: -0.47 (0.22), residues: 388 sheet: -0.17 (0.31), residues: 264 loop : -0.36 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.121 0.025 TRP B 82 HIS 0.022 0.005 HIS B 54 PHE 0.105 0.018 PHE R 345 TYR 0.377 0.025 TYR B 105 ARG 0.014 0.002 ARG R 222 Details of bonding type rmsd hydrogen bonds : bond 0.14465 ( 472) hydrogen bonds : angle 7.30597 ( 1326) SS BOND : bond 0.00616 ( 4) SS BOND : angle 1.96859 ( 8) covalent geometry : bond 0.01219 ( 8946) covalent geometry : angle 1.88561 (12126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 1.371 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 22 ASN cc_start: 0.8139 (m-40) cc_final: 0.7930 (m-40) REVERT: A 26 ASP cc_start: 0.7501 (m-30) cc_final: 0.7209 (m-30) REVERT: A 207 GLU cc_start: 0.7262 (tt0) cc_final: 0.6856 (tt0) REVERT: B 214 ARG cc_start: 0.6868 (mmp80) cc_final: 0.6569 (mmp-170) REVERT: G 14 LYS cc_start: 0.7418 (tptp) cc_final: 0.7070 (tttt) REVERT: R 170 PHE cc_start: 0.6066 (p90) cc_final: 0.5835 (p90) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 2.6616 time to fit residues: 587.4632 Evaluate side-chains 157 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.8980 chunk 83 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 213 HIS A 244 HIS A 294 ASN A 322 HIS B 35 ASN B 266 HIS B 340 ASN E 171 ASN G 24 ASN R 47 ASN R 352 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.173408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.127119 restraints weight = 24961.613| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.59 r_work: 0.3230 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8950 Z= 0.168 Angle : 0.646 7.575 12134 Z= 0.352 Chirality : 0.044 0.153 1389 Planarity : 0.005 0.081 1527 Dihedral : 7.690 79.456 1236 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.77 % Allowed : 7.28 % Favored : 90.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: 0.25 (0.24), residues: 1104 helix: 1.26 (0.25), residues: 385 sheet: -0.38 (0.30), residues: 268 loop : -0.31 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 99 HIS 0.004 0.001 HIS A 244 PHE 0.025 0.002 PHE R 345 TYR 0.044 0.002 TYR B 105 ARG 0.005 0.001 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.04874 ( 472) hydrogen bonds : angle 5.63928 ( 1326) SS BOND : bond 0.00259 ( 4) SS BOND : angle 1.09981 ( 8) covalent geometry : bond 0.00363 ( 8946) covalent geometry : angle 0.64608 (12126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 184 time to evaluate : 1.315 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: A 22 ASN cc_start: 0.8517 (m-40) cc_final: 0.8290 (m110) REVERT: A 26 ASP cc_start: 0.7917 (m-30) cc_final: 0.7606 (m-30) REVERT: A 32 ARG cc_start: 0.7629 (mmt-90) cc_final: 0.7398 (mmt-90) REVERT: A 244 HIS cc_start: 0.7797 (m90) cc_final: 0.7455 (m-70) REVERT: A 345 LYS cc_start: 0.8537 (mttt) cc_final: 0.8189 (mttm) REVERT: B 175 GLN cc_start: 0.8329 (tp40) cc_final: 0.8104 (mp10) REVERT: B 197 ARG cc_start: 0.8209 (mmp-170) cc_final: 0.7782 (mmm-85) REVERT: B 214 ARG cc_start: 0.7336 (mmp80) cc_final: 0.6889 (mmm160) REVERT: B 312 ASP cc_start: 0.7711 (m-30) cc_final: 0.7511 (m-30) REVERT: E 160 ARG cc_start: 0.7684 (ttm170) cc_final: 0.6941 (ttm-80) REVERT: E 244 LYS cc_start: 0.7682 (ptmm) cc_final: 0.7450 (ptmt) REVERT: G 20 LYS cc_start: 0.7401 (OUTLIER) cc_final: 0.6480 (tttm) REVERT: R 113 MET cc_start: 0.7501 (mmt) cc_final: 0.7225 (mmt) REVERT: R 216 LYS cc_start: 0.6793 (ttpp) cc_final: 0.6544 (mptt) REVERT: R 389 GLU cc_start: 0.7201 (mp0) cc_final: 0.6960 (mp0) outliers start: 17 outliers final: 7 residues processed: 190 average time/residue: 2.7313 time to fit residues: 552.2781 Evaluate side-chains 163 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 155 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 333 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 67 optimal weight: 6.9990 chunk 105 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 86 optimal weight: 4.9990 chunk 83 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 89 optimal weight: 9.9990 chunk 54 optimal weight: 0.5980 chunk 99 optimal weight: 3.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 331 ASN A 333 GLN B 266 HIS R 137 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.167215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.119542 restraints weight = 25124.632| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.71 r_work: 0.3085 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.080 8950 Z= 0.355 Angle : 0.709 8.383 12134 Z= 0.387 Chirality : 0.047 0.157 1389 Planarity : 0.006 0.093 1527 Dihedral : 7.245 69.569 1236 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.19 % Allowed : 11.34 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.55 % 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: 1104 helix: 1.40 (0.25), residues: 387 sheet: -0.55 (0.31), residues: 270 loop : -0.51 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 99 HIS 0.012 0.002 HIS A 213 PHE 0.025 0.003 PHE R 345 TYR 0.051 0.003 TYR B 105 ARG 0.004 0.001 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.04987 ( 472) hydrogen bonds : angle 5.65596 ( 1326) SS BOND : bond 0.00341 ( 4) SS BOND : angle 0.98088 ( 8) covalent geometry : bond 0.00799 ( 8946) covalent geometry : angle 0.70861 (12126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 166 time to evaluate : 1.553 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: A 26 ASP cc_start: 0.8092 (m-30) cc_final: 0.7829 (m-30) REVERT: A 33 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7565 (tt0) REVERT: A 318 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7741 (tt0) REVERT: B 175 GLN cc_start: 0.8520 (tp40) cc_final: 0.8292 (mp10) REVERT: B 197 ARG cc_start: 0.8218 (mmp-170) cc_final: 0.7814 (mmm-85) REVERT: B 290 ASP cc_start: 0.7777 (OUTLIER) cc_final: 0.7535 (p0) REVERT: E 160 ARG cc_start: 0.7815 (ttm170) cc_final: 0.7049 (ttm-80) REVERT: G 14 LYS cc_start: 0.6898 (tptp) cc_final: 0.6461 (tttt) REVERT: G 20 LYS cc_start: 0.7466 (OUTLIER) cc_final: 0.6460 (tttm) REVERT: G 32 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8040 (ttmt) REVERT: R 83 MET cc_start: 0.7379 (mtp) cc_final: 0.7069 (mtp) REVERT: R 170 PHE cc_start: 0.6060 (OUTLIER) cc_final: 0.5102 (p90) REVERT: R 216 LYS cc_start: 0.6819 (ttpp) cc_final: 0.6546 (mptt) REVERT: R 387 ASN cc_start: 0.6517 (t0) cc_final: 0.6150 (t0) REVERT: R 389 GLU cc_start: 0.7149 (mp0) cc_final: 0.6938 (mp0) outliers start: 21 outliers final: 10 residues processed: 178 average time/residue: 2.6337 time to fit residues: 500.1951 Evaluate side-chains 162 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 147 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 170 PHE Chi-restraints excluded: chain R residue 352 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 40 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 89 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 74 optimal weight: 0.4980 chunk 108 optimal weight: 4.9990 chunk 94 optimal weight: 8.9990 chunk 69 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.170340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.131379 restraints weight = 25212.933| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.87 r_work: 0.3187 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8950 Z= 0.155 Angle : 0.572 5.511 12134 Z= 0.308 Chirality : 0.042 0.151 1389 Planarity : 0.004 0.065 1527 Dihedral : 5.977 34.460 1236 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.50 % Allowed : 12.70 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: 0.41 (0.25), residues: 1104 helix: 1.85 (0.26), residues: 388 sheet: -0.59 (0.31), residues: 279 loop : -0.48 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS A 213 PHE 0.016 0.002 PHE R 345 TYR 0.017 0.002 TYR B 105 ARG 0.004 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.04071 ( 472) hydrogen bonds : angle 5.32146 ( 1326) SS BOND : bond 0.00324 ( 4) SS BOND : angle 1.73493 ( 8) covalent geometry : bond 0.00332 ( 8946) covalent geometry : angle 0.57055 (12126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 1.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 ARG cc_start: 0.6337 (OUTLIER) cc_final: 0.6120 (mtt90) REVERT: A 318 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7747 (tt0) REVERT: A 345 LYS cc_start: 0.8573 (mttt) cc_final: 0.8224 (mttm) REVERT: B 219 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7532 (mmm-85) REVERT: E 160 ARG cc_start: 0.7769 (ttm170) cc_final: 0.7033 (ttm-80) REVERT: G 14 LYS cc_start: 0.6927 (tptp) cc_final: 0.6502 (tttt) REVERT: G 20 LYS cc_start: 0.7572 (OUTLIER) cc_final: 0.6553 (tttm) REVERT: G 32 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8083 (ttmt) REVERT: R 170 PHE cc_start: 0.6137 (OUTLIER) cc_final: 0.5070 (p90) REVERT: R 216 LYS cc_start: 0.6832 (ttpp) cc_final: 0.6555 (mmtt) REVERT: R 387 ASN cc_start: 0.6376 (t0) cc_final: 0.5957 (t0) REVERT: R 389 GLU cc_start: 0.7215 (mp0) cc_final: 0.6972 (mp0) outliers start: 24 outliers final: 11 residues processed: 171 average time/residue: 2.6331 time to fit residues: 480.2133 Evaluate side-chains 167 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 170 PHE Chi-restraints excluded: chain R residue 352 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 4 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 108 optimal weight: 0.2980 chunk 92 optimal weight: 3.9990 chunk 82 optimal weight: 0.4980 chunk 7 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 195 HIS A 331 ASN B 268 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.171840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.133800 restraints weight = 25403.638| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.78 r_work: 0.3214 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.4193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8950 Z= 0.141 Angle : 0.540 6.779 12134 Z= 0.291 Chirality : 0.041 0.146 1389 Planarity : 0.004 0.042 1527 Dihedral : 5.576 33.757 1236 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.71 % Allowed : 14.05 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.63 (0.26), residues: 1104 helix: 2.17 (0.26), residues: 389 sheet: -0.58 (0.31), residues: 274 loop : -0.43 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS A 213 PHE 0.014 0.002 PHE R 345 TYR 0.013 0.001 TYR B 105 ARG 0.005 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.03772 ( 472) hydrogen bonds : angle 5.07757 ( 1326) SS BOND : bond 0.00210 ( 4) SS BOND : angle 1.11996 ( 8) covalent geometry : bond 0.00305 ( 8946) covalent geometry : angle 0.53959 (12126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 1.793 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: A 52 GLN cc_start: 0.6126 (OUTLIER) cc_final: 0.5761 (mt0) REVERT: A 313 ARG cc_start: 0.6205 (OUTLIER) cc_final: 0.5993 (mtt90) REVERT: A 318 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7698 (tt0) REVERT: A 345 LYS cc_start: 0.8415 (mttt) cc_final: 0.8181 (mttm) REVERT: B 134 ARG cc_start: 0.8423 (mtm110) cc_final: 0.8202 (ptp90) REVERT: B 219 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7499 (mmm-85) REVERT: E 116 THR cc_start: 0.8667 (OUTLIER) cc_final: 0.8464 (m) REVERT: E 160 ARG cc_start: 0.7802 (ttm170) cc_final: 0.7107 (ttm-80) REVERT: E 191 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.8461 (mtp180) REVERT: G 14 LYS cc_start: 0.6892 (tptp) cc_final: 0.6465 (tttt) REVERT: G 20 LYS cc_start: 0.7770 (ttpt) cc_final: 0.6680 (tttm) REVERT: G 32 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8070 (ttmt) REVERT: R 170 PHE cc_start: 0.6174 (OUTLIER) cc_final: 0.5133 (p90) REVERT: R 389 GLU cc_start: 0.7252 (mp0) cc_final: 0.6916 (mp0) outliers start: 26 outliers final: 11 residues processed: 168 average time/residue: 2.7905 time to fit residues: 498.3422 Evaluate side-chains 166 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 148 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 191 ARG Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 170 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 16 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 chunk 75 optimal weight: 8.9990 chunk 80 optimal weight: 7.9990 chunk 104 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS B 230 ASN R 352 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.169371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.130462 restraints weight = 25394.597| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.85 r_work: 0.3176 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.4303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 8950 Z= 0.209 Angle : 0.579 5.687 12134 Z= 0.313 Chirality : 0.042 0.148 1389 Planarity : 0.004 0.054 1527 Dihedral : 5.665 32.768 1236 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.71 % Allowed : 14.26 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.58 (0.26), residues: 1104 helix: 2.15 (0.26), residues: 392 sheet: -0.65 (0.31), residues: 273 loop : -0.47 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 82 HIS 0.007 0.001 HIS A 213 PHE 0.017 0.002 PHE R 345 TYR 0.015 0.002 TYR B 105 ARG 0.006 0.001 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03985 ( 472) hydrogen bonds : angle 5.15348 ( 1326) SS BOND : bond 0.00228 ( 4) SS BOND : angle 1.01575 ( 8) covalent geometry : bond 0.00462 ( 8946) covalent geometry : angle 0.57815 (12126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 150 time to evaluate : 1.491 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: A 52 GLN cc_start: 0.6227 (OUTLIER) cc_final: 0.5845 (mt0) REVERT: A 313 ARG cc_start: 0.6458 (OUTLIER) cc_final: 0.6241 (mtt90) REVERT: A 318 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7714 (tt0) REVERT: A 345 LYS cc_start: 0.8599 (mttt) cc_final: 0.8200 (mttm) REVERT: B 134 ARG cc_start: 0.8487 (mtm110) cc_final: 0.8260 (ptp90) REVERT: B 215 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7300 (mp0) REVERT: B 219 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7522 (mmm-85) REVERT: E 116 THR cc_start: 0.8701 (OUTLIER) cc_final: 0.8492 (m) REVERT: E 160 ARG cc_start: 0.7794 (ttm170) cc_final: 0.7004 (ttm-80) REVERT: E 191 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.7611 (mtp180) REVERT: G 14 LYS cc_start: 0.6933 (tptp) cc_final: 0.6524 (tttt) REVERT: G 32 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.8042 (ttmt) REVERT: R 89 LEU cc_start: 0.6901 (OUTLIER) cc_final: 0.6475 (mt) REVERT: R 113 MET cc_start: 0.7097 (mmp) cc_final: 0.6882 (mmp) REVERT: R 170 PHE cc_start: 0.6223 (OUTLIER) cc_final: 0.5198 (p90) REVERT: R 389 GLU cc_start: 0.7292 (mp0) cc_final: 0.6941 (mp0) outliers start: 26 outliers final: 12 residues processed: 164 average time/residue: 2.9373 time to fit residues: 511.2634 Evaluate side-chains 168 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 191 ARG Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 170 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 50 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 8 optimal weight: 0.3980 chunk 44 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN R 352 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.170693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.132950 restraints weight = 25255.978| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.76 r_work: 0.3210 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.4392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8950 Z= 0.137 Angle : 0.531 5.305 12134 Z= 0.286 Chirality : 0.041 0.148 1389 Planarity : 0.004 0.050 1527 Dihedral : 5.366 31.633 1236 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.39 % Allowed : 15.30 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.76 (0.26), residues: 1104 helix: 2.34 (0.26), residues: 393 sheet: -0.61 (0.31), residues: 272 loop : -0.38 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS A 213 PHE 0.013 0.002 PHE R 345 TYR 0.013 0.001 TYR R 88 ARG 0.007 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.03636 ( 472) hydrogen bonds : angle 4.95164 ( 1326) SS BOND : bond 0.00228 ( 4) SS BOND : angle 0.78704 ( 8) covalent geometry : bond 0.00296 ( 8946) covalent geometry : angle 0.53073 (12126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 152 time to evaluate : 1.465 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: A 52 GLN cc_start: 0.6117 (OUTLIER) cc_final: 0.5793 (mt0) REVERT: A 313 ARG cc_start: 0.6334 (OUTLIER) cc_final: 0.6091 (mtt90) REVERT: A 318 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7673 (tt0) REVERT: A 345 LYS cc_start: 0.8396 (mttt) cc_final: 0.8139 (mttm) REVERT: B 134 ARG cc_start: 0.8436 (mtm110) cc_final: 0.8223 (ptp90) REVERT: B 219 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.7510 (mmm-85) REVERT: B 234 PHE cc_start: 0.9081 (OUTLIER) cc_final: 0.8491 (m-80) REVERT: B 276 VAL cc_start: 0.8977 (OUTLIER) cc_final: 0.8730 (p) REVERT: E 13 GLN cc_start: 0.7828 (mm-40) cc_final: 0.7513 (tp40) REVERT: E 160 ARG cc_start: 0.7788 (ttm170) cc_final: 0.7085 (ttm-80) REVERT: E 191 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.8422 (mtp180) REVERT: G 14 LYS cc_start: 0.6886 (tptp) cc_final: 0.6471 (tttt) REVERT: G 32 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8069 (ttmt) REVERT: R 89 LEU cc_start: 0.6869 (OUTLIER) cc_final: 0.6472 (mt) REVERT: R 170 PHE cc_start: 0.6269 (OUTLIER) cc_final: 0.5341 (p90) REVERT: R 389 GLU cc_start: 0.7301 (mp0) cc_final: 0.6959 (mp0) outliers start: 23 outliers final: 9 residues processed: 167 average time/residue: 2.8356 time to fit residues: 503.3296 Evaluate side-chains 169 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 151 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 191 ARG Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 170 PHE Chi-restraints excluded: chain R residue 352 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 65 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 352 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.169220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.131183 restraints weight = 25211.493| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.76 r_work: 0.3169 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.4411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8950 Z= 0.198 Angle : 0.570 6.548 12134 Z= 0.308 Chirality : 0.042 0.147 1389 Planarity : 0.004 0.049 1527 Dihedral : 5.459 31.237 1236 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.39 % Allowed : 15.71 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.72 (0.26), residues: 1104 helix: 2.27 (0.26), residues: 393 sheet: -0.61 (0.31), residues: 273 loop : -0.38 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.006 0.001 HIS R 349 PHE 0.017 0.002 PHE R 345 TYR 0.014 0.002 TYR R 88 ARG 0.005 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.03829 ( 472) hydrogen bonds : angle 5.02858 ( 1326) SS BOND : bond 0.00153 ( 4) SS BOND : angle 1.39478 ( 8) covalent geometry : bond 0.00438 ( 8946) covalent geometry : angle 0.56893 (12126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 1.516 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: A 52 GLN cc_start: 0.6115 (OUTLIER) cc_final: 0.5792 (mt0) REVERT: A 313 ARG cc_start: 0.6470 (OUTLIER) cc_final: 0.6205 (mtt90) REVERT: A 318 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7681 (tt0) REVERT: A 345 LYS cc_start: 0.8578 (mttt) cc_final: 0.8151 (mttm) REVERT: B 134 ARG cc_start: 0.8465 (mtm110) cc_final: 0.8245 (ptp90) REVERT: B 219 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7514 (mmm-85) REVERT: B 234 PHE cc_start: 0.9119 (OUTLIER) cc_final: 0.8611 (m-80) REVERT: B 276 VAL cc_start: 0.9018 (OUTLIER) cc_final: 0.8708 (t) REVERT: E 13 GLN cc_start: 0.7839 (mm-40) cc_final: 0.7519 (tp-100) REVERT: E 160 ARG cc_start: 0.7791 (ttm170) cc_final: 0.7000 (ttm-80) REVERT: E 191 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.8305 (mtp180) REVERT: G 14 LYS cc_start: 0.6891 (tptp) cc_final: 0.6476 (tttt) REVERT: G 32 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.8063 (ttmt) REVERT: R 89 LEU cc_start: 0.6885 (OUTLIER) cc_final: 0.6506 (mt) REVERT: R 170 PHE cc_start: 0.6203 (OUTLIER) cc_final: 0.5187 (p90) REVERT: R 389 GLU cc_start: 0.7317 (mp0) cc_final: 0.6977 (mp0) outliers start: 23 outliers final: 10 residues processed: 161 average time/residue: 2.8919 time to fit residues: 494.1792 Evaluate side-chains 166 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 147 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 191 ARG Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 170 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 99 optimal weight: 0.9990 chunk 105 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 109 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 HIS B 230 ASN E 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.170977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.133430 restraints weight = 25475.452| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.77 r_work: 0.3229 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.4526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8950 Z= 0.126 Angle : 0.526 6.299 12134 Z= 0.281 Chirality : 0.041 0.147 1389 Planarity : 0.004 0.053 1527 Dihedral : 5.202 32.063 1236 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.08 % Allowed : 15.92 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.86 (0.26), residues: 1104 helix: 2.43 (0.26), residues: 394 sheet: -0.57 (0.31), residues: 272 loop : -0.31 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS R 349 PHE 0.013 0.001 PHE R 45 TYR 0.013 0.001 TYR R 88 ARG 0.007 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.03511 ( 472) hydrogen bonds : angle 4.84027 ( 1326) SS BOND : bond 0.00197 ( 4) SS BOND : angle 1.06649 ( 8) covalent geometry : bond 0.00277 ( 8946) covalent geometry : angle 0.52529 (12126) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 1.700 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: A 52 GLN cc_start: 0.6076 (OUTLIER) cc_final: 0.5809 (mt0) REVERT: A 313 ARG cc_start: 0.6417 (OUTLIER) cc_final: 0.6109 (mtt90) REVERT: A 318 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7707 (tt0) REVERT: A 341 ASP cc_start: 0.8714 (t0) cc_final: 0.8497 (t70) REVERT: A 345 LYS cc_start: 0.8433 (mttt) cc_final: 0.8121 (mttm) REVERT: B 134 ARG cc_start: 0.8437 (mtm110) cc_final: 0.8226 (ptp90) REVERT: B 219 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7503 (mmm-85) REVERT: B 276 VAL cc_start: 0.8967 (OUTLIER) cc_final: 0.8734 (p) REVERT: E 13 GLN cc_start: 0.7838 (mm-40) cc_final: 0.7539 (tp-100) REVERT: E 191 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.8349 (mtp180) REVERT: G 14 LYS cc_start: 0.6906 (tptp) cc_final: 0.6492 (tttt) REVERT: G 32 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8066 (ttmt) REVERT: R 89 LEU cc_start: 0.6880 (OUTLIER) cc_final: 0.6408 (mt) REVERT: R 170 PHE cc_start: 0.6148 (OUTLIER) cc_final: 0.5238 (p90) REVERT: R 389 GLU cc_start: 0.7337 (mp0) cc_final: 0.7003 (mp0) outliers start: 20 outliers final: 9 residues processed: 161 average time/residue: 2.8761 time to fit residues: 492.9809 Evaluate side-chains 165 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 1.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 191 ARG Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 170 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 31 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN R 61 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.169820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.132013 restraints weight = 25296.608| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.79 r_work: 0.3195 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.4561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8950 Z= 0.167 Angle : 0.554 7.180 12134 Z= 0.297 Chirality : 0.041 0.146 1389 Planarity : 0.004 0.048 1527 Dihedral : 5.283 30.206 1236 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.08 % Allowed : 16.44 % Favored : 81.48 % 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: 0.85 (0.26), residues: 1104 helix: 2.41 (0.26), residues: 394 sheet: -0.56 (0.31), residues: 272 loop : -0.32 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS A 213 PHE 0.015 0.002 PHE R 345 TYR 0.012 0.001 TYR R 88 ARG 0.006 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.03629 ( 472) hydrogen bonds : angle 4.90160 ( 1326) SS BOND : bond 0.00178 ( 4) SS BOND : angle 1.17383 ( 8) covalent geometry : bond 0.00371 ( 8946) covalent geometry : angle 0.55347 (12126) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 1.469 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: A 52 GLN cc_start: 0.6189 (OUTLIER) cc_final: 0.5943 (mt0) REVERT: A 313 ARG cc_start: 0.6487 (OUTLIER) cc_final: 0.6175 (mtt90) REVERT: A 318 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7624 (tt0) REVERT: A 341 ASP cc_start: 0.8741 (t0) cc_final: 0.8536 (t70) REVERT: A 345 LYS cc_start: 0.8475 (mttt) cc_final: 0.8199 (mttm) REVERT: B 234 PHE cc_start: 0.9085 (OUTLIER) cc_final: 0.8542 (m-80) REVERT: B 276 VAL cc_start: 0.8975 (OUTLIER) cc_final: 0.8664 (t) REVERT: E 13 GLN cc_start: 0.7850 (mm-40) cc_final: 0.7554 (tp-100) REVERT: E 76 LYS cc_start: 0.8183 (mtpt) cc_final: 0.7784 (mtpt) REVERT: E 191 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.8394 (mtp180) REVERT: G 14 LYS cc_start: 0.6892 (tptp) cc_final: 0.6477 (tttt) REVERT: G 32 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8054 (ttmt) REVERT: R 89 LEU cc_start: 0.6772 (OUTLIER) cc_final: 0.6493 (mt) REVERT: R 170 PHE cc_start: 0.5969 (OUTLIER) cc_final: 0.5160 (p90) REVERT: R 389 GLU cc_start: 0.7359 (mp0) cc_final: 0.7015 (mp0) outliers start: 20 outliers final: 10 residues processed: 156 average time/residue: 2.9145 time to fit residues: 482.4016 Evaluate side-chains 163 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 145 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 191 ARG Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 170 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 62 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 6 optimal weight: 0.0770 chunk 5 optimal weight: 4.9990 chunk 61 optimal weight: 0.3980 chunk 11 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.8742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.171361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.134006 restraints weight = 25263.171| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.76 r_work: 0.3230 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8950 Z= 0.131 Angle : 0.532 6.644 12134 Z= 0.283 Chirality : 0.041 0.146 1389 Planarity : 0.004 0.051 1527 Dihedral : 5.129 31.130 1236 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.08 % Allowed : 16.34 % Favored : 81.58 % 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: 0.93 (0.26), residues: 1104 helix: 2.47 (0.26), residues: 395 sheet: -0.56 (0.31), residues: 272 loop : -0.25 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS R 349 PHE 0.015 0.002 PHE R 386 TYR 0.011 0.001 TYR A 296 ARG 0.007 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.03455 ( 472) hydrogen bonds : angle 4.80438 ( 1326) SS BOND : bond 0.00193 ( 4) SS BOND : angle 0.99153 ( 8) covalent geometry : bond 0.00289 ( 8946) covalent geometry : angle 0.53138 (12126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14936.51 seconds wall clock time: 255 minutes 50.91 seconds (15350.91 seconds total)