Starting phenix.real_space_refine on Sun Jun 15 07:16:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8irt_35685/06_2025/8irt_35685_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8irt_35685/06_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_35685/06_2025/8irt_35685.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8irt_35685/06_2025/8irt_35685.map" model { file = "/net/cci-nas-00/data/ceres_data/8irt_35685/06_2025/8irt_35685_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8irt_35685/06_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-5710/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: 9.49, per 1000 atoms: 0.54 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: 5.35 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: 2.44 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: 10.18 Time building geometry restraints manager: 5.99 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: 0.010 Normalize map: mean=0, sd=1: 24.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.340 Extract box with map and model: 0.750 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 48.300 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.060 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: 0.020 Load rotamer database and sin/cos tables:78.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 153.130 ------------------------------------------------------------------------------- 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 : 1.158 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: 3.4021 time to fit residues: 754.3756 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 : 1.405 ------------------------------------------------------------------------------- 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 = 66)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.127116 restraints weight = 24961.621| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.59 r_work: 0.3231 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 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 : 1.295 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: 0.8520 (m-40) cc_final: 0.8297 (m110) REVERT: A 26 ASP cc_start: 0.7917 (m-30) cc_final: 0.7603 (m-30) REVERT: A 32 ARG cc_start: 0.7632 (mmt-90) cc_final: 0.7400 (mmt-90) REVERT: A 244 HIS cc_start: 0.7790 (m90) cc_final: 0.7445 (m-70) REVERT: A 345 LYS cc_start: 0.8531 (mttt) cc_final: 0.8178 (mttm) REVERT: B 175 GLN cc_start: 0.8330 (tp40) cc_final: 0.8106 (mp10) REVERT: B 197 ARG cc_start: 0.8207 (mmp-170) cc_final: 0.7778 (mmm-85) REVERT: B 214 ARG cc_start: 0.7341 (mmp80) cc_final: 0.6892 (mmm160) REVERT: B 312 ASP cc_start: 0.7709 (m-30) cc_final: 0.7507 (m-30) REVERT: E 160 ARG cc_start: 0.7672 (ttm170) cc_final: 0.6922 (ttm-80) REVERT: E 244 LYS cc_start: 0.7671 (ptmm) cc_final: 0.7438 (ptmt) REVERT: G 20 LYS cc_start: 0.7377 (OUTLIER) cc_final: 0.6455 (tttm) REVERT: R 113 MET cc_start: 0.7506 (mmt) cc_final: 0.7230 (mmt) REVERT: R 216 LYS cc_start: 0.6792 (ttpp) cc_final: 0.6537 (mptt) REVERT: R 389 GLU cc_start: 0.7199 (mp0) cc_final: 0.6951 (mp0) outliers start: 17 outliers final: 7 residues processed: 190 average time/residue: 2.7889 time to fit residues: 562.7324 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 : 1.315 ------------------------------------------------------------------------------- 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: 7.9990 chunk 105 optimal weight: 10.0000 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: 10.0000 chunk 54 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- 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 = 0.3873 r_free = 0.3873 target = 0.166984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.119903 restraints weight = 25110.309| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.69 r_work: 0.3080 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.082 8950 Z= 0.367 Angle : 0.716 8.450 12134 Z= 0.392 Chirality : 0.048 0.157 1389 Planarity : 0.006 0.093 1527 Dihedral : 7.235 69.042 1236 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.19 % Allowed : 11.45 % Favored : 86.37 % 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: 1.39 (0.25), residues: 387 sheet: -0.51 (0.31), residues: 268 loop : -0.54 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 99 HIS 0.013 0.002 HIS A 213 PHE 0.025 0.003 PHE R 345 TYR 0.050 0.003 TYR B 105 ARG 0.004 0.001 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.05030 ( 472) hydrogen bonds : angle 5.66973 ( 1326) SS BOND : bond 0.00338 ( 4) SS BOND : angle 0.98554 ( 8) covalent geometry : bond 0.00824 ( 8946) covalent geometry : angle 0.71572 (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 186 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 165 time to evaluate : 1.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.8102 (m-30) cc_final: 0.7838 (m-30) REVERT: A 318 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7735 (tt0) REVERT: B 175 GLN cc_start: 0.8531 (tp40) cc_final: 0.8292 (mp10) REVERT: B 197 ARG cc_start: 0.8214 (mmp-170) cc_final: 0.7805 (mmm-85) REVERT: B 290 ASP cc_start: 0.7833 (OUTLIER) cc_final: 0.7601 (p0) REVERT: E 160 ARG cc_start: 0.7824 (ttm170) cc_final: 0.7052 (ttm-80) REVERT: G 14 LYS cc_start: 0.6880 (tptp) cc_final: 0.6439 (tttt) REVERT: G 20 LYS cc_start: 0.7488 (OUTLIER) cc_final: 0.6481 (tttm) REVERT: G 32 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8055 (ttmt) REVERT: R 170 PHE cc_start: 0.6074 (OUTLIER) cc_final: 0.5112 (p90) REVERT: R 216 LYS cc_start: 0.6829 (ttpp) cc_final: 0.6556 (mptt) REVERT: R 387 ASN cc_start: 0.6547 (t0) cc_final: 0.6180 (t0) REVERT: R 389 GLU cc_start: 0.7171 (mp0) cc_final: 0.6960 (mp0) outliers start: 21 outliers final: 10 residues processed: 177 average time/residue: 2.7068 time to fit residues: 510.6190 Evaluate side-chains 162 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 148 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 81 optimal weight: 1.9990 chunk 89 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 74 optimal weight: 0.3980 chunk 108 optimal weight: 0.5980 chunk 94 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3921 r_free = 0.3921 target = 0.171391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.133433 restraints weight = 25203.782| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.78 r_work: 0.3215 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8950 Z= 0.149 Angle : 0.564 5.707 12134 Z= 0.304 Chirality : 0.042 0.150 1389 Planarity : 0.004 0.057 1527 Dihedral : 5.891 34.231 1236 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.50 % Allowed : 12.80 % Favored : 84.70 % 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: 0.47 (0.25), residues: 1104 helix: 1.88 (0.26), residues: 388 sheet: -0.52 (0.31), residues: 273 loop : -0.46 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS A 213 PHE 0.015 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 0.03981 ( 472) hydrogen bonds : angle 5.26759 ( 1326) SS BOND : bond 0.00281 ( 4) SS BOND : angle 1.79640 ( 8) covalent geometry : bond 0.00311 ( 8946) covalent geometry : angle 0.56237 (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 182 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 158 time to evaluate : 1.473 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: 0.6282 (OUTLIER) cc_final: 0.6059 (mtt90) REVERT: A 318 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7643 (tt0) REVERT: A 345 LYS cc_start: 0.8515 (mttt) cc_final: 0.8154 (mttm) REVERT: B 134 ARG cc_start: 0.8421 (mtm110) cc_final: 0.8176 (ptp90) REVERT: B 219 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.7489 (mmm-85) REVERT: B 336 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8660 (mt) REVERT: E 116 THR cc_start: 0.8698 (OUTLIER) cc_final: 0.8464 (m) REVERT: E 160 ARG cc_start: 0.7736 (ttm170) cc_final: 0.6970 (ttm-80) REVERT: G 14 LYS cc_start: 0.6902 (tptp) cc_final: 0.6476 (tttt) REVERT: G 20 LYS cc_start: 0.7715 (OUTLIER) cc_final: 0.6686 (tttm) REVERT: G 32 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8073 (ttmt) REVERT: R 170 PHE cc_start: 0.6164 (OUTLIER) cc_final: 0.5084 (p90) REVERT: R 216 LYS cc_start: 0.6793 (ttpp) cc_final: 0.6525 (mmtt) REVERT: R 389 GLU cc_start: 0.7200 (mp0) cc_final: 0.6852 (mp0) outliers start: 24 outliers final: 9 residues processed: 170 average time/residue: 2.7302 time to fit residues: 493.9525 Evaluate side-chains 162 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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: 0.7980 chunk 13 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 48 optimal weight: 0.0270 chunk 80 optimal weight: 7.9990 overall best weight: 0.9240 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.171741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.133599 restraints weight = 25410.943| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.79 r_work: 0.3215 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8950 Z= 0.142 Angle : 0.540 6.784 12134 Z= 0.292 Chirality : 0.041 0.146 1389 Planarity : 0.004 0.041 1527 Dihedral : 5.554 33.591 1236 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.60 % Allowed : 13.74 % Favored : 83.66 % 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: 0.65 (0.26), residues: 1104 helix: 2.19 (0.26), residues: 389 sheet: -0.55 (0.30), residues: 282 loop : -0.43 (0.30), residues: 433 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 0.014 0.001 TYR B 105 ARG 0.004 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.03775 ( 472) hydrogen bonds : angle 5.07003 ( 1326) SS BOND : bond 0.00207 ( 4) SS BOND : angle 1.16448 ( 8) covalent geometry : bond 0.00306 ( 8946) covalent geometry : angle 0.53981 (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 177 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 152 time to evaluate : 1.415 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: 0.6186 (OUTLIER) cc_final: 0.5844 (mt0) REVERT: A 313 ARG cc_start: 0.6205 (OUTLIER) cc_final: 0.5996 (mtt90) REVERT: A 318 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7677 (tt0) REVERT: A 341 ASP cc_start: 0.8710 (t0) cc_final: 0.8473 (t70) REVERT: A 345 LYS cc_start: 0.8419 (mttt) cc_final: 0.8215 (mttm) REVERT: B 134 ARG cc_start: 0.8418 (mtm110) cc_final: 0.8216 (ptp90) REVERT: B 219 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7506 (mmm-85) REVERT: E 160 ARG cc_start: 0.7778 (ttm170) cc_final: 0.7107 (ttm-80) REVERT: G 14 LYS cc_start: 0.6899 (tptp) cc_final: 0.6473 (tttt) REVERT: G 20 LYS cc_start: 0.7776 (ttpt) cc_final: 0.6685 (tttm) REVERT: G 32 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.8073 (ttmt) REVERT: R 170 PHE cc_start: 0.6187 (OUTLIER) cc_final: 0.5188 (p90) REVERT: R 389 GLU cc_start: 0.7239 (mp0) cc_final: 0.6915 (mp0) outliers start: 25 outliers final: 12 residues processed: 167 average time/residue: 2.8858 time to fit residues: 511.3452 Evaluate side-chains 164 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 147 time to evaluate : 1.343 ------------------------------------------------------------------------------- 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 197 ARG 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 166 LEU Chi-restraints excluded: chain E residue 174 LEU 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: 10.0000 chunk 63 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 75 optimal weight: 7.9990 chunk 80 optimal weight: 7.9990 chunk 104 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- 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 = 0.3902 r_free = 0.3902 target = 0.169429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.130306 restraints weight = 25380.072| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.91 r_work: 0.3182 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.4293 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= 0.204 Angle : 0.574 5.664 12134 Z= 0.311 Chirality : 0.042 0.148 1389 Planarity : 0.004 0.051 1527 Dihedral : 5.634 32.537 1236 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.71 % Allowed : 14.15 % Favored : 83.14 % 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: 0.64 (0.26), residues: 1104 helix: 2.21 (0.26), residues: 391 sheet: -0.63 (0.31), residues: 273 loop : -0.43 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.007 0.001 HIS A 213 PHE 0.017 0.002 PHE R 345 TYR 0.014 0.002 TYR B 105 ARG 0.006 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03962 ( 472) hydrogen bonds : angle 5.13300 ( 1326) SS BOND : bond 0.00228 ( 4) SS BOND : angle 1.02560 ( 8) covalent geometry : bond 0.00450 ( 8946) covalent geometry : angle 0.57361 (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 177 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 1.609 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 313 ARG cc_start: 0.6442 (OUTLIER) cc_final: 0.6222 (mtt90) REVERT: A 318 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7698 (tt0) REVERT: A 345 LYS cc_start: 0.8552 (mttt) cc_final: 0.8251 (mttm) REVERT: B 134 ARG cc_start: 0.8508 (mtm110) cc_final: 0.8281 (ptp90) REVERT: B 215 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7296 (mp0) REVERT: B 219 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7523 (mmm-85) REVERT: E 160 ARG cc_start: 0.7764 (ttm170) cc_final: 0.6965 (ttm-80) REVERT: G 14 LYS cc_start: 0.6922 (tptp) cc_final: 0.6512 (tttt) REVERT: G 32 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.8055 (ttmt) REVERT: R 89 LEU cc_start: 0.6889 (OUTLIER) cc_final: 0.6463 (mt) REVERT: R 170 PHE cc_start: 0.6154 (OUTLIER) cc_final: 0.5154 (p90) REVERT: R 389 GLU cc_start: 0.7293 (mp0) cc_final: 0.6943 (mp0) outliers start: 26 outliers final: 13 residues processed: 165 average time/residue: 2.9152 time to fit residues: 511.7880 Evaluate side-chains 164 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 1.327 ------------------------------------------------------------------------------- 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 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 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: 0.7980 chunk 63 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.3918 r_free = 0.3918 target = 0.170841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.132760 restraints weight = 25206.316| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.77 r_work: 0.3188 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.4403 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= 0.159 Angle : 0.543 5.774 12134 Z= 0.293 Chirality : 0.041 0.148 1389 Planarity : 0.004 0.047 1527 Dihedral : 5.447 31.781 1236 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.39 % Allowed : 15.50 % Favored : 82.10 % 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: 0.73 (0.26), residues: 1104 helix: 2.28 (0.26), residues: 394 sheet: -0.59 (0.31), residues: 272 loop : -0.39 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS A 213 PHE 0.014 0.002 PHE R 345 TYR 0.012 0.001 TYR R 88 ARG 0.004 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03722 ( 472) hydrogen bonds : angle 5.03297 ( 1326) SS BOND : bond 0.00235 ( 4) SS BOND : angle 0.84288 ( 8) covalent geometry : bond 0.00347 ( 8946) covalent geometry : angle 0.54299 (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 171 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 1.430 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: 0.5803 (mt0) REVERT: A 313 ARG cc_start: 0.6470 (OUTLIER) cc_final: 0.6206 (mtt90) REVERT: A 318 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7687 (tt0) REVERT: A 345 LYS cc_start: 0.8573 (mttt) cc_final: 0.8145 (mttm) REVERT: B 134 ARG cc_start: 0.8475 (mtm110) cc_final: 0.8235 (ptp90) REVERT: B 215 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7311 (mp0) REVERT: B 219 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7520 (mmm-85) REVERT: B 234 PHE cc_start: 0.9107 (OUTLIER) cc_final: 0.8512 (m-80) REVERT: B 276 VAL cc_start: 0.8981 (OUTLIER) cc_final: 0.8763 (p) REVERT: E 13 GLN cc_start: 0.7825 (mm-40) cc_final: 0.7518 (tp40) REVERT: E 160 ARG cc_start: 0.7745 (ttm170) cc_final: 0.6986 (ttm-80) REVERT: G 14 LYS cc_start: 0.6891 (tptp) cc_final: 0.6491 (tttt) REVERT: G 32 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.8061 (ttmt) REVERT: R 89 LEU cc_start: 0.6859 (OUTLIER) cc_final: 0.6465 (mt) REVERT: R 170 PHE cc_start: 0.6275 (OUTLIER) cc_final: 0.5347 (p90) REVERT: R 389 GLU cc_start: 0.7275 (mp0) cc_final: 0.6975 (mp0) outliers start: 23 outliers final: 12 residues processed: 162 average time/residue: 2.8537 time to fit residues: 491.2240 Evaluate side-chains 175 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 1.669 ------------------------------------------------------------------------------- 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 215 GLU 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 B residue 336 LEU Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 174 LEU 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: 0.9990 chunk 20 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 84 optimal weight: 10.0000 chunk 40 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 8 optimal weight: 0.0040 chunk 29 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.171585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.133647 restraints weight = 25230.666| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 1.82 r_work: 0.3232 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.4493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8950 Z= 0.124 Angle : 0.530 5.954 12134 Z= 0.285 Chirality : 0.041 0.146 1389 Planarity : 0.004 0.048 1527 Dihedral : 5.258 32.005 1236 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.19 % Allowed : 15.82 % 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: 0.84 (0.26), residues: 1104 helix: 2.39 (0.26), residues: 394 sheet: -0.58 (0.31), residues: 272 loop : -0.31 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS R 349 PHE 0.013 0.001 PHE R 45 TYR 0.013 0.001 TYR R 88 ARG 0.010 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.03560 ( 472) hydrogen bonds : angle 4.91555 ( 1326) SS BOND : bond 0.00123 ( 4) SS BOND : angle 1.22309 ( 8) covalent geometry : bond 0.00268 ( 8946) covalent geometry : angle 0.52891 (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 177 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 1.397 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 26 ASP cc_start: 0.8048 (m-30) cc_final: 0.7759 (m-30) REVERT: A 52 GLN cc_start: 0.6093 (OUTLIER) cc_final: 0.5804 (mt0) REVERT: A 255 ASN cc_start: 0.8308 (m-40) cc_final: 0.8055 (m-40) REVERT: A 313 ARG cc_start: 0.6418 (OUTLIER) cc_final: 0.6121 (mtt90) REVERT: A 318 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7680 (tt0) REVERT: A 345 LYS cc_start: 0.8442 (mttt) cc_final: 0.8118 (mttm) REVERT: B 134 ARG cc_start: 0.8414 (mtm110) cc_final: 0.8202 (ptp90) REVERT: B 219 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7498 (mmm-85) REVERT: B 234 PHE cc_start: 0.9072 (OUTLIER) cc_final: 0.8558 (m-80) REVERT: B 276 VAL cc_start: 0.8963 (OUTLIER) cc_final: 0.8729 (p) REVERT: E 13 GLN cc_start: 0.7846 (mm-40) cc_final: 0.7510 (tp-100) REVERT: E 160 ARG cc_start: 0.7753 (ttm170) cc_final: 0.7060 (ttm-80) REVERT: E 191 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.6509 (mtp180) REVERT: G 14 LYS cc_start: 0.6893 (tptp) cc_final: 0.6482 (tttt) REVERT: G 32 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.8062 (ttmt) REVERT: R 89 LEU cc_start: 0.6876 (OUTLIER) cc_final: 0.6379 (mt) REVERT: R 170 PHE cc_start: 0.6189 (OUTLIER) cc_final: 0.5265 (p90) REVERT: R 389 GLU cc_start: 0.7357 (mp0) cc_final: 0.7020 (mp0) outliers start: 21 outliers final: 9 residues processed: 169 average time/residue: 2.8632 time to fit residues: 513.3079 Evaluate side-chains 164 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 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 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: 2.9990 chunk 105 optimal weight: 0.0970 chunk 4 optimal weight: 5.9990 chunk 68 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 22 optimal weight: 8.9990 chunk 19 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN E 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.172562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.134914 restraints weight = 25398.653| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.77 r_work: 0.3224 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 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 : 0.003 0.035 8950 Z= 0.132 Angle : 0.528 6.827 12134 Z= 0.283 Chirality : 0.041 0.146 1389 Planarity : 0.004 0.047 1527 Dihedral : 5.135 31.332 1236 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.87 % Allowed : 16.23 % Favored : 81.89 % 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: 0.91 (0.26), residues: 1104 helix: 2.46 (0.26), residues: 394 sheet: -0.58 (0.31), residues: 272 loop : -0.25 (0.31), residues: 438 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 0.013 0.001 PHE R 345 TYR 0.012 0.001 TYR R 88 ARG 0.006 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03489 ( 472) hydrogen bonds : angle 4.83209 ( 1326) SS BOND : bond 0.00154 ( 4) SS BOND : angle 1.10559 ( 8) covalent geometry : bond 0.00289 ( 8946) covalent geometry : angle 0.52719 (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 169 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 151 time to evaluate : 1.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.8042 (m-30) cc_final: 0.7750 (m-30) REVERT: A 52 GLN cc_start: 0.6164 (OUTLIER) cc_final: 0.5959 (mt0) REVERT: A 313 ARG cc_start: 0.6389 (OUTLIER) cc_final: 0.6079 (mtt90) REVERT: A 318 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7703 (tt0) REVERT: A 345 LYS cc_start: 0.8532 (mttt) cc_final: 0.8127 (mttm) REVERT: B 134 ARG cc_start: 0.8431 (mtm110) cc_final: 0.8220 (ptp90) REVERT: B 276 VAL cc_start: 0.8956 (OUTLIER) cc_final: 0.8717 (p) REVERT: E 13 GLN cc_start: 0.7831 (mm-40) cc_final: 0.7535 (tp-100) REVERT: E 191 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.6477 (mtp180) REVERT: G 14 LYS cc_start: 0.6910 (tptp) cc_final: 0.6494 (tttt) REVERT: G 20 LYS cc_start: 0.7777 (ttpt) cc_final: 0.6685 (tttm) REVERT: G 32 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.8067 (ttmt) REVERT: R 89 LEU cc_start: 0.6869 (OUTLIER) cc_final: 0.6398 (mt) REVERT: R 170 PHE cc_start: 0.6154 (OUTLIER) cc_final: 0.5284 (p90) REVERT: R 389 GLU cc_start: 0.7347 (mp0) cc_final: 0.7022 (mp0) outliers start: 18 outliers final: 9 residues processed: 161 average time/residue: 3.1480 time to fit residues: 540.1641 Evaluate side-chains 161 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 1.461 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 31 optimal weight: 0.5980 chunk 70 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 97 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 83 optimal weight: 9.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.171374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.133234 restraints weight = 25305.934| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.81 r_work: 0.3225 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.4632 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= 0.130 Angle : 0.533 6.393 12134 Z= 0.285 Chirality : 0.041 0.145 1389 Planarity : 0.004 0.047 1527 Dihedral : 5.059 30.901 1236 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.87 % Allowed : 16.65 % 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: 0.94 (0.26), residues: 1104 helix: 2.47 (0.26), residues: 395 sheet: -0.57 (0.31), residues: 272 loop : -0.22 (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 0.013 0.001 PHE R 45 TYR 0.012 0.001 TYR A 296 ARG 0.006 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03434 ( 472) hydrogen bonds : angle 4.78726 ( 1326) SS BOND : bond 0.00176 ( 4) SS BOND : angle 0.99726 ( 8) covalent geometry : bond 0.00287 ( 8946) covalent geometry : angle 0.53232 (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 164 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 1.552 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 313 ARG cc_start: 0.6342 (OUTLIER) cc_final: 0.6039 (mtt90) REVERT: A 318 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7697 (tt0) REVERT: A 345 LYS cc_start: 0.8436 (mttt) cc_final: 0.8136 (mttm) REVERT: B 234 PHE cc_start: 0.9061 (OUTLIER) cc_final: 0.8525 (m-80) REVERT: B 276 VAL cc_start: 0.8956 (OUTLIER) cc_final: 0.8727 (p) REVERT: B 333 ASP cc_start: 0.8745 (p0) cc_final: 0.8495 (p0) REVERT: E 13 GLN cc_start: 0.7828 (mm-40) cc_final: 0.7540 (tp-100) REVERT: E 191 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.6245 (mtp180) REVERT: G 14 LYS cc_start: 0.6899 (tptp) cc_final: 0.6485 (tttt) REVERT: G 20 LYS cc_start: 0.7716 (ttpt) cc_final: 0.6589 (tttm) REVERT: G 32 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8071 (ttmt) REVERT: R 89 LEU cc_start: 0.6746 (OUTLIER) cc_final: 0.6472 (mt) REVERT: R 170 PHE cc_start: 0.5985 (OUTLIER) cc_final: 0.5079 (p90) REVERT: R 389 GLU cc_start: 0.7351 (mp0) cc_final: 0.7042 (mp0) outliers start: 18 outliers final: 7 residues processed: 154 average time/residue: 2.9673 time to fit residues: 484.0293 Evaluate side-chains 153 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 139 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 E residue 166 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 62 optimal weight: 0.4980 chunk 44 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 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 220 GLN B 230 ASN R 65 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.172215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.134333 restraints weight = 25261.328| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.81 r_work: 0.3233 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.4706 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= 0.128 Angle : 0.529 6.825 12134 Z= 0.282 Chirality : 0.041 0.145 1389 Planarity : 0.003 0.048 1527 Dihedral : 4.993 30.369 1236 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.98 % Allowed : 16.55 % 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: 0.98 (0.26), residues: 1104 helix: 2.53 (0.26), residues: 395 sheet: -0.53 (0.30), residues: 280 loop : -0.22 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS A 213 PHE 0.013 0.001 PHE R 45 TYR 0.012 0.001 TYR A 296 ARG 0.007 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03382 ( 472) hydrogen bonds : angle 4.73911 ( 1326) SS BOND : bond 0.00177 ( 4) SS BOND : angle 0.96552 ( 8) covalent geometry : bond 0.00284 ( 8946) covalent geometry : angle 0.52877 (12126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16469.59 seconds wall clock time: 283 minutes 28.86 seconds (17008.86 seconds total)