Starting phenix.real_space_refine on Wed Aug 5 23:03:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mn6_48414/08_2026/9mn6_48414.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mn6_48414/08_2026/9mn6_48414.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mn6_48414/08_2026/9mn6_48414.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mn6_48414/08_2026/9mn6_48414.map" model { file = "/net/cci-nas-00/data/ceres_data/9mn6_48414/08_2026/9mn6_48414.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mn6_48414/08_2026/9mn6_48414.cif" } resolution = 2.71 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 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: 6 Type Number sf(0) Gaussians P 69 5.49 5 Mg 1 5.21 5 S 63 5.16 5 C 7338 2.51 5 N 2123 2.21 5 O 2261 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11855 Number of models: 1 Model: "" Number of chains: 6 Chain: "N" Number of atoms: 618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 618 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "R" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 133 Classifications: {'RNA': 6} Modifications used: {'rna3p_pur': 5} Link IDs: {'rna3p': 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 612 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "E" Number of atoms: 7953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 997, 7953 Classifications: {'peptide': 997} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 64, 'TRANS': 932} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2507 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 19, 'TRANS': 289} Chain breaks: 1 Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.62, per 1000 atoms: 0.22 Number of scatterers: 11855 At special positions: 0 Unit cell: (97.82, 129.94, 110.23, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 63 16.00 P 69 15.00 Mg 1 11.99 O 2261 8.00 N 2123 7.00 C 7338 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.96 Conformation dependent library (CDL) restraints added in 489.0 milliseconds 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2478 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 9 sheets defined 59.5% alpha, 6.0% beta 21 base pairs and 42 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'E' and resid 220 through 237 Processing helix chain 'E' and resid 238 through 252 removed outlier: 3.797A pdb=" N GLN E 252 " --> pdb=" O VAL E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 259 Processing helix chain 'E' and resid 260 through 275 removed outlier: 3.964A pdb=" N VAL E 267 " --> pdb=" O MET E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 291 removed outlier: 3.737A pdb=" N TYR E 282 " --> pdb=" O LYS E 278 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY E 291 " --> pdb=" O VAL E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 309 removed outlier: 3.549A pdb=" N TYR E 299 " --> pdb=" O ASP E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 327 removed outlier: 3.938A pdb=" N ILE E 316 " --> pdb=" O ASP E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 335 Processing helix chain 'E' and resid 340 through 355 removed outlier: 4.020A pdb=" N LYS E 353 " --> pdb=" O LYS E 349 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL E 354 " --> pdb=" O ALA E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 410 Processing helix chain 'E' and resid 424 through 462 Processing helix chain 'E' and resid 467 through 472 Processing helix chain 'E' and resid 475 through 489 Processing helix chain 'E' and resid 497 through 520 Processing helix chain 'E' and resid 521 through 538 removed outlier: 3.701A pdb=" N ALA E 525 " --> pdb=" O GLY E 521 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS E 532 " --> pdb=" O ASN E 528 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N CYS E 535 " --> pdb=" O ARG E 531 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N LEU E 536 " --> pdb=" O LYS E 532 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU E 537 " --> pdb=" O TYR E 533 " (cutoff:3.500A) Processing helix chain 'E' and resid 548 through 556 Processing helix chain 'E' and resid 568 through 587 Processing helix chain 'E' and resid 624 through 635 removed outlier: 3.604A pdb=" N ALA E 635 " --> pdb=" O LEU E 631 " (cutoff:3.500A) Processing helix chain 'E' and resid 679 through 687 Processing helix chain 'E' and resid 692 through 704 Processing helix chain 'E' and resid 710 through 723 Processing helix chain 'E' and resid 726 through 730 Processing helix chain 'E' and resid 734 through 738 Processing helix chain 'E' and resid 760 through 789 Processing helix chain 'E' and resid 818 through 824 Processing helix chain 'E' and resid 837 through 850 removed outlier: 3.634A pdb=" N GLY E 850 " --> pdb=" O VAL E 846 " (cutoff:3.500A) Processing helix chain 'E' and resid 856 through 867 Processing helix chain 'E' and resid 867 through 877 Processing helix chain 'E' and resid 884 through 888 Processing helix chain 'E' and resid 890 through 906 Processing helix chain 'E' and resid 925 through 936 Processing helix chain 'E' and resid 939 through 944 Processing helix chain 'E' and resid 954 through 973 removed outlier: 3.781A pdb=" N GLY E 958 " --> pdb=" O ASP E 954 " (cutoff:3.500A) Processing helix chain 'E' and resid 975 through 982 removed outlier: 3.520A pdb=" N GLN E 979 " --> pdb=" O MET E 975 " (cutoff:3.500A) Processing helix chain 'E' and resid 983 through 985 No H-bonds generated for 'chain 'E' and resid 983 through 985' Processing helix chain 'E' and resid 986 through 998 removed outlier: 3.903A pdb=" N VAL E 990 " --> pdb=" O THR E 986 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLN E 992 " --> pdb=" O LYS E 988 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N THR E 993 " --> pdb=" O VAL E 989 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL E 998 " --> pdb=" O VAL E 994 " (cutoff:3.500A) Processing helix chain 'E' and resid 1002 through 1016 removed outlier: 3.605A pdb=" N ARG E1013 " --> pdb=" O GLN E1009 " (cutoff:3.500A) Processing helix chain 'E' and resid 1021 through 1023 No H-bonds generated for 'chain 'E' and resid 1021 through 1023' Processing helix chain 'E' and resid 1024 through 1040 Processing helix chain 'E' and resid 1044 through 1064 removed outlier: 3.744A pdb=" N MET E1064 " --> pdb=" O LEU E1060 " (cutoff:3.500A) Processing helix chain 'E' and resid 1111 through 1141 Proline residue: E1120 - end of helix removed outlier: 3.705A pdb=" N ILE E1124 " --> pdb=" O PRO E1120 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG E1141 " --> pdb=" O LEU E1137 " (cutoff:3.500A) Processing helix chain 'E' and resid 1159 through 1176 Processing helix chain 'E' and resid 1178 through 1192 Processing helix chain 'E' and resid 1194 through 1196 No H-bonds generated for 'chain 'E' and resid 1194 through 1196' Processing helix chain 'E' and resid 1197 through 1209 removed outlier: 5.733A pdb=" N GLN E1203 " --> pdb=" O LEU E1199 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N LEU E1204 " --> pdb=" O GLU E1200 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN E1209 " --> pdb=" O LYS E1205 " (cutoff:3.500A) Processing helix chain 'E' and resid 1218 through 1225 Processing helix chain 'B' and resid 80 through 90 removed outlier: 3.916A pdb=" N GLY B 90 " --> pdb=" O GLN B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 115 Processing helix chain 'B' and resid 126 through 129 removed outlier: 3.863A pdb=" N PHE B 129 " --> pdb=" O ASP B 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 126 through 129' Processing helix chain 'B' and resid 130 through 140 removed outlier: 4.075A pdb=" N GLU B 134 " --> pdb=" O ILE B 130 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN B 139 " --> pdb=" O SER B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 154 removed outlier: 3.647A pdb=" N LEU B 154 " --> pdb=" O PHE B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 176 Processing helix chain 'B' and resid 199 through 213 Processing helix chain 'B' and resid 215 through 221 removed outlier: 3.727A pdb=" N LYS B 219 " --> pdb=" O SER B 216 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY B 221 " --> pdb=" O TYR B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 256 removed outlier: 3.761A pdb=" N VAL B 252 " --> pdb=" O HIS B 248 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU B 256 " --> pdb=" O VAL B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 308 removed outlier: 3.719A pdb=" N LEU B 307 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N PHE B 308 " --> pdb=" O GLN B 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 304 through 308' Processing helix chain 'B' and resid 316 through 328 removed outlier: 3.638A pdb=" N PHE B 320 " --> pdb=" O ASN B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 343 removed outlier: 3.768A pdb=" N SER B 341 " --> pdb=" O ASP B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 355 Processing helix chain 'B' and resid 361 through 365 Processing helix chain 'B' and resid 366 through 379 removed outlier: 3.589A pdb=" N LYS B 371 " --> pdb=" O PRO B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 395 removed outlier: 3.589A pdb=" N ASP B 395 " --> pdb=" O THR B 392 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 411 through 415 Processing sheet with id=AA2, first strand: chain 'E' and resid 495 through 496 removed outlier: 3.545A pdb=" N GLU E 495 " --> pdb=" O LEU E 621 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 588 through 589 Processing sheet with id=AA4, first strand: chain 'E' and resid 794 through 795 Processing sheet with id=AA5, first strand: chain 'E' and resid 798 through 800 Processing sheet with id=AA6, first strand: chain 'E' and resid 831 through 832 Processing sheet with id=AA7, first strand: chain 'E' and resid 1147 through 1149 Processing sheet with id=AA8, first strand: chain 'E' and resid 1069 through 1071 Processing sheet with id=AA9, first strand: chain 'B' and resid 147 through 148 removed outlier: 7.779A pdb=" N ILE B 147 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N ALA B 122 " --> pdb=" O ILE B 147 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N LEU B 99 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU B 123 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N GLU B 101 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N VAL B 191 " --> pdb=" O ASN B 226 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N PHE B 228 " --> pdb=" O VAL B 191 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N GLY B 193 " --> pdb=" O PHE B 228 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N LEU B 296 " --> pdb=" O MET B 265 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N MET B 265 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU B 298 " --> pdb=" O LEU B 263 " (cutoff:3.500A) 542 hydrogen bonds defined for protein. 1548 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 53 hydrogen bonds 106 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 42 stacking parallelities Total time for adding SS restraints: 2.33 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3145 1.34 - 1.45: 2471 1.45 - 1.57: 6426 1.57 - 1.69: 135 1.69 - 1.81: 96 Bond restraints: 12273 Sorted by residual: bond pdb=" C PRO B 164 " pdb=" N PRO B 165 " ideal model delta sigma weight residual 1.336 1.386 -0.050 1.20e-02 6.94e+03 1.73e+01 bond pdb=" C3' DA N 36 " pdb=" O3' DA N 36 " ideal model delta sigma weight residual 1.435 1.484 -0.049 1.30e-02 5.92e+03 1.41e+01 bond pdb=" C3' DG T 18 " pdb=" C2' DG T 18 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.37e+01 bond pdb=" C3' DC N 34 " pdb=" O3' DC N 34 " ideal model delta sigma weight residual 1.435 1.479 -0.044 1.30e-02 5.92e+03 1.15e+01 bond pdb=" C3' DC N 34 " pdb=" C2' DC N 34 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.12e+01 ... (remaining 12268 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.06: 16652 3.06 - 6.13: 233 6.13 - 9.19: 34 9.19 - 12.26: 6 12.26 - 15.32: 1 Bond angle restraints: 16926 Sorted by residual: angle pdb=" O4' DA N 36 " pdb=" C4' DA N 36 " pdb=" C3' DA N 36 " ideal model delta sigma weight residual 106.00 102.45 3.55 6.00e-01 2.78e+00 3.49e+01 angle pdb=" CA ASP E 237 " pdb=" CB ASP E 237 " pdb=" CG ASP E 237 " ideal model delta sigma weight residual 112.60 118.25 -5.65 1.00e+00 1.00e+00 3.19e+01 angle pdb=" C HIS E1150 " pdb=" N ASP E1151 " pdb=" CA ASP E1151 " ideal model delta sigma weight residual 121.54 131.89 -10.35 1.91e+00 2.74e-01 2.94e+01 angle pdb=" O4' DT T 11 " pdb=" C4' DT T 11 " pdb=" C3' DT T 11 " ideal model delta sigma weight residual 106.00 103.09 2.91 6.00e-01 2.78e+00 2.36e+01 angle pdb=" O4' DA N 40 " pdb=" C4' DA N 40 " pdb=" C3' DA N 40 " ideal model delta sigma weight residual 106.00 103.22 2.78 6.00e-01 2.78e+00 2.14e+01 ... (remaining 16921 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.73: 6966 35.73 - 71.47: 330 71.47 - 107.20: 5 107.20 - 142.93: 2 142.93 - 178.67: 2 Dihedral angle restraints: 7305 sinusoidal: 3488 harmonic: 3817 Sorted by residual: dihedral pdb=" CA SER E1148 " pdb=" C SER E1148 " pdb=" N VAL E1149 " pdb=" CA VAL E1149 " ideal model delta harmonic sigma weight residual 180.00 149.96 30.04 0 5.00e+00 4.00e-02 3.61e+01 dihedral pdb=" CA MET B 194 " pdb=" C MET B 194 " pdb=" N PHE B 195 " pdb=" CA PHE B 195 " ideal model delta harmonic sigma weight residual 180.00 150.07 29.93 0 5.00e+00 4.00e-02 3.58e+01 dihedral pdb=" CA GLN E 252 " pdb=" C GLN E 252 " pdb=" N ARG E 253 " pdb=" CA ARG E 253 " ideal model delta harmonic sigma weight residual 180.00 -150.41 -29.59 0 5.00e+00 4.00e-02 3.50e+01 ... (remaining 7302 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.134: 1845 0.134 - 0.269: 29 0.269 - 0.403: 1 0.403 - 0.537: 3 0.537 - 0.671: 4 Chirality restraints: 1882 Sorted by residual: chirality pdb=" P DG N 39 " pdb=" OP1 DG N 39 " pdb=" OP2 DG N 39 " pdb=" O5' DG N 39 " both_signs ideal model delta sigma weight residual True 2.34 -3.01 -0.67 2.00e-01 2.50e+01 1.13e+01 chirality pdb=" P DA N 42 " pdb=" OP1 DA N 42 " pdb=" OP2 DA N 42 " pdb=" O5' DA N 42 " both_signs ideal model delta sigma weight residual True 2.34 -2.93 -0.59 2.00e-01 2.50e+01 8.79e+00 chirality pdb=" P DG N 44 " pdb=" OP1 DG N 44 " pdb=" OP2 DG N 44 " pdb=" O5' DG N 44 " both_signs ideal model delta sigma weight residual True 2.34 -2.91 -0.58 2.00e-01 2.50e+01 8.29e+00 ... (remaining 1879 not shown) Planarity restraints: 1937 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 803 " -0.382 9.50e-02 1.11e+02 1.72e-01 1.91e+01 pdb=" NE ARG E 803 " 0.029 2.00e-02 2.50e+03 pdb=" CZ ARG E 803 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG E 803 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG E 803 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN B 103 " -0.051 5.00e-02 4.00e+02 7.77e-02 9.65e+00 pdb=" N PRO B 104 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO B 104 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 104 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS E1150 " 0.013 2.00e-02 2.50e+03 2.76e-02 7.59e+00 pdb=" C HIS E1150 " -0.048 2.00e-02 2.50e+03 pdb=" O HIS E1150 " 0.018 2.00e-02 2.50e+03 pdb=" N ASP E1151 " 0.016 2.00e-02 2.50e+03 ... (remaining 1934 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 72 2.59 - 3.17: 9150 3.17 - 3.75: 19365 3.75 - 4.32: 26187 4.32 - 4.90: 41875 Nonbonded interactions: 96649 Sorted by model distance: nonbonded pdb=" O GLY E 923 " pdb="MG MG E1302 " model vdw 2.016 2.170 nonbonded pdb=" O2A ATP E1301 " pdb="MG MG E1302 " model vdw 2.021 2.170 nonbonded pdb=" OD2 ASP E 922 " pdb="MG MG E1302 " model vdw 2.056 2.170 nonbonded pdb=" O LYS B 236 " pdb=" OG SER B 251 " model vdw 2.229 3.040 nonbonded pdb=" O VAL E1025 " pdb=" OG SER E1029 " model vdw 2.237 3.040 ... (remaining 96644 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: 3.850 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.740 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5381 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 : 0.005 0.060 12273 Z= 0.331 Angle : 0.940 15.321 16926 Z= 0.573 Chirality : 0.061 0.671 1882 Planarity : 0.009 0.172 1937 Dihedral : 17.858 178.665 4827 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.17 % Allowed : 0.35 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.21), residues: 1298 helix: -0.17 (0.18), residues: 691 sheet: -1.59 (0.51), residues: 90 loop : -0.80 (0.25), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG E 803 TYR 0.022 0.002 TYR B 88 PHE 0.027 0.003 PHE E 470 TRP 0.026 0.002 TRP E1026 HIS 0.012 0.002 HIS B 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.33 (12273) covalent geometry : angle 0.93974 / 0.57 (16926) hydrogen bonds : bond 0.15019 / 16.99 ( 595) hydrogen bonds : angle 5.90289 / 7.06 ( 1654) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 241 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 342 GLU cc_start: 0.6326 (tm-30) cc_final: 0.6112 (tm-30) REVERT: E 515 GLN cc_start: 0.6622 (tp40) cc_final: 0.6258 (tp40) REVERT: E 632 GLU cc_start: 0.7085 (mp0) cc_final: 0.6615 (mp0) REVERT: E 943 SER cc_start: 0.7385 (m) cc_final: 0.7122 (m) REVERT: E 947 GLU cc_start: 0.7336 (tt0) cc_final: 0.7133 (tt0) REVERT: E 951 VAL cc_start: 0.8044 (m) cc_final: 0.7820 (t) REVERT: B 266 GLU cc_start: 0.7249 (tp30) cc_final: 0.7017 (tp30) REVERT: B 295 LYS cc_start: 0.6421 (ttmm) cc_final: 0.5952 (ttmm) REVERT: B 309 THR cc_start: 0.6516 (p) cc_final: 0.6280 (p) outliers start: 2 outliers final: 1 residues processed: 243 average time/residue: 0.6131 time to fit residues: 160.7456 Evaluate side-chains 210 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 209 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 239 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.4980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.0670 chunk 91 optimal weight: 0.0270 chunk 55 optimal weight: 0.4980 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 223 GLN E 252 GLN E 265 ASN E 304 GLN E 528 ASN ** E 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 920 HIS E 969 GLN E 979 GLN E1103 ASN E1138 HIS E1165 GLN B 97 HIS B 294 GLN B 311 ASN ** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.184404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.156502 restraints weight = 16545.195| |-----------------------------------------------------------------------------| r_work (start): 0.4032 rms_B_bonded: 1.79 r_work: 0.3934 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3795 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 12273 Z= 0.153 Angle : 0.656 8.484 16926 Z= 0.347 Chirality : 0.043 0.245 1882 Planarity : 0.006 0.049 1937 Dihedral : 20.078 179.575 2202 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.57 % Allowed : 10.05 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.23), residues: 1298 helix: 0.83 (0.19), residues: 699 sheet: -1.42 (0.53), residues: 80 loop : -0.33 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 331 TYR 0.014 0.001 TYR E1227 PHE 0.017 0.001 PHE B 370 TRP 0.011 0.001 TRP B 205 HIS 0.012 0.001 HIS B 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (12273) covalent geometry : angle 0.65558 / 0.35 (16926) hydrogen bonds : bond 0.04984 / 5.59 ( 595) hydrogen bonds : angle 4.50046 / 5.50 ( 1654) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 215 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 342 GLU cc_start: 0.7430 (tm-30) cc_final: 0.7176 (tm-30) REVERT: E 792 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7577 (mtp180) REVERT: E 845 LEU cc_start: 0.8691 (tt) cc_final: 0.8488 (tp) REVERT: E 1051 GLN cc_start: 0.6872 (tt0) cc_final: 0.6649 (tt0) REVERT: B 259 GLU cc_start: 0.5040 (mp0) cc_final: 0.4670 (mp0) REVERT: B 266 GLU cc_start: 0.8190 (tp30) cc_final: 0.7698 (tp30) REVERT: B 295 LYS cc_start: 0.7428 (ttmm) cc_final: 0.6724 (ttmm) outliers start: 18 outliers final: 9 residues processed: 220 average time/residue: 0.6215 time to fit residues: 147.9789 Evaluate side-chains 215 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 205 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 415 VAL Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain E residue 502 ARG Chi-restraints excluded: chain E residue 792 ARG Chi-restraints excluded: chain E residue 988 LYS Chi-restraints excluded: chain E residue 1192 CYS Chi-restraints excluded: chain B residue 224 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 97 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 49 optimal weight: 0.0470 chunk 16 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 81 optimal weight: 0.0570 overall best weight: 0.6202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 369 ASN E 528 ASN E 585 GLN ** E 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 844 HIS E 920 HIS E 992 GLN E1165 GLN B 311 ASN B 322 HIS ** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.182719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.154172 restraints weight = 16548.075| |-----------------------------------------------------------------------------| r_work (start): 0.4001 rms_B_bonded: 1.79 r_work: 0.3902 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3760 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12273 Z= 0.163 Angle : 0.620 7.541 16926 Z= 0.329 Chirality : 0.042 0.255 1882 Planarity : 0.005 0.051 1937 Dihedral : 20.000 179.011 2202 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.75 % Allowed : 11.71 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.23), residues: 1298 helix: 1.21 (0.19), residues: 703 sheet: -1.32 (0.47), residues: 90 loop : -0.24 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 331 TYR 0.015 0.001 TYR B 247 PHE 0.023 0.002 PHE B 370 TRP 0.024 0.002 TRP E 441 HIS 0.008 0.001 HIS B 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 (12273) covalent geometry : angle 0.62049 / 0.33 (16926) hydrogen bonds : bond 0.04511 / 5.06 ( 595) hydrogen bonds : angle 4.21250 / 5.13 ( 1654) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 214 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 289 ASP cc_start: 0.7377 (t0) cc_final: 0.7159 (t0) REVERT: E 787 GLN cc_start: 0.7776 (OUTLIER) cc_final: 0.7449 (tt0) REVERT: E 792 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.7691 (mtp180) REVERT: B 265 MET cc_start: 0.8104 (ttt) cc_final: 0.7845 (ttm) REVERT: B 266 GLU cc_start: 0.8367 (tp30) cc_final: 0.7937 (tp30) REVERT: B 295 LYS cc_start: 0.7528 (ttmm) cc_final: 0.6804 (ttmm) REVERT: B 309 THR cc_start: 0.7107 (p) cc_final: 0.6896 (p) outliers start: 20 outliers final: 9 residues processed: 220 average time/residue: 0.6342 time to fit residues: 150.9134 Evaluate side-chains 215 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 204 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 263 MET Chi-restraints excluded: chain E residue 415 VAL Chi-restraints excluded: chain E residue 502 ARG Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 787 GLN Chi-restraints excluded: chain E residue 792 ARG Chi-restraints excluded: chain E residue 976 ARG Chi-restraints excluded: chain B residue 224 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 4 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 109 optimal weight: 6.9990 chunk 93 optimal weight: 0.9980 chunk 131 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 51 optimal weight: 0.0670 chunk 41 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 265 ASN E 369 ASN E 528 ASN ** E 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 920 HIS ** E1096 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1165 GLN B 243 ASN B 311 ASN ** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.181933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.153387 restraints weight = 16500.285| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 1.78 r_work: 0.3892 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3751 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 12273 Z= 0.174 Angle : 0.626 8.415 16926 Z= 0.330 Chirality : 0.042 0.255 1882 Planarity : 0.005 0.047 1937 Dihedral : 19.938 179.966 2202 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.10 % Allowed : 13.02 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.23), residues: 1298 helix: 1.40 (0.20), residues: 701 sheet: -1.32 (0.47), residues: 90 loop : -0.25 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 331 TYR 0.015 0.001 TYR E1227 PHE 0.020 0.002 PHE B 370 TRP 0.028 0.002 TRP E 441 HIS 0.005 0.001 HIS E 608 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (12273) covalent geometry : angle 0.62624 / 0.33 (16926) hydrogen bonds : bond 0.04376 / 4.90 ( 595) hydrogen bonds : angle 4.17285 / 5.08 ( 1654) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 216 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 289 ASP cc_start: 0.7400 (t0) cc_final: 0.7129 (t0) REVERT: E 772 MET cc_start: 0.7382 (mtp) cc_final: 0.7176 (mtm) REVERT: E 787 GLN cc_start: 0.7800 (OUTLIER) cc_final: 0.7486 (tt0) REVERT: E 792 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.7743 (mtp180) REVERT: B 258 CYS cc_start: 0.3927 (OUTLIER) cc_final: 0.3667 (t) REVERT: B 259 GLU cc_start: 0.5417 (mp0) cc_final: 0.4940 (mp0) REVERT: B 266 GLU cc_start: 0.8372 (tp30) cc_final: 0.7773 (tp30) REVERT: B 295 LYS cc_start: 0.7571 (ttmm) cc_final: 0.6894 (ttmm) REVERT: B 309 THR cc_start: 0.7215 (p) cc_final: 0.7005 (p) outliers start: 24 outliers final: 12 residues processed: 229 average time/residue: 0.5939 time to fit residues: 147.4530 Evaluate side-chains 224 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 209 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 263 MET Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 415 VAL Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain E residue 502 ARG Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 787 GLN Chi-restraints excluded: chain E residue 792 ARG Chi-restraints excluded: chain E residue 976 ARG Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 258 CYS Chi-restraints excluded: chain B residue 262 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 52 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 99 optimal weight: 0.5980 chunk 9 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 369 ASN E 528 ASN E 597 HIS E 617 GLN ** E 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 920 HIS ** E1096 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1165 GLN B 175 ASN B 255 GLN B 311 ASN ** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.177680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.148522 restraints weight = 16315.787| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 1.79 r_work: 0.3828 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3682 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 12273 Z= 0.300 Angle : 0.746 9.234 16926 Z= 0.388 Chirality : 0.049 0.262 1882 Planarity : 0.006 0.050 1937 Dihedral : 19.946 179.924 2202 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.67 % Allowed : 12.94 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.23), residues: 1298 helix: 0.94 (0.19), residues: 706 sheet: -1.66 (0.46), residues: 90 loop : -0.45 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 331 TYR 0.023 0.002 TYR B 247 PHE 0.035 0.003 PHE B 370 TRP 0.033 0.003 TRP E 441 HIS 0.009 0.002 HIS B 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00705 / 0.30 (12273) covalent geometry : angle 0.74578 / 0.39 (16926) hydrogen bonds : bond 0.05428 / 6.05 ( 595) hydrogen bonds : angle 4.33813 / 5.40 ( 1654) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 232 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 289 ASP cc_start: 0.7458 (t0) cc_final: 0.7179 (t0) REVERT: E 342 GLU cc_start: 0.7590 (tm-30) cc_final: 0.7335 (tm-30) REVERT: E 573 MET cc_start: 0.7692 (OUTLIER) cc_final: 0.7483 (mmt) REVERT: E 781 TYR cc_start: 0.8154 (m-10) cc_final: 0.7417 (m-10) REVERT: E 787 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.7595 (tt0) REVERT: E 792 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.7837 (mtp180) REVERT: E 1224 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7275 (mtp85) REVERT: B 258 CYS cc_start: 0.4245 (OUTLIER) cc_final: 0.3780 (t) REVERT: B 259 GLU cc_start: 0.5783 (mp0) cc_final: 0.5219 (mp0) REVERT: B 265 MET cc_start: 0.8426 (ttt) cc_final: 0.8116 (ttm) REVERT: B 295 LYS cc_start: 0.7624 (ttmm) cc_final: 0.6859 (ttmm) REVERT: B 309 THR cc_start: 0.7448 (p) cc_final: 0.7202 (p) outliers start: 42 outliers final: 15 residues processed: 253 average time/residue: 0.5987 time to fit residues: 163.5328 Evaluate side-chains 244 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 224 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 263 MET Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 415 VAL Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain E residue 502 ARG Chi-restraints excluded: chain E residue 573 MET Chi-restraints excluded: chain E residue 618 ILE Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 659 HIS Chi-restraints excluded: chain E residue 787 GLN Chi-restraints excluded: chain E residue 792 ARG Chi-restraints excluded: chain E residue 1224 ARG Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 258 CYS Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 373 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 129 optimal weight: 0.1980 chunk 112 optimal weight: 0.9990 chunk 133 optimal weight: 0.6980 chunk 22 optimal weight: 0.0570 chunk 62 optimal weight: 0.8980 chunk 108 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 126 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 369 ASN E 528 ASN ** E 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1096 GLN E1165 GLN B 175 ASN B 311 ASN ** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.180376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.151476 restraints weight = 16334.672| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 1.77 r_work: 0.3868 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3725 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 12273 Z= 0.157 Angle : 0.638 9.389 16926 Z= 0.335 Chirality : 0.042 0.263 1882 Planarity : 0.006 0.050 1937 Dihedral : 19.866 177.792 2200 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.06 % Allowed : 15.12 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.24), residues: 1298 helix: 1.40 (0.20), residues: 700 sheet: -1.56 (0.49), residues: 84 loop : -0.24 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 782 TYR 0.014 0.001 TYR E1227 PHE 0.019 0.001 PHE B 195 TRP 0.031 0.002 TRP E 441 HIS 0.007 0.001 HIS B 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (12273) covalent geometry : angle 0.63838 / 0.33 (16926) hydrogen bonds : bond 0.04384 / 4.95 ( 595) hydrogen bonds : angle 4.16724 / 5.12 ( 1654) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 217 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 289 ASP cc_start: 0.7409 (t0) cc_final: 0.7131 (t0) REVERT: E 342 GLU cc_start: 0.7623 (tm-30) cc_final: 0.7319 (tm-30) REVERT: E 787 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.7518 (tt0) REVERT: E 792 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.7799 (mtp180) REVERT: B 258 CYS cc_start: 0.4101 (OUTLIER) cc_final: 0.3756 (t) REVERT: B 259 GLU cc_start: 0.5767 (mp0) cc_final: 0.5313 (mp0) REVERT: B 265 MET cc_start: 0.8349 (ttt) cc_final: 0.8023 (ttm) REVERT: B 266 GLU cc_start: 0.8548 (tp30) cc_final: 0.7849 (tp30) REVERT: B 295 LYS cc_start: 0.7600 (ttmm) cc_final: 0.6886 (ttmm) REVERT: B 309 THR cc_start: 0.7285 (p) cc_final: 0.7044 (p) outliers start: 35 outliers final: 14 residues processed: 234 average time/residue: 0.6125 time to fit residues: 154.8685 Evaluate side-chains 230 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 213 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 263 MET Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 398 CYS Chi-restraints excluded: chain E residue 415 VAL Chi-restraints excluded: chain E residue 451 GLU Chi-restraints excluded: chain E residue 502 ARG Chi-restraints excluded: chain E residue 537 LEU Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 659 HIS Chi-restraints excluded: chain E residue 787 GLN Chi-restraints excluded: chain E residue 792 ARG Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 258 CYS Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 373 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 11 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 133 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 81 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 369 ASN E 528 ASN ** E 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1165 GLN B 311 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.179820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.150779 restraints weight = 16297.168| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 1.77 r_work: 0.3859 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3715 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12273 Z= 0.177 Angle : 0.642 10.956 16926 Z= 0.333 Chirality : 0.043 0.262 1882 Planarity : 0.005 0.050 1937 Dihedral : 19.814 178.534 2200 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.53 % Allowed : 16.35 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.24), residues: 1298 helix: 1.36 (0.20), residues: 707 sheet: -1.46 (0.48), residues: 90 loop : -0.36 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 331 TYR 0.015 0.001 TYR E1227 PHE 0.015 0.001 PHE B 195 TRP 0.040 0.002 TRP E 441 HIS 0.006 0.001 HIS E 608 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.18 (12273) covalent geometry : angle 0.64217 / 0.33 (16926) hydrogen bonds : bond 0.04400 / 4.93 ( 595) hydrogen bonds : angle 4.11946 / 5.07 ( 1654) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 217 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 289 ASP cc_start: 0.7414 (t0) cc_final: 0.7142 (t0) REVERT: E 342 GLU cc_start: 0.7661 (tm-30) cc_final: 0.7413 (tm-30) REVERT: E 787 GLN cc_start: 0.7805 (OUTLIER) cc_final: 0.7523 (tt0) REVERT: E 792 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.7820 (mtp180) REVERT: B 154 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8419 (mp) REVERT: B 258 CYS cc_start: 0.4112 (OUTLIER) cc_final: 0.3755 (t) REVERT: B 259 GLU cc_start: 0.5766 (mp0) cc_final: 0.5297 (mp0) REVERT: B 266 GLU cc_start: 0.8589 (tp30) cc_final: 0.7929 (tp30) REVERT: B 295 LYS cc_start: 0.7626 (ttmm) cc_final: 0.6904 (ttmm) REVERT: B 309 THR cc_start: 0.7307 (p) cc_final: 0.7066 (p) outliers start: 29 outliers final: 15 residues processed: 233 average time/residue: 0.6260 time to fit residues: 157.8794 Evaluate side-chains 235 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 216 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 263 MET Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 415 VAL Chi-restraints excluded: chain E residue 451 GLU Chi-restraints excluded: chain E residue 502 ARG Chi-restraints excluded: chain E residue 618 ILE Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 644 VAL Chi-restraints excluded: chain E residue 787 GLN Chi-restraints excluded: chain E residue 792 ARG Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 258 CYS Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 373 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 0 optimal weight: 30.0000 chunk 128 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 101 optimal weight: 0.0970 chunk 24 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 369 ASN E 528 ASN E 608 HIS ** E 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1035 GLN E1165 GLN B 264 HIS B 311 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.180718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.151714 restraints weight = 16312.414| |-----------------------------------------------------------------------------| r_work (start): 0.3969 rms_B_bonded: 1.76 r_work: 0.3868 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3725 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12273 Z= 0.156 Angle : 0.624 9.986 16926 Z= 0.325 Chirality : 0.042 0.264 1882 Planarity : 0.005 0.050 1937 Dihedral : 19.742 178.248 2200 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.27 % Allowed : 16.70 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.24), residues: 1298 helix: 1.50 (0.20), residues: 703 sheet: -1.49 (0.48), residues: 90 loop : -0.23 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 222 TYR 0.014 0.001 TYR E1227 PHE 0.015 0.001 PHE B 195 TRP 0.045 0.002 TRP E 441 HIS 0.005 0.001 HIS E1030 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 (12273) covalent geometry : angle 0.62426 / 0.32 (16926) hydrogen bonds : bond 0.04163 / 4.67 ( 595) hydrogen bonds : angle 4.06474 / 4.98 ( 1654) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 219 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 289 ASP cc_start: 0.7409 (t0) cc_final: 0.7150 (t0) REVERT: E 342 GLU cc_start: 0.7718 (tm-30) cc_final: 0.7460 (tm-30) REVERT: E 787 GLN cc_start: 0.7793 (OUTLIER) cc_final: 0.7500 (tt0) REVERT: E 801 ASP cc_start: 0.8061 (p0) cc_final: 0.7787 (p0) REVERT: B 258 CYS cc_start: 0.4016 (OUTLIER) cc_final: 0.3712 (t) REVERT: B 259 GLU cc_start: 0.5699 (mp0) cc_final: 0.5267 (mp0) REVERT: B 265 MET cc_start: 0.8305 (ttt) cc_final: 0.8042 (tpt) REVERT: B 295 LYS cc_start: 0.7666 (ttmm) cc_final: 0.7424 (ttmm) REVERT: B 309 THR cc_start: 0.7288 (p) cc_final: 0.7051 (p) outliers start: 26 outliers final: 13 residues processed: 231 average time/residue: 0.5756 time to fit residues: 144.2577 Evaluate side-chains 232 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 217 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 415 VAL Chi-restraints excluded: chain E residue 451 GLU Chi-restraints excluded: chain E residue 502 ARG Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 644 VAL Chi-restraints excluded: chain E residue 787 GLN Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 258 CYS Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 264 HIS Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 373 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 96 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 120 optimal weight: 0.9990 chunk 111 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 369 ASN E 528 ASN ** E 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1051 GLN ** B 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.179347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.150194 restraints weight = 16242.071| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 1.76 r_work: 0.3853 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3707 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 12273 Z= 0.206 Angle : 0.654 10.629 16926 Z= 0.340 Chirality : 0.044 0.265 1882 Planarity : 0.006 0.051 1937 Dihedral : 19.710 178.708 2200 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.19 % Allowed : 17.31 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.24), residues: 1298 helix: 1.42 (0.20), residues: 703 sheet: -1.56 (0.49), residues: 90 loop : -0.28 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 331 TYR 0.016 0.002 TYR E1227 PHE 0.011 0.002 PHE E 721 TRP 0.052 0.002 TRP E 441 HIS 0.015 0.001 HIS B 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.21 (12273) covalent geometry : angle 0.65352 / 0.34 (16926) hydrogen bonds : bond 0.04455 / 5.01 ( 595) hydrogen bonds : angle 4.10847 / 5.07 ( 1654) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 215 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 289 ASP cc_start: 0.7418 (t0) cc_final: 0.7158 (t0) REVERT: E 342 GLU cc_start: 0.7681 (tm-30) cc_final: 0.7421 (tm-30) REVERT: B 259 GLU cc_start: 0.5759 (mp0) cc_final: 0.5305 (mp0) REVERT: B 295 LYS cc_start: 0.7674 (ttmm) cc_final: 0.6929 (ttmm) REVERT: B 309 THR cc_start: 0.7348 (p) cc_final: 0.7105 (p) outliers start: 25 outliers final: 16 residues processed: 227 average time/residue: 0.5941 time to fit residues: 146.3023 Evaluate side-chains 231 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 215 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 415 VAL Chi-restraints excluded: chain E residue 451 GLU Chi-restraints excluded: chain E residue 502 ARG Chi-restraints excluded: chain E residue 618 ILE Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 644 VAL Chi-restraints excluded: chain E residue 1219 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 373 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 119 optimal weight: 0.5980 chunk 90 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 80 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 49 optimal weight: 0.0020 chunk 7 optimal weight: 0.3980 chunk 38 optimal weight: 0.8980 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 369 ASN E 528 ASN ** E 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 787 GLN ** E1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.180735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.151562 restraints weight = 16462.592| |-----------------------------------------------------------------------------| r_work (start): 0.3974 rms_B_bonded: 1.78 r_work: 0.3874 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3731 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12273 Z= 0.150 Angle : 0.629 11.115 16926 Z= 0.327 Chirality : 0.042 0.265 1882 Planarity : 0.005 0.050 1937 Dihedral : 19.653 178.028 2200 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.66 % Allowed : 18.27 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.24), residues: 1298 helix: 1.56 (0.20), residues: 704 sheet: -1.51 (0.48), residues: 90 loop : -0.24 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 222 TYR 0.017 0.001 TYR E 931 PHE 0.013 0.001 PHE B 195 TRP 0.064 0.002 TRP E 441 HIS 0.005 0.001 HIS E1030 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (12273) covalent geometry : angle 0.62883 / 0.33 (16926) hydrogen bonds : bond 0.04128 / 4.66 ( 595) hydrogen bonds : angle 4.03237 / 4.95 ( 1654) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 221 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 289 ASP cc_start: 0.7393 (t0) cc_final: 0.7145 (t0) REVERT: E 323 MET cc_start: 0.6655 (tpt) cc_final: 0.6422 (tpp) REVERT: E 342 GLU cc_start: 0.7736 (tm-30) cc_final: 0.7470 (tm-30) REVERT: E 616 GLN cc_start: 0.7077 (mt0) cc_final: 0.6701 (mt0) REVERT: E 1060 LEU cc_start: 0.7939 (mp) cc_final: 0.7703 (mt) REVERT: B 258 CYS cc_start: 0.3860 (OUTLIER) cc_final: 0.3535 (t) REVERT: B 259 GLU cc_start: 0.5729 (mp0) cc_final: 0.5308 (mp0) REVERT: B 265 MET cc_start: 0.8144 (ttm) cc_final: 0.7476 (tpt) REVERT: B 295 LYS cc_start: 0.7677 (ttmm) cc_final: 0.6903 (ttmm) REVERT: B 309 THR cc_start: 0.7296 (p) cc_final: 0.7057 (p) outliers start: 19 outliers final: 15 residues processed: 231 average time/residue: 0.5439 time to fit residues: 135.7170 Evaluate side-chains 235 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 219 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 415 VAL Chi-restraints excluded: chain E residue 451 GLU Chi-restraints excluded: chain E residue 502 ARG Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 644 VAL Chi-restraints excluded: chain E residue 787 GLN Chi-restraints excluded: chain E residue 931 TYR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 258 CYS Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 373 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 84 optimal weight: 0.0570 chunk 41 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 75 optimal weight: 0.2980 chunk 72 optimal weight: 0.7980 chunk 123 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 120 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 369 ASN E 528 ASN ** E 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 847 ASN ** E1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 HIS B 311 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.180758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.151570 restraints weight = 16266.479| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 1.78 r_work: 0.3864 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3720 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 12273 Z= 0.169 Angle : 0.643 10.573 16926 Z= 0.333 Chirality : 0.042 0.266 1882 Planarity : 0.006 0.050 1937 Dihedral : 19.622 178.306 2200 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.66 % Allowed : 18.27 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.24), residues: 1298 helix: 1.54 (0.20), residues: 704 sheet: -1.55 (0.47), residues: 90 loop : -0.27 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 222 TYR 0.053 0.002 TYR E 931 PHE 0.013 0.001 PHE B 195 TRP 0.065 0.002 TRP E 441 HIS 0.006 0.001 HIS E 608 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 (12273) covalent geometry : angle 0.64252 / 0.33 (16926) hydrogen bonds : bond 0.04186 / 4.73 ( 595) hydrogen bonds : angle 4.02861 / 4.98 ( 1654) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5123.54 seconds wall clock time: 87 minutes 50.89 seconds (5270.89 seconds total)