Starting phenix.real_space_refine on Fri Jul 3 04:57:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mn6_48414/07_2026/9mn6_48414.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mn6_48414/07_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_48414/07_2026/9mn6_48414.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mn6_48414/07_2026/9mn6_48414.map" model { file = "/net/cci-nas-00/data/ceres_data/9mn6_48414/07_2026/9mn6_48414.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mn6_48414/07_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-dev-6108/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: 2.25, per 1000 atoms: 0.19 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: 0.84 Conformation dependent library (CDL) restraints added in 387.6 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: 1.08 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: 2.48 Time building geometry restraints manager: 1.04 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=" O3' DA N 41 " pdb=" P DA N 42 " pdb=" O5' DA N 42 " ideal model delta sigma weight residual 104.00 111.62 -7.62 1.50e+00 4.44e-01 2.58e+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 ... (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: 4.590 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: 0.020 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.450 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.530 ------------------------------------------------------------------------------- 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= 0.330 Angle : 0.935 15.321 16926 Z= 0.568 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 0.00517 / 0.33 (12273) covalent geometry : angle 0.93540 / 0.57 (16926) hydrogen bonds : bond 0.15019 / 16.96 ( 595) hydrogen bonds : angle 5.90289 / 7.03 ( 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 : 0.406 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: 0.5488 time to fit residues: 144.0059 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 : 0.318 ------------------------------------------------------------------------------- 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 = 0.184423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.156461 restraints weight = 16523.033| |-----------------------------------------------------------------------------| r_work (start): 0.4031 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: 4.46 restraints_weight: 0.2500 r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 12273 Z= 0.153 Angle : 0.651 8.028 16926 Z= 0.345 Chirality : 0.042 0.229 1882 Planarity : 0.006 0.048 1937 Dihedral : 20.093 179.751 2202 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % 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: 0.29 (0.23), residues: 1298 helix: 0.85 (0.19), residues: 699 sheet: -1.42 (0.53), residues: 80 loop : -0.32 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 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 0.00324 / 0.15 (12273) covalent geometry : angle 0.65133 / 0.34 (16926) hydrogen bonds : bond 0.04856 / 5.43 ( 595) hydrogen bonds : angle 4.46173 / 5.45 ( 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 : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 342 GLU cc_start: 0.7440 (tm-30) cc_final: 0.7182 (tm-30) REVERT: E 792 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7576 (mtp180) REVERT: E 1051 GLN cc_start: 0.6915 (tt0) cc_final: 0.6703 (tt0) REVERT: B 259 GLU cc_start: 0.4957 (mp0) cc_final: 0.4516 (mp0) REVERT: B 266 GLU cc_start: 0.8208 (tp30) cc_final: 0.7703 (tp30) REVERT: B 295 LYS cc_start: 0.7433 (ttmm) cc_final: 0.6742 (ttmm) outliers start: 18 outliers final: 9 residues processed: 221 average time/residue: 0.5181 time to fit residues: 124.4472 Evaluate side-chains 212 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 202 time to evaluate : 0.405 ------------------------------------------------------------------------------- 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 1002 THR 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: 0.0470 chunk 134 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 chunk 9 optimal weight: 0.2980 chunk 103 optimal weight: 1.9990 chunk 81 optimal weight: 0.0670 overall best weight: 0.4216 ------------------------------------------------------------------------------- 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 844 HIS E 920 HIS E 992 GLN E1035 GLN E1165 GLN B 311 ASN B 322 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.184077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.155804 restraints weight = 16621.100| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 1.79 r_work: 0.3921 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3781 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12273 Z= 0.141 Angle : 0.601 7.332 16926 Z= 0.319 Chirality : 0.041 0.237 1882 Planarity : 0.005 0.051 1937 Dihedral : 20.018 178.323 2202 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.84 % Allowed : 11.28 % Favored : 86.89 % 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: 0.73 (0.23), residues: 1298 helix: 1.27 (0.19), residues: 704 sheet: -1.42 (0.52), residues: 80 loop : -0.18 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 331 TYR 0.013 0.001 TYR E1227 PHE 0.016 0.001 PHE B 370 TRP 0.025 0.001 TRP E 441 HIS 0.007 0.001 HIS B 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (12273) covalent geometry : angle 0.60072 / 0.32 (16926) hydrogen bonds : bond 0.04323 / 4.84 ( 595) hydrogen bonds : angle 4.20388 / 5.09 ( 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 227 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 206 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 289 ASP cc_start: 0.7359 (t0) cc_final: 0.7145 (t0) REVERT: E 342 GLU cc_start: 0.7501 (tm-30) cc_final: 0.7202 (tm-30) REVERT: E 369 ASN cc_start: 0.8566 (t0) cc_final: 0.8300 (t0) REVERT: E 787 GLN cc_start: 0.7760 (OUTLIER) cc_final: 0.7444 (tt0) REVERT: E 792 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.7669 (mtp180) REVERT: B 265 MET cc_start: 0.8003 (ttt) cc_final: 0.7551 (tpt) REVERT: B 295 LYS cc_start: 0.7510 (ttmm) cc_final: 0.6724 (ttmm) outliers start: 21 outliers final: 11 residues processed: 214 average time/residue: 0.5365 time to fit residues: 124.5847 Evaluate side-chains 213 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 200 time to evaluate : 0.329 ------------------------------------------------------------------------------- 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 268 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 E residue 1023 GLU Chi-restraints excluded: chain E residue 1192 CYS 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: 5.9990 chunk 89 optimal weight: 1.9990 chunk 57 optimal weight: 0.0970 chunk 67 optimal weight: 1.9990 chunk 109 optimal weight: 6.9990 chunk 93 optimal weight: 0.0670 chunk 131 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 51 optimal weight: 0.0020 chunk 41 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 overall best weight: 0.2924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 265 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.184150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.155772 restraints weight = 16647.520| |-----------------------------------------------------------------------------| r_work (start): 0.4026 rms_B_bonded: 1.80 r_work: 0.3927 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3786 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 12273 Z= 0.126 Angle : 0.586 8.827 16926 Z= 0.309 Chirality : 0.040 0.231 1882 Planarity : 0.005 0.046 1937 Dihedral : 19.950 178.946 2202 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.45 % Allowed : 12.67 % 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: 1.03 (0.24), residues: 1298 helix: 1.57 (0.20), residues: 702 sheet: -1.38 (0.53), residues: 80 loop : -0.12 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 344 TYR 0.011 0.001 TYR E1227 PHE 0.014 0.001 PHE B 195 TRP 0.025 0.001 TRP E 441 HIS 0.005 0.001 HIS E1030 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.13 (12273) covalent geometry : angle 0.58633 / 0.31 (16926) hydrogen bonds : bond 0.03964 / 4.46 ( 595) hydrogen bonds : angle 4.05842 / 4.90 ( 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 242 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 214 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 289 ASP cc_start: 0.7367 (t0) cc_final: 0.7108 (t0) REVERT: E 342 GLU cc_start: 0.7498 (tm-30) cc_final: 0.7178 (tm-30) REVERT: E 787 GLN cc_start: 0.7773 (OUTLIER) cc_final: 0.7467 (tt0) REVERT: B 258 CYS cc_start: 0.3855 (OUTLIER) cc_final: 0.3623 (t) REVERT: B 259 GLU cc_start: 0.5297 (mp0) cc_final: 0.4818 (mp0) REVERT: B 295 LYS cc_start: 0.7523 (ttmm) cc_final: 0.6831 (ttmm) outliers start: 28 outliers final: 12 residues processed: 224 average time/residue: 0.5071 time to fit residues: 123.4711 Evaluate side-chains 214 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 200 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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 638 THR Chi-restraints excluded: chain E residue 787 GLN Chi-restraints excluded: chain E residue 976 ARG Chi-restraints excluded: chain E residue 1159 ASP Chi-restraints excluded: chain E residue 1192 CYS 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: 0.6980 chunk 129 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 chunk 99 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 127 optimal weight: 0.6980 chunk 40 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 528 ASN E 585 GLN ** 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.181694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.153168 restraints weight = 16476.637| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 1.77 r_work: 0.3891 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3749 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 12273 Z= 0.176 Angle : 0.622 8.474 16926 Z= 0.325 Chirality : 0.042 0.233 1882 Planarity : 0.006 0.078 1937 Dihedral : 19.855 178.790 2202 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.36 % Allowed : 13.72 % Favored : 83.92 % 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: 0.97 (0.24), residues: 1298 helix: 1.53 (0.20), residues: 703 sheet: -1.28 (0.49), residues: 90 loop : -0.16 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 450 TYR 0.016 0.001 TYR B 247 PHE 0.023 0.002 PHE B 370 TRP 0.028 0.002 TRP E 441 HIS 0.006 0.001 HIS E1030 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.18 (12273) covalent geometry : angle 0.62161 / 0.33 (16926) hydrogen bonds : bond 0.04324 / 4.83 ( 595) hydrogen bonds : angle 4.06536 / 4.92 ( 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 240 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 213 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 289 ASP cc_start: 0.7412 (t0) cc_final: 0.7138 (t0) REVERT: E 342 GLU cc_start: 0.7507 (tm-30) cc_final: 0.7295 (tm-30) REVERT: E 787 GLN cc_start: 0.7792 (OUTLIER) cc_final: 0.7471 (tt0) REVERT: E 792 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.7788 (mtp180) REVERT: E 801 ASP cc_start: 0.8052 (p0) cc_final: 0.7811 (p0) REVERT: E 1040 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8149 (mp) REVERT: B 259 GLU cc_start: 0.5405 (mp0) cc_final: 0.4853 (mp0) REVERT: B 265 MET cc_start: 0.7991 (ttt) cc_final: 0.7614 (tpt) REVERT: B 266 GLU cc_start: 0.8364 (tp30) cc_final: 0.7738 (tp30) REVERT: B 295 LYS cc_start: 0.7608 (ttmm) cc_final: 0.6874 (ttmm) REVERT: B 309 THR cc_start: 0.7210 (p) cc_final: 0.7003 (p) outliers start: 27 outliers final: 15 residues processed: 223 average time/residue: 0.5422 time to fit residues: 131.0886 Evaluate side-chains 222 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 204 time to evaluate : 0.335 ------------------------------------------------------------------------------- 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 280 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 618 ILE 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 E residue 1040 LEU Chi-restraints excluded: chain E residue 1192 CYS Chi-restraints excluded: chain E residue 1230 SER Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 365 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 129 optimal weight: 1.9990 chunk 112 optimal weight: 0.2980 chunk 133 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 108 optimal weight: 0.5980 chunk 63 optimal weight: 0.8980 chunk 126 optimal weight: 0.3980 chunk 39 optimal weight: 0.3980 chunk 40 optimal weight: 2.9990 chunk 58 optimal weight: 8.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 920 HIS ** E1096 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1165 GLN B 311 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.182549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.154141 restraints weight = 16493.638| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 1.78 r_work: 0.3898 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3757 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 12273 Z= 0.139 Angle : 0.590 8.525 16926 Z= 0.309 Chirality : 0.040 0.235 1882 Planarity : 0.005 0.069 1937 Dihedral : 19.786 179.771 2202 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.36 % Allowed : 14.69 % Favored : 82.95 % 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: 1.10 (0.24), residues: 1298 helix: 1.67 (0.20), residues: 704 sheet: -1.30 (0.49), residues: 90 loop : -0.13 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG E 450 TYR 0.013 0.001 TYR E1227 PHE 0.018 0.001 PHE B 195 TRP 0.031 0.001 TRP E 441 HIS 0.004 0.001 HIS E1030 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (12273) covalent geometry : angle 0.58954 / 0.31 (16926) hydrogen bonds : bond 0.03987 / 4.49 ( 595) hydrogen bonds : angle 3.98409 / 4.81 ( 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 237 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 210 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 289 ASP cc_start: 0.7402 (t0) cc_final: 0.7132 (t0) REVERT: E 342 GLU cc_start: 0.7532 (tm-30) cc_final: 0.7298 (tm-30) REVERT: E 787 GLN cc_start: 0.7771 (OUTLIER) cc_final: 0.7465 (tt0) REVERT: E 792 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.7796 (mtp180) REVERT: E 801 ASP cc_start: 0.8007 (p0) cc_final: 0.7725 (p0) REVERT: E 1060 LEU cc_start: 0.7942 (mp) cc_final: 0.7722 (mt) REVERT: B 258 CYS cc_start: 0.3834 (OUTLIER) cc_final: 0.3520 (t) REVERT: B 259 GLU cc_start: 0.5529 (mp0) cc_final: 0.5058 (mp0) REVERT: B 265 MET cc_start: 0.7971 (ttt) cc_final: 0.7541 (tpt) REVERT: B 266 GLU cc_start: 0.8373 (tp30) cc_final: 0.7725 (tp30) REVERT: B 295 LYS cc_start: 0.7619 (ttmm) cc_final: 0.6883 (ttmm) REVERT: B 309 THR cc_start: 0.7169 (p) cc_final: 0.6957 (p) outliers start: 27 outliers final: 11 residues processed: 226 average time/residue: 0.5528 time to fit residues: 135.0773 Evaluate side-chains 219 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 205 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 280 LEU 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 E residue 1192 CYS 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 365 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 11 optimal weight: 0.9980 chunk 61 optimal weight: 0.3980 chunk 27 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 133 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 81 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 920 HIS ** E1096 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1165 GLN B 311 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.181572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.153131 restraints weight = 16424.819| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 1.76 r_work: 0.3889 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3748 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 12273 Z= 0.157 Angle : 0.604 9.013 16926 Z= 0.315 Chirality : 0.041 0.235 1882 Planarity : 0.005 0.076 1937 Dihedral : 19.741 179.700 2202 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.36 % Allowed : 15.12 % Favored : 82.52 % 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: 1.10 (0.24), residues: 1298 helix: 1.67 (0.20), residues: 703 sheet: -1.28 (0.49), residues: 90 loop : -0.14 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG E 450 TYR 0.014 0.001 TYR E1227 PHE 0.016 0.002 PHE B 195 TRP 0.040 0.002 TRP E 441 HIS 0.004 0.001 HIS E1030 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 (12273) covalent geometry : angle 0.60363 / 0.31 (16926) hydrogen bonds : bond 0.04100 / 4.60 ( 595) hydrogen bonds : angle 3.95809 / 4.81 ( 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 233 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 206 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 277 PHE cc_start: 0.7666 (OUTLIER) cc_final: 0.7402 (m-10) REVERT: E 289 ASP cc_start: 0.7392 (t0) cc_final: 0.7121 (t0) REVERT: E 342 GLU cc_start: 0.7562 (tm-30) cc_final: 0.7119 (tm-30) REVERT: E 787 GLN cc_start: 0.7795 (OUTLIER) cc_final: 0.7482 (tt0) REVERT: E 792 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.7801 (mtp180) REVERT: E 801 ASP cc_start: 0.8006 (p0) cc_final: 0.7750 (p0) REVERT: B 265 MET cc_start: 0.8059 (ttt) cc_final: 0.7567 (tpt) REVERT: B 295 LYS cc_start: 0.7621 (ttmm) cc_final: 0.6874 (ttmm) REVERT: B 309 THR cc_start: 0.7197 (p) cc_final: 0.6988 (p) outliers start: 27 outliers final: 14 residues processed: 220 average time/residue: 0.5132 time to fit residues: 122.5489 Evaluate side-chains 222 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 205 time to evaluate : 0.285 ------------------------------------------------------------------------------- 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 277 PHE Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 415 VAL 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 787 GLN Chi-restraints excluded: chain E residue 792 ARG Chi-restraints excluded: chain E residue 976 ARG Chi-restraints excluded: chain E residue 1192 CYS Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 262 VAL 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: 0.9980 chunk 12 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 0 optimal weight: 30.0000 chunk 128 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 101 optimal weight: 0.4980 chunk 24 optimal weight: 0.6980 chunk 15 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 920 HIS ** E1096 GLN ** 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 = 0.4318 r_free = 0.4318 target = 0.181341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.152854 restraints weight = 16319.911| |-----------------------------------------------------------------------------| r_work (start): 0.3987 rms_B_bonded: 1.76 r_work: 0.3887 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3747 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12273 Z= 0.157 Angle : 0.602 9.670 16926 Z= 0.314 Chirality : 0.041 0.238 1882 Planarity : 0.005 0.070 1937 Dihedral : 19.707 179.959 2202 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.45 % Allowed : 15.30 % Favored : 82.26 % 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: 1.11 (0.24), residues: 1298 helix: 1.67 (0.20), residues: 703 sheet: -1.30 (0.50), residues: 90 loop : -0.12 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 450 TYR 0.014 0.001 TYR E1227 PHE 0.017 0.001 PHE B 195 TRP 0.049 0.002 TRP E 441 HIS 0.005 0.001 HIS E 608 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 (12273) covalent geometry : angle 0.60186 / 0.31 (16926) hydrogen bonds : bond 0.04068 / 4.57 ( 595) hydrogen bonds : angle 3.97531 / 4.83 ( 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 244 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 216 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 277 PHE cc_start: 0.7650 (OUTLIER) cc_final: 0.7394 (m-10) REVERT: E 289 ASP cc_start: 0.7393 (t0) cc_final: 0.7130 (t0) REVERT: E 787 GLN cc_start: 0.7763 (OUTLIER) cc_final: 0.7467 (tt0) REVERT: E 792 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.7823 (mtp180) REVERT: B 206 LYS cc_start: 0.7628 (mttp) cc_final: 0.7277 (pptt) REVERT: B 259 GLU cc_start: 0.5443 (mp0) cc_final: 0.5041 (mp0) REVERT: B 265 MET cc_start: 0.8132 (ttt) cc_final: 0.7723 (ttm) REVERT: B 295 LYS cc_start: 0.7638 (ttmm) cc_final: 0.6943 (ttmm) REVERT: B 309 THR cc_start: 0.7173 (p) cc_final: 0.6956 (p) outliers start: 28 outliers final: 14 residues processed: 231 average time/residue: 0.5045 time to fit residues: 126.4952 Evaluate side-chains 229 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 212 time to evaluate : 0.428 ------------------------------------------------------------------------------- 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 277 PHE Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 415 VAL 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 787 GLN Chi-restraints excluded: chain E residue 792 ARG Chi-restraints excluded: chain E residue 976 ARG Chi-restraints excluded: chain E residue 1192 CYS Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 262 VAL 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: 0.6980 chunk 59 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 54 optimal weight: 0.5980 chunk 106 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 304 GLN E 369 ASN E 528 ASN ** E 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 920 HIS E 926 ASN B 311 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.180404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.151694 restraints weight = 16265.363| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 1.76 r_work: 0.3875 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3734 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12273 Z= 0.183 Angle : 0.639 10.817 16926 Z= 0.332 Chirality : 0.043 0.239 1882 Planarity : 0.006 0.092 1937 Dihedral : 19.688 179.981 2202 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.19 % Allowed : 16.08 % Favored : 81.73 % 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: 0.94 (0.24), residues: 1298 helix: 1.52 (0.20), residues: 710 sheet: -1.41 (0.51), residues: 84 loop : -0.21 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG E 450 TYR 0.015 0.001 TYR E1227 PHE 0.015 0.002 PHE B 195 TRP 0.052 0.002 TRP E 441 HIS 0.005 0.001 HIS E1030 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 (12273) covalent geometry : angle 0.63869 / 0.33 (16926) hydrogen bonds : bond 0.04259 / 4.78 ( 595) hydrogen bonds : angle 4.02024 / 4.89 ( 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 235 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 210 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 277 PHE cc_start: 0.7649 (OUTLIER) cc_final: 0.7406 (m-10) REVERT: E 787 GLN cc_start: 0.7796 (OUTLIER) cc_final: 0.7505 (tt0) REVERT: E 792 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.7824 (mtp180) REVERT: B 206 LYS cc_start: 0.7639 (mttp) cc_final: 0.7334 (pptt) REVERT: B 259 GLU cc_start: 0.5546 (mp0) cc_final: 0.5153 (mp0) REVERT: B 265 MET cc_start: 0.8238 (ttt) cc_final: 0.7786 (ttm) REVERT: B 295 LYS cc_start: 0.7665 (ttmm) cc_final: 0.6946 (ttmm) REVERT: B 309 THR cc_start: 0.7224 (p) cc_final: 0.6999 (p) outliers start: 25 outliers final: 14 residues processed: 222 average time/residue: 0.5112 time to fit residues: 122.9351 Evaluate side-chains 223 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 206 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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 277 PHE Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 415 VAL 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 787 GLN Chi-restraints excluded: chain E residue 792 ARG Chi-restraints excluded: chain E residue 976 ARG Chi-restraints excluded: chain E residue 1192 CYS Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 262 VAL 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: 0.8980 chunk 30 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 304 GLN ** E 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 369 ASN E 528 ASN E 608 HIS ** E 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 847 ASN E 920 HIS ** E1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1096 GLN B 311 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.180303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.151536 restraints weight = 16462.375| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 1.77 r_work: 0.3874 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3733 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12273 Z= 0.174 Angle : 0.634 11.076 16926 Z= 0.329 Chirality : 0.043 0.241 1882 Planarity : 0.006 0.095 1937 Dihedral : 19.679 179.635 2202 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.01 % Allowed : 16.17 % 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: 0.91 (0.24), residues: 1298 helix: 1.49 (0.20), residues: 710 sheet: -1.47 (0.50), residues: 84 loop : -0.20 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG E 450 TYR 0.031 0.002 TYR E 931 PHE 0.017 0.002 PHE B 195 TRP 0.066 0.002 TRP E 441 HIS 0.005 0.001 HIS E1030 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (12273) covalent geometry : angle 0.63363 / 0.33 (16926) hydrogen bonds : bond 0.04227 / 4.76 ( 595) hydrogen bonds : angle 4.04191 / 4.92 ( 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 235 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 212 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 277 PHE cc_start: 0.7659 (OUTLIER) cc_final: 0.7423 (m-10) REVERT: E 342 GLU cc_start: 0.7955 (tp30) cc_final: 0.7652 (tm-30) REVERT: E 787 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.7523 (tt0) REVERT: E 792 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.7842 (mtp180) REVERT: B 206 LYS cc_start: 0.7635 (mttp) cc_final: 0.7320 (pptt) REVERT: B 259 GLU cc_start: 0.5572 (mp0) cc_final: 0.5197 (mp0) REVERT: B 265 MET cc_start: 0.8254 (ttt) cc_final: 0.7760 (ttm) REVERT: B 295 LYS cc_start: 0.7610 (ttmm) cc_final: 0.6872 (ttmm) REVERT: B 309 THR cc_start: 0.7226 (p) cc_final: 0.6999 (p) outliers start: 23 outliers final: 13 residues processed: 223 average time/residue: 0.5162 time to fit residues: 124.6847 Evaluate side-chains 226 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 210 time to evaluate : 0.255 ------------------------------------------------------------------------------- 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 277 PHE Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 415 VAL 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 787 GLN Chi-restraints excluded: chain E residue 792 ARG Chi-restraints excluded: chain E residue 1192 CYS Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 262 VAL 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: 0.0010 chunk 41 optimal weight: 0.5980 chunk 88 optimal weight: 0.9980 chunk 75 optimal weight: 0.3980 chunk 72 optimal weight: 0.6980 chunk 123 optimal weight: 0.6980 chunk 98 optimal weight: 0.7980 chunk 58 optimal weight: 0.0060 chunk 101 optimal weight: 0.1980 chunk 120 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 overall best weight: 0.2402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 369 ASN E 522 GLN E 528 ASN ** E 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 847 ASN E 920 HIS ** E1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.182915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.154366 restraints weight = 16366.504| |-----------------------------------------------------------------------------| r_work (start): 0.4004 rms_B_bonded: 1.77 r_work: 0.3907 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3768 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12273 Z= 0.125 Angle : 0.595 10.129 16926 Z= 0.310 Chirality : 0.041 0.242 1882 Planarity : 0.005 0.063 1937 Dihedral : 19.603 179.050 2202 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.22 % Allowed : 17.83 % Favored : 80.94 % 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: 1.21 (0.24), residues: 1298 helix: 1.74 (0.20), residues: 700 sheet: -1.55 (0.48), residues: 84 loop : 0.01 (0.29), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E1034 TYR 0.020 0.001 TYR E 931 PHE 0.020 0.001 PHE E 612 TRP 0.078 0.002 TRP E 441 HIS 0.004 0.001 HIS B 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 (12273) covalent geometry : angle 0.59506 / 0.31 (16926) hydrogen bonds : bond 0.03752 / 4.24 ( 595) hydrogen bonds : angle 3.94435 / 4.78 ( 1654) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4407.19 seconds wall clock time: 75 minutes 34.07 seconds (4534.07 seconds total)