Starting phenix.real_space_refine on Thu Aug 6 05:21:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kln_62410/08_2026/9kln_62410.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kln_62410/08_2026/9kln_62410.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kln_62410/08_2026/9kln_62410.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kln_62410/08_2026/9kln_62410.map" model { file = "/net/cci-nas-00/data/ceres_data/9kln_62410/08_2026/9kln_62410.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kln_62410/08_2026/9kln_62410.cif" } resolution = 2.55 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= 0.000 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 143 5.49 5 Mg 2 5.21 5 S 36 5.16 5 C 8118 2.51 5 N 2535 2.21 5 O 2915 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 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: 13749 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 10685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1385, 10685 Classifications: {'peptide': 1385} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 57, 'TRANS': 1327} Chain breaks: 13 Unresolved non-hydrogen bonds: 263 Unresolved non-hydrogen angles: 327 Unresolved non-hydrogen dihedrals: 218 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 19, 'ASP:plan': 10, 'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 3, 'ARG:plan': 4, 'TRP:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 177 Chain: "B" Number of atoms: 2204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 2204 Classifications: {'RNA': 103} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 6, 'rna3p_pur': 48, 'rna3p_pyr': 40} Link IDs: {'rna2p': 15, 'rna3p': 87} Chain breaks: 1 Chain: "C" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 668 Classifications: {'DNA': 33} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 32} Chain: "D" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 182 Classifications: {'DNA': 9} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 8} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2, 'water': 8} Link IDs: {None: 9} Time building chain proxies: 2.75, per 1000 atoms: 0.20 Number of scatterers: 13749 At special positions: 0 Unit cell: (104.648, 119.48, 126.896, 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 36 16.00 P 143 15.00 Mg 2 11.99 O 2915 8.00 N 2535 7.00 C 8118 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: 1.01 Conformation dependent library (CDL) restraints added in 574.8 milliseconds 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2586 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 8 sheets defined 55.4% alpha, 9.0% beta 50 base pairs and 96 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'A' and resid 24 through 52 Processing helix chain 'A' and resid 53 through 54 No H-bonds generated for 'chain 'A' and resid 53 through 54' Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 70 through 85 Processing helix chain 'A' and resid 95 through 97 No H-bonds generated for 'chain 'A' and resid 95 through 97' Processing helix chain 'A' and resid 106 through 125 Processing helix chain 'A' and resid 128 through 139 Processing helix chain 'A' and resid 141 through 145 Processing helix chain 'A' and resid 156 through 168 Processing helix chain 'A' and resid 175 through 185 removed outlier: 4.096A pdb=" N MET A 179 " --> pdb=" O ASP A 175 " (cutoff:3.500A) Proline residue: A 182 - end of helix Processing helix chain 'A' and resid 186 through 192 Processing helix chain 'A' and resid 214 through 228 Processing helix chain 'A' and resid 234 through 252 Processing helix chain 'A' and resid 258 through 269 Processing helix chain 'A' and resid 278 through 287 removed outlier: 3.725A pdb=" N VAL A 282 " --> pdb=" O ASN A 278 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU A 285 " --> pdb=" O GLY A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 305 removed outlier: 3.548A pdb=" N GLY A 300 " --> pdb=" O ARG A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 330 Processing helix chain 'A' and resid 337 through 352 removed outlier: 3.690A pdb=" N ARG A 350 " --> pdb=" O ASP A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 369 removed outlier: 3.662A pdb=" N THR A 369 " --> pdb=" O ILE A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 416 Processing helix chain 'A' and resid 417 through 418 No H-bonds generated for 'chain 'A' and resid 417 through 418' Processing helix chain 'A' and resid 419 through 424 Processing helix chain 'A' and resid 425 through 444 Processing helix chain 'A' and resid 459 through 467 removed outlier: 3.835A pdb=" N ALA A 465 " --> pdb=" O LYS A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 488 Processing helix chain 'A' and resid 496 through 504 Processing helix chain 'A' and resid 509 through 513 Processing helix chain 'A' and resid 524 through 543 removed outlier: 3.634A pdb=" N ILE A 528 " --> pdb=" O ALA A 524 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG A 541 " --> pdb=" O GLU A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 579 Processing helix chain 'A' and resid 615 through 622 Processing helix chain 'A' and resid 641 through 648 Processing helix chain 'A' and resid 660 through 664 removed outlier: 3.566A pdb=" N GLU A 664 " --> pdb=" O LEU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 686 Processing helix chain 'A' and resid 691 through 704 Processing helix chain 'A' and resid 721 through 726 Processing helix chain 'A' and resid 742 through 746 removed outlier: 3.662A pdb=" N LYS A 746 " --> pdb=" O ILE A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 752 Processing helix chain 'A' and resid 783 through 794 Processing helix chain 'A' and resid 868 through 882 removed outlier: 3.505A pdb=" N TRP A 873 " --> pdb=" O ASN A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 895 Processing helix chain 'A' and resid 900 through 914 Processing helix chain 'A' and resid 936 through 966 removed outlier: 4.144A pdb=" N LYS A 953 " --> pdb=" O ARG A 949 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N TYR A 954 " --> pdb=" O LEU A 950 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N THR A 966 " --> pdb=" O ALA A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 988 Processing helix chain 'A' and resid 998 through 1015 removed outlier: 3.584A pdb=" N ASP A1005 " --> pdb=" O ASP A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1023 through 1029 Processing helix chain 'A' and resid 1054 through 1073 Proline residue: A1066 - end of helix Processing helix chain 'A' and resid 1075 through 1108 removed outlier: 3.602A pdb=" N LYS A1098 " --> pdb=" O ALA A1094 " (cutoff:3.500A) Processing helix chain 'A' and resid 1111 through 1115 Processing helix chain 'A' and resid 1116 through 1120 removed outlier: 3.996A pdb=" N ILE A1119 " --> pdb=" O THR A1116 " (cutoff:3.500A) Processing helix chain 'A' and resid 1126 through 1139 Processing helix chain 'A' and resid 1140 through 1146 Processing helix chain 'A' and resid 1162 through 1190 Processing helix chain 'A' and resid 1234 through 1243 Processing helix chain 'A' and resid 1244 through 1258 Processing helix chain 'A' and resid 1269 through 1273 removed outlier: 3.818A pdb=" N GLN A1273 " --> pdb=" O THR A1270 " (cutoff:3.500A) Processing helix chain 'A' and resid 1295 through 1309 Processing helix chain 'A' and resid 1311 through 1323 removed outlier: 3.575A pdb=" N ARG A1315 " --> pdb=" O THR A1311 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA A1323 " --> pdb=" O ALA A1319 " (cutoff:3.500A) Processing helix chain 'A' and resid 1328 through 1336 removed outlier: 3.933A pdb=" N GLY A1336 " --> pdb=" O GLU A1332 " (cutoff:3.500A) Processing helix chain 'A' and resid 1355 through 1360 removed outlier: 3.628A pdb=" N LYS A1359 " --> pdb=" O PRO A1356 " (cutoff:3.500A) Processing helix chain 'A' and resid 1363 through 1377 Processing helix chain 'A' and resid 1457 through 1481 removed outlier: 3.640A pdb=" N ASN A1481 " --> pdb=" O LEU A1477 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 561 through 562 Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 90 removed outlier: 3.750A pdb=" N ALA A 101 " --> pdb=" O TRP A 153 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ASN A 155 " --> pdb=" O ILE A 99 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE A 99 " --> pdb=" O ASN A 155 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 356 through 357 removed outlier: 4.331A pdb=" N LEU A 356 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 635 through 637 removed outlier: 6.167A pdb=" N ALA A 635 " --> pdb=" O THR A 657 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 805 through 812 removed outlier: 3.676A pdb=" N ARG A 810 " --> pdb=" O GLU A 825 " (cutoff:3.500A) removed outlier: 21.329A pdb=" N GLU A 824 " --> pdb=" O PHE A 854 " (cutoff:3.500A) removed outlier: 16.706A pdb=" N PHE A 854 " --> pdb=" O GLU A 824 " (cutoff:3.500A) removed outlier: 13.223A pdb=" N SER A 826 " --> pdb=" O ARG A 852 " (cutoff:3.500A) removed outlier: 9.188A pdb=" N ARG A 852 " --> pdb=" O SER A 826 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N VAL A 828 " --> pdb=" O LEU A 850 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL A 778 " --> pdb=" O ASP A 851 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N GLN A 853 " --> pdb=" O CYS A 776 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N CYS A 776 " --> pdb=" O GLN A 853 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N LEU A 855 " --> pdb=" O ALA A 774 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ALA A 774 " --> pdb=" O LEU A 855 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU A1220 " --> pdb=" O VAL A 766 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N VAL A1217 " --> pdb=" O ARG A1263 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N VAL A1265 " --> pdb=" O VAL A1217 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE A1219 " --> pdb=" O VAL A1265 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 969 through 972 Processing sheet with id=AA7, first strand: chain 'A' and resid 1338 through 1341 Processing sheet with id=AA8, first strand: chain 'A' and resid 1387 through 1390 586 hydrogen bonds defined for protein. 1659 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 129 hydrogen bonds 250 hydrogen bond angles 0 basepair planarities 50 basepair parallelities 96 stacking parallelities Total time for adding SS restraints: 3.86 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3027 1.33 - 1.45: 3875 1.45 - 1.57: 7074 1.57 - 1.70: 284 1.70 - 1.82: 57 Bond restraints: 14317 Sorted by residual: bond pdb=" CA GLY A 228 " pdb=" C GLY A 228 " ideal model delta sigma weight residual 1.517 1.569 -0.052 9.60e-03 1.09e+04 2.92e+01 bond pdb=" C GLY A 228 " pdb=" N THR A 229 " ideal model delta sigma weight residual 1.332 1.400 -0.068 1.36e-02 5.41e+03 2.52e+01 bond pdb=" C3' DA C 4 " pdb=" C2' DA C 4 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 bond pdb=" C3' DA C 16 " pdb=" O3' DA C 16 " ideal model delta sigma weight residual 1.435 1.397 0.038 1.30e-02 5.92e+03 8.49e+00 bond pdb=" C3' DG D 4 " pdb=" C2' DG D 4 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.19e+00 ... (remaining 14312 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 18907 1.70 - 3.39: 850 3.39 - 5.09: 169 5.09 - 6.79: 98 6.79 - 8.48: 14 Bond angle restraints: 20038 Sorted by residual: angle pdb=" O4' G B 92 " pdb=" C1' G B 92 " pdb=" N9 G B 92 " ideal model delta sigma weight residual 108.20 112.92 -4.72 8.00e-01 1.56e+00 3.47e+01 angle pdb=" O4' DC C 12 " pdb=" C4' DC C 12 " pdb=" C3' DC C 12 " ideal model delta sigma weight residual 106.00 102.69 3.31 6.00e-01 2.78e+00 3.04e+01 angle pdb=" C4' G B 92 " pdb=" O4' G B 92 " pdb=" C1' G B 92 " ideal model delta sigma weight residual 109.70 105.86 3.84 7.00e-01 2.04e+00 3.01e+01 angle pdb=" C4' G B 27 " pdb=" C3' G B 27 " pdb=" C2' G B 27 " ideal model delta sigma weight residual 102.60 98.08 4.52 1.00e+00 1.00e+00 2.04e+01 angle pdb=" C1' C B 45 " pdb=" N1 C B 45 " pdb=" C2 C B 45 " ideal model delta sigma weight residual 118.80 123.72 -4.92 1.10e+00 8.26e-01 2.00e+01 ... (remaining 20033 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.73: 7913 34.73 - 69.45: 657 69.45 - 104.18: 54 104.18 - 138.90: 0 138.90 - 173.63: 1 Dihedral angle restraints: 8625 sinusoidal: 4637 harmonic: 3988 Sorted by residual: dihedral pdb=" CD ARG A 166 " pdb=" NE ARG A 166 " pdb=" CZ ARG A 166 " pdb=" NH1 ARG A 166 " ideal model delta sinusoidal sigma weight residual 0.00 -84.15 84.15 1 1.00e+01 1.00e-02 8.62e+01 dihedral pdb=" O4' C B 45 " pdb=" C1' C B 45 " pdb=" N1 C B 45 " pdb=" C2 C B 45 " ideal model delta sinusoidal sigma weight residual 200.00 26.37 173.63 1 1.50e+01 4.44e-03 8.51e+01 dihedral pdb=" CD ARG A1196 " pdb=" NE ARG A1196 " pdb=" CZ ARG A1196 " pdb=" NH1 ARG A1196 " ideal model delta sinusoidal sigma weight residual 0.00 60.90 -60.90 1 1.00e+01 1.00e-02 4.93e+01 ... (remaining 8622 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 2093 0.115 - 0.230: 122 0.230 - 0.345: 17 0.345 - 0.459: 34 0.459 - 0.574: 14 Chirality restraints: 2280 Sorted by residual: chirality pdb=" P C B 82 " pdb=" OP1 C B 82 " pdb=" OP2 C B 82 " pdb=" O5' C B 82 " both_signs ideal model delta sigma weight residual True 2.41 -2.98 -0.57 2.00e-01 2.50e+01 8.25e+00 chirality pdb=" P DC D 5 " pdb=" OP1 DC D 5 " pdb=" OP2 DC D 5 " pdb=" O5' DC D 5 " both_signs ideal model delta sigma weight residual True 2.34 -2.91 -0.57 2.00e-01 2.50e+01 8.14e+00 chirality pdb=" P DA C 31 " pdb=" OP1 DA C 31 " pdb=" OP2 DA C 31 " pdb=" O5' DA C 31 " both_signs ideal model delta sigma weight residual True 2.34 -2.88 -0.54 2.00e-01 2.50e+01 7.40e+00 ... (remaining 2277 not shown) Planarity restraints: 2055 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 166 " 1.096 9.50e-02 1.11e+02 4.91e-01 1.46e+02 pdb=" NE ARG A 166 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG A 166 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 166 " 0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG A 166 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1196 " 0.958 9.50e-02 1.11e+02 4.29e-01 1.12e+02 pdb=" NE ARG A1196 " -0.058 2.00e-02 2.50e+03 pdb=" CZ ARG A1196 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A1196 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A1196 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1193 " -0.638 9.50e-02 1.11e+02 2.86e-01 4.99e+01 pdb=" NE ARG A1193 " 0.038 2.00e-02 2.50e+03 pdb=" CZ ARG A1193 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG A1193 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A1193 " -0.020 2.00e-02 2.50e+03 ... (remaining 2052 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 150 2.61 - 3.19: 11382 3.19 - 3.76: 23462 3.76 - 4.33: 31963 4.33 - 4.90: 49582 Nonbonded interactions: 116539 Sorted by model distance: nonbonded pdb="MG MG B 202 " pdb=" O HOH B 302 " model vdw 2.042 2.170 nonbonded pdb=" OP2 C B 39 " pdb="MG MG B 202 " model vdw 2.048 2.170 nonbonded pdb="MG MG B 201 " pdb=" O HOH B 308 " model vdw 2.069 2.170 nonbonded pdb="MG MG B 202 " pdb=" O HOH B 304 " model vdw 2.086 2.170 nonbonded pdb=" OP2 U B 33 " pdb="MG MG B 201 " model vdw 2.098 2.170 ... (remaining 116534 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: 1.900 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: 15.280 Find NCS groups from input model: 0.070 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:6.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 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 : 0.007 0.068 14317 Z= 0.468 Angle : 0.900 8.482 20038 Z= 0.562 Chirality : 0.086 0.574 2280 Planarity : 0.016 0.491 2055 Dihedral : 21.238 173.626 6039 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.05 % Favored : 95.87 % Rotamer: Outliers : 2.00 % Allowed : 21.93 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1357 helix: 1.53 (0.20), residues: 701 sheet: -0.45 (0.45), residues: 126 loop : -0.64 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 771 TYR 0.016 0.002 TYR A 954 PHE 0.013 0.002 PHE A 386 TRP 0.017 0.002 TRP A 30 HIS 0.005 0.001 HIS A 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00710 / 0.47 (14317) covalent geometry : angle 0.89963 / 0.56 (20038) hydrogen bonds : bond 0.16209 / 10.58 ( 715) hydrogen bonds : angle 6.64484 / 4.70 ( 1909) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 175 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 ASP cc_start: 0.8445 (m-30) cc_final: 0.7958 (m-30) REVERT: A 326 LYS cc_start: 0.5713 (tttt) cc_final: 0.5408 (mtmt) REVERT: A 375 ASP cc_start: 0.8291 (p0) cc_final: 0.7564 (t0) REVERT: A 413 ARG cc_start: 0.7050 (ttm170) cc_final: 0.6664 (mtt90) REVERT: A 439 ARG cc_start: 0.6255 (mmm160) cc_final: 0.5628 (mpp-170) REVERT: A 485 LEU cc_start: 0.5470 (OUTLIER) cc_final: 0.5184 (mt) REVERT: A 539 LYS cc_start: 0.7427 (mtpp) cc_final: 0.6961 (mttp) REVERT: A 652 ARG cc_start: 0.8165 (ttt-90) cc_final: 0.7680 (tpm170) REVERT: A 696 GLU cc_start: 0.8477 (mm-30) cc_final: 0.8119 (mt-10) REVERT: A 878 MET cc_start: 0.8395 (ttm) cc_final: 0.8120 (ttp) REVERT: A 916 LYS cc_start: 0.8920 (mtpp) cc_final: 0.8571 (mttp) REVERT: A 941 MET cc_start: 0.9101 (mmm) cc_final: 0.8690 (mmp) REVERT: A 1158 LYS cc_start: 0.8959 (mtpp) cc_final: 0.8691 (mtmt) REVERT: A 1247 VAL cc_start: 0.9360 (t) cc_final: 0.9064 (p) REVERT: A 1248 LYS cc_start: 0.8596 (tttt) cc_final: 0.8266 (tppt) REVERT: A 1294 ASN cc_start: 0.6451 (OUTLIER) cc_final: 0.6089 (m110) REVERT: A 1329 MET cc_start: 0.3283 (mmp) cc_final: 0.2790 (mtp) REVERT: A 1352 ASP cc_start: 0.8038 (t70) cc_final: 0.7589 (t0) REVERT: A 1464 GLU cc_start: 0.8432 (mm-30) cc_final: 0.8083 (tm-30) outliers start: 21 outliers final: 2 residues processed: 192 average time/residue: 0.7802 time to fit residues: 160.3907 Evaluate side-chains 102 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 98 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 982 GLU Chi-restraints excluded: chain A residue 1292 PHE Chi-restraints excluded: chain A residue 1294 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 10.0000 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 676 GLN A 813 GLN ** A1306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1471 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.136159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.093868 restraints weight = 19716.141| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.06 r_work: 0.3076 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 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 : 0.003 0.034 14317 Z= 0.159 Angle : 0.571 10.358 20038 Z= 0.326 Chirality : 0.039 0.192 2280 Planarity : 0.005 0.061 2055 Dihedral : 20.084 176.765 3569 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.10 % Allowed : 23.07 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.98 (0.23), residues: 1357 helix: 1.78 (0.20), residues: 701 sheet: -0.27 (0.47), residues: 123 loop : -0.62 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1020 TYR 0.020 0.002 TYR A1458 PHE 0.012 0.001 PHE A 386 TRP 0.018 0.001 TRP A 30 HIS 0.003 0.001 HIS A 770 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.16 (14317) covalent geometry : angle 0.57113 / 0.33 (20038) hydrogen bonds : bond 0.05770 / 3.91 ( 715) hydrogen bonds : angle 4.23570 / 3.08 ( 1909) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 105 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 ASP cc_start: 0.8428 (m-30) cc_final: 0.7927 (m-30) REVERT: A 326 LYS cc_start: 0.6577 (tttt) cc_final: 0.6083 (mtmt) REVERT: A 375 ASP cc_start: 0.8387 (p0) cc_final: 0.7583 (t0) REVERT: A 413 ARG cc_start: 0.6908 (ttm170) cc_final: 0.6542 (mtt90) REVERT: A 439 ARG cc_start: 0.6359 (mmm160) cc_final: 0.5669 (mpp-170) REVERT: A 485 LEU cc_start: 0.5568 (OUTLIER) cc_final: 0.5176 (mt) REVERT: A 539 LYS cc_start: 0.7131 (mtpp) cc_final: 0.6714 (mttp) REVERT: A 541 ARG cc_start: 0.8285 (ptp-110) cc_final: 0.7756 (ptt-90) REVERT: A 652 ARG cc_start: 0.8098 (ttt-90) cc_final: 0.7592 (tpm170) REVERT: A 696 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8010 (mt-10) REVERT: A 732 GLN cc_start: 0.6634 (mp10) cc_final: 0.6302 (mm110) REVERT: A 780 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8141 (tt0) REVERT: A 814 LYS cc_start: 0.7192 (OUTLIER) cc_final: 0.6560 (mtmt) REVERT: A 878 MET cc_start: 0.8271 (ttm) cc_final: 0.7915 (ttp) REVERT: A 939 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8112 (mm-30) REVERT: A 1158 LYS cc_start: 0.8891 (mtpp) cc_final: 0.8675 (mtmt) REVERT: A 1247 VAL cc_start: 0.9262 (t) cc_final: 0.8948 (p) REVERT: A 1329 MET cc_start: 0.3096 (mmp) cc_final: 0.2721 (mtt) REVERT: A 1352 ASP cc_start: 0.7884 (t70) cc_final: 0.7338 (t0) REVERT: A 1400 GLU cc_start: 0.6347 (mm-30) cc_final: 0.5913 (tm-30) REVERT: A 1464 GLU cc_start: 0.8421 (mm-30) cc_final: 0.8035 (tm-30) outliers start: 43 outliers final: 16 residues processed: 142 average time/residue: 0.6356 time to fit residues: 98.3659 Evaluate side-chains 112 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 703 LYS Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 822 THR Chi-restraints excluded: chain A residue 897 TRP Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 939 GLU Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 982 GLU Chi-restraints excluded: chain A residue 1039 GLN Chi-restraints excluded: chain A residue 1087 GLU Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1195 SER Chi-restraints excluded: chain A residue 1408 VAL Chi-restraints excluded: chain A residue 1478 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 108 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 45 optimal weight: 0.0770 chunk 51 optimal weight: 5.9990 chunk 134 optimal weight: 9.9990 chunk 80 optimal weight: 4.9990 chunk 74 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 overall best weight: 0.9142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 813 GLN ** A1306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.136755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.094620 restraints weight = 19874.527| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.06 r_work: 0.3089 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14317 Z= 0.132 Angle : 0.507 15.261 20038 Z= 0.290 Chirality : 0.036 0.170 2280 Planarity : 0.004 0.046 2055 Dihedral : 19.943 178.260 3565 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 4.10 % Allowed : 23.07 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.22 (0.23), residues: 1357 helix: 2.00 (0.19), residues: 699 sheet: -0.15 (0.47), residues: 122 loop : -0.54 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1462 TYR 0.018 0.001 TYR A1387 PHE 0.010 0.001 PHE A1485 TRP 0.017 0.001 TRP A 30 HIS 0.003 0.001 HIS A 770 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.13 (14317) covalent geometry : angle 0.50677 / 0.29 (20038) hydrogen bonds : bond 0.04930 / 3.33 ( 715) hydrogen bonds : angle 3.91484 / 2.84 ( 1909) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 97 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.8043 (ttp80) cc_final: 0.7210 (ttm170) REVERT: A 284 LYS cc_start: 0.6763 (OUTLIER) cc_final: 0.6393 (mttm) REVERT: A 326 LYS cc_start: 0.6545 (tttt) cc_final: 0.6030 (mtmt) REVERT: A 362 ARG cc_start: 0.7514 (mpp80) cc_final: 0.6878 (mmm160) REVERT: A 375 ASP cc_start: 0.8385 (p0) cc_final: 0.7460 (t0) REVERT: A 413 ARG cc_start: 0.6925 (ttm170) cc_final: 0.6518 (mtt90) REVERT: A 485 LEU cc_start: 0.5621 (OUTLIER) cc_final: 0.5222 (mt) REVERT: A 541 ARG cc_start: 0.8296 (ptp-110) cc_final: 0.7776 (ptt-90) REVERT: A 624 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.7803 (mp) REVERT: A 652 ARG cc_start: 0.8081 (ttt-90) cc_final: 0.7555 (tpm170) REVERT: A 696 GLU cc_start: 0.8567 (mm-30) cc_final: 0.8246 (mm-30) REVERT: A 732 GLN cc_start: 0.6659 (mp10) cc_final: 0.6283 (mm110) REVERT: A 780 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8168 (tt0) REVERT: A 813 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.8434 (mm-40) REVERT: A 878 MET cc_start: 0.8212 (ttm) cc_final: 0.7867 (ttp) REVERT: A 939 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.8040 (mm-30) REVERT: A 1000 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.8027 (ptpt) REVERT: A 1158 LYS cc_start: 0.8866 (mtpp) cc_final: 0.8562 (mtmt) REVERT: A 1245 SER cc_start: 0.7918 (m) cc_final: 0.7644 (m) REVERT: A 1247 VAL cc_start: 0.9211 (t) cc_final: 0.8917 (p) REVERT: A 1329 MET cc_start: 0.2957 (mmp) cc_final: 0.2674 (mtt) REVERT: A 1352 ASP cc_start: 0.7865 (t70) cc_final: 0.7294 (t0) REVERT: A 1359 LYS cc_start: 0.8018 (OUTLIER) cc_final: 0.7697 (mtpt) REVERT: A 1400 GLU cc_start: 0.6379 (mm-30) cc_final: 0.6066 (tm-30) REVERT: A 1464 GLU cc_start: 0.8411 (mm-30) cc_final: 0.8030 (tm-30) outliers start: 43 outliers final: 16 residues processed: 136 average time/residue: 0.6733 time to fit residues: 99.2080 Evaluate side-chains 115 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 PHE Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 703 LYS Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 813 GLN Chi-restraints excluded: chain A residue 822 THR Chi-restraints excluded: chain A residue 897 TRP Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 939 GLU Chi-restraints excluded: chain A residue 982 GLU Chi-restraints excluded: chain A residue 1000 LYS Chi-restraints excluded: chain A residue 1039 GLN Chi-restraints excluded: chain A residue 1087 GLU Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1359 LYS Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1408 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 6 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 21 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 133 optimal weight: 8.9990 chunk 104 optimal weight: 2.9990 chunk 149 optimal weight: 10.0000 chunk 135 optimal weight: 9.9990 chunk 102 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 129 optimal weight: 0.5980 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.134878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.093425 restraints weight = 20923.761| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.02 r_work: 0.3104 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 14317 Z= 0.234 Angle : 0.583 13.760 20038 Z= 0.324 Chirality : 0.042 0.211 2280 Planarity : 0.005 0.042 2055 Dihedral : 19.908 176.769 3565 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.96 % Allowed : 22.69 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.07 (0.23), residues: 1357 helix: 1.87 (0.19), residues: 700 sheet: -0.25 (0.46), residues: 122 loop : -0.59 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1276 TYR 0.017 0.002 TYR A 829 PHE 0.016 0.002 PHE A 386 TRP 0.018 0.002 TRP A 30 HIS 0.005 0.001 HIS A 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.23 (14317) covalent geometry : angle 0.58345 / 0.32 (20038) hydrogen bonds : bond 0.05346 / 3.61 ( 715) hydrogen bonds : angle 3.98832 / 2.91 ( 1909) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 96 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.8145 (ttp80) cc_final: 0.7341 (ttm170) REVERT: A 284 LYS cc_start: 0.6870 (OUTLIER) cc_final: 0.6477 (mttm) REVERT: A 326 LYS cc_start: 0.6642 (tttt) cc_final: 0.6095 (mtmt) REVERT: A 413 ARG cc_start: 0.6949 (ttm170) cc_final: 0.6556 (mtt90) REVERT: A 485 LEU cc_start: 0.5733 (OUTLIER) cc_final: 0.5310 (mt) REVERT: A 541 ARG cc_start: 0.8385 (ptp-110) cc_final: 0.7680 (ptp90) REVERT: A 624 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.7817 (mp) REVERT: A 652 ARG cc_start: 0.8047 (ttt-90) cc_final: 0.7549 (tpm170) REVERT: A 696 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8357 (mm-30) REVERT: A 825 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7763 (mm-30) REVERT: A 982 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7631 (mt-10) REVERT: A 1158 LYS cc_start: 0.8891 (mtpp) cc_final: 0.8594 (mtmt) REVERT: A 1245 SER cc_start: 0.8031 (m) cc_final: 0.7770 (m) REVERT: A 1247 VAL cc_start: 0.9202 (t) cc_final: 0.8942 (p) REVERT: A 1329 MET cc_start: 0.2792 (mmp) cc_final: 0.2465 (mtt) REVERT: A 1352 ASP cc_start: 0.7882 (t70) cc_final: 0.7316 (t0) REVERT: A 1359 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7869 (mtpt) REVERT: A 1400 GLU cc_start: 0.6356 (mm-30) cc_final: 0.6102 (tm-30) REVERT: A 1464 GLU cc_start: 0.8371 (mm-30) cc_final: 0.8015 (tm-30) outliers start: 52 outliers final: 22 residues processed: 141 average time/residue: 0.7059 time to fit residues: 108.1438 Evaluate side-chains 117 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 89 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 703 LYS Chi-restraints excluded: chain A residue 822 THR Chi-restraints excluded: chain A residue 825 GLU Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 982 GLU Chi-restraints excluded: chain A residue 1039 GLN Chi-restraints excluded: chain A residue 1087 GLU Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1347 VAL Chi-restraints excluded: chain A residue 1359 LYS Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1408 VAL Chi-restraints excluded: chain A residue 1477 LEU Chi-restraints excluded: chain A residue 1478 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 108 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 114 optimal weight: 9.9990 chunk 119 optimal weight: 0.8980 chunk 85 optimal weight: 0.6980 chunk 38 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 676 GLN A1306 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.137400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.096657 restraints weight = 20962.123| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.00 r_work: 0.3147 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14317 Z= 0.133 Angle : 0.507 16.534 20038 Z= 0.287 Chirality : 0.036 0.201 2280 Planarity : 0.004 0.039 2055 Dihedral : 19.834 177.642 3565 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.91 % Allowed : 24.21 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.28 (0.23), residues: 1357 helix: 2.07 (0.19), residues: 700 sheet: -0.28 (0.46), residues: 124 loop : -0.51 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1462 TYR 0.015 0.001 TYR A 931 PHE 0.012 0.001 PHE A 435 TRP 0.017 0.001 TRP A 30 HIS 0.003 0.001 HIS A 556 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.13 (14317) covalent geometry : angle 0.50706 / 0.29 (20038) hydrogen bonds : bond 0.04655 / 3.17 ( 715) hydrogen bonds : angle 3.82012 / 2.79 ( 1909) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 98 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.8090 (ttp80) cc_final: 0.7325 (ttm170) REVERT: A 284 LYS cc_start: 0.6881 (OUTLIER) cc_final: 0.6485 (mttm) REVERT: A 326 LYS cc_start: 0.6606 (tttt) cc_final: 0.6061 (mtmt) REVERT: A 330 SER cc_start: 0.7568 (m) cc_final: 0.7303 (p) REVERT: A 413 ARG cc_start: 0.6950 (ttm170) cc_final: 0.6560 (mtt90) REVERT: A 485 LEU cc_start: 0.5704 (OUTLIER) cc_final: 0.5251 (mt) REVERT: A 652 ARG cc_start: 0.8034 (ttt-90) cc_final: 0.7565 (tpm170) REVERT: A 696 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8404 (mm-30) REVERT: A 732 GLN cc_start: 0.6786 (mp10) cc_final: 0.6373 (mm110) REVERT: A 878 MET cc_start: 0.8362 (ttm) cc_final: 0.7959 (ttp) REVERT: A 982 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7578 (mt-10) REVERT: A 1158 LYS cc_start: 0.8842 (mtpp) cc_final: 0.8551 (mtmt) REVERT: A 1245 SER cc_start: 0.7991 (m) cc_final: 0.7739 (m) REVERT: A 1247 VAL cc_start: 0.9229 (t) cc_final: 0.8992 (p) REVERT: A 1329 MET cc_start: 0.2884 (mmp) cc_final: 0.2551 (mtt) REVERT: A 1352 ASP cc_start: 0.7871 (t70) cc_final: 0.7279 (t0) REVERT: A 1359 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7835 (mtpt) REVERT: A 1464 GLU cc_start: 0.8341 (mm-30) cc_final: 0.7927 (tm-30) outliers start: 41 outliers final: 19 residues processed: 133 average time/residue: 0.6892 time to fit residues: 99.6170 Evaluate side-chains 116 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 PHE Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 822 THR Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 982 GLU Chi-restraints excluded: chain A residue 1039 GLN Chi-restraints excluded: chain A residue 1087 GLU Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1359 LYS Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1408 VAL Chi-restraints excluded: chain A residue 1477 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 81 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 111 optimal weight: 6.9990 chunk 78 optimal weight: 0.0980 chunk 31 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 92 optimal weight: 7.9990 chunk 93 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 chunk 90 optimal weight: 6.9990 chunk 128 optimal weight: 0.7980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 813 GLN A1301 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.137513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.096339 restraints weight = 20771.880| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.01 r_work: 0.3154 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14317 Z= 0.130 Angle : 0.494 14.968 20038 Z= 0.281 Chirality : 0.036 0.202 2280 Planarity : 0.004 0.046 2055 Dihedral : 19.667 178.937 3565 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.91 % Allowed : 24.69 % Favored : 71.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.44 (0.23), residues: 1357 helix: 2.21 (0.20), residues: 702 sheet: -0.25 (0.46), residues: 124 loop : -0.45 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 771 TYR 0.019 0.001 TYR A1458 PHE 0.011 0.001 PHE A 435 TRP 0.018 0.001 TRP A 30 HIS 0.002 0.001 HIS A 876 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.13 (14317) covalent geometry : angle 0.49358 / 0.28 (20038) hydrogen bonds : bond 0.04415 / 2.99 ( 715) hydrogen bonds : angle 3.69112 / 2.68 ( 1909) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 92 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.8086 (ttp80) cc_final: 0.7336 (ttm170) REVERT: A 86 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8768 (mm) REVERT: A 284 LYS cc_start: 0.6929 (OUTLIER) cc_final: 0.6504 (mttm) REVERT: A 326 LYS cc_start: 0.6648 (tttt) cc_final: 0.6043 (mtmt) REVERT: A 413 ARG cc_start: 0.6985 (ttm170) cc_final: 0.6583 (mtt90) REVERT: A 485 LEU cc_start: 0.5893 (OUTLIER) cc_final: 0.5449 (mt) REVERT: A 541 ARG cc_start: 0.8546 (ptp-110) cc_final: 0.8135 (ptt90) REVERT: A 652 ARG cc_start: 0.8006 (ttt-90) cc_final: 0.7591 (tpm170) REVERT: A 696 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8360 (mm-30) REVERT: A 825 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7697 (mm-30) REVERT: A 1158 LYS cc_start: 0.8874 (mtpp) cc_final: 0.8582 (mtmt) REVERT: A 1245 SER cc_start: 0.8013 (m) cc_final: 0.7765 (m) REVERT: A 1247 VAL cc_start: 0.9206 (t) cc_final: 0.8967 (p) REVERT: A 1309 LYS cc_start: 0.8180 (tppt) cc_final: 0.7617 (tptp) REVERT: A 1329 MET cc_start: 0.2719 (mmp) cc_final: 0.2502 (mtp) REVERT: A 1352 ASP cc_start: 0.7885 (t70) cc_final: 0.7312 (t0) REVERT: A 1359 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7799 (mtpt) REVERT: A 1464 GLU cc_start: 0.8331 (mm-30) cc_final: 0.7896 (tm-30) outliers start: 41 outliers final: 20 residues processed: 128 average time/residue: 0.6815 time to fit residues: 94.9063 Evaluate side-chains 113 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 88 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 PHE Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 822 THR Chi-restraints excluded: chain A residue 825 GLU Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 1039 GLN Chi-restraints excluded: chain A residue 1087 GLU Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1359 LYS Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1408 VAL Chi-restraints excluded: chain A residue 1477 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 22 optimal weight: 9.9990 chunk 96 optimal weight: 4.9990 chunk 137 optimal weight: 10.0000 chunk 139 optimal weight: 10.0000 chunk 63 optimal weight: 9.9990 chunk 128 optimal weight: 0.9980 chunk 39 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 56 optimal weight: 0.6980 chunk 148 optimal weight: 20.0000 chunk 43 optimal weight: 0.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 813 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.132471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.090789 restraints weight = 19646.338| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.89 r_work: 0.3023 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14317 Z= 0.243 Angle : 0.582 15.423 20038 Z= 0.321 Chirality : 0.041 0.220 2280 Planarity : 0.005 0.052 2055 Dihedral : 19.729 175.861 3562 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.48 % Allowed : 24.12 % Favored : 71.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.18 (0.23), residues: 1357 helix: 1.97 (0.19), residues: 702 sheet: -0.32 (0.46), residues: 123 loop : -0.54 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 771 TYR 0.015 0.002 TYR A 829 PHE 0.016 0.002 PHE A 386 TRP 0.014 0.002 TRP A 30 HIS 0.006 0.001 HIS A 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.24 (14317) covalent geometry : angle 0.58249 / 0.32 (20038) hydrogen bonds : bond 0.05218 / 3.52 ( 715) hydrogen bonds : angle 3.89483 / 2.84 ( 1909) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 92 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.8195 (ttp80) cc_final: 0.7388 (ttm170) REVERT: A 86 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8827 (mm) REVERT: A 284 LYS cc_start: 0.6911 (OUTLIER) cc_final: 0.6499 (mttm) REVERT: A 326 LYS cc_start: 0.6615 (tttt) cc_final: 0.6071 (mtmt) REVERT: A 413 ARG cc_start: 0.7027 (ttm170) cc_final: 0.6582 (mtt90) REVERT: A 485 LEU cc_start: 0.5841 (OUTLIER) cc_final: 0.5367 (mt) REVERT: A 541 ARG cc_start: 0.8533 (ptp-110) cc_final: 0.8042 (ptt90) REVERT: A 652 ARG cc_start: 0.8056 (ttt-90) cc_final: 0.7599 (tpm170) REVERT: A 696 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8294 (mm-30) REVERT: A 736 LYS cc_start: 0.8269 (pttt) cc_final: 0.7647 (ptpt) REVERT: A 825 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7592 (mm-30) REVERT: A 1000 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.8141 (ptpp) REVERT: A 1158 LYS cc_start: 0.8928 (mtpp) cc_final: 0.8649 (mtmt) REVERT: A 1245 SER cc_start: 0.8038 (m) cc_final: 0.7784 (m) REVERT: A 1247 VAL cc_start: 0.9198 (t) cc_final: 0.8950 (p) REVERT: A 1309 LYS cc_start: 0.8195 (tppt) cc_final: 0.7584 (tptp) REVERT: A 1329 MET cc_start: 0.2836 (mmp) cc_final: 0.2375 (mtp) REVERT: A 1352 ASP cc_start: 0.7883 (t70) cc_final: 0.7274 (t0) REVERT: A 1359 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7873 (mtpt) outliers start: 47 outliers final: 22 residues processed: 136 average time/residue: 0.6750 time to fit residues: 100.0675 Evaluate side-chains 115 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 87 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 822 THR Chi-restraints excluded: chain A residue 825 GLU Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 1000 LYS Chi-restraints excluded: chain A residue 1039 GLN Chi-restraints excluded: chain A residue 1087 GLU Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1359 LYS Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1408 VAL Chi-restraints excluded: chain A residue 1477 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 14 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 144 optimal weight: 20.0000 chunk 66 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 146 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 813 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.133647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.092054 restraints weight = 19626.241| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.89 r_work: 0.3044 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14317 Z= 0.169 Angle : 0.538 15.885 20038 Z= 0.300 Chirality : 0.038 0.222 2280 Planarity : 0.004 0.077 2055 Dihedral : 19.716 176.750 3562 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.24 % Allowed : 25.26 % Favored : 71.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.24 (0.23), residues: 1357 helix: 2.03 (0.19), residues: 702 sheet: -0.32 (0.46), residues: 124 loop : -0.51 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 771 TYR 0.020 0.002 TYR A1387 PHE 0.017 0.001 PHE A 435 TRP 0.014 0.001 TRP A 30 HIS 0.003 0.001 HIS A 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.17 (14317) covalent geometry : angle 0.53806 / 0.30 (20038) hydrogen bonds : bond 0.04807 / 3.25 ( 715) hydrogen bonds : angle 3.82497 / 2.79 ( 1909) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 87 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.8170 (ttp80) cc_final: 0.7375 (ttm170) REVERT: A 86 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8781 (mm) REVERT: A 284 LYS cc_start: 0.6931 (OUTLIER) cc_final: 0.6511 (mttm) REVERT: A 322 GLU cc_start: 0.6751 (mt-10) cc_final: 0.6527 (mt-10) REVERT: A 326 LYS cc_start: 0.6555 (tttt) cc_final: 0.6024 (mtmt) REVERT: A 413 ARG cc_start: 0.7020 (ttm170) cc_final: 0.6580 (mtt90) REVERT: A 485 LEU cc_start: 0.5842 (OUTLIER) cc_final: 0.5394 (mt) REVERT: A 541 ARG cc_start: 0.8537 (ptp-110) cc_final: 0.8084 (ptt90) REVERT: A 624 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.7854 (mp) REVERT: A 652 ARG cc_start: 0.8046 (ttt-90) cc_final: 0.7591 (tpm170) REVERT: A 696 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8302 (mm-30) REVERT: A 736 LYS cc_start: 0.8236 (pttt) cc_final: 0.7609 (ptpt) REVERT: A 825 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7550 (mm-30) REVERT: A 878 MET cc_start: 0.8456 (ttm) cc_final: 0.8075 (ttp) REVERT: A 1158 LYS cc_start: 0.8912 (mtpp) cc_final: 0.8640 (mtmt) REVERT: A 1245 SER cc_start: 0.8012 (m) cc_final: 0.7765 (m) REVERT: A 1247 VAL cc_start: 0.9205 (t) cc_final: 0.8970 (p) REVERT: A 1309 LYS cc_start: 0.8134 (tppt) cc_final: 0.7490 (tptp) REVERT: A 1329 MET cc_start: 0.2818 (mmp) cc_final: 0.2358 (mtp) REVERT: A 1352 ASP cc_start: 0.7863 (t70) cc_final: 0.7226 (t0) REVERT: A 1359 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7881 (mtpt) REVERT: A 1464 GLU cc_start: 0.8346 (tp30) cc_final: 0.7645 (tm-30) outliers start: 34 outliers final: 25 residues processed: 119 average time/residue: 0.7073 time to fit residues: 91.4086 Evaluate side-chains 116 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 85 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 PHE Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 822 THR Chi-restraints excluded: chain A residue 825 GLU Chi-restraints excluded: chain A residue 851 ASP Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 1039 GLN Chi-restraints excluded: chain A residue 1087 GLU Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1359 LYS Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1408 VAL Chi-restraints excluded: chain A residue 1477 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 124 optimal weight: 0.0000 chunk 7 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 148 optimal weight: 20.0000 chunk 29 optimal weight: 10.0000 chunk 121 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 71 optimal weight: 0.2980 chunk 15 optimal weight: 2.9990 chunk 141 optimal weight: 8.9990 chunk 65 optimal weight: 0.2980 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 813 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.135513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.094211 restraints weight = 19729.989| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.90 r_work: 0.3080 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14317 Z= 0.125 Angle : 0.500 15.919 20038 Z= 0.283 Chirality : 0.036 0.211 2280 Planarity : 0.004 0.062 2055 Dihedral : 19.607 179.609 3562 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.43 % Allowed : 25.07 % Favored : 71.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.43 (0.23), residues: 1357 helix: 2.19 (0.19), residues: 702 sheet: -0.28 (0.46), residues: 124 loop : -0.41 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A 771 TYR 0.018 0.001 TYR A1387 PHE 0.015 0.001 PHE A 435 TRP 0.017 0.001 TRP A 30 HIS 0.003 0.001 HIS A 876 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 (14317) covalent geometry : angle 0.49967 / 0.28 (20038) hydrogen bonds : bond 0.04318 / 2.93 ( 715) hydrogen bonds : angle 3.68926 / 2.68 ( 1909) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 87 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.8117 (ttp80) cc_final: 0.7378 (ttm170) REVERT: A 86 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8766 (mm) REVERT: A 284 LYS cc_start: 0.6969 (OUTLIER) cc_final: 0.6546 (mttm) REVERT: A 326 LYS cc_start: 0.6590 (tttt) cc_final: 0.5994 (mtmt) REVERT: A 413 ARG cc_start: 0.6989 (ttm170) cc_final: 0.6549 (mtt90) REVERT: A 485 LEU cc_start: 0.5874 (OUTLIER) cc_final: 0.5486 (mt) REVERT: A 652 ARG cc_start: 0.8044 (ttt-90) cc_final: 0.7593 (tpm170) REVERT: A 696 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8273 (mm-30) REVERT: A 736 LYS cc_start: 0.8210 (pttt) cc_final: 0.7574 (ptpt) REVERT: A 825 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7465 (mm-30) REVERT: A 878 MET cc_start: 0.8408 (ttm) cc_final: 0.8016 (ttp) REVERT: A 939 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8050 (mm-30) REVERT: A 1000 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.8082 (ptpp) REVERT: A 1022 GLU cc_start: 0.8979 (mm-30) cc_final: 0.8764 (mm-30) REVERT: A 1158 LYS cc_start: 0.8912 (mtpp) cc_final: 0.8641 (mtmt) REVERT: A 1245 SER cc_start: 0.8018 (m) cc_final: 0.7779 (m) REVERT: A 1247 VAL cc_start: 0.9196 (t) cc_final: 0.8967 (p) REVERT: A 1309 LYS cc_start: 0.8121 (tppt) cc_final: 0.7431 (tptp) REVERT: A 1329 MET cc_start: 0.2802 (mmp) cc_final: 0.2356 (mtp) REVERT: A 1352 ASP cc_start: 0.7871 (t70) cc_final: 0.7261 (t0) REVERT: A 1464 GLU cc_start: 0.8363 (tp30) cc_final: 0.7676 (tm-30) outliers start: 36 outliers final: 22 residues processed: 120 average time/residue: 0.7345 time to fit residues: 95.6010 Evaluate side-chains 112 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 84 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 PHE Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 822 THR Chi-restraints excluded: chain A residue 825 GLU Chi-restraints excluded: chain A residue 851 ASP Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 939 GLU Chi-restraints excluded: chain A residue 1000 LYS Chi-restraints excluded: chain A residue 1039 GLN Chi-restraints excluded: chain A residue 1087 GLU Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1408 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 94 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 104 optimal weight: 2.9990 chunk 130 optimal weight: 0.0670 chunk 7 optimal weight: 0.7980 chunk 46 optimal weight: 10.0000 chunk 124 optimal weight: 0.4980 chunk 20 optimal weight: 8.9990 chunk 122 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 19 optimal weight: 0.8980 overall best weight: 1.0520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 813 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.135474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.093766 restraints weight = 19748.241| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.96 r_work: 0.3071 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14317 Z= 0.128 Angle : 0.501 15.802 20038 Z= 0.281 Chirality : 0.036 0.209 2280 Planarity : 0.004 0.062 2055 Dihedral : 19.533 179.550 3562 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.24 % Allowed : 25.36 % Favored : 71.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.49 (0.23), residues: 1357 helix: 2.21 (0.19), residues: 710 sheet: -0.32 (0.45), residues: 124 loop : -0.36 (0.27), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 771 TYR 0.018 0.001 TYR A1387 PHE 0.016 0.001 PHE A 435 TRP 0.017 0.001 TRP A 30 HIS 0.002 0.001 HIS A 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.13 (14317) covalent geometry : angle 0.50083 / 0.28 (20038) hydrogen bonds : bond 0.04219 / 2.86 ( 715) hydrogen bonds : angle 3.62890 / 2.63 ( 1909) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 89 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.8002 (ttp80) cc_final: 0.7246 (ttm170) REVERT: A 86 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8660 (mm) REVERT: A 284 LYS cc_start: 0.6846 (OUTLIER) cc_final: 0.6444 (mttm) REVERT: A 326 LYS cc_start: 0.6651 (tttt) cc_final: 0.6026 (mtmt) REVERT: A 413 ARG cc_start: 0.6880 (ttm170) cc_final: 0.6459 (mtt90) REVERT: A 485 LEU cc_start: 0.5864 (OUTLIER) cc_final: 0.5483 (mt) REVERT: A 541 ARG cc_start: 0.8539 (ptp-110) cc_final: 0.8061 (ptt90) REVERT: A 652 ARG cc_start: 0.8021 (ttt-90) cc_final: 0.7552 (tpm170) REVERT: A 696 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8254 (mm-30) REVERT: A 732 GLN cc_start: 0.6613 (mp10) cc_final: 0.6204 (mm110) REVERT: A 736 LYS cc_start: 0.8128 (pttt) cc_final: 0.7498 (ptpt) REVERT: A 825 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7366 (mm-30) REVERT: A 878 MET cc_start: 0.8295 (ttm) cc_final: 0.7884 (ttp) REVERT: A 939 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7979 (mm-30) REVERT: A 1022 GLU cc_start: 0.8937 (mm-30) cc_final: 0.8703 (mm-30) REVERT: A 1158 LYS cc_start: 0.8841 (mtpp) cc_final: 0.8535 (mtmt) REVERT: A 1245 SER cc_start: 0.7991 (m) cc_final: 0.7737 (m) REVERT: A 1247 VAL cc_start: 0.9134 (t) cc_final: 0.8899 (p) REVERT: A 1309 LYS cc_start: 0.8068 (tppt) cc_final: 0.7381 (tptp) REVERT: A 1329 MET cc_start: 0.3005 (mmp) cc_final: 0.2398 (mtp) REVERT: A 1352 ASP cc_start: 0.7787 (t70) cc_final: 0.7166 (t0) REVERT: A 1464 GLU cc_start: 0.8346 (tp30) cc_final: 0.7577 (tm-30) outliers start: 34 outliers final: 22 residues processed: 120 average time/residue: 0.7114 time to fit residues: 92.5576 Evaluate side-chains 113 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 86 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 PHE Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 822 THR Chi-restraints excluded: chain A residue 825 GLU Chi-restraints excluded: chain A residue 851 ASP Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 939 GLU Chi-restraints excluded: chain A residue 1087 GLU Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1408 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 37 optimal weight: 5.9990 chunk 122 optimal weight: 9.9990 chunk 116 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 47 optimal weight: 0.0040 chunk 22 optimal weight: 0.2980 chunk 0 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 73 optimal weight: 7.9990 chunk 109 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.8194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 688 GLN A 813 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.135936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.094308 restraints weight = 19867.336| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.97 r_work: 0.3080 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14317 Z= 0.117 Angle : 0.496 15.861 20038 Z= 0.279 Chirality : 0.035 0.208 2280 Planarity : 0.004 0.060 2055 Dihedral : 19.527 179.262 3562 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.57 % Allowed : 25.93 % Favored : 71.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.53 (0.23), residues: 1357 helix: 2.24 (0.19), residues: 710 sheet: -0.31 (0.45), residues: 124 loop : -0.33 (0.27), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 771 TYR 0.019 0.001 TYR A1387 PHE 0.017 0.001 PHE A 435 TRP 0.015 0.001 TRP A1102 HIS 0.002 0.001 HIS A 556 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.12 (14317) covalent geometry : angle 0.49649 / 0.28 (20038) hydrogen bonds : bond 0.04139 / 2.81 ( 715) hydrogen bonds : angle 3.58770 / 2.60 ( 1909) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5416.17 seconds wall clock time: 92 minutes 58.16 seconds (5578.16 seconds total)