Starting phenix.real_space_refine on Fri Jul 3 10:39:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kln_62410/07_2026/9kln_62410.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kln_62410/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9kln_62410/07_2026/9kln_62410.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kln_62410/07_2026/9kln_62410.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kln_62410/07_2026/9kln_62410.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kln_62410/07_2026/9kln_62410.map" } 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-dev-6108/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: 3.29, per 1000 atoms: 0.24 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: 1.22 Conformation dependent library (CDL) restraints added in 570.2 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: 1.67 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: 4.26 Time building geometry restraints manager: 1.60 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: 18947 1.70 - 3.39: 809 3.39 - 5.09: 170 5.09 - 6.79: 98 6.79 - 8.48: 14 Bond angle restraints: 20038 Sorted by residual: angle pdb=" O3' A B 20 " pdb=" P G B 21 " pdb=" O5' G B 21 " ideal model delta sigma weight residual 104.00 95.59 8.41 1.50e+00 4.44e-01 3.14e+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 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 angle pdb=" O4' DG C 9 " pdb=" C4' DG C 9 " pdb=" C3' DG C 9 " ideal model delta sigma weight residual 106.00 103.36 2.64 6.00e-01 2.78e+00 1.94e+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: 2109 0.115 - 0.230: 106 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: 2.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.790 Find NCS groups from input model: 0.060 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: 0.010 Load rotamer database and sin/cos tables:6.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.630 ------------------------------------------------------------------------------- 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= 0.454 Angle : 0.889 8.482 20038 Z= 0.548 Chirality : 0.085 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 0.00706 / 0.45 (14317) covalent geometry : angle 0.88946 / 0.55 (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 : 0.426 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 1245 SER cc_start: 0.8196 (t) cc_final: 0.7962 (p) 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: 0.7627 time to fit residues: 156.8053 Evaluate side-chains 101 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 97 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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: 9.9990 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 = 0.136138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.093933 restraints weight = 19722.243| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.07 r_work: 0.3080 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14317 Z= 0.165 Angle : 0.559 10.443 20038 Z= 0.323 Chirality : 0.039 0.356 2280 Planarity : 0.005 0.062 2055 Dihedral : 20.183 177.459 3569 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.29 % Allowed : 22.69 % Favored : 73.02 % 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: 1.77 (0.20), residues: 701 sheet: -0.26 (0.47), residues: 123 loop : -0.61 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1196 TYR 0.020 0.002 TYR A1458 PHE 0.010 0.001 PHE A 386 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 0.00318 / 0.17 (14317) covalent geometry : angle 0.55926 / 0.32 (20038) hydrogen bonds : bond 0.05641 / 3.83 ( 715) hydrogen bonds : angle 4.21330 / 3.06 ( 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 152 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 107 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.8064 (ttp80) cc_final: 0.7191 (ttm170) REVERT: A 175 ASP cc_start: 0.8415 (m-30) cc_final: 0.7911 (m-30) REVERT: A 284 LYS cc_start: 0.6732 (OUTLIER) cc_final: 0.6394 (mttm) REVERT: A 326 LYS cc_start: 0.6552 (tttt) cc_final: 0.6055 (mtmt) REVERT: A 375 ASP cc_start: 0.8406 (p0) cc_final: 0.7600 (t0) REVERT: A 413 ARG cc_start: 0.6879 (ttm170) cc_final: 0.6515 (mtt90) REVERT: A 439 ARG cc_start: 0.6344 (mmm160) cc_final: 0.5651 (mpp-170) REVERT: A 485 LEU cc_start: 0.5547 (OUTLIER) cc_final: 0.5161 (mt) REVERT: A 539 LYS cc_start: 0.7039 (mtpp) cc_final: 0.6643 (mttp) REVERT: A 541 ARG cc_start: 0.8288 (ptp-110) cc_final: 0.7757 (ptt-90) REVERT: A 652 ARG cc_start: 0.8097 (ttt-90) cc_final: 0.7580 (tpm170) REVERT: A 696 GLU cc_start: 0.8530 (mm-30) cc_final: 0.7980 (mt-10) REVERT: A 732 GLN cc_start: 0.6592 (mp10) cc_final: 0.6218 (mm110) REVERT: A 780 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.7958 (tt0) REVERT: A 878 MET cc_start: 0.8220 (ttm) cc_final: 0.7860 (ttp) REVERT: A 939 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.8062 (mm-30) REVERT: A 1158 LYS cc_start: 0.8862 (mtpp) cc_final: 0.8638 (mtmt) REVERT: A 1245 SER cc_start: 0.8073 (t) cc_final: 0.7867 (m) REVERT: A 1247 VAL cc_start: 0.9223 (t) cc_final: 0.8911 (p) REVERT: A 1329 MET cc_start: 0.3055 (mmp) cc_final: 0.2688 (mtt) REVERT: A 1352 ASP cc_start: 0.7841 (t70) cc_final: 0.7283 (t0) REVERT: A 1400 GLU cc_start: 0.6307 (mm-30) cc_final: 0.5860 (tm-30) REVERT: A 1464 GLU cc_start: 0.8426 (mm-30) cc_final: 0.8026 (tm-30) outliers start: 45 outliers final: 17 residues processed: 146 average time/residue: 0.6841 time to fit residues: 108.4052 Evaluate side-chains 115 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 650 ILE 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 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: 3.9990 chunk 23 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 45 optimal weight: 0.0270 chunk 51 optimal weight: 3.9990 chunk 134 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 chunk 74 optimal weight: 0.0050 chunk 5 optimal weight: 4.9990 chunk 105 optimal weight: 0.8980 chunk 53 optimal weight: 0.1980 overall best weight: 0.8254 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.136855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.094637 restraints weight = 19845.838| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.07 r_work: 0.3091 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14317 Z= 0.128 Angle : 0.496 15.504 20038 Z= 0.287 Chirality : 0.037 0.362 2280 Planarity : 0.004 0.044 2055 Dihedral : 20.021 178.401 3565 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 4.29 % Allowed : 22.69 % Favored : 73.02 % 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: 1.23 (0.23), residues: 1357 helix: 2.02 (0.19), residues: 699 sheet: -0.14 (0.47), residues: 122 loop : -0.55 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1462 TYR 0.017 0.001 TYR A1387 PHE 0.010 0.001 PHE A 562 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 0.00240 / 0.13 (14317) covalent geometry : angle 0.49590 / 0.29 (20038) hydrogen bonds : bond 0.04875 / 3.28 ( 715) hydrogen bonds : angle 3.91719 / 2.85 ( 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 142 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 97 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.8078 (ttp80) cc_final: 0.7249 (ttm170) REVERT: A 326 LYS cc_start: 0.6546 (tttt) cc_final: 0.6030 (mtmt) REVERT: A 375 ASP cc_start: 0.8386 (p0) cc_final: 0.7464 (t0) REVERT: A 413 ARG cc_start: 0.6947 (ttm170) cc_final: 0.6540 (mtt90) REVERT: A 485 LEU cc_start: 0.5650 (OUTLIER) cc_final: 0.5254 (mt) REVERT: A 541 ARG cc_start: 0.8315 (ptp-110) cc_final: 0.7790 (ptt-90) REVERT: A 624 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.7794 (mp) REVERT: A 652 ARG cc_start: 0.8079 (ttt-90) cc_final: 0.7571 (tpm170) REVERT: A 696 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8269 (mm-30) REVERT: A 732 GLN cc_start: 0.6674 (mp10) cc_final: 0.6286 (mm110) REVERT: A 780 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8164 (tt0) REVERT: A 813 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8428 (mm-40) REVERT: A 878 MET cc_start: 0.8231 (ttm) cc_final: 0.7893 (ttp) REVERT: A 939 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.8073 (mm-30) REVERT: A 1158 LYS cc_start: 0.8880 (mtpp) cc_final: 0.8582 (mtmt) REVERT: A 1245 SER cc_start: 0.7969 (t) cc_final: 0.7551 (p) REVERT: A 1247 VAL cc_start: 0.9224 (t) cc_final: 0.8931 (p) REVERT: A 1329 MET cc_start: 0.2992 (mmp) cc_final: 0.2704 (mtt) REVERT: A 1352 ASP cc_start: 0.7874 (t70) cc_final: 0.7344 (t0) REVERT: A 1359 LYS cc_start: 0.8040 (OUTLIER) cc_final: 0.7712 (mtpt) REVERT: A 1400 GLU cc_start: 0.6373 (mm-30) cc_final: 0.6080 (tm-30) REVERT: A 1464 GLU cc_start: 0.8416 (mm-30) cc_final: 0.8035 (tm-30) outliers start: 45 outliers final: 16 residues processed: 137 average time/residue: 0.6527 time to fit residues: 97.0818 Evaluate side-chains 113 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.436 ------------------------------------------------------------------------------- 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 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 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: 4.9990 chunk 133 optimal weight: 9.9990 chunk 104 optimal weight: 0.6980 chunk 149 optimal weight: 9.9990 chunk 135 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 129 optimal weight: 0.0670 overall best weight: 2.3524 ------------------------------------------------------------------------------- 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 = 0.3795 r_free = 0.3795 target = 0.135556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.094222 restraints weight = 20927.699| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.03 r_work: 0.3117 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 14317 Z= 0.217 Angle : 0.548 13.565 20038 Z= 0.311 Chirality : 0.040 0.410 2280 Planarity : 0.005 0.043 2055 Dihedral : 19.967 177.839 3565 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.58 % Allowed : 23.16 % Favored : 72.26 % 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: 700 sheet: -0.20 (0.47), residues: 122 loop : -0.57 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1462 TYR 0.016 0.002 TYR A1458 PHE 0.015 0.001 PHE A 386 TRP 0.018 0.002 TRP A 30 HIS 0.004 0.001 HIS A 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.22 (14317) covalent geometry : angle 0.54802 / 0.31 (20038) hydrogen bonds : bond 0.05090 / 3.43 ( 715) hydrogen bonds : angle 3.93180 / 2.87 ( 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 143 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 95 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.8128 (ttp80) cc_final: 0.7319 (ttm170) REVERT: A 326 LYS cc_start: 0.6656 (tttt) cc_final: 0.6113 (mtmt) REVERT: A 413 ARG cc_start: 0.6942 (ttm170) cc_final: 0.6553 (mtt90) REVERT: A 485 LEU cc_start: 0.5708 (OUTLIER) cc_final: 0.5291 (mt) REVERT: A 624 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.7829 (mp) REVERT: A 652 ARG cc_start: 0.8037 (ttt-90) cc_final: 0.7551 (tpm170) REVERT: A 696 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8349 (mm-30) REVERT: A 825 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7777 (mm-30) REVERT: A 982 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7613 (mt-10) REVERT: A 1158 LYS cc_start: 0.8883 (mtpp) cc_final: 0.8587 (mtmt) REVERT: A 1247 VAL cc_start: 0.9232 (t) cc_final: 0.8971 (p) REVERT: A 1329 MET cc_start: 0.2769 (mmp) cc_final: 0.2464 (mtt) REVERT: A 1352 ASP cc_start: 0.7901 (t70) cc_final: 0.7348 (t0) REVERT: A 1359 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7837 (mtpt) REVERT: A 1400 GLU cc_start: 0.6340 (mm-30) cc_final: 0.6100 (tm-30) REVERT: A 1464 GLU cc_start: 0.8379 (mm-30) cc_final: 0.8012 (tm-30) outliers start: 48 outliers final: 21 residues processed: 139 average time/residue: 0.6902 time to fit residues: 103.7000 Evaluate side-chains 116 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 90 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 PHE 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 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: 0.9980 chunk 101 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 114 optimal weight: 8.9990 chunk 119 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 505 GLN A1306 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.137127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.095909 restraints weight = 20922.964| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.02 r_work: 0.3147 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14317 Z= 0.139 Angle : 0.495 14.646 20038 Z= 0.284 Chirality : 0.037 0.407 2280 Planarity : 0.004 0.044 2055 Dihedral : 19.872 179.019 3565 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.81 % Allowed : 24.50 % Favored : 71.69 % 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: 1.32 (0.23), residues: 1357 helix: 2.09 (0.19), residues: 701 sheet: -0.23 (0.46), residues: 124 loop : -0.49 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1462 TYR 0.013 0.001 TYR A 931 PHE 0.010 0.001 PHE A 386 TRP 0.016 0.001 TRP A 30 HIS 0.003 0.001 HIS A 876 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.14 (14317) covalent geometry : angle 0.49485 / 0.28 (20038) hydrogen bonds : bond 0.04558 / 3.08 ( 715) hydrogen bonds : angle 3.80443 / 2.77 ( 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 135 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 95 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.8084 (ttp80) cc_final: 0.7317 (ttm170) REVERT: A 326 LYS cc_start: 0.6639 (tttt) cc_final: 0.6052 (mtmt) REVERT: A 330 SER cc_start: 0.7584 (m) cc_final: 0.7316 (p) REVERT: A 413 ARG cc_start: 0.6945 (ttm170) cc_final: 0.6551 (mtt90) REVERT: A 485 LEU cc_start: 0.5706 (OUTLIER) cc_final: 0.5253 (mt) REVERT: A 541 ARG cc_start: 0.8509 (ptp-110) cc_final: 0.8088 (ptt90) REVERT: A 652 ARG cc_start: 0.8023 (ttt-90) cc_final: 0.7552 (tpm170) REVERT: A 696 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8354 (mm-30) REVERT: A 732 GLN cc_start: 0.6716 (mp10) cc_final: 0.6223 (mm110) REVERT: A 771 ARG cc_start: 0.7501 (ptm-80) cc_final: 0.7298 (ptm160) REVERT: A 825 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7762 (mm-30) REVERT: A 939 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8063 (mm-30) REVERT: A 982 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7530 (mm-30) REVERT: A 1000 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.8048 (ptpp) REVERT: A 1158 LYS cc_start: 0.8878 (mtpp) cc_final: 0.8594 (mtmt) REVERT: A 1247 VAL cc_start: 0.9211 (t) cc_final: 0.8968 (p) REVERT: A 1329 MET cc_start: 0.2871 (mmp) cc_final: 0.2558 (mtt) REVERT: A 1352 ASP cc_start: 0.7870 (t70) cc_final: 0.7317 (t0) REVERT: A 1359 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7796 (mtpt) REVERT: A 1464 GLU cc_start: 0.8348 (mm-30) cc_final: 0.7926 (tm-30) outliers start: 40 outliers final: 20 residues processed: 131 average time/residue: 0.6107 time to fit residues: 86.9019 Evaluate side-chains 118 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 PHE 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 643 LEU Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 691 SER 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 939 GLU Chi-restraints excluded: chain A residue 943 SER 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 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: 5.9990 chunk 111 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 92 optimal weight: 0.0970 chunk 93 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 128 optimal weight: 0.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 = 0.3811 r_free = 0.3811 target = 0.136919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.095675 restraints weight = 20766.579| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.01 r_work: 0.3139 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 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 0.030 14317 Z= 0.151 Angle : 0.498 15.533 20038 Z= 0.285 Chirality : 0.038 0.411 2280 Planarity : 0.004 0.040 2055 Dihedral : 19.759 179.576 3565 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.00 % Allowed : 24.79 % Favored : 71.21 % 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: 1.41 (0.23), residues: 1357 helix: 2.19 (0.19), residues: 702 sheet: -0.29 (0.46), residues: 124 loop : -0.45 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1462 TYR 0.017 0.001 TYR A1458 PHE 0.012 0.001 PHE A 435 TRP 0.015 0.001 TRP A 30 HIS 0.003 0.001 HIS A 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.15 (14317) covalent geometry : angle 0.49780 / 0.28 (20038) hydrogen bonds : bond 0.04470 / 3.02 ( 715) hydrogen bonds : angle 3.70375 / 2.70 ( 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: 42 poor density : 91 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.8099 (ttp80) cc_final: 0.7350 (ttm170) REVERT: A 326 LYS cc_start: 0.6645 (tttt) cc_final: 0.6041 (mtmt) REVERT: A 413 ARG cc_start: 0.6949 (ttm170) cc_final: 0.6544 (mtt90) REVERT: A 485 LEU cc_start: 0.5896 (OUTLIER) cc_final: 0.5442 (mt) REVERT: A 541 ARG cc_start: 0.8539 (ptp-110) cc_final: 0.8056 (ptt90) REVERT: A 652 ARG cc_start: 0.8013 (ttt-90) cc_final: 0.7598 (tpm170) REVERT: A 696 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8373 (mm-30) REVERT: A 771 ARG cc_start: 0.7545 (ptm-80) cc_final: 0.7345 (ptm160) REVERT: A 825 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7711 (mm-30) REVERT: A 939 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8055 (mm-30) REVERT: A 1000 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.8061 (ptpp) REVERT: A 1158 LYS cc_start: 0.8881 (mtpp) cc_final: 0.8589 (mtmt) REVERT: A 1247 VAL cc_start: 0.9201 (t) cc_final: 0.8958 (p) REVERT: A 1309 LYS cc_start: 0.8201 (tppt) cc_final: 0.7634 (tptp) REVERT: A 1329 MET cc_start: 0.2725 (mmp) cc_final: 0.2517 (mtp) REVERT: A 1352 ASP cc_start: 0.7860 (t70) cc_final: 0.7298 (t0) REVERT: A 1359 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7838 (mtpt) REVERT: A 1464 GLU cc_start: 0.8344 (mm-30) cc_final: 0.7897 (tm-30) outliers start: 42 outliers final: 23 residues processed: 129 average time/residue: 0.6750 time to fit residues: 94.6221 Evaluate side-chains 114 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 86 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 PHE Chi-restraints excluded: chain A residue 165 VAL 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 709 LEU Chi-restraints excluded: chain A residue 813 GLN 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 939 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 22 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 137 optimal weight: 5.9990 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: 7.9990 chunk 56 optimal weight: 0.9990 chunk 148 optimal weight: 20.0000 chunk 43 optimal weight: 0.7980 overall best weight: 2.7586 ------------------------------------------------------------------------------- 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 = 0.3751 r_free = 0.3751 target = 0.133009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.091289 restraints weight = 19647.944| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.91 r_work: 0.3031 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 14317 Z= 0.237 Angle : 0.552 15.241 20038 Z= 0.311 Chirality : 0.041 0.426 2280 Planarity : 0.004 0.037 2055 Dihedral : 19.754 177.383 3562 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 4.67 % Allowed : 23.93 % 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: 1.26 (0.23), residues: 1357 helix: 2.05 (0.19), residues: 703 sheet: -0.32 (0.46), residues: 124 loop : -0.52 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1462 TYR 0.015 0.002 TYR A 829 PHE 0.016 0.002 PHE A 386 TRP 0.014 0.002 TRP A1102 HIS 0.005 0.001 HIS A 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.24 (14317) covalent geometry : angle 0.55201 / 0.31 (20038) hydrogen bonds : bond 0.04995 / 3.36 ( 715) hydrogen bonds : angle 3.84584 / 2.80 ( 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 140 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 91 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.8185 (ttp80) cc_final: 0.7378 (ttm170) REVERT: A 86 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8815 (mm) REVERT: A 326 LYS cc_start: 0.6608 (tttt) cc_final: 0.6027 (mtmt) REVERT: A 413 ARG cc_start: 0.7014 (ttm170) cc_final: 0.6569 (mtt90) REVERT: A 485 LEU cc_start: 0.5878 (OUTLIER) cc_final: 0.5410 (mt) REVERT: A 505 GLN cc_start: 0.6096 (OUTLIER) cc_final: 0.5648 (mp-120) REVERT: A 652 ARG cc_start: 0.8041 (ttt-90) cc_final: 0.7593 (tpm170) REVERT: A 696 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8303 (mm-30) REVERT: A 736 LYS cc_start: 0.8250 (pttt) cc_final: 0.7636 (ptpt) REVERT: A 939 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8136 (mm-30) REVERT: A 1000 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.8160 (ptpp) REVERT: A 1158 LYS cc_start: 0.8923 (mtpp) cc_final: 0.8646 (mtmt) REVERT: A 1247 VAL cc_start: 0.9188 (t) cc_final: 0.8951 (p) REVERT: A 1309 LYS cc_start: 0.8199 (tppt) cc_final: 0.7618 (tptp) REVERT: A 1329 MET cc_start: 0.2811 (mmp) cc_final: 0.2377 (mtp) REVERT: A 1352 ASP cc_start: 0.7909 (t70) cc_final: 0.7286 (t0) REVERT: A 1359 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7892 (mtpt) outliers start: 49 outliers final: 22 residues processed: 134 average time/residue: 0.5978 time to fit residues: 87.0340 Evaluate side-chains 114 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 86 time to evaluate : 0.428 ------------------------------------------------------------------------------- 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 351 CYS Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 505 GLN 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 768 LEU Chi-restraints excluded: chain A residue 822 THR 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 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: 3.9990 chunk 144 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 146 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 = 0.3742 r_free = 0.3742 target = 0.132351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.090742 restraints weight = 19676.956| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.90 r_work: 0.3022 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 14317 Z= 0.238 Angle : 0.564 15.695 20038 Z= 0.318 Chirality : 0.041 0.435 2280 Planarity : 0.005 0.037 2055 Dihedral : 19.788 177.378 3562 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.81 % Allowed : 24.98 % Favored : 71.21 % 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: 1.14 (0.23), residues: 1357 helix: 1.95 (0.19), residues: 703 sheet: -0.36 (0.46), residues: 124 loop : -0.56 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 771 TYR 0.018 0.002 TYR A1458 PHE 0.015 0.002 PHE A 386 TRP 0.014 0.002 TRP A1102 HIS 0.005 0.001 HIS A 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.24 (14317) covalent geometry : angle 0.56428 / 0.32 (20038) hydrogen bonds : bond 0.05071 / 3.43 ( 715) hydrogen bonds : angle 3.92405 / 2.86 ( 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 124 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 84 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: A 41 ARG cc_start: 0.8206 (ttp80) cc_final: 0.7432 (ttm170) REVERT: A 86 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8794 (mm) REVERT: A 326 LYS cc_start: 0.6583 (tttt) cc_final: 0.6008 (mtmt) REVERT: A 413 ARG cc_start: 0.7038 (ttm170) cc_final: 0.6586 (mtt90) REVERT: A 485 LEU cc_start: 0.5854 (OUTLIER) cc_final: 0.5471 (mt) REVERT: A 505 GLN cc_start: 0.6232 (OUTLIER) cc_final: 0.5774 (mp-120) REVERT: A 541 ARG cc_start: 0.8568 (ptp-110) cc_final: 0.8065 (ptt90) REVERT: A 652 ARG cc_start: 0.8078 (ttt-90) cc_final: 0.7599 (tpm170) REVERT: A 696 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8240 (mm-30) REVERT: A 736 LYS cc_start: 0.8253 (pttt) cc_final: 0.7631 (ptpt) REVERT: A 825 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7501 (mm-30) REVERT: A 939 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8179 (mm-30) REVERT: A 1000 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.8104 (ptpp) REVERT: A 1158 LYS cc_start: 0.8943 (mtpp) cc_final: 0.8657 (mtmt) REVERT: A 1247 VAL cc_start: 0.9186 (t) cc_final: 0.8952 (p) REVERT: A 1309 LYS cc_start: 0.8208 (tppt) cc_final: 0.7499 (tptp) REVERT: A 1329 MET cc_start: 0.3046 (mmp) cc_final: 0.2420 (mtp) REVERT: A 1352 ASP cc_start: 0.7876 (t70) cc_final: 0.7237 (t0) REVERT: A 1464 GLU cc_start: 0.8411 (tp30) cc_final: 0.7855 (tm-30) outliers start: 40 outliers final: 20 residues processed: 122 average time/residue: 0.7091 time to fit residues: 93.6450 Evaluate side-chains 108 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 82 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 351 CYS Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 505 GLN 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 939 GLU 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 1394 THR Chi-restraints excluded: chain A residue 1408 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 124 optimal weight: 0.0070 chunk 7 optimal weight: 0.0270 chunk 70 optimal weight: 5.9990 chunk 148 optimal weight: 20.0000 chunk 29 optimal weight: 9.9990 chunk 121 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 141 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 overall best weight: 1.2060 ------------------------------------------------------------------------------- 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 = 0.3770 r_free = 0.3770 target = 0.134343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.092499 restraints weight = 19805.651| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.96 r_work: 0.3049 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14317 Z= 0.137 Angle : 0.504 15.987 20038 Z= 0.288 Chirality : 0.037 0.422 2280 Planarity : 0.004 0.037 2055 Dihedral : 19.726 178.739 3562 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.96 % Allowed : 26.22 % Favored : 70.83 % 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: 1.39 (0.23), residues: 1357 helix: 2.15 (0.19), residues: 703 sheet: -0.25 (0.47), residues: 124 loop : -0.45 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1462 TYR 0.013 0.001 TYR A 931 PHE 0.018 0.001 PHE A 435 TRP 0.022 0.001 TRP A 431 HIS 0.003 0.001 HIS A 876 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.14 (14317) covalent geometry : angle 0.50380 / 0.29 (20038) hydrogen bonds : bond 0.04454 / 3.03 ( 715) hydrogen bonds : angle 3.76518 / 2.74 ( 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 117 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 86 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: A 41 ARG cc_start: 0.8015 (ttp80) cc_final: 0.7237 (ttm170) REVERT: A 86 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8673 (mm) REVERT: A 326 LYS cc_start: 0.6556 (tttt) cc_final: 0.5980 (mtmt) REVERT: A 413 ARG cc_start: 0.6945 (ttm170) cc_final: 0.6511 (mtt90) REVERT: A 485 LEU cc_start: 0.5861 (OUTLIER) cc_final: 0.5489 (mt) REVERT: A 505 GLN cc_start: 0.6260 (OUTLIER) cc_final: 0.6025 (mp-120) REVERT: A 541 ARG cc_start: 0.8528 (ptp-110) cc_final: 0.8030 (ptt90) REVERT: A 652 ARG cc_start: 0.8038 (ttt-90) cc_final: 0.7563 (tpm170) REVERT: A 736 LYS cc_start: 0.8156 (pttt) cc_final: 0.7535 (ptpt) REVERT: A 825 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7407 (mm-30) REVERT: A 878 MET cc_start: 0.8336 (ttm) cc_final: 0.7910 (ttp) REVERT: A 939 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.8075 (mm-30) REVERT: A 1158 LYS cc_start: 0.8804 (mtpp) cc_final: 0.8507 (mtmt) REVERT: A 1247 VAL cc_start: 0.9136 (t) cc_final: 0.8902 (p) REVERT: A 1309 LYS cc_start: 0.8175 (tppt) cc_final: 0.7467 (tptp) REVERT: A 1329 MET cc_start: 0.3058 (mmp) cc_final: 0.2416 (mtp) REVERT: A 1352 ASP cc_start: 0.7788 (t70) cc_final: 0.7116 (t0) outliers start: 31 outliers final: 19 residues processed: 113 average time/residue: 0.6610 time to fit residues: 81.0411 Evaluate side-chains 108 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 0.457 ------------------------------------------------------------------------------- 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 351 CYS Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 505 GLN 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 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 1039 GLN Chi-restraints excluded: chain A residue 1087 GLU Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1320 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: 4.9990 chunk 97 optimal weight: 10.0000 chunk 104 optimal weight: 2.9990 chunk 130 optimal weight: 10.0000 chunk 7 optimal weight: 0.6980 chunk 46 optimal weight: 10.0000 chunk 124 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 122 optimal weight: 9.9990 chunk 45 optimal weight: 7.9990 chunk 19 optimal weight: 0.8980 overall best weight: 3.3186 ------------------------------------------------------------------------------- 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 = 0.3733 r_free = 0.3733 target = 0.131509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.089548 restraints weight = 19800.665| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.99 r_work: 0.3001 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 14317 Z= 0.277 Angle : 0.587 15.397 20038 Z= 0.328 Chirality : 0.043 0.437 2280 Planarity : 0.005 0.042 2055 Dihedral : 19.760 176.859 3562 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.05 % Allowed : 26.22 % Favored : 70.73 % 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: 1.14 (0.22), residues: 1357 helix: 1.94 (0.19), residues: 703 sheet: -0.35 (0.46), residues: 125 loop : -0.56 (0.26), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 771 TYR 0.018 0.002 TYR A1387 PHE 0.018 0.002 PHE A 435 TRP 0.026 0.002 TRP A 431 HIS 0.005 0.001 HIS A 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00596 / 0.28 (14317) covalent geometry : angle 0.58660 / 0.33 (20038) hydrogen bonds : bond 0.05260 / 3.55 ( 715) hydrogen bonds : angle 3.94347 / 2.88 ( 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 118 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 86 time to evaluate : 0.776 Fit side-chains revert: symmetry clash REVERT: A 41 ARG cc_start: 0.8060 (ttp80) cc_final: 0.7258 (ttm170) REVERT: A 86 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8728 (mm) REVERT: A 326 LYS cc_start: 0.6626 (tttt) cc_final: 0.6045 (mtmt) REVERT: A 413 ARG cc_start: 0.6952 (ttm170) cc_final: 0.6499 (mtt90) REVERT: A 454 ARG cc_start: 0.7491 (ttt180) cc_final: 0.7022 (tpt90) REVERT: A 485 LEU cc_start: 0.5812 (OUTLIER) cc_final: 0.5462 (mt) REVERT: A 505 GLN cc_start: 0.6273 (OUTLIER) cc_final: 0.5877 (mp-120) REVERT: A 541 ARG cc_start: 0.8511 (ptp-110) cc_final: 0.7955 (ptt90) REVERT: A 652 ARG cc_start: 0.8079 (ttt-90) cc_final: 0.7565 (tpm170) REVERT: A 736 LYS cc_start: 0.8195 (pttt) cc_final: 0.7553 (ptpt) REVERT: A 825 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7420 (mm-30) REVERT: A 939 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8160 (mm-30) REVERT: A 1158 LYS cc_start: 0.8889 (mtpp) cc_final: 0.8567 (mtmt) REVERT: A 1247 VAL cc_start: 0.9128 (t) cc_final: 0.8883 (p) REVERT: A 1309 LYS cc_start: 0.8163 (tppt) cc_final: 0.7352 (tptt) REVERT: A 1329 MET cc_start: 0.2913 (mmp) cc_final: 0.2137 (mtt) REVERT: A 1352 ASP cc_start: 0.7790 (t70) cc_final: 0.7111 (t0) outliers start: 32 outliers final: 17 residues processed: 114 average time/residue: 0.6938 time to fit residues: 85.6252 Evaluate side-chains 107 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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 351 CYS Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 505 GLN 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 822 THR Chi-restraints excluded: chain A residue 825 GLU Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 939 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 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: 1.9990 chunk 122 optimal weight: 10.0000 chunk 116 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 47 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 109 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.3760 r_free = 0.3760 target = 0.133630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.091842 restraints weight = 19856.743| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 1.96 r_work: 0.3037 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.3203 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= 0.141 Angle : 0.529 16.699 20038 Z= 0.297 Chirality : 0.038 0.419 2280 Planarity : 0.004 0.043 2055 Dihedral : 19.768 176.817 3562 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.38 % Allowed : 26.79 % Favored : 70.83 % 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: 1.31 (0.23), residues: 1357 helix: 2.07 (0.19), residues: 703 sheet: -0.27 (0.47), residues: 124 loop : -0.46 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 771 TYR 0.021 0.002 TYR A1387 PHE 0.024 0.001 PHE A 435 TRP 0.037 0.002 TRP A 431 HIS 0.003 0.001 HIS A 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.14 (14317) covalent geometry : angle 0.52861 / 0.30 (20038) hydrogen bonds : bond 0.04623 / 3.14 ( 715) hydrogen bonds : angle 3.81507 / 2.79 ( 1909) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5201.02 seconds wall clock time: 89 minutes 7.45 seconds (5347.45 seconds total)