Starting phenix.refine on Fri Dec 27 17:58:26 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4811713.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4811713.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4811713.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } pdb_interpretation { nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.61, per 1000 atoms: 0.48 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.43 Conformation dependent library (CDL) restraints added in 108.2 milliseconds Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.63 - 0.89: 408 0.89 - 1.16: 1214 1.16 - 1.42: 658 1.42 - 1.68: 840 1.68 - 1.95: 33 Bond restraints: 3153 Sorted by residual: bond pdb=" CA THR A 34 " pdb=" C THR A 34 " ideal model delta sigma weight residual 1.523 1.283 0.240 1.23e-02 6.61e+03 3.80e+02 bond pdb=" C ALA A 111 " pdb=" N LEU A 112 " ideal model delta sigma weight residual 1.334 1.099 0.236 1.33e-02 5.65e+03 3.14e+02 bond pdb=" C GLN A 180 " pdb=" N VAL A 181 " ideal model delta sigma weight residual 1.335 1.528 -0.193 1.09e-02 8.42e+03 3.13e+02 bond pdb=" C LEU A 112 " pdb=" O LEU A 112 " ideal model delta sigma weight residual 1.237 1.439 -0.203 1.16e-02 7.43e+03 3.06e+02 bond pdb=" CA TYR A 141 " pdb=" C TYR A 141 " ideal model delta sigma weight residual 1.524 1.741 -0.217 1.25e-02 6.40e+03 3.01e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.88: 3236 4.88 - 9.75: 1905 9.75 - 14.63: 533 14.63 - 19.51: 98 19.51 - 24.38: 5 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O GLU A 16 " pdb=" C GLU A 16 " pdb=" N MET A 17 " ideal model delta sigma weight residual 122.12 139.86 -17.74 1.06e+00 8.90e-01 2.80e+02 angle pdb=" OD1AASN A 97 " pdb=" CG AASN A 97 " pdb=" ND2AASN A 97 " ideal model delta sigma weight residual 122.60 138.54 -15.94 1.00e+00 1.00e+00 2.54e+02 angle pdb=" OD1 ASN A 135 " pdb=" CG ASN A 135 " pdb=" ND2 ASN A 135 " ideal model delta sigma weight residual 122.60 108.18 14.42 1.00e+00 1.00e+00 2.08e+02 angle pdb=" C LEU A 72 " pdb=" N PRO A 73 " pdb=" CA PRO A 73 " ideal model delta sigma weight residual 120.21 107.69 12.52 9.60e-01 1.09e+00 1.70e+02 angle pdb=" CA LYS A 89 " pdb=" C LYS A 89 " pdb=" O LYS A 89 " ideal model delta sigma weight residual 120.98 107.15 13.84 1.10e+00 8.26e-01 1.58e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 940 17.50 - 35.00: 118 35.00 - 52.49: 37 52.49 - 69.99: 14 69.99 - 87.48: 2 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA LYS A 182 " pdb=" C LYS A 182 " pdb=" N ALA A 183 " pdb=" CA ALA A 183 " ideal model delta harmonic sigma weight residual -180.00 -152.82 -27.18 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" N ARG A 156 " pdb=" CA ARG A 156 " ideal model delta harmonic sigma weight residual 180.00 -155.34 -24.66 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA VAL A 123 " pdb=" C VAL A 123 " pdb=" N THR A 124 " pdb=" CA THR A 124 " ideal model delta harmonic sigma weight residual 180.00 157.53 22.47 0 5.00e+00 4.00e-02 2.02e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.215: 98 0.215 - 0.429: 75 0.429 - 0.643: 43 0.643 - 0.857: 20 0.857 - 1.071: 7 Chirality restraints: 243 Sorted by residual: chirality pdb=" CB VAL A 177 " pdb=" CA VAL A 177 " pdb=" CG1 VAL A 177 " pdb=" CG2 VAL A 177 " both_signs ideal model delta sigma weight residual False -2.63 -3.70 1.07 2.00e-01 2.50e+01 2.87e+01 chirality pdb=" CA VAL A 35 " pdb=" N VAL A 35 " pdb=" C VAL A 35 " pdb=" CB VAL A 35 " both_signs ideal model delta sigma weight residual False 2.44 3.47 -1.02 2.00e-01 2.50e+01 2.62e+01 chirality pdb=" CB VAL A 20 " pdb=" CA VAL A 20 " pdb=" CG1 VAL A 20 " pdb=" CG2 VAL A 20 " both_signs ideal model delta sigma weight residual False -2.63 -1.71 -0.92 2.00e-01 2.50e+01 2.13e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 45 " -0.018 2.00e-02 2.50e+03 8.86e-02 1.18e+02 pdb=" CD GLN A 45 " -0.135 2.00e-02 2.50e+03 pdb=" OE1 GLN A 45 " 0.100 2.00e-02 2.50e+03 pdb=" NE2 GLN A 45 " 0.065 2.00e-02 2.50e+03 pdb="HE21 GLN A 45 " 0.079 2.00e-02 2.50e+03 pdb="HE22 GLN A 45 " -0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " 0.030 2.00e-02 2.50e+03 5.99e-02 1.08e+02 pdb=" CG TYR A 141 " -0.073 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " -0.112 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " -0.047 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " 0.072 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " -0.040 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " 0.054 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " 0.066 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " 0.084 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " -0.003 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.092 2.00e-02 2.50e+03 5.81e-02 1.01e+02 pdb=" CG PHE A 119 " -0.122 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.027 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.090 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.034 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.004 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.033 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.060 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.045 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.008 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.26: 705 2.26 - 2.85: 7714 2.85 - 3.43: 10703 3.43 - 4.02: 15316 4.02 - 4.60: 22151 Nonbonded interactions: 56589 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.681 2.100 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.753 2.100 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.824 2.100 nonbonded pdb=" O VAL A 51 " pdb=" H ACYS A 53 " model vdw sym.op. 1.826 1.850 x-y,-y,-z-4/3 nonbonded pdb="HH21 ARG A 145 " pdb=" OE2 GLU A 163 " model vdw 1.835 1.850 ... (remaining 56584 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 6 Type Number sf(0) Gaussians S 10 15.96 2 O1- 2 8.97 3 O 551 7.97 2 N 265 6.97 2 C 957 5.97 2 H 1596 1.00 2 sf(0) = scattering factor at diffraction angle 0. =========================== Regularize ADP if needed ========================== ========================== Anomalous scatterer groups ========================= All atoms refined with f_prime=0 and f_double_prime=0. ====================== Modifying start model if requested ===================== ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 3381 n_use_u_iso = 1596 n_use_u_aniso = 1785 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 0 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 total number of scatterers = 3381 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (3381 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 1596 aniso = 1785) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = True (876 atoms) group_anomalous = False ============================ Non-default parameters =========================== A complete record of all parameters was written to the .eff file above. Below are only the non-defaults. #phil __ON__ refinement { electron_density_maps { map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT" mtz_label_phases = "PH2FOFCWT" fill_missing_f_obs = True } map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT_no_fill" mtz_label_phases = "PH2FOFCWT_no_fill" } map_coefficients { map_type = "mFo-DFc" mtz_label_amplitudes = "FOFCWT" mtz_label_phases = "PHFOFCWT" } map_coefficients { map_type = "anomalous" mtz_label_amplitudes = "ANOM" mtz_label_phases = "PANOM" } map { map_type = "2mFo-DFc" fill_missing_f_obs = True } map { map_type = "2mFo-DFc" } map { map_type = "mFo-DFc" } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } hydrogens { refine = individual *riding Auto } pdb_interpretation { c_beta_restraints = False nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } output { prefix = "shake_4811713_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2605 r_free= 0.1946 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.791021 | | target function (ml) not normalized (work): 232508.831690 | | target function (ml) not normalized (free): 11810.494274 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 49.25 - 3.58 1.00 2941 171 0.3031 0.2102 7.1064 4.9319| | 2: 3.57 - 2.84 1.00 2876 122 0.2438 0.1842 4.3423 4.3481| | 3: 2.84 - 2.48 1.00 2833 165 0.2322 0.1592 4.1221 4.1469| | 4: 2.47 - 2.25 1.00 2825 136 0.2330 0.1513 3.8192 3.8424| | 5: 2.25 - 2.09 1.00 2756 127 0.2501 0.1541 3.7937 3.8087| | 6: 2.09 - 1.97 1.00 2846 113 0.2513 0.1739 3.4544 3.5281| | 7: 1.97 - 1.87 1.00 2787 165 0.2583 0.1748 3.1442 3.1666| | 8: 1.87 - 1.79 1.00 2789 144 0.2468 0.1688 3.0502 3.0597| | 9: 1.79 - 1.72 1.00 2745 138 0.2396 0.2167 2.8966 3.041| | 10: 1.72 - 1.66 1.00 2789 158 0.2411 0.1992 2.8114 2.9156| | 11: 1.66 - 1.61 1.00 2740 147 0.2519 0.1765 2.7636 2.762| | 12: 1.61 - 1.56 1.00 2787 146 0.2505 0.2099 2.6228 2.6987| | 13: 1.56 - 1.52 1.00 2745 130 0.2518 0.1726 2.5468 2.5634| | 14: 1.52 - 1.48 1.00 2803 134 0.2564 0.1957 2.5001 2.5651| | 15: 1.48 - 1.45 1.00 2738 128 0.2622 0.2232 2.4389 2.4763| | 16: 1.45 - 1.42 1.00 2756 161 0.2639 0.2264 2.3947 2.5084| | 17: 1.42 - 1.39 1.00 2785 139 0.2734 0.2106 2.3338 2.3617| | 18: 1.39 - 1.36 1.00 2741 179 0.2664 0.2418 2.283 2.3263| | 19: 1.36 - 1.34 1.00 2807 134 0.2727 0.2202 2.2627 2.2532| | 20: 1.34 - 1.32 1.00 2696 147 0.2687 0.2352 2.1953 2.2162| | 21: 1.32 - 1.30 1.00 2785 112 0.2664 0.2415 2.1614 2.1816| | 22: 1.29 - 1.27 1.00 2704 152 0.2704 0.2417 2.1241 2.1457| | 23: 1.27 - 1.26 1.00 2802 156 0.2828 0.2692 2.112 2.2615| | 24: 1.26 - 1.24 1.00 2744 132 0.2835 0.2474 2.0855 2.1431| | 25: 1.24 - 1.22 1.00 2734 148 0.2758 0.2395 2.0341 2.0442| | 26: 1.22 - 1.21 1.00 2727 135 0.2838 0.2347 2.0033 2.0825| | 27: 1.21 - 1.19 1.00 2814 148 0.2975 0.2682 1.9981 2.006| | 28: 1.19 - 1.18 1.00 2671 147 0.2989 0.2706 1.9806 1.9654| | 29: 1.18 - 1.16 1.00 2800 134 0.2981 0.2717 1.9614 2.0193| | 30: 1.16 - 1.15 1.00 2740 148 0.3027 0.2751 1.9295 1.9434| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 49.25 - 3.58 2941 171 0.87 18.65 0.76 0.23 1461.62| | 2: 3.57 - 2.84 2876 122 0.81 25.95 1.27 0.23 1461.62| | 3: 2.84 - 2.48 2833 165 0.74 31.63 1.24 0.24 1211.48| | 4: 2.47 - 2.25 2825 136 0.81 25.42 1.26 0.25 562.34| | 5: 2.25 - 2.09 2756 127 0.77 29.07 1.29 0.25 562.34| | 6: 2.09 - 1.97 2846 113 0.84 22.42 1.29 0.25 306.88| | 7: 1.97 - 1.87 2787 165 0.90 16.39 1.29 0.26 89.01| | 8: 1.87 - 1.79 2789 144 0.86 20.72 1.25 0.26 89.01| | 9: 1.79 - 1.72 2745 138 0.88 18.66 1.23 0.25 55.37| | 10: 1.72 - 1.66 2789 158 0.87 20.13 1.22 0.25 48.63| | 11: 1.66 - 1.61 2740 147 0.86 21.42 1.24 0.25 46.93| | 12: 1.61 - 1.56 2787 146 0.89 18.35 1.24 0.25 29.69| | 13: 1.56 - 1.52 2745 130 0.87 20.47 1.24 0.25 29.69| | 14: 1.52 - 1.48 2803 134 0.86 20.82 1.24 0.25 26.57| | 15: 1.48 - 1.45 2738 128 0.87 20.23 1.24 0.25 20.88| | 16: 1.45 - 1.42 2756 161 0.86 21.37 1.23 0.25 20.88| | 17: 1.42 - 1.39 2785 139 0.87 20.73 1.24 0.25 17.73| | 18: 1.39 - 1.36 2741 179 0.86 21.12 1.22 0.25 15.90| | 19: 1.36 - 1.34 2807 134 0.86 21.97 1.22 0.25 15.90| | 20: 1.34 - 1.32 2696 147 0.87 20.98 1.21 0.25 13.08| | 21: 1.32 - 1.30 2785 112 0.86 21.84 1.20 0.25 12.88| | 22: 1.29 - 1.27 2704 152 0.85 22.33 1.21 0.25 12.58| | 23: 1.27 - 1.26 2802 156 0.86 22.11 1.22 0.24 11.05| | 24: 1.26 - 1.24 2744 132 0.85 22.63 1.21 0.24 11.05| | 25: 1.24 - 1.22 2734 148 0.85 23.29 1.20 0.24 10.41| | 26: 1.22 - 1.21 2727 135 0.84 23.52 1.20 0.24 9.70| | 27: 1.21 - 1.19 2814 148 0.84 24.43 1.20 0.24 9.70| | 28: 1.19 - 1.18 2671 147 0.84 24.57 1.19 0.23 8.94| | 29: 1.18 - 1.16 2800 134 0.83 24.91 1.16 0.23 8.65| | 30: 1.16 - 1.15 2740 148 0.82 26.16 1.15 0.23 8.65| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 8.65 max = 1461.62 mean = 212.11| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.99 mean = 22.41| |phase err.(test): min = 0.00 max = 89.97 mean = 22.48| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.081 0.246 1557 Z= 5.331 Angle : 5.362 18.216 2118 Z= 3.708 Chirality : 0.400 1.071 243 Planarity : 0.032 0.088 284 Dihedral : 13.917 87.482 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.24 % Allowed : 1.86 % Favored : 96.89 % Cbeta Deviations : 35.14 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.47), residues: 224 helix: -2.61 (0.39), residues: 109 sheet: -0.63 (0.78), residues: 28 loop : -0.13 (0.57), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.105 0.033 ARG A 156 TYR 0.093 0.036 TYR A 141 PHE 0.115 0.031 PHE A 119 HIS 0.077 0.029 HIS A 126 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2605 r_free= 0.1946 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.791021 | | target function (ml) not normalized (work): 232508.831690 | | target function (ml) not normalized (free): 11810.494274 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2564 0.2606 0.1946 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2564 0.2606 0.1946 n_refl.: 87602 remove outliers: r(all,work,free)=0.1975 0.1979 0.1946 n_refl.: 87594 overall B=0.20 to atoms: r(all,work,free)=0.2000 0.2005 0.1960 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1634 0.1627 0.1773 n_refl.: 87594 remove outliers: r(all,work,free)=0.1633 0.1626 0.1773 n_refl.: 87593 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 98.94 88 5 0.3785 386.510 369.685 0.687 1.000 0.401 11.894-9.307 99.02 97 4 0.1797 613.953 593.270 0.921 1.001 0.375 9.237-7.194 100.00 213 7 0.2165 502.138 488.963 0.951 1.002 0.370 7.162-5.571 100.00 427 22 0.2148 376.827 365.576 0.930 1.002 0.308 5.546-4.326 100.00 867 58 0.1260 517.290 512.829 0.962 1.002 0.233 4.315-3.360 100.00 1859 96 0.1129 491.946 488.141 1.005 1.002 0.199 3.356-2.611 100.00 3867 181 0.1430 323.183 319.721 0.996 1.002 0.043 2.608-2.026 99.99 8198 413 0.1325 214.241 212.129 1.006 1.002 0.000 2.025-1.573 100.00 17313 902 0.1649 104.624 104.141 1.010 1.002 0.000 1.573-1.221 100.00 36679 1900 0.2064 46.395 45.108 1.000 1.002 0.000 1.221-1.150 99.97 13689 708 0.2581 29.232 26.844 0.963 1.002 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0469 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1626 r_free=0.1773 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1626 r_free=0.1773 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.721344 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2016.807295 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1761 0.1883 0.0122 0.001 0.4 5.4 0.0 0.0 0 0.125 0.1563 0.1713 0.0150 0.001 0.4 4.2 0.0 0.0 0 0.250 0.1450 0.1630 0.0180 0.002 0.5 3.8 0.0 0.0 0 0.500 0.1387 0.1584 0.0197 0.002 0.5 3.8 0.0 0.0 0 0.750 0.1360 0.1569 0.0209 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1341 0.1547 0.0206 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1289 0.1511 0.0222 0.002 0.6 3.2 0.5 0.0 0 2.000 0.1270 0.1501 0.0231 0.003 0.6 3.8 0.5 0.0 0 3.000 0.1256 0.1490 0.0234 0.003 0.7 3.8 0.5 0.0 0 4.000 0.1247 0.1477 0.0230 0.004 0.7 4.2 0.5 0.0 0 5.000 0.1241 0.1474 0.0233 0.004 0.8 4.2 0.5 0.0 0 6.000 0.1237 0.1471 0.0234 0.005 0.8 3.5 0.5 0.0 0 7.000 0.1232 0.1470 0.0238 0.005 0.8 3.8 0.5 0.0 0 8.000 0.1232 0.1470 0.0238 0.006 0.9 3.8 0.5 0.0 0 9.000 0.1228 0.1468 0.0240 0.006 0.9 4.5 0.5 0.0 0 10.000 0.1226 0.1470 0.0243 0.007 0.9 3.8 0.5 0.0 0 11.000 0.1223 0.1475 0.0252 0.007 0.9 4.2 0.5 0.6 0 12.861 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1228 0.1468 0.0240 0.006 0.9 4.5 0.5 0.0 0 10.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.28 14.68 2.40 3.013 19.063 2016.807 0.017 12.28 14.67 2.39 2.989 19.063 60.504 0.017 12.35 14.68 2.33 2.666 19.063 252.101 0.017 12.75 15.40 2.64 2.850 19.320 1008.404 0.017 12.49 15.41 2.92 3.124 19.519 2016.807 0.016 12.43 15.46 3.03 3.260 19.606 3025.211 0.015 12.34 15.45 3.11 3.357 19.653 4033.615 0.015 12.34 15.51 3.16 3.379 19.650 5042.018 0.015 12.24 15.39 3.15 3.252 19.573 6050.422 0.015 12.20 15.42 3.22 3.308 19.608 7058.826 0.015 12.23 15.50 3.27 3.465 19.670 8067.229 0.015 12.22 15.54 3.32 3.433 19.645 9075.633 0.015 12.17 15.48 3.31 3.537 19.701 10084.036 0.015 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 60.504 Accepted refinement result: 12.28 14.67 2.39 2.989 19.063 60.504 0.017 Individual atomic B min max mean iso aniso Overall: 9.06 119.50 20.09 3.86 0 1785 Protein: 9.06 115.95 17.00 3.86 0 1519 Water: 11.56 119.50 38.24 N/A 0 258 Other: 19.27 26.48 21.91 N/A 0 8 Chain A: 9.06 119.50 20.09 N/A 0 1785 Histogram: Values Number of atoms 9.06 - 20.10 1276 20.10 - 31.14 224 31.14 - 42.19 127 42.19 - 53.23 89 53.23 - 64.28 44 64.28 - 75.32 11 75.32 - 86.37 7 86.37 - 97.41 4 97.41 - 108.46 1 108.46 - 119.50 2 =========================== Idealize ADP of riding H ========================== r_work=0.1228 r_free=0.1467 r_work=0.1230 r_free=0.1471 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1230 r_free = 0.1471 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1223 r_free = 0.1462 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1223 r_free= 0.1462 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016931 | | target function (ls_wunit_k1) not normalized (work): 1410.332814 | | target function (ls_wunit_k1) not normalized (free): 109.547487 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1234 0.1223 0.1462 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1674 0.1675 0.1701 n_refl.: 87593 remove outliers: r(all,work,free)=0.1674 0.1675 0.1701 n_refl.: 87593 overall B=0.03 to atoms: r(all,work,free)=0.1680 0.1681 0.1705 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1231 0.1220 0.1454 n_refl.: 87593 remove outliers: r(all,work,free)=0.1230 0.1219 0.1454 n_refl.: 87592 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3550 300.775 281.468 0.650 1.002 0.380 11.894-9.307 99.02 97 4 0.1686 481.825 469.851 0.918 1.003 0.370 9.237-7.194 100.00 213 7 0.1934 394.073 387.079 0.960 1.003 0.350 7.162-5.571 100.00 427 22 0.1843 295.730 289.746 0.934 1.003 0.258 5.546-4.326 100.00 867 58 0.1005 405.964 402.933 0.959 1.003 0.199 4.315-3.360 100.00 1859 96 0.0876 386.075 384.993 1.006 1.003 0.180 3.356-2.611 100.00 3867 181 0.1181 253.631 252.418 1.008 1.002 0.100 2.608-2.026 99.99 8198 413 0.1021 168.134 167.409 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1086 82.108 82.288 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1427 36.410 35.925 1.021 0.997 0.000 1.221-1.150 99.97 13689 708 0.2244 22.941 21.427 0.979 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0473 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1219 r_free=0.1454 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.1221 r_free=0.1454 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1221 r_free=0.1454 | n_water=258 | time (s): 1.580 (total time: 1.580) Filter (dist) r_work=0.1229 r_free=0.1450 | n_water=252 | time (s): 22.060 (total time: 23.640) Filter (q & B) r_work=0.1232 r_free=0.1450 | n_water=249 | time (s): 2.990 (total time: 26.630) Compute maps r_work=0.1232 r_free=0.1450 | n_water=249 | time (s): 1.420 (total time: 28.050) Filter (map) r_work=0.1245 r_free=0.1458 | n_water=227 | time (s): 2.360 (total time: 30.410) Find peaks r_work=0.1245 r_free=0.1458 | n_water=227 | time (s): 0.440 (total time: 30.850) Add new water r_work=0.1387 r_free=0.1633 | n_water=442 | time (s): 2.930 (total time: 33.780) Refine new water occ: r_work=0.1293 r_free=0.1480 adp: r_work=0.1214 r_free=0.1435 occ: r_work=0.1227 r_free=0.1420 adp: r_work=0.1195 r_free=0.1409 occ: r_work=0.1198 r_free=0.1397 adp: r_work=0.1187 r_free=0.1397 ADP+occupancy (water only), MIN, final r_work=0.1187 r_free=0.1397 r_work=0.1187 r_free=0.1397 | n_water=442 | time (s): 61.890 (total time: 95.670) Filter (q & B) r_work=0.1192 r_free=0.1403 | n_water=420 | time (s): 3.400 (total time: 99.070) Filter (dist only) r_work=0.1192 r_free=0.1402 | n_water=419 | time (s): 34.980 (total time: 134.050) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 28.313773 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1876.643227 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1680 0.1796 0.0116 0.001 0.4 7.7 0.0 0.0 0 0.125 0.1492 0.1632 0.0140 0.001 0.4 6.1 0.0 0.0 0 0.250 0.1411 0.1565 0.0154 0.001 0.4 5.4 0.0 0.0 0 0.500 0.1347 0.1513 0.0166 0.001 0.5 4.5 0.0 0.0 0 0.750 0.1320 0.1498 0.0178 0.002 0.5 4.5 0.0 0.0 0 1.000 0.1322 0.1500 0.0178 0.002 0.5 4.5 0.0 0.0 0 1.000 0.1254 0.1456 0.0202 0.002 0.5 4.5 0.5 0.0 0 2.000 0.1227 0.1441 0.0214 0.003 0.6 4.5 0.5 0.0 0 3.000 0.1209 0.1436 0.0228 0.003 0.7 4.2 0.5 0.0 0 4.000 0.1201 0.1430 0.0230 0.004 0.7 4.5 0.5 0.0 0 5.000 0.1198 0.1434 0.0236 0.004 0.7 5.1 0.5 0.0 0 6.000 0.1194 0.1433 0.0239 0.005 0.8 5.1 0.5 0.0 0 7.000 0.1191 0.1423 0.0231 0.005 0.8 5.1 0.5 0.0 0 8.000 0.1189 0.1422 0.0233 0.006 0.8 4.5 0.5 0.0 0 9.000 0.1185 0.1426 0.0240 0.006 0.9 5.1 0.5 0.0 0 10.000 0.1184 0.1420 0.0237 0.007 0.9 4.5 0.5 0.0 0 11.000 0.1181 0.1419 0.0239 0.007 0.9 4.5 0.5 0.0 0 12.000 0.1180 0.1417 0.0238 0.007 0.9 5.4 0.5 0.0 0 13.000 0.1179 0.1420 0.0241 0.008 0.9 4.8 0.5 0.0 0 14.157 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1180 0.1417 0.0238 0.007 0.9 5.4 0.5 0.0 0 13.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.80 14.17 2.38 4.034 21.798 1876.643 0.016 11.80 14.16 2.37 4.011 21.798 56.299 0.016 11.86 14.15 2.29 3.866 21.796 234.580 0.016 12.11 14.66 2.55 3.638 21.875 938.322 0.015 12.00 14.89 2.89 3.486 22.163 1876.643 0.015 11.88 14.90 3.02 3.506 22.213 2814.965 0.014 11.76 14.79 3.03 3.505 22.170 3753.286 0.014 11.74 14.83 3.09 3.521 22.199 4691.608 0.014 11.61 14.69 3.08 3.513 22.186 5629.930 0.014 11.63 14.72 3.10 3.546 22.121 6568.251 0.014 11.54 14.64 3.09 3.552 22.136 7506.573 0.014 11.58 14.72 3.15 3.577 22.223 8444.895 0.014 11.58 14.75 3.17 3.601 22.220 9383.216 0.014 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 234.580 Accepted refinement result: 11.86 14.15 2.29 3.866 21.796 234.580 0.016 Individual atomic B min max mean iso aniso Overall: 9.12 115.16 22.18 3.33 192 1754 Protein: 9.12 115.16 17.03 3.33 0 1519 Water: 11.51 76.74 40.87 N/A 192 227 Other: 19.38 26.44 21.98 N/A 0 8 Chain A: 9.12 115.16 19.48 N/A 0 1754 Chain S: 15.73 60.14 46.89 N/A 192 0 Histogram: Values Number of atoms 9.12 - 19.73 1262 19.73 - 30.33 242 30.33 - 40.93 168 40.93 - 51.54 134 51.54 - 62.14 118 62.14 - 72.75 11 72.75 - 83.35 5 83.35 - 93.96 4 93.96 - 104.56 0 104.56 - 115.16 2 =========================== Idealize ADP of riding H ========================== r_work=0.1186 r_free=0.1415 r_work=0.1186 r_free=0.1415 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1186 r_free = 0.1415 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1185 r_free = 0.1416 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1185 r_free= 0.1416 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015190 | | target function (ls_wunit_k1) not normalized (work): 1265.242881 | | target function (ls_wunit_k1) not normalized (free): 103.052879 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1197 0.1185 0.1416 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1579 0.1577 0.1659 n_refl.: 87592 remove outliers: r(all,work,free)=0.1579 0.1577 0.1659 n_refl.: 87592 overall B=0.01 to atoms: r(all,work,free)=0.1580 0.1578 0.1660 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1193 0.1182 0.1413 n_refl.: 87592 remove outliers: r(all,work,free)=0.1192 0.1181 0.1413 n_refl.: 87589 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 92.71 84 5 0.3369 296.688 272.232 0.593 1.003 0.350 11.894-9.307 99.02 97 4 0.1629 481.825 473.939 0.915 1.003 0.332 9.237-7.194 100.00 213 7 0.1769 394.073 390.663 0.984 1.003 0.290 7.162-5.571 100.00 427 22 0.1610 295.730 290.961 0.932 1.003 0.214 5.546-4.326 100.00 867 58 0.0881 405.964 403.353 0.960 1.003 0.200 4.315-3.360 100.00 1859 96 0.0786 386.075 384.848 1.005 1.003 0.190 3.356-2.611 100.00 3867 181 0.1073 253.631 252.747 1.009 1.002 0.120 2.608-2.026 99.99 8198 413 0.1009 168.134 167.634 1.021 1.001 0.000 2.025-1.573 100.00 17313 902 0.1092 82.108 82.310 1.031 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1439 36.410 35.944 1.025 0.997 0.000 1.221-1.150 99.97 13689 708 0.2248 22.941 21.453 0.988 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0106 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1181 r_free=0.1413 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1181 r_free=0.1413 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1181 r_free=0.1413 | n_water=419 | time (s): 1.670 (total time: 1.670) Filter (dist) r_work=0.1180 r_free=0.1411 | n_water=413 | time (s): 36.090 (total time: 37.760) Filter (q & B) r_work=0.1180 r_free=0.1411 | n_water=413 | time (s): 1.220 (total time: 38.980) Compute maps r_work=0.1180 r_free=0.1411 | n_water=413 | time (s): 1.520 (total time: 40.500) Filter (map) r_work=0.1218 r_free=0.1392 | n_water=293 | time (s): 3.490 (total time: 43.990) Find peaks r_work=0.1218 r_free=0.1392 | n_water=293 | time (s): 0.550 (total time: 44.540) Add new water r_work=0.1334 r_free=0.1493 | n_water=468 | time (s): 2.840 (total time: 47.380) Refine new water occ: r_work=0.1244 r_free=0.1427 adp: r_work=0.1245 r_free=0.1428 occ: r_work=0.1222 r_free=0.1414 adp: r_work=0.1220 r_free=0.1413 occ: r_work=0.1206 r_free=0.1408 adp: r_work=0.1200 r_free=0.1403 ADP+occupancy (water only), MIN, final r_work=0.1200 r_free=0.1403 r_work=0.1200 r_free=0.1403 | n_water=468 | time (s): 214.700 (total time: 262.080) Filter (q & B) r_work=0.1204 r_free=0.1403 | n_water=438 | time (s): 3.160 (total time: 265.240) Filter (dist only) r_work=0.1204 r_free=0.1401 | n_water=436 | time (s): 38.620 (total time: 303.860) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.708027 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 56.026316 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1247 0.1373 0.0126 0.002 0.6 4.2 0.5 0.0 0 0.085 0.1192 0.1340 0.0148 0.003 0.7 3.8 0.5 0.0 0 0.256 0.1177 0.1331 0.0155 0.004 0.8 3.5 0.5 0.0 0 0.512 0.1167 0.1324 0.0158 0.005 0.9 3.5 0.5 0.0 0 0.769 0.1161 0.1320 0.0160 0.006 1.0 3.8 0.5 0.0 0 1.025 0.1158 0.1321 0.0163 0.007 1.0 3.2 0.5 0.0 0 1.281 0.1156 0.1321 0.0165 0.007 1.0 3.5 0.5 0.0 0 1.537 0.1154 0.1321 0.0167 0.008 1.1 3.5 0.5 0.0 0 1.793 0.1165 0.1324 0.0159 0.005 0.9 3.5 0.5 0.0 0 0.854 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1161 0.1320 0.0160 0.006 1.0 3.8 0.5 0.0 0 1.025 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.61 13.20 1.60 3.786 21.293 56.026 3.619 11.61 13.20 1.60 3.786 21.293 1.681 3.619 11.61 13.20 1.59 3.776 21.293 7.003 3.619 11.66 13.28 1.62 3.720 21.275 28.013 3.614 11.66 13.38 1.72 3.740 21.246 56.026 3.613 11.59 13.35 1.76 3.764 21.238 84.039 3.607 11.55 13.33 1.78 3.779 21.228 112.053 3.604 11.51 13.31 1.80 3.792 21.222 140.066 3.601 11.49 13.29 1.80 3.806 21.209 168.079 3.599 11.49 13.30 1.82 3.820 21.205 196.092 3.599 11.47 13.29 1.82 3.829 21.202 224.105 3.597 11.46 13.29 1.83 3.837 21.202 252.118 3.597 11.45 13.26 1.81 3.843 21.199 280.132 3.595 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 7.003 Accepted refinement result: 11.61 13.20 1.59 3.776 21.293 7.003 3.619 Individual atomic B min max mean iso aniso Overall: 9.14 115.05 21.29 3.30 213 1750 Protein: 9.14 115.05 17.04 3.30 0 1519 Water: 11.53 76.74 36.11 N/A 213 223 Other: 19.34 26.40 21.97 N/A 0 8 Chain A: 9.14 115.05 19.41 N/A 0 1750 Chain S: 15.72 60.04 36.79 N/A 213 0 Histogram: Values Number of atoms 9.14 - 19.73 1264 19.73 - 30.32 283 30.32 - 40.91 206 40.91 - 51.50 132 51.50 - 62.09 57 62.09 - 72.68 10 72.68 - 83.28 5 83.28 - 93.87 4 93.87 - 104.46 0 104.46 - 115.05 2 =========================== Idealize ADP of riding H ========================== r_work=0.1161 r_free=0.1320 r_work=0.1161 r_free=0.1321 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1161 r_free = 0.1321 target_work(ml) = 3.619 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1153 r_free = 0.1325 target_work(ml) = 3.614 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87589 (all), 4.90 % free)------------| | | | r_work= 0.1153 r_free= 0.1325 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.614097 | | target function (ml) not normalized (work): 301028.970691 | | target function (ml) not normalized (free): 15841.593804 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1161 0.1153 0.1325 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1495 0.1496 0.1514 n_refl.: 87589 remove outliers: r(all,work,free)=0.1495 0.1496 0.1514 n_refl.: 87589 overall B=-0.01 to atoms: r(all,work,free)=0.1494 0.1495 0.1514 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1156 0.1148 0.1320 n_refl.: 87589 remove outliers: r(all,work,free)=0.1155 0.1146 0.1320 n_refl.: 87585 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 92.71 84 5 0.4026 296.688 268.676 0.490 1.001 0.318 11.894-9.307 98.04 96 4 0.2290 481.949 465.431 0.877 1.003 0.310 9.237-7.194 98.64 210 7 0.2286 386.570 384.984 0.958 1.003 0.200 7.162-5.571 100.00 427 22 0.2088 295.730 285.325 0.919 1.003 0.160 5.546-4.326 100.00 867 58 0.1127 405.964 401.134 0.962 1.003 0.160 4.315-3.360 100.00 1859 96 0.0934 386.075 383.462 1.004 1.003 0.150 3.356-2.611 100.00 3867 181 0.1131 253.631 251.670 1.008 1.002 0.090 2.608-2.026 99.99 8198 413 0.0934 168.134 167.483 1.023 1.001 0.000 2.025-1.573 100.00 17313 902 0.0904 82.108 82.407 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1261 36.410 36.000 1.029 0.997 0.000 1.221-1.150 99.97 13689 708 0.2170 22.941 21.479 0.990 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0182 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1146 r_free=0.1320 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1146 r_free=0.1320 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1146 r_free=0.1320 | n_water=436 | time (s): 2.360 (total time: 2.360) Filter (dist) r_work=0.1147 r_free=0.1318 | n_water=434 | time (s): 48.380 (total time: 50.740) Filter (q & B) r_work=0.1147 r_free=0.1318 | n_water=433 | time (s): 3.850 (total time: 54.590) Compute maps r_work=0.1147 r_free=0.1318 | n_water=433 | time (s): 1.820 (total time: 56.410) Filter (map) r_work=0.1169 r_free=0.1315 | n_water=330 | time (s): 3.820 (total time: 60.230) Find peaks r_work=0.1169 r_free=0.1315 | n_water=330 | time (s): 0.680 (total time: 60.910) Add new water r_work=0.1232 r_free=0.1374 | n_water=480 | time (s): 3.700 (total time: 64.610) Refine new water occ: r_work=0.1170 r_free=0.1322 adp: r_work=0.1171 r_free=0.1323 occ: r_work=0.1156 r_free=0.1312 adp: r_work=0.1155 r_free=0.1311 occ: r_work=0.1145 r_free=0.1303 adp: r_work=0.1142 r_free=0.1301 ADP+occupancy (water only), MIN, final r_work=0.1142 r_free=0.1301 r_work=0.1142 r_free=0.1301 | n_water=480 | time (s): 261.890 (total time: 326.500) Filter (q & B) r_work=0.1147 r_free=0.1311 | n_water=447 | time (s): 3.890 (total time: 330.390) Filter (dist only) r_work=0.1147 r_free=0.1312 | n_water=445 | time (s): 47.510 (total time: 377.900) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.791536 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 39.305447 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1207 0.1346 0.0139 0.002 0.6 4.2 0.5 0.0 0 0.090 0.1164 0.1317 0.0153 0.003 0.8 3.8 0.5 0.0 0 0.269 0.1155 0.1317 0.0163 0.005 0.9 3.8 0.5 0.0 0 0.537 0.1149 0.1315 0.0166 0.006 0.9 3.2 0.5 0.0 0 0.806 0.1145 0.1314 0.0168 0.007 1.0 3.5 0.5 0.0 0 1.075 0.1143 0.1310 0.0167 0.007 1.1 3.5 0.5 0.0 0 1.344 0.1141 0.1310 0.0170 0.008 1.1 3.8 0.5 0.0 0 1.612 0.1139 0.1312 0.0173 0.008 1.1 3.5 0.5 0.0 0 1.881 0.1148 0.1314 0.0166 0.006 1.0 3.5 0.5 0.0 0 0.896 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1143 0.1310 0.0167 0.007 1.1 3.5 0.5 0.0 0 1.344 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.43 13.10 1.67 3.772 21.244 39.305 3.607 11.43 13.10 1.67 3.772 21.244 1.179 3.607 11.43 13.10 1.67 3.772 21.244 4.913 3.607 11.47 13.15 1.68 3.703 21.235 19.653 3.605 11.44 13.18 1.74 3.721 21.225 39.305 3.601 11.48 13.26 1.78 3.739 21.198 58.958 3.602 11.40 13.21 1.81 3.757 21.196 78.611 3.596 11.38 13.20 1.82 3.768 21.193 98.264 3.594 11.36 13.20 1.83 3.779 21.188 117.916 3.592 11.35 13.20 1.85 3.792 21.180 137.569 3.591 11.37 13.23 1.86 3.808 21.168 157.222 3.591 11.34 13.21 1.87 3.815 21.169 176.875 3.590 11.34 13.20 1.87 3.824 21.166 196.527 3.589 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 4.913 Accepted refinement result: 11.43 13.10 1.67 3.772 21.244 4.913 3.607 Individual atomic B min max mean iso aniso Overall: 9.13 115.04 21.21 3.30 224 1748 Protein: 9.13 115.04 17.03 3.30 0 1519 Water: 11.52 76.74 35.46 N/A 224 221 Other: 19.33 26.39 21.97 N/A 0 8 Chain A: 9.13 115.04 19.35 N/A 0 1748 Chain S: 15.72 60.03 35.69 N/A 224 0 Histogram: Values Number of atoms 9.13 - 19.72 1263 19.72 - 30.31 296 30.31 - 40.90 210 40.90 - 51.49 132 51.49 - 62.09 51 62.09 - 72.68 10 72.68 - 83.27 4 83.27 - 93.86 4 93.86 - 104.45 0 104.45 - 115.04 2 =========================== Idealize ADP of riding H ========================== r_work=0.1143 r_free=0.1310 r_work=0.1143 r_free=0.1310 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1143 r_free = 0.1310 target_work(ml) = 3.607 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1138 r_free = 0.1307 target_work(ml) = 3.605 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87585 (all), 4.90 % free)------------| | | | r_work= 0.1138 r_free= 0.1307 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.605182 | | target function (ml) not normalized (work): 300272.029981 | | target function (ml) not normalized (free): 15811.958727 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1146 0.1138 0.1307 n_refl.: 87585 re-set all scales: r(all,work,free)=0.1484 0.1485 0.1506 n_refl.: 87585 remove outliers: r(all,work,free)=0.1484 0.1485 0.1506 n_refl.: 87585 overall B=-0.01 to atoms: r(all,work,free)=0.1483 0.1484 0.1506 n_refl.: 87585 bulk-solvent and scaling: r(all,work,free)=0.1145 0.1137 0.1309 n_refl.: 87585 remove outliers: r(all,work,free)=0.1144 0.1135 0.1309 n_refl.: 87581 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 90.62 82 5 0.4011 293.418 254.999 0.464 1.001 0.314 11.894-9.307 97.06 95 4 0.2441 483.917 467.739 0.867 1.002 0.310 9.237-7.194 98.18 209 7 0.2340 385.565 379.296 0.932 1.003 0.170 7.162-5.571 100.00 427 22 0.2171 295.730 285.133 0.912 1.003 0.145 5.546-4.326 100.00 867 58 0.1126 405.964 401.115 0.964 1.003 0.140 4.315-3.360 100.00 1859 96 0.0934 386.075 383.808 1.003 1.003 0.107 3.356-2.611 100.00 3867 181 0.1106 253.631 251.768 1.009 1.002 0.050 2.608-2.026 99.99 8198 413 0.0917 168.134 167.561 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0884 82.108 82.447 1.036 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1249 36.410 36.018 1.029 0.997 0.000 1.221-1.150 99.97 13689 708 0.2169 22.941 21.485 0.990 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0152 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1135 r_free=0.1309 After: r_work=0.1136 r_free=0.1309 ================================== NQH flips ================================== r_work=0.1136 r_free=0.1309 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1136 r_free=0.1309 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1136 r_free=0.1309 | n_water=445 | time (s): 2.440 (total time: 2.440) Filter (dist) r_work=0.1136 r_free=0.1309 | n_water=445 | time (s): 44.530 (total time: 46.970) Filter (q & B) r_work=0.1136 r_free=0.1309 | n_water=444 | time (s): 3.920 (total time: 50.890) Compute maps r_work=0.1136 r_free=0.1309 | n_water=444 | time (s): 1.870 (total time: 52.760) Filter (map) r_work=0.1163 r_free=0.1304 | n_water=342 | time (s): 3.950 (total time: 56.710) Find peaks r_work=0.1163 r_free=0.1304 | n_water=342 | time (s): 0.700 (total time: 57.410) Add new water r_work=0.1209 r_free=0.1344 | n_water=481 | time (s): 3.710 (total time: 61.120) Refine new water occ: r_work=0.1153 r_free=0.1305 adp: r_work=0.1153 r_free=0.1306 occ: r_work=0.1140 r_free=0.1295 adp: r_work=0.1140 r_free=0.1296 occ: r_work=0.1132 r_free=0.1287 adp: r_work=0.1130 r_free=0.1286 ADP+occupancy (water only), MIN, final r_work=0.1130 r_free=0.1286 r_work=0.1130 r_free=0.1286 | n_water=481 | time (s): 239.330 (total time: 300.450) Filter (q & B) r_work=0.1136 r_free=0.1289 | n_water=446 | time (s): 3.820 (total time: 304.270) Filter (dist only) r_work=0.1136 r_free=0.1289 | n_water=445 | time (s): 46.720 (total time: 350.990) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.789179 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 44.596818 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1225 0.1346 0.0120 0.004 0.7 6.4 0.0 0.0 0 0.089 0.1172 0.1312 0.0139 0.004 0.8 7.7 0.0 0.0 0 0.268 0.1156 0.1302 0.0146 0.005 0.9 7.4 0.5 0.0 0 0.537 0.1146 0.1295 0.0149 0.006 1.0 7.4 0.5 0.0 0 0.805 0.1140 0.1290 0.0151 0.007 1.1 7.0 0.5 0.0 0 1.074 0.1136 0.1289 0.0153 0.007 1.1 7.4 0.5 0.0 0 1.342 0.1135 0.1289 0.0154 0.008 1.1 7.4 0.5 0.0 0 1.610 0.1134 0.1288 0.0154 0.008 1.1 7.4 0.5 0.0 0 1.879 0.1144 0.1293 0.0149 0.006 1.0 7.0 0.5 0.0 0 0.895 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1134 0.1288 0.0154 0.008 1.1 7.4 0.5 0.0 0 1.879 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.34 12.88 1.54 3.772 21.198 44.597 3.600 11.34 12.88 1.54 3.772 21.198 1.338 3.600 11.34 12.88 1.54 3.771 21.198 5.575 3.600 11.35 12.90 1.55 3.707 21.191 22.298 3.594 11.40 13.02 1.62 3.732 21.163 44.597 3.598 11.36 13.03 1.66 3.746 21.150 66.895 3.593 11.29 12.98 1.69 3.764 21.149 89.194 3.587 11.27 12.98 1.71 3.775 21.145 111.492 3.586 11.26 12.98 1.72 3.789 21.138 133.790 3.584 11.26 13.00 1.74 3.807 21.127 156.089 3.584 11.24 12.98 1.73 3.814 21.128 178.387 3.583 11.24 12.97 1.73 3.824 21.123 200.686 3.581 11.21 12.95 1.74 3.827 21.127 222.984 3.580 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.338 Accepted refinement result: 11.34 12.88 1.54 3.772 21.198 1.338 3.600 Individual atomic B min max mean iso aniso Overall: 9.12 115.04 21.13 3.30 224 1748 Protein: 9.12 115.04 17.02 3.30 0 1519 Water: 11.51 76.73 35.14 N/A 224 221 Other: 19.32 26.39 21.96 N/A 0 8 Chain A: 9.12 115.04 19.35 N/A 0 1748 Chain S: 15.64 60.03 35.06 N/A 224 0 Histogram: Values Number of atoms 9.12 - 19.72 1263 19.72 - 30.31 297 30.31 - 40.90 219 40.90 - 51.49 123 51.49 - 62.08 50 62.08 - 72.67 10 72.67 - 83.26 4 83.26 - 93.85 4 93.85 - 104.45 0 104.45 - 115.04 2 =========================== Idealize ADP of riding H ========================== r_work=0.1134 r_free=0.1288 r_work=0.1134 r_free=0.1288 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1134 r_free = 0.1288 target_work(ml) = 3.600 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1131 r_free = 0.1287 target_work(ml) = 3.599 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87581 (all), 4.91 % free)------------| | | | r_work= 0.1131 r_free= 0.1287 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.598653 | | target function (ml) not normalized (work): 299713.841469 | | target function (ml) not normalized (free): 15779.678501 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2923 171 0.1344 0.1339 5.6724 5.5727| | 2: 3.57 - 2.84 1.00 2888 124 0.1065 0.1383 5.1503 5.2308| | 3: 2.83 - 2.48 1.00 2820 163 0.1093 0.1164 4.9292 4.96| | 4: 2.47 - 2.25 1.00 2825 136 0.0897 0.1046 4.6167 4.6674| | 5: 2.25 - 2.09 1.00 2756 127 0.0864 0.0989 4.5629 4.6179| | 6: 2.09 - 1.97 1.00 2846 113 0.0846 0.1021 4.2561 4.3606| | 7: 1.97 - 1.87 1.00 2787 165 0.0876 0.1112 3.9736 4.074| | 8: 1.87 - 1.79 1.00 2789 144 0.0916 0.1101 3.8839 3.9856| | 9: 1.79 - 1.72 1.00 2745 138 0.0869 0.1132 3.6377 3.7891| | 10: 1.72 - 1.66 1.00 2831 160 0.0917 0.1188 3.5607 3.7151| | 11: 1.66 - 1.61 1.00 2712 147 0.0860 0.1035 3.4882 3.5617| | 12: 1.61 - 1.56 1.00 2773 144 0.0896 0.1152 3.3222 3.4691| | 13: 1.56 - 1.52 1.00 2745 130 0.0940 0.1041 3.3015 3.3906| | 14: 1.52 - 1.48 1.00 2803 134 0.0976 0.1054 3.2321 3.3243| | 15: 1.48 - 1.45 1.00 2738 128 0.0992 0.1212 3.1432 3.2565| | 16: 1.45 - 1.42 1.00 2756 161 0.1050 0.1224 3.1291 3.2314| | 17: 1.42 - 1.39 1.00 2785 139 0.1135 0.1295 3.1122 3.2139| | 18: 1.39 - 1.36 1.00 2741 179 0.1197 0.1317 3.0996 3.2276| | 19: 1.36 - 1.34 1.00 2807 134 0.1257 0.1556 3.1054 3.2675| | 20: 1.34 - 1.32 1.00 2696 147 0.1364 0.1441 3.1068 3.1415| | 21: 1.32 - 1.30 1.00 2785 112 0.1473 0.1522 3.1111 3.1024| | 22: 1.29 - 1.27 1.00 2704 152 0.1558 0.1995 3.1194 3.2998| | 23: 1.27 - 1.26 1.00 2802 156 0.1645 0.1778 3.1298 3.1939| | 24: 1.26 - 1.24 1.00 2744 132 0.1706 0.1835 3.1241 3.223| | 25: 1.24 - 1.22 1.00 2733 148 0.1877 0.2148 3.1384 3.2555| | 26: 1.22 - 1.21 1.00 2727 135 0.1910 0.1774 3.1453 3.202| | 27: 1.21 - 1.19 1.00 2814 148 0.2071 0.2169 3.168 3.1582| | 28: 1.19 - 1.18 1.00 2671 147 0.2196 0.2298 3.1636 3.1698| | 29: 1.18 - 1.16 1.00 2800 134 0.2269 0.2386 3.1461 3.2269| | 30: 1.16 - 1.15 1.00 2739 148 0.2450 0.2465 3.1418 3.1695| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.58 2923 171 0.95 8.19 1.00 0.97 5499.41| | 2: 3.57 - 2.84 2888 124 0.93 12.22 1.01 0.97 5499.41| | 3: 2.83 - 2.48 2820 163 0.90 16.13 0.99 0.97 4598.42| | 4: 2.47 - 2.25 2825 136 0.92 13.22 1.00 0.98 2275.07| | 5: 2.25 - 2.09 2756 127 0.91 15.30 1.01 0.98 2275.07| | 6: 2.09 - 1.97 2846 113 0.93 12.22 1.02 0.98 1321.30| | 7: 1.97 - 1.87 2787 165 0.95 9.27 1.02 0.97 507.85| | 8: 1.87 - 1.79 2789 144 0.93 12.63 1.00 0.97 507.85| | 9: 1.79 - 1.72 2745 138 0.94 10.00 0.98 0.97 286.31| | 10: 1.72 - 1.66 2831 160 0.94 11.06 0.98 0.97 241.95| | 11: 1.66 - 1.61 2712 147 0.94 11.69 0.98 0.97 231.79| | 12: 1.61 - 1.56 2773 144 0.96 8.84 0.99 0.97 135.99| | 13: 1.56 - 1.52 2745 130 0.95 10.32 1.02 0.97 135.99| | 14: 1.52 - 1.48 2803 134 0.94 10.67 1.02 0.98 121.93| | 15: 1.48 - 1.45 2738 128 0.95 9.84 1.02 0.98 96.17| | 16: 1.45 - 1.42 2756 161 0.94 10.96 1.02 0.98 96.17| | 17: 1.42 - 1.39 2785 139 0.95 10.79 1.01 0.98 87.60| | 18: 1.39 - 1.36 2741 179 0.94 11.43 1.01 0.98 82.64| | 19: 1.36 - 1.34 2807 134 0.94 11.78 0.99 0.98 82.64| | 20: 1.34 - 1.32 2696 147 0.94 12.06 0.98 0.96 79.05| | 21: 1.32 - 1.30 2785 112 0.94 13.02 0.98 0.96 78.79| | 22: 1.29 - 1.27 2704 152 0.93 13.59 0.98 0.96 79.26| | 23: 1.27 - 1.26 2802 156 0.92 14.80 0.97 0.94 81.64| | 24: 1.26 - 1.24 2744 132 0.93 14.82 0.96 0.94 81.64| | 25: 1.24 - 1.22 2733 148 0.91 16.34 0.96 0.94 83.78| | 26: 1.22 - 1.21 2727 135 0.90 18.13 1.02 0.93 86.15| | 27: 1.21 - 1.19 2814 148 0.89 18.77 1.02 0.93 86.15| | 28: 1.19 - 1.18 2671 147 0.88 20.41 1.01 0.92 89.98| | 29: 1.18 - 1.16 2800 134 0.88 20.57 0.99 0.92 91.42| | 30: 1.16 - 1.15 2739 148 0.86 22.10 0.98 0.92 91.42| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 78.79 max = 5499.41 mean = 854.77| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.93 mean = 13.35| |phase err.(test): min = 0.00 max = 89.65 mean = 13.35| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1139 0.1131 0.1287 n_refl.: 87581 re-set all scales: r(all,work,free)=0.1461 0.1463 0.1462 n_refl.: 87581 remove outliers: r(all,work,free)=0.1461 0.1463 0.1462 n_refl.: 87581 overall B=-0.00 to atoms: r(all,work,free)=0.1460 0.1463 0.1461 n_refl.: 87581 bulk-solvent and scaling: r(all,work,free)=0.1138 0.1131 0.1284 n_refl.: 87581 remove outliers: r(all,work,free)=0.1137 0.1129 0.1284 n_refl.: 87577 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.3979 293.642 256.805 0.466 1.002 0.324 11.894-9.307 97.06 95 4 0.2391 483.917 469.786 0.869 1.003 0.320 9.237-7.194 97.27 207 7 0.2273 386.811 379.563 0.925 1.003 0.162 7.162-5.571 100.00 427 22 0.2190 295.730 284.940 0.913 1.003 0.160 5.546-4.326 100.00 867 58 0.1139 405.964 400.821 0.961 1.003 0.115 4.315-3.360 100.00 1859 96 0.0912 386.075 384.007 1.003 1.003 0.110 3.356-2.611 100.00 3867 181 0.1109 253.631 251.786 1.010 1.002 0.019 2.608-2.026 99.99 8198 413 0.0905 168.134 167.599 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0882 82.108 82.463 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1246 36.410 36.026 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2167 22.941 21.497 0.989 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0135 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2605 0.1946 0.081 5.362 8.8 119.3 19.9 258 0.000 1_bss: 0.1626 0.1773 0.081 5.362 9.1 119.5 20.1 258 0.000 1_settarget: 0.1626 0.1773 0.081 5.362 9.1 119.5 20.1 258 0.000 1_nqh: 0.1626 0.1773 0.081 5.362 9.1 119.5 20.1 258 0.000 1_weight: 0.1626 0.1773 0.081 5.362 9.1 119.5 20.1 258 0.000 1_xyzrec: 0.1228 0.1468 0.006 0.883 9.1 119.5 20.1 258 0.136 1_adp: 0.1228 0.1467 0.006 0.883 9.1 119.5 20.1 258 0.136 1_regHadp: 0.1230 0.1471 0.006 0.883 9.1 119.5 20.1 258 0.136 1_occ: 0.1223 0.1462 0.006 0.883 9.1 119.5 20.1 258 0.136 2_bss: 0.1219 0.1454 0.006 0.883 9.1 119.5 20.1 258 0.136 2_settarget: 0.1219 0.1454 0.006 0.883 9.1 119.5 20.1 258 0.136 2_updatecdl: 0.1219 0.1454 0.006 0.897 9.1 119.5 20.1 258 0.136 2_nqh: 0.1221 0.1454 0.006 0.897 9.1 119.5 20.1 258 0.139 2_sol: 0.1192 0.1402 0.006 0.897 9.1 116.0 22.2 419 n/a 2_weight: 0.1192 0.1402 0.006 0.897 9.1 116.0 22.2 419 n/a 2_xyzrec: 0.1180 0.1417 0.007 0.920 9.1 116.0 22.2 419 n/a 2_adp: 0.1186 0.1415 0.007 0.920 9.1 115.2 22.2 419 n/a 2_regHadp: 0.1186 0.1415 0.007 0.920 9.1 115.2 22.2 419 n/a 2_occ: 0.1185 0.1416 0.007 0.920 9.1 115.2 22.2 419 n/a 3_bss: 0.1181 0.1413 0.007 0.920 9.1 115.2 22.2 419 n/a 3_settarget: 0.1181 0.1413 0.007 0.920 9.1 115.2 22.2 419 n/a 3_updatecdl: 0.1181 0.1413 0.007 0.920 9.1 115.2 22.2 419 n/a 3_nqh: 0.1181 0.1413 0.007 0.920 9.1 115.2 22.2 419 n/a 3_sol: 0.1204 0.1401 0.007 0.920 9.1 115.2 21.3 436 n/a 3_weight: 0.1204 0.1401 0.007 0.920 9.1 115.2 21.3 436 n/a 3_xyzrec: 0.1161 0.1320 0.006 0.964 9.1 115.2 21.3 436 n/a 3_adp: 0.1161 0.1320 0.006 0.964 9.1 115.0 21.3 436 n/a 3_regHadp: 0.1161 0.1321 0.006 0.964 9.1 115.0 21.3 436 n/a 3_occ: 0.1153 0.1325 0.006 0.964 9.1 115.0 21.3 436 n/a 4_bss: 0.1146 0.1320 0.006 0.964 9.1 115.0 21.3 436 n/a 4_settarget: 0.1146 0.1320 0.006 0.964 9.1 115.0 21.3 436 n/a 4_updatecdl: 0.1146 0.1320 0.006 0.965 9.1 115.0 21.3 436 n/a 4_nqh: 0.1146 0.1320 0.006 0.965 9.1 115.0 21.3 436 n/a 4_sol: 0.1147 0.1312 0.006 0.965 9.1 115.0 21.2 445 n/a 4_weight: 0.1147 0.1312 0.006 0.965 9.1 115.0 21.2 445 n/a 4_xyzrec: 0.1143 0.1310 0.007 1.053 9.1 115.0 21.2 445 n/a 4_adp: 0.1143 0.1310 0.007 1.053 9.1 115.0 21.2 445 n/a 4_regHadp: 0.1143 0.1310 0.007 1.053 9.1 115.0 21.2 445 n/a 4_occ: 0.1138 0.1307 0.007 1.053 9.1 115.0 21.2 445 n/a 5_bss: 0.1135 0.1309 0.007 1.053 9.1 115.0 21.2 445 n/a 5_settarget: 0.1135 0.1309 0.007 1.053 9.1 115.0 21.2 445 n/a 5_updatecdl: 0.1135 0.1309 0.007 1.054 9.1 115.0 21.2 445 n/a 5_setrh: 0.1136 0.1309 0.007 1.054 9.1 115.0 21.2 445 n/a 5_nqh: 0.1136 0.1309 0.007 1.054 9.1 115.0 21.2 445 n/a 5_sol: 0.1136 0.1289 0.007 1.054 9.1 115.0 21.1 445 n/a 5_weight: 0.1136 0.1289 0.007 1.054 9.1 115.0 21.1 445 n/a 5_xyzrec: 0.1134 0.1288 0.008 1.115 9.1 115.0 21.1 445 n/a 5_adp: 0.1134 0.1288 0.008 1.115 9.1 115.0 21.1 445 n/a 5_regHadp: 0.1134 0.1288 0.008 1.115 9.1 115.0 21.1 445 n/a 5_occ: 0.1131 0.1287 0.008 1.115 9.1 115.0 21.1 445 n/a end: 0.1129 0.1284 0.008 1.115 9.1 115.0 21.1 445 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_4811713_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_4811713_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.3200 Refinement macro-cycles (run) : 13513.2200 Write final files (write_after_run_outputs) : 94.2900 Total : 13610.8300 Total CPU time: 3.79 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:06:14 PST -0800 (1735365974.32 s) Start R-work = 0.1626, R-free = 0.1773 Final R-work = 0.1129, R-free = 0.1284 =============================================================================== Job complete usr+sys time: 13789.70 seconds wall clock time: 250 minutes 27.10 seconds (15027.10 seconds total)