Starting phenix.refine on Fri Dec 27 17:58:27 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7509253.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 { 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_7509253.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7509253.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } 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: 1.46, per 1000 atoms: 0.43 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: 0.39 Conformation dependent library (CDL) restraints added in 149.5 milliseconds Time building geometry restraints manager: 0.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.62 - 0.91: 515 0.91 - 1.20: 1164 1.20 - 1.48: 846 1.48 - 1.77: 619 1.77 - 2.05: 9 Bond restraints: 3153 Sorted by residual: bond pdb=" NE ARG A 27 " pdb=" CZ ARG A 27 " ideal model delta sigma weight residual 1.326 1.556 -0.230 1.10e-02 8.26e+03 4.37e+02 bond pdb=" C GLU A 163 " pdb=" N PHE A 164 " ideal model delta sigma weight residual 1.334 1.554 -0.220 1.20e-02 6.94e+03 3.36e+02 bond pdb=" C ALYS A 132 " pdb=" O ALYS A 132 " ideal model delta sigma weight residual 1.236 1.024 0.212 1.16e-02 7.43e+03 3.34e+02 bond pdb=" C SER A 142 " pdb=" O SER A 142 " ideal model delta sigma weight residual 1.234 1.456 -0.222 1.26e-02 6.30e+03 3.10e+02 bond pdb=" CA ALA A 79 " pdb=" C ALA A 79 " ideal model delta sigma weight residual 1.523 1.288 0.235 1.35e-02 5.49e+03 3.04e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.85: 3238 4.85 - 9.70: 1869 9.70 - 14.54: 583 14.54 - 19.39: 79 19.39 - 24.24: 8 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA ALYS A 132 " pdb=" C ALYS A 132 " pdb=" N MET A 133 " ideal model delta sigma weight residual 116.79 99.92 16.87 1.28e+00 6.10e-01 1.74e+02 angle pdb=" CA THR A 140 " pdb=" C THR A 140 " pdb=" O THR A 140 " ideal model delta sigma weight residual 120.36 134.46 -14.10 1.08e+00 8.57e-01 1.70e+02 angle pdb=" CA GLY A 174 " pdb=" C GLY A 174 " pdb=" O GLY A 174 " ideal model delta sigma weight residual 122.43 132.88 -10.45 8.10e-01 1.52e+00 1.66e+02 angle pdb=" O AGLU A 90 " pdb=" C AGLU A 90 " pdb=" N ILE A 91 " ideal model delta sigma weight residual 122.07 108.94 13.13 1.03e+00 9.43e-01 1.63e+02 angle pdb=" CG HIS A 126 " pdb=" CD2 HIS A 126 " pdb=" NE2 HIS A 126 " ideal model delta sigma weight residual 107.20 95.14 12.06 1.00e+00 1.00e+00 1.45e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 15.53: 912 15.53 - 31.06: 132 31.06 - 46.59: 37 46.59 - 62.12: 24 62.12 - 77.65: 6 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: 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 180.00 151.40 28.60 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA ILE A 117 " pdb=" C ILE A 117 " pdb=" N GLY A 118 " pdb=" CA GLY A 118 " ideal model delta harmonic sigma weight residual 180.00 155.03 24.97 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA GLY A 74 " pdb=" C GLY A 74 " pdb=" N GLY A 75 " pdb=" CA GLY A 75 " ideal model delta harmonic sigma weight residual -180.00 -156.37 -23.63 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.003 - 0.198: 92 0.198 - 0.392: 83 0.392 - 0.587: 41 0.587 - 0.782: 19 0.782 - 0.977: 8 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA SER A 161 " pdb=" N SER A 161 " pdb=" C SER A 161 " pdb=" CB SER A 161 " both_signs ideal model delta sigma weight residual False 2.51 1.53 0.98 2.00e-01 2.50e+01 2.38e+01 chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.65 -0.94 2.00e-01 2.50e+01 2.21e+01 chirality pdb=" CB VAL A 23 " pdb=" CA VAL A 23 " pdb=" CG1 VAL A 23 " pdb=" CG2 VAL A 23 " both_signs ideal model delta sigma weight residual False -2.63 -3.51 0.88 2.00e-01 2.50e+01 1.95e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 5 " 0.084 9.50e-02 1.11e+02 7.51e-02 1.10e+02 pdb=" NE ARG A 5 " -0.079 2.00e-02 2.50e+03 pdb=" CZ ARG A 5 " 0.021 2.00e-02 2.50e+03 pdb=" NH1 ARG A 5 " 0.029 2.00e-02 2.50e+03 pdb=" NH2 ARG A 5 " 0.128 2.00e-02 2.50e+03 pdb="HH11 ARG A 5 " 0.070 2.00e-02 2.50e+03 pdb="HH12 ARG A 5 " -0.115 2.00e-02 2.50e+03 pdb="HH21 ARG A 5 " -0.032 2.00e-02 2.50e+03 pdb="HH22 ARG A 5 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB AASN A 97 " -0.069 2.00e-02 2.50e+03 8.55e-02 1.10e+02 pdb=" CG AASN A 97 " 0.109 2.00e-02 2.50e+03 pdb=" OD1AASN A 97 " -0.038 2.00e-02 2.50e+03 pdb=" ND2AASN A 97 " 0.126 2.00e-02 2.50e+03 pdb="HD21AASN A 97 " -0.092 2.00e-02 2.50e+03 pdb="HD22AASN A 97 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 115 " -0.055 2.00e-02 2.50e+03 6.88e-02 1.06e+02 pdb=" CG HIS A 115 " 0.020 2.00e-02 2.50e+03 pdb=" ND1 HIS A 115 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 HIS A 115 " 0.051 2.00e-02 2.50e+03 pdb=" CE1 HIS A 115 " -0.104 2.00e-02 2.50e+03 pdb=" NE2 HIS A 115 " -0.031 2.00e-02 2.50e+03 pdb=" HD2 HIS A 115 " 0.065 2.00e-02 2.50e+03 pdb=" HE1 HIS A 115 " 0.119 2.00e-02 2.50e+03 pdb=" HE2 HIS A 115 " -0.078 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.37: 1340 2.37 - 2.92: 8350 2.92 - 3.48: 10476 3.48 - 4.04: 15047 4.04 - 4.60: 21459 Nonbonded interactions: 56672 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.807 2.100 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.814 1.850 x-y,-y,-z-4/3 nonbonded pdb=" O ALA A 14 " pdb=" H SER A 47 " model vdw 1.827 1.850 nonbonded pdb=" H GLY A 120 " pdb=" O HIS A 138 " model vdw 1.838 1.850 nonbonded pdb=" H VAL A 35 " pdb=" OD2 ASP A 55 " model vdw 1.862 1.850 ... (remaining 56667 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_7509253_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= 0.2608 r_free= 0.1947 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.794938 | | target function (ml) not normalized (work): 232835.119798 | | target function (ml) not normalized (free): 11838.361063 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3034 0.2057 7.0665 4.9502| | 2: 3.57 - 2.84 1.00 2876 122 0.2427 0.1728 4.3487 4.3309| | 3: 2.84 - 2.48 1.00 2833 165 0.2384 0.1730 4.13 4.1585| | 4: 2.47 - 2.25 1.00 2825 136 0.2362 0.1446 3.834 3.8285| | 5: 2.25 - 2.09 1.00 2756 127 0.2481 0.1680 3.7976 3.8327| | 6: 2.09 - 1.97 1.00 2846 113 0.2539 0.1836 3.4679 3.5515| | 7: 1.97 - 1.87 1.00 2787 165 0.2517 0.1723 3.148 3.1546| | 8: 1.87 - 1.79 1.00 2789 144 0.2449 0.2047 3.0712 3.1842| | 9: 1.79 - 1.72 1.00 2745 138 0.2405 0.1827 2.8884 2.9164| | 10: 1.72 - 1.66 1.00 2789 158 0.2369 0.1929 2.8042 2.8793| | 11: 1.66 - 1.61 1.00 2740 147 0.2497 0.1967 2.7636 2.8396| | 12: 1.61 - 1.56 1.00 2787 146 0.2488 0.2009 2.6239 2.6805| | 13: 1.56 - 1.52 1.00 2745 130 0.2540 0.1895 2.5702 2.6281| | 14: 1.52 - 1.48 1.00 2803 134 0.2606 0.1853 2.5105 2.5274| | 15: 1.48 - 1.45 1.00 2738 128 0.2638 0.2131 2.433 2.4933| | 16: 1.45 - 1.42 1.00 2756 161 0.2702 0.2226 2.3968 2.4226| | 17: 1.42 - 1.39 1.00 2785 139 0.2672 0.2006 2.3623 2.3378| | 18: 1.39 - 1.36 1.00 2741 179 0.2702 0.2195 2.2837 2.3442| | 19: 1.36 - 1.34 1.00 2807 134 0.2637 0.2309 2.2496 2.281| | 20: 1.34 - 1.32 1.00 2696 147 0.2684 0.2406 2.1976 2.264| | 21: 1.32 - 1.30 1.00 2785 112 0.2719 0.2524 2.1665 2.2815| | 22: 1.29 - 1.27 1.00 2704 152 0.2726 0.2588 2.1386 2.2031| | 23: 1.27 - 1.26 1.00 2802 156 0.2772 0.2224 2.1033 2.123| | 24: 1.26 - 1.24 1.00 2744 132 0.2780 0.2619 2.08 2.2039| | 25: 1.24 - 1.22 1.00 2734 148 0.2805 0.2587 2.0452 2.1129| | 26: 1.22 - 1.21 1.00 2727 135 0.2795 0.2364 2.0132 2.1153| | 27: 1.21 - 1.19 1.00 2814 148 0.2984 0.2577 2.0218 1.9528| | 28: 1.19 - 1.18 1.00 2671 147 0.2973 0.2829 1.9846 2.0206| | 29: 1.18 - 1.16 1.00 2800 134 0.3004 0.2545 1.9628 1.9723| | 30: 1.16 - 1.15 1.00 2740 148 0.3045 0.2901 1.9277 1.9579| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.84 0.76 0.23 1473.46| | 2: 3.57 - 2.84 2876 122 0.80 26.05 1.27 0.23 1473.46| | 3: 2.84 - 2.48 2833 165 0.74 31.94 1.25 0.24 1222.60| | 4: 2.47 - 2.25 2825 136 0.81 25.62 1.26 0.25 571.57| | 5: 2.25 - 2.09 2756 127 0.77 29.35 1.28 0.25 571.57| | 6: 2.09 - 1.97 2846 113 0.83 22.97 1.29 0.25 314.63| | 7: 1.97 - 1.87 2787 165 0.90 16.90 1.28 0.26 95.49| | 8: 1.87 - 1.79 2789 144 0.85 21.56 1.24 0.26 95.49| | 9: 1.79 - 1.72 2745 138 0.88 19.08 1.24 0.25 58.24| | 10: 1.72 - 1.66 2789 158 0.86 20.66 1.22 0.25 50.78| | 11: 1.66 - 1.61 2740 147 0.85 21.89 1.24 0.25 49.02| | 12: 1.61 - 1.56 2787 146 0.88 18.94 1.23 0.25 31.13| | 13: 1.56 - 1.52 2745 130 0.86 21.10 1.24 0.25 31.13| | 14: 1.52 - 1.48 2803 134 0.86 21.24 1.24 0.25 27.62| | 15: 1.48 - 1.45 2738 128 0.87 20.66 1.24 0.25 21.18| | 16: 1.45 - 1.42 2756 161 0.85 22.02 1.24 0.25 21.18| | 17: 1.42 - 1.39 2785 139 0.87 20.82 1.22 0.25 17.94| | 18: 1.39 - 1.36 2741 179 0.86 21.58 1.23 0.25 16.07| | 19: 1.36 - 1.34 2807 134 0.85 22.22 1.21 0.25 16.07| | 20: 1.34 - 1.32 2696 147 0.87 21.06 1.21 0.25 13.40| | 21: 1.32 - 1.30 2785 112 0.85 22.36 1.21 0.25 13.21| | 22: 1.29 - 1.27 2704 152 0.85 22.68 1.20 0.25 12.90| | 23: 1.27 - 1.26 2802 156 0.86 22.16 1.21 0.24 11.36| | 24: 1.26 - 1.24 2744 132 0.85 23.01 1.20 0.24 11.36| | 25: 1.24 - 1.22 2734 148 0.84 23.83 1.20 0.24 10.71| | 26: 1.22 - 1.21 2727 135 0.84 23.80 1.19 0.23 9.99| | 27: 1.21 - 1.19 2814 148 0.83 24.80 1.20 0.23 9.99| | 28: 1.19 - 1.18 2671 147 0.83 24.99 1.19 0.23 9.20| | 29: 1.18 - 1.16 2800 134 0.83 25.52 1.16 0.23 8.91| | 30: 1.16 - 1.15 2740 148 0.81 26.74 1.15 0.23 8.91| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 8.91 max = 1473.46 mean = 215.14| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 90.00 mean = 22.82| |phase err.(test): min = 0.00 max = 89.80 mean = 22.65| |-----------------------------------------------------------------------------| ----------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 : 0.082 0.249 1557 Z= 5.469 Angle : 5.342 18.550 2118 Z= 3.795 Chirality : 0.368 0.977 243 Planarity : 0.032 0.115 284 Dihedral : 13.964 77.646 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.16 % Favored : 97.30 % Rotamer: Outliers : 1.86 % Allowed : 3.11 % Favored : 95.03 % Cbeta Deviations : 31.35 % 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: -2.44 (0.49), residues: 224 helix: -2.44 (0.39), residues: 103 sheet: -0.73 (0.80), residues: 38 loop : -0.56 (0.66), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.085 0.021 ARG A 98 TYR 0.108 0.046 TYR A 139 PHE 0.094 0.039 PHE A 164 HIS 0.035 0.016 HIS A 115 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= 0.2608 r_free= 0.1947 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.794938 | | target function (ml) not normalized (work): 232835.119798 | | target function (ml) not normalized (free): 11838.361063 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2567 0.2608 0.1948 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2567 0.2608 0.1948 n_refl.: 87602 remove outliers: r(all,work,free)=0.1981 0.1985 0.1948 n_refl.: 87594 overall B=0.21 to atoms: r(all,work,free)=0.2005 0.2010 0.1963 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1647 0.1641 0.1767 n_refl.: 87594 remove outliers: r(all,work,free)=0.1646 0.1640 0.1767 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 98.94 88 5 0.3787 386.167 359.553 0.668 1.002 0.401 11.894-9.307 98.04 96 4 0.1696 615.897 590.567 0.934 1.003 0.380 9.237-7.194 100.00 213 7 0.2163 501.692 492.185 0.955 1.003 0.359 7.162-5.571 100.00 427 22 0.2229 376.492 364.974 0.926 1.003 0.282 5.546-4.326 100.00 867 58 0.1273 516.831 511.684 0.962 1.003 0.219 4.315-3.360 100.00 1859 96 0.1146 491.510 487.780 1.009 1.003 0.209 3.356-2.611 100.00 3867 181 0.1421 322.896 319.922 0.998 1.002 0.043 2.608-2.026 99.99 8198 413 0.1370 214.051 211.765 1.010 1.001 0.000 2.025-1.573 100.00 17313 902 0.1644 104.531 103.868 1.009 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2078 46.353 45.046 1.005 0.996 0.000 1.221-1.150 99.97 13689 708 0.2597 29.206 26.944 0.975 0.993 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0472 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1640 r_free=0.1767 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=0.1640 r_free=0.1767 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.790914 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2012.982750 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 0.1621 0.1741 0.0120 0.002 0.5 3.8 0.0 0.0 0 0.125 0.1504 0.1643 0.0139 0.002 0.5 3.5 0.0 0.0 0 0.250 0.1417 0.1575 0.0158 0.002 0.5 3.8 0.0 0.0 0 0.500 0.1374 0.1549 0.0175 0.002 0.5 3.5 0.0 0.0 0 0.750 0.1346 0.1531 0.0185 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1352 0.1543 0.0191 0.002 0.5 2.9 0.0 0.0 0 1.000 0.1286 0.1498 0.0212 0.002 0.6 3.2 0.5 0.0 0 2.000 0.1266 0.1485 0.0218 0.003 0.6 3.2 0.5 0.0 0 3.000 0.1255 0.1480 0.0225 0.004 0.7 3.5 0.5 0.0 0 4.000 0.1242 0.1471 0.0229 0.004 0.7 3.5 0.5 0.0 0 5.000 0.1243 0.1478 0.0235 0.005 0.8 3.5 0.5 0.0 0 6.000 0.1238 0.1473 0.0235 0.005 0.8 3.5 0.5 0.0 0 7.000 0.1233 0.1465 0.0232 0.006 0.8 3.5 0.5 0.0 0 8.000 0.1233 0.1471 0.0238 0.006 0.9 3.8 0.5 0.0 0 9.000 0.1228 0.1467 0.0238 0.006 0.9 3.5 0.5 0.0 0 10.000 0.1228 0.1463 0.0235 0.007 0.9 3.2 0.5 0.0 0 11.000 0.1226 0.1465 0.0239 0.007 0.9 3.2 0.5 0.0 0 12.000 0.1225 0.1468 0.0243 0.008 1.0 3.5 0.5 0.0 0 13.895 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1228 0.1463 0.0235 0.007 0.9 3.2 0.5 0.0 0 11.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.28 14.63 2.35 3.013 19.064 2012.983 0.017 12.28 14.63 2.35 3.011 19.064 60.389 0.017 12.35 14.59 2.24 2.667 19.063 251.623 0.017 12.71 15.29 2.59 2.930 19.357 1006.491 0.016 12.54 15.42 2.88 3.300 19.614 2012.983 0.016 12.39 15.41 3.01 3.299 19.624 3019.474 0.015 12.30 15.34 3.04 3.328 19.631 4025.965 0.015 12.26 15.40 3.14 3.292 19.604 5032.457 0.015 12.24 15.40 3.16 3.392 19.653 6038.948 0.015 12.22 15.40 3.18 3.205 19.527 7045.440 0.015 12.17 15.37 3.20 3.429 19.662 8051.931 0.015 12.18 15.44 3.26 3.501 19.687 9058.422 0.015 12.17 15.44 3.28 3.502 19.671 10064.914 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: 251.623 Accepted refinement result: 12.35 14.59 2.24 2.667 19.063 251.623 0.017 Individual atomic B min max mean iso aniso Overall: 9.07 119.45 20.09 3.31 0 1785 Protein: 9.07 114.99 17.00 3.31 0 1519 Water: 11.47 119.45 38.23 N/A 0 258 Other: 19.71 26.59 22.06 N/A 0 8 Chain A: 9.07 119.45 20.09 N/A 0 1785 Histogram: Values Number of atoms 9.07 - 20.11 1272 20.11 - 31.15 227 31.15 - 42.18 125 42.18 - 53.22 94 53.22 - 64.26 42 64.26 - 75.30 11 75.30 - 86.33 7 86.33 - 97.37 4 97.37 - 108.41 1 108.41 - 119.45 2 =========================== Idealize ADP of riding H ========================== r_work=0.1235 r_free=0.1459 r_work=0.1236 r_free=0.1462 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1236 r_free = 0.1462 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 = 0.1230 r_free = 0.1457 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1230 r_free= 0.1457 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016693 | | target function (ls_wunit_k1) not normalized (work): 1390.467353 | | target function (ls_wunit_k1) not normalized (free): 108.897971 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1241 0.1230 0.1457 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1673 0.1674 0.1687 n_refl.: 87592 remove outliers: r(all,work,free)=0.1673 0.1674 0.1687 n_refl.: 87592 overall B=0.03 to atoms: r(all,work,free)=0.1679 0.1681 0.1691 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1239 0.1228 0.1450 n_refl.: 87592 remove outliers: r(all,work,free)=0.1238 0.1228 0.1450 n_refl.: 87591 ======================== 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 0.3547 301.545 282.963 0.638 1.003 0.374 11.894-9.307 98.04 96 4 0.1586 485.019 472.615 0.928 1.003 0.370 9.237-7.194 100.00 213 7 0.1903 395.082 389.239 0.962 1.003 0.350 7.162-5.571 100.00 427 22 0.1844 296.487 290.419 0.935 1.003 0.254 5.546-4.326 100.00 867 58 0.1000 407.004 403.839 0.962 1.003 0.209 4.315-3.360 100.00 1859 96 0.0863 387.064 386.035 1.010 1.003 0.190 3.356-2.611 100.00 3867 181 0.1175 254.281 253.115 1.010 1.002 0.090 2.608-2.026 99.99 8198 413 0.1019 168.565 167.844 1.019 1.001 0.000 2.025-1.573 100.00 17313 902 0.1116 82.318 82.508 1.026 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1456 36.503 36.008 1.019 0.997 0.000 1.221-1.150 99.97 13689 708 0.2256 23.000 21.485 0.982 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0519 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1228 r_free=0.1450 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 r_work=0.1230 r_free=0.1451 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1230 r_free=0.1451 | n_water=258 | time (s): 1.930 (total time: 1.930) Filter (dist) r_work=0.1237 r_free=0.1449 | n_water=252 | time (s): 21.150 (total time: 23.080) Filter (q & B) r_work=0.1240 r_free=0.1449 | n_water=249 | time (s): 2.510 (total time: 25.590) Compute maps r_work=0.1240 r_free=0.1449 | n_water=249 | time (s): 1.630 (total time: 27.220) Filter (map) r_work=0.1255 r_free=0.1458 | n_water=226 | time (s): 2.930 (total time: 30.150) Find peaks r_work=0.1255 r_free=0.1458 | n_water=226 | time (s): 0.670 (total time: 30.820) Add new water r_work=0.1399 r_free=0.1631 | n_water=440 | time (s): 3.010 (total time: 33.830) Refine new water occ: r_work=0.1300 r_free=0.1489 adp: r_work=0.1224 r_free=0.1435 occ: r_work=0.1236 r_free=0.1424 adp: r_work=0.1204 r_free=0.1409 occ: r_work=0.1207 r_free=0.1397 adp: r_work=0.1198 r_free=0.1397 ADP+occupancy (water only), MIN, final r_work=0.1198 r_free=0.1397 r_work=0.1198 r_free=0.1397 | n_water=440 | time (s): 59.820 (total time: 93.650) Filter (q & B) r_work=0.1202 r_free=0.1400 | n_water=421 | time (s): 3.310 (total time: 96.960) Filter (dist only) r_work=0.1203 r_free=0.1398 | n_water=420 | time (s): 35.240 (total time: 132.200) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 29.064494 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1500.148036 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 0.1649 0.1764 0.0115 0.001 0.4 7.0 0.0 0.0 0 0.125 0.1510 0.1641 0.0131 0.002 0.4 6.4 0.0 0.0 0 0.250 0.1411 0.1561 0.0150 0.001 0.4 5.4 0.0 0.0 0 0.500 0.1359 0.1521 0.0162 0.001 0.4 5.1 0.0 0.0 0 0.750 0.1323 0.1498 0.0175 0.002 0.5 4.8 0.0 0.0 0 1.000 0.1302 0.1478 0.0176 0.002 0.5 4.5 0.0 0.0 0 1.000 0.1253 0.1452 0.0199 0.002 0.5 3.8 0.5 0.0 0 2.000 0.1230 0.1436 0.0206 0.003 0.6 4.2 0.5 0.0 0 3.000 0.1213 0.1426 0.0213 0.003 0.7 4.8 0.5 0.0 0 4.000 0.1209 0.1419 0.0210 0.004 0.7 4.8 0.5 0.0 0 5.000 0.1204 0.1417 0.0213 0.004 0.7 5.1 0.5 0.0 0 6.000 0.1201 0.1421 0.0220 0.005 0.8 5.1 0.5 0.0 0 7.000 0.1195 0.1411 0.0216 0.005 0.8 4.2 0.5 0.0 0 8.000 0.1192 0.1418 0.0226 0.006 0.8 4.8 0.5 0.0 0 9.000 0.1190 0.1421 0.0231 0.006 0.9 4.8 0.5 0.0 0 10.000 0.1188 0.1417 0.0229 0.007 0.9 5.1 0.5 0.0 0 11.000 0.1187 0.1420 0.0233 0.007 0.9 5.1 0.5 0.0 0 12.000 0.1184 0.1416 0.0232 0.007 0.9 5.8 0.5 0.0 0 13.000 0.1182 0.1415 0.0233 0.008 0.9 5.1 0.5 0.0 0 14.532 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1195 0.1411 0.0216 0.005 0.8 4.2 0.5 0.0 0 8.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.95 14.11 2.16 3.775 21.766 1500.148 0.016 11.95 14.11 2.16 3.775 21.766 45.004 0.016 11.95 14.11 2.16 3.772 21.766 187.519 0.016 12.21 14.67 2.46 3.578 21.800 750.074 0.016 12.15 14.89 2.74 3.483 22.110 1500.148 0.015 12.02 14.92 2.90 3.502 21.905 2250.222 0.015 11.83 14.72 2.89 3.529 21.870 3000.296 0.015 11.76 14.70 2.94 3.519 21.907 3750.370 0.014 11.82 14.80 2.98 3.521 22.093 4500.444 0.014 11.77 14.75 2.98 3.528 22.110 5250.518 0.014 11.75 14.79 3.04 3.543 22.139 6000.592 0.014 11.72 14.77 3.05 3.544 22.045 6750.666 0.014 11.71 14.81 3.10 3.594 22.158 7500.740 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: 45.004 Accepted refinement result: 11.95 14.11 2.16 3.775 21.766 45.004 0.016 Individual atomic B min max mean iso aniso Overall: 9.10 115.02 22.16 3.31 194 1753 Protein: 9.10 115.02 17.03 3.31 0 1519 Water: 10.91 76.70 40.71 N/A 194 226 Other: 19.75 26.62 22.09 N/A 0 8 Chain A: 9.10 115.02 19.48 N/A 0 1753 Chain S: 10.91 60.00 46.35 N/A 194 0 Histogram: Values Number of atoms 9.10 - 19.70 1259 19.70 - 30.29 248 30.29 - 40.88 165 40.88 - 51.47 134 51.47 - 62.06 117 62.06 - 72.65 13 72.65 - 83.25 5 83.25 - 93.84 4 93.84 - 104.43 0 104.43 - 115.02 2 =========================== Idealize ADP of riding H ========================== r_work=0.1195 r_free=0.1411 r_work=0.1195 r_free=0.1411 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1195 r_free = 0.1411 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1192 r_free = 0.1415 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.=87591 (all), 4.90 % free)------------| | | | r_work= 0.1192 r_free= 0.1415 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.015268 | | target function (ls_wunit_k1) not normalized (work): 1271.749723 | | target function (ls_wunit_k1) not normalized (free): 100.582387 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1203 0.1192 0.1415 n_refl.: 87591 re-set all scales: r(all,work,free)=0.1578 0.1578 0.1612 n_refl.: 87591 remove outliers: r(all,work,free)=0.1578 0.1578 0.1612 n_refl.: 87591 overall B=0.01 to atoms: r(all,work,free)=0.1580 0.1580 0.1614 n_refl.: 87591 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1190 0.1410 n_refl.: 87591 remove outliers: r(all,work,free)=0.1199 0.1188 0.1410 n_refl.: 87588 ======================== 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 0.3360 297.447 273.979 0.589 1.003 0.350 11.894-9.307 98.04 96 4 0.1656 485.019 475.899 0.919 1.003 0.333 9.237-7.194 100.00 213 7 0.1749 395.082 393.957 0.979 1.003 0.290 7.162-5.571 100.00 427 22 0.1626 296.487 292.473 0.935 1.003 0.220 5.546-4.326 100.00 867 58 0.0897 407.004 403.463 0.958 1.003 0.194 4.315-3.360 100.00 1859 96 0.0790 387.064 386.003 1.005 1.003 0.180 3.356-2.611 100.00 3867 181 0.1080 254.281 253.296 1.011 1.002 0.100 2.608-2.026 99.99 8198 413 0.1002 168.565 168.042 1.020 1.001 0.000 2.025-1.573 100.00 17313 902 0.1109 82.318 82.535 1.030 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1450 36.503 36.034 1.023 0.997 0.000 1.221-1.150 99.97 13689 708 0.2257 23.000 21.511 0.987 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0159 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1188 r_free=0.1410 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN B Total number of N/Q/H flips: 1 r_work=0.1189 r_free=0.1410 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1189 r_free=0.1410 | n_water=420 | time (s): 1.660 (total time: 1.660) Filter (dist) r_work=0.1188 r_free=0.1412 | n_water=419 | time (s): 33.880 (total time: 35.540) Filter (q & B) r_work=0.1188 r_free=0.1412 | n_water=419 | time (s): 1.210 (total time: 36.750) Compute maps r_work=0.1188 r_free=0.1412 | n_water=419 | time (s): 1.530 (total time: 38.280) Filter (map) r_work=0.1230 r_free=0.1384 | n_water=286 | time (s): 3.380 (total time: 41.660) Find peaks r_work=0.1230 r_free=0.1384 | n_water=286 | time (s): 0.520 (total time: 42.180) Add new water r_work=0.1339 r_free=0.1500 | n_water=471 | time (s): 3.330 (total time: 45.510) Refine new water occ: r_work=0.1241 r_free=0.1414 adp: r_work=0.1242 r_free=0.1415 occ: r_work=0.1220 r_free=0.1394 adp: r_work=0.1219 r_free=0.1395 occ: r_work=0.1205 r_free=0.1377 adp: r_work=0.1200 r_free=0.1376 ADP+occupancy (water only), MIN, final r_work=0.1200 r_free=0.1376 r_work=0.1200 r_free=0.1376 | n_water=471 | time (s): 179.520 (total time: 225.030) Filter (q & B) r_work=0.1206 r_free=0.1381 | n_water=437 | time (s): 2.990 (total time: 228.020) Filter (dist only) r_work=0.1206 r_free=0.1380 | n_water=436 | time (s): 36.440 (total time: 264.460) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.785401 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 41.773849 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 0.1233 0.1343 0.0110 0.002 0.6 4.2 0.5 0.0 0 0.089 0.1184 0.1309 0.0125 0.003 0.7 3.5 0.5 0.0 0 0.268 0.1169 0.1299 0.0130 0.004 0.8 3.2 0.5 0.0 0 0.536 0.1162 0.1298 0.0136 0.005 0.9 3.5 0.5 0.0 0 0.803 0.1156 0.1299 0.0142 0.006 1.0 3.8 0.5 0.0 0 1.071 0.1154 0.1298 0.0144 0.007 1.0 3.5 0.5 0.0 0 1.339 0.1152 0.1299 0.0147 0.007 1.1 3.8 0.5 0.0 0 1.607 0.1151 0.1305 0.0154 0.008 1.1 3.8 0.5 0.0 0 1.875 0.1160 0.1300 0.0140 0.005 0.9 3.5 0.5 0.0 0 0.893 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1154 0.1298 0.0144 0.007 1.0 3.5 0.5 0.0 0 1.339 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.54 12.98 1.44 3.778 21.268 41.774 3.618 11.54 12.98 1.44 3.778 21.268 1.253 3.618 11.54 12.98 1.44 3.777 21.268 5.222 3.618 11.57 13.04 1.46 3.711 21.261 20.887 3.611 11.63 13.18 1.56 3.730 21.229 41.774 3.614 11.57 13.17 1.61 3.745 21.215 62.661 3.608 11.49 13.12 1.63 3.769 21.212 83.548 3.603 11.46 13.09 1.63 3.778 21.206 104.435 3.600 11.44 13.11 1.67 3.791 21.202 125.322 3.599 11.43 13.14 1.71 3.807 21.190 146.208 3.598 11.40 13.11 1.71 3.814 21.189 167.095 3.596 11.39 13.09 1.70 3.822 21.186 187.982 3.595 11.38 13.08 1.70 3.828 21.184 208.869 3.594 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.253 Accepted refinement result: 11.54 12.98 1.44 3.778 21.268 1.253 3.618 Individual atomic B min max mean iso aniso Overall: 9.11 115.03 21.24 3.31 213 1750 Protein: 9.11 115.03 17.04 3.31 0 1519 Water: 10.92 76.71 35.86 N/A 213 223 Other: 19.76 26.63 22.10 N/A 0 8 Chain A: 9.11 115.03 19.45 N/A 0 1750 Chain S: 10.92 60.01 35.96 N/A 213 0 Histogram: Values Number of atoms 9.11 - 19.71 1264 19.71 - 30.30 279 30.30 - 40.89 215 40.89 - 51.48 127 51.48 - 62.07 54 62.07 - 72.66 13 72.66 - 83.26 5 83.26 - 93.85 4 93.85 - 104.44 0 104.44 - 115.03 2 =========================== Idealize ADP of riding H ========================== r_work=0.1154 r_free=0.1298 r_work=0.1154 r_free=0.1298 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1154 r_free = 0.1298 target_work(ml) = 3.618 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1148 r_free = 0.1304 target_work(ml) = 3.612 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87588 (all), 4.90 % free)------------| | | | r_work= 0.1148 r_free= 0.1304 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.611651 | | target function (ml) not normalized (work): 300821.626030 | | target function (ml) not normalized (free): 15832.429150 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1155 0.1148 0.1304 n_refl.: 87588 re-set all scales: r(all,work,free)=0.1488 0.1488 0.1514 n_refl.: 87588 remove outliers: r(all,work,free)=0.1488 0.1488 0.1514 n_refl.: 87588 overall B=-0.00 to atoms: r(all,work,free)=0.1487 0.1488 0.1514 n_refl.: 87588 bulk-solvent and scaling: r(all,work,free)=0.1152 0.1145 0.1303 n_refl.: 87588 remove outliers: r(all,work,free)=0.1150 0.1142 0.1303 n_refl.: 87580 ======================== 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 0.3921 294.170 259.699 0.500 1.000 0.330 11.894-9.307 96.08 94 4 0.2051 478.322 467.218 0.887 1.001 0.330 9.237-7.194 98.18 209 7 0.2174 386.553 387.497 0.965 1.001 0.205 7.162-5.571 100.00 427 22 0.2066 296.487 286.078 0.926 1.002 0.190 5.546-4.326 100.00 867 58 0.1088 407.004 401.891 0.964 1.002 0.180 4.315-3.360 100.00 1859 96 0.0928 387.064 384.549 1.002 1.002 0.170 3.356-2.611 100.00 3867 181 0.1147 254.281 252.228 1.006 1.002 0.053 2.608-2.026 99.99 8198 413 0.0938 168.565 167.879 1.022 1.002 0.000 2.025-1.573 100.00 17313 902 0.0902 82.318 82.623 1.032 1.002 0.000 1.573-1.221 100.00 36679 1900 0.1260 36.503 36.075 1.023 1.001 0.000 1.221-1.150 99.97 13689 708 0.2166 23.000 21.446 0.980 1.001 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0025 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1142 r_free=0.1303 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.1146 r_free=0.1304 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1146 r_free=0.1304 | n_water=436 | time (s): 2.530 (total time: 2.530) Filter (dist) r_work=0.1146 r_free=0.1305 | n_water=434 | time (s): 49.030 (total time: 51.560) Filter (q & B) r_work=0.1146 r_free=0.1304 | n_water=432 | time (s): 3.840 (total time: 55.400) Compute maps r_work=0.1146 r_free=0.1304 | n_water=432 | time (s): 1.830 (total time: 57.230) Filter (map) r_work=0.1166 r_free=0.1306 | n_water=321 | time (s): 3.790 (total time: 61.020) Find peaks r_work=0.1166 r_free=0.1306 | n_water=321 | time (s): 0.690 (total time: 61.710) Add new water r_work=0.1247 r_free=0.1391 | n_water=489 | time (s): 3.730 (total time: 65.440) Refine new water occ: r_work=0.1173 r_free=0.1336 adp: r_work=0.1174 r_free=0.1338 occ: r_work=0.1156 r_free=0.1319 adp: r_work=0.1155 r_free=0.1320 occ: r_work=0.1142 r_free=0.1307 adp: r_work=0.1138 r_free=0.1304 ADP+occupancy (water only), MIN, final r_work=0.1138 r_free=0.1304 r_work=0.1138 r_free=0.1304 | n_water=489 | time (s): 261.360 (total time: 326.800) Filter (q & B) r_work=0.1148 r_free=0.1308 | n_water=443 | time (s): 3.860 (total time: 330.660) Filter (dist only) r_work=0.1154 r_free=0.1306 | n_water=441 | time (s): 45.100 (total time: 375.760) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.787788 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 35.727324 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 0.1211 0.1341 0.0130 0.002 0.6 4.2 0.5 0.0 0 0.089 0.1173 0.1316 0.0143 0.003 0.8 3.2 0.5 0.0 0 0.268 0.1160 0.1309 0.0149 0.004 0.9 3.5 0.5 0.0 0 0.536 0.1154 0.1306 0.0153 0.006 0.9 3.8 0.5 0.0 0 0.805 0.1150 0.1304 0.0154 0.006 1.0 3.8 0.5 0.0 0 1.073 0.1147 0.1304 0.0156 0.007 1.1 3.5 0.5 0.0 0 1.341 0.1145 0.1301 0.0156 0.008 1.1 3.8 0.5 0.0 0 1.609 0.1144 0.1301 0.0157 0.009 1.1 4.2 0.5 0.0 0 1.877 0.1152 0.1304 0.0152 0.006 1.0 4.2 0.5 0.0 0 0.894 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1145 0.1301 0.0156 0.008 1.1 3.8 0.5 0.0 0 1.609 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.45 13.01 1.56 3.779 21.219 35.727 3.610 11.45 13.01 1.56 3.779 21.219 1.072 3.610 11.45 13.01 1.56 3.779 21.219 4.466 3.610 11.49 13.05 1.56 3.709 21.212 17.864 3.606 11.60 13.24 1.65 3.717 21.188 35.727 3.611 11.48 13.17 1.69 3.751 21.177 53.591 3.604 11.46 13.19 1.73 3.761 21.170 71.455 3.601 11.41 13.16 1.75 3.774 21.167 89.318 3.597 11.39 13.16 1.76 3.780 21.167 107.182 3.596 11.36 13.13 1.77 3.788 21.166 125.046 3.593 11.37 13.18 1.81 3.803 21.154 142.909 3.594 11.35 13.15 1.81 3.811 21.152 160.773 3.592 11.35 13.18 1.82 3.822 21.148 178.637 3.592 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.072 Accepted refinement result: 11.45 13.01 1.56 3.779 21.219 1.072 3.610 Individual atomic B min max mean iso aniso Overall: 9.11 115.03 21.15 3.31 221 1747 Protein: 9.11 115.03 17.04 3.31 0 1519 Water: 10.92 76.71 35.30 N/A 221 220 Other: 19.76 26.63 22.10 N/A 0 8 Chain A: 9.11 115.03 19.42 N/A 0 1747 Chain S: 10.92 60.01 34.81 N/A 221 0 Histogram: Values Number of atoms 9.11 - 19.70 1266 19.70 - 30.30 290 30.30 - 40.89 215 40.89 - 51.48 119 51.48 - 62.07 54 62.07 - 72.66 13 72.66 - 83.25 5 83.25 - 93.85 4 93.85 - 104.44 0 104.44 - 115.03 2 =========================== Idealize ADP of riding H ========================== r_work=0.1145 r_free=0.1301 r_work=0.1145 r_free=0.1301 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1145 r_free = 0.1301 target_work(ml) = 3.610 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1139 r_free = 0.1301 target_work(ml) = 3.607 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87580 (all), 4.91 % free)------------| | | | r_work= 0.1139 r_free= 0.1301 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.607490 | | target function (ml) not normalized (work): 300446.180552 | | target function (ml) not normalized (free): 15829.016208 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1146 0.1139 0.1301 n_refl.: 87580 re-set all scales: r(all,work,free)=0.1462 0.1461 0.1512 n_refl.: 87580 remove outliers: r(all,work,free)=0.1462 0.1461 0.1512 n_refl.: 87580 overall B=-0.01 to atoms: r(all,work,free)=0.1461 0.1459 0.1511 n_refl.: 87580 bulk-solvent and scaling: r(all,work,free)=0.1143 0.1135 0.1298 n_refl.: 87580 remove outliers: r(all,work,free)=0.1141 0.1133 0.1298 n_refl.: 87574 ======================== 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 87.50 79 5 0.3841 290.933 259.000 0.457 1.001 0.310 11.894-9.307 93.14 91 4 0.2211 473.237 453.415 0.857 1.002 0.243 9.237-7.194 98.18 209 7 0.2315 386.553 380.496 0.924 1.002 0.180 7.162-5.571 100.00 427 22 0.2067 296.487 286.037 0.907 1.002 0.150 5.546-4.326 100.00 867 58 0.1101 407.004 401.655 0.956 1.002 0.135 4.315-3.360 100.00 1859 96 0.0921 387.064 384.939 0.993 1.002 0.130 3.356-2.611 100.00 3867 181 0.1125 254.281 252.437 1.000 1.002 0.034 2.608-2.026 99.99 8198 413 0.0926 168.565 167.937 1.015 1.001 0.000 2.025-1.573 100.00 17313 902 0.0889 82.318 82.659 1.025 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1250 36.503 36.123 1.018 0.998 0.000 1.221-1.150 99.97 13689 708 0.2166 23.000 21.560 0.980 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0190 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1133 r_free=0.1298 After: r_work=0.1134 r_free=0.1298 ================================== NQH flips ================================== r_work=0.1134 r_free=0.1298 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=0.1134 r_free=0.1298 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1134 r_free=0.1298 | n_water=441 | time (s): 2.480 (total time: 2.480) Filter (dist) r_work=0.1134 r_free=0.1298 | n_water=441 | time (s): 43.000 (total time: 45.480) Filter (q & B) r_work=0.1135 r_free=0.1297 | n_water=440 | time (s): 3.960 (total time: 49.440) Compute maps r_work=0.1135 r_free=0.1297 | n_water=440 | time (s): 1.850 (total time: 51.290) Filter (map) r_work=0.1156 r_free=0.1290 | n_water=344 | time (s): 3.900 (total time: 55.190) Find peaks r_work=0.1156 r_free=0.1290 | n_water=344 | time (s): 0.700 (total time: 55.890) Add new water r_work=0.1207 r_free=0.1346 | n_water=500 | time (s): 3.680 (total time: 59.570) Refine new water occ: r_work=0.1147 r_free=0.1294 adp: r_work=0.1148 r_free=0.1295 occ: r_work=0.1136 r_free=0.1281 adp: r_work=0.1134 r_free=0.1281 occ: r_work=0.1127 r_free=0.1274 adp: r_work=0.1123 r_free=0.1272 ADP+occupancy (water only), MIN, final r_work=0.1123 r_free=0.1272 r_work=0.1123 r_free=0.1272 | n_water=500 | time (s): 219.230 (total time: 278.800) Filter (q & B) r_work=0.1132 r_free=0.1282 | n_water=455 | time (s): 3.850 (total time: 282.650) Filter (dist only) r_work=0.1132 r_free=0.1283 | n_water=453 | time (s): 46.890 (total time: 329.540) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.780764 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 34.760208 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 0.1227 0.1343 0.0116 0.004 0.7 9.0 0.0 0.0 0 0.089 0.1172 0.1306 0.0134 0.004 0.8 9.3 0.0 0.0 0 0.267 0.1153 0.1294 0.0140 0.005 0.9 8.6 0.5 0.0 0 0.534 0.1143 0.1286 0.0143 0.006 1.0 9.3 0.5 0.0 0 0.801 0.1137 0.1284 0.0147 0.006 1.1 8.6 0.5 0.0 0 1.068 0.1133 0.1283 0.0150 0.007 1.1 8.6 0.5 0.0 0 1.336 0.1132 0.1283 0.0151 0.008 1.1 8.3 0.5 0.0 0 1.603 0.1131 0.1283 0.0151 0.008 1.1 8.3 0.5 0.0 0 1.870 0.1139 0.1284 0.0145 0.006 1.0 9.0 0.5 0.0 0 0.890 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1132 0.1283 0.0151 0.008 1.1 8.3 0.5 0.0 0 1.603 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.32 12.83 1.51 3.779 21.241 34.760 3.603 11.32 12.83 1.51 3.779 21.241 1.043 3.603 11.32 12.83 1.51 3.779 21.241 4.345 3.603 11.36 12.87 1.51 3.708 21.234 17.380 3.599 11.39 12.99 1.59 3.730 21.214 34.760 3.601 11.36 13.02 1.66 3.750 21.199 52.140 3.598 11.33 13.02 1.69 3.758 21.193 69.520 3.594 11.28 12.98 1.70 3.773 21.191 86.901 3.591 11.27 12.97 1.71 3.779 21.191 104.281 3.589 11.23 12.95 1.71 3.787 21.190 121.661 3.587 11.21 12.92 1.71 3.792 21.190 139.041 3.585 11.22 12.97 1.75 3.809 21.180 156.421 3.586 11.21 12.96 1.75 3.816 21.179 173.801 3.585 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.043 Accepted refinement result: 11.32 12.83 1.51 3.779 21.241 1.043 3.603 Individual atomic B min max mean iso aniso Overall: 9.11 115.02 21.20 3.31 234 1746 Protein: 9.11 115.02 17.03 3.31 0 1519 Water: 10.91 76.70 35.15 N/A 234 219 Other: 19.75 26.62 22.09 N/A 0 8 Chain A: 9.11 115.02 19.40 N/A 0 1746 Chain S: 10.91 60.00 34.63 N/A 234 0 Histogram: Values Number of atoms 9.11 - 19.70 1266 19.70 - 30.29 296 30.29 - 40.88 215 40.88 - 51.47 129 51.47 - 62.06 50 62.06 - 72.66 13 72.66 - 83.25 5 83.25 - 93.84 4 93.84 - 104.43 0 104.43 - 115.02 2 =========================== Idealize ADP of riding H ========================== r_work=0.1132 r_free=0.1283 r_work=0.1132 r_free=0.1283 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1132 r_free = 0.1283 target_work(ml) = 3.603 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1128 r_free = 0.1281 target_work(ml) = 3.601 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87574 (all), 4.91 % free)------------| | | | r_work= 0.1128 r_free= 0.1281 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.601409 | | target function (ml) not normalized (work): 299918.146958 | | target function (ml) not normalized (free): 15797.934189 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2916 171 0.1295 0.1314 5.613 5.5695| | 2: 3.57 - 2.84 1.00 2888 124 0.1066 0.1348 5.1452 5.1995| | 3: 2.83 - 2.48 1.00 2820 163 0.1106 0.1201 4.9274 4.9578| | 4: 2.47 - 2.25 1.00 2825 136 0.0901 0.1031 4.6121 4.6625| | 5: 2.25 - 2.09 1.00 2756 127 0.0871 0.0969 4.5585 4.612| | 6: 2.09 - 1.97 1.00 2846 113 0.0865 0.0986 4.261 4.3471| | 7: 1.97 - 1.87 1.00 2787 165 0.0877 0.1125 3.9752 4.0998| | 8: 1.87 - 1.79 1.00 2789 144 0.0919 0.1089 3.8896 3.99| | 9: 1.79 - 1.72 1.00 2745 138 0.0889 0.1173 3.6511 3.8112| | 10: 1.72 - 1.66 1.00 2831 160 0.0923 0.1222 3.5677 3.7253| | 11: 1.66 - 1.61 1.00 2712 147 0.0874 0.1046 3.4981 3.5717| | 12: 1.61 - 1.56 1.00 2773 144 0.0911 0.1170 3.3352 3.4749| | 13: 1.56 - 1.52 1.00 2745 130 0.0946 0.1064 3.3125 3.4077| | 14: 1.52 - 1.48 1.00 2803 134 0.0987 0.1022 3.2459 3.3226| | 15: 1.48 - 1.45 1.00 2738 128 0.1001 0.1226 3.1554 3.27| | 16: 1.45 - 1.42 1.00 2756 161 0.1052 0.1220 3.1384 3.2318| | 17: 1.42 - 1.39 1.00 2785 139 0.1139 0.1294 3.1203 3.2354| | 18: 1.39 - 1.36 1.00 2741 179 0.1199 0.1315 3.1057 3.2342| | 19: 1.36 - 1.34 1.00 2807 134 0.1259 0.1551 3.1123 3.2596| | 20: 1.34 - 1.32 1.00 2696 147 0.1372 0.1460 3.1148 3.1507| | 21: 1.32 - 1.30 1.00 2785 112 0.1477 0.1524 3.1164 3.1189| | 22: 1.29 - 1.27 1.00 2704 152 0.1560 0.1976 3.1237 3.2923| | 23: 1.27 - 1.26 1.00 2802 156 0.1650 0.1793 3.1337 3.2042| | 24: 1.26 - 1.24 1.00 2744 132 0.1707 0.1834 3.1275 3.2267| | 25: 1.24 - 1.22 1.00 2733 148 0.1878 0.2168 3.1428 3.2627| | 26: 1.22 - 1.21 1.00 2727 135 0.1907 0.1754 3.1489 3.2026| | 27: 1.21 - 1.19 1.00 2814 148 0.2073 0.2166 3.1726 3.1658| | 28: 1.19 - 1.18 1.00 2671 147 0.2200 0.2287 3.1664 3.1712| | 29: 1.18 - 1.16 1.00 2800 134 0.2266 0.2392 3.1487 3.2325| | 30: 1.16 - 1.15 1.00 2739 148 0.2442 0.2448 3.1432 3.1681| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2916 171 0.95 8.18 1.00 0.98 5365.67| | 2: 3.57 - 2.84 2888 124 0.93 12.08 1.01 0.98 5365.67| | 3: 2.83 - 2.48 2820 163 0.90 15.91 0.99 0.98 4489.38| | 4: 2.47 - 2.25 2825 136 0.92 13.01 1.00 0.99 2229.73| | 5: 2.25 - 2.09 2756 127 0.91 15.02 1.01 0.99 2229.73| | 6: 2.09 - 1.97 2846 113 0.93 12.10 1.02 0.99 1300.75| | 7: 1.97 - 1.87 2787 165 0.95 9.21 1.02 0.99 508.46| | 8: 1.87 - 1.79 2789 144 0.93 12.56 1.00 0.99 508.46| | 9: 1.79 - 1.72 2745 138 0.94 10.10 0.98 0.98 289.32| | 10: 1.72 - 1.66 2831 160 0.94 11.12 0.98 0.98 245.44| | 11: 1.66 - 1.61 2712 147 0.93 11.76 0.98 0.98 235.20| | 12: 1.61 - 1.56 2773 144 0.95 8.92 0.99 0.98 138.70| | 13: 1.56 - 1.52 2745 130 0.95 10.44 1.02 0.98 138.70| | 14: 1.52 - 1.48 2803 134 0.94 10.78 1.02 0.99 124.31| | 15: 1.48 - 1.45 2738 128 0.95 9.92 1.02 0.99 97.95| | 16: 1.45 - 1.42 2756 161 0.94 11.07 1.02 0.99 97.95| | 17: 1.42 - 1.39 2785 139 0.95 10.94 1.01 0.99 89.13| | 18: 1.39 - 1.36 2741 179 0.94 11.54 1.01 0.99 84.03| | 19: 1.36 - 1.34 2807 134 0.94 11.86 1.00 0.99 84.03| | 20: 1.34 - 1.32 2696 147 0.94 12.12 0.98 0.97 80.17| | 21: 1.32 - 1.30 2785 112 0.94 13.10 0.98 0.97 79.90| | 22: 1.29 - 1.27 2704 152 0.93 13.63 0.98 0.97 80.32| | 23: 1.27 - 1.26 2802 156 0.92 14.87 0.97 0.95 82.47| | 24: 1.26 - 1.24 2744 132 0.92 14.87 0.96 0.95 82.47| | 25: 1.24 - 1.22 2733 148 0.91 16.37 0.96 0.95 84.44| | 26: 1.22 - 1.21 2727 135 0.90 18.13 1.02 0.94 86.63| | 27: 1.21 - 1.19 2814 148 0.89 18.77 1.02 0.94 86.63| | 28: 1.19 - 1.18 2671 147 0.88 20.40 1.01 0.94 90.18| | 29: 1.18 - 1.16 2800 134 0.88 20.50 0.98 0.93 91.52| | 30: 1.16 - 1.15 2739 148 0.86 22.02 0.98 0.93 91.52| |alpha: min = 0.93 max = 0.99 mean = 0.97| |beta: min = 79.90 max = 5365.67 mean = 838.74| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.99 mean = 13.36| |phase err.(test): min = 0.00 max = 89.82 mean = 13.34| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1136 0.1128 0.1281 n_refl.: 87574 re-set all scales: r(all,work,free)=0.1448 0.1447 0.1489 n_refl.: 87574 remove outliers: r(all,work,free)=0.1448 0.1447 0.1489 n_refl.: 87574 overall B=-0.00 to atoms: r(all,work,free)=0.1447 0.1446 0.1488 n_refl.: 87574 bulk-solvent and scaling: r(all,work,free)=0.1136 0.1129 0.1281 n_refl.: 87574 remove outliers: r(all,work,free)=0.1135 0.1127 0.1281 n_refl.: 87570 ======================== 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 86.46 78 5 0.3901 286.072 255.346 0.440 1.000 0.281 11.894-9.307 91.18 89 4 0.2127 473.342 460.852 0.870 1.002 0.223 9.237-7.194 97.73 208 7 0.2213 387.637 381.368 0.926 1.002 0.190 7.162-5.571 100.00 427 22 0.2053 296.487 286.640 0.912 1.002 0.141 5.546-4.326 100.00 867 58 0.1109 407.004 401.785 0.965 1.002 0.130 4.315-3.360 100.00 1859 96 0.0920 387.064 384.834 1.003 1.002 0.120 3.356-2.611 100.00 3867 181 0.1109 254.281 252.422 1.011 1.002 0.050 2.608-2.026 99.99 8198 413 0.0914 168.565 167.935 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0892 82.318 82.664 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1252 36.503 36.113 1.027 0.998 0.000 1.221-1.150 99.97 13689 708 0.2168 23.000 21.550 0.989 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0131 ================= 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 : 0.2608 0.1947 0.082 5.342 8.8 119.3 19.9 258 0.000 1_bss: 0.1640 0.1767 0.082 5.342 9.1 119.5 20.1 258 0.000 1_settarget: 0.1640 0.1767 0.082 5.342 9.1 119.5 20.1 258 0.000 1_nqh: 0.1640 0.1767 0.082 5.342 9.1 119.5 20.1 258 0.000 1_weight: 0.1640 0.1767 0.082 5.342 9.1 119.5 20.1 258 0.000 1_xyzrec: 0.1228 0.1463 0.007 0.908 9.1 119.5 20.1 258 0.130 1_adp: 0.1235 0.1459 0.007 0.908 9.1 119.4 20.1 258 0.130 1_regHadp: 0.1236 0.1462 0.007 0.908 9.1 119.4 20.1 258 0.130 1_occ: 0.1230 0.1457 0.007 0.908 9.1 119.4 20.1 258 0.130 2_bss: 0.1228 0.1450 0.007 0.908 9.1 119.5 20.1 258 0.130 2_settarget: 0.1228 0.1450 0.007 0.908 9.1 119.5 20.1 258 0.130 2_updatecdl: 0.1228 0.1450 0.007 0.916 9.1 119.5 20.1 258 0.130 2_nqh: 0.1230 0.1451 0.007 0.916 9.1 119.5 20.1 258 0.136 2_sol: 0.1203 0.1398 0.007 0.916 9.1 115.0 22.2 420 n/a 2_weight: 0.1203 0.1398 0.007 0.916 9.1 115.0 22.2 420 n/a 2_xyzrec: 0.1195 0.1411 0.005 0.797 9.1 115.0 22.2 420 n/a 2_adp: 0.1195 0.1411 0.005 0.797 9.1 115.0 22.2 420 n/a 2_regHadp: 0.1195 0.1411 0.005 0.797 9.1 115.0 22.2 420 n/a 2_occ: 0.1192 0.1415 0.005 0.797 9.1 115.0 22.2 420 n/a 3_bss: 0.1188 0.1410 0.005 0.797 9.1 115.0 22.2 420 n/a 3_settarget: 0.1188 0.1410 0.005 0.797 9.1 115.0 22.2 420 n/a 3_updatecdl: 0.1188 0.1410 0.005 0.797 9.1 115.0 22.2 420 n/a 3_nqh: 0.1189 0.1410 0.005 0.797 9.1 115.0 22.2 420 n/a 3_sol: 0.1206 0.1380 0.005 0.797 9.1 115.0 21.2 436 n/a 3_weight: 0.1206 0.1380 0.005 0.797 9.1 115.0 21.2 436 n/a 3_xyzrec: 0.1154 0.1298 0.007 1.011 9.1 115.0 21.2 436 n/a 3_adp: 0.1154 0.1298 0.007 1.011 9.1 115.0 21.2 436 n/a 3_regHadp: 0.1154 0.1298 0.007 1.011 9.1 115.0 21.2 436 n/a 3_occ: 0.1148 0.1304 0.007 1.011 9.1 115.0 21.2 436 n/a 4_bss: 0.1142 0.1303 0.007 1.011 9.1 115.0 21.2 436 n/a 4_settarget: 0.1142 0.1303 0.007 1.011 9.1 115.0 21.2 436 n/a 4_updatecdl: 0.1142 0.1303 0.007 1.015 9.1 115.0 21.2 436 n/a 4_nqh: 0.1146 0.1304 0.007 1.015 9.1 115.0 21.2 436 n/a 4_sol: 0.1154 0.1306 0.007 1.015 9.1 115.0 21.2 441 n/a 4_weight: 0.1154 0.1306 0.007 1.015 9.1 115.0 21.2 441 n/a 4_xyzrec: 0.1145 0.1301 0.008 1.084 9.1 115.0 21.2 441 n/a 4_adp: 0.1145 0.1301 0.008 1.084 9.1 115.0 21.2 441 n/a 4_regHadp: 0.1145 0.1301 0.008 1.084 9.1 115.0 21.2 441 n/a 4_occ: 0.1139 0.1301 0.008 1.084 9.1 115.0 21.2 441 n/a 5_bss: 0.1133 0.1298 0.008 1.084 9.1 115.0 21.1 441 n/a 5_settarget: 0.1133 0.1298 0.008 1.084 9.1 115.0 21.1 441 n/a 5_updatecdl: 0.1133 0.1298 0.008 1.086 9.1 115.0 21.1 441 n/a 5_setrh: 0.1134 0.1298 0.008 1.086 9.1 115.0 21.1 441 n/a 5_nqh: 0.1134 0.1298 0.008 1.086 9.1 115.0 21.1 441 n/a 5_sol: 0.1132 0.1283 0.008 1.086 9.1 115.0 21.2 453 n/a 5_weight: 0.1132 0.1283 0.008 1.086 9.1 115.0 21.2 453 n/a 5_xyzrec: 0.1132 0.1283 0.008 1.097 9.1 115.0 21.2 453 n/a 5_adp: 0.1132 0.1283 0.008 1.097 9.1 115.0 21.2 453 n/a 5_regHadp: 0.1132 0.1283 0.008 1.097 9.1 115.0 21.2 453 n/a 5_occ: 0.1128 0.1281 0.008 1.097 9.1 115.0 21.2 453 n/a end: 0.1127 0.1281 0.008 1.097 9.1 115.0 21.2 453 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_7509253_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_7509253_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.1900 Refinement macro-cycles (run) : 13612.2200 Write final files (write_after_run_outputs) : 89.2800 Total : 13704.6900 Total CPU time: 3.81 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:11:23 PST -0800 (1735366283.35 s) Start R-work = 0.1640, R-free = 0.1767 Final R-work = 0.1127, R-free = 0.1281 =============================================================================== Job complete usr+sys time: 13882.64 seconds wall clock time: 255 minutes 30.33 seconds (15330.33 seconds total)