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_9394591.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 { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_9394591.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_9394591.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" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" } 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 3 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: 1.33, per 1000 atoms: 0.39 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: 0.28 Conformation dependent library (CDL) restraints added in 159.6 milliseconds Time building geometry restraints manager: 0.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.65 - 0.92: 541 0.92 - 1.18: 1132 1.18 - 1.45: 732 1.45 - 1.72: 732 1.72 - 1.99: 16 Bond restraints: 3153 Sorted by residual: bond pdb=" N LYS A 89 " pdb=" CA LYS A 89 " ideal model delta sigma weight residual 1.459 1.692 -0.233 1.21e-02 6.83e+03 3.70e+02 bond pdb=" N THR A 140 " pdb=" CA THR A 140 " ideal model delta sigma weight residual 1.458 1.232 0.226 1.22e-02 6.72e+03 3.42e+02 bond pdb=" N LEU A 72 " pdb=" CA LEU A 72 " ideal model delta sigma weight residual 1.463 1.662 -0.198 1.08e-02 8.57e+03 3.37e+02 bond pdb=" C BGLU A 94 " pdb=" O BGLU A 94 " ideal model delta sigma weight residual 1.236 1.027 0.209 1.15e-02 7.56e+03 3.32e+02 bond pdb=" C GLY A 78 " pdb=" O GLY A 78 " ideal model delta sigma weight residual 1.234 1.440 -0.206 1.19e-02 7.06e+03 2.99e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.42: 3027 4.42 - 8.84: 1845 8.84 - 13.25: 728 13.25 - 17.67: 156 17.67 - 22.09: 21 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O AGLY A 65 " pdb=" C AGLY A 65 " pdb=" N APRO A 66 " ideal model delta sigma weight residual 121.77 137.63 -15.86 1.00e+00 1.00e+00 2.52e+02 angle pdb=" O VAL A 146 " pdb=" C VAL A 146 " pdb=" N GLU A 147 " ideal model delta sigma weight residual 123.05 139.49 -16.44 1.11e+00 8.12e-01 2.19e+02 angle pdb=" O THR A 160 " pdb=" C THR A 160 " pdb=" N SER A 161 " ideal model delta sigma weight residual 122.34 140.17 -17.83 1.25e+00 6.40e-01 2.04e+02 angle pdb=" O ALA A 167 " pdb=" C ALA A 167 " pdb=" N ILE A 168 " ideal model delta sigma weight residual 122.12 137.16 -15.04 1.06e+00 8.90e-01 2.01e+02 angle pdb=" O ASN A 173 " pdb=" C ASN A 173 " pdb=" N GLY A 174 " ideal model delta sigma weight residual 122.35 139.54 -17.19 1.23e+00 6.61e-01 1.95e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 21.29: 991 21.29 - 42.57: 82 42.57 - 63.85: 33 63.85 - 85.13: 4 85.13 - 106.41: 1 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA ARG A 156 " pdb=" C ARG A 156 " pdb=" N GLY A 157 " pdb=" CA GLY A 157 " ideal model delta harmonic sigma weight residual -180.00 -156.27 -23.73 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA THR A 140 " pdb=" C THR A 140 " pdb=" N TYR A 141 " pdb=" CA TYR A 141 " ideal model delta harmonic sigma weight residual -180.00 -157.74 -22.26 0 5.00e+00 4.00e-02 1.98e+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 -158.38 -21.62 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.007 - 0.319: 137 0.319 - 0.631: 79 0.631 - 0.943: 21 0.943 - 1.255: 5 1.255 - 1.568: 1 Chirality restraints: 243 Sorted by residual: 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 -1.02 -1.57 2.00e-01 2.50e+01 6.14e+01 chirality pdb=" CA ARG A 156 " pdb=" N ARG A 156 " pdb=" C ARG A 156 " pdb=" CB ARG A 156 " both_signs ideal model delta sigma weight residual False 2.51 1.40 1.11 2.00e-01 2.50e+01 3.06e+01 chirality pdb=" CA GLU A 143 " pdb=" N GLU A 143 " pdb=" C GLU A 143 " pdb=" CB GLU A 143 " both_signs ideal model delta sigma weight residual False 2.51 1.42 1.09 2.00e-01 2.50e+01 2.98e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 48 " -0.158 9.50e-02 1.11e+02 9.57e-02 1.46e+02 pdb=" NE ARG A 48 " 0.061 2.00e-02 2.50e+03 pdb=" CZ ARG A 48 " -0.133 2.00e-02 2.50e+03 pdb=" NH1 ARG A 48 " -0.089 2.00e-02 2.50e+03 pdb=" NH2 ARG A 48 " -0.088 2.00e-02 2.50e+03 pdb="HH11 ARG A 48 " 0.065 2.00e-02 2.50e+03 pdb="HH12 ARG A 48 " 0.081 2.00e-02 2.50e+03 pdb="HH21 ARG A 48 " 0.096 2.00e-02 2.50e+03 pdb="HH22 ARG A 48 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " 0.012 2.00e-02 2.50e+03 5.91e-02 1.05e+02 pdb=" CG TYR A 139 " 0.103 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.101 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.107 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " 0.046 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " -0.018 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " -0.018 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " -0.033 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.048 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " 0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 126 " 0.022 2.00e-02 2.50e+03 6.36e-02 9.11e+01 pdb=" CG HIS A 126 " 0.061 2.00e-02 2.50e+03 pdb=" ND1 HIS A 126 " -0.064 2.00e-02 2.50e+03 pdb=" CD2 HIS A 126 " -0.104 2.00e-02 2.50e+03 pdb=" CE1 HIS A 126 " 0.102 2.00e-02 2.50e+03 pdb=" NE2 HIS A 126 " -0.042 2.00e-02 2.50e+03 pdb=" HD2 HIS A 126 " 0.011 2.00e-02 2.50e+03 pdb=" HE1 HIS A 126 " -0.043 2.00e-02 2.50e+03 pdb=" HE2 HIS A 126 " 0.057 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.23: 526 2.23 - 2.82: 7384 2.82 - 3.41: 10808 3.41 - 4.01: 15431 4.01 - 4.60: 22530 Nonbonded interactions: 56679 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.633 2.100 nonbonded pdb=" H GLY A 120 " pdb=" O HIS A 138 " model vdw 1.816 1.850 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.819 1.850 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.839 1.850 nonbonded pdb=" O PRO A 22 " pdb=" H MET A 26 " model vdw 1.853 1.850 ... (remaining 56674 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_9394591_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= 0.2614 r_free= 0.1972 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.794106 | | target function (ml) not normalized (work): 232765.799277 | | target function (ml) not normalized (free): 11827.826047 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3050 0.2123 6.9982 4.9567| | 2: 3.57 - 2.84 1.00 2876 122 0.2417 0.1753 4.3552 4.3359| | 3: 2.84 - 2.48 1.00 2833 165 0.2356 0.1821 4.1386 4.1945| | 4: 2.47 - 2.25 1.00 2825 136 0.2342 0.1565 3.8418 3.8638| | 5: 2.25 - 2.09 1.00 2756 127 0.2461 0.1639 3.8064 3.8339| | 6: 2.09 - 1.97 1.00 2846 113 0.2546 0.1663 3.4787 3.5349| | 7: 1.97 - 1.87 1.00 2787 165 0.2558 0.1826 3.1583 3.1674| | 8: 1.87 - 1.79 1.00 2789 144 0.2469 0.1919 3.0654 3.1307| | 9: 1.79 - 1.72 1.00 2745 138 0.2417 0.1951 2.8927 2.9675| | 10: 1.72 - 1.66 1.00 2789 158 0.2477 0.1994 2.8002 2.9127| | 11: 1.66 - 1.61 1.00 2740 147 0.2541 0.1779 2.7646 2.7356| | 12: 1.61 - 1.56 1.00 2787 146 0.2518 0.1966 2.625 2.6361| | 13: 1.56 - 1.52 1.00 2745 130 0.2572 0.1716 2.5723 2.5291| | 14: 1.52 - 1.48 1.00 2803 134 0.2604 0.2132 2.5123 2.5885| | 15: 1.48 - 1.45 1.00 2738 128 0.2609 0.2244 2.4373 2.5014| | 16: 1.45 - 1.42 1.00 2756 161 0.2672 0.2108 2.3957 2.4239| | 17: 1.42 - 1.39 1.00 2785 139 0.2667 0.2003 2.3443 2.3553| | 18: 1.39 - 1.36 1.00 2741 179 0.2695 0.2250 2.2924 2.3639| | 19: 1.36 - 1.34 1.00 2807 134 0.2673 0.2325 2.2477 2.3067| | 20: 1.34 - 1.32 1.00 2696 147 0.2692 0.2338 2.2016 2.235| | 21: 1.32 - 1.30 1.00 2785 112 0.2722 0.2294 2.1621 2.1829| | 22: 1.29 - 1.27 1.00 2704 152 0.2748 0.2525 2.1295 2.1689| | 23: 1.27 - 1.26 1.00 2802 156 0.2832 0.2552 2.1211 2.2196| | 24: 1.26 - 1.24 1.00 2744 132 0.2761 0.2514 2.083 2.1567| | 25: 1.24 - 1.22 1.00 2734 148 0.2854 0.2764 2.0415 2.1566| | 26: 1.22 - 1.21 1.00 2727 135 0.2924 0.2210 2.0347 2.0363| | 27: 1.21 - 1.19 1.00 2814 148 0.2965 0.2592 2.0021 1.9545| | 28: 1.19 - 1.18 1.00 2671 147 0.2961 0.2728 1.9836 2.006| | 29: 1.18 - 1.16 1.00 2800 134 0.2977 0.2682 1.9579 2.0092| | 30: 1.16 - 1.15 1.00 2740 148 0.3030 0.2838 1.9265 1.962| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 19.15 0.76 0.23 1507.46| | 2: 3.57 - 2.84 2876 122 0.80 26.37 1.27 0.23 1507.46| | 3: 2.84 - 2.48 2833 165 0.74 32.30 1.24 0.23 1250.49| | 4: 2.47 - 2.25 2825 136 0.81 25.84 1.26 0.25 583.60| | 5: 2.25 - 2.09 2756 127 0.77 29.70 1.28 0.25 583.60| | 6: 2.09 - 1.97 2846 113 0.83 23.09 1.29 0.25 319.56| | 7: 1.97 - 1.87 2787 165 0.90 16.86 1.28 0.25 94.37| | 8: 1.87 - 1.79 2789 144 0.85 21.61 1.25 0.25 94.37| | 9: 1.79 - 1.72 2745 138 0.88 19.03 1.24 0.25 56.55| | 10: 1.72 - 1.66 2789 158 0.86 20.53 1.23 0.25 48.97| | 11: 1.66 - 1.61 2740 147 0.85 21.50 1.24 0.25 47.14| | 12: 1.61 - 1.56 2787 146 0.89 18.29 1.23 0.25 28.62| | 13: 1.56 - 1.52 2745 130 0.87 20.27 1.24 0.25 28.62| | 14: 1.52 - 1.48 2803 134 0.87 20.60 1.24 0.25 25.76| | 15: 1.48 - 1.45 2738 128 0.87 20.13 1.23 0.25 20.53| | 16: 1.45 - 1.42 2756 161 0.86 21.61 1.23 0.25 20.53| | 17: 1.42 - 1.39 2785 139 0.87 20.71 1.22 0.25 17.65| | 18: 1.39 - 1.36 2741 179 0.86 21.25 1.22 0.25 15.98| | 19: 1.36 - 1.34 2807 134 0.85 22.21 1.22 0.25 15.98| | 20: 1.34 - 1.32 2696 147 0.86 21.38 1.22 0.24 13.44| | 21: 1.32 - 1.30 2785 112 0.85 22.59 1.21 0.24 13.26| | 22: 1.29 - 1.27 2704 152 0.85 23.20 1.22 0.24 12.95| | 23: 1.27 - 1.26 2802 156 0.85 22.50 1.22 0.24 11.40| | 24: 1.26 - 1.24 2744 132 0.85 22.99 1.20 0.24 11.40| | 25: 1.24 - 1.22 2734 148 0.84 24.20 1.20 0.23 10.82| | 26: 1.22 - 1.21 2727 135 0.83 24.66 1.19 0.23 10.17| | 27: 1.21 - 1.19 2814 148 0.83 25.25 1.21 0.23 10.17| | 28: 1.19 - 1.18 2671 147 0.82 25.70 1.18 0.23 9.58| | 29: 1.18 - 1.16 2800 134 0.82 26.20 1.16 0.22 9.36| | 30: 1.16 - 1.15 2740 148 0.80 27.79 1.15 0.22 9.36| |alpha: min = 0.22 max = 0.25 mean = 0.24| |beta: min = 9.36 max = 1507.46 mean = 218.97| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.99 mean = 22.92| |phase err.(test): min = 0.00 max = 89.13 mean = 22.84| |-----------------------------------------------------------------------------| ----------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 : 0.083 0.235 1557 Z= 5.484 Angle : 5.353 19.110 2118 Z= 3.755 Chirality : 0.409 1.568 243 Planarity : 0.030 0.106 284 Dihedral : 14.604 106.413 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.16 % Favored : 97.30 % Rotamer: Outliers : 2.48 % Allowed : 2.48 % Favored : 95.03 % Cbeta Deviations : 31.89 % 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: -3.09 (0.46), residues: 224 helix: -2.93 (0.38), residues: 102 sheet: -0.89 (0.76), residues: 38 loop : -1.07 (0.56), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.082 0.019 ARG A 145 TYR 0.100 0.043 TYR A 139 PHE 0.112 0.044 PHE A 119 HIS 0.099 0.041 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= 0.2614 r_free= 0.1972 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.794106 | | target function (ml) not normalized (work): 232765.799277 | | target function (ml) not normalized (free): 11827.826047 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2573 0.2615 0.1972 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2573 0.2615 0.1972 n_refl.: 87602 remove outliers: r(all,work,free)=0.1987 0.1990 0.1972 n_refl.: 87594 overall B=0.21 to atoms: r(all,work,free)=0.2013 0.2016 0.1987 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1654 0.1646 0.1803 n_refl.: 87594 remove outliers: r(all,work,free)=0.1653 0.1645 0.1803 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 0.3904 386.431 358.235 0.737 0.915 0.416 11.894-9.307 99.02 97 4 0.1834 613.826 594.828 1.011 0.916 0.403 9.237-7.194 100.00 213 7 0.2125 502.034 490.401 1.049 0.916 0.360 7.162-5.571 100.00 427 22 0.2163 376.749 364.057 1.016 0.917 0.288 5.546-4.326 100.00 867 58 0.1277 517.183 511.330 1.054 0.917 0.218 4.315-3.360 100.00 1859 96 0.1151 491.845 487.713 1.096 0.918 0.189 3.356-2.611 100.00 3867 181 0.1460 323.116 319.507 1.082 0.920 0.109 2.608-2.026 99.99 8198 413 0.1351 214.197 212.292 1.091 0.922 0.000 2.025-1.573 100.00 17313 902 0.1661 104.603 103.818 1.093 0.926 0.000 1.573-1.221 100.00 36679 1900 0.2079 46.385 45.050 1.071 0.933 0.000 1.221-1.150 99.97 13689 708 0.2584 29.226 26.936 1.031 0.939 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0490 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1645 r_free=0.1803 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=0.1646 r_free=0.1805 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.247012 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1996.403563 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 0.1730 0.1838 0.0109 0.001 0.4 4.5 0.0 0.0 0 0.125 0.1587 0.1721 0.0133 0.001 0.4 4.2 0.0 0.0 0 0.250 0.1445 0.1613 0.0168 0.002 0.5 3.5 0.0 0.0 0 0.500 0.1386 0.1579 0.0193 0.002 0.5 3.5 0.0 0.0 0 0.750 0.1372 0.1574 0.0202 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1352 0.1549 0.0197 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1299 0.1515 0.0217 0.002 0.6 3.2 0.5 0.0 0 2.000 0.1274 0.1503 0.0229 0.003 0.6 3.5 0.5 0.0 0 3.000 0.1260 0.1494 0.0233 0.003 0.7 3.5 0.5 0.0 0 4.000 0.1248 0.1479 0.0231 0.004 0.7 3.5 0.5 0.0 0 5.000 0.1244 0.1477 0.0233 0.004 0.8 4.2 0.5 0.0 0 6.000 0.1240 0.1475 0.0235 0.005 0.8 4.2 0.5 0.0 0 7.000 0.1235 0.1470 0.0235 0.005 0.8 3.5 0.5 0.0 0 8.000 0.1229 0.1465 0.0236 0.006 0.9 3.2 0.5 0.0 0 9.000 0.1230 0.1472 0.0242 0.006 0.9 4.5 0.5 0.0 0 10.000 0.1227 0.1471 0.0244 0.007 0.9 3.8 0.5 0.0 0 11.000 0.1226 0.1474 0.0248 0.007 0.9 3.8 0.5 0.6 0 12.000 0.1223 0.1474 0.0251 0.007 1.0 4.5 0.5 0.6 0 13.124 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1229 0.1465 0.0236 0.006 0.9 3.2 0.5 0.0 0 9.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.29 14.65 2.36 3.013 19.073 1996.404 0.017 12.29 14.65 2.36 2.989 19.073 59.892 0.017 12.36 14.63 2.27 2.660 19.072 249.550 0.017 12.69 15.28 2.59 2.740 19.240 998.202 0.017 12.58 15.49 2.91 3.372 19.680 1996.404 0.016 12.46 15.47 3.00 3.372 19.684 2994.605 0.015 12.35 15.42 3.08 3.382 19.676 3992.807 0.015 12.28 15.37 3.09 3.318 19.626 4991.009 0.015 12.21 15.33 3.12 3.272 19.594 5989.211 0.015 12.24 15.40 3.16 3.366 19.639 6987.412 0.015 12.17 15.37 3.20 3.350 19.617 7985.614 0.015 12.17 15.37 3.20 3.342 19.603 8983.816 0.015 12.15 15.42 3.28 3.399 19.617 9982.018 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: 249.550 Accepted refinement result: 12.36 14.63 2.27 2.660 19.072 249.550 0.017 Individual atomic B min max mean iso aniso Overall: 9.09 119.45 20.10 3.29 0 1785 Protein: 9.09 114.92 17.01 3.30 0 1519 Water: 11.47 119.45 38.24 N/A 0 258 Other: 19.73 26.62 22.08 N/A 0 8 Chain A: 9.09 119.45 20.10 N/A 0 1785 Histogram: Values Number of atoms 9.09 - 20.13 1272 20.13 - 31.16 227 31.16 - 42.20 125 42.20 - 53.24 94 53.24 - 64.27 42 64.27 - 75.31 11 75.31 - 86.35 7 86.35 - 97.38 4 97.38 - 108.42 1 108.42 - 119.45 2 =========================== Idealize ADP of riding H ========================== r_work=0.1236 r_free=0.1463 r_work=0.1237 r_free=0.1467 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1237 r_free = 0.1467 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 = 0.1232 r_free = 0.1461 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.22 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= 0.1232 r_free= 0.1461 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.017051 | | target function (ls_wunit_k1) not normalized (work): 1420.305374 | | target function (ls_wunit_k1) not normalized (free): 111.683557 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1243 0.1232 0.1461 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1679 0.1680 0.1690 n_refl.: 87593 remove outliers: r(all,work,free)=0.1679 0.1680 0.1690 n_refl.: 87593 overall B=0.03 to atoms: r(all,work,free)=0.1684 0.1686 0.1693 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1241 0.1231 0.1453 n_refl.: 87593 remove outliers: r(all,work,free)=0.1241 0.1230 0.1453 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 94.79 86 5 0.3570 297.346 280.935 0.638 1.002 0.376 11.894-9.307 99.02 97 4 0.1687 481.831 468.850 0.917 1.003 0.373 9.237-7.194 100.00 213 7 0.1904 394.079 387.765 0.964 1.003 0.350 7.162-5.571 100.00 427 22 0.1868 295.734 289.306 0.937 1.003 0.259 5.546-4.326 100.00 867 58 0.1013 405.970 402.883 0.963 1.003 0.204 4.315-3.360 100.00 1859 96 0.0873 386.080 384.988 1.010 1.002 0.180 3.356-2.611 100.00 3867 181 0.1177 253.635 252.469 1.009 1.002 0.110 2.608-2.026 99.99 8198 413 0.1023 168.137 167.397 1.019 1.001 0.000 2.025-1.573 100.00 17313 902 0.1114 82.109 82.297 1.027 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1451 36.411 35.911 1.020 0.997 0.000 1.221-1.150 99.97 13689 708 0.2254 22.941 21.424 0.983 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0438 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1230 r_free=0.1453 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=0.1230 r_free=0.1453 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1230 r_free=0.1453 | n_water=258 | time (s): 1.780 (total time: 1.780) Filter (dist) r_work=0.1241 r_free=0.1448 | n_water=250 | time (s): 21.550 (total time: 23.330) Filter (q & B) r_work=0.1244 r_free=0.1449 | n_water=247 | time (s): 2.700 (total time: 26.030) Compute maps r_work=0.1244 r_free=0.1449 | n_water=247 | time (s): 1.290 (total time: 27.320) Filter (map) r_work=0.1259 r_free=0.1456 | n_water=226 | time (s): 2.450 (total time: 29.770) Find peaks r_work=0.1259 r_free=0.1456 | n_water=226 | time (s): 0.460 (total time: 30.230) Add new water r_work=0.1399 r_free=0.1598 | n_water=427 | time (s): 2.650 (total time: 32.880) Refine new water occ: r_work=0.1308 r_free=0.1481 adp: r_work=0.1228 r_free=0.1419 occ: r_work=0.1239 r_free=0.1417 adp: r_work=0.1208 r_free=0.1399 occ: r_work=0.1212 r_free=0.1399 adp: r_work=0.1202 r_free=0.1394 ADP+occupancy (water only), MIN, final r_work=0.1202 r_free=0.1394 r_work=0.1202 r_free=0.1394 | n_water=427 | time (s): 55.180 (total time: 88.060) Filter (q & B) r_work=0.1204 r_free=0.1397 | n_water=413 | time (s): 2.570 (total time: 90.630) Filter (dist only) r_work=0.1204 r_free=0.1395 | n_water=412 | time (s): 34.850 (total time: 125.480) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 28.496911 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1489.845458 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 0.1685 0.1791 0.0106 0.001 0.4 8.0 0.0 0.0 0 0.125 0.1574 0.1697 0.0123 0.001 0.4 8.0 0.0 0.0 0 0.250 0.1427 0.1578 0.0150 0.001 0.4 7.4 0.0 0.0 0 0.500 0.1368 0.1534 0.0167 0.002 0.5 5.8 0.0 0.0 0 0.750 0.1323 0.1496 0.0173 0.002 0.5 6.1 0.0 0.0 0 1.000 0.1322 0.1500 0.0178 0.002 0.5 5.8 0.0 0.0 0 1.000 0.1258 0.1457 0.0199 0.002 0.5 5.8 0.5 0.0 0 2.000 0.1233 0.1443 0.0210 0.003 0.6 5.8 0.5 0.0 0 3.000 0.1220 0.1440 0.0220 0.003 0.7 6.7 0.5 0.0 0 4.000 0.1212 0.1434 0.0222 0.004 0.7 6.1 0.5 0.0 0 5.000 0.1208 0.1428 0.0220 0.004 0.7 6.4 0.5 0.0 0 6.000 0.1206 0.1429 0.0223 0.005 0.8 6.4 0.5 0.0 0 7.000 0.1202 0.1419 0.0217 0.005 0.8 6.4 0.5 0.0 0 8.000 0.1198 0.1419 0.0221 0.006 0.8 6.1 0.5 0.0 0 9.000 0.1196 0.1417 0.0221 0.006 0.8 6.4 0.5 0.0 0 10.000 0.1190 0.1409 0.0219 0.007 0.9 7.0 0.5 0.0 0 11.000 0.1192 0.1418 0.0227 0.007 0.9 5.8 0.5 0.0 0 12.000 0.1189 0.1421 0.0232 0.008 0.9 6.4 0.5 0.0 0 13.000 0.1189 0.1424 0.0235 0.008 0.9 7.4 0.5 0.6 0 14.248 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1190 0.1409 0.0219 0.007 0.9 7.0 0.5 0.0 0 11.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.90 14.09 2.19 3.769 21.709 1489.845 0.016 11.90 14.09 2.19 3.769 21.709 44.695 0.016 11.90 14.09 2.19 3.769 21.709 186.231 0.016 12.16 14.67 2.51 3.578 21.760 744.923 0.015 12.09 14.87 2.78 3.470 22.046 1489.845 0.015 11.89 14.71 2.82 3.483 22.104 2234.768 0.015 11.84 14.77 2.93 3.480 22.101 2979.691 0.014 11.79 14.76 2.97 3.494 22.073 3724.614 0.014 11.79 14.88 3.09 3.513 22.039 4469.536 0.014 11.69 14.67 2.98 3.526 22.030 5214.459 0.014 11.74 14.83 3.10 3.569 22.115 5959.382 0.014 11.70 14.84 3.15 3.571 22.064 6704.305 0.014 11.65 14.82 3.17 3.583 22.105 7449.227 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: 186.231 Accepted refinement result: 11.90 14.09 2.19 3.769 21.709 186.231 0.016 Individual atomic B min max mean iso aniso Overall: 9.12 114.95 22.05 3.29 186 1753 Protein: 9.12 114.95 17.04 3.30 0 1519 Water: 11.50 76.69 40.54 N/A 186 226 Other: 19.76 26.64 22.11 N/A 0 8 Chain A: 9.12 114.95 19.47 N/A 0 1753 Chain S: 14.46 60.00 46.37 N/A 186 0 Histogram: Values Number of atoms 9.12 - 19.70 1261 19.70 - 30.29 250 30.29 - 40.87 162 40.87 - 51.45 129 51.45 - 62.04 114 62.04 - 72.62 12 72.62 - 83.20 5 83.20 - 93.78 4 93.78 - 104.37 0 104.37 - 114.95 2 =========================== Idealize ADP of riding H ========================== r_work=0.1190 r_free=0.1409 r_work=0.1190 r_free=0.1409 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1190 r_free = 0.1409 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 = 0.1190 r_free = 0.1405 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.27 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= 0.1190 r_free= 0.1405 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.015187 | | target function (ls_wunit_k1) not normalized (work): 1264.967422 | | target function (ls_wunit_k1) not normalized (free): 104.188669 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1190 0.1405 n_refl.: 87591 re-set all scales: r(all,work,free)=0.1587 0.1585 0.1648 n_refl.: 87591 remove outliers: r(all,work,free)=0.1587 0.1585 0.1648 n_refl.: 87591 overall B=0.01 to atoms: r(all,work,free)=0.1587 0.1586 0.1648 n_refl.: 87591 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1187 0.1398 n_refl.: 87591 remove outliers: r(all,work,free)=0.1196 0.1186 0.1398 n_refl.: 87590 ======================== 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 93.75 85 5 0.3480 299.330 270.091 0.577 1.003 0.350 11.894-9.307 99.02 97 4 0.1654 481.831 475.981 0.916 1.003 0.333 9.237-7.194 100.00 213 7 0.1763 394.079 394.585 0.980 1.003 0.290 7.162-5.571 100.00 427 22 0.1614 295.734 291.477 0.935 1.003 0.214 5.546-4.326 100.00 867 58 0.0890 405.970 403.020 0.960 1.003 0.200 4.315-3.360 100.00 1859 96 0.0793 386.080 385.057 1.008 1.002 0.200 3.356-2.611 100.00 3867 181 0.1084 253.635 252.749 1.010 1.002 0.120 2.608-2.026 99.99 8198 413 0.1007 168.137 167.620 1.021 1.001 0.000 2.025-1.573 100.00 17313 902 0.1099 82.109 82.338 1.031 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1441 36.411 35.950 1.025 0.997 0.000 1.221-1.150 99.97 13689 708 0.2251 22.941 21.460 0.988 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0081 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1186 r_free=0.1398 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A Total number of N/Q/H flips: 1 r_work=0.1189 r_free=0.1398 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1189 r_free=0.1398 | n_water=412 | time (s): 1.730 (total time: 1.730) Filter (dist) r_work=0.1188 r_free=0.1397 | n_water=408 | time (s): 37.380 (total time: 39.110) Filter (q & B) r_work=0.1188 r_free=0.1397 | n_water=408 | time (s): 0.800 (total time: 39.910) Compute maps r_work=0.1188 r_free=0.1397 | n_water=408 | time (s): 1.490 (total time: 41.400) Filter (map) r_work=0.1220 r_free=0.1390 | n_water=289 | time (s): 3.090 (total time: 44.490) Find peaks r_work=0.1220 r_free=0.1390 | n_water=289 | time (s): 0.650 (total time: 45.140) Add new water r_work=0.1336 r_free=0.1480 | n_water=469 | time (s): 3.430 (total time: 48.570) Refine new water occ: r_work=0.1247 r_free=0.1419 adp: r_work=0.1247 r_free=0.1419 occ: r_work=0.1226 r_free=0.1405 adp: r_work=0.1224 r_free=0.1403 occ: r_work=0.1211 r_free=0.1397 adp: r_work=0.1204 r_free=0.1391 ADP+occupancy (water only), MIN, final r_work=0.1204 r_free=0.1391 r_work=0.1204 r_free=0.1391 | n_water=469 | time (s): 208.840 (total time: 257.410) Filter (q & B) r_work=0.1209 r_free=0.1394 | n_water=439 | time (s): 2.770 (total time: 260.180) Filter (dist only) r_work=0.1209 r_free=0.1392 | n_water=438 | time (s): 38.280 (total time: 298.460) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.789209 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 41.992243 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 0.1235 0.1367 0.0132 0.002 0.6 5.1 0.5 0.0 0 0.089 0.1192 0.1330 0.0138 0.003 0.7 4.2 0.5 0.0 0 0.268 0.1174 0.1316 0.0141 0.004 0.8 3.5 0.5 0.0 0 0.537 0.1167 0.1313 0.0146 0.005 0.9 3.2 0.5 0.0 0 0.805 0.1164 0.1310 0.0146 0.006 1.0 3.8 0.5 0.0 0 1.074 0.1161 0.1311 0.0150 0.007 1.0 3.8 0.5 0.0 0 1.342 0.1158 0.1309 0.0151 0.007 1.1 3.8 0.5 0.0 0 1.610 0.1157 0.1308 0.0150 0.008 1.1 3.8 0.5 0.0 0 1.879 0.1166 0.1313 0.0147 0.006 0.9 3.5 0.5 0.0 0 0.895 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1157 0.1308 0.0150 0.008 1.1 3.8 0.5 0.0 0 1.879 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.57 13.08 1.50 3.772 21.311 41.992 3.616 11.57 13.08 1.50 3.772 21.311 1.260 3.616 11.57 13.07 1.50 3.770 21.311 5.249 3.616 11.60 13.13 1.53 3.705 21.302 20.996 3.609 11.65 13.24 1.59 3.730 21.268 41.992 3.611 11.57 13.21 1.64 3.751 21.254 62.988 3.604 11.51 13.17 1.66 3.769 21.250 83.984 3.600 11.47 13.14 1.67 3.780 21.247 104.981 3.596 11.46 13.15 1.69 3.795 21.234 125.977 3.595 11.46 13.17 1.71 3.812 21.221 146.973 3.594 11.44 13.15 1.71 3.821 21.221 167.969 3.592 11.42 13.13 1.71 3.828 21.221 188.965 3.591 11.40 13.11 1.71 3.835 21.217 209.961 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: 5.249 Accepted refinement result: 11.57 13.07 1.50 3.770 21.311 5.249 3.616 Individual atomic B min max mean iso aniso Overall: 9.13 114.93 21.32 3.29 214 1751 Protein: 9.13 114.93 17.04 3.29 0 1519 Water: 11.51 76.70 36.13 N/A 214 224 Other: 19.75 26.64 22.11 N/A 0 8 Chain A: 9.13 114.93 19.45 N/A 0 1751 Chain S: 14.47 60.01 36.56 N/A 214 0 Histogram: Values Number of atoms 9.13 - 19.71 1262 19.71 - 30.29 289 30.29 - 40.87 205 40.87 - 51.45 124 51.45 - 62.03 62 62.03 - 72.61 11 72.61 - 83.19 6 83.19 - 93.77 4 93.77 - 104.35 0 104.35 - 114.93 2 =========================== Idealize ADP of riding H ========================== r_work=0.1157 r_free=0.1307 r_work=0.1157 r_free=0.1307 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1157 r_free = 0.1307 target_work(ml) = 3.616 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1150 r_free = 0.1316 target_work(ml) = 3.611 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87590 (all), 4.90 % free)------------| | | | r_work= 0.1150 r_free= 0.1316 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.611161 | | target function (ml) not normalized (work): 300788.047507 | | target function (ml) not normalized (free): 15834.129489 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1158 0.1150 0.1316 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1491 0.1489 0.1552 n_refl.: 87590 remove outliers: r(all,work,free)=0.1491 0.1489 0.1552 n_refl.: 87590 overall B=-0.01 to atoms: r(all,work,free)=0.1489 0.1488 0.1551 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1154 0.1145 0.1318 n_refl.: 87590 remove outliers: r(all,work,free)=0.1152 0.1143 0.1318 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 0.3936 296.692 268.684 0.507 1.001 0.330 11.894-9.307 98.04 96 4 0.2268 481.956 467.134 0.883 1.002 0.330 9.237-7.194 98.64 210 7 0.2217 386.576 386.164 0.962 1.003 0.210 7.162-5.571 100.00 427 22 0.2135 295.734 284.741 0.918 1.003 0.175 5.546-4.326 100.00 867 58 0.1120 405.970 401.449 0.963 1.003 0.170 4.315-3.360 100.00 1859 96 0.0933 386.080 383.633 1.005 1.002 0.160 3.356-2.611 100.00 3867 181 0.1140 253.635 251.578 1.007 1.002 0.043 2.608-2.026 99.99 8198 413 0.0931 168.137 167.377 1.024 1.001 0.000 2.025-1.573 100.00 17313 902 0.0896 82.109 82.381 1.036 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1257 36.411 35.988 1.029 0.997 0.000 1.221-1.150 99.97 13689 708 0.2166 22.941 21.481 0.992 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0206 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1143 r_free=0.1318 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=0.1143 r_free=0.1318 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1143 r_free=0.1318 | n_water=438 | time (s): 2.480 (total time: 2.480) Filter (dist) r_work=0.1143 r_free=0.1317 | n_water=437 | time (s): 49.420 (total time: 51.900) Filter (q & B) r_work=0.1143 r_free=0.1317 | n_water=437 | time (s): 1.860 (total time: 53.760) Compute maps r_work=0.1143 r_free=0.1317 | n_water=437 | time (s): 1.960 (total time: 55.720) Filter (map) r_work=0.1169 r_free=0.1304 | n_water=320 | time (s): 4.090 (total time: 59.810) Find peaks r_work=0.1169 r_free=0.1304 | n_water=320 | time (s): 0.700 (total time: 60.510) Add new water r_work=0.1249 r_free=0.1396 | n_water=477 | time (s): 3.700 (total time: 64.210) Refine new water occ: r_work=0.1178 r_free=0.1324 adp: r_work=0.1179 r_free=0.1326 occ: r_work=0.1163 r_free=0.1312 adp: r_work=0.1162 r_free=0.1312 occ: r_work=0.1149 r_free=0.1300 adp: r_work=0.1146 r_free=0.1299 ADP+occupancy (water only), MIN, final r_work=0.1146 r_free=0.1299 r_work=0.1146 r_free=0.1299 | n_water=477 | time (s): 229.500 (total time: 293.710) Filter (q & B) r_work=0.1151 r_free=0.1309 | n_water=440 | time (s): 3.960 (total time: 297.670) Filter (dist only) r_work=0.1158 r_free=0.1307 | n_water=438 | time (s): 45.290 (total time: 342.960) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.798518 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 41.453280 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 0.1226 0.1353 0.0128 0.002 0.6 4.5 0.5 0.0 0 0.090 0.1187 0.1326 0.0140 0.003 0.7 3.5 0.5 0.0 0 0.270 0.1172 0.1317 0.0145 0.005 0.9 4.2 0.5 0.0 0 0.540 0.1165 0.1314 0.0149 0.006 1.0 4.2 0.5 0.0 0 0.809 0.1162 0.1315 0.0153 0.006 1.0 3.8 0.5 0.0 0 1.079 0.1159 0.1314 0.0155 0.007 1.1 4.2 0.5 0.0 0 1.349 0.1157 0.1314 0.0157 0.008 1.1 4.2 0.5 0.0 0 1.619 0.1155 0.1313 0.0158 0.009 1.1 4.2 0.5 0.0 0 1.888 0.1164 0.1316 0.0152 0.006 1.0 3.8 0.5 0.0 0 0.899 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1155 0.1313 0.0158 0.009 1.1 4.2 0.5 0.0 0 1.888 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.55 13.13 1.58 3.769 21.180 41.453 3.612 11.55 13.13 1.58 3.769 21.180 1.244 3.612 11.55 13.13 1.58 3.769 21.180 5.182 3.612 11.58 13.17 1.59 3.705 21.171 20.727 3.606 11.67 13.35 1.68 3.723 21.137 41.453 3.610 11.59 13.30 1.72 3.748 21.126 62.180 3.603 11.51 13.24 1.73 3.766 21.123 82.907 3.598 11.49 13.22 1.73 3.775 21.121 103.633 3.595 11.47 13.21 1.75 3.787 21.115 124.360 3.594 11.47 13.25 1.78 3.808 21.100 145.086 3.593 11.45 13.23 1.78 3.816 21.100 165.813 3.592 11.44 13.22 1.79 3.824 21.095 186.540 3.591 11.41 13.19 1.77 3.825 21.100 207.266 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: 1.244 Accepted refinement result: 11.55 13.13 1.58 3.769 21.180 1.244 3.612 Individual atomic B min max mean iso aniso Overall: 9.12 114.92 21.08 3.29 216 1749 Protein: 9.12 114.92 17.03 3.29 0 1519 Water: 11.50 76.69 35.11 N/A 216 222 Other: 19.74 26.63 22.10 N/A 0 8 Chain A: 9.12 114.92 19.44 N/A 0 1749 Chain S: 14.46 60.00 34.40 N/A 216 0 Histogram: Values Number of atoms 9.12 - 19.70 1264 19.70 - 30.28 294 30.28 - 40.86 213 40.86 - 51.44 122 51.44 - 62.02 49 62.02 - 72.60 11 72.60 - 83.18 6 83.18 - 93.76 4 93.76 - 104.34 0 104.34 - 114.92 2 =========================== Idealize ADP of riding H ========================== r_work=0.1155 r_free=0.1313 r_work=0.1155 r_free=0.1313 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1155 r_free = 0.1313 target_work(ml) = 3.612 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1150 r_free = 0.1306 target_work(ml) = 3.608 | | occupancies: max = 1.00 min = 0.15 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= 0.1150 r_free= 0.1306 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.608123 | | target function (ml) not normalized (work): 300516.986058 | | target function (ml) not normalized (free): 15823.881180 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1158 0.1150 0.1306 n_refl.: 87585 re-set all scales: r(all,work,free)=0.1483 0.1483 0.1517 n_refl.: 87585 remove outliers: r(all,work,free)=0.1483 0.1483 0.1517 n_refl.: 87585 overall B=-0.01 to atoms: r(all,work,free)=0.1482 0.1482 0.1516 n_refl.: 87585 bulk-solvent and scaling: r(all,work,free)=0.1155 0.1147 0.1310 n_refl.: 87585 remove outliers: r(all,work,free)=0.1153 0.1145 0.1310 n_refl.: 87579 ======================== 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 0.4134 287.893 258.733 0.452 1.000 0.306 11.894-9.307 95.10 93 4 0.2483 468.998 457.127 0.856 1.002 0.229 9.237-7.194 98.18 209 7 0.2376 385.571 380.240 0.933 1.002 0.158 7.162-5.571 100.00 427 22 0.2281 295.734 283.669 0.908 1.002 0.138 5.546-4.326 100.00 867 58 0.1156 405.970 400.811 0.964 1.002 0.130 4.315-3.360 100.00 1859 96 0.0934 386.080 383.907 1.006 1.002 0.120 3.356-2.611 100.00 3867 181 0.1128 253.635 251.523 1.010 1.002 0.029 2.608-2.026 99.99 8198 413 0.0926 168.137 167.427 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0885 82.109 82.401 1.036 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1251 36.411 35.994 1.029 0.997 0.000 1.221-1.150 99.97 13689 708 0.2168 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=1.0151 b_overall=-0.0179 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1145 r_free=0.1310 After: r_work=0.1146 r_free=0.1310 ================================== NQH flips ================================== r_work=0.1146 r_free=0.1310 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=0.1309 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1146 r_free=0.1309 | n_water=438 | time (s): 2.260 (total time: 2.260) Filter (dist) r_work=0.1146 r_free=0.1308 | n_water=437 | time (s): 44.790 (total time: 47.050) Filter (q & B) r_work=0.1147 r_free=0.1307 | n_water=435 | time (s): 3.890 (total time: 50.940) Compute maps r_work=0.1147 r_free=0.1307 | n_water=435 | time (s): 1.860 (total time: 52.800) Filter (map) r_work=0.1176 r_free=0.1330 | n_water=332 | time (s): 3.850 (total time: 56.650) Find peaks r_work=0.1176 r_free=0.1330 | n_water=332 | time (s): 0.700 (total time: 57.350) Add new water r_work=0.1225 r_free=0.1388 | n_water=479 | time (s): 3.730 (total time: 61.080) Refine new water occ: r_work=0.1165 r_free=0.1325 adp: r_work=0.1165 r_free=0.1328 occ: r_work=0.1153 r_free=0.1308 adp: r_work=0.1153 r_free=0.1312 occ: r_work=0.1143 r_free=0.1297 adp: r_work=0.1141 r_free=0.1299 ADP+occupancy (water only), MIN, final r_work=0.1141 r_free=0.1299 r_work=0.1141 r_free=0.1299 | n_water=479 | time (s): 313.960 (total time: 375.040) Filter (q & B) r_work=0.1148 r_free=0.1308 | n_water=442 | time (s): 3.940 (total time: 378.980) Filter (dist only) r_work=0.1149 r_free=0.1308 | n_water=440 | time (s): 46.440 (total time: 425.420) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.761087 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 36.548690 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 0.1232 0.1355 0.0123 0.004 0.7 5.4 0.5 0.0 0 0.088 0.1194 0.1329 0.0135 0.004 0.8 6.7 0.0 0.0 0 0.264 0.1175 0.1319 0.0143 0.005 0.9 6.4 0.5 0.0 0 0.528 0.1167 0.1314 0.0148 0.006 1.0 6.4 0.5 0.0 0 0.792 0.1162 0.1312 0.0150 0.006 1.0 6.4 0.5 0.0 0 1.057 0.1157 0.1310 0.0153 0.007 1.1 6.4 0.5 0.0 0 1.321 0.1152 0.1307 0.0156 0.008 1.1 6.4 0.5 0.0 0 1.585 0.1150 0.1307 0.0157 0.009 1.2 6.4 0.5 0.0 0 1.849 0.1164 0.1313 0.0149 0.006 1.0 6.4 0.5 0.0 0 0.881 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1150 0.1307 0.0157 0.009 1.2 6.4 0.5 0.0 0 1.849 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.50 13.07 1.57 3.769 21.143 36.549 3.608 11.50 13.07 1.57 3.769 21.143 1.096 3.608 11.50 13.07 1.57 3.769 21.143 4.569 3.608 11.54 13.11 1.57 3.701 21.136 18.274 3.605 11.55 13.20 1.65 3.725 21.117 36.549 3.605 11.54 13.26 1.72 3.745 21.096 54.823 3.604 11.49 13.24 1.74 3.757 21.090 73.097 3.599 11.45 13.20 1.75 3.771 21.089 91.372 3.596 11.43 13.19 1.76 3.779 21.086 109.646 3.594 11.40 13.17 1.77 3.786 21.087 127.920 3.591 11.40 13.20 1.80 3.803 21.076 146.195 3.591 11.41 13.23 1.82 3.818 21.068 164.469 3.591 11.40 13.23 1.82 3.826 21.065 182.743 3.591 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.096 Accepted refinement result: 11.50 13.07 1.57 3.769 21.143 1.096 3.608 Individual atomic B min max mean iso aniso Overall: 9.11 114.92 21.02 3.29 220 1747 Protein: 9.11 114.92 17.03 3.29 0 1519 Water: 11.49 76.68 34.80 N/A 220 220 Other: 19.74 26.62 22.10 N/A 0 8 Chain A: 9.11 114.92 19.40 N/A 0 1747 Chain S: 14.45 60.00 33.94 N/A 220 0 Histogram: Values Number of atoms 9.11 - 19.69 1265 19.69 - 30.27 302 30.27 - 40.85 211 40.85 - 51.43 115 51.43 - 62.01 51 62.01 - 72.59 11 72.59 - 83.17 6 83.17 - 93.76 4 93.76 - 104.34 0 104.34 - 114.92 2 =========================== Idealize ADP of riding H ========================== r_work=0.1150 r_free=0.1307 r_work=0.1150 r_free=0.1307 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1150 r_free = 0.1307 target_work(ml) = 3.608 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1145 r_free = 0.1302 target_work(ml) = 3.607 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87579 (all), 4.91 % free)------------| | | | r_work= 0.1145 r_free= 0.1302 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.606700 | | target function (ml) not normalized (work): 300376.823113 | | target function (ml) not normalized (free): 15819.749096 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2921 171 0.1375 0.1412 5.6659 5.6457| | 2: 3.57 - 2.84 1.00 2888 124 0.1084 0.1384 5.1815 5.2331| | 3: 2.83 - 2.48 1.00 2820 163 0.1110 0.1216 4.9678 5.0026| | 4: 2.47 - 2.25 1.00 2825 136 0.0904 0.1011 4.6457 4.6871| | 5: 2.25 - 2.09 1.00 2756 127 0.0870 0.0924 4.5918 4.6361| | 6: 2.09 - 1.97 1.00 2846 113 0.0864 0.0984 4.2778 4.3526| | 7: 1.97 - 1.87 1.00 2787 165 0.0881 0.1109 3.97 4.0761| | 8: 1.87 - 1.79 1.00 2789 144 0.0923 0.1106 3.8811 3.9774| | 9: 1.79 - 1.72 1.00 2745 138 0.0877 0.1199 3.6394 3.826| | 10: 1.72 - 1.66 1.00 2831 160 0.0924 0.1151 3.5608 3.6985| | 11: 1.66 - 1.61 1.00 2712 147 0.0873 0.1029 3.4928 3.5673| | 12: 1.61 - 1.56 1.00 2773 144 0.0907 0.1158 3.3307 3.4588| | 13: 1.56 - 1.52 1.00 2745 130 0.0952 0.1089 3.3113 3.416| | 14: 1.52 - 1.48 1.00 2803 134 0.0984 0.1031 3.2435 3.3252| | 15: 1.48 - 1.45 1.00 2738 128 0.1007 0.1248 3.1576 3.2633| | 16: 1.45 - 1.42 1.00 2756 161 0.1053 0.1274 3.1359 3.2562| | 17: 1.42 - 1.39 1.00 2785 139 0.1152 0.1301 3.1242 3.2322| | 18: 1.39 - 1.36 1.00 2741 179 0.1201 0.1329 3.1069 3.2418| | 19: 1.36 - 1.34 1.00 2807 134 0.1262 0.1570 3.1146 3.2621| | 20: 1.34 - 1.32 1.00 2696 147 0.1372 0.1453 3.1117 3.1482| | 21: 1.32 - 1.30 1.00 2785 112 0.1473 0.1542 3.1144 3.1143| | 22: 1.29 - 1.27 1.00 2704 152 0.1555 0.1988 3.1198 3.3| | 23: 1.27 - 1.26 1.00 2802 156 0.1647 0.1804 3.1319 3.2022| | 24: 1.26 - 1.24 1.00 2744 132 0.1707 0.1814 3.1245 3.2133| | 25: 1.24 - 1.22 1.00 2733 148 0.1883 0.2151 3.1424 3.2538| | 26: 1.22 - 1.21 1.00 2727 135 0.1907 0.1779 3.1461 3.1992| | 27: 1.21 - 1.19 1.00 2814 148 0.2076 0.2161 3.1691 3.1609| | 28: 1.19 - 1.18 1.00 2671 147 0.2204 0.2299 3.1644 3.1703| | 29: 1.18 - 1.16 1.00 2800 134 0.2265 0.2392 3.1469 3.2267| | 30: 1.16 - 1.15 1.00 2739 148 0.2449 0.2479 3.1419 3.1727| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2921 171 0.95 8.98 1.00 0.97 6103.55| | 2: 3.57 - 2.84 2888 124 0.92 13.08 1.01 0.97 6103.55| | 3: 2.83 - 2.48 2820 163 0.89 17.05 0.99 0.97 5086.16| | 4: 2.47 - 2.25 2825 136 0.92 13.82 1.00 0.98 2462.65| | 5: 2.25 - 2.09 2756 127 0.90 16.11 1.01 0.98 2462.65| | 6: 2.09 - 1.97 2846 113 0.92 12.42 1.02 0.97 1400.23| | 7: 1.97 - 1.87 2787 165 0.95 9.10 1.02 0.97 494.14| | 8: 1.87 - 1.79 2789 144 0.93 12.42 1.00 0.97 494.14| | 9: 1.79 - 1.72 2745 138 0.94 9.99 0.98 0.97 284.11| | 10: 1.72 - 1.66 2831 160 0.94 11.09 0.98 0.97 242.05| | 11: 1.66 - 1.61 2712 147 0.94 11.69 0.98 0.97 232.09| | 12: 1.61 - 1.56 2773 144 0.95 8.95 0.99 0.97 138.14| | 13: 1.56 - 1.52 2745 130 0.95 10.49 1.03 0.97 138.14| | 14: 1.52 - 1.48 2803 134 0.94 10.83 1.02 0.97 124.31| | 15: 1.48 - 1.45 2738 128 0.95 10.05 1.02 0.98 98.96| | 16: 1.45 - 1.42 2756 161 0.94 11.20 1.02 0.98 98.96| | 17: 1.42 - 1.39 2785 139 0.95 11.05 1.01 0.98 89.95| | 18: 1.39 - 1.36 2741 179 0.94 11.61 1.01 0.98 84.73| | 19: 1.36 - 1.34 2807 134 0.94 11.95 1.00 0.98 84.73| | 20: 1.34 - 1.32 2696 147 0.94 12.20 0.98 0.96 80.31| | 21: 1.32 - 1.30 2785 112 0.94 13.18 0.98 0.96 80.00| | 22: 1.29 - 1.27 2704 152 0.93 13.68 0.98 0.96 80.35| | 23: 1.27 - 1.26 2802 156 0.92 14.88 0.97 0.94 82.15| | 24: 1.26 - 1.24 2744 132 0.92 14.89 0.96 0.94 82.15| | 25: 1.24 - 1.22 2733 148 0.91 16.36 0.96 0.94 84.14| | 26: 1.22 - 1.21 2727 135 0.90 18.14 1.02 0.93 86.34| | 27: 1.21 - 1.19 2814 148 0.89 18.83 1.02 0.93 86.34| | 28: 1.19 - 1.18 2671 147 0.88 20.47 1.01 0.92 90.20| | 29: 1.18 - 1.16 2800 134 0.88 20.57 0.99 0.92 91.65| | 30: 1.16 - 1.15 2739 148 0.86 22.09 0.98 0.92 91.65| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 80.00 max = 6103.55 mean = 928.42| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 90.00 mean = 13.56| |phase err.(test): min = 0.00 max = 89.61 mean = 13.57| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1152 0.1145 0.1302 n_refl.: 87579 re-set all scales: r(all,work,free)=0.1475 0.1475 0.1500 n_refl.: 87579 remove outliers: r(all,work,free)=0.1475 0.1475 0.1500 n_refl.: 87579 overall B=-0.00 to atoms: r(all,work,free)=0.1474 0.1474 0.1499 n_refl.: 87579 bulk-solvent and scaling: r(all,work,free)=0.1153 0.1145 0.1304 n_refl.: 87579 remove outliers: r(all,work,free)=0.1152 0.1144 0.1304 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 89.58 81 5 0.4338 283.186 244.404 0.430 1.000 0.304 11.894-9.307 94.12 92 4 0.2423 472.875 452.053 0.848 1.002 0.218 9.237-7.194 98.18 209 7 0.2404 385.571 377.526 0.921 1.002 0.140 7.162-5.571 100.00 427 22 0.2255 295.734 284.695 0.906 1.003 0.125 5.546-4.326 100.00 867 58 0.1151 405.970 400.808 0.962 1.003 0.120 4.315-3.360 100.00 1859 96 0.0940 386.080 383.795 1.006 1.002 0.110 3.356-2.611 100.00 3867 181 0.1123 253.635 251.707 1.011 1.002 0.029 2.608-2.026 99.99 8198 413 0.0917 168.137 167.509 1.026 1.001 0.000 2.025-1.573 100.00 17313 902 0.0891 82.109 82.447 1.036 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1253 36.411 36.012 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2170 22.941 21.486 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=-0.0142 ================= 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 : 0.2614 0.1972 0.083 5.353 8.8 119.3 19.9 258 0.000 1_bss: 0.1645 0.1803 0.083 5.353 9.1 119.5 20.1 258 0.000 1_settarget: 0.1645 0.1803 0.083 5.353 9.1 119.5 20.1 258 0.000 1_nqh: 0.1646 0.1805 0.083 5.353 9.1 119.5 20.1 258 0.006 1_weight: 0.1646 0.1805 0.083 5.353 9.1 119.5 20.1 258 0.006 1_xyzrec: 0.1229 0.1465 0.006 0.851 9.1 119.5 20.1 258 0.137 1_adp: 0.1236 0.1463 0.006 0.851 9.1 119.5 20.1 258 0.137 1_regHadp: 0.1237 0.1467 0.006 0.851 9.1 119.5 20.1 258 0.137 1_occ: 0.1232 0.1461 0.006 0.851 9.1 119.5 20.1 258 0.137 2_bss: 0.1230 0.1453 0.006 0.851 9.1 119.5 20.1 258 0.137 2_settarget: 0.1230 0.1453 0.006 0.851 9.1 119.5 20.1 258 0.137 2_updatecdl: 0.1230 0.1453 0.006 0.860 9.1 119.5 20.1 258 0.137 2_nqh: 0.1230 0.1453 0.006 0.860 9.1 119.5 20.1 258 0.137 2_sol: 0.1204 0.1395 0.006 0.860 9.1 115.0 22.1 412 n/a 2_weight: 0.1204 0.1395 0.006 0.860 9.1 115.0 22.1 412 n/a 2_xyzrec: 0.1190 0.1409 0.007 0.872 9.1 115.0 22.1 412 n/a 2_adp: 0.1190 0.1409 0.007 0.872 9.1 115.0 22.1 412 n/a 2_regHadp: 0.1190 0.1409 0.007 0.872 9.1 115.0 22.1 412 n/a 2_occ: 0.1190 0.1405 0.007 0.872 9.1 115.0 22.1 412 n/a 3_bss: 0.1186 0.1398 0.007 0.872 9.1 115.0 22.1 412 n/a 3_settarget: 0.1186 0.1398 0.007 0.872 9.1 115.0 22.1 412 n/a 3_updatecdl: 0.1186 0.1398 0.007 0.870 9.1 115.0 22.1 412 n/a 3_nqh: 0.1189 0.1398 0.007 0.870 9.1 115.0 22.1 412 n/a 3_sol: 0.1209 0.1392 0.007 0.870 9.1 115.0 21.3 438 n/a 3_weight: 0.1209 0.1392 0.007 0.870 9.1 115.0 21.3 438 n/a 3_xyzrec: 0.1157 0.1308 0.008 1.090 9.1 115.0 21.3 438 n/a 3_adp: 0.1157 0.1307 0.008 1.090 9.1 114.9 21.3 438 n/a 3_regHadp: 0.1157 0.1307 0.008 1.090 9.1 114.9 21.3 438 n/a 3_occ: 0.1150 0.1316 0.008 1.090 9.1 114.9 21.3 438 n/a 4_bss: 0.1143 0.1318 0.008 1.090 9.1 114.9 21.3 438 n/a 4_settarget: 0.1143 0.1318 0.008 1.090 9.1 114.9 21.3 438 n/a 4_updatecdl: 0.1143 0.1318 0.008 1.092 9.1 114.9 21.3 438 n/a 4_nqh: 0.1143 0.1318 0.008 1.092 9.1 114.9 21.3 438 n/a 4_sol: 0.1158 0.1307 0.008 1.092 9.1 114.9 21.1 438 n/a 4_weight: 0.1158 0.1307 0.008 1.092 9.1 114.9 21.1 438 n/a 4_xyzrec: 0.1155 0.1313 0.009 1.130 9.1 114.9 21.1 438 n/a 4_adp: 0.1155 0.1313 0.009 1.130 9.1 114.9 21.1 438 n/a 4_regHadp: 0.1155 0.1313 0.009 1.130 9.1 114.9 21.1 438 n/a 4_occ: 0.1150 0.1306 0.009 1.130 9.1 114.9 21.1 438 n/a 5_bss: 0.1145 0.1310 0.009 1.130 9.1 114.9 21.1 438 n/a 5_settarget: 0.1145 0.1310 0.009 1.130 9.1 114.9 21.1 438 n/a 5_updatecdl: 0.1145 0.1310 0.009 1.131 9.1 114.9 21.1 438 n/a 5_setrh: 0.1146 0.1310 0.009 1.131 9.1 114.9 21.1 438 n/a 5_nqh: 0.1146 0.1309 0.009 1.131 9.1 114.9 21.1 438 n/a 5_sol: 0.1149 0.1308 0.009 1.131 9.1 114.9 21.0 440 n/a 5_weight: 0.1149 0.1308 0.009 1.131 9.1 114.9 21.0 440 n/a 5_xyzrec: 0.1150 0.1307 0.009 1.181 9.1 114.9 21.0 440 n/a 5_adp: 0.1150 0.1307 0.009 1.181 9.1 114.9 21.0 440 n/a 5_regHadp: 0.1150 0.1307 0.009 1.181 9.1 114.9 21.0 440 n/a 5_occ: 0.1145 0.1302 0.009 1.181 9.1 114.9 21.0 440 n/a end: 0.1144 0.1304 0.009 1.181 9.1 114.9 21.0 440 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_9394591_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_9394591_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.1500 Refinement macro-cycles (run) : 14213.7900 Write final files (write_after_run_outputs) : 67.0000 Total : 14283.9400 Total CPU time: 3.97 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:20:28 PST -0800 (1735366828.76 s) Start R-work = 0.1645, R-free = 0.1803 Final R-work = 0.1144, R-free = 0.1304 =============================================================================== Job complete usr+sys time: 14420.86 seconds wall clock time: 263 minutes 57.27 seconds (15837.27 seconds total)