Starting phenix.refine on Sat Dec 28 21:06:35 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6462862.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.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_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6462862.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6462862.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } 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 } } 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: 2.28, per 1000 atoms: 0.67 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: 0.90 Conformation dependent library (CDL) restraints added in 303.6 milliseconds Time building geometry restraints manager: 0.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.92: 532 0.92 - 1.17: 1105 1.17 - 1.43: 688 1.43 - 1.69: 810 1.69 - 1.95: 18 Bond restraints: 3153 Sorted by residual: bond pdb=" N ALEU A 153 " pdb=" CA ALEU A 153 " ideal model delta sigma weight residual 1.456 1.726 -0.269 1.21e-02 6.83e+03 4.96e+02 bond pdb=" C VAL A 69 " pdb=" O VAL A 69 " ideal model delta sigma weight residual 1.235 1.423 -0.188 1.02e-02 9.61e+03 3.40e+02 bond pdb=" N BLYS A 132 " pdb=" CA BLYS A 132 " ideal model delta sigma weight residual 1.459 1.669 -0.210 1.19e-02 7.06e+03 3.12e+02 bond pdb=" N ASP A 60 " pdb=" CA ASP A 60 " ideal model delta sigma weight residual 1.459 1.255 0.204 1.17e-02 7.31e+03 3.03e+02 bond pdb=" N LEU A 72 " pdb=" CA LEU A 72 " ideal model delta sigma weight residual 1.454 1.661 -0.207 1.21e-02 6.83e+03 2.91e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.22: 2904 4.22 - 8.44: 1893 8.44 - 12.65: 760 12.65 - 16.87: 193 16.87 - 21.09: 27 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA ILE A 117 " pdb=" C ILE A 117 " pdb=" O ILE A 117 " ideal model delta sigma weight residual 120.84 136.82 -15.98 1.16e+00 7.43e-01 1.90e+02 angle pdb=" CA LYS A 12 " pdb=" C LYS A 12 " pdb=" O LYS A 12 " ideal model delta sigma weight residual 120.96 105.98 14.98 1.09e+00 8.42e-01 1.89e+02 angle pdb=" O VAL A 169 " pdb=" C VAL A 169 " pdb=" N GLU A 170 " ideal model delta sigma weight residual 121.91 135.32 -13.41 9.80e-01 1.04e+00 1.87e+02 angle pdb=" O ARG A 28 " pdb=" C ARG A 28 " pdb=" N ALA A 29 " ideal model delta sigma weight residual 122.12 107.87 14.25 1.06e+00 8.90e-01 1.81e+02 angle pdb=" C LEU A 72 " pdb=" CA LEU A 72 " pdb=" CB LEU A 72 " ideal model delta sigma weight residual 110.17 123.12 -12.95 9.90e-01 1.02e+00 1.71e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 957 17.98 - 35.96: 103 35.96 - 53.93: 38 53.93 - 71.91: 10 71.91 - 89.89: 3 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA VAL A 69 " pdb=" C VAL A 69 " pdb=" N VAL A 70 " pdb=" CA VAL A 70 " ideal model delta harmonic sigma weight residual 180.00 156.74 23.26 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA SER A 85 " pdb=" C SER A 85 " pdb=" N ALA A 86 " pdb=" CA ALA A 86 " ideal model delta harmonic sigma weight residual 180.00 158.26 21.74 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CG ATYR A 67 " pdb=" CD1ATYR A 67 " pdb=" CE1ATYR A 67 " pdb=" HE1ATYR A 67 " ideal model delta harmonic sigma weight residual -180.00 -159.84 -20.16 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.272: 117 0.272 - 0.544: 84 0.544 - 0.815: 28 0.815 - 1.086: 12 1.086 - 1.358: 2 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA ASP A 49 " pdb=" N ASP A 49 " pdb=" C ASP A 49 " pdb=" CB ASP A 49 " both_signs ideal model delta sigma weight residual False 2.51 1.15 1.36 2.00e-01 2.50e+01 4.61e+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 -1.35 -1.24 2.00e-01 2.50e+01 3.83e+01 chirality pdb=" CA ALA A 86 " pdb=" N ALA A 86 " pdb=" C ALA A 86 " pdb=" CB ALA A 86 " both_signs ideal model delta sigma weight residual False 2.48 1.47 1.01 2.00e-01 2.50e+01 2.57e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.072 2.00e-02 2.50e+03 6.94e-02 1.44e+02 pdb=" CG PHE A 164 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.134 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.038 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.017 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.079 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.065 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.034 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.066 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.058 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.110 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " -0.016 2.00e-02 2.50e+03 6.26e-02 1.18e+02 pdb=" CG PHE A 162 " 0.069 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " 0.096 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " -0.089 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " -0.013 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " 0.010 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " -0.095 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " -0.085 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " 0.019 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " 0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " -0.079 2.00e-02 2.50e+03 5.99e-02 1.08e+02 pdb=" CG ATYR A 67 " -0.065 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " 0.035 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.069 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " 0.115 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " 0.027 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " -0.011 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " -0.042 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " 0.043 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " 0.021 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " -0.088 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " -0.026 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 398 2.19 - 2.80: 7074 2.80 - 3.40: 10882 3.40 - 4.00: 15533 4.00 - 4.60: 22718 Nonbonded interactions: 56605 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.592 2.100 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.789 2.450 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.803 2.450 nonbonded pdb=" H THR A 125 " pdb=" HH TYR A 141 " model vdw 1.810 2.100 nonbonded pdb=" H THR A 124 " pdb=" HG1 THR A 154 " model vdw 1.823 2.100 ... (remaining 56600 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 } 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 } } output { prefix = "shake_6462862_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= 0.2612 r_free= 0.1931 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.789482 | | target function (ml) not normalized (work): 232380.616952 | | target function (ml) not normalized (free): 11799.032408 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3030 0.2091 7.0263 4.9478| | 2: 3.57 - 2.84 1.00 2876 122 0.2428 0.1855 4.3526 4.3486| | 3: 2.84 - 2.48 1.00 2833 165 0.2387 0.1664 4.1332 4.1735| | 4: 2.47 - 2.25 1.00 2825 136 0.2344 0.1429 3.8325 3.832| | 5: 2.25 - 2.09 1.00 2756 127 0.2471 0.1560 3.8002 3.8215| | 6: 2.09 - 1.97 1.00 2846 113 0.2519 0.1743 3.4686 3.5688| | 7: 1.97 - 1.87 1.00 2787 165 0.2619 0.1753 3.1528 3.1764| | 8: 1.87 - 1.79 1.00 2789 144 0.2483 0.1799 3.0605 3.1021| | 9: 1.79 - 1.72 1.00 2745 138 0.2435 0.1912 2.9112 2.963| | 10: 1.72 - 1.66 1.00 2789 158 0.2405 0.1967 2.7873 2.8858| | 11: 1.66 - 1.61 1.00 2740 147 0.2490 0.1756 2.7383 2.7351| | 12: 1.61 - 1.56 1.00 2787 146 0.2495 0.2035 2.6311 2.7271| | 13: 1.56 - 1.52 1.00 2745 130 0.2594 0.1702 2.5884 2.5296| | 14: 1.52 - 1.48 1.00 2803 134 0.2562 0.2152 2.5022 2.5682| | 15: 1.48 - 1.45 1.00 2738 128 0.2639 0.1974 2.4146 2.4521| | 16: 1.45 - 1.42 1.00 2756 161 0.2624 0.1940 2.3792 2.3948| | 17: 1.42 - 1.39 1.00 2785 139 0.2707 0.1958 2.3311 2.3007| | 18: 1.39 - 1.36 1.00 2741 179 0.2701 0.2298 2.2628 2.3541| | 19: 1.36 - 1.34 1.00 2807 134 0.2655 0.2276 2.2422 2.2993| | 20: 1.34 - 1.32 1.00 2696 147 0.2683 0.2187 2.2067 2.2198| | 21: 1.32 - 1.30 1.00 2785 112 0.2736 0.2338 2.1697 2.1633| | 22: 1.29 - 1.27 1.00 2704 152 0.2770 0.2580 2.1497 2.2329| | 23: 1.27 - 1.26 1.00 2802 156 0.2710 0.2602 2.0866 2.2206| | 24: 1.26 - 1.24 1.00 2744 132 0.2701 0.2433 2.064 2.1097| | 25: 1.24 - 1.22 1.00 2734 148 0.2842 0.2523 2.0363 2.0674| | 26: 1.22 - 1.21 1.00 2727 135 0.2840 0.2267 2.0085 2.047| | 27: 1.21 - 1.19 1.00 2814 148 0.2968 0.2570 2.0062 1.9761| | 28: 1.19 - 1.18 1.00 2671 147 0.2988 0.2820 1.9851 1.9826| | 29: 1.18 - 1.16 1.00 2800 134 0.2996 0.2915 1.9617 2.0574| | 30: 1.16 - 1.15 1.00 2740 148 0.3067 0.2876 1.941 1.9708| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.96 0.76 0.23 1499.57| | 2: 3.57 - 2.84 2876 122 0.80 26.22 1.27 0.23 1499.57| | 3: 2.84 - 2.48 2833 165 0.74 32.22 1.25 0.23 1242.65| | 4: 2.47 - 2.25 2825 136 0.81 25.65 1.26 0.25 575.90| | 5: 2.25 - 2.09 2756 127 0.77 29.47 1.28 0.25 575.90| | 6: 2.09 - 1.97 2846 113 0.84 22.53 1.29 0.25 313.32| | 7: 1.97 - 1.87 2787 165 0.90 16.62 1.29 0.25 89.37| | 8: 1.87 - 1.79 2789 144 0.86 21.08 1.25 0.25 89.37| | 9: 1.79 - 1.72 2745 138 0.88 18.42 1.23 0.25 54.08| | 10: 1.72 - 1.66 2789 158 0.87 19.85 1.22 0.25 47.01| | 11: 1.66 - 1.61 2740 147 0.86 21.32 1.24 0.25 45.35| | 12: 1.61 - 1.56 2787 146 0.89 18.03 1.23 0.25 28.48| | 13: 1.56 - 1.52 2745 130 0.87 20.07 1.24 0.25 28.48| | 14: 1.52 - 1.48 2803 134 0.87 20.35 1.23 0.25 25.54| | 15: 1.48 - 1.45 2738 128 0.87 20.05 1.25 0.25 20.15| | 16: 1.45 - 1.42 2756 161 0.86 21.41 1.23 0.25 20.15| | 17: 1.42 - 1.39 2785 139 0.87 20.79 1.23 0.25 17.23| | 18: 1.39 - 1.36 2741 179 0.86 21.18 1.24 0.25 15.53| | 19: 1.36 - 1.34 2807 134 0.86 21.94 1.22 0.25 15.53| | 20: 1.34 - 1.32 2696 147 0.87 20.94 1.21 0.24 12.98| | 21: 1.32 - 1.30 2785 112 0.86 21.95 1.21 0.24 12.80| | 22: 1.29 - 1.27 2704 152 0.85 22.34 1.20 0.24 12.52| | 23: 1.27 - 1.26 2802 156 0.86 22.23 1.20 0.24 11.11| | 24: 1.26 - 1.24 2744 132 0.85 22.57 1.20 0.24 11.11| | 25: 1.24 - 1.22 2734 148 0.84 23.97 1.22 0.24 10.59| | 26: 1.22 - 1.21 2727 135 0.84 24.29 1.20 0.23 10.01| | 27: 1.21 - 1.19 2814 148 0.83 24.94 1.20 0.23 10.01| | 28: 1.19 - 1.18 2671 147 0.82 25.76 1.19 0.23 9.40| | 29: 1.18 - 1.16 2800 134 0.82 26.21 1.16 0.22 9.18| | 30: 1.16 - 1.15 2740 148 0.80 27.52 1.15 0.22 9.18| |alpha: min = 0.22 max = 0.25 mean = 0.24| |beta: min = 9.18 max = 1499.57 mean = 216.69| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.99 mean = 22.63| |phase err.(test): min = 0.00 max = 89.88 mean = 22.40| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.081 0.269 1557 Z= 5.407 Angle : 5.189 18.284 2118 Z= 3.660 Chirality : 0.408 1.358 243 Planarity : 0.032 0.088 284 Dihedral : 13.844 89.886 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.54 % Allowed : 5.41 % Favored : 94.05 % Rotamer: Outliers : 1.24 % Allowed : 3.73 % Favored : 95.03 % Cbeta Deviations : 35.14 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.21 (0.42), residues: 224 helix: -2.76 (0.33), residues: 107 sheet: -2.02 (0.79), residues: 24 loop : -1.05 (0.51), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.093 0.026 ARG A 98 TYR 0.072 0.044 TYR A 139 PHE 0.095 0.041 PHE A 164 HIS 0.045 0.026 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= 0.2612 r_free= 0.1931 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.789482 | | target function (ml) not normalized (work): 232380.616952 | | target function (ml) not normalized (free): 11799.032408 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2570 0.2613 0.1932 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2570 0.2613 0.1932 n_refl.: 87602 remove outliers: r(all,work,free)=0.1983 0.1988 0.1932 n_refl.: 87594 overall B=0.21 to atoms: r(all,work,free)=0.2008 0.2013 0.1945 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1646 0.1640 0.1760 n_refl.: 87594 remove outliers: r(all,work,free)=0.1646 0.1640 0.1760 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 0.3874 386.351 358.039 0.667 1.002 0.407 11.894-9.307 99.02 97 4 0.1833 613.700 593.975 0.927 1.003 0.375 9.237-7.194 100.00 213 7 0.2158 501.931 492.314 0.956 1.004 0.344 7.162-5.571 100.00 427 22 0.2215 376.671 364.196 0.925 1.004 0.288 5.546-4.326 100.00 867 58 0.1277 517.076 511.670 0.960 1.004 0.229 4.315-3.360 100.00 1859 96 0.1149 491.743 488.443 1.004 1.003 0.173 3.356-2.611 100.00 3867 181 0.1441 323.050 319.565 0.998 1.002 0.067 2.608-2.026 99.99 8198 413 0.1341 214.153 212.147 1.006 1.001 0.000 2.025-1.573 100.00 17313 902 0.1664 104.581 103.882 1.013 0.998 0.000 1.573-1.221 100.00 36679 1900 0.2064 46.375 45.008 1.006 0.994 0.000 1.221-1.150 99.97 13689 708 0.2596 29.220 26.899 0.976 0.991 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0476 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1640 r_free=0.1760 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN Total number of N/Q/H flips: 1 r_work=0.1641 r_free=0.1762 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.973374 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2004.749329 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 0.1214 0.1464 0.0250 0.007 0.9 1.0 0.5 0.0 0 11.487 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.14 14.64 2.50 3.013 19.066 2004.749 0.017 12.44 15.40 2.96 3.294 19.613 2004.749 0.016 Individual atomic B min max mean iso aniso Overall: 8.57 118.63 21.13 2.89 0 1785 Protein: 8.57 118.63 17.97 2.88 0 1519 Water: 11.16 114.51 39.48 N/A 0 258 Other: 23.34 37.25 29.84 N/A 0 8 Chain A: 8.57 118.63 21.13 N/A 0 1785 Histogram: Values Number of atoms 8.57 - 19.57 1204 19.57 - 30.58 233 30.58 - 41.59 156 41.59 - 52.59 106 52.59 - 63.60 54 63.60 - 74.61 16 74.61 - 85.61 9 85.61 - 96.62 4 96.62 - 107.62 0 107.62 - 118.63 3 =========================== Idealize ADP of riding H ========================== r_work=0.1244 r_free=0.1540 r_work=0.1249 r_free=0.1546 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1249 r_free = 0.1546 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1248 r_free = 0.1548 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.25 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= 0.1248 r_free= 0.1548 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.015416 | | target function (ls_wunit_k1) not normalized (work): 1284.131517 | | target function (ls_wunit_k1) not normalized (free): 114.563524 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1263 0.1248 0.1548 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1704 0.1703 0.1770 n_refl.: 87593 remove outliers: r(all,work,free)=0.1704 0.1703 0.1770 n_refl.: 87593 overall B=0.13 to atoms: r(all,work,free)=0.1726 0.1725 0.1786 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1262 0.1248 0.1542 n_refl.: 87593 remove outliers: r(all,work,free)=0.1261 0.1247 0.1542 n_refl.: 87592 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3634 298.194 278.189 0.631 1.002 0.380 11.894-9.307 99.02 97 4 0.1610 477.690 465.886 0.905 1.003 0.380 9.237-7.194 100.00 213 7 0.1814 390.692 385.416 0.948 1.003 0.340 7.162-5.571 100.00 427 22 0.1715 293.193 287.848 0.920 1.003 0.253 5.546-4.326 100.00 867 58 0.0917 402.481 399.696 0.947 1.003 0.199 4.315-3.360 100.00 1859 96 0.0777 382.762 381.726 0.995 1.003 0.180 3.356-2.611 100.00 3867 181 0.1020 251.455 250.765 1.000 1.002 0.057 2.608-2.026 99.99 8198 413 0.0978 166.692 166.109 1.010 1.001 0.000 2.025-1.573 100.00 17313 902 0.1218 81.404 81.572 1.018 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1659 36.098 35.560 1.007 0.997 0.000 1.221-1.150 99.97 13689 708 0.2366 22.744 21.259 0.970 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0512 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1247 r_free=0.1542 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 180 GLN Total number of N/Q/H flips: 2 r_work=0.1250 r_free=0.1543 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1250 r_free=0.1543 | n_water=258 | time (s): 2.170 (total time: 2.170) Filter (dist) r_work=0.1259 r_free=0.1542 | n_water=252 | time (s): 28.080 (total time: 30.250) Filter (q & B) r_work=0.1263 r_free=0.1542 | n_water=249 | time (s): 3.880 (total time: 34.130) Compute maps r_work=0.1263 r_free=0.1542 | n_water=249 | time (s): 1.960 (total time: 36.090) Filter (map) r_work=0.1275 r_free=0.1550 | n_water=237 | time (s): 3.860 (total time: 39.950) Find peaks r_work=0.1275 r_free=0.1550 | n_water=237 | time (s): 0.710 (total time: 40.660) Add new water r_work=0.1427 r_free=0.1701 | n_water=459 | time (s): 4.080 (total time: 44.740) Refine new water occ: r_work=0.1339 r_free=0.1562 adp: r_work=0.1260 r_free=0.1512 occ: r_work=0.1273 r_free=0.1500 adp: r_work=0.1239 r_free=0.1489 occ: r_work=0.1243 r_free=0.1475 adp: r_work=0.1232 r_free=0.1475 ADP+occupancy (water only), MIN, final r_work=0.1232 r_free=0.1475 r_work=0.1232 r_free=0.1475 | n_water=459 | time (s): 79.070 (total time: 123.810) Filter (q & B) r_work=0.1237 r_free=0.1482 | n_water=440 | time (s): 4.030 (total time: 127.840) Filter (dist only) r_work=0.1237 r_free=0.1482 | n_water=440 | time (s): 42.300 (total time: 170.140) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 28.825074 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1540.228991 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 0.1229 0.1507 0.0278 0.007 0.9 1.9 0.5 0.0 0 14.413 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.29 15.07 2.78 3.810 23.357 1540.229 0.015 11.96 14.73 2.78 4.316 23.119 1540.229 0.015 Individual atomic B min max mean iso aniso Overall: 8.81 113.76 23.31 2.63 203 1764 Protein: 8.81 113.76 17.66 2.63 0 1519 Water: 11.27 75.97 42.75 N/A 203 237 Other: 23.27 33.85 27.67 N/A 0 8 Chain A: 8.81 113.76 20.40 N/A 0 1764 Chain S: 14.28 75.97 48.61 N/A 203 0 Histogram: Values Number of atoms 8.81 - 19.31 1211 19.31 - 29.80 253 29.80 - 40.30 178 40.30 - 50.79 139 50.79 - 61.29 120 61.29 - 71.78 51 71.78 - 82.28 9 82.28 - 92.77 3 92.77 - 103.27 1 103.27 - 113.76 2 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1473 r_work=0.1195 r_free=0.1473 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1195 r_free = 0.1473 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1467 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1196 r_free= 0.1467 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.013772 | | target function (ls_wunit_k1) not normalized (work): 1147.170708 | | target function (ls_wunit_k1) not normalized (free): 99.832426 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1209 0.1196 0.1467 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1601 0.1597 0.1716 n_refl.: 87592 remove outliers: r(all,work,free)=0.1601 0.1597 0.1716 n_refl.: 87592 overall B=0.03 to atoms: r(all,work,free)=0.1605 0.1601 0.1719 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1206 0.1193 0.1462 n_refl.: 87592 remove outliers: r(all,work,free)=0.1204 0.1191 0.1462 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 91.67 83 5 0.3275 290.910 272.939 0.587 1.002 0.360 11.894-9.307 99.02 97 4 0.1516 477.690 472.195 0.909 1.003 0.333 9.237-7.194 100.00 213 7 0.1674 390.692 391.773 0.978 1.003 0.254 7.162-5.571 100.00 427 22 0.1462 293.193 289.842 0.938 1.003 0.224 5.546-4.326 100.00 867 58 0.0824 402.481 399.923 0.957 1.003 0.200 4.315-3.360 100.00 1859 96 0.0698 382.762 381.729 1.001 1.003 0.190 3.356-2.611 100.00 3867 181 0.0952 251.455 250.846 1.010 1.002 0.150 2.608-2.026 99.99 8198 413 0.0963 166.692 166.313 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1177 81.404 81.591 1.029 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1606 36.098 35.610 1.020 0.997 0.000 1.221-1.150 99.97 13689 708 0.2331 22.744 21.287 0.980 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0454 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1191 r_free=0.1462 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1191 r_free=0.1462 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1191 r_free=0.1462 | n_water=440 | time (s): 1.700 (total time: 1.700) Filter (dist) r_work=0.1191 r_free=0.1461 | n_water=438 | time (s): 42.030 (total time: 43.730) Filter (q & B) r_work=0.1192 r_free=0.1461 | n_water=437 | time (s): 2.690 (total time: 46.420) Compute maps r_work=0.1192 r_free=0.1461 | n_water=437 | time (s): 1.650 (total time: 48.070) Filter (map) r_work=0.1228 r_free=0.1464 | n_water=295 | time (s): 3.800 (total time: 51.870) Find peaks r_work=0.1228 r_free=0.1464 | n_water=295 | time (s): 0.710 (total time: 52.580) Add new water r_work=0.1349 r_free=0.1580 | n_water=492 | time (s): 3.080 (total time: 55.660) Refine new water occ: r_work=0.1250 r_free=0.1487 adp: r_work=0.1251 r_free=0.1490 occ: r_work=0.1229 r_free=0.1465 adp: r_work=0.1226 r_free=0.1466 occ: r_work=0.1214 r_free=0.1454 adp: r_work=0.1206 r_free=0.1450 ADP+occupancy (water only), MIN, final r_work=0.1206 r_free=0.1450 r_work=0.1206 r_free=0.1450 | n_water=492 | time (s): 244.960 (total time: 300.620) Filter (q & B) r_work=0.1211 r_free=0.1459 | n_water=456 | time (s): 3.670 (total time: 304.290) Filter (dist only) r_work=0.1211 r_free=0.1457 | n_water=455 | time (s): 41.570 (total time: 345.860) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.012246 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 50.739981 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 0.1218 0.1426 0.0207 0.006 0.9 2.2 0.5 0.0 0 1.006 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.18 14.26 2.07 3.628 22.159 50.740 3.714 12.04 13.89 1.84 4.125 21.981 50.740 3.645 Individual atomic B min max mean iso aniso Overall: 9.27 108.79 21.80 2.34 218 1764 Protein: 9.27 108.79 17.22 2.34 0 1519 Water: 11.54 71.37 37.04 N/A 218 237 Other: 19.01 30.00 24.66 N/A 0 8 Chain A: 9.27 108.79 19.97 N/A 0 1764 Chain S: 15.33 68.78 36.57 N/A 218 0 Histogram: Values Number of atoms 9.27 - 19.22 1235 19.22 - 29.17 270 29.17 - 39.12 214 39.12 - 49.08 147 49.08 - 59.03 80 59.03 - 68.98 23 68.98 - 78.93 7 78.93 - 88.89 3 88.89 - 98.84 1 98.84 - 108.79 2 =========================== Idealize ADP of riding H ========================== r_work=0.1205 r_free=0.1389 r_work=0.1205 r_free=0.1390 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1205 r_free = 0.1390 target_work(ml) = 3.645 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1200 r_free = 0.1387 target_work(ml) = 3.643 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87588 (all), 4.90 % free)------------| | | | r_work= 0.1200 r_free= 0.1387 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.643121 | | target function (ml) not normalized (work): 303442.811403 | | target function (ml) not normalized (free): 16033.694612 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1209 0.1200 0.1387 n_refl.: 87588 re-set all scales: r(all,work,free)=0.1528 0.1526 0.1591 n_refl.: 87588 remove outliers: r(all,work,free)=0.1528 0.1526 0.1591 n_refl.: 87588 overall B=-0.01 to atoms: r(all,work,free)=0.1526 0.1524 0.1590 n_refl.: 87588 bulk-solvent and scaling: r(all,work,free)=0.1201 0.1193 0.1367 n_refl.: 87588 remove outliers: r(all,work,free)=0.1198 0.1189 0.1367 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 89.58 81 5 0.3812 287.555 258.702 0.460 1.000 0.296 11.894-9.307 96.08 94 4 0.2411 471.125 451.752 0.852 1.001 0.279 9.237-7.194 98.18 209 7 0.2293 382.257 384.261 0.950 1.002 0.185 7.162-5.571 100.00 427 22 0.1988 293.193 284.072 0.911 1.002 0.170 5.546-4.326 100.00 867 58 0.1101 402.481 397.936 0.953 1.002 0.160 4.315-3.360 100.00 1859 96 0.0908 382.762 380.259 0.993 1.002 0.160 3.356-2.611 100.00 3867 181 0.1146 251.455 249.535 0.999 1.002 0.072 2.608-2.026 99.99 8198 413 0.1044 166.692 165.708 1.012 1.001 0.000 2.025-1.573 100.00 17313 902 0.1007 81.404 81.561 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1287 36.098 35.667 1.021 0.997 0.000 1.221-1.150 99.97 13689 708 0.2129 22.744 21.363 0.980 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0296 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1189 r_free=0.1367 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=0.1190 r_free=0.1369 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1190 r_free=0.1369 | n_water=455 | time (s): 1.890 (total time: 1.890) Filter (dist) r_work=0.1190 r_free=0.1370 | n_water=454 | time (s): 42.430 (total time: 44.320) Filter (q & B) r_work=0.1190 r_free=0.1370 | n_water=454 | time (s): 0.990 (total time: 45.310) Compute maps r_work=0.1190 r_free=0.1370 | n_water=454 | time (s): 1.800 (total time: 47.110) Filter (map) r_work=0.1216 r_free=0.1375 | n_water=315 | time (s): 3.310 (total time: 50.420) Find peaks r_work=0.1216 r_free=0.1375 | n_water=315 | time (s): 0.460 (total time: 50.880) Add new water r_work=0.1280 r_free=0.1427 | n_water=488 | time (s): 2.870 (total time: 53.750) Refine new water occ: r_work=0.1204 r_free=0.1353 adp: r_work=0.1205 r_free=0.1355 occ: r_work=0.1189 r_free=0.1345 adp: r_work=0.1188 r_free=0.1346 occ: r_work=0.1179 r_free=0.1344 adp: r_work=0.1176 r_free=0.1342 ADP+occupancy (water only), MIN, final r_work=0.1176 r_free=0.1342 r_work=0.1176 r_free=0.1342 | n_water=488 | time (s): 267.290 (total time: 321.040) Filter (q & B) r_work=0.1184 r_free=0.1353 | n_water=443 | time (s): 3.880 (total time: 324.920) Filter (dist only) r_work=0.1185 r_free=0.1352 | n_water=442 | time (s): 39.650 (total time: 364.570) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.913765 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 46.827557 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 0.1190 0.1359 0.0169 0.006 0.9 1.9 0.5 0.0 0 0.957 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.90 13.59 1.69 3.430 21.484 46.828 3.632 11.77 13.51 1.73 3.725 21.395 46.828 3.618 Individual atomic B min max mean iso aniso Overall: 9.30 105.18 21.28 2.18 208 1761 Protein: 9.30 105.18 17.01 2.18 0 1519 Water: 11.51 70.30 35.93 N/A 208 234 Other: 19.01 27.38 23.34 N/A 0 8 Chain A: 9.30 105.18 19.66 N/A 0 1761 Chain S: 15.77 57.47 35.00 N/A 208 0 Histogram: Values Number of atoms 9.30 - 18.89 1227 18.89 - 28.48 280 28.48 - 38.07 209 38.07 - 47.65 139 47.65 - 57.24 74 57.24 - 66.83 27 66.83 - 76.42 8 76.42 - 86.01 2 86.01 - 95.59 1 95.59 - 105.18 2 =========================== Idealize ADP of riding H ========================== r_work=0.1178 r_free=0.1351 r_work=0.1178 r_free=0.1351 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1178 r_free = 0.1351 target_work(ml) = 3.618 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1173 r_free = 0.1348 target_work(ml) = 3.616 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87579 (all), 4.91 % free)------------| | | | r_work= 0.1173 r_free= 0.1348 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.616146 | | target function (ml) not normalized (work): 301163.483521 | | target function (ml) not normalized (free): 15921.669321 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1182 0.1173 0.1348 n_refl.: 87579 re-set all scales: r(all,work,free)=0.1499 0.1497 0.1552 n_refl.: 87579 remove outliers: r(all,work,free)=0.1499 0.1497 0.1552 n_refl.: 87579 overall B=-0.01 to atoms: r(all,work,free)=0.1497 0.1495 0.1550 n_refl.: 87579 bulk-solvent and scaling: r(all,work,free)=0.1182 0.1173 0.1347 n_refl.: 87579 remove outliers: r(all,work,free)=0.1180 0.1172 0.1347 n_refl.: 87575 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.3934 282.859 254.302 0.462 1.000 0.312 11.894-9.307 94.12 92 4 0.2217 476.984 457.116 0.850 1.002 0.300 9.237-7.194 97.73 208 7 0.2261 383.329 377.922 0.928 1.002 0.180 7.162-5.571 100.00 427 22 0.2076 293.193 283.330 0.908 1.002 0.160 5.546-4.326 100.00 867 58 0.1104 402.481 398.733 0.953 1.002 0.153 4.315-3.360 100.00 1859 96 0.0917 382.762 380.370 0.995 1.002 0.137 3.356-2.611 100.00 3867 181 0.1153 251.455 249.744 0.999 1.002 0.053 2.608-2.026 99.99 8198 413 0.1030 166.692 165.847 1.012 1.001 0.000 2.025-1.573 100.00 17313 902 0.0971 81.404 81.688 1.027 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1243 36.098 35.734 1.022 0.996 0.000 1.221-1.150 99.97 13689 708 0.2121 22.744 21.379 0.981 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0328 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1172 r_free=0.1347 After: r_work=0.1172 r_free=0.1347 ================================== NQH flips ================================== r_work=0.1172 r_free=0.1347 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1172 r_free=0.1347 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1172 r_free=0.1347 | n_water=442 | time (s): 2.240 (total time: 2.240) Filter (dist) r_work=0.1172 r_free=0.1347 | n_water=442 | time (s): 39.790 (total time: 42.030) Filter (q & B) r_work=0.1173 r_free=0.1349 | n_water=437 | time (s): 3.550 (total time: 45.580) Compute maps r_work=0.1173 r_free=0.1349 | n_water=437 | time (s): 1.700 (total time: 47.280) Filter (map) r_work=0.1190 r_free=0.1364 | n_water=341 | time (s): 3.100 (total time: 50.380) Find peaks r_work=0.1190 r_free=0.1364 | n_water=341 | time (s): 0.690 (total time: 51.070) Add new water r_work=0.1244 r_free=0.1406 | n_water=498 | time (s): 3.220 (total time: 54.290) Refine new water occ: r_work=0.1185 r_free=0.1340 adp: r_work=0.1185 r_free=0.1344 occ: r_work=0.1173 r_free=0.1328 adp: r_work=0.1171 r_free=0.1332 occ: r_work=0.1164 r_free=0.1320 adp: r_work=0.1160 r_free=0.1323 ADP+occupancy (water only), MIN, final r_work=0.1160 r_free=0.1323 r_work=0.1160 r_free=0.1323 | n_water=498 | time (s): 172.560 (total time: 226.850) Filter (q & B) r_work=0.1168 r_free=0.1329 | n_water=456 | time (s): 3.060 (total time: 229.910) Filter (dist only) r_work=0.1169 r_free=0.1328 | n_water=455 | time (s): 41.280 (total time: 271.190) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.000077 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 38.722157 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 0.1188 0.1357 0.0169 0.007 1.0 3.8 0.5 0.0 0 1.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.88 13.57 1.69 3.315 21.297 38.722 3.622 11.96 13.62 1.66 3.554 21.217 38.722 3.619 Individual atomic B min max mean iso aniso Overall: 9.26 101.34 21.21 2.02 223 1759 Protein: 9.26 101.34 16.80 2.02 0 1519 Water: 11.41 69.55 35.90 N/A 223 232 Other: 18.97 26.66 23.07 N/A 0 8 Chain A: 9.26 101.34 19.40 N/A 0 1759 Chain S: 15.95 60.24 35.49 N/A 223 0 Histogram: Values Number of atoms 9.26 - 18.46 1223 18.46 - 27.67 282 27.67 - 36.88 202 36.88 - 46.09 150 46.09 - 55.30 77 55.30 - 64.51 32 64.51 - 73.72 11 73.72 - 82.93 2 82.93 - 92.13 1 92.13 - 101.34 2 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1362 r_work=0.1196 r_free=0.1361 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1196 r_free = 0.1361 target_work(ml) = 3.619 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1193 r_free = 0.1355 target_work(ml) = 3.617 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87575 (all), 4.91 % free)------------| | | | r_work= 0.1193 r_free= 0.1355 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.617401 | | target function (ml) not normalized (work): 301253.519841 | | target function (ml) not normalized (free): 15915.677781 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2917 171 0.1375 0.1374 5.655 5.6079| | 2: 3.57 - 2.84 1.00 2888 124 0.1111 0.1377 5.175 5.2123| | 3: 2.83 - 2.48 1.00 2820 163 0.1227 0.1282 4.9848 5.0052| | 4: 2.47 - 2.25 1.00 2825 136 0.1035 0.1153 4.6891 4.7491| | 5: 2.25 - 2.09 1.00 2756 127 0.1000 0.1126 4.6254 4.7147| | 6: 2.09 - 1.97 1.00 2846 113 0.0976 0.1188 4.3388 4.4554| | 7: 1.97 - 1.87 1.00 2787 165 0.0992 0.1200 4.0703 4.1557| | 8: 1.87 - 1.79 1.00 2789 144 0.1028 0.1271 3.9895 4.0843| | 9: 1.79 - 1.72 1.00 2745 138 0.0961 0.1301 3.7161 3.9016| | 10: 1.72 - 1.66 1.00 2831 160 0.1015 0.1262 3.638 3.7788| | 11: 1.66 - 1.61 1.00 2712 147 0.0974 0.1091 3.5743 3.6036| | 12: 1.61 - 1.56 1.00 2773 144 0.0920 0.1192 3.3495 3.4957| | 13: 1.56 - 1.52 1.00 2745 130 0.0990 0.1050 3.3414 3.4328| | 14: 1.52 - 1.48 1.00 2803 134 0.0999 0.1096 3.2618 3.3211| | 15: 1.48 - 1.45 1.00 2738 128 0.1021 0.1364 3.1692 3.3408| | 16: 1.45 - 1.42 1.00 2756 161 0.1074 0.1238 3.151 3.2338| | 17: 1.42 - 1.39 1.00 2785 139 0.1129 0.1269 3.1146 3.2222| | 18: 1.39 - 1.36 1.00 2741 179 0.1159 0.1379 3.0853 3.2644| | 19: 1.36 - 1.34 1.00 2807 134 0.1226 0.1601 3.0924 3.2669| | 20: 1.34 - 1.32 1.00 2696 147 0.1324 0.1503 3.0862 3.1381| | 21: 1.32 - 1.30 1.00 2785 112 0.1421 0.1589 3.0865 3.1429| | 22: 1.29 - 1.27 1.00 2704 152 0.1489 0.1915 3.0871 3.2832| | 23: 1.27 - 1.26 1.00 2802 156 0.1575 0.1866 3.1025 3.2094| | 24: 1.26 - 1.24 1.00 2744 132 0.1631 0.1771 3.0949 3.2012| | 25: 1.24 - 1.22 1.00 2733 148 0.1792 0.2322 3.1076 3.2863| | 26: 1.22 - 1.21 1.00 2727 135 0.1861 0.1784 3.123 3.2005| | 27: 1.21 - 1.19 1.00 2814 148 0.2016 0.2103 3.1414 3.1534| | 28: 1.19 - 1.18 1.00 2671 147 0.2149 0.2335 3.1407 3.1683| | 29: 1.18 - 1.16 1.00 2800 134 0.2220 0.2361 3.1266 3.2222| | 30: 1.16 - 1.15 1.00 2739 148 0.2379 0.2495 3.1146 3.167| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2917 171 0.95 8.52 1.00 0.97 5743.77| | 2: 3.57 - 2.84 2888 124 0.93 12.65 1.01 0.97 5743.77| | 3: 2.83 - 2.48 2820 163 0.89 16.85 0.99 0.97 4826.58| | 4: 2.47 - 2.25 2825 136 0.91 14.05 1.00 0.98 2461.43| | 5: 2.25 - 2.09 2756 127 0.90 16.23 1.01 0.98 2461.43| | 6: 2.09 - 1.97 2846 113 0.92 13.34 1.02 0.98 1467.31| | 7: 1.97 - 1.87 2787 165 0.94 10.77 1.02 0.97 619.46| | 8: 1.87 - 1.79 2789 144 0.91 14.33 1.00 0.97 619.46| | 9: 1.79 - 1.72 2745 138 0.93 11.44 0.98 0.97 338.65| | 10: 1.72 - 1.66 2831 160 0.93 12.34 0.98 0.97 282.42| | 11: 1.66 - 1.61 2712 147 0.93 12.91 0.98 0.97 269.49| | 12: 1.61 - 1.56 2773 144 0.95 9.53 0.99 0.97 147.53| | 13: 1.56 - 1.52 2745 130 0.94 11.14 1.02 0.97 147.53| | 14: 1.52 - 1.48 2803 134 0.94 11.33 1.02 0.97 131.59| | 15: 1.48 - 1.45 2738 128 0.95 10.40 1.01 0.98 102.39| | 16: 1.45 - 1.42 2756 161 0.94 11.58 1.02 0.98 102.39| | 17: 1.42 - 1.39 2785 139 0.94 11.43 1.01 0.98 92.30| | 18: 1.39 - 1.36 2741 179 0.94 11.68 1.01 0.98 86.46| | 19: 1.36 - 1.34 2807 134 0.94 12.19 1.00 0.98 86.46| | 20: 1.34 - 1.32 2696 147 0.94 12.43 0.99 0.97 81.68| | 21: 1.32 - 1.30 2785 112 0.94 13.33 0.99 0.96 81.34| | 22: 1.29 - 1.27 2704 152 0.93 13.90 0.98 0.96 81.59| | 23: 1.27 - 1.26 2802 156 0.92 14.87 0.98 0.95 82.85| | 24: 1.26 - 1.24 2744 132 0.92 14.99 0.97 0.95 82.85| | 25: 1.24 - 1.22 2733 148 0.91 16.40 0.96 0.94 84.51| | 26: 1.22 - 1.21 2727 135 0.90 18.17 1.02 0.93 86.34| | 27: 1.21 - 1.19 2814 148 0.89 18.81 1.02 0.93 86.34| | 28: 1.19 - 1.18 2671 147 0.88 20.37 1.01 0.93 89.69| | 29: 1.18 - 1.16 2800 134 0.88 20.64 0.99 0.92 90.94| | 30: 1.16 - 1.15 2739 148 0.86 22.11 0.98 0.92 90.94| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 81.34 max = 5743.77 mean = 910.70| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.99 mean = 13.94| |phase err.(test): min = 0.00 max = 89.20 mean = 14.06| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1193 0.1355 n_refl.: 87575 re-set all scales: r(all,work,free)=0.1508 0.1506 0.1573 n_refl.: 87575 remove outliers: r(all,work,free)=0.1508 0.1506 0.1573 n_refl.: 87575 overall B=-0.01 to atoms: r(all,work,free)=0.1506 0.1504 0.1571 n_refl.: 87575 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1192 0.1359 n_refl.: 87575 remove outliers: r(all,work,free)=0.1200 0.1192 0.1359 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 88.54 80 5 0.4054 282.859 250.698 0.437 1.000 0.296 11.894-9.307 93.14 91 4 0.2307 470.758 457.982 0.861 1.002 0.235 9.237-7.194 97.73 208 7 0.2409 383.329 376.667 0.914 1.002 0.161 7.162-5.571 100.00 427 22 0.2164 293.193 282.119 0.897 1.002 0.137 5.546-4.326 100.00 867 58 0.1156 402.481 398.186 0.954 1.002 0.130 4.315-3.360 100.00 1859 96 0.0973 382.762 380.197 0.995 1.002 0.120 3.356-2.611 100.00 3867 181 0.1179 251.455 249.473 1.000 1.002 0.110 2.608-2.026 99.99 8198 413 0.1047 166.692 165.708 1.014 1.000 0.000 2.025-1.573 100.00 17313 902 0.0983 81.404 81.651 1.028 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1234 36.098 35.716 1.024 0.995 0.000 1.221-1.150 99.97 13689 708 0.2118 22.744 21.372 0.983 0.993 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0354 ================= 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 : 0.2612 0.1931 0.081 5.189 8.8 119.3 19.9 258 0.000 1_bss: 0.1640 0.1760 0.081 5.189 9.1 119.5 20.1 258 0.000 1_settarget: 0.1640 0.1760 0.081 5.189 9.1 119.5 20.1 258 0.000 1_nqh: 0.1641 0.1762 0.081 5.189 9.1 119.5 20.1 258 0.003 1_weight: 0.1641 0.1762 0.081 5.189 9.1 119.5 20.1 258 0.003 1_xyzrec: 0.1214 0.1464 0.007 0.929 9.1 119.5 20.1 258 0.128 1_adp: 0.1244 0.1540 0.007 0.929 8.6 118.6 21.1 258 0.128 1_regHadp: 0.1249 0.1546 0.007 0.929 8.6 118.6 21.1 258 0.128 1_occ: 0.1248 0.1548 0.007 0.929 8.6 118.6 21.1 258 0.128 2_bss: 0.1247 0.1542 0.007 0.929 8.7 118.8 21.3 258 0.128 2_settarget: 0.1247 0.1542 0.007 0.929 8.7 118.8 21.3 258 0.128 2_updatecdl: 0.1247 0.1542 0.007 0.931 8.7 118.8 21.3 258 0.128 2_nqh: 0.1250 0.1543 0.007 0.931 8.7 118.8 21.3 258 0.128 2_sol: 0.1237 0.1482 0.007 0.931 8.7 118.8 23.7 440 n/a 2_weight: 0.1237 0.1482 0.007 0.931 8.7 118.8 23.7 440 n/a 2_xyzrec: 0.1229 0.1507 0.007 0.905 8.7 118.8 23.7 440 n/a 2_adp: 0.1196 0.1473 0.007 0.905 8.8 113.8 23.3 440 n/a 2_regHadp: 0.1195 0.1473 0.007 0.905 8.8 113.8 23.3 440 n/a 2_occ: 0.1196 0.1467 0.007 0.905 8.8 113.8 23.3 440 n/a 3_bss: 0.1191 0.1462 0.007 0.905 8.8 113.8 23.3 440 n/a 3_settarget: 0.1191 0.1462 0.007 0.905 8.8 113.8 23.3 440 n/a 3_updatecdl: 0.1191 0.1462 0.007 0.905 8.8 113.8 23.3 440 n/a 3_nqh: 0.1191 0.1462 0.007 0.905 8.8 113.8 23.3 440 n/a 3_sol: 0.1211 0.1457 0.007 0.905 8.8 113.8 22.1 455 n/a 3_weight: 0.1211 0.1457 0.007 0.905 8.8 113.8 22.1 455 n/a 3_xyzrec: 0.1218 0.1426 0.006 0.922 8.8 113.8 22.1 455 n/a 3_adp: 0.1205 0.1389 0.006 0.922 9.3 108.8 21.8 455 n/a 3_regHadp: 0.1205 0.1390 0.006 0.922 9.3 108.8 21.8 455 n/a 3_occ: 0.1200 0.1387 0.006 0.922 9.3 108.8 21.8 455 n/a 4_bss: 0.1189 0.1367 0.006 0.922 9.3 108.8 21.8 455 n/a 4_settarget: 0.1189 0.1367 0.006 0.922 9.3 108.8 21.8 455 n/a 4_updatecdl: 0.1189 0.1367 0.006 0.922 9.3 108.8 21.8 455 n/a 4_nqh: 0.1190 0.1369 0.006 0.922 9.3 108.8 21.8 455 n/a 4_sol: 0.1185 0.1352 0.006 0.922 9.3 108.8 21.4 442 n/a 4_weight: 0.1185 0.1352 0.006 0.922 9.3 108.8 21.4 442 n/a 4_xyzrec: 0.1190 0.1359 0.006 0.946 9.3 108.8 21.4 442 n/a 4_adp: 0.1178 0.1351 0.006 0.946 9.3 105.2 21.3 442 n/a 4_regHadp: 0.1178 0.1351 0.006 0.946 9.3 105.2 21.3 442 n/a 4_occ: 0.1173 0.1348 0.006 0.946 9.3 105.2 21.3 442 n/a 5_bss: 0.1172 0.1347 0.006 0.946 9.3 105.2 21.3 442 n/a 5_settarget: 0.1172 0.1347 0.006 0.946 9.3 105.2 21.3 442 n/a 5_updatecdl: 0.1172 0.1347 0.006 0.945 9.3 105.2 21.3 442 n/a 5_setrh: 0.1172 0.1347 0.006 0.945 9.3 105.2 21.3 442 n/a 5_nqh: 0.1172 0.1347 0.006 0.945 9.3 105.2 21.3 442 n/a 5_sol: 0.1169 0.1328 0.006 0.945 9.3 105.2 21.4 455 n/a 5_weight: 0.1169 0.1328 0.006 0.945 9.3 105.2 21.4 455 n/a 5_xyzrec: 0.1188 0.1357 0.007 1.050 9.3 105.2 21.4 455 n/a 5_adp: 0.1196 0.1362 0.007 1.050 9.3 101.3 21.2 455 n/a 5_regHadp: 0.1196 0.1361 0.007 1.050 9.3 101.3 21.2 455 n/a 5_occ: 0.1193 0.1355 0.007 1.050 9.3 101.3 21.2 455 n/a end: 0.1192 0.1359 0.007 1.050 9.2 101.3 21.2 455 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_6462862_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_6462862_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.8900 Refinement macro-cycles (run) : 3631.7600 Write final files (write_after_run_outputs) : 56.9800 Total : 3693.6300 Total CPU time: 62.19 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:13:19 PST -0800 (1735452799.27 s) Start R-work = 0.1640, R-free = 0.1760 Final R-work = 0.1192, R-free = 0.1359 =============================================================================== Job complete usr+sys time: 3830.21 seconds wall clock time: 68 minutes 28.38 seconds (4108.38 seconds total)