Starting phenix.refine on Sat Dec 28 21:06:32 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7410891.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 { 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_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7410891.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7410891.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 1 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 2.39, per 1000 atoms: 0.71 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: 0.76 Conformation dependent library (CDL) restraints added in 210.6 milliseconds Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.63 - 0.89: 410 0.89 - 1.14: 1196 1.14 - 1.40: 576 1.40 - 1.65: 902 1.65 - 1.90: 69 Bond restraints: 3153 Sorted by residual: bond pdb=" N ALA A 165 " pdb=" CA ALA A 165 " ideal model delta sigma weight residual 1.459 1.238 0.221 1.21e-02 6.83e+03 3.35e+02 bond pdb=" ND1 HIS A 126 " pdb=" CE1 HIS A 126 " ideal model delta sigma weight residual 1.321 1.156 0.165 1.00e-02 1.00e+04 2.72e+02 bond pdb=" CA VAL A 33 " pdb=" CB VAL A 33 " ideal model delta sigma weight residual 1.539 1.730 -0.191 1.18e-02 7.18e+03 2.63e+02 bond pdb=" C BLYS A 175 " pdb=" N GLU A 176 " ideal model delta sigma weight residual 1.334 1.540 -0.206 1.27e-02 6.20e+03 2.62e+02 bond pdb=" C GLY A 78 " pdb=" O GLY A 78 " ideal model delta sigma weight residual 1.234 1.428 -0.195 1.21e-02 6.83e+03 2.59e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.93: 3251 4.93 - 9.86: 1858 9.86 - 14.79: 582 14.79 - 19.71: 81 19.71 - 24.64: 5 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA ALEU A 153 " pdb=" C ALEU A 153 " pdb=" O ALEU A 153 " ideal model delta sigma weight residual 120.30 134.74 -14.44 1.07e+00 8.73e-01 1.82e+02 angle pdb=" O LEU A 92 " pdb=" C LEU A 92 " pdb=" N BLYS A 93 " ideal model delta sigma weight residual 122.07 135.58 -13.51 1.03e+00 9.43e-01 1.72e+02 angle pdb=" O ASP A 60 " pdb=" C ASP A 60 " pdb=" N ALA A 61 " ideal model delta sigma weight residual 122.07 135.53 -13.46 1.03e+00 9.43e-01 1.71e+02 angle pdb=" CA LEU A 82 " pdb=" C LEU A 82 " pdb=" O LEU A 82 " ideal model delta sigma weight residual 120.90 134.82 -13.92 1.07e+00 8.73e-01 1.69e+02 angle pdb=" NE ARG A 28 " pdb=" CZ ARG A 28 " pdb=" NH2 ARG A 28 " ideal model delta sigma weight residual 119.20 108.24 10.96 9.00e-01 1.23e+00 1.48e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.42: 921 16.42 - 32.83: 132 32.83 - 49.24: 41 49.24 - 65.66: 14 65.66 - 82.07: 3 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: 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 -154.17 -25.83 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA CYS A 106 " pdb=" C CYS A 106 " pdb=" N ALA A 107 " pdb=" CA ALA A 107 " ideal model delta harmonic sigma weight residual 180.00 157.29 22.71 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA THR A 125 " pdb=" C THR A 125 " pdb=" N HIS A 126 " pdb=" CA HIS A 126 " ideal model delta harmonic sigma weight residual 180.00 157.87 22.13 0 5.00e+00 4.00e-02 1.96e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.270: 111 0.270 - 0.539: 83 0.539 - 0.809: 39 0.809 - 1.079: 8 1.079 - 1.348: 2 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 -1.24 -1.35 2.00e-01 2.50e+01 4.55e+01 chirality pdb=" CA MET A 26 " pdb=" N MET A 26 " pdb=" C MET A 26 " pdb=" CB MET A 26 " both_signs ideal model delta sigma weight residual False 2.51 1.35 1.16 2.00e-01 2.50e+01 3.35e+01 chirality pdb=" CA PRO A 22 " pdb=" N PRO A 22 " pdb=" C PRO A 22 " pdb=" CB PRO A 22 " both_signs ideal model delta sigma weight residual False 2.72 1.70 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 " -0.102 2.00e-02 2.50e+03 7.30e-02 1.60e+02 pdb=" CG PHE A 164 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.087 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.128 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.091 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.083 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.082 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.008 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.046 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.055 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " -0.065 2.00e-02 2.50e+03 6.85e-02 1.41e+02 pdb=" CG ATYR A 67 " 0.032 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " -0.015 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.098 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " 0.080 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " 0.068 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " 0.064 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " -0.121 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " -0.066 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " -0.022 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " 0.027 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " -0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 138 " 0.070 2.00e-02 2.50e+03 6.39e-02 9.18e+01 pdb=" CG HIS A 138 " -0.055 2.00e-02 2.50e+03 pdb=" ND1 HIS A 138 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 HIS A 138 " -0.060 2.00e-02 2.50e+03 pdb=" CE1 HIS A 138 " 0.068 2.00e-02 2.50e+03 pdb=" NE2 HIS A 138 " -0.078 2.00e-02 2.50e+03 pdb=" HD1 HIS A 138 " -0.084 2.00e-02 2.50e+03 pdb=" HD2 HIS A 138 " 0.053 2.00e-02 2.50e+03 pdb=" HE1 HIS A 138 " 0.061 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.34: 1162 2.34 - 2.90: 8204 2.90 - 3.47: 10467 3.47 - 4.03: 15210 4.03 - 4.60: 21605 Nonbonded interactions: 56648 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.771 2.100 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.817 2.450 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.853 2.450 nonbonded pdb=" HE2 HIS A 126 " pdb=" O PRO A 184 " model vdw sym.op. 1.873 2.450 x-y,-y,-z-4/3 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.878 2.450 ... (remaining 56643 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_7410891_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= 0.2603 r_free= 0.1941 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.795928 | | target function (ml) not normalized (work): 232917.562073 | | target function (ml) not normalized (free): 11855.320496 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3025 0.2057 7.0711 4.9433| | 2: 3.57 - 2.84 1.00 2876 122 0.2453 0.1776 4.3504 4.3388| | 3: 2.84 - 2.48 1.00 2833 165 0.2319 0.1658 4.1247 4.148| | 4: 2.47 - 2.25 1.00 2825 136 0.2332 0.1366 3.8335 3.821| | 5: 2.25 - 2.09 1.00 2756 127 0.2495 0.1673 3.7978 3.8319| | 6: 2.09 - 1.97 1.00 2846 113 0.2513 0.1648 3.4684 3.5539| | 7: 1.97 - 1.87 1.00 2787 165 0.2562 0.1853 3.1367 3.244| | 8: 1.87 - 1.79 1.00 2789 144 0.2456 0.2014 3.0683 3.158| | 9: 1.79 - 1.72 1.00 2745 138 0.2420 0.1865 2.8912 2.9255| | 10: 1.72 - 1.66 1.00 2789 158 0.2438 0.1885 2.8157 2.8644| | 11: 1.66 - 1.61 1.00 2740 147 0.2523 0.1953 2.7568 2.767| | 12: 1.61 - 1.56 1.00 2787 146 0.2487 0.2124 2.6256 2.7061| | 13: 1.56 - 1.52 1.00 2745 130 0.2507 0.1970 2.5833 2.6492| | 14: 1.52 - 1.48 1.00 2803 134 0.2575 0.2034 2.5003 2.5773| | 15: 1.48 - 1.45 1.00 2738 128 0.2615 0.2158 2.4551 2.55| | 16: 1.45 - 1.42 1.00 2756 161 0.2652 0.2283 2.4053 2.4795| | 17: 1.42 - 1.39 1.00 2785 139 0.2667 0.2090 2.3414 2.3799| | 18: 1.39 - 1.36 1.00 2741 179 0.2665 0.2240 2.2938 2.3523| | 19: 1.36 - 1.34 1.00 2807 134 0.2633 0.2336 2.2527 2.2763| | 20: 1.34 - 1.32 1.00 2696 147 0.2699 0.2101 2.2188 2.1414| | 21: 1.32 - 1.30 1.00 2785 112 0.2666 0.2531 2.1675 2.3024| | 22: 1.29 - 1.27 1.00 2704 152 0.2702 0.2575 2.1226 2.2332| | 23: 1.27 - 1.26 1.00 2802 156 0.2770 0.2371 2.1143 2.168| | 24: 1.26 - 1.24 1.00 2744 132 0.2782 0.2303 2.0633 2.0632| | 25: 1.24 - 1.22 1.00 2734 148 0.2861 0.2520 2.0608 2.0657| | 26: 1.22 - 1.21 1.00 2727 135 0.2836 0.2346 2.013 2.0873| | 27: 1.21 - 1.19 1.00 2814 148 0.2968 0.2691 2.0014 2.0417| | 28: 1.19 - 1.18 1.00 2671 147 0.3000 0.2655 1.9872 2.0097| | 29: 1.18 - 1.16 1.00 2800 134 0.2962 0.2637 1.9645 1.9855| | 30: 1.16 - 1.15 1.00 2740 148 0.3060 0.2856 1.9368 1.9876| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.73 0.76 0.23 1478.00| | 2: 3.57 - 2.84 2876 122 0.80 26.07 1.27 0.23 1478.00| | 3: 2.84 - 2.48 2833 165 0.74 32.05 1.24 0.24 1226.07| | 4: 2.47 - 2.25 2825 136 0.81 25.66 1.25 0.25 572.28| | 5: 2.25 - 2.09 2756 127 0.77 29.42 1.29 0.25 572.28| | 6: 2.09 - 1.97 2846 113 0.83 22.80 1.29 0.25 314.18| | 7: 1.97 - 1.87 2787 165 0.90 16.89 1.29 0.26 94.06| | 8: 1.87 - 1.79 2789 144 0.85 21.44 1.24 0.26 94.06| | 9: 1.79 - 1.72 2745 138 0.87 19.04 1.23 0.26 57.09| | 10: 1.72 - 1.66 2789 158 0.86 20.58 1.23 0.26 49.69| | 11: 1.66 - 1.61 2740 147 0.85 21.67 1.25 0.26 48.01| | 12: 1.61 - 1.56 2787 146 0.88 19.02 1.23 0.25 30.93| | 13: 1.56 - 1.52 2745 130 0.86 20.80 1.23 0.25 30.93| | 14: 1.52 - 1.48 2803 134 0.86 21.37 1.24 0.25 27.69| | 15: 1.48 - 1.45 2738 128 0.87 20.61 1.23 0.25 21.76| | 16: 1.45 - 1.42 2756 161 0.85 22.28 1.23 0.25 21.76| | 17: 1.42 - 1.39 2785 139 0.86 21.11 1.23 0.25 18.28| | 18: 1.39 - 1.36 2741 179 0.86 21.42 1.22 0.25 16.27| | 19: 1.36 - 1.34 2807 134 0.85 22.41 1.21 0.25 16.27| | 20: 1.34 - 1.32 2696 147 0.86 21.47 1.20 0.25 13.44| | 21: 1.32 - 1.30 2785 112 0.86 22.13 1.20 0.25 13.24| | 22: 1.29 - 1.27 2704 152 0.85 22.65 1.21 0.24 12.91| | 23: 1.27 - 1.26 2802 156 0.86 22.21 1.21 0.24 11.21| | 24: 1.26 - 1.24 2744 132 0.85 22.98 1.21 0.24 11.21| | 25: 1.24 - 1.22 2734 148 0.84 23.71 1.20 0.24 10.60| | 26: 1.22 - 1.21 2727 135 0.84 23.83 1.20 0.24 9.93| | 27: 1.21 - 1.19 2814 148 0.83 24.81 1.21 0.24 9.93| | 28: 1.19 - 1.18 2671 147 0.83 24.89 1.19 0.23 9.16| | 29: 1.18 - 1.16 2800 134 0.83 24.98 1.15 0.23 8.87| | 30: 1.16 - 1.15 2740 148 0.81 26.55 1.15 0.23 8.87| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 8.87 max = 1478.00 mean = 215.44| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.99 mean = 22.79| |phase err.(test): min = 0.00 max = 89.99 mean = 22.70| |-----------------------------------------------------------------------------| ----------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 : 0.080 0.247 1557 Z= 5.376 Angle : 5.408 18.959 2118 Z= 3.798 Chirality : 0.413 1.348 243 Planarity : 0.034 0.086 284 Dihedral : 13.735 82.074 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.48 % Allowed : 1.86 % Favored : 95.65 % Cbeta Deviations : 36.22 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.44), residues: 224 helix: -2.57 (0.34), residues: 103 sheet: -0.77 (0.90), residues: 28 loop : -0.42 (0.52), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.101 0.024 ARG A 5 TYR 0.069 0.030 TYR A 139 PHE 0.120 0.045 PHE A 164 HIS 0.042 0.017 HIS A 138 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= 0.2603 r_free= 0.1941 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.795928 | | target function (ml) not normalized (work): 232917.562073 | | target function (ml) not normalized (free): 11855.320496 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2562 0.2604 0.1941 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2562 0.2604 0.1941 n_refl.: 87602 remove outliers: r(all,work,free)=0.1981 0.1985 0.1941 n_refl.: 87594 overall B=0.22 to atoms: r(all,work,free)=0.2007 0.2012 0.1955 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1651 0.1645 0.1756 n_refl.: 87594 remove outliers: r(all,work,free)=0.1650 0.1644 0.1756 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 97.87 87 5 0.3780 389.574 365.819 0.695 1.000 0.407 11.894-9.307 99.02 97 4 0.1807 613.625 595.566 0.929 1.001 0.390 9.237-7.194 100.00 213 7 0.2169 501.870 492.178 0.959 1.001 0.344 7.162-5.571 100.00 427 22 0.2236 376.625 365.126 0.928 1.002 0.288 5.546-4.326 100.00 867 58 0.1291 517.013 511.174 0.966 1.002 0.234 4.315-3.360 100.00 1859 96 0.1150 491.683 487.838 1.004 1.002 0.209 3.356-2.611 100.00 3867 181 0.1443 323.011 319.548 0.997 1.002 0.052 2.608-2.026 99.99 8198 413 0.1352 214.126 211.859 1.005 1.002 0.000 2.025-1.573 100.00 17313 902 0.1653 104.568 103.807 1.010 1.002 0.000 1.573-1.221 100.00 36679 1900 0.2084 46.370 45.072 0.997 1.002 0.000 1.221-1.150 99.97 13689 708 0.2594 29.216 26.885 0.965 1.002 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0017 b_overall=0.0510 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1644 r_free=0.1756 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1644 r_free=0.1756 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.655750 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2021.918518 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 0.1213 0.1469 0.0256 0.007 0.9 1.3 0.5 0.0 0 12.328 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.13 14.69 2.56 3.013 19.081 2021.919 0.017 12.48 15.50 3.02 3.252 19.576 2021.919 0.016 Individual atomic B min max mean iso aniso Overall: 8.60 118.89 21.05 2.88 0 1785 Protein: 8.60 118.89 17.92 2.88 0 1519 Water: 11.04 114.55 39.19 N/A 0 258 Other: 23.23 36.75 29.30 N/A 0 8 Chain A: 8.60 118.89 21.05 N/A 0 1785 Histogram: Values Number of atoms 8.60 - 19.63 1209 19.63 - 30.66 227 30.66 - 41.69 165 41.69 - 52.72 102 52.72 - 63.75 53 63.75 - 74.77 16 74.77 - 85.80 6 85.80 - 96.83 4 96.83 - 107.86 0 107.86 - 118.89 3 =========================== Idealize ADP of riding H ========================== r_work=0.1248 r_free=0.1549 r_work=0.1252 r_free=0.1554 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1252 r_free = 0.1554 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 = 0.1252 r_free = 0.1556 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1252 r_free= 0.1556 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.015415 | | target function (ls_wunit_k1) not normalized (work): 1284.007399 | | target function (ls_wunit_k1) not normalized (free): 115.253959 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1267 0.1252 0.1556 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1706 0.1705 0.1776 n_refl.: 87592 remove outliers: r(all,work,free)=0.1706 0.1705 0.1776 n_refl.: 87592 overall B=0.14 to atoms: r(all,work,free)=0.1729 0.1728 0.1792 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1263 0.1249 0.1549 n_refl.: 87592 remove outliers: r(all,work,free)=0.1263 0.1248 0.1549 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 0.3525 300.986 280.429 0.685 0.923 0.373 11.894-9.307 99.02 97 4 0.1617 478.082 466.307 0.980 0.924 0.368 9.237-7.194 100.00 213 7 0.1821 391.012 385.579 1.028 0.924 0.340 7.162-5.571 100.00 427 22 0.1721 293.433 287.938 0.999 0.925 0.254 5.546-4.326 100.00 867 58 0.0915 402.811 400.131 1.028 0.925 0.209 4.315-3.360 100.00 1859 96 0.0772 383.076 382.028 1.075 0.927 0.190 3.356-2.611 100.00 3867 181 0.1018 251.661 250.952 1.077 0.929 0.100 2.608-2.026 99.99 8198 413 0.0980 166.828 166.206 1.085 0.932 0.000 2.025-1.573 100.00 17313 902 0.1219 81.470 81.635 1.085 0.937 0.000 1.573-1.221 100.00 36679 1900 0.1665 36.127 35.584 1.061 0.946 0.000 1.221-1.150 99.97 13689 708 0.2373 22.763 21.291 1.015 0.953 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0532 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1248 r_free=0.1549 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.1250 r_free=0.1550 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1250 r_free=0.1550 | n_water=258 | time (s): 2.380 (total time: 2.380) Filter (dist) r_work=0.1260 r_free=0.1547 | n_water=251 | time (s): 27.750 (total time: 30.130) Filter (q & B) r_work=0.1263 r_free=0.1546 | n_water=248 | time (s): 3.800 (total time: 33.930) Compute maps r_work=0.1263 r_free=0.1546 | n_water=248 | time (s): 2.000 (total time: 35.930) Filter (map) r_work=0.1276 r_free=0.1555 | n_water=236 | time (s): 4.030 (total time: 39.960) Find peaks r_work=0.1276 r_free=0.1555 | n_water=236 | time (s): 0.770 (total time: 40.730) Add new water r_work=0.1430 r_free=0.1715 | n_water=455 | time (s): 3.900 (total time: 44.630) Refine new water occ: r_work=0.1339 r_free=0.1586 adp: r_work=0.1262 r_free=0.1537 occ: r_work=0.1276 r_free=0.1528 adp: r_work=0.1239 r_free=0.1513 occ: r_work=0.1242 r_free=0.1502 adp: r_work=0.1232 r_free=0.1501 ADP+occupancy (water only), MIN, final r_work=0.1232 r_free=0.1501 r_work=0.1232 r_free=0.1501 | n_water=455 | time (s): 77.950 (total time: 122.580) Filter (q & B) r_work=0.1238 r_free=0.1509 | n_water=433 | time (s): 4.140 (total time: 126.720) Filter (dist only) r_work=0.1238 r_free=0.1509 | n_water=433 | time (s): 41.230 (total time: 167.950) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.032197 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1527.200983 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 0.1234 0.1529 0.0295 0.007 0.9 2.2 0.5 0.0 0 13.016 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.34 15.29 2.95 3.801 23.248 1527.201 0.015 11.99 14.99 2.99 4.235 23.052 1527.201 0.015 Individual atomic B min max mean iso aniso Overall: 8.81 114.60 23.23 2.61 197 1763 Protein: 8.81 114.60 17.70 2.62 0 1519 Water: 10.98 71.75 42.54 N/A 197 236 Other: 22.21 33.47 27.03 N/A 0 8 Chain A: 8.81 114.60 20.39 N/A 0 1763 Chain S: 14.51 69.74 48.63 N/A 197 0 Histogram: Values Number of atoms 8.81 - 19.39 1210 19.39 - 29.97 249 29.97 - 40.55 191 40.55 - 51.13 138 51.13 - 61.70 106 61.70 - 72.28 55 72.28 - 82.86 5 82.86 - 93.44 3 93.44 - 104.02 1 104.02 - 114.60 2 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1498 r_work=0.1199 r_free=0.1498 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1498 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 = 0.1198 r_free = 0.1500 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.20 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= 0.1198 r_free= 0.1500 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.013873 | | target function (ls_wunit_k1) not normalized (work): 1155.533903 | | target function (ls_wunit_k1) not normalized (free): 106.080239 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1213 0.1198 0.1500 n_refl.: 87591 re-set all scales: r(all,work,free)=0.1610 0.1605 0.1737 n_refl.: 87591 remove outliers: r(all,work,free)=0.1610 0.1605 0.1737 n_refl.: 87591 overall B=0.03 to atoms: r(all,work,free)=0.1615 0.1610 0.1740 n_refl.: 87591 bulk-solvent and scaling: r(all,work,free)=0.1211 0.1196 0.1497 n_refl.: 87591 remove outliers: r(all,work,free)=0.1210 0.1195 0.1497 n_refl.: 87589 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 92.71 84 5 0.3330 299.590 272.372 0.601 1.002 0.370 11.894-9.307 99.02 97 4 0.1468 478.082 475.225 0.912 1.003 0.350 9.237-7.194 100.00 213 7 0.1666 391.012 391.032 0.980 1.003 0.280 7.162-5.571 100.00 427 22 0.1509 293.433 289.521 0.938 1.003 0.220 5.546-4.326 100.00 867 58 0.0814 402.811 400.451 0.957 1.003 0.210 4.315-3.360 100.00 1859 96 0.0710 383.076 382.103 1.002 1.002 0.201 3.356-2.611 100.00 3867 181 0.0952 251.661 250.874 1.009 1.002 0.072 2.608-2.026 99.99 8198 413 0.0961 166.828 166.434 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1183 81.470 81.663 1.028 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1611 36.127 35.618 1.018 0.998 0.000 1.221-1.150 99.97 13689 708 0.2337 22.763 21.288 0.978 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0528 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1195 r_free=0.1497 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1195 r_free=0.1497 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1195 r_free=0.1497 | n_water=433 | time (s): 1.610 (total time: 1.610) Filter (dist) r_work=0.1195 r_free=0.1497 | n_water=431 | time (s): 38.580 (total time: 40.190) Filter (q & B) r_work=0.1195 r_free=0.1497 | n_water=431 | time (s): 1.290 (total time: 41.480) Compute maps r_work=0.1195 r_free=0.1497 | n_water=431 | time (s): 1.560 (total time: 43.040) Filter (map) r_work=0.1237 r_free=0.1492 | n_water=294 | time (s): 2.730 (total time: 45.770) Find peaks r_work=0.1237 r_free=0.1492 | n_water=294 | time (s): 0.630 (total time: 46.400) Add new water r_work=0.1359 r_free=0.1598 | n_water=478 | time (s): 3.410 (total time: 49.810) Refine new water occ: r_work=0.1266 r_free=0.1514 adp: r_work=0.1267 r_free=0.1515 occ: r_work=0.1242 r_free=0.1499 adp: r_work=0.1241 r_free=0.1498 occ: r_work=0.1225 r_free=0.1491 adp: r_work=0.1219 r_free=0.1485 ADP+occupancy (water only), MIN, final r_work=0.1219 r_free=0.1485 r_work=0.1219 r_free=0.1485 | n_water=478 | time (s): 253.530 (total time: 303.340) Filter (q & B) r_work=0.1223 r_free=0.1490 | n_water=443 | time (s): 2.610 (total time: 305.950) Filter (dist only) r_work=0.1223 r_free=0.1489 | n_water=442 | time (s): 35.630 (total time: 341.580) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.114477 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 49.673929 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 0.1224 0.1452 0.0228 0.006 0.9 1.9 0.5 0.0 0 1.057 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.24 14.52 2.28 3.629 22.143 49.674 3.721 12.10 14.02 1.93 4.165 21.932 49.674 3.649 Individual atomic B min max mean iso aniso Overall: 9.29 109.84 21.66 2.33 209 1760 Protein: 9.29 109.84 17.22 2.33 0 1519 Water: 11.49 70.49 36.88 N/A 209 233 Other: 18.98 29.75 24.31 N/A 0 8 Chain A: 9.29 109.84 19.86 N/A 0 1760 Chain S: 14.94 66.18 36.83 N/A 209 0 Histogram: Values Number of atoms 9.29 - 19.34 1238 19.34 - 29.40 267 29.40 - 39.45 211 39.45 - 49.51 145 49.51 - 59.56 73 59.56 - 69.62 21 69.62 - 79.68 8 79.68 - 89.73 3 89.73 - 99.79 1 99.79 - 109.84 2 =========================== Idealize ADP of riding H ========================== r_work=0.1210 r_free=0.1402 r_work=0.1211 r_free=0.1403 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1211 r_free = 0.1403 target_work(ml) = 3.649 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1204 r_free = 0.1394 target_work(ml) = 3.646 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87589 (all), 4.90 % free)------------| | | | r_work= 0.1204 r_free= 0.1394 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.645682 | | target function (ml) not normalized (work): 303659.816165 | | target function (ml) not normalized (free): 16040.603669 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1213 0.1204 0.1394 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1542 0.1540 0.1603 n_refl.: 87589 remove outliers: r(all,work,free)=0.1542 0.1540 0.1603 n_refl.: 87589 overall B=-0.01 to atoms: r(all,work,free)=0.1540 0.1538 0.1601 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1205 0.1197 0.1367 n_refl.: 87589 remove outliers: r(all,work,free)=0.1202 0.1193 0.1367 n_refl.: 87581 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 89.58 81 5 0.3793 293.750 262.611 0.493 0.999 0.324 11.894-9.307 98.04 96 4 0.2266 478.205 463.440 0.860 1.001 0.320 9.237-7.194 98.18 209 7 0.2231 382.570 385.475 0.952 1.002 0.190 7.162-5.571 100.00 427 22 0.1983 293.433 284.765 0.913 1.002 0.173 5.546-4.326 100.00 867 58 0.1117 402.811 398.316 0.952 1.002 0.170 4.315-3.360 100.00 1859 96 0.0929 383.076 380.384 0.993 1.002 0.170 3.356-2.611 100.00 3867 181 0.1151 251.661 249.712 0.999 1.002 0.072 2.608-2.026 99.99 8198 413 0.1050 166.828 165.803 1.011 1.001 0.000 2.025-1.573 100.00 17313 902 0.1011 81.470 81.602 1.026 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1288 36.127 35.694 1.020 0.998 0.000 1.221-1.150 99.97 13689 708 0.2128 22.763 21.374 0.979 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0286 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1193 r_free=0.1367 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=0.1193 r_free=0.1367 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1367 | n_water=442 | time (s): 2.170 (total time: 2.170) Filter (dist) r_work=0.1193 r_free=0.1367 | n_water=442 | time (s): 33.680 (total time: 35.850) Filter (q & B) r_work=0.1193 r_free=0.1367 | n_water=442 | time (s): 1.070 (total time: 36.920) Compute maps r_work=0.1193 r_free=0.1367 | n_water=442 | time (s): 1.780 (total time: 38.700) Filter (map) r_work=0.1212 r_free=0.1371 | n_water=316 | time (s): 3.590 (total time: 42.290) Find peaks r_work=0.1212 r_free=0.1371 | n_water=316 | time (s): 0.690 (total time: 42.980) Add new water r_work=0.1288 r_free=0.1435 | n_water=480 | time (s): 3.410 (total time: 46.390) Refine new water occ: r_work=0.1216 r_free=0.1365 adp: r_work=0.1217 r_free=0.1367 occ: r_work=0.1201 r_free=0.1352 adp: r_work=0.1199 r_free=0.1353 occ: r_work=0.1188 r_free=0.1347 adp: r_work=0.1185 r_free=0.1345 ADP+occupancy (water only), MIN, final r_work=0.1185 r_free=0.1345 r_work=0.1185 r_free=0.1345 | n_water=480 | time (s): 163.590 (total time: 209.980) Filter (q & B) r_work=0.1191 r_free=0.1349 | n_water=446 | time (s): 2.670 (total time: 212.650) Filter (dist only) r_work=0.1191 r_free=0.1348 | n_water=445 | time (s): 37.940 (total time: 250.590) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.386664 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 50.275970 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 0.1365 0.0176 0.006 1.0 3.8 0.5 0.0 0 1.193 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.88 13.65 1.76 3.429 21.500 50.276 3.632 11.75 13.55 1.80 3.724 21.401 50.276 3.617 Individual atomic B min max mean iso aniso Overall: 9.26 106.30 21.29 2.19 214 1758 Protein: 9.26 106.30 17.01 2.20 0 1519 Water: 11.58 69.41 35.87 N/A 214 231 Other: 18.67 27.04 22.88 N/A 0 8 Chain A: 9.26 106.30 19.58 N/A 0 1758 Chain S: 14.78 58.36 35.35 N/A 214 0 Histogram: Values Number of atoms 9.26 - 18.97 1236 18.97 - 28.67 280 28.67 - 38.37 214 38.37 - 48.08 134 48.08 - 57.78 71 57.78 - 67.48 23 67.48 - 77.19 9 77.19 - 86.89 2 86.89 - 96.60 1 96.60 - 106.30 2 =========================== Idealize ADP of riding H ========================== r_work=0.1175 r_free=0.1355 r_work=0.1176 r_free=0.1356 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1176 r_free = 0.1356 target_work(ml) = 3.617 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1171 r_free = 0.1356 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.=87581 (all), 4.91 % free)------------| | | | r_work= 0.1171 r_free= 0.1356 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.615752 | | target function (ml) not normalized (work): 301137.893422 | | target function (ml) not normalized (free): 15931.560510 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1180 0.1171 0.1356 n_refl.: 87581 re-set all scales: r(all,work,free)=0.1499 0.1499 0.1543 n_refl.: 87581 remove outliers: r(all,work,free)=0.1499 0.1499 0.1543 n_refl.: 87581 overall B=-0.02 to atoms: r(all,work,free)=0.1496 0.1495 0.1541 n_refl.: 87581 bulk-solvent and scaling: r(all,work,free)=0.1178 0.1169 0.1355 n_refl.: 87581 remove outliers: r(all,work,free)=0.1177 0.1168 0.1355 n_refl.: 87580 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 89.58 81 5 0.4001 293.750 257.211 0.460 1.000 0.324 11.894-9.307 97.06 95 4 0.2399 480.166 456.971 0.843 1.002 0.320 9.237-7.194 98.18 209 7 0.2428 382.570 376.981 0.916 1.002 0.144 7.162-5.571 100.00 427 22 0.2103 293.433 283.815 0.903 1.002 0.137 5.546-4.326 100.00 867 58 0.1120 402.811 398.621 0.953 1.002 0.130 4.315-3.360 100.00 1859 96 0.0921 383.076 380.730 0.993 1.002 0.130 3.356-2.611 100.00 3867 181 0.1148 251.661 249.850 1.000 1.002 0.110 2.608-2.026 99.99 8198 413 0.1015 166.828 165.939 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0957 81.470 81.747 1.028 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1233 36.127 35.761 1.023 0.998 0.000 1.221-1.150 99.97 13689 708 0.2116 22.763 21.403 0.981 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0459 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1168 r_free=0.1355 After: r_work=0.1169 r_free=0.1355 ================================== NQH flips ================================== r_work=0.1169 r_free=0.1355 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=0.1169 r_free=0.1355 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1169 r_free=0.1355 | n_water=445 | time (s): 1.830 (total time: 1.830) Filter (dist) r_work=0.1169 r_free=0.1355 | n_water=444 | time (s): 39.020 (total time: 40.850) Filter (q & B) r_work=0.1169 r_free=0.1358 | n_water=441 | time (s): 2.530 (total time: 43.380) Compute maps r_work=0.1169 r_free=0.1358 | n_water=441 | time (s): 1.480 (total time: 44.860) Filter (map) r_work=0.1191 r_free=0.1364 | n_water=337 | time (s): 3.640 (total time: 48.500) Find peaks r_work=0.1191 r_free=0.1364 | n_water=337 | time (s): 0.600 (total time: 49.100) Add new water r_work=0.1246 r_free=0.1421 | n_water=492 | time (s): 3.170 (total time: 52.270) Refine new water occ: r_work=0.1184 r_free=0.1348 adp: r_work=0.1184 r_free=0.1351 occ: r_work=0.1171 r_free=0.1337 adp: r_work=0.1170 r_free=0.1338 occ: r_work=0.1161 r_free=0.1331 adp: r_work=0.1158 r_free=0.1331 ADP+occupancy (water only), MIN, final r_work=0.1158 r_free=0.1331 r_work=0.1158 r_free=0.1331 | n_water=492 | time (s): 172.210 (total time: 224.480) Filter (q & B) r_work=0.1165 r_free=0.1330 | n_water=451 | time (s): 2.500 (total time: 226.980) Filter (dist only) r_work=0.1165 r_free=0.1329 | n_water=450 | time (s): 37.970 (total time: 264.950) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.932787 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 41.153235 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 0.1193 0.1362 0.0168 0.007 1.1 2.9 0.5 0.0 0 0.966 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.93 13.62 1.68 3.321 21.267 41.153 3.625 11.96 13.60 1.64 3.432 21.223 41.153 3.622 Individual atomic B min max mean iso aniso Overall: 9.25 103.48 21.23 2.08 219 1758 Protein: 9.25 103.48 16.88 2.09 0 1519 Water: 11.55 68.99 35.85 N/A 219 231 Other: 19.15 26.98 23.02 N/A 0 8 Chain A: 9.25 103.48 19.45 N/A 0 1758 Chain S: 15.21 58.31 35.49 N/A 219 0 Histogram: Values Number of atoms 9.25 - 18.67 1227 18.67 - 28.09 279 28.09 - 37.51 212 37.51 - 46.94 142 46.94 - 56.36 75 56.36 - 65.78 26 65.78 - 75.21 11 75.21 - 84.63 2 84.63 - 94.05 1 94.05 - 103.48 2 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1360 r_work=0.1196 r_free=0.1360 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1196 r_free = 0.1360 target_work(ml) = 3.622 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1359 target_work(ml) = 3.622 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87580 (all), 4.91 % free)------------| | | | r_work= 0.1195 r_free= 0.1359 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.621784 | | target function (ml) not normalized (work): 301636.638800 | | target function (ml) not normalized (free): 15933.090120 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2922 171 0.1396 0.1361 5.6806 5.5969| | 2: 3.57 - 2.84 1.00 2888 124 0.1108 0.1459 5.1854 5.2663| | 3: 2.83 - 2.48 1.00 2820 163 0.1219 0.1277 4.9921 5.0203| | 4: 2.47 - 2.25 1.00 2825 136 0.1021 0.1079 4.6951 4.7335| | 5: 2.25 - 2.09 1.00 2756 127 0.1004 0.1144 4.6366 4.7153| | 6: 2.09 - 1.97 1.00 2846 113 0.0973 0.1205 4.3463 4.4835| | 7: 1.97 - 1.87 1.00 2787 165 0.1000 0.1192 4.0752 4.1619| | 8: 1.87 - 1.79 1.00 2789 144 0.1033 0.1296 3.9939 4.0927| | 9: 1.79 - 1.72 1.00 2745 138 0.0962 0.1266 3.7195 3.8786| | 10: 1.72 - 1.66 1.00 2831 160 0.1009 0.1281 3.6383 3.7789| | 11: 1.66 - 1.61 1.00 2712 147 0.0972 0.1107 3.572 3.6178| | 12: 1.61 - 1.56 1.00 2773 144 0.0932 0.1178 3.3559 3.4756| | 13: 1.56 - 1.52 1.00 2745 130 0.0988 0.1064 3.3446 3.4317| | 14: 1.52 - 1.48 1.00 2803 134 0.0997 0.1104 3.2646 3.3364| | 15: 1.48 - 1.45 1.00 2738 128 0.1017 0.1362 3.171 3.3322| | 16: 1.45 - 1.42 1.00 2756 161 0.1072 0.1255 3.1551 3.2492| | 17: 1.42 - 1.39 1.00 2785 139 0.1129 0.1315 3.119 3.2451| | 18: 1.39 - 1.36 1.00 2741 179 0.1165 0.1385 3.0923 3.2649| | 19: 1.36 - 1.34 1.00 2807 134 0.1223 0.1574 3.0962 3.2696| | 20: 1.34 - 1.32 1.00 2696 147 0.1325 0.1493 3.0901 3.1467| | 21: 1.32 - 1.30 1.00 2785 112 0.1419 0.1662 3.09 3.1756| | 22: 1.29 - 1.27 1.00 2704 152 0.1479 0.1898 3.0869 3.2733| | 23: 1.27 - 1.26 1.00 2802 156 0.1578 0.1839 3.1034 3.2095| | 24: 1.26 - 1.24 1.00 2744 132 0.1631 0.1781 3.0968 3.2042| | 25: 1.24 - 1.22 1.00 2733 148 0.1795 0.2350 3.1097 3.3004| | 26: 1.22 - 1.21 1.00 2727 135 0.1864 0.1774 3.1244 3.1944| | 27: 1.21 - 1.19 1.00 2814 148 0.2017 0.2101 3.1409 3.15| | 28: 1.19 - 1.18 1.00 2671 147 0.2142 0.2328 3.1387 3.1611| | 29: 1.18 - 1.16 1.00 2800 134 0.2222 0.2379 3.1281 3.2253| | 30: 1.16 - 1.15 1.00 2739 148 0.2377 0.2506 3.1156 3.166| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2922 171 0.95 8.85 1.00 0.97 5969.21| | 2: 3.57 - 2.84 2888 124 0.92 12.94 1.01 0.97 5969.21| | 3: 2.83 - 2.48 2820 163 0.89 17.13 0.99 0.97 5011.14| | 4: 2.47 - 2.25 2825 136 0.91 14.30 1.00 0.98 2540.58| | 5: 2.25 - 2.09 2756 127 0.90 16.57 1.01 0.98 2540.58| | 6: 2.09 - 1.97 2846 113 0.92 13.41 1.02 0.98 1506.10| | 7: 1.97 - 1.87 2787 165 0.94 10.75 1.02 0.97 623.82| | 8: 1.87 - 1.79 2789 144 0.91 14.41 1.00 0.97 623.82| | 9: 1.79 - 1.72 2745 138 0.93 11.42 0.98 0.97 339.96| | 10: 1.72 - 1.66 2831 160 0.93 12.30 0.97 0.97 283.11| | 11: 1.66 - 1.61 2712 147 0.93 12.92 0.98 0.97 270.20| | 12: 1.61 - 1.56 2773 144 0.95 9.59 0.99 0.97 148.42| | 13: 1.56 - 1.52 2745 130 0.94 11.17 1.02 0.97 148.42| | 14: 1.52 - 1.48 2803 134 0.94 11.29 1.02 0.97 132.60| | 15: 1.48 - 1.45 2738 128 0.95 10.48 1.01 0.98 103.62| | 16: 1.45 - 1.42 2756 161 0.94 11.62 1.01 0.98 103.62| | 17: 1.42 - 1.39 2785 139 0.94 11.54 1.01 0.98 93.65| | 18: 1.39 - 1.36 2741 179 0.94 11.79 1.01 0.98 87.88| | 19: 1.36 - 1.34 2807 134 0.94 12.38 1.00 0.98 87.88| | 20: 1.34 - 1.32 2696 147 0.94 12.50 0.99 0.97 83.00| | 21: 1.32 - 1.30 2785 112 0.93 13.43 0.98 0.96 82.66| | 22: 1.29 - 1.27 2704 152 0.93 13.94 0.98 0.96 82.78| | 23: 1.27 - 1.26 2802 156 0.92 14.97 0.98 0.95 83.41| | 24: 1.26 - 1.24 2744 132 0.92 15.05 0.97 0.95 83.41| | 25: 1.24 - 1.22 2733 148 0.91 16.42 0.96 0.94 84.91| | 26: 1.22 - 1.21 2727 135 0.90 18.19 1.02 0.93 86.57| | 27: 1.21 - 1.19 2814 148 0.89 18.80 1.02 0.93 86.57| | 28: 1.19 - 1.18 2671 147 0.88 20.27 1.01 0.93 89.68| | 29: 1.18 - 1.16 2800 134 0.88 20.57 0.99 0.93 90.85| | 30: 1.16 - 1.15 2739 148 0.86 22.02 0.98 0.93 90.85| |alpha: min = 0.93 max = 0.98 mean = 0.96| |beta: min = 82.66 max = 5969.21 mean = 940.48| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.96 mean = 14.02| |phase err.(test): min = 0.00 max = 87.80 mean = 14.13| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1203 0.1194 0.1359 n_refl.: 87580 re-set all scales: r(all,work,free)=0.1513 0.1513 0.1550 n_refl.: 87580 remove outliers: r(all,work,free)=0.1513 0.1513 0.1550 n_refl.: 87580 overall B=-0.01 to atoms: r(all,work,free)=0.1511 0.1510 0.1549 n_refl.: 87580 bulk-solvent and scaling: r(all,work,free)=0.1203 0.1195 0.1361 n_refl.: 87580 remove outliers: r(all,work,free)=0.1201 0.1192 0.1361 n_refl.: 87573 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 87.50 79 5 0.4011 285.668 255.160 0.438 1.001 0.283 11.894-9.307 93.14 91 4 0.2278 473.646 457.802 0.864 1.002 0.263 9.237-7.194 97.73 208 7 0.2458 382.094 376.722 0.907 1.002 0.130 7.162-5.571 100.00 427 22 0.2161 293.433 283.528 0.897 1.002 0.129 5.546-4.326 100.00 867 58 0.1169 402.811 398.458 0.955 1.002 0.127 4.315-3.360 100.00 1859 96 0.0979 383.076 380.189 0.994 1.002 0.125 3.356-2.611 100.00 3867 181 0.1177 251.661 249.665 1.001 1.002 0.120 2.608-2.026 99.99 8198 413 0.1041 166.828 165.830 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0984 81.470 81.715 1.028 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1235 36.127 35.752 1.022 0.997 0.000 1.221-1.150 99.97 13689 708 0.2120 22.763 21.381 0.980 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0353 ================= 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 : 0.2603 0.1941 0.080 5.408 8.8 119.3 19.9 258 0.000 1_bss: 0.1644 0.1756 0.080 5.408 9.1 119.5 20.1 258 0.000 1_settarget: 0.1644 0.1756 0.080 5.408 9.1 119.5 20.1 258 0.000 1_nqh: 0.1644 0.1756 0.080 5.408 9.1 119.5 20.1 258 0.000 1_weight: 0.1644 0.1756 0.080 5.408 9.1 119.5 20.1 258 0.000 1_xyzrec: 0.1213 0.1469 0.007 0.947 9.1 119.5 20.1 258 0.123 1_adp: 0.1248 0.1549 0.007 0.947 8.6 118.9 21.0 258 0.123 1_regHadp: 0.1252 0.1554 0.007 0.947 8.6 118.9 21.0 258 0.123 1_occ: 0.1252 0.1556 0.007 0.947 8.6 118.9 21.0 258 0.123 2_bss: 0.1248 0.1549 0.007 0.947 8.7 119.0 21.2 258 0.123 2_settarget: 0.1248 0.1549 0.007 0.947 8.7 119.0 21.2 258 0.123 2_updatecdl: 0.1248 0.1549 0.007 0.957 8.7 119.0 21.2 258 0.123 2_nqh: 0.1250 0.1550 0.007 0.957 8.7 119.0 21.2 258 0.126 2_sol: 0.1238 0.1509 0.007 0.957 8.7 119.0 23.6 433 n/a 2_weight: 0.1238 0.1509 0.007 0.957 8.7 119.0 23.6 433 n/a 2_xyzrec: 0.1234 0.1529 0.007 0.876 8.7 119.0 23.6 433 n/a 2_adp: 0.1199 0.1498 0.007 0.876 8.8 114.6 23.2 433 n/a 2_regHadp: 0.1199 0.1498 0.007 0.876 8.8 114.6 23.2 433 n/a 2_occ: 0.1198 0.1500 0.007 0.876 8.8 114.6 23.2 433 n/a 3_bss: 0.1195 0.1497 0.007 0.876 8.8 114.6 23.3 433 n/a 3_settarget: 0.1195 0.1497 0.007 0.876 8.8 114.6 23.3 433 n/a 3_updatecdl: 0.1195 0.1497 0.007 0.874 8.8 114.6 23.3 433 n/a 3_nqh: 0.1195 0.1497 0.007 0.874 8.8 114.6 23.3 433 n/a 3_sol: 0.1223 0.1489 0.007 0.874 8.8 114.6 22.0 442 n/a 3_weight: 0.1223 0.1489 0.007 0.874 8.8 114.6 22.0 442 n/a 3_xyzrec: 0.1224 0.1452 0.006 0.920 8.8 114.6 22.0 442 n/a 3_adp: 0.1210 0.1402 0.006 0.920 9.3 109.8 21.7 442 n/a 3_regHadp: 0.1211 0.1403 0.006 0.920 9.3 109.8 21.7 442 n/a 3_occ: 0.1204 0.1394 0.006 0.920 9.3 109.8 21.7 442 n/a 4_bss: 0.1193 0.1367 0.006 0.920 9.3 109.8 21.7 442 n/a 4_settarget: 0.1193 0.1367 0.006 0.920 9.3 109.8 21.7 442 n/a 4_updatecdl: 0.1193 0.1367 0.006 0.921 9.3 109.8 21.7 442 n/a 4_nqh: 0.1193 0.1367 0.006 0.921 9.3 109.8 21.7 442 n/a 4_sol: 0.1191 0.1348 0.006 0.921 9.3 109.8 21.5 445 n/a 4_weight: 0.1191 0.1348 0.006 0.921 9.3 109.8 21.5 445 n/a 4_xyzrec: 0.1188 0.1365 0.006 0.986 9.3 109.8 21.5 445 n/a 4_adp: 0.1175 0.1355 0.006 0.986 9.3 106.3 21.3 445 n/a 4_regHadp: 0.1176 0.1356 0.006 0.986 9.3 106.3 21.3 445 n/a 4_occ: 0.1171 0.1356 0.006 0.986 9.3 106.3 21.3 445 n/a 5_bss: 0.1168 0.1355 0.006 0.986 9.2 106.3 21.3 445 n/a 5_settarget: 0.1168 0.1355 0.006 0.986 9.2 106.3 21.3 445 n/a 5_updatecdl: 0.1168 0.1355 0.006 0.986 9.2 106.3 21.3 445 n/a 5_setrh: 0.1169 0.1355 0.006 0.986 9.2 106.3 21.3 445 n/a 5_nqh: 0.1169 0.1355 0.006 0.986 9.2 106.3 21.3 445 n/a 5_sol: 0.1165 0.1329 0.006 0.986 9.2 106.3 21.3 450 n/a 5_weight: 0.1165 0.1329 0.006 0.986 9.2 106.3 21.3 450 n/a 5_xyzrec: 0.1193 0.1362 0.007 1.062 9.2 106.3 21.3 450 n/a 5_adp: 0.1196 0.1360 0.007 1.062 9.2 103.5 21.2 450 n/a 5_regHadp: 0.1196 0.1360 0.007 1.062 9.2 103.5 21.2 450 n/a 5_occ: 0.1195 0.1359 0.007 1.062 9.2 103.5 21.2 450 n/a end: 0.1192 0.1361 0.007 1.062 9.2 103.5 21.2 450 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_7410891_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_7410891_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.9800 Refinement macro-cycles (run) : 3524.6200 Write final files (write_after_run_outputs) : 69.8000 Total : 3599.4000 Total CPU time: 60.62 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:11:35 PST -0800 (1735452695.78 s) Start R-work = 0.1644, R-free = 0.1756 Final R-work = 0.1192, R-free = 0.1361 =============================================================================== Job complete usr+sys time: 3739.42 seconds wall clock time: 66 minutes 50.84 seconds (4010.84 seconds total)