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_8666014.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" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8666014.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8666014.pdb" 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" } 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: 2.27, 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: 0.56 Conformation dependent library (CDL) restraints added in 216.9 milliseconds Time building geometry restraints manager: 0.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.63 - 0.90: 430 0.90 - 1.16: 1197 1.16 - 1.43: 670 1.43 - 1.69: 835 1.69 - 1.96: 21 Bond restraints: 3153 Sorted by residual: bond pdb=" C ALA A 183 " pdb=" O ALA A 183 " ideal model delta sigma weight residual 1.244 1.430 -0.186 1.00e-02 1.00e+04 3.46e+02 bond pdb=" C LEU A 77 " pdb=" N GLY A 78 " ideal model delta sigma weight residual 1.334 1.544 -0.211 1.14e-02 7.69e+03 3.42e+02 bond pdb=" N GLY A 174 " pdb=" CA GLY A 174 " ideal model delta sigma weight residual 1.447 1.251 0.196 1.08e-02 8.57e+03 3.29e+02 bond pdb=" C ASP A 60 " pdb=" O ASP A 60 " ideal model delta sigma weight residual 1.236 1.451 -0.215 1.19e-02 7.06e+03 3.26e+02 bond pdb=" CD ARG A 145 " pdb=" NE ARG A 145 " ideal model delta sigma weight residual 1.458 1.209 0.249 1.40e-02 5.10e+03 3.15e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.39: 2961 4.39 - 8.79: 1912 8.79 - 13.18: 728 13.18 - 17.57: 152 17.57 - 21.97: 24 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA LEU A 72 " pdb=" C LEU A 72 " pdb=" O LEU A 72 " ideal model delta sigma weight residual 119.71 106.85 12.86 8.10e-01 1.52e+00 2.52e+02 angle pdb=" CA GLY A 137 " pdb=" C GLY A 137 " pdb=" O GLY A 137 " ideal model delta sigma weight residual 119.82 103.97 15.85 1.14e+00 7.69e-01 1.93e+02 angle pdb=" C LEU A 82 " pdb=" N SER A 83 " pdb=" CA SER A 83 " ideal model delta sigma weight residual 120.28 139.74 -19.46 1.44e+00 4.82e-01 1.83e+02 angle pdb=" ND1 HIS A 115 " pdb=" CE1 HIS A 115 " pdb=" NE2 HIS A 115 " ideal model delta sigma weight residual 108.40 95.27 13.13 1.00e+00 1.00e+00 1.72e+02 angle pdb=" ND1 HIS A 126 " pdb=" CG HIS A 126 " pdb=" CD2 HIS A 126 " ideal model delta sigma weight residual 106.10 118.65 -12.55 1.00e+00 1.00e+00 1.57e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.76: 925 16.76 - 33.53: 131 33.53 - 50.29: 34 50.29 - 67.05: 16 67.05 - 83.81: 5 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: 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 180.00 156.16 23.84 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA SER A 121 " pdb=" C SER A 121 " pdb=" N LYS A 122 " pdb=" CA LYS A 122 " ideal model delta harmonic sigma weight residual 180.00 158.51 21.49 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA LEU A 72 " pdb=" C LEU A 72 " pdb=" N PRO A 73 " pdb=" CA PRO A 73 " ideal model delta harmonic sigma weight residual 180.00 159.53 20.47 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.007 - 0.240: 108 0.240 - 0.472: 75 0.472 - 0.705: 36 0.705 - 0.937: 19 0.937 - 1.170: 5 Chirality restraints: 243 Sorted by residual: chirality pdb=" CG LEU A 58 " pdb=" CB LEU A 58 " pdb=" CD1 LEU A 58 " pdb=" CD2 LEU A 58 " both_signs ideal model delta sigma weight residual False -2.59 -1.42 -1.17 2.00e-01 2.50e+01 3.42e+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 -1.52 -1.07 2.00e-01 2.50e+01 2.88e+01 chirality pdb=" CA BGLU A 90 " pdb=" N BGLU A 90 " pdb=" C BGLU A 90 " pdb=" CB BGLU A 90 " both_signs ideal model delta sigma weight residual False 2.51 1.51 1.00 2.00e-01 2.50e+01 2.51e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " 0.072 2.00e-02 2.50e+03 6.70e-02 1.35e+02 pdb=" CG TYR A 141 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " -0.110 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " -0.107 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " 0.097 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " -0.034 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " 0.011 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " 0.028 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " -0.040 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " 0.107 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " 0.058 2.00e-02 2.50e+03 6.22e-02 1.16e+02 pdb=" CG BTYR A 67 " 0.012 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.128 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " 0.050 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " 0.093 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " 0.053 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " -0.074 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " 0.046 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " -0.003 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " -0.061 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " -0.010 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " 0.041 2.00e-02 2.50e+03 5.42e-02 8.82e+01 pdb=" CG TYR A 139 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.085 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.079 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.007 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.040 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " -0.087 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " 0.029 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.078 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " -0.052 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.32: 1084 2.32 - 2.89: 8132 2.89 - 3.46: 10475 3.46 - 4.03: 15267 4.03 - 4.60: 21704 Nonbonded interactions: 56662 Sorted by model distance: nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.755 2.100 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.775 2.100 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.779 2.450 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.814 2.450 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.827 2.450 ... (remaining 56657 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_8666014_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= 0.2600 r_free= 0.1963 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.787673 | | target function (ml) not normalized (work): 232229.914467 | | target function (ml) not normalized (free): 11810.873337 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3033 0.2194 7.022 4.9608| | 2: 3.57 - 2.84 1.00 2876 122 0.2424 0.1722 4.3528 4.3443| | 3: 2.84 - 2.48 1.00 2833 165 0.2330 0.1749 4.1334 4.1891| | 4: 2.47 - 2.25 1.00 2825 136 0.2353 0.1480 3.8344 3.8183| | 5: 2.25 - 2.09 1.00 2756 127 0.2458 0.1638 3.8059 3.8341| | 6: 2.09 - 1.97 1.00 2846 113 0.2536 0.1533 3.4748 3.4992| | 7: 1.97 - 1.87 1.00 2787 165 0.2511 0.1818 3.1343 3.2157| | 8: 1.87 - 1.79 1.00 2789 144 0.2453 0.1832 3.0569 3.1052| | 9: 1.79 - 1.72 1.00 2745 138 0.2412 0.1901 2.9022 2.9428| | 10: 1.72 - 1.66 1.00 2789 158 0.2393 0.1968 2.7987 2.8944| | 11: 1.66 - 1.61 1.00 2740 147 0.2496 0.2176 2.7534 2.8529| | 12: 1.61 - 1.56 1.00 2787 146 0.2509 0.1886 2.632 2.6199| | 13: 1.56 - 1.52 1.00 2745 130 0.2519 0.1693 2.5404 2.5569| | 14: 1.52 - 1.48 1.00 2803 134 0.2545 0.2057 2.5087 2.5808| | 15: 1.48 - 1.45 1.00 2738 128 0.2621 0.2156 2.4134 2.496| | 16: 1.45 - 1.42 1.00 2756 161 0.2675 0.2207 2.3848 2.417| | 17: 1.42 - 1.39 1.00 2785 139 0.2708 0.2246 2.3463 2.4075| | 18: 1.39 - 1.36 1.00 2741 179 0.2659 0.2297 2.2584 2.3119| | 19: 1.36 - 1.34 1.00 2807 134 0.2673 0.2536 2.2421 2.3562| | 20: 1.34 - 1.32 1.00 2696 147 0.2736 0.2266 2.2097 2.2585| | 21: 1.32 - 1.30 1.00 2785 112 0.2699 0.2031 2.1689 2.14| | 22: 1.29 - 1.27 1.00 2704 152 0.2748 0.2379 2.1478 2.144| | 23: 1.27 - 1.26 1.00 2802 156 0.2729 0.2486 2.0896 2.1688| | 24: 1.26 - 1.24 1.00 2744 132 0.2753 0.2522 2.0655 2.1617| | 25: 1.24 - 1.22 1.00 2734 148 0.2887 0.2324 2.0507 2.0403| | 26: 1.22 - 1.21 1.00 2727 135 0.2828 0.2328 1.9959 2.1194| | 27: 1.21 - 1.19 1.00 2814 148 0.2944 0.2583 1.9999 1.9651| | 28: 1.19 - 1.18 1.00 2671 147 0.2979 0.2778 1.9778 1.9888| | 29: 1.18 - 1.16 1.00 2800 134 0.2962 0.2772 1.9592 2.011| | 30: 1.16 - 1.15 1.00 2740 148 0.3040 0.2696 1.9153 1.9167| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 49.25 - 3.58 2941 171 0.87 19.04 0.76 0.23 1508.78| | 2: 3.57 - 2.84 2876 122 0.80 26.29 1.27 0.23 1508.78| | 3: 2.84 - 2.48 2833 165 0.74 32.28 1.24 0.24 1250.38| | 4: 2.47 - 2.25 2825 136 0.81 25.90 1.26 0.25 579.78| | 5: 2.25 - 2.09 2756 127 0.77 29.43 1.28 0.25 579.78| | 6: 2.09 - 1.97 2846 113 0.83 22.60 1.29 0.25 315.73| | 7: 1.97 - 1.87 2787 165 0.90 16.35 1.28 0.26 90.53| | 8: 1.87 - 1.79 2789 144 0.86 21.05 1.25 0.26 90.53| | 9: 1.79 - 1.72 2745 138 0.88 18.46 1.23 0.25 55.06| | 10: 1.72 - 1.66 2789 158 0.86 20.27 1.22 0.25 47.96| | 11: 1.66 - 1.61 2740 147 0.86 21.27 1.24 0.25 46.34| | 12: 1.61 - 1.56 2787 146 0.89 18.43 1.23 0.25 29.90| | 13: 1.56 - 1.52 2745 130 0.86 20.61 1.24 0.25 29.90| | 14: 1.52 - 1.48 2803 134 0.86 20.81 1.23 0.25 26.95| | 15: 1.48 - 1.45 2738 128 0.86 20.70 1.24 0.25 21.55| | 16: 1.45 - 1.42 2756 161 0.85 22.16 1.25 0.25 21.55| | 17: 1.42 - 1.39 2785 139 0.86 21.21 1.24 0.25 18.27| | 18: 1.39 - 1.36 2741 179 0.86 21.69 1.23 0.25 16.37| | 19: 1.36 - 1.34 2807 134 0.85 22.65 1.22 0.25 16.37| | 20: 1.34 - 1.32 2696 147 0.86 21.27 1.21 0.24 13.38| | 21: 1.32 - 1.30 2785 112 0.86 22.13 1.20 0.24 13.17| | 22: 1.29 - 1.27 2704 152 0.85 22.71 1.20 0.24 12.82| | 23: 1.27 - 1.26 2802 156 0.86 22.21 1.21 0.24 11.04| | 24: 1.26 - 1.24 2744 132 0.85 22.92 1.20 0.24 11.04| | 25: 1.24 - 1.22 2734 148 0.84 23.69 1.21 0.24 10.40| | 26: 1.22 - 1.21 2727 135 0.84 23.86 1.19 0.23 9.69| | 27: 1.21 - 1.19 2814 148 0.84 24.35 1.20 0.23 9.69| | 28: 1.19 - 1.18 2671 147 0.83 24.99 1.18 0.23 8.97| | 29: 1.18 - 1.16 2800 134 0.83 24.76 1.16 0.23 8.69| | 30: 1.16 - 1.15 2740 148 0.81 26.63 1.16 0.23 8.69| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 8.69 max = 1508.78 mean = 218.40| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.96 mean = 22.69| |phase err.(test): min = 0.00 max = 89.19 mean = 22.55| |-----------------------------------------------------------------------------| ----------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 0.249 1557 Z= 5.435 Angle : 5.396 19.459 2118 Z= 3.758 Chirality : 0.408 1.170 243 Planarity : 0.030 0.091 284 Dihedral : 13.832 83.813 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.16 % Favored : 97.30 % Rotamer: Outliers : 1.24 % Allowed : 2.48 % Favored : 96.27 % Cbeta Deviations : 32.43 % 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: -3.35 (0.45), residues: 224 helix: -3.25 (0.33), residues: 105 sheet: -0.98 (0.72), residues: 38 loop : -0.95 (0.59), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.081 0.023 ARG A 98 TYR 0.085 0.037 TYR A 139 PHE 0.090 0.027 PHE A 164 HIS 0.047 0.017 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= 0.2600 r_free= 0.1963 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.787673 | | target function (ml) not normalized (work): 232229.914467 | | target function (ml) not normalized (free): 11810.873337 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2559 0.2600 0.1963 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2559 0.2600 0.1963 n_refl.: 87602 remove outliers: r(all,work,free)=0.1972 0.1975 0.1963 n_refl.: 87594 overall B=0.19 to atoms: r(all,work,free)=0.1996 0.1999 0.1976 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1635 0.1628 0.1779 n_refl.: 87594 remove outliers: r(all,work,free)=0.1635 0.1627 0.1779 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 0.3852 386.280 356.231 0.660 1.002 0.401 11.894-9.307 99.02 97 4 0.1832 613.587 595.457 0.925 1.003 0.380 9.237-7.194 100.00 213 7 0.2207 501.839 491.027 0.961 1.004 0.344 7.162-5.571 100.00 427 22 0.2123 376.602 366.532 0.931 1.004 0.330 5.546-4.326 100.00 867 58 0.1296 516.982 512.007 0.965 1.003 0.230 4.315-3.360 100.00 1859 96 0.1128 491.653 488.217 1.006 1.003 0.199 3.356-2.611 100.00 3867 181 0.1443 322.991 319.632 0.996 1.002 0.048 2.608-2.026 99.99 8198 413 0.1337 214.113 212.197 1.008 1.001 0.000 2.025-1.573 100.00 17313 902 0.1642 104.562 103.886 1.010 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2047 46.367 45.078 1.006 0.996 0.000 1.221-1.150 99.97 13689 708 0.2568 29.214 26.945 0.976 0.993 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0438 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1627 r_free=0.1779 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 180 GLN Total number of N/Q/H flips: 2 r_work=0.1635 r_free=0.1785 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.917006 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2026.140199 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 0.1462 0.0249 0.007 0.9 1.3 0.5 0.0 0 11.959 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.13 14.62 2.49 3.013 19.050 2026.140 0.017 12.47 15.39 2.92 3.201 19.533 2026.140 0.016 Individual atomic B min max mean iso aniso Overall: 8.60 118.87 20.99 2.87 0 1785 Protein: 8.60 118.87 17.88 2.87 0 1519 Water: 11.12 114.72 39.04 N/A 0 258 Other: 23.20 36.91 29.23 N/A 0 8 Chain A: 8.60 118.87 20.99 N/A 0 1785 Histogram: Values Number of atoms 8.60 - 19.63 1212 19.63 - 30.65 226 30.65 - 41.68 168 41.68 - 52.71 97 52.71 - 63.73 52 63.73 - 74.76 18 74.76 - 85.79 5 85.79 - 96.81 3 96.81 - 107.84 1 107.84 - 118.87 3 =========================== Idealize ADP of riding H ========================== r_work=0.1247 r_free=0.1539 r_work=0.1252 r_free=0.1544 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1252 r_free = 0.1544 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 = 0.1250 r_free = 0.1548 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.21 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= 0.1250 r_free= 0.1548 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.015413 | | target function (ls_wunit_k1) not normalized (work): 1283.870767 | | target function (ls_wunit_k1) not normalized (free): 112.620636 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1265 0.1250 0.1548 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1707 0.1706 0.1774 n_refl.: 87593 remove outliers: r(all,work,free)=0.1707 0.1706 0.1774 n_refl.: 87593 overall B=0.13 to atoms: r(all,work,free)=0.1728 0.1728 0.1789 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1263 0.1249 0.1541 n_refl.: 87593 remove outliers: r(all,work,free)=0.1262 0.1248 0.1541 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 0.3619 298.951 279.242 0.635 1.002 0.380 11.894-9.307 99.02 97 4 0.1614 478.903 467.442 0.909 1.002 0.380 9.237-7.194 100.00 213 7 0.1810 391.684 387.055 0.950 1.003 0.314 7.162-5.571 100.00 427 22 0.1701 293.937 288.847 0.924 1.003 0.263 5.546-4.326 100.00 867 58 0.0908 403.503 400.970 0.950 1.003 0.214 4.315-3.360 100.00 1859 96 0.0771 383.734 382.712 0.996 1.002 0.200 3.356-2.611 100.00 3867 181 0.1015 252.093 251.344 0.998 1.002 0.052 2.608-2.026 99.99 8198 413 0.0974 167.115 166.527 1.011 1.001 0.000 2.025-1.573 100.00 17313 902 0.1222 81.610 81.779 1.017 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1674 36.189 35.649 1.006 0.999 0.000 1.221-1.150 99.97 13689 708 0.2376 22.802 21.307 0.969 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0504 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1248 r_free=0.1541 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=0.1252 r_free=0.1541 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1252 r_free=0.1541 | n_water=258 | time (s): 2.270 (total time: 2.270) Filter (dist) r_work=0.1261 r_free=0.1539 | n_water=252 | time (s): 27.970 (total time: 30.240) Filter (q & B) r_work=0.1264 r_free=0.1538 | n_water=249 | time (s): 3.620 (total time: 33.860) Compute maps r_work=0.1264 r_free=0.1538 | n_water=249 | time (s): 1.880 (total time: 35.740) Filter (map) r_work=0.1287 r_free=0.1549 | n_water=234 | time (s): 3.690 (total time: 39.430) Find peaks r_work=0.1287 r_free=0.1549 | n_water=234 | time (s): 0.710 (total time: 40.140) Add new water r_work=0.1443 r_free=0.1701 | n_water=449 | time (s): 3.660 (total time: 43.800) Refine new water occ: r_work=0.1346 r_free=0.1567 adp: r_work=0.1263 r_free=0.1517 occ: r_work=0.1276 r_free=0.1509 adp: r_work=0.1241 r_free=0.1497 occ: r_work=0.1243 r_free=0.1486 adp: r_work=0.1234 r_free=0.1490 ADP+occupancy (water only), MIN, final r_work=0.1234 r_free=0.1490 r_work=0.1234 r_free=0.1490 | n_water=449 | time (s): 80.890 (total time: 124.690) Filter (q & B) r_work=0.1239 r_free=0.1492 | n_water=434 | time (s): 4.080 (total time: 128.770) Filter (dist only) r_work=0.1239 r_free=0.1492 | n_water=434 | time (s): 40.260 (total time: 169.030) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.465357 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1469.493743 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1235 0.1523 0.0288 0.007 0.9 2.2 0.5 0.0 0 13.233 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.35 15.23 2.88 3.787 23.193 1469.494 0.015 12.04 14.92 2.88 4.115 23.033 1469.494 0.015 Individual atomic B min max mean iso aniso Overall: 8.67 115.53 23.25 2.59 200 1761 Protein: 8.67 115.53 17.72 2.60 0 1519 Water: 10.93 73.29 42.51 N/A 200 234 Other: 23.88 35.57 28.61 N/A 0 8 Chain A: 8.67 115.53 20.40 N/A 0 1761 Chain S: 15.40 66.37 48.40 N/A 200 0 Histogram: Values Number of atoms 8.67 - 19.36 1203 19.36 - 30.04 253 30.04 - 40.73 196 40.73 - 51.42 140 51.42 - 62.10 109 62.10 - 72.79 48 72.79 - 83.47 6 83.47 - 94.16 3 94.16 - 104.84 1 104.84 - 115.53 2 =========================== Idealize ADP of riding H ========================== r_work=0.1204 r_free=0.1492 r_work=0.1204 r_free=0.1492 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1204 r_free = 0.1492 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 = 0.1205 r_free = 0.1484 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.21 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= 0.1205 r_free= 0.1484 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.013925 | | target function (ls_wunit_k1) not normalized (work): 1159.919812 | | target function (ls_wunit_k1) not normalized (free): 102.792845 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1219 0.1205 0.1484 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1614 0.1610 0.1724 n_refl.: 87592 remove outliers: r(all,work,free)=0.1614 0.1610 0.1724 n_refl.: 87592 overall B=0.04 to atoms: r(all,work,free)=0.1620 0.1616 0.1727 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1216 0.1202 0.1483 n_refl.: 87592 remove outliers: r(all,work,free)=0.1215 0.1201 0.1483 n_refl.: 87590 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 93.75 85 5 0.3462 297.511 270.786 0.595 1.002 0.370 11.894-9.307 99.02 97 4 0.1478 478.903 475.864 0.919 1.003 0.357 9.237-7.194 100.00 213 7 0.1583 391.684 393.784 0.978 1.003 0.280 7.162-5.571 100.00 427 22 0.1498 293.937 290.610 0.945 1.003 0.257 5.546-4.326 100.00 867 58 0.0837 403.503 400.777 0.957 1.003 0.215 4.315-3.360 100.00 1859 96 0.0712 383.734 382.634 1.002 1.003 0.210 3.356-2.611 100.00 3867 181 0.0964 252.093 251.663 1.009 1.002 0.077 2.608-2.026 99.99 8198 413 0.0960 167.115 166.672 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1185 81.610 81.797 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1626 36.189 35.691 1.017 0.998 0.000 1.221-1.150 99.97 13689 708 0.2347 22.802 21.327 0.977 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0581 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1201 r_free=0.1483 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.1204 r_free=0.1484 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1204 r_free=0.1484 | n_water=434 | time (s): 2.250 (total time: 2.250) Filter (dist) r_work=0.1203 r_free=0.1486 | n_water=432 | time (s): 39.540 (total time: 41.790) Filter (q & B) r_work=0.1203 r_free=0.1486 | n_water=432 | time (s): 0.920 (total time: 42.710) Compute maps r_work=0.1203 r_free=0.1486 | n_water=432 | time (s): 1.300 (total time: 44.010) Filter (map) r_work=0.1244 r_free=0.1490 | n_water=295 | time (s): 3.340 (total time: 47.350) Find peaks r_work=0.1244 r_free=0.1490 | n_water=295 | time (s): 0.720 (total time: 48.070) Add new water r_work=0.1375 r_free=0.1621 | n_water=483 | time (s): 3.360 (total time: 51.430) Refine new water occ: r_work=0.1272 r_free=0.1532 adp: r_work=0.1273 r_free=0.1529 occ: r_work=0.1251 r_free=0.1517 adp: r_work=0.1249 r_free=0.1511 occ: r_work=0.1235 r_free=0.1504 adp: r_work=0.1229 r_free=0.1495 ADP+occupancy (water only), MIN, final r_work=0.1229 r_free=0.1495 r_work=0.1229 r_free=0.1495 | n_water=483 | time (s): 212.390 (total time: 263.820) Filter (q & B) r_work=0.1234 r_free=0.1503 | n_water=448 | time (s): 2.850 (total time: 266.670) Filter (dist only) r_work=0.1234 r_free=0.1503 | n_water=448 | time (s): 36.560 (total time: 303.230) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.145444 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 43.925452 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 0.1237 0.1454 0.0216 0.006 0.9 3.2 0.5 0.0 0 1.073 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.37 14.54 2.16 3.628 22.153 43.925 3.730 12.18 14.11 1.92 4.211 21.930 43.925 3.658 Individual atomic B min max mean iso aniso Overall: 9.24 110.57 21.61 2.31 218 1757 Protein: 9.24 110.57 17.22 2.31 0 1519 Water: 11.36 72.15 36.46 N/A 218 230 Other: 19.82 31.61 25.67 N/A 0 8 Chain A: 9.24 110.57 19.83 N/A 0 1757 Chain S: 15.52 65.94 36.04 N/A 218 0 Histogram: Values Number of atoms 9.24 - 19.38 1238 19.38 - 29.51 283 29.51 - 39.64 214 39.64 - 49.77 139 49.77 - 59.90 69 59.90 - 70.04 19 70.04 - 80.17 8 80.17 - 90.30 2 90.30 - 100.43 1 100.43 - 110.57 2 =========================== Idealize ADP of riding H ========================== r_work=0.1219 r_free=0.1411 r_work=0.1220 r_free=0.1412 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1220 r_free = 0.1412 target_work(ml) = 3.658 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1213 r_free = 0.1405 target_work(ml) = 3.655 | | 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.=87590 (all), 4.90 % free)------------| | | | r_work= 0.1213 r_free= 0.1405 coordinate error (max.-lik. estimate): 0.06 A | | | | normalized target function (ml) (work): 3.655341 | | target function (ml) not normalized (work): 304467.993893 | | target function (ml) not normalized (free): 16068.260255 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1222 0.1213 0.1405 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1545 0.1545 0.1580 n_refl.: 87590 remove outliers: r(all,work,free)=0.1545 0.1545 0.1580 n_refl.: 87590 overall B=-0.02 to atoms: r(all,work,free)=0.1542 0.1542 0.1578 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1211 0.1203 0.1377 n_refl.: 87590 remove outliers: r(all,work,free)=0.1207 0.1199 0.1377 n_refl.: 87580 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 90.62 82 5 0.3977 291.639 263.162 0.466 0.999 0.297 11.894-9.307 96.08 94 4 0.2390 472.322 456.076 0.852 1.001 0.280 9.237-7.194 98.18 209 7 0.2380 383.228 385.279 0.940 1.001 0.203 7.162-5.571 100.00 427 22 0.2033 293.937 282.729 0.910 1.002 0.173 5.546-4.326 100.00 867 58 0.1112 403.503 399.060 0.951 1.002 0.155 4.315-3.360 100.00 1859 96 0.0932 383.734 381.242 0.995 1.002 0.144 3.356-2.611 100.00 3867 181 0.1136 252.093 250.262 1.001 1.002 0.057 2.608-2.026 99.99 8198 413 0.1046 167.115 166.097 1.012 1.001 0.000 2.025-1.573 100.00 17313 902 0.1019 81.610 81.743 1.027 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1298 36.189 35.775 1.021 1.000 0.000 1.221-1.150 99.97 13689 708 0.2139 22.802 21.422 0.979 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0440 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1199 r_free=0.1377 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=0.1199 r_free=0.1377 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1199 r_free=0.1377 | n_water=448 | time (s): 1.980 (total time: 1.980) Filter (dist) r_work=0.1199 r_free=0.1376 | n_water=447 | time (s): 38.270 (total time: 40.250) Filter (q & B) r_work=0.1198 r_free=0.1374 | n_water=445 | time (s): 3.190 (total time: 43.440) Compute maps r_work=0.1198 r_free=0.1374 | n_water=445 | time (s): 1.430 (total time: 44.870) Filter (map) r_work=0.1225 r_free=0.1372 | n_water=310 | time (s): 2.750 (total time: 47.620) Find peaks r_work=0.1225 r_free=0.1372 | n_water=310 | time (s): 0.600 (total time: 48.220) Add new water r_work=0.1292 r_free=0.1447 | n_water=479 | time (s): 3.160 (total time: 51.380) Refine new water occ: r_work=0.1217 r_free=0.1381 adp: r_work=0.1218 r_free=0.1380 occ: r_work=0.1201 r_free=0.1371 adp: r_work=0.1200 r_free=0.1369 occ: r_work=0.1190 r_free=0.1366 adp: r_work=0.1186 r_free=0.1361 ADP+occupancy (water only), MIN, final r_work=0.1186 r_free=0.1361 r_work=0.1186 r_free=0.1361 | n_water=479 | time (s): 201.940 (total time: 253.320) Filter (q & B) r_work=0.1194 r_free=0.1360 | n_water=440 | time (s): 3.540 (total time: 256.860) Filter (dist only) r_work=0.1194 r_free=0.1359 | n_water=439 | time (s): 37.610 (total time: 294.470) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.984625 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 50.136510 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 0.1196 0.1370 0.0174 0.006 1.0 3.2 0.5 0.0 0 0.992 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.96 13.70 1.74 3.418 21.446 50.137 3.640 11.80 13.62 1.81 3.855 21.313 50.137 3.620 Individual atomic B min max mean iso aniso Overall: 9.26 105.55 21.13 2.18 210 1756 Protein: 9.26 105.55 16.91 2.19 0 1519 Water: 11.43 70.51 35.71 N/A 210 229 Other: 19.70 28.53 23.84 N/A 0 8 Chain A: 9.26 105.55 19.46 N/A 0 1756 Chain S: 15.33 61.02 35.16 N/A 210 0 Histogram: Values Number of atoms 9.26 - 18.89 1228 18.89 - 28.52 278 28.52 - 38.14 219 38.14 - 47.77 132 47.77 - 57.40 70 57.40 - 67.03 25 67.03 - 76.66 9 76.66 - 86.29 2 86.29 - 95.92 1 95.92 - 105.55 2 =========================== Idealize ADP of riding H ========================== r_work=0.1180 r_free=0.1362 r_work=0.1181 r_free=0.1362 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1181 r_free = 0.1362 target_work(ml) = 3.620 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1177 r_free = 0.1357 target_work(ml) = 3.618 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87580 (all), 4.91 % free)------------| | | | r_work= 0.1177 r_free= 0.1357 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.618429 | | target function (ml) not normalized (work): 301357.266140 | | target function (ml) not normalized (free): 15924.022530 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1186 0.1177 0.1357 n_refl.: 87580 re-set all scales: r(all,work,free)=0.1500 0.1499 0.1559 n_refl.: 87580 remove outliers: r(all,work,free)=0.1500 0.1499 0.1559 n_refl.: 87580 overall B=-0.02 to atoms: r(all,work,free)=0.1497 0.1495 0.1557 n_refl.: 87580 bulk-solvent and scaling: r(all,work,free)=0.1185 0.1176 0.1357 n_refl.: 87580 remove outliers: r(all,work,free)=0.1184 0.1175 0.1357 n_refl.: 87577 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 89.58 81 5 0.4087 294.255 254.802 0.445 0.999 0.312 11.894-9.307 95.10 93 4 0.2278 474.258 453.741 0.845 1.001 0.300 9.237-7.194 97.73 208 7 0.2457 384.303 378.048 0.911 1.002 0.150 7.162-5.571 100.00 427 22 0.2133 293.937 283.882 0.904 1.002 0.139 5.546-4.326 100.00 867 58 0.1145 403.503 399.183 0.950 1.002 0.139 4.315-3.360 100.00 1859 96 0.0935 383.734 381.498 0.995 1.002 0.126 3.356-2.611 100.00 3867 181 0.1152 252.093 250.450 1.001 1.002 0.048 2.608-2.026 99.99 8198 413 0.1023 167.115 166.278 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0961 81.610 81.907 1.028 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1234 36.189 35.842 1.023 0.998 0.000 1.221-1.150 99.97 13689 708 0.2126 22.802 21.450 0.981 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0471 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1175 r_free=0.1357 After: r_work=0.1176 r_free=0.1357 ================================== NQH flips ================================== r_work=0.1176 r_free=0.1357 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=0.1176 r_free=0.1357 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1176 r_free=0.1357 | n_water=439 | time (s): 1.600 (total time: 1.600) Filter (dist) r_work=0.1176 r_free=0.1357 | n_water=439 | time (s): 36.900 (total time: 38.500) Filter (q & B) r_work=0.1176 r_free=0.1357 | n_water=438 | time (s): 2.600 (total time: 41.100) Compute maps r_work=0.1176 r_free=0.1357 | n_water=438 | time (s): 1.690 (total time: 42.790) Filter (map) r_work=0.1200 r_free=0.1372 | n_water=332 | time (s): 3.280 (total time: 46.070) Find peaks r_work=0.1200 r_free=0.1372 | n_water=332 | time (s): 0.690 (total time: 46.760) Add new water r_work=0.1248 r_free=0.1428 | n_water=479 | time (s): 3.190 (total time: 49.950) Refine new water occ: r_work=0.1188 r_free=0.1366 adp: r_work=0.1188 r_free=0.1368 occ: r_work=0.1178 r_free=0.1355 adp: r_work=0.1177 r_free=0.1356 occ: r_work=0.1170 r_free=0.1350 adp: r_work=0.1167 r_free=0.1350 ADP+occupancy (water only), MIN, final r_work=0.1167 r_free=0.1350 r_work=0.1167 r_free=0.1350 | n_water=479 | time (s): 169.960 (total time: 219.910) Filter (q & B) r_work=0.1173 r_free=0.1356 | n_water=445 | time (s): 3.050 (total time: 222.960) Filter (dist only) r_work=0.1173 r_free=0.1354 | n_water=443 | time (s): 37.630 (total time: 260.590) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.893047 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 47.326066 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 0.1205 0.1375 0.0171 0.007 1.0 6.1 0.5 0.0 0 0.947 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.05 13.75 1.71 3.291 21.050 47.326 3.630 12.08 13.75 1.67 3.445 20.994 47.326 3.625 Individual atomic B min max mean iso aniso Overall: 9.29 102.22 20.92 2.05 214 1756 Protein: 9.29 102.22 16.75 2.05 0 1519 Water: 11.24 69.86 35.15 N/A 214 229 Other: 19.51 27.36 23.49 N/A 0 8 Chain A: 9.29 102.22 19.29 N/A 0 1756 Chain S: 14.40 57.44 34.23 N/A 214 0 Histogram: Values Number of atoms 9.29 - 18.58 1223 18.58 - 27.87 288 27.87 - 37.17 208 37.17 - 46.46 141 46.46 - 55.75 69 55.75 - 65.04 26 65.04 - 74.34 10 74.34 - 83.63 2 83.63 - 92.92 1 92.92 - 102.22 2 =========================== Idealize ADP of riding H ========================== r_work=0.1208 r_free=0.1375 r_work=0.1208 r_free=0.1375 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1208 r_free = 0.1375 target_work(ml) = 3.625 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1205 r_free = 0.1374 target_work(ml) = 3.624 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87577 (all), 4.91 % free)------------| | | | r_work= 0.1205 r_free= 0.1374 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.624374 | | target function (ml) not normalized (work): 301841.512786 | | target function (ml) not normalized (free): 15946.047802 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2919 171 0.1443 0.1480 5.704 5.6802| | 2: 3.57 - 2.84 1.00 2888 124 0.1135 0.1402 5.2193 5.2452| | 3: 2.83 - 2.48 1.00 2820 163 0.1231 0.1268 5.0198 5.0322| | 4: 2.47 - 2.25 1.00 2825 136 0.1035 0.1137 4.7196 4.7682| | 5: 2.25 - 2.09 1.00 2756 127 0.1006 0.1127 4.6647 4.7337| | 6: 2.09 - 1.97 1.00 2846 113 0.0972 0.1208 4.3617 4.5051| | 7: 1.97 - 1.87 1.00 2787 165 0.0997 0.1193 4.0792 4.1691| | 8: 1.87 - 1.79 1.00 2789 144 0.1026 0.1218 3.9899 4.0684| | 9: 1.79 - 1.72 1.00 2745 138 0.0956 0.1296 3.7134 3.8921| | 10: 1.72 - 1.66 1.00 2831 160 0.1010 0.1269 3.6341 3.7623| | 11: 1.66 - 1.61 1.00 2712 147 0.0968 0.1116 3.565 3.6202| | 12: 1.61 - 1.56 1.00 2773 144 0.0918 0.1134 3.3436 3.4562| | 13: 1.56 - 1.52 1.00 2745 130 0.0972 0.1080 3.3322 3.4364| | 14: 1.52 - 1.48 1.00 2803 134 0.0984 0.1111 3.2579 3.3417| | 15: 1.48 - 1.45 1.00 2738 128 0.1003 0.1340 3.1651 3.3212| | 16: 1.45 - 1.42 1.00 2756 161 0.1065 0.1258 3.1504 3.2383| | 17: 1.42 - 1.39 1.00 2785 139 0.1118 0.1289 3.1142 3.2336| | 18: 1.39 - 1.36 1.00 2741 179 0.1155 0.1392 3.0874 3.2767| | 19: 1.36 - 1.34 1.00 2807 134 0.1212 0.1596 3.0916 3.263| | 20: 1.34 - 1.32 1.00 2696 147 0.1316 0.1471 3.0881 3.1444| | 21: 1.32 - 1.30 1.00 2785 112 0.1410 0.1607 3.0863 3.1598| | 22: 1.29 - 1.27 1.00 2704 152 0.1476 0.1915 3.0874 3.2812| | 23: 1.27 - 1.26 1.00 2802 156 0.1576 0.1856 3.1036 3.216| | 24: 1.26 - 1.24 1.00 2744 132 0.1633 0.1777 3.0958 3.1941| | 25: 1.24 - 1.22 1.00 2733 148 0.1797 0.2298 3.1096 3.2879| | 26: 1.22 - 1.21 1.00 2727 135 0.1862 0.1777 3.1238 3.1986| | 27: 1.21 - 1.19 1.00 2814 148 0.2014 0.2103 3.1418 3.1557| | 28: 1.19 - 1.18 1.00 2671 147 0.2145 0.2299 3.1407 3.1606| | 29: 1.18 - 1.16 1.00 2800 134 0.2219 0.2376 3.127 3.2256| | 30: 1.16 - 1.15 1.00 2739 148 0.2377 0.2482 3.1174 3.1618| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2919 171 0.94 9.30 1.00 0.97 6558.56| | 2: 3.57 - 2.84 2888 124 0.92 13.68 1.01 0.97 6558.56| | 3: 2.83 - 2.48 2820 163 0.88 17.93 0.99 0.97 5491.75| | 4: 2.47 - 2.25 2825 136 0.91 14.97 1.00 0.98 2740.77| | 5: 2.25 - 2.09 2756 127 0.89 17.19 1.01 0.98 2740.77| | 6: 2.09 - 1.97 2846 113 0.91 13.82 1.02 0.97 1599.74| | 7: 1.97 - 1.87 2787 165 0.94 10.79 1.02 0.97 626.60| | 8: 1.87 - 1.79 2789 144 0.91 14.42 1.00 0.97 626.60| | 9: 1.79 - 1.72 2745 138 0.93 11.42 0.98 0.97 337.18| | 10: 1.72 - 1.66 2831 160 0.93 12.17 0.98 0.97 279.22| | 11: 1.66 - 1.61 2712 147 0.93 12.85 0.98 0.97 266.53| | 12: 1.61 - 1.56 2773 144 0.95 9.52 0.99 0.97 146.82| | 13: 1.56 - 1.52 2745 130 0.94 11.09 1.02 0.97 146.82| | 14: 1.52 - 1.48 2803 134 0.94 11.23 1.02 0.97 131.27| | 15: 1.48 - 1.45 2738 128 0.95 10.33 1.01 0.98 102.79| | 16: 1.45 - 1.42 2756 161 0.94 11.52 1.02 0.98 102.79| | 17: 1.42 - 1.39 2785 139 0.94 11.36 1.01 0.98 93.09| | 18: 1.39 - 1.36 2741 179 0.94 11.77 1.01 0.98 87.48| | 19: 1.36 - 1.34 2807 134 0.94 12.32 1.00 0.98 87.48| | 20: 1.34 - 1.32 2696 147 0.94 12.43 0.99 0.97 82.66| | 21: 1.32 - 1.30 2785 112 0.94 13.35 0.98 0.96 82.32| | 22: 1.29 - 1.27 2704 152 0.93 13.91 0.98 0.96 82.46| | 23: 1.27 - 1.26 2802 156 0.92 14.83 0.98 0.95 83.21| | 24: 1.26 - 1.24 2744 132 0.92 14.98 0.97 0.95 83.21| | 25: 1.24 - 1.22 2733 148 0.91 16.42 0.96 0.94 84.73| | 26: 1.22 - 1.21 2727 135 0.90 18.14 1.02 0.93 86.42| | 27: 1.21 - 1.19 2814 148 0.89 18.76 1.02 0.93 86.42| | 28: 1.19 - 1.18 2671 147 0.88 20.23 1.01 0.93 89.65| | 29: 1.18 - 1.16 2800 134 0.88 20.55 0.99 0.93 90.87| | 30: 1.16 - 1.15 2739 148 0.86 21.95 0.98 0.93 90.87| |alpha: min = 0.93 max = 0.98 mean = 0.96| |beta: min = 82.32 max = 6558.56 mean = 1013.81| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.99 mean = 14.09| |phase err.(test): min = 0.00 max = 88.28 mean = 14.23| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1214 0.1205 0.1374 n_refl.: 87577 re-set all scales: r(all,work,free)=0.1522 0.1522 0.1568 n_refl.: 87577 remove outliers: r(all,work,free)=0.1522 0.1522 0.1568 n_refl.: 87577 overall B=-0.01 to atoms: r(all,work,free)=0.1520 0.1519 0.1566 n_refl.: 87577 bulk-solvent and scaling: r(all,work,free)=0.1214 0.1206 0.1375 n_refl.: 87577 remove outliers: r(all,work,free)=0.1214 0.1205 0.1375 n_refl.: 87576 ======================== 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 0.4160 294.255 254.057 0.446 1.001 0.304 11.894-9.307 94.12 92 4 0.2331 478.195 456.054 0.844 1.002 0.300 9.237-7.194 97.73 208 7 0.2605 384.303 377.140 0.906 1.002 0.120 7.162-5.571 100.00 427 22 0.2271 293.937 282.570 0.897 1.003 0.120 5.546-4.326 100.00 867 58 0.1222 403.503 398.777 0.951 1.002 0.120 4.315-3.360 100.00 1859 96 0.1013 383.734 381.091 0.994 1.002 0.120 3.356-2.611 100.00 3867 181 0.1194 252.093 250.172 1.002 1.002 0.048 2.608-2.026 99.99 8198 413 0.1048 167.115 166.143 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0981 81.610 81.858 1.028 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1225 36.189 35.826 1.023 0.996 0.000 1.221-1.150 99.97 13689 708 0.2119 22.802 21.434 0.982 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0391 ================= 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 : 0.2600 0.1963 0.081 5.396 8.8 119.3 19.9 258 0.000 1_bss: 0.1627 0.1779 0.081 5.396 9.0 119.5 20.1 258 0.000 1_settarget: 0.1627 0.1779 0.081 5.396 9.0 119.5 20.1 258 0.000 1_nqh: 0.1635 0.1785 0.081 5.396 9.0 119.5 20.1 258 0.006 1_weight: 0.1635 0.1785 0.081 5.396 9.0 119.5 20.1 258 0.006 1_xyzrec: 0.1213 0.1462 0.007 0.927 9.0 119.5 20.1 258 0.131 1_adp: 0.1247 0.1539 0.007 0.927 8.6 118.9 21.0 258 0.131 1_regHadp: 0.1252 0.1544 0.007 0.927 8.6 118.9 21.0 258 0.131 1_occ: 0.1250 0.1548 0.007 0.927 8.6 118.9 21.0 258 0.131 2_bss: 0.1248 0.1541 0.007 0.927 8.7 119.0 21.1 258 0.131 2_settarget: 0.1248 0.1541 0.007 0.927 8.7 119.0 21.1 258 0.131 2_updatecdl: 0.1248 0.1541 0.007 0.942 8.7 119.0 21.1 258 0.131 2_nqh: 0.1252 0.1541 0.007 0.942 8.7 119.0 21.1 258 0.131 2_sol: 0.1239 0.1492 0.007 0.942 8.7 119.0 23.5 434 n/a 2_weight: 0.1239 0.1492 0.007 0.942 8.7 119.0 23.5 434 n/a 2_xyzrec: 0.1235 0.1523 0.007 0.884 8.7 119.0 23.5 434 n/a 2_adp: 0.1204 0.1492 0.007 0.884 8.7 115.5 23.3 434 n/a 2_regHadp: 0.1204 0.1492 0.007 0.884 8.7 115.5 23.3 434 n/a 2_occ: 0.1205 0.1484 0.007 0.884 8.7 115.5 23.3 434 n/a 3_bss: 0.1201 0.1483 0.007 0.884 8.7 115.6 23.3 434 n/a 3_settarget: 0.1201 0.1483 0.007 0.884 8.7 115.6 23.3 434 n/a 3_updatecdl: 0.1201 0.1483 0.007 0.884 8.7 115.6 23.3 434 n/a 3_nqh: 0.1204 0.1484 0.007 0.884 8.7 115.6 23.3 434 n/a 3_sol: 0.1234 0.1503 0.007 0.884 8.7 115.6 22.0 448 n/a 3_weight: 0.1234 0.1503 0.007 0.884 8.7 115.6 22.0 448 n/a 3_xyzrec: 0.1237 0.1454 0.006 0.928 8.7 115.6 22.0 448 n/a 3_adp: 0.1219 0.1411 0.006 0.928 9.2 110.6 21.6 448 n/a 3_regHadp: 0.1220 0.1412 0.006 0.928 9.2 110.6 21.6 448 n/a 3_occ: 0.1213 0.1405 0.006 0.928 9.2 110.6 21.6 448 n/a 4_bss: 0.1199 0.1377 0.006 0.928 9.2 110.6 21.6 448 n/a 4_settarget: 0.1199 0.1377 0.006 0.928 9.2 110.6 21.6 448 n/a 4_updatecdl: 0.1199 0.1377 0.006 0.927 9.2 110.6 21.6 448 n/a 4_nqh: 0.1199 0.1377 0.006 0.927 9.2 110.6 21.6 448 n/a 4_sol: 0.1194 0.1359 0.006 0.927 9.2 110.6 21.4 439 n/a 4_weight: 0.1194 0.1359 0.006 0.927 9.2 110.6 21.4 439 n/a 4_xyzrec: 0.1196 0.1370 0.006 0.952 9.2 110.6 21.4 439 n/a 4_adp: 0.1180 0.1362 0.006 0.952 9.3 105.6 21.1 439 n/a 4_regHadp: 0.1181 0.1362 0.006 0.952 9.3 105.6 21.1 439 n/a 4_occ: 0.1177 0.1357 0.006 0.952 9.3 105.6 21.1 439 n/a 5_bss: 0.1175 0.1357 0.006 0.952 9.2 105.5 21.1 439 n/a 5_settarget: 0.1175 0.1357 0.006 0.952 9.2 105.5 21.1 439 n/a 5_updatecdl: 0.1175 0.1357 0.006 0.953 9.2 105.5 21.1 439 n/a 5_setrh: 0.1176 0.1357 0.006 0.953 9.2 105.5 21.1 439 n/a 5_nqh: 0.1176 0.1357 0.006 0.953 9.2 105.5 21.1 439 n/a 5_sol: 0.1173 0.1354 0.006 0.953 9.2 105.5 21.0 443 n/a 5_weight: 0.1173 0.1354 0.006 0.953 9.2 105.5 21.0 443 n/a 5_xyzrec: 0.1205 0.1375 0.007 1.045 9.2 105.5 21.0 443 n/a 5_adp: 0.1208 0.1375 0.007 1.045 9.3 102.2 20.9 443 n/a 5_regHadp: 0.1208 0.1375 0.007 1.045 9.3 102.2 20.9 443 n/a 5_occ: 0.1205 0.1374 0.007 1.045 9.3 102.2 20.9 443 n/a end: 0.1205 0.1375 0.007 1.045 9.3 102.2 20.9 443 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_8666014_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_8666014_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 5.1200 Refinement macro-cycles (run) : 3501.6100 Write final files (write_after_run_outputs) : 64.9200 Total : 3571.6500 Total CPU time: 60.15 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:11:30 PST -0800 (1735452690.19 s) Start R-work = 0.1627, R-free = 0.1779 Final R-work = 0.1205, R-free = 0.1375 =============================================================================== Job complete usr+sys time: 3708.03 seconds wall clock time: 66 minutes 41.79 seconds (4001.79 seconds total)