Starting phenix.refine on Sat Dec 28 21:06:33 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6470396.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6470396.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6470396.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 2 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: 2.03, per 1000 atoms: 0.60 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: 0.75 Conformation dependent library (CDL) restraints added in 195.9 milliseconds Time building geometry restraints manager: 0.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.91: 498 0.91 - 1.15: 1124 1.15 - 1.40: 600 1.40 - 1.65: 853 1.65 - 1.90: 78 Bond restraints: 3153 Sorted by residual: bond pdb=" C BGLU A 94 " pdb=" O BGLU A 94 " ideal model delta sigma weight residual 1.237 1.448 -0.211 1.19e-02 7.06e+03 3.15e+02 bond pdb=" ND1 HIS A 126 " pdb=" CE1 HIS A 126 " ideal model delta sigma weight residual 1.321 1.150 0.171 1.00e-02 1.00e+04 2.93e+02 bond pdb=" CA ALA A 114 " pdb=" C ALA A 114 " ideal model delta sigma weight residual 1.523 1.739 -0.216 1.30e-02 5.92e+03 2.76e+02 bond pdb=" C LYS A 63 " pdb=" O LYS A 63 " ideal model delta sigma weight residual 1.236 1.444 -0.209 1.29e-02 6.01e+03 2.61e+02 bond pdb=" CA ALA A 14 " pdb=" C ALA A 14 " ideal model delta sigma weight residual 1.525 1.731 -0.207 1.28e-02 6.10e+03 2.61e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.01: 3319 5.01 - 10.01: 1843 10.01 - 15.02: 551 15.02 - 20.03: 59 20.03 - 25.03: 5 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O AGLU A 96 " pdb=" C AGLU A 96 " pdb=" N AASN A 97 " ideal model delta sigma weight residual 122.07 106.39 15.68 1.03e+00 9.43e-01 2.32e+02 angle pdb=" O BCYS A 53 " pdb=" C BCYS A 53 " pdb=" N PRO A 54 " ideal model delta sigma weight residual 121.19 135.28 -14.09 9.40e-01 1.13e+00 2.25e+02 angle pdb=" NE ARG A 28 " pdb=" CZ ARG A 28 " pdb=" NH1 ARG A 28 " ideal model delta sigma weight residual 121.50 106.70 14.80 1.00e+00 1.00e+00 2.19e+02 angle pdb=" O ALA A 111 " pdb=" C ALA A 111 " pdb=" N LEU A 112 " ideal model delta sigma weight residual 122.12 136.28 -14.16 1.06e+00 8.90e-01 1.78e+02 angle pdb=" N ILE A 9 " pdb=" CA ILE A 9 " pdb=" CB ILE A 9 " ideal model delta sigma weight residual 111.21 126.44 -15.23 1.17e+00 7.31e-01 1.69e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.02 - 16.51: 919 16.51 - 33.00: 130 33.00 - 49.49: 43 49.49 - 65.98: 16 65.98 - 82.47: 3 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA ALYS A 41 " pdb=" C ALYS A 41 " pdb=" N ASP A 42 " pdb=" CA ASP A 42 " ideal model delta harmonic sigma weight residual -180.00 -155.85 -24.15 0 5.00e+00 4.00e-02 2.33e+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 180.00 157.64 22.36 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA GLY A 74 " pdb=" C GLY A 74 " pdb=" N GLY A 75 " pdb=" CA GLY A 75 " ideal model delta harmonic sigma weight residual 180.00 -158.79 -21.21 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.003 - 0.290: 124 0.290 - 0.576: 87 0.576 - 0.862: 28 0.862 - 1.148: 3 1.148 - 1.434: 1 Chirality restraints: 243 Sorted by residual: chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.16 -1.43 2.00e-01 2.50e+01 5.14e+01 chirality pdb=" CB VAL A 44 " pdb=" CA VAL A 44 " pdb=" CG1 VAL A 44 " pdb=" CG2 VAL A 44 " both_signs ideal model delta sigma weight residual False -2.63 -3.64 1.01 2.00e-01 2.50e+01 2.54e+01 chirality pdb=" CA BGLU A 96 " pdb=" N BGLU A 96 " pdb=" C BGLU A 96 " pdb=" CB BGLU A 96 " both_signs ideal model delta sigma weight residual False 2.51 1.59 0.92 2.00e-01 2.50e+01 2.11e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " -0.074 2.00e-02 2.50e+03 5.88e-02 1.04e+02 pdb=" CG ATYR A 67 " -0.079 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " 0.115 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.013 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " -0.074 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " 0.029 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " -0.006 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " -0.067 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " 0.053 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " 0.028 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " 0.020 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 115 " -0.035 2.00e-02 2.50e+03 6.75e-02 1.03e+02 pdb=" CG HIS A 115 " -0.006 2.00e-02 2.50e+03 pdb=" ND1 HIS A 115 " 0.115 2.00e-02 2.50e+03 pdb=" CD2 HIS A 115 " -0.055 2.00e-02 2.50e+03 pdb=" CE1 HIS A 115 " -0.029 2.00e-02 2.50e+03 pdb=" NE2 HIS A 115 " -0.113 2.00e-02 2.50e+03 pdb=" HD2 HIS A 115 " 0.073 2.00e-02 2.50e+03 pdb=" HE1 HIS A 115 " -0.016 2.00e-02 2.50e+03 pdb=" HE2 HIS A 115 " 0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " 0.036 2.00e-02 2.50e+03 5.67e-02 9.65e+01 pdb=" CG TYR A 141 " -0.078 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " 0.051 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " -0.022 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " 0.038 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " 0.078 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " 0.009 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " 0.067 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " -0.086 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " -0.093 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.34: 1194 2.34 - 2.91: 8234 2.91 - 3.47: 10532 3.47 - 4.04: 15142 4.04 - 4.60: 21506 Nonbonded interactions: 56608 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.780 2.100 nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.791 2.100 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.801 2.450 x-y,-y,-z-4/3 nonbonded pdb=" H LYS A 122 " pdb=" OD2 ASP A 149 " model vdw 1.825 2.450 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.834 2.450 ... (remaining 56603 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_6470396_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= 0.2604 r_free= 0.1929 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.786796 | | target function (ml) not normalized (work): 232156.846880 | | target function (ml) not normalized (free): 11812.053274 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3035 0.2054 7.1158 4.9435| | 2: 3.57 - 2.84 1.00 2876 122 0.2419 0.1779 4.3448 4.3276| | 3: 2.84 - 2.48 1.00 2833 165 0.2346 0.1598 4.121 4.13| | 4: 2.47 - 2.25 1.00 2825 136 0.2322 0.1395 3.8283 3.8233| | 5: 2.25 - 2.09 1.00 2756 127 0.2506 0.1609 3.7892 3.8127| | 6: 2.09 - 1.97 1.00 2846 113 0.2580 0.1685 3.4757 3.4885| | 7: 1.97 - 1.87 1.00 2787 165 0.2559 0.1895 3.1299 3.2281| | 8: 1.87 - 1.79 1.00 2789 144 0.2446 0.1901 3.0508 3.1652| | 9: 1.79 - 1.72 1.00 2745 138 0.2422 0.1914 2.8966 2.9627| | 10: 1.72 - 1.66 1.00 2789 158 0.2442 0.1884 2.8094 2.8665| | 11: 1.66 - 1.61 1.00 2740 147 0.2481 0.1769 2.7303 2.7315| | 12: 1.61 - 1.56 1.00 2787 146 0.2479 0.2192 2.6119 2.7033| | 13: 1.56 - 1.52 1.00 2745 130 0.2530 0.1912 2.5587 2.6293| | 14: 1.52 - 1.48 1.00 2803 134 0.2542 0.1982 2.4971 2.5443| | 15: 1.48 - 1.45 1.00 2738 128 0.2535 0.2267 2.3983 2.5317| | 16: 1.45 - 1.42 1.00 2756 161 0.2617 0.2220 2.3682 2.4624| | 17: 1.42 - 1.39 1.00 2785 139 0.2643 0.2016 2.3114 2.3174| | 18: 1.39 - 1.36 1.00 2741 179 0.2642 0.2242 2.2596 2.3173| | 19: 1.36 - 1.34 1.00 2807 134 0.2716 0.2322 2.2431 2.2481| | 20: 1.34 - 1.32 1.00 2696 147 0.2625 0.2202 2.2065 2.1839| | 21: 1.32 - 1.30 1.00 2785 112 0.2699 0.2215 2.1618 2.1567| | 22: 1.29 - 1.27 1.00 2704 152 0.2763 0.2503 2.1228 2.1938| | 23: 1.27 - 1.26 1.00 2802 156 0.2782 0.2460 2.1077 2.1813| | 24: 1.26 - 1.24 1.00 2744 132 0.2766 0.2536 2.0676 2.1902| | 25: 1.24 - 1.22 1.00 2734 148 0.2847 0.2732 2.0522 2.1287| | 26: 1.22 - 1.21 1.00 2727 135 0.2872 0.2058 2.0141 2.0334| | 27: 1.21 - 1.19 1.00 2814 148 0.2967 0.2621 1.9978 1.9944| | 28: 1.19 - 1.18 1.00 2671 147 0.3034 0.2689 1.9919 1.9789| | 29: 1.18 - 1.16 1.00 2800 134 0.2983 0.2941 1.9591 2.0843| | 30: 1.16 - 1.15 1.00 2740 148 0.3011 0.2764 1.9223 1.9647| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.65 0.76 0.23 1461.79| | 2: 3.57 - 2.84 2876 122 0.81 25.75 1.27 0.23 1461.79| | 3: 2.84 - 2.48 2833 165 0.74 31.79 1.24 0.24 1211.77| | 4: 2.47 - 2.25 2825 136 0.81 25.35 1.25 0.25 562.91| | 5: 2.25 - 2.09 2756 127 0.77 29.29 1.29 0.25 562.91| | 6: 2.09 - 1.97 2846 113 0.83 22.60 1.30 0.25 307.60| | 7: 1.97 - 1.87 2787 165 0.90 16.38 1.28 0.26 89.86| | 8: 1.87 - 1.79 2789 144 0.86 20.84 1.25 0.26 89.86| | 9: 1.79 - 1.72 2745 138 0.88 18.86 1.23 0.25 56.16| | 10: 1.72 - 1.66 2789 158 0.86 20.45 1.22 0.25 49.42| | 11: 1.66 - 1.61 2740 147 0.85 21.64 1.25 0.25 47.68| | 12: 1.61 - 1.56 2787 146 0.88 18.79 1.23 0.25 30.11| | 13: 1.56 - 1.52 2745 130 0.86 20.85 1.24 0.25 30.11| | 14: 1.52 - 1.48 2803 134 0.86 20.79 1.23 0.25 26.82| | 15: 1.48 - 1.45 2738 128 0.87 20.17 1.23 0.25 20.79| | 16: 1.45 - 1.42 2756 161 0.85 21.81 1.24 0.25 20.79| | 17: 1.42 - 1.39 2785 139 0.87 20.70 1.23 0.25 17.49| | 18: 1.39 - 1.36 2741 179 0.86 21.07 1.23 0.25 15.58| | 19: 1.36 - 1.34 2807 134 0.86 21.96 1.23 0.25 15.58| | 20: 1.34 - 1.32 2696 147 0.87 20.68 1.19 0.24 12.82| | 21: 1.32 - 1.30 2785 112 0.86 21.97 1.20 0.24 12.63| | 22: 1.29 - 1.27 2704 152 0.85 22.55 1.21 0.24 12.37| | 23: 1.27 - 1.26 2802 156 0.86 22.22 1.22 0.24 11.05| | 24: 1.26 - 1.24 2744 132 0.85 22.87 1.20 0.24 11.05| | 25: 1.24 - 1.22 2734 148 0.84 23.64 1.20 0.23 10.53| | 26: 1.22 - 1.21 2727 135 0.84 24.16 1.19 0.23 9.97| | 27: 1.21 - 1.19 2814 148 0.83 25.07 1.21 0.23 9.97| | 28: 1.19 - 1.18 2671 147 0.82 25.58 1.19 0.23 9.41| | 29: 1.18 - 1.16 2800 134 0.82 25.82 1.17 0.23 9.20| | 30: 1.16 - 1.15 2740 148 0.81 27.15 1.16 0.23 9.20| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 9.20 max = 1461.79 mean = 212.38| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.98 mean = 22.65| |phase err.(test): min = 0.00 max = 89.65 mean = 22.45| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.083 0.236 1557 Z= 5.511 Angle : 5.297 17.365 2118 Z= 3.728 Chirality : 0.379 1.434 243 Planarity : 0.033 0.094 284 Dihedral : 14.260 82.471 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.24 % Allowed : 3.11 % Favored : 95.65 % Cbeta Deviations : 27.03 % 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: -3.02 (0.45), residues: 224 helix: -2.90 (0.39), residues: 103 sheet: -0.84 (0.85), residues: 28 loop : -1.00 (0.52), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.075 0.021 ARG A 156 TYR 0.078 0.030 TYR A 139 PHE 0.110 0.041 PHE A 162 HIS 0.075 0.030 HIS A 126 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2604 r_free= 0.1929 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.786796 | | target function (ml) not normalized (work): 232156.846880 | | target function (ml) not normalized (free): 11812.053274 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2562 0.2605 0.1929 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2562 0.2605 0.1929 n_refl.: 87602 remove outliers: r(all,work,free)=0.1971 0.1975 0.1929 n_refl.: 87594 overall B=0.19 to atoms: r(all,work,free)=0.1994 0.2000 0.1941 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1631 0.1625 0.1748 n_refl.: 87594 remove outliers: r(all,work,free)=0.1629 0.1623 0.1748 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 97.87 87 5 0.3750 389.599 354.282 0.729 0.917 0.401 11.894-9.307 98.04 96 4 0.1712 616.156 590.608 1.004 0.917 0.380 9.237-7.194 100.00 213 7 0.2181 501.903 490.898 1.045 0.917 0.358 7.162-5.571 100.00 427 22 0.2191 376.650 365.014 1.021 0.918 0.296 5.546-4.326 100.00 867 58 0.1255 517.047 511.590 1.052 0.918 0.224 4.315-3.360 100.00 1859 96 0.1129 491.716 489.013 1.099 0.919 0.199 3.356-2.611 100.00 3867 181 0.1428 323.032 319.929 1.082 0.921 0.119 2.608-2.026 99.99 8198 413 0.1369 214.141 211.639 1.091 0.924 0.000 2.025-1.573 100.00 17313 902 0.1627 104.575 104.056 1.091 0.928 0.000 1.573-1.221 100.00 36679 1900 0.2032 46.373 45.159 1.068 0.935 0.000 1.221-1.150 99.97 13689 708 0.2572 29.218 26.972 1.034 0.941 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0017 b_overall=0.0446 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1623 r_free=0.1748 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=0.1625 r_free=0.1749 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.609734 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1992.909061 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1211 0.1457 0.0246 0.007 0.9 1.6 0.5 0.0 0 12.305 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.11 14.57 2.46 3.013 19.052 1992.909 0.017 12.39 15.35 2.96 3.171 19.531 1992.909 0.015 Individual atomic B min max mean iso aniso Overall: 8.55 118.37 20.99 2.87 0 1785 Protein: 8.55 118.37 17.86 2.87 0 1519 Water: 11.08 114.72 39.15 N/A 0 258 Other: 22.90 35.89 28.85 N/A 0 8 Chain A: 8.55 118.37 20.99 N/A 0 1785 Histogram: Values Number of atoms 8.55 - 19.53 1207 19.53 - 30.51 231 30.51 - 41.50 163 41.50 - 52.48 99 52.48 - 63.46 56 63.46 - 74.44 17 74.44 - 85.43 5 85.43 - 96.41 4 96.41 - 107.39 0 107.39 - 118.37 3 =========================== Idealize ADP of riding H ========================== r_work=0.1240 r_free=0.1535 r_work=0.1244 r_free=0.1540 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1244 r_free = 0.1540 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1242 r_free = 0.1542 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87591 (all), 4.90 % free)------------| | | | r_work= 0.1242 r_free= 0.1542 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.015151 | | target function (ls_wunit_k1) not normalized (work): 1262.023686 | | target function (ls_wunit_k1) not normalized (free): 112.802980 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1257 0.1242 0.1542 n_refl.: 87591 re-set all scales: r(all,work,free)=0.1694 0.1692 0.1765 n_refl.: 87591 remove outliers: r(all,work,free)=0.1694 0.1692 0.1765 n_refl.: 87591 overall B=0.14 to atoms: r(all,work,free)=0.1717 0.1716 0.1782 n_refl.: 87591 bulk-solvent and scaling: r(all,work,free)=0.1256 0.1242 0.1538 n_refl.: 87591 remove outliers: r(all,work,free)=0.1256 0.1242 0.1538 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 94.79 86 5 0.3475 301.383 281.600 0.642 1.003 0.380 11.894-9.307 98.04 96 4 0.1507 480.655 470.554 0.915 1.003 0.369 9.237-7.194 100.00 213 7 0.1798 391.527 386.571 0.947 1.003 0.340 7.162-5.571 100.00 427 22 0.1732 293.820 288.609 0.923 1.003 0.253 5.546-4.326 100.00 867 58 0.0921 403.342 400.659 0.950 1.003 0.204 4.315-3.360 100.00 1859 96 0.0776 383.581 382.738 0.996 1.002 0.190 3.356-2.611 100.00 3867 181 0.1022 251.993 251.271 0.998 1.002 0.057 2.608-2.026 99.99 8198 413 0.0975 167.048 166.452 1.010 1.001 0.000 2.025-1.573 100.00 17313 902 0.1210 81.578 81.767 1.018 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1648 36.175 35.633 1.006 0.998 0.000 1.221-1.150 99.97 13689 708 0.2362 22.793 21.296 0.969 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0551 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1242 r_free=0.1538 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1242 r_free=0.1538 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1242 r_free=0.1538 | n_water=258 | time (s): 2.460 (total time: 2.460) Filter (dist) r_work=0.1251 r_free=0.1536 | n_water=252 | time (s): 28.210 (total time: 30.670) Filter (q & B) r_work=0.1254 r_free=0.1535 | n_water=249 | time (s): 3.830 (total time: 34.500) Compute maps r_work=0.1254 r_free=0.1535 | n_water=249 | time (s): 1.940 (total time: 36.440) Filter (map) r_work=0.1266 r_free=0.1543 | n_water=237 | time (s): 3.930 (total time: 40.370) Find peaks r_work=0.1266 r_free=0.1543 | n_water=237 | time (s): 0.720 (total time: 41.090) Add new water r_work=0.1422 r_free=0.1705 | n_water=455 | time (s): 3.930 (total time: 45.020) Refine new water occ: r_work=0.1330 r_free=0.1559 adp: r_work=0.1252 r_free=0.1515 occ: r_work=0.1266 r_free=0.1504 adp: r_work=0.1230 r_free=0.1491 occ: r_work=0.1234 r_free=0.1482 adp: r_work=0.1224 r_free=0.1480 ADP+occupancy (water only), MIN, final r_work=0.1224 r_free=0.1480 r_work=0.1224 r_free=0.1480 | n_water=455 | time (s): 98.630 (total time: 143.650) Filter (q & B) r_work=0.1230 r_free=0.1485 | n_water=435 | time (s): 3.900 (total time: 147.550) Filter (dist only) r_work=0.1230 r_free=0.1484 | n_water=433 | time (s): 45.240 (total time: 192.790) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.496517 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1592.939028 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 0.1228 0.1520 0.0292 0.007 0.9 1.6 0.5 0.0 0 12.248 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.28 15.20 2.92 3.784 23.178 1592.939 0.015 11.99 14.96 2.97 4.235 22.995 1592.939 0.015 Individual atomic B min max mean iso aniso Overall: 8.80 113.51 23.19 2.61 196 1764 Protein: 8.80 113.51 17.60 2.61 0 1519 Water: 11.12 73.85 42.67 N/A 196 237 Other: 24.10 34.80 28.52 N/A 0 8 Chain A: 8.80 113.51 20.34 N/A 0 1764 Chain S: 13.79 73.85 48.76 N/A 196 0 Histogram: Values Number of atoms 8.80 - 19.27 1213 19.27 - 29.74 241 29.74 - 40.22 194 40.22 - 50.69 130 50.69 - 61.16 111 61.16 - 71.63 54 71.63 - 82.10 11 82.10 - 92.57 3 92.57 - 103.04 1 103.04 - 113.51 2 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1496 r_work=0.1199 r_free=0.1495 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1495 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1201 r_free = 0.1492 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87590 (all), 4.90 % free)------------| | | | r_work= 0.1201 r_free= 0.1492 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.014060 | | target function (ls_wunit_k1) not normalized (work): 1171.115081 | | target function (ls_wunit_k1) not normalized (free): 105.432138 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1215 0.1201 0.1492 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1598 0.1593 0.1712 n_refl.: 87590 remove outliers: r(all,work,free)=0.1598 0.1593 0.1712 n_refl.: 87590 overall B=0.04 to atoms: r(all,work,free)=0.1604 0.1600 0.1717 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1210 0.1196 0.1488 n_refl.: 87590 remove outliers: r(all,work,free)=0.1208 0.1194 0.1488 n_refl.: 87586 ======================== 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 0.3206 294.116 273.861 0.623 0.939 0.354 11.894-9.307 98.04 96 4 0.1431 480.655 476.908 0.987 0.939 0.350 9.237-7.194 100.00 213 7 0.1732 391.527 391.881 1.044 0.939 0.280 7.162-5.571 100.00 427 22 0.1502 293.820 290.166 0.997 0.939 0.223 5.546-4.326 100.00 867 58 0.0831 403.342 400.622 1.022 0.940 0.212 4.315-3.360 100.00 1859 96 0.0713 383.581 382.526 1.068 0.940 0.208 3.356-2.611 100.00 3867 181 0.0968 251.993 251.281 1.073 0.941 0.062 2.608-2.026 99.99 8198 413 0.0959 167.048 166.524 1.080 0.943 0.000 2.025-1.573 100.00 17313 902 0.1170 81.578 81.777 1.086 0.945 0.000 1.573-1.221 100.00 36679 1900 0.1606 36.175 35.680 1.067 0.950 0.000 1.221-1.150 99.97 13689 708 0.2335 22.793 21.355 1.022 0.953 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0648 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1194 r_free=0.1488 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1194 r_free=0.1488 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1194 r_free=0.1488 | n_water=433 | time (s): 1.630 (total time: 1.630) Filter (dist) r_work=0.1194 r_free=0.1489 | n_water=432 | time (s): 39.860 (total time: 41.490) Filter (q & B) r_work=0.1194 r_free=0.1489 | n_water=432 | time (s): 1.170 (total time: 42.660) Compute maps r_work=0.1194 r_free=0.1489 | n_water=432 | time (s): 1.660 (total time: 44.320) Filter (map) r_work=0.1243 r_free=0.1497 | n_water=287 | time (s): 3.280 (total time: 47.600) Find peaks r_work=0.1243 r_free=0.1497 | n_water=287 | time (s): 0.700 (total time: 48.300) Add new water r_work=0.1369 r_free=0.1608 | n_water=472 | time (s): 3.240 (total time: 51.540) Refine new water occ: r_work=0.1266 r_free=0.1529 adp: r_work=0.1267 r_free=0.1531 occ: r_work=0.1243 r_free=0.1506 adp: r_work=0.1240 r_free=0.1507 occ: r_work=0.1228 r_free=0.1491 adp: r_work=0.1219 r_free=0.1489 ADP+occupancy (water only), MIN, final r_work=0.1219 r_free=0.1489 r_work=0.1219 r_free=0.1489 | n_water=472 | time (s): 147.950 (total time: 199.490) Filter (q & B) r_work=0.1224 r_free=0.1494 | n_water=440 | time (s): 2.680 (total time: 202.170) Filter (dist only) r_work=0.1224 r_free=0.1493 | n_water=438 | time (s): 37.760 (total time: 239.930) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.029144 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 51.217452 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 0.1447 0.0223 0.005 0.9 1.6 0.5 0.0 0 1.015 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.24 14.47 2.23 3.611 22.020 51.217 3.721 12.15 14.05 1.90 4.069 21.834 51.217 3.651 Individual atomic B min max mean iso aniso Overall: 9.21 109.21 21.58 2.32 205 1760 Protein: 9.21 109.21 17.19 2.32 0 1519 Water: 11.50 70.93 36.70 N/A 205 233 Other: 21.17 31.61 26.59 N/A 0 8 Chain A: 9.21 109.21 19.87 N/A 0 1760 Chain S: 15.38 64.45 36.21 N/A 205 0 Histogram: Values Number of atoms 9.21 - 19.21 1234 19.21 - 29.21 270 29.21 - 39.21 216 39.21 - 49.21 135 49.21 - 59.21 76 59.21 - 69.21 21 69.21 - 79.21 7 79.21 - 89.21 3 89.21 - 99.21 1 99.21 - 109.21 2 =========================== Idealize ADP of riding H ========================== r_work=0.1215 r_free=0.1405 r_work=0.1216 r_free=0.1406 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1216 r_free = 0.1406 target_work(ml) = 3.651 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1208 r_free = 0.1402 target_work(ml) = 3.647 | | 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.=87586 (all), 4.90 % free)------------| | | | r_work= 0.1208 r_free= 0.1402 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.647203 | | target function (ml) not normalized (work): 303775.505858 | | target function (ml) not normalized (free): 16048.676509 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1218 0.1208 0.1402 n_refl.: 87586 re-set all scales: r(all,work,free)=0.1537 0.1536 0.1602 n_refl.: 87586 remove outliers: r(all,work,free)=0.1537 0.1536 0.1602 n_refl.: 87586 overall B=-0.01 to atoms: r(all,work,free)=0.1536 0.1534 0.1601 n_refl.: 87586 bulk-solvent and scaling: r(all,work,free)=0.1210 0.1202 0.1379 n_refl.: 87586 remove outliers: r(all,work,free)=0.1209 0.1200 0.1379 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 0.3855 288.580 264.946 0.494 1.001 0.330 11.894-9.307 97.06 95 4 0.2227 480.799 462.046 0.866 1.002 0.268 9.237-7.194 98.64 210 7 0.2322 384.073 383.167 0.944 1.002 0.220 7.162-5.571 100.00 427 22 0.1976 293.820 285.189 0.910 1.002 0.170 5.546-4.326 100.00 867 58 0.1102 403.342 398.518 0.954 1.002 0.170 4.315-3.360 100.00 1859 96 0.0934 383.581 380.948 0.994 1.002 0.160 3.356-2.611 100.00 3867 181 0.1175 251.993 250.024 0.998 1.002 0.072 2.608-2.026 99.99 8198 413 0.1062 167.048 165.978 1.011 1.001 0.000 2.025-1.573 100.00 17313 902 0.1013 81.578 81.730 1.026 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1285 36.175 35.751 1.020 0.999 0.000 1.221-1.150 99.97 13689 708 0.2125 22.793 21.413 0.977 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0274 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1200 r_free=0.1379 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A Total number of N/Q/H flips: 1 r_work=0.1200 r_free=0.1381 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1200 r_free=0.1381 | n_water=438 | time (s): 1.700 (total time: 1.700) Filter (dist) r_work=0.1203 r_free=0.1385 | n_water=437 | time (s): 36.470 (total time: 38.170) Filter (q & B) r_work=0.1203 r_free=0.1385 | n_water=437 | time (s): 1.130 (total time: 39.300) Compute maps r_work=0.1203 r_free=0.1385 | n_water=437 | time (s): 1.420 (total time: 40.720) Filter (map) r_work=0.1219 r_free=0.1389 | n_water=315 | time (s): 2.890 (total time: 43.610) Find peaks r_work=0.1219 r_free=0.1389 | n_water=315 | time (s): 0.560 (total time: 44.170) Add new water r_work=0.1288 r_free=0.1453 | n_water=465 | time (s): 3.200 (total time: 47.370) Refine new water occ: r_work=0.1219 r_free=0.1391 adp: r_work=0.1219 r_free=0.1391 occ: r_work=0.1206 r_free=0.1380 adp: r_work=0.1205 r_free=0.1379 occ: r_work=0.1195 r_free=0.1376 adp: r_work=0.1192 r_free=0.1372 ADP+occupancy (water only), MIN, final r_work=0.1192 r_free=0.1372 r_work=0.1192 r_free=0.1372 | n_water=465 | time (s): 187.250 (total time: 234.620) Filter (q & B) r_work=0.1196 r_free=0.1377 | n_water=437 | time (s): 3.570 (total time: 238.190) Filter (dist only) r_work=0.1196 r_free=0.1376 | n_water=436 | time (s): 36.650 (total time: 274.840) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.009888 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 40.563477 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 0.1199 0.1391 0.0192 0.006 0.9 1.6 0.5 0.0 0 1.005 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.99 13.91 1.92 3.423 21.404 40.563 3.639 11.93 13.82 1.89 3.708 21.318 40.563 3.629 Individual atomic B min max mean iso aniso Overall: 9.27 105.61 21.15 2.14 206 1757 Protein: 9.27 105.61 16.99 2.14 0 1519 Water: 11.59 70.03 35.57 N/A 206 230 Other: 21.26 29.69 25.50 N/A 0 8 Chain A: 9.27 105.61 19.60 N/A 0 1757 Chain S: 15.49 55.16 34.41 N/A 206 0 Histogram: Values Number of atoms 9.27 - 18.90 1231 18.90 - 28.54 280 28.54 - 38.17 203 38.17 - 47.80 141 47.80 - 57.44 70 57.44 - 67.07 25 67.07 - 76.71 8 76.71 - 86.34 2 86.34 - 95.97 1 95.97 - 105.61 2 =========================== Idealize ADP of riding H ========================== r_work=0.1193 r_free=0.1382 r_work=0.1194 r_free=0.1383 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1194 r_free = 0.1383 target_work(ml) = 3.629 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1190 r_free = 0.1381 target_work(ml) = 3.628 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87581 (all), 4.91 % free)------------| | | | r_work= 0.1190 r_free= 0.1381 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.628298 | | target function (ml) not normalized (work): 302182.770955 | | target function (ml) not normalized (free): 15962.592981 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1199 0.1190 0.1381 n_refl.: 87581 re-set all scales: r(all,work,free)=0.1517 0.1516 0.1568 n_refl.: 87581 remove outliers: r(all,work,free)=0.1517 0.1516 0.1568 n_refl.: 87581 overall B=-0.02 to atoms: r(all,work,free)=0.1514 0.1513 0.1566 n_refl.: 87581 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1188 0.1381 n_refl.: 87581 remove outliers: r(all,work,free)=0.1195 0.1186 0.1381 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 88.54 80 5 0.4147 283.878 249.093 0.453 1.002 0.324 11.894-9.307 94.12 92 4 0.2220 484.912 467.996 0.858 1.002 0.320 9.237-7.194 98.18 209 7 0.2448 383.074 377.599 0.915 1.002 0.150 7.162-5.571 100.00 427 22 0.2136 293.820 283.650 0.899 1.002 0.132 5.546-4.326 100.00 867 58 0.1149 403.342 398.719 0.953 1.002 0.130 4.315-3.360 100.00 1859 96 0.0949 383.581 381.034 0.994 1.002 0.119 3.356-2.611 100.00 3867 181 0.1156 251.993 250.135 1.001 1.002 0.048 2.608-2.026 99.99 8198 413 0.1041 167.048 166.031 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0975 81.578 81.820 1.028 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1248 36.175 35.785 1.023 0.998 0.000 1.221-1.150 99.97 13689 708 0.2124 22.793 21.413 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=-0.0457 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1186 r_free=0.1381 After: r_work=0.1186 r_free=0.1381 ================================== NQH flips ================================== r_work=0.1186 r_free=0.1381 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=0.1186 r_free=0.1381 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1186 r_free=0.1381 | n_water=436 | time (s): 2.140 (total time: 2.140) Filter (dist) r_work=0.1186 r_free=0.1381 | n_water=436 | time (s): 34.740 (total time: 36.880) Filter (q & B) r_work=0.1187 r_free=0.1381 | n_water=435 | time (s): 3.600 (total time: 40.480) Compute maps r_work=0.1187 r_free=0.1381 | n_water=435 | time (s): 1.670 (total time: 42.150) Filter (map) r_work=0.1214 r_free=0.1390 | n_water=329 | time (s): 3.380 (total time: 45.530) Find peaks r_work=0.1214 r_free=0.1390 | n_water=329 | time (s): 0.650 (total time: 46.180) Add new water r_work=0.1265 r_free=0.1447 | n_water=486 | time (s): 2.870 (total time: 49.050) Refine new water occ: r_work=0.1199 r_free=0.1378 adp: r_work=0.1200 r_free=0.1381 occ: r_work=0.1187 r_free=0.1366 adp: r_work=0.1186 r_free=0.1369 occ: r_work=0.1177 r_free=0.1360 adp: r_work=0.1175 r_free=0.1360 ADP+occupancy (water only), MIN, final r_work=0.1175 r_free=0.1360 r_work=0.1175 r_free=0.1360 | n_water=486 | time (s): 213.010 (total time: 262.060) Filter (q & B) r_work=0.1183 r_free=0.1364 | n_water=447 | time (s): 2.690 (total time: 264.750) Filter (dist only) r_work=0.1183 r_free=0.1363 | n_water=445 | time (s): 38.690 (total time: 303.440) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.959205 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 45.688797 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 0.1210 0.1383 0.0173 0.008 1.0 2.6 0.5 0.0 0 0.980 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.10 13.83 1.73 3.300 21.146 45.689 3.635 12.10 13.84 1.74 3.663 21.041 45.689 3.626 Individual atomic B min max mean iso aniso Overall: 9.22 101.24 20.91 2.02 217 1755 Protein: 9.22 101.24 16.70 2.02 0 1519 Water: 11.50 68.84 35.17 N/A 217 228 Other: 21.16 29.27 25.13 N/A 0 8 Chain A: 9.22 101.24 19.26 N/A 0 1755 Chain S: 14.52 55.96 34.19 N/A 217 0 Histogram: Values Number of atoms 9.22 - 18.42 1219 18.42 - 27.63 280 27.63 - 36.83 217 36.83 - 46.03 146 46.03 - 55.23 70 55.23 - 64.43 24 64.43 - 73.64 11 73.64 - 82.84 2 82.84 - 92.04 1 92.04 - 101.24 2 =========================== Idealize ADP of riding H ========================== r_work=0.1210 r_free=0.1384 r_work=0.1211 r_free=0.1384 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1211 r_free = 0.1384 target_work(ml) = 3.626 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1208 r_free = 0.1381 target_work(ml) = 3.625 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87576 (all), 4.91 % free)------------| | | | r_work= 0.1208 r_free= 0.1381 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.624564 | | target function (ml) not normalized (work): 301853.652712 | | target function (ml) not normalized (free): 15960.504254 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2918 171 0.1432 0.1434 5.696 5.6639| | 2: 3.57 - 2.84 1.00 2888 124 0.1141 0.1422 5.2207 5.2649| | 3: 2.83 - 2.48 1.00 2820 163 0.1259 0.1348 5.0251 5.0567| | 4: 2.47 - 2.25 1.00 2825 136 0.1048 0.1136 4.7267 4.7603| | 5: 2.25 - 2.09 1.00 2756 127 0.1022 0.1159 4.6675 4.7326| | 6: 2.09 - 1.97 1.00 2846 113 0.0991 0.1225 4.3641 4.505| | 7: 1.97 - 1.87 1.00 2787 165 0.1004 0.1213 4.086 4.1788| | 8: 1.87 - 1.79 1.00 2789 144 0.1026 0.1273 4.0001 4.0976| | 9: 1.79 - 1.72 1.00 2745 138 0.0947 0.1244 3.7155 3.8816| | 10: 1.72 - 1.66 1.00 2831 160 0.0988 0.1256 3.6297 3.7659| | 11: 1.66 - 1.61 1.00 2712 147 0.0956 0.1091 3.5674 3.6006| | 12: 1.61 - 1.56 1.00 2773 144 0.0912 0.1190 3.3441 3.4963| | 13: 1.56 - 1.52 1.00 2745 130 0.0980 0.1082 3.3408 3.4418| | 14: 1.52 - 1.48 1.00 2803 134 0.0984 0.1135 3.2594 3.3519| | 15: 1.48 - 1.45 1.00 2738 128 0.1000 0.1357 3.1624 3.3369| | 16: 1.45 - 1.42 1.00 2756 161 0.1062 0.1260 3.1488 3.2498| | 17: 1.42 - 1.39 1.00 2785 139 0.1110 0.1293 3.1115 3.2254| | 18: 1.39 - 1.36 1.00 2741 179 0.1147 0.1372 3.0836 3.2571| | 19: 1.36 - 1.34 1.00 2807 134 0.1206 0.1596 3.0881 3.2578| | 20: 1.34 - 1.32 1.00 2696 147 0.1319 0.1480 3.0884 3.1358| | 21: 1.32 - 1.30 1.00 2785 112 0.1413 0.1613 3.0853 3.1545| | 22: 1.29 - 1.27 1.00 2704 152 0.1476 0.1913 3.0839 3.2849| | 23: 1.27 - 1.26 1.00 2802 156 0.1566 0.1882 3.1003 3.2142| | 24: 1.26 - 1.24 1.00 2744 132 0.1621 0.1808 3.0927 3.2023| | 25: 1.24 - 1.22 1.00 2733 148 0.1790 0.2303 3.109 3.2934| | 26: 1.22 - 1.21 1.00 2727 135 0.1854 0.1811 3.1215 3.2041| | 27: 1.21 - 1.19 1.00 2814 148 0.2010 0.2106 3.1421 3.1519| | 28: 1.19 - 1.18 1.00 2671 147 0.2142 0.2323 3.1415 3.1706| | 29: 1.18 - 1.16 1.00 2800 134 0.2216 0.2385 3.1259 3.2291| | 30: 1.16 - 1.15 1.00 2739 148 0.2367 0.2515 3.1128 3.1695| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2918 171 0.94 9.43 1.00 0.97 6528.37| | 2: 3.57 - 2.84 2888 124 0.92 13.64 1.01 0.97 6528.37| | 3: 2.83 - 2.48 2820 163 0.88 17.92 0.99 0.97 5471.82| | 4: 2.47 - 2.25 2825 136 0.91 14.96 1.00 0.97 2747.33| | 5: 2.25 - 2.09 2756 127 0.89 17.22 1.01 0.97 2747.33| | 6: 2.09 - 1.97 2846 113 0.91 13.95 1.02 0.97 1612.15| | 7: 1.97 - 1.87 2787 165 0.94 11.03 1.02 0.97 643.98| | 8: 1.87 - 1.79 2789 144 0.91 14.62 1.00 0.97 643.98| | 9: 1.79 - 1.72 2745 138 0.93 11.53 0.98 0.97 344.70| | 10: 1.72 - 1.66 2831 160 0.93 12.36 0.98 0.97 284.77| | 11: 1.66 - 1.61 2712 147 0.93 13.00 0.98 0.97 271.72| | 12: 1.61 - 1.56 2773 144 0.95 9.62 0.99 0.97 148.67| | 13: 1.56 - 1.52 2745 130 0.94 11.19 1.02 0.97 148.67| | 14: 1.52 - 1.48 2803 134 0.94 11.33 1.02 0.97 132.79| | 15: 1.48 - 1.45 2738 128 0.95 10.42 1.01 0.98 103.69| | 16: 1.45 - 1.42 2756 161 0.94 11.61 1.02 0.98 103.69| | 17: 1.42 - 1.39 2785 139 0.94 11.42 1.01 0.98 93.26| | 18: 1.39 - 1.36 2741 179 0.94 11.71 1.01 0.98 87.22| | 19: 1.36 - 1.34 2807 134 0.94 12.24 1.00 0.98 87.22| | 20: 1.34 - 1.32 2696 147 0.94 12.41 0.99 0.96 82.07| | 21: 1.32 - 1.30 2785 112 0.94 13.35 0.98 0.96 81.71| | 22: 1.29 - 1.27 2704 152 0.93 13.86 0.98 0.96 81.96| | 23: 1.27 - 1.26 2802 156 0.92 14.85 0.98 0.95 83.22| | 24: 1.26 - 1.24 2744 132 0.92 15.00 0.97 0.95 83.22| | 25: 1.24 - 1.22 2733 148 0.91 16.44 0.96 0.94 85.09| | 26: 1.22 - 1.21 2727 135 0.90 18.23 1.02 0.93 87.16| | 27: 1.21 - 1.19 2814 148 0.89 18.86 1.02 0.93 87.16| | 28: 1.19 - 1.18 2671 147 0.88 20.44 1.01 0.92 90.85| | 29: 1.18 - 1.16 2800 134 0.88 20.78 0.99 0.92 92.24| | 30: 1.16 - 1.15 2739 148 0.86 22.22 0.98 0.92 92.24| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 81.71 max = 6528.37 mean = 1013.96| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.96 mean = 14.18| |phase err.(test): min = 0.00 max = 89.93 mean = 14.28| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1216 0.1208 0.1381 n_refl.: 87576 re-set all scales: r(all,work,free)=0.1527 0.1528 0.1551 n_refl.: 87576 remove outliers: r(all,work,free)=0.1527 0.1528 0.1551 n_refl.: 87576 overall B=-0.01 to atoms: r(all,work,free)=0.1524 0.1525 0.1549 n_refl.: 87576 bulk-solvent and scaling: r(all,work,free)=0.1217 0.1209 0.1379 n_refl.: 87576 remove outliers: r(all,work,free)=0.1216 0.1208 0.1379 n_refl.: 87574 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.4208 283.878 252.801 0.427 1.002 0.285 11.894-9.307 93.14 91 4 0.2455 485.078 462.018 0.861 1.002 0.260 9.237-7.194 97.73 208 7 0.2525 384.149 375.901 0.907 1.002 0.125 7.162-5.571 100.00 427 22 0.2254 293.820 281.897 0.889 1.002 0.120 5.546-4.326 100.00 867 58 0.1206 403.342 398.267 0.953 1.002 0.120 4.315-3.360 100.00 1859 96 0.1006 383.581 380.629 0.994 1.002 0.120 3.356-2.611 100.00 3867 181 0.1213 251.993 250.240 1.001 1.002 0.100 2.608-2.026 99.99 8198 413 0.1064 167.048 165.960 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0977 81.578 81.863 1.027 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1223 36.175 35.821 1.020 1.000 0.000 1.221-1.150 99.97 13689 708 0.2112 22.793 21.403 0.975 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0393 ================= 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 : 0.2604 0.1929 0.083 5.297 8.8 119.3 19.9 258 0.000 1_bss: 0.1623 0.1748 0.083 5.297 9.0 119.5 20.1 258 0.000 1_settarget: 0.1623 0.1748 0.083 5.297 9.0 119.5 20.1 258 0.000 1_nqh: 0.1625 0.1749 0.083 5.297 9.0 119.5 20.1 258 0.003 1_weight: 0.1625 0.1749 0.083 5.297 9.0 119.5 20.1 258 0.003 1_xyzrec: 0.1211 0.1457 0.007 0.943 9.0 119.5 20.1 258 0.128 1_adp: 0.1240 0.1535 0.007 0.943 8.5 118.4 21.0 258 0.128 1_regHadp: 0.1244 0.1540 0.007 0.943 8.5 118.4 21.0 258 0.128 1_occ: 0.1242 0.1542 0.007 0.943 8.5 118.4 21.0 258 0.128 2_bss: 0.1242 0.1538 0.007 0.943 8.7 118.5 21.1 258 0.128 2_settarget: 0.1242 0.1538 0.007 0.943 8.7 118.5 21.1 258 0.128 2_updatecdl: 0.1242 0.1538 0.007 0.946 8.7 118.5 21.1 258 0.128 2_nqh: 0.1242 0.1538 0.007 0.946 8.7 118.5 21.1 258 0.128 2_sol: 0.1230 0.1484 0.007 0.946 8.7 118.5 23.5 433 n/a 2_weight: 0.1230 0.1484 0.007 0.946 8.7 118.5 23.5 433 n/a 2_xyzrec: 0.1228 0.1520 0.007 0.874 8.7 118.5 23.5 433 n/a 2_adp: 0.1199 0.1496 0.007 0.874 8.8 113.5 23.2 433 n/a 2_regHadp: 0.1199 0.1495 0.007 0.874 8.8 113.5 23.2 433 n/a 2_occ: 0.1201 0.1492 0.007 0.874 8.8 113.5 23.2 433 n/a 3_bss: 0.1194 0.1488 0.007 0.874 8.8 113.6 23.2 433 n/a 3_settarget: 0.1194 0.1488 0.007 0.874 8.8 113.6 23.2 433 n/a 3_updatecdl: 0.1194 0.1488 0.007 0.876 8.8 113.6 23.2 433 n/a 3_nqh: 0.1194 0.1488 0.007 0.876 8.8 113.6 23.2 433 n/a 3_sol: 0.1224 0.1493 0.007 0.876 8.8 113.6 21.9 438 n/a 3_weight: 0.1224 0.1493 0.007 0.876 8.8 113.6 21.9 438 n/a 3_xyzrec: 0.1224 0.1447 0.005 0.922 8.8 113.6 21.9 438 n/a 3_adp: 0.1215 0.1405 0.005 0.922 9.2 109.2 21.6 438 n/a 3_regHadp: 0.1216 0.1406 0.005 0.922 9.2 109.2 21.6 438 n/a 3_occ: 0.1208 0.1402 0.005 0.922 9.2 109.2 21.6 438 n/a 4_bss: 0.1200 0.1379 0.005 0.922 9.2 109.2 21.6 438 n/a 4_settarget: 0.1200 0.1379 0.005 0.922 9.2 109.2 21.6 438 n/a 4_updatecdl: 0.1200 0.1379 0.005 0.920 9.2 109.2 21.6 438 n/a 4_nqh: 0.1200 0.1381 0.005 0.920 9.2 109.2 21.6 438 n/a 4_sol: 0.1196 0.1376 0.005 0.920 9.2 109.2 21.3 436 n/a 4_weight: 0.1196 0.1376 0.005 0.920 9.2 109.2 21.3 436 n/a 4_xyzrec: 0.1199 0.1391 0.006 0.948 9.2 109.2 21.3 436 n/a 4_adp: 0.1193 0.1382 0.006 0.948 9.3 105.6 21.2 436 n/a 4_regHadp: 0.1194 0.1383 0.006 0.948 9.3 105.6 21.2 436 n/a 4_occ: 0.1190 0.1381 0.006 0.948 9.3 105.6 21.2 436 n/a 5_bss: 0.1186 0.1381 0.006 0.948 9.3 105.6 21.1 436 n/a 5_settarget: 0.1186 0.1381 0.006 0.948 9.3 105.6 21.1 436 n/a 5_updatecdl: 0.1186 0.1381 0.006 0.949 9.3 105.6 21.1 436 n/a 5_setrh: 0.1186 0.1381 0.006 0.949 9.3 105.6 21.1 436 n/a 5_nqh: 0.1186 0.1381 0.006 0.949 9.3 105.6 21.1 436 n/a 5_sol: 0.1183 0.1363 0.006 0.949 9.3 105.6 21.1 445 n/a 5_weight: 0.1183 0.1363 0.006 0.949 9.3 105.6 21.1 445 n/a 5_xyzrec: 0.1210 0.1383 0.008 1.034 9.3 105.6 21.1 445 n/a 5_adp: 0.1210 0.1384 0.008 1.034 9.2 101.2 20.9 445 n/a 5_regHadp: 0.1211 0.1384 0.008 1.034 9.2 101.2 20.9 445 n/a 5_occ: 0.1208 0.1381 0.008 1.034 9.2 101.2 20.9 445 n/a end: 0.1208 0.1379 0.008 1.034 9.2 101.2 20.9 445 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_6470396_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_6470396_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.8200 Refinement macro-cycles (run) : 3559.4400 Write final files (write_after_run_outputs) : 64.7900 Total : 3629.0500 Total CPU time: 61.09 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:12:05 PST -0800 (1735452725.27 s) Start R-work = 0.1623, R-free = 0.1748 Final R-work = 0.1208, R-free = 0.1379 =============================================================================== Job complete usr+sys time: 3758.96 seconds wall clock time: 67 minutes 10.35 seconds (4030.35 seconds total)