Starting phenix.refine on Sat Dec 28 21:06:34 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6318584.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 { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6318584.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6318584.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" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } 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: 2.29, per 1000 atoms: 0.68 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: 0.73 Conformation dependent library (CDL) restraints added in 290.5 milliseconds Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.68 - 0.94: 708 0.94 - 1.20: 988 1.20 - 1.47: 751 1.47 - 1.73: 691 1.73 - 1.99: 15 Bond restraints: 3153 Sorted by residual: bond pdb=" C GLN A 95 " pdb=" O GLN A 95 " ideal model delta sigma weight residual 1.236 0.983 0.254 1.15e-02 7.56e+03 4.88e+02 bond pdb=" C MET A 134 " pdb=" O MET A 134 " ideal model delta sigma weight residual 1.235 0.961 0.274 1.33e-02 5.65e+03 4.26e+02 bond pdb=" C ILE A 105 " pdb=" O ILE A 105 " ideal model delta sigma weight residual 1.236 1.432 -0.196 1.01e-02 9.80e+03 3.78e+02 bond pdb=" CA TYR A 141 " pdb=" C TYR A 141 " ideal model delta sigma weight residual 1.525 1.273 0.252 1.32e-02 5.74e+03 3.64e+02 bond pdb=" C SER A 161 " pdb=" N PHE A 162 " ideal model delta sigma weight residual 1.334 1.569 -0.234 1.27e-02 6.20e+03 3.40e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.89: 3191 4.89 - 9.78: 1922 9.78 - 14.67: 560 14.67 - 19.56: 96 19.56 - 24.46: 8 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O ALA A 111 " pdb=" C ALA A 111 " pdb=" N LEU A 112 " ideal model delta sigma weight residual 122.12 138.68 -16.56 1.06e+00 8.90e-01 2.44e+02 angle pdb=" O GLY A 78 " pdb=" C GLY A 78 " pdb=" N ALA A 79 " ideal model delta sigma weight residual 122.18 107.91 14.27 9.60e-01 1.09e+00 2.21e+02 angle pdb=" O BGLN A 80 " pdb=" C BGLN A 80 " pdb=" N ASN A 81 " ideal model delta sigma weight residual 122.12 137.79 -15.67 1.06e+00 8.90e-01 2.18e+02 angle pdb=" O BPRO A 66 " pdb=" C BPRO A 66 " pdb=" N BTYR A 67 " ideal model delta sigma weight residual 121.10 145.56 -24.46 1.90e+00 2.77e-01 1.66e+02 angle pdb=" O ALA A 183 " pdb=" C ALA A 183 " pdb=" N PRO A 184 " ideal model delta sigma weight residual 120.55 108.59 11.96 9.50e-01 1.11e+00 1.59e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 949 17.96 - 35.93: 116 35.93 - 53.89: 30 53.89 - 71.85: 14 71.85 - 89.81: 2 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" N ARG A 156 " pdb=" CA ARG A 156 " ideal model delta harmonic sigma weight residual -180.00 -150.12 -29.88 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CA CYS A 106 " pdb=" C CYS A 106 " pdb=" N ALA A 107 " pdb=" CA ALA A 107 " ideal model delta harmonic sigma weight residual 180.00 155.61 24.39 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA BLYS A 99 " pdb=" C BLYS A 99 " pdb=" N GLY A 100 " pdb=" CA GLY A 100 " ideal model delta harmonic sigma weight residual 180.00 158.71 21.29 0 5.00e+00 4.00e-02 1.81e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.213: 86 0.213 - 0.425: 82 0.425 - 0.637: 48 0.637 - 0.849: 21 0.849 - 1.061: 6 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA THR A 110 " pdb=" N THR A 110 " pdb=" C THR A 110 " pdb=" CB THR A 110 " both_signs ideal model delta sigma weight residual False 2.53 1.46 1.06 2.00e-01 2.50e+01 2.82e+01 chirality pdb=" CA ALA A 171 " pdb=" N ALA A 171 " pdb=" C ALA A 171 " pdb=" CB ALA A 171 " both_signs ideal model delta sigma weight residual False 2.48 1.49 0.99 2.00e-01 2.50e+01 2.46e+01 chirality pdb=" CA THR A 19 " pdb=" N THR A 19 " pdb=" C THR A 19 " pdb=" CB THR A 19 " both_signs ideal model delta sigma weight residual False 2.53 3.50 -0.97 2.00e-01 2.50e+01 2.36e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " -0.129 2.00e-02 2.50e+03 6.32e-02 1.20e+02 pdb=" CG TYR A 141 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " 0.030 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " 0.032 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " 0.089 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " -0.079 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " 0.096 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " 0.023 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " -0.046 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.004 2.00e-02 2.50e+03 6.28e-02 1.18e+02 pdb=" CG BTYR A 67 " -0.070 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.004 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " 0.110 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " 0.106 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " 0.004 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " -0.039 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " 0.052 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " -0.015 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " 0.022 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " -0.061 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.102 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.017 2.00e-02 2.50e+03 5.97e-02 1.07e+02 pdb=" CG PHE A 164 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.063 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.047 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.068 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.092 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.037 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.085 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.065 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.080 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 785 2.28 - 2.86: 7830 2.86 - 3.44: 10690 3.44 - 4.02: 15318 4.02 - 4.60: 21984 Nonbonded interactions: 56607 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.699 2.100 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.825 2.450 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.837 2.450 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.850 2.100 nonbonded pdb=" O GLU A 147 " pdb=" H ATHR A 154 " model vdw 1.854 2.450 ... (remaining 56602 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_6318584_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= 0.2598 r_free= 0.1926 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.787914 | | target function (ml) not normalized (work): 232249.964631 | | target function (ml) not normalized (free): 11789.298437 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3016 0.2097 7.1251 4.9474| | 2: 3.57 - 2.84 1.00 2876 122 0.2439 0.1748 4.3431 4.3369| | 3: 2.84 - 2.48 1.00 2833 165 0.2332 0.1618 4.1202 4.1419| | 4: 2.47 - 2.25 1.00 2825 136 0.2337 0.1367 3.8233 3.8191| | 5: 2.25 - 2.09 1.00 2756 127 0.2450 0.1511 3.7956 3.8081| | 6: 2.09 - 1.97 1.00 2846 113 0.2532 0.1683 3.4511 3.5157| | 7: 1.97 - 1.87 1.00 2787 165 0.2521 0.1780 3.1146 3.1834| | 8: 1.87 - 1.79 1.00 2789 144 0.2486 0.2085 3.0472 3.1731| | 9: 1.79 - 1.72 1.00 2745 138 0.2413 0.1890 2.9013 2.9375| | 10: 1.72 - 1.66 1.00 2789 158 0.2430 0.2011 2.8147 2.862| | 11: 1.66 - 1.61 1.00 2740 147 0.2433 0.1866 2.7488 2.7841| | 12: 1.61 - 1.56 1.00 2787 146 0.2476 0.2165 2.6021 2.7399| | 13: 1.56 - 1.52 1.00 2745 130 0.2589 0.1887 2.5955 2.5828| | 14: 1.52 - 1.48 1.00 2803 134 0.2592 0.1866 2.5122 2.5298| | 15: 1.48 - 1.45 1.00 2738 128 0.2612 0.2257 2.4248 2.5516| | 16: 1.45 - 1.42 1.00 2756 161 0.2653 0.2124 2.3726 2.4059| | 17: 1.42 - 1.39 1.00 2785 139 0.2636 0.2052 2.3234 2.3246| | 18: 1.39 - 1.36 1.00 2741 179 0.2668 0.2046 2.2646 2.2808| | 19: 1.36 - 1.34 1.00 2807 134 0.2693 0.2400 2.2546 2.3161| | 20: 1.34 - 1.32 1.00 2696 147 0.2692 0.2176 2.1961 2.1704| | 21: 1.32 - 1.30 1.00 2785 112 0.2681 0.2253 2.1577 2.1937| | 22: 1.29 - 1.27 1.00 2704 152 0.2714 0.2561 2.1242 2.2086| | 23: 1.27 - 1.26 1.00 2802 156 0.2775 0.2289 2.0958 2.1346| | 24: 1.26 - 1.24 1.00 2744 132 0.2792 0.2671 2.0628 2.1564| | 25: 1.24 - 1.22 1.00 2734 148 0.2803 0.2588 2.0403 2.0873| | 26: 1.22 - 1.21 1.00 2727 135 0.2820 0.2422 2.0019 2.0802| | 27: 1.21 - 1.19 1.00 2814 148 0.2974 0.2634 2.0071 2.0185| | 28: 1.19 - 1.18 1.00 2671 147 0.2972 0.2708 1.9828 2.002| | 29: 1.18 - 1.16 1.00 2800 134 0.2990 0.2532 1.9542 1.9927| | 30: 1.16 - 1.15 1.00 2740 148 0.3047 0.2683 1.92 1.9127| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.63 0.76 0.23 1461.59| | 2: 3.57 - 2.84 2876 122 0.81 25.83 1.27 0.23 1461.59| | 3: 2.84 - 2.48 2833 165 0.74 31.61 1.24 0.24 1211.41| | 4: 2.47 - 2.25 2825 136 0.81 25.43 1.25 0.25 562.16| | 5: 2.25 - 2.09 2756 127 0.78 28.92 1.28 0.25 562.16| | 6: 2.09 - 1.97 2846 113 0.84 22.51 1.29 0.25 306.97| | 7: 1.97 - 1.87 2787 165 0.90 16.30 1.28 0.26 89.32| | 8: 1.87 - 1.79 2789 144 0.86 21.08 1.25 0.26 89.32| | 9: 1.79 - 1.72 2745 138 0.88 18.68 1.23 0.25 56.02| | 10: 1.72 - 1.66 2789 158 0.86 20.46 1.22 0.25 49.35| | 11: 1.66 - 1.61 2740 147 0.86 21.37 1.23 0.25 47.61| | 12: 1.61 - 1.56 2787 146 0.88 18.63 1.24 0.25 29.92| | 13: 1.56 - 1.52 2745 130 0.86 20.53 1.24 0.25 29.92| | 14: 1.52 - 1.48 2803 134 0.86 20.72 1.24 0.25 26.54| | 15: 1.48 - 1.45 2738 128 0.87 19.75 1.24 0.25 20.34| | 16: 1.45 - 1.42 2756 161 0.86 21.56 1.24 0.25 20.34| | 17: 1.42 - 1.39 2785 139 0.87 20.39 1.23 0.25 17.07| | 18: 1.39 - 1.36 2741 179 0.87 20.75 1.23 0.25 15.17| | 19: 1.36 - 1.34 2807 134 0.86 21.44 1.22 0.25 15.17| | 20: 1.34 - 1.32 2696 147 0.87 20.59 1.21 0.25 12.73| | 21: 1.32 - 1.30 2785 112 0.86 21.56 1.20 0.25 12.55| | 22: 1.29 - 1.27 2704 152 0.86 21.96 1.22 0.25 12.30| | 23: 1.27 - 1.26 2802 156 0.86 22.02 1.21 0.24 11.02| | 24: 1.26 - 1.24 2744 132 0.85 22.79 1.21 0.24 11.02| | 25: 1.24 - 1.22 2734 148 0.85 23.28 1.20 0.24 10.40| | 26: 1.22 - 1.21 2727 135 0.84 23.74 1.20 0.23 9.72| | 27: 1.21 - 1.19 2814 148 0.83 24.53 1.20 0.23 9.72| | 28: 1.19 - 1.18 2671 147 0.84 24.46 1.18 0.23 8.71| | 29: 1.18 - 1.16 2800 134 0.84 24.55 1.17 0.23 8.33| | 30: 1.16 - 1.15 2740 148 0.82 25.68 1.16 0.23 8.33| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 8.33 max = 1461.59 mean = 212.03| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 90.00 mean = 22.33| |phase err.(test): min = 0.00 max = 89.63 mean = 22.24| |-----------------------------------------------------------------------------| ----------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 0.274 1557 Z= 5.356 Angle : 5.348 24.455 2118 Z= 3.727 Chirality : 0.406 1.061 243 Planarity : 0.030 0.124 284 Dihedral : 14.099 89.814 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 0.00 % Allowed : 3.73 % 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: -2.49 (0.47), residues: 224 helix: -2.38 (0.39), residues: 108 sheet: -0.28 (0.83), residues: 30 loop : -0.84 (0.57), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.099 0.019 ARG A 27 TYR 0.102 0.042 TYR A 141 PHE 0.098 0.032 PHE A 119 HIS 0.041 0.022 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= 0.2598 r_free= 0.1926 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.787914 | | target function (ml) not normalized (work): 232249.964631 | | target function (ml) not normalized (free): 11789.298437 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2557 0.2598 0.1926 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2557 0.2598 0.1926 n_refl.: 87602 remove outliers: r(all,work,free)=0.1968 0.1972 0.1926 n_refl.: 87594 overall B=0.20 to atoms: r(all,work,free)=0.1992 0.1997 0.1939 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1632 0.1626 0.1753 n_refl.: 87594 remove outliers: r(all,work,free)=0.1631 0.1625 0.1753 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 98.94 88 5 0.3811 386.364 359.801 0.731 0.916 0.401 11.894-9.307 98.04 96 4 0.1750 616.211 586.454 1.010 0.917 0.380 9.237-7.194 100.00 213 7 0.2127 501.948 492.395 1.045 0.917 0.334 7.162-5.571 100.00 427 22 0.2213 376.684 363.154 1.011 0.918 0.310 5.546-4.326 100.00 867 58 0.1274 517.094 510.752 1.052 0.919 0.219 4.315-3.360 100.00 1859 96 0.1136 491.760 488.167 1.096 0.920 0.199 3.356-2.611 100.00 3867 181 0.1442 323.061 320.022 1.085 0.921 0.109 2.608-2.026 99.99 8198 413 0.1340 214.160 212.103 1.091 0.923 0.000 2.025-1.573 100.00 17313 902 0.1623 104.585 103.980 1.090 0.927 0.000 1.573-1.221 100.00 36679 1900 0.2052 46.377 45.062 1.072 0.933 0.000 1.221-1.150 99.97 13689 708 0.2578 29.221 27.004 1.035 0.938 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0449 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1625 r_free=0.1753 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** A 97 ASN B Total number of N/Q/H flips: 1 r_work=0.1625 r_free=0.1753 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.357332 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2021.193992 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 0.1212 0.1459 0.0247 0.007 1.0 0.6 0.5 0.0 0 12.679 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.12 14.59 2.47 3.013 19.055 2021.194 0.017 12.45 15.43 2.98 3.306 19.621 2021.194 0.015 Individual atomic B min max mean iso aniso Overall: 8.61 118.85 21.15 2.87 0 1785 Protein: 8.61 118.85 18.00 2.87 0 1519 Water: 11.16 114.49 39.45 N/A 0 258 Other: 23.33 37.04 29.60 N/A 0 8 Chain A: 8.61 118.85 21.15 N/A 0 1785 Histogram: Values Number of atoms 8.61 - 19.64 1207 19.64 - 30.66 229 30.66 - 41.69 160 41.69 - 52.71 102 52.71 - 63.73 56 63.73 - 74.76 17 74.76 - 85.78 7 85.78 - 96.80 4 96.80 - 107.83 0 107.83 - 118.85 3 =========================== Idealize ADP of riding H ========================== r_work=0.1245 r_free=0.1543 r_work=0.1250 r_free=0.1548 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1250 r_free = 0.1548 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 = 0.1249 r_free = 0.1549 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1249 r_free= 0.1549 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.015255 | | target function (ls_wunit_k1) not normalized (work): 1270.657182 | | target function (ls_wunit_k1) not normalized (free): 112.961362 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1264 0.1249 0.1549 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1709 0.1708 0.1777 n_refl.: 87592 remove outliers: r(all,work,free)=0.1709 0.1708 0.1777 n_refl.: 87592 overall B=0.12 to atoms: r(all,work,free)=0.1728 0.1727 0.1790 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1262 0.1248 0.1545 n_refl.: 87592 remove outliers: r(all,work,free)=0.1262 0.1248 0.1545 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 95.83 87 5 0.3616 298.083 278.045 0.632 1.003 0.380 11.894-9.307 98.04 96 4 0.1493 479.450 468.162 0.912 1.003 0.367 9.237-7.194 100.00 213 7 0.1819 390.546 385.919 0.948 1.003 0.314 7.162-5.571 100.00 427 22 0.1699 293.083 288.016 0.921 1.003 0.290 5.546-4.326 100.00 867 58 0.0919 402.331 399.630 0.948 1.003 0.199 4.315-3.360 100.00 1859 96 0.0771 382.619 381.654 0.995 1.003 0.180 3.356-2.611 100.00 3867 181 0.1015 251.361 250.694 0.999 1.002 0.110 2.608-2.026 99.99 8198 413 0.0979 166.629 166.042 1.010 1.002 0.000 2.025-1.573 100.00 17313 902 0.1224 81.373 81.526 1.017 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1666 36.084 35.539 1.006 0.999 0.000 1.221-1.150 99.97 13689 708 0.2371 22.736 21.248 0.969 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0457 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1248 r_free=0.1545 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=0.1249 r_free=0.1546 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1249 r_free=0.1546 | n_water=258 | time (s): 2.400 (total time: 2.400) Filter (dist) r_work=0.1258 r_free=0.1544 | n_water=252 | time (s): 26.220 (total time: 28.620) Filter (q & B) r_work=0.1261 r_free=0.1544 | n_water=249 | time (s): 3.620 (total time: 32.240) Compute maps r_work=0.1261 r_free=0.1544 | n_water=249 | time (s): 1.750 (total time: 33.990) Filter (map) r_work=0.1279 r_free=0.1549 | n_water=235 | time (s): 3.710 (total time: 37.700) Find peaks r_work=0.1279 r_free=0.1549 | n_water=235 | time (s): 0.710 (total time: 38.410) Add new water r_work=0.1433 r_free=0.1709 | n_water=458 | time (s): 3.640 (total time: 42.050) Refine new water occ: r_work=0.1340 r_free=0.1584 adp: r_work=0.1261 r_free=0.1535 occ: r_work=0.1276 r_free=0.1520 adp: r_work=0.1238 r_free=0.1507 occ: r_work=0.1241 r_free=0.1489 adp: r_work=0.1231 r_free=0.1491 ADP+occupancy (water only), MIN, final r_work=0.1231 r_free=0.1491 r_work=0.1231 r_free=0.1491 | n_water=458 | time (s): 118.340 (total time: 160.390) Filter (q & B) r_work=0.1237 r_free=0.1493 | n_water=435 | time (s): 3.940 (total time: 164.330) Filter (dist only) r_work=0.1237 r_free=0.1493 | n_water=435 | time (s): 41.130 (total time: 205.460) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.498986 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1566.804353 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 0.1233 0.1511 0.0279 0.007 0.9 1.9 0.5 0.0 0 12.249 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.33 15.11 2.79 3.811 23.382 1566.804 0.015 11.99 14.69 2.69 4.331 23.161 1566.804 0.015 Individual atomic B min max mean iso aniso Overall: 8.79 113.97 23.35 2.63 200 1762 Protein: 8.79 113.97 17.68 2.63 0 1519 Water: 11.23 74.11 43.08 N/A 200 235 Other: 23.07 34.02 27.89 N/A 0 8 Chain A: 8.79 113.97 20.41 N/A 0 1762 Chain S: 15.51 74.11 49.28 N/A 200 0 Histogram: Values Number of atoms 8.79 - 19.30 1209 19.30 - 29.82 244 29.82 - 40.34 188 40.34 - 50.86 137 50.86 - 61.38 115 61.38 - 71.90 50 71.90 - 82.42 13 82.42 - 92.93 3 92.93 - 103.45 1 103.45 - 113.97 2 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1469 r_work=0.1199 r_free=0.1468 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1468 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1459 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.=87591 (all), 4.90 % free)------------| | | | r_work= 0.1199 r_free= 0.1459 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.013849 | | target function (ls_wunit_k1) not normalized (work): 1153.553659 | | target function (ls_wunit_k1) not normalized (free): 98.168516 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1212 0.1199 0.1459 n_refl.: 87591 re-set all scales: r(all,work,free)=0.1608 0.1605 0.1693 n_refl.: 87591 remove outliers: r(all,work,free)=0.1608 0.1605 0.1693 n_refl.: 87591 overall B=0.04 to atoms: r(all,work,free)=0.1614 0.1611 0.1697 n_refl.: 87591 bulk-solvent and scaling: r(all,work,free)=0.1210 0.1197 0.1452 n_refl.: 87591 remove outliers: r(all,work,free)=0.1208 0.1195 0.1452 n_refl.: 87587 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 91.67 83 5 0.3331 290.801 273.153 0.567 1.002 0.338 11.894-9.307 98.04 96 4 0.1528 479.450 475.749 0.916 1.003 0.330 9.237-7.194 100.00 213 7 0.1652 390.546 391.885 0.981 1.003 0.270 7.162-5.571 100.00 427 22 0.1511 293.083 289.870 0.937 1.003 0.255 5.546-4.326 100.00 867 58 0.0833 402.331 399.380 0.957 1.003 0.209 4.315-3.360 100.00 1859 96 0.0707 382.619 381.704 1.002 1.002 0.198 3.356-2.611 100.00 3867 181 0.0952 251.361 250.828 1.010 1.002 0.072 2.608-2.026 99.99 8198 413 0.0962 166.629 166.184 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1181 81.373 81.565 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1611 36.084 35.587 1.017 0.999 0.000 1.221-1.150 99.97 13689 708 0.2336 22.736 21.270 0.976 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0591 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1195 r_free=0.1452 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1195 r_free=0.1452 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1195 r_free=0.1452 | n_water=435 | time (s): 2.220 (total time: 2.220) Filter (dist) r_work=0.1195 r_free=0.1453 | n_water=433 | time (s): 39.610 (total time: 41.830) Filter (q & B) r_work=0.1195 r_free=0.1453 | n_water=433 | time (s): 0.940 (total time: 42.770) Compute maps r_work=0.1195 r_free=0.1453 | n_water=433 | time (s): 1.190 (total time: 43.960) Filter (map) r_work=0.1235 r_free=0.1462 | n_water=293 | time (s): 3.570 (total time: 47.530) Find peaks r_work=0.1235 r_free=0.1462 | n_water=293 | time (s): 0.710 (total time: 48.240) Add new water r_work=0.1355 r_free=0.1561 | n_water=475 | time (s): 3.370 (total time: 51.610) Refine new water occ: r_work=0.1256 r_free=0.1485 adp: r_work=0.1256 r_free=0.1486 occ: r_work=0.1236 r_free=0.1469 adp: r_work=0.1233 r_free=0.1468 occ: r_work=0.1223 r_free=0.1458 adp: r_work=0.1215 r_free=0.1455 ADP+occupancy (water only), MIN, final r_work=0.1215 r_free=0.1455 r_work=0.1215 r_free=0.1455 | n_water=475 | time (s): 155.450 (total time: 207.060) Filter (q & B) r_work=0.1220 r_free=0.1458 | n_water=441 | time (s): 3.180 (total time: 210.240) Filter (dist only) r_work=0.1220 r_free=0.1458 | n_water=441 | time (s): 34.260 (total time: 244.500) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.000934 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 46.401971 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 0.1225 0.1435 0.0210 0.006 0.9 1.9 0.5 0.0 0 1.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.25 14.35 2.10 3.632 22.154 46.402 3.719 12.16 13.91 1.76 4.161 21.950 46.402 3.651 Individual atomic B min max mean iso aniso Overall: 9.26 109.30 21.72 2.31 208 1760 Protein: 9.26 109.30 17.22 2.31 0 1519 Water: 11.58 71.25 37.14 N/A 208 233 Other: 18.83 30.05 24.40 N/A 0 8 Chain A: 9.26 109.30 19.91 N/A 0 1760 Chain S: 16.47 63.84 36.95 N/A 208 0 Histogram: Values Number of atoms 9.26 - 19.26 1233 19.26 - 29.27 279 29.27 - 39.27 204 39.27 - 49.28 137 49.28 - 59.28 78 59.28 - 69.28 24 69.28 - 79.29 7 79.29 - 89.29 3 89.29 - 99.30 1 99.30 - 109.30 2 =========================== Idealize ADP of riding H ========================== r_work=0.1216 r_free=0.1391 r_work=0.1217 r_free=0.1392 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1217 r_free = 0.1392 target_work(ml) = 3.651 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1210 r_free = 0.1398 target_work(ml) = 3.648 | | 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.=87587 (all), 4.90 % free)------------| | | | r_work= 0.1210 r_free= 0.1398 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.648087 | | target function (ml) not normalized (work): 303852.812735 | | target function (ml) not normalized (free): 16038.773414 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1219 0.1210 0.1398 n_refl.: 87587 re-set all scales: r(all,work,free)=0.1549 0.1548 0.1587 n_refl.: 87587 remove outliers: r(all,work,free)=0.1549 0.1548 0.1587 n_refl.: 87587 overall B=-0.01 to atoms: r(all,work,free)=0.1547 0.1546 0.1586 n_refl.: 87587 bulk-solvent and scaling: r(all,work,free)=0.1213 0.1204 0.1381 n_refl.: 87587 remove outliers: r(all,work,free)=0.1211 0.1202 0.1381 n_refl.: 87582 ======================== 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 0.3802 287.448 259.767 0.478 1.000 0.324 11.894-9.307 98.04 96 4 0.2292 479.450 466.816 0.867 1.002 0.320 9.237-7.194 98.64 210 7 0.2246 387.099 385.526 0.951 1.002 0.190 7.162-5.571 100.00 427 22 0.2012 293.083 284.099 0.920 1.002 0.190 5.546-4.326 100.00 867 58 0.1090 402.331 397.927 0.954 1.002 0.179 4.315-3.360 100.00 1859 96 0.0930 382.619 380.059 0.992 1.002 0.179 3.356-2.611 100.00 3867 181 0.1178 251.361 249.343 0.998 1.002 0.067 2.608-2.026 99.99 8198 413 0.1053 166.629 165.613 1.011 1.002 0.000 2.025-1.573 100.00 17313 902 0.1020 81.373 81.509 1.025 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1298 36.084 35.666 1.019 0.999 0.000 1.221-1.150 99.97 13689 708 0.2139 22.736 21.349 0.977 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0290 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1202 r_free=0.1381 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1202 r_free=0.1381 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1202 r_free=0.1381 | n_water=441 | time (s): 2.200 (total time: 2.200) Filter (dist) r_work=0.1202 r_free=0.1383 | n_water=440 | time (s): 36.660 (total time: 38.860) Filter (q & B) r_work=0.1202 r_free=0.1384 | n_water=439 | time (s): 3.540 (total time: 42.400) Compute maps r_work=0.1202 r_free=0.1384 | n_water=439 | time (s): 1.440 (total time: 43.840) Filter (map) r_work=0.1220 r_free=0.1382 | n_water=314 | time (s): 2.450 (total time: 46.290) Find peaks r_work=0.1220 r_free=0.1382 | n_water=314 | time (s): 0.450 (total time: 46.740) Add new water r_work=0.1300 r_free=0.1455 | n_water=484 | time (s): 2.480 (total time: 49.220) Refine new water occ: r_work=0.1223 r_free=0.1378 adp: r_work=0.1223 r_free=0.1380 occ: r_work=0.1206 r_free=0.1368 adp: r_work=0.1203 r_free=0.1368 occ: r_work=0.1194 r_free=0.1363 adp: r_work=0.1189 r_free=0.1361 ADP+occupancy (water only), MIN, final r_work=0.1189 r_free=0.1361 r_work=0.1189 r_free=0.1361 | n_water=484 | time (s): 230.150 (total time: 279.370) Filter (q & B) r_work=0.1196 r_free=0.1362 | n_water=447 | time (s): 2.550 (total time: 281.920) Filter (dist only) r_work=0.1196 r_free=0.1359 | n_water=446 | time (s): 35.180 (total time: 317.100) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.132557 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 49.681003 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 0.1365 0.0166 0.006 1.0 2.9 0.5 0.0 0 1.066 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.99 13.65 1.66 3.419 21.554 49.681 3.636 11.79 13.50 1.72 3.764 21.448 49.681 3.617 Individual atomic B min max mean iso aniso Overall: 9.28 105.74 21.38 2.18 214 1759 Protein: 9.28 105.74 16.98 2.18 0 1519 Water: 11.41 69.89 36.36 N/A 214 232 Other: 18.58 27.10 22.79 N/A 0 8 Chain A: 9.28 105.74 19.61 N/A 0 1759 Chain S: 16.01 59.59 35.97 N/A 214 0 Histogram: Values Number of atoms 9.28 - 18.92 1229 18.92 - 28.57 286 28.57 - 38.22 201 38.22 - 47.86 139 47.86 - 57.51 79 57.51 - 67.15 26 67.15 - 76.80 8 76.80 - 86.44 2 86.44 - 96.09 1 96.09 - 105.74 2 =========================== Idealize ADP of riding H ========================== r_work=0.1179 r_free=0.1350 r_work=0.1179 r_free=0.1350 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1179 r_free = 0.1350 target_work(ml) = 3.617 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1174 r_free = 0.1349 target_work(ml) = 3.615 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87582 (all), 4.91 % free)------------| | | | r_work= 0.1174 r_free= 0.1349 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.615428 | | target function (ml) not normalized (work): 301114.516783 | | target function (ml) not normalized (free): 15907.864965 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1183 0.1174 0.1349 n_refl.: 87582 re-set all scales: r(all,work,free)=0.1502 0.1502 0.1543 n_refl.: 87582 remove outliers: r(all,work,free)=0.1502 0.1502 0.1543 n_refl.: 87582 overall B=-0.01 to atoms: r(all,work,free)=0.1500 0.1500 0.1542 n_refl.: 87582 bulk-solvent and scaling: r(all,work,free)=0.1183 0.1175 0.1347 n_refl.: 87582 remove outliers: r(all,work,free)=0.1181 0.1172 0.1347 n_refl.: 87575 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.3962 282.754 263.446 0.450 0.999 0.285 11.894-9.307 94.12 92 4 0.2358 473.028 458.102 0.853 1.000 0.260 9.237-7.194 97.73 208 7 0.2412 383.186 380.915 0.935 1.000 0.186 7.162-5.571 100.00 427 22 0.2101 293.083 282.455 0.908 1.001 0.165 5.546-4.326 100.00 867 58 0.1120 402.331 397.505 0.955 1.001 0.160 4.315-3.360 100.00 1859 96 0.0943 382.619 379.416 0.993 1.001 0.160 3.356-2.611 100.00 3867 181 0.1148 251.361 249.451 0.999 1.001 0.057 2.608-2.026 99.99 8198 413 0.1016 166.629 165.710 1.011 1.002 0.000 2.025-1.573 100.00 17313 902 0.0959 81.373 81.636 1.025 1.002 0.000 1.573-1.221 100.00 36679 1900 0.1242 36.084 35.714 1.017 1.002 0.000 1.221-1.150 99.97 13689 708 0.2124 22.736 21.314 0.971 1.002 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0319 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1172 r_free=0.1347 After: r_work=0.1173 r_free=0.1347 ================================== NQH flips ================================== r_work=0.1173 r_free=0.1347 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1173 r_free=0.1347 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1173 r_free=0.1347 | n_water=446 | time (s): 1.900 (total time: 1.900) Filter (dist) r_work=0.1173 r_free=0.1347 | n_water=446 | time (s): 33.700 (total time: 35.600) Filter (q & B) r_work=0.1174 r_free=0.1350 | n_water=442 | time (s): 3.240 (total time: 38.840) Compute maps r_work=0.1174 r_free=0.1350 | n_water=442 | time (s): 1.630 (total time: 40.470) Filter (map) r_work=0.1194 r_free=0.1350 | n_water=335 | time (s): 3.500 (total time: 43.970) Find peaks r_work=0.1194 r_free=0.1350 | n_water=335 | time (s): 0.570 (total time: 44.540) Add new water r_work=0.1253 r_free=0.1389 | n_water=496 | time (s): 2.770 (total time: 47.310) Refine new water occ: r_work=0.1186 r_free=0.1331 adp: r_work=0.1186 r_free=0.1333 occ: r_work=0.1173 r_free=0.1326 adp: r_work=0.1171 r_free=0.1325 occ: r_work=0.1163 r_free=0.1328 adp: r_work=0.1158 r_free=0.1325 ADP+occupancy (water only), MIN, final r_work=0.1158 r_free=0.1325 r_work=0.1158 r_free=0.1325 | n_water=496 | time (s): 165.960 (total time: 213.270) Filter (q & B) r_work=0.1165 r_free=0.1328 | n_water=455 | time (s): 2.560 (total time: 215.830) Filter (dist only) r_work=0.1165 r_free=0.1326 | n_water=453 | time (s): 39.080 (total time: 254.910) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.979356 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 37.800210 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1190 0.1356 0.0166 0.007 1.0 3.2 0.5 0.0 0 0.990 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.90 13.56 1.66 3.306 21.267 37.800 3.621 11.95 13.60 1.64 3.391 21.231 37.800 3.619 Individual atomic B min max mean iso aniso Overall: 9.26 103.15 21.28 2.07 223 1757 Protein: 9.26 103.15 16.88 2.07 0 1519 Water: 11.43 69.57 36.02 N/A 223 230 Other: 18.79 26.49 22.72 N/A 0 8 Chain A: 9.26 103.15 19.46 N/A 0 1757 Chain S: 15.91 58.17 35.61 N/A 223 0 Histogram: Values Number of atoms 9.26 - 18.65 1224 18.65 - 28.04 283 28.04 - 37.43 204 37.43 - 46.82 146 46.82 - 56.21 80 56.21 - 65.60 28 65.60 - 74.98 10 74.98 - 84.37 2 84.37 - 93.76 1 93.76 - 103.15 2 =========================== Idealize ADP of riding H ========================== r_work=0.1195 r_free=0.1360 r_work=0.1196 r_free=0.1360 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1196 r_free = 0.1360 target_work(ml) = 3.619 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1193 r_free = 0.1362 target_work(ml) = 3.618 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87575 (all), 4.91 % free)------------| | | | r_work= 0.1193 r_free= 0.1362 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.617944 | | target function (ml) not normalized (work): 301298.796200 | | target function (ml) not normalized (free): 15908.924270 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2917 171 0.1402 0.1372 5.6723 5.5961| | 2: 3.57 - 2.84 1.00 2888 124 0.1098 0.1416 5.172 5.2353| | 3: 2.83 - 2.48 1.00 2820 163 0.1207 0.1330 4.9815 5.0033| | 4: 2.47 - 2.25 1.00 2825 136 0.1012 0.1131 4.6842 4.7272| | 5: 2.25 - 2.09 1.00 2756 127 0.0995 0.1099 4.625 4.6941| | 6: 2.09 - 1.97 1.00 2846 113 0.0981 0.1191 4.3416 4.4667| | 7: 1.97 - 1.87 1.00 2787 165 0.0998 0.1245 4.0719 4.1828| | 8: 1.87 - 1.79 1.00 2789 144 0.1033 0.1287 3.9901 4.0919| | 9: 1.79 - 1.72 1.00 2745 138 0.0962 0.1295 3.7165 3.8908| | 10: 1.72 - 1.66 1.00 2831 160 0.1015 0.1262 3.6375 3.7674| | 11: 1.66 - 1.61 1.00 2712 147 0.0981 0.1105 3.5724 3.6144| | 12: 1.61 - 1.56 1.00 2773 144 0.0929 0.1096 3.3525 3.441| | 13: 1.56 - 1.52 1.00 2745 130 0.0991 0.1070 3.3381 3.4308| | 14: 1.52 - 1.48 1.00 2803 134 0.0998 0.1083 3.2598 3.3298| | 15: 1.48 - 1.45 1.00 2738 128 0.1022 0.1384 3.1693 3.3355| | 16: 1.45 - 1.42 1.00 2756 161 0.1076 0.1244 3.1523 3.2377| | 17: 1.42 - 1.39 1.00 2785 139 0.1126 0.1316 3.1145 3.2426| | 18: 1.39 - 1.36 1.00 2741 179 0.1171 0.1367 3.0897 3.2512| | 19: 1.36 - 1.34 1.00 2807 134 0.1220 0.1607 3.0927 3.2846| | 20: 1.34 - 1.32 1.00 2696 147 0.1320 0.1467 3.0858 3.1328| | 21: 1.32 - 1.30 1.00 2785 112 0.1417 0.1627 3.0869 3.1623| | 22: 1.29 - 1.27 1.00 2704 152 0.1474 0.1921 3.0824 3.2805| | 23: 1.27 - 1.26 1.00 2802 156 0.1586 0.1813 3.1042 3.1929| | 24: 1.26 - 1.24 1.00 2744 132 0.1639 0.1786 3.0969 3.2063| | 25: 1.24 - 1.22 1.00 2733 148 0.1801 0.2339 3.1094 3.2961| | 26: 1.22 - 1.21 1.00 2727 135 0.1867 0.1784 3.1245 3.1957| | 27: 1.21 - 1.19 1.00 2814 148 0.2019 0.2093 3.1408 3.1396| | 28: 1.19 - 1.18 1.00 2671 147 0.2144 0.2336 3.1386 3.1643| | 29: 1.18 - 1.16 1.00 2800 134 0.2229 0.2370 3.1289 3.223| | 30: 1.16 - 1.15 1.00 2739 148 0.2379 0.2515 3.1157 3.1669| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.58 2917 171 0.95 8.60 1.00 0.97 5824.22| | 2: 3.57 - 2.84 2888 124 0.92 12.78 1.01 0.97 5824.22| | 3: 2.83 - 2.48 2820 163 0.89 16.98 0.99 0.97 4891.89| | 4: 2.47 - 2.25 2825 136 0.91 14.15 1.00 0.98 2487.72| | 5: 2.25 - 2.09 2756 127 0.90 16.31 1.01 0.98 2487.72| | 6: 2.09 - 1.97 2846 113 0.92 13.35 1.02 0.98 1478.53| | 7: 1.97 - 1.87 2787 165 0.94 10.75 1.02 0.97 617.82| | 8: 1.87 - 1.79 2789 144 0.91 14.30 1.00 0.97 617.82| | 9: 1.79 - 1.72 2745 138 0.93 11.40 0.98 0.97 336.46| | 10: 1.72 - 1.66 2831 160 0.93 12.25 0.98 0.97 280.11| | 11: 1.66 - 1.61 2712 147 0.93 12.82 0.98 0.97 267.26| | 12: 1.61 - 1.56 2773 144 0.95 9.49 0.99 0.97 146.10| | 13: 1.56 - 1.52 2745 130 0.94 11.07 1.02 0.97 146.10| | 14: 1.52 - 1.48 2803 134 0.94 11.21 1.02 0.98 130.71| | 15: 1.48 - 1.45 2738 128 0.95 10.40 1.01 0.98 102.53| | 16: 1.45 - 1.42 2756 161 0.94 11.54 1.02 0.98 102.53| | 17: 1.42 - 1.39 2785 139 0.94 11.45 1.01 0.98 92.77| | 18: 1.39 - 1.36 2741 179 0.94 11.80 1.01 0.98 87.13| | 19: 1.36 - 1.34 2807 134 0.94 12.28 1.00 0.98 87.13| | 20: 1.34 - 1.32 2696 147 0.94 12.48 0.99 0.96 82.30| | 21: 1.32 - 1.30 2785 112 0.94 13.38 0.98 0.96 81.96| | 22: 1.29 - 1.27 2704 152 0.93 13.87 0.98 0.96 82.08| | 23: 1.27 - 1.26 2802 156 0.92 14.92 0.97 0.95 82.72| | 24: 1.26 - 1.24 2744 132 0.92 14.96 0.97 0.95 82.72| | 25: 1.24 - 1.22 2733 148 0.91 16.38 0.96 0.94 84.29| | 26: 1.22 - 1.21 2727 135 0.90 18.15 1.03 0.93 86.04| | 27: 1.21 - 1.19 2814 148 0.89 18.78 1.02 0.93 86.04| | 28: 1.19 - 1.18 2671 147 0.88 20.28 1.01 0.93 89.49| | 29: 1.18 - 1.16 2800 134 0.88 20.62 0.99 0.93 90.79| | 30: 1.16 - 1.15 2739 148 0.86 22.08 0.99 0.93 90.79| |alpha: min = 0.93 max = 0.98 mean = 0.96| |beta: min = 81.96 max = 5824.22 mean = 920.28| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.91 mean = 13.94| |phase err.(test): min = 0.00 max = 89.56 mean = 14.08| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1193 0.1362 n_refl.: 87575 re-set all scales: r(all,work,free)=0.1510 0.1509 0.1565 n_refl.: 87575 remove outliers: r(all,work,free)=0.1510 0.1509 0.1565 n_refl.: 87575 overall B=-0.01 to atoms: r(all,work,free)=0.1508 0.1507 0.1564 n_refl.: 87575 bulk-solvent and scaling: r(all,work,free)=0.1201 0.1192 0.1364 n_refl.: 87575 remove outliers: r(all,work,free)=0.1201 0.1192 0.1364 n_refl.: 87575 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.4171 282.754 248.697 0.432 1.000 0.310 11.894-9.307 94.12 92 4 0.2403 473.028 454.129 0.853 1.001 0.249 9.237-7.194 97.73 208 7 0.2484 383.186 376.727 0.914 1.001 0.162 7.162-5.571 100.00 427 22 0.2215 293.083 282.795 0.903 1.001 0.133 5.546-4.326 100.00 867 58 0.1165 402.331 397.332 0.955 1.001 0.130 4.315-3.360 100.00 1859 96 0.0978 382.619 379.776 0.994 1.001 0.130 3.356-2.611 100.00 3867 181 0.1165 251.361 249.485 1.000 1.001 0.053 2.608-2.026 99.99 8198 413 0.1034 166.629 165.645 1.012 1.001 0.000 2.025-1.573 100.00 17313 902 0.0986 81.373 81.641 1.026 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1236 36.084 35.724 1.019 1.000 0.000 1.221-1.150 99.97 13689 708 0.2121 22.736 21.325 0.974 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0324 ================= 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 : 0.2598 0.1926 0.081 5.348 8.8 119.3 19.9 258 0.000 1_bss: 0.1625 0.1753 0.081 5.348 9.0 119.5 20.1 258 0.000 1_settarget: 0.1625 0.1753 0.081 5.348 9.0 119.5 20.1 258 0.000 1_nqh: 0.1625 0.1753 0.081 5.348 9.0 119.5 20.1 258 0.003 1_weight: 0.1625 0.1753 0.081 5.348 9.0 119.5 20.1 258 0.003 1_xyzrec: 0.1212 0.1459 0.007 0.956 9.0 119.5 20.1 258 0.124 1_adp: 0.1245 0.1543 0.007 0.956 8.6 118.9 21.2 258 0.124 1_regHadp: 0.1250 0.1548 0.007 0.956 8.6 118.9 21.2 258 0.124 1_occ: 0.1249 0.1549 0.007 0.956 8.6 118.9 21.2 258 0.124 2_bss: 0.1248 0.1545 0.007 0.956 8.7 119.0 21.3 258 0.124 2_settarget: 0.1248 0.1545 0.007 0.956 8.7 119.0 21.3 258 0.124 2_updatecdl: 0.1248 0.1545 0.007 0.964 8.7 119.0 21.3 258 0.124 2_nqh: 0.1249 0.1546 0.007 0.964 8.7 119.0 21.3 258 0.127 2_sol: 0.1237 0.1493 0.007 0.964 8.7 119.0 23.8 435 n/a 2_weight: 0.1237 0.1493 0.007 0.964 8.7 119.0 23.8 435 n/a 2_xyzrec: 0.1233 0.1511 0.007 0.880 8.7 119.0 23.8 435 n/a 2_adp: 0.1199 0.1469 0.007 0.880 8.8 114.0 23.4 435 n/a 2_regHadp: 0.1199 0.1468 0.007 0.880 8.8 114.0 23.4 435 n/a 2_occ: 0.1199 0.1459 0.007 0.880 8.8 114.0 23.4 435 n/a 3_bss: 0.1195 0.1452 0.007 0.880 8.8 114.0 23.4 435 n/a 3_settarget: 0.1195 0.1452 0.007 0.880 8.8 114.0 23.4 435 n/a 3_updatecdl: 0.1195 0.1452 0.007 0.880 8.8 114.0 23.4 435 n/a 3_nqh: 0.1195 0.1452 0.007 0.880 8.8 114.0 23.4 435 n/a 3_sol: 0.1220 0.1458 0.007 0.880 8.8 114.0 22.1 441 n/a 3_weight: 0.1220 0.1458 0.007 0.880 8.8 114.0 22.1 441 n/a 3_xyzrec: 0.1225 0.1435 0.006 0.919 8.8 114.0 22.1 441 n/a 3_adp: 0.1216 0.1391 0.006 0.919 9.3 109.3 21.7 441 n/a 3_regHadp: 0.1217 0.1392 0.006 0.919 9.3 109.3 21.7 441 n/a 3_occ: 0.1210 0.1398 0.006 0.919 9.3 109.3 21.7 441 n/a 4_bss: 0.1202 0.1381 0.006 0.919 9.2 109.3 21.7 441 n/a 4_settarget: 0.1202 0.1381 0.006 0.919 9.2 109.3 21.7 441 n/a 4_updatecdl: 0.1202 0.1381 0.006 0.918 9.2 109.3 21.7 441 n/a 4_nqh: 0.1202 0.1381 0.006 0.918 9.2 109.3 21.7 441 n/a 4_sol: 0.1196 0.1359 0.006 0.918 9.2 109.3 21.6 446 n/a 4_weight: 0.1196 0.1359 0.006 0.918 9.2 109.3 21.6 446 n/a 4_xyzrec: 0.1199 0.1365 0.006 0.965 9.2 109.3 21.6 446 n/a 4_adp: 0.1179 0.1350 0.006 0.965 9.3 105.7 21.4 446 n/a 4_regHadp: 0.1179 0.1350 0.006 0.965 9.3 105.7 21.4 446 n/a 4_occ: 0.1174 0.1349 0.006 0.965 9.3 105.7 21.4 446 n/a 5_bss: 0.1172 0.1347 0.006 0.965 9.3 105.7 21.4 446 n/a 5_settarget: 0.1172 0.1347 0.006 0.965 9.3 105.7 21.4 446 n/a 5_updatecdl: 0.1172 0.1347 0.006 0.966 9.3 105.7 21.4 446 n/a 5_setrh: 0.1173 0.1347 0.006 0.966 9.3 105.7 21.4 446 n/a 5_nqh: 0.1173 0.1347 0.006 0.966 9.3 105.7 21.4 446 n/a 5_sol: 0.1165 0.1326 0.006 0.966 9.3 105.7 21.3 453 n/a 5_weight: 0.1165 0.1326 0.006 0.966 9.3 105.7 21.3 453 n/a 5_xyzrec: 0.1190 0.1356 0.007 1.040 9.3 105.7 21.3 453 n/a 5_adp: 0.1195 0.1360 0.007 1.040 9.3 103.2 21.3 453 n/a 5_regHadp: 0.1196 0.1360 0.007 1.040 9.3 103.2 21.3 453 n/a 5_occ: 0.1193 0.1362 0.007 1.040 9.3 103.2 21.3 453 n/a end: 0.1192 0.1364 0.007 1.040 9.3 103.1 21.3 453 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_6318584_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_6318584_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.7800 Refinement macro-cycles (run) : 3441.3800 Write final files (write_after_run_outputs) : 74.0200 Total : 3520.1800 Total CPU time: 59.28 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:10:53 PST -0800 (1735452653.35 s) Start R-work = 0.1625, R-free = 0.1753 Final R-work = 0.1192, R-free = 0.1364 =============================================================================== Job complete usr+sys time: 3662.99 seconds wall clock time: 66 minutes 11.12 seconds (3971.12 seconds total)