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_3081210.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_3081210.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3081210.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 2.26, per 1000 atoms: 0.67 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 241.0 milliseconds Time building geometry restraints manager: 0.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.65 - 0.91: 512 0.91 - 1.16: 1125 1.16 - 1.41: 641 1.41 - 1.67: 832 1.67 - 1.92: 43 Bond restraints: 3153 Sorted by residual: bond pdb=" CG HIS A 138 " pdb=" ND1 HIS A 138 " ideal model delta sigma weight residual 1.378 1.156 0.222 1.10e-02 8.26e+03 4.09e+02 bond pdb=" ND1 HIS A 115 " pdb=" CE1 HIS A 115 " ideal model delta sigma weight residual 1.321 1.511 -0.190 1.00e-02 1.00e+04 3.61e+02 bond pdb=" C BCYS A 53 " pdb=" N PRO A 54 " ideal model delta sigma weight residual 1.330 1.539 -0.209 1.22e-02 6.72e+03 2.94e+02 bond pdb=" CA LEU A 72 " pdb=" C LEU A 72 " ideal model delta sigma weight residual 1.521 1.741 -0.220 1.32e-02 5.74e+03 2.78e+02 bond pdb=" N VAL A 186 " pdb=" CA VAL A 186 " ideal model delta sigma weight residual 1.459 1.251 0.208 1.25e-02 6.40e+03 2.76e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.14: 3403 5.14 - 10.27: 1796 10.27 - 15.41: 522 15.41 - 20.54: 53 20.54 - 25.68: 3 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O GLU A 163 " pdb=" C GLU A 163 " pdb=" N PHE A 164 " ideal model delta sigma weight residual 122.08 106.03 16.05 1.07e+00 8.73e-01 2.25e+02 angle pdb=" CA ALYS A 93 " pdb=" C ALYS A 93 " pdb=" O ALYS A 93 " ideal model delta sigma weight residual 120.63 136.22 -15.59 1.08e+00 8.57e-01 2.08e+02 angle pdb=" O VAL A 44 " pdb=" C VAL A 44 " pdb=" N GLN A 45 " ideal model delta sigma weight residual 123.10 139.29 -16.19 1.17e+00 7.31e-01 1.91e+02 angle pdb=" O LYS A 12 " pdb=" C LYS A 12 " pdb=" N GLY A 13 " ideal model delta sigma weight residual 122.87 139.41 -16.54 1.23e+00 6.61e-01 1.81e+02 angle pdb=" N SER A 47 " pdb=" CA SER A 47 " pdb=" C SER A 47 " ideal model delta sigma weight residual 111.33 127.40 -16.07 1.21e+00 6.83e-01 1.76e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.02 - 17.25: 946 17.25 - 34.49: 110 34.49 - 51.72: 34 51.72 - 68.95: 17 68.95 - 86.19: 4 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA LEU A 72 " pdb=" C LEU A 72 " pdb=" N PRO A 73 " pdb=" CA PRO A 73 " ideal model delta harmonic sigma weight residual 180.00 159.53 20.47 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA ASP A 49 " pdb=" C ASP A 49 " pdb=" N VAL A 50 " pdb=" CA VAL A 50 " ideal model delta harmonic sigma weight residual 180.00 160.39 19.61 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA PRO A 73 " pdb=" C PRO A 73 " pdb=" N GLY A 74 " pdb=" CA GLY A 74 " ideal model delta harmonic sigma weight residual 180.00 160.46 19.54 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.227: 86 0.227 - 0.455: 74 0.455 - 0.682: 55 0.682 - 0.910: 20 0.910 - 1.137: 8 Chirality restraints: 243 Sorted by residual: chirality pdb=" CG LEU A 7 " pdb=" CB LEU A 7 " pdb=" CD1 LEU A 7 " pdb=" CD2 LEU A 7 " both_signs ideal model delta sigma weight residual False -2.59 -3.73 1.14 2.00e-01 2.50e+01 3.23e+01 chirality pdb=" CA ARG A 98 " pdb=" N ARG A 98 " pdb=" C ARG A 98 " pdb=" CB ARG A 98 " both_signs ideal model delta sigma weight residual False 2.51 1.42 1.09 2.00e-01 2.50e+01 2.96e+01 chirality pdb=" CA SER A 57 " pdb=" N SER A 57 " pdb=" C SER A 57 " pdb=" CB SER A 57 " both_signs ideal model delta sigma weight residual False 2.51 3.55 -1.04 2.00e-01 2.50e+01 2.69e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " -0.076 2.00e-02 2.50e+03 6.41e-02 1.23e+02 pdb=" CG TYR A 139 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.064 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.041 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " 0.051 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.113 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.076 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " -0.024 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " 0.047 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " 0.074 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.062 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " 0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " -0.031 2.00e-02 2.50e+03 5.29e-02 8.38e+01 pdb=" CG ATYR A 67 " 0.033 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " 0.062 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.096 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " -0.058 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " -0.026 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " -0.053 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " 0.029 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " -0.072 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " -0.009 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " 0.064 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.007 2.00e-02 2.50e+03 5.28e-02 8.37e+01 pdb=" CG PHE A 164 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.044 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.067 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.099 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.027 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.020 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.042 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.045 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.100 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.037 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.028 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.25: 643 2.25 - 2.84: 7583 2.84 - 3.43: 10714 3.43 - 4.01: 15390 4.01 - 4.60: 22239 Nonbonded interactions: 56569 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.663 2.100 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.772 2.450 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.777 2.450 nonbonded pdb=" HE2 HIS A 126 " pdb=" O PRO A 184 " model vdw sym.op. 1.804 2.450 x-y,-y,-z-4/3 nonbonded pdb=" H LEU A 10 " pdb=" O ALA A 36 " model vdw 1.833 2.450 ... (remaining 56564 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_3081210_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= 0.2607 r_free= 0.1968 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.795834 | | target function (ml) not normalized (work): 232909.761221 | | target function (ml) not normalized (free): 11891.762093 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3028 0.2156 6.9714 4.9676| | 2: 3.57 - 2.84 1.00 2876 122 0.2442 0.1781 4.3623 4.354| | 3: 2.84 - 2.48 1.00 2833 165 0.2324 0.1642 4.1345 4.1691| | 4: 2.47 - 2.25 1.00 2825 136 0.2318 0.1408 3.8381 3.8218| | 5: 2.25 - 2.09 1.00 2756 127 0.2481 0.1478 3.8063 3.8199| | 6: 2.09 - 1.97 1.00 2846 113 0.2555 0.1660 3.4775 3.5407| | 7: 1.97 - 1.87 1.00 2787 165 0.2581 0.1892 3.1282 3.1878| | 8: 1.87 - 1.79 1.00 2789 144 0.2496 0.1888 3.0544 3.1252| | 9: 1.79 - 1.72 1.00 2745 138 0.2463 0.1800 2.8857 2.8951| | 10: 1.72 - 1.66 1.00 2789 158 0.2409 0.2028 2.8217 2.8912| | 11: 1.66 - 1.61 1.00 2740 147 0.2459 0.2111 2.7528 2.8345| | 12: 1.61 - 1.56 1.00 2787 146 0.2484 0.2057 2.6406 2.683| | 13: 1.56 - 1.52 1.00 2745 130 0.2567 0.1973 2.5907 2.6527| | 14: 1.52 - 1.48 1.00 2803 134 0.2582 0.2030 2.5276 2.5532| | 15: 1.48 - 1.45 1.00 2738 128 0.2627 0.2111 2.453 2.5215| | 16: 1.45 - 1.42 1.00 2756 161 0.2691 0.2293 2.3985 2.4788| | 17: 1.42 - 1.39 1.00 2785 139 0.2651 0.2215 2.3292 2.3988| | 18: 1.39 - 1.36 1.00 2741 179 0.2643 0.2218 2.3 2.3512| | 19: 1.36 - 1.34 1.00 2807 134 0.2651 0.2424 2.252 2.3033| | 20: 1.34 - 1.32 1.00 2696 147 0.2635 0.2261 2.1991 2.2092| | 21: 1.32 - 1.30 1.00 2785 112 0.2722 0.2658 2.1771 2.2466| | 22: 1.29 - 1.27 1.00 2704 152 0.2767 0.2474 2.1427 2.2081| | 23: 1.27 - 1.26 1.00 2802 156 0.2831 0.2615 2.1351 2.2156| | 24: 1.26 - 1.24 1.00 2744 132 0.2774 0.2534 2.091 2.1598| | 25: 1.24 - 1.22 1.00 2734 148 0.2826 0.2586 2.0503 2.1088| | 26: 1.22 - 1.21 1.00 2727 135 0.2880 0.2447 2.0206 2.1539| | 27: 1.21 - 1.19 1.00 2814 148 0.2967 0.2902 2.0097 2.0837| | 28: 1.19 - 1.18 1.00 2671 147 0.2983 0.2596 1.9896 1.9608| | 29: 1.18 - 1.16 1.00 2800 134 0.2953 0.2815 1.9561 2.0349| | 30: 1.16 - 1.15 1.00 2740 148 0.3057 0.2943 1.9285 1.9648| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 49.25 - 3.58 2941 171 0.87 19.16 0.76 0.23 1522.05| | 2: 3.57 - 2.84 2876 122 0.80 26.54 1.27 0.23 1522.05| | 3: 2.84 - 2.48 2833 165 0.73 32.41 1.24 0.23 1260.23| | 4: 2.47 - 2.25 2825 136 0.81 25.66 1.26 0.25 580.75| | 5: 2.25 - 2.09 2756 127 0.77 29.56 1.28 0.25 580.75| | 6: 2.09 - 1.97 2846 113 0.83 22.78 1.29 0.25 314.92| | 7: 1.97 - 1.87 2787 165 0.90 16.45 1.29 0.26 88.20| | 8: 1.87 - 1.79 2789 144 0.86 20.68 1.26 0.26 88.20| | 9: 1.79 - 1.72 2745 138 0.88 18.96 1.24 0.25 56.10| | 10: 1.72 - 1.66 2789 158 0.86 20.42 1.22 0.25 49.67| | 11: 1.66 - 1.61 2740 147 0.85 21.62 1.23 0.25 48.05| | 12: 1.61 - 1.56 2787 146 0.88 19.15 1.23 0.25 31.68| | 13: 1.56 - 1.52 2745 130 0.86 20.99 1.24 0.25 31.68| | 14: 1.52 - 1.48 2803 134 0.86 21.46 1.23 0.25 28.31| | 15: 1.48 - 1.45 2738 128 0.87 20.73 1.23 0.25 22.13| | 16: 1.45 - 1.42 2756 161 0.84 22.71 1.24 0.25 22.13| | 17: 1.42 - 1.39 2785 139 0.86 21.42 1.23 0.25 18.73| | 18: 1.39 - 1.36 2741 179 0.86 21.76 1.21 0.25 16.76| | 19: 1.36 - 1.34 2807 134 0.85 22.86 1.21 0.25 16.76| | 20: 1.34 - 1.32 2696 147 0.86 21.66 1.20 0.24 14.01| | 21: 1.32 - 1.30 2785 112 0.85 23.01 1.20 0.24 13.81| | 22: 1.29 - 1.27 2704 152 0.84 23.62 1.22 0.24 13.53| | 23: 1.27 - 1.26 2802 156 0.85 23.21 1.21 0.24 12.10| | 24: 1.26 - 1.24 2744 132 0.84 23.96 1.19 0.24 12.10| | 25: 1.24 - 1.22 2734 148 0.83 24.72 1.20 0.23 11.37| | 26: 1.22 - 1.21 2727 135 0.83 25.03 1.19 0.23 10.56| | 27: 1.21 - 1.19 2814 148 0.82 25.85 1.21 0.23 10.56| | 28: 1.19 - 1.18 2671 147 0.82 25.56 1.18 0.23 9.30| | 29: 1.18 - 1.16 2800 134 0.83 25.08 1.17 0.22 8.83| | 30: 1.16 - 1.15 2740 148 0.81 26.99 1.15 0.22 8.83| |alpha: min = 0.22 max = 0.26 mean = 0.24| |beta: min = 8.83 max = 1522.05 mean = 220.18| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 90.00 mean = 23.13| |phase err.(test): min = 0.00 max = 89.97 mean = 23.15| |-----------------------------------------------------------------------------| ----------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 0.228 1557 Z= 5.393 Angle : 5.341 17.586 2118 Z= 3.715 Chirality : 0.444 1.137 243 Planarity : 0.031 0.085 284 Dihedral : 13.921 86.187 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 1.86 % Allowed : 1.86 % Favored : 96.27 % Cbeta Deviations : 35.14 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.26 (0.48), residues: 224 helix: -3.12 (0.36), residues: 109 sheet: -0.94 (0.83), residues: 38 loop : -0.82 (0.61), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.099 0.019 ARG A 5 TYR 0.086 0.039 TYR A 139 PHE 0.083 0.029 PHE A 164 HIS 0.076 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= 0.2607 r_free= 0.1968 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.795834 | | target function (ml) not normalized (work): 232909.761221 | | target function (ml) not normalized (free): 11891.762093 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2567 0.2608 0.1968 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2567 0.2608 0.1968 n_refl.: 87602 remove outliers: r(all,work,free)=0.1986 0.1989 0.1968 n_refl.: 87594 overall B=0.22 to atoms: r(all,work,free)=0.2012 0.2015 0.1983 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1649 0.1642 0.1795 n_refl.: 87594 remove outliers: r(all,work,free)=0.1649 0.1641 0.1795 n_refl.: 87593 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 98.94 88 5 0.3856 386.476 355.570 0.664 1.002 0.401 11.894-9.307 99.02 97 4 0.1897 613.898 593.956 0.922 1.003 0.375 9.237-7.194 100.00 213 7 0.2101 502.093 490.181 0.958 1.003 0.349 7.162-5.571 100.00 427 22 0.2191 376.793 365.433 0.934 1.003 0.303 5.546-4.326 100.00 867 58 0.1290 517.244 510.846 0.963 1.003 0.243 4.315-3.360 100.00 1859 96 0.1126 491.902 488.179 1.005 1.003 0.209 3.356-2.611 100.00 3867 181 0.1455 323.154 319.467 0.996 1.002 0.109 2.608-2.026 99.99 8198 413 0.1345 214.222 212.008 1.006 1.001 0.000 2.025-1.573 100.00 17313 902 0.1655 104.615 103.898 1.014 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2084 46.390 45.049 1.003 0.995 0.000 1.221-1.150 99.97 13689 708 0.2584 29.229 26.956 0.977 0.993 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0493 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1641 r_free=0.1795 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=0.1641 r_free=0.1795 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.917506 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2012.684581 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1214 0.1461 0.0247 0.007 0.9 1.0 0.5 0.0 0 11.959 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.14 14.61 2.47 3.013 19.074 2012.685 0.017 12.49 15.46 2.97 3.301 19.607 2012.685 0.016 Individual atomic B min max mean iso aniso Overall: 8.46 118.99 21.11 2.87 0 1785 Protein: 8.46 118.99 17.99 2.87 0 1519 Water: 11.13 114.51 39.24 N/A 0 258 Other: 23.44 37.23 29.80 N/A 0 8 Chain A: 8.46 118.99 21.11 N/A 0 1785 Histogram: Values Number of atoms 8.46 - 19.51 1201 19.51 - 30.56 234 30.56 - 41.62 164 41.62 - 52.67 106 52.67 - 63.72 50 63.72 - 74.78 18 74.78 - 85.83 5 85.83 - 96.88 3 96.88 - 107.93 1 107.93 - 118.99 3 =========================== Idealize ADP of riding H ========================== r_work=0.1249 r_free=0.1546 r_work=0.1254 r_free=0.1550 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1254 r_free = 0.1550 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 = 0.1254 r_free = 0.1552 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1254 r_free= 0.1552 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.015475 | | target function (ls_wunit_k1) not normalized (work): 1289.057828 | | target function (ls_wunit_k1) not normalized (free): 114.432290 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1268 0.1254 0.1552 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1709 0.1708 0.1775 n_refl.: 87593 remove outliers: r(all,work,free)=0.1709 0.1708 0.1775 n_refl.: 87593 overall B=0.14 to atoms: r(all,work,free)=0.1732 0.1731 0.1791 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1266 0.1252 0.1547 n_refl.: 87593 remove outliers: r(all,work,free)=0.1266 0.1251 0.1547 n_refl.: 87592 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3604 298.407 277.939 0.633 1.002 0.380 11.894-9.307 99.02 97 4 0.1608 478.031 466.610 0.906 1.003 0.380 9.237-7.194 100.00 213 7 0.1827 390.971 385.465 0.949 1.003 0.340 7.162-5.571 100.00 427 22 0.1720 293.402 288.276 0.924 1.003 0.258 5.546-4.326 100.00 867 58 0.0913 402.768 400.278 0.949 1.003 0.214 4.315-3.360 100.00 1859 96 0.0773 383.035 382.042 0.995 1.003 0.200 3.356-2.611 100.00 3867 181 0.1018 251.634 250.967 0.998 1.002 0.120 2.608-2.026 99.99 8198 413 0.0981 166.811 166.227 1.010 1.001 0.000 2.025-1.573 100.00 17313 902 0.1227 81.462 81.636 1.018 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1671 36.123 35.569 1.005 0.998 0.000 1.221-1.150 99.97 13689 708 0.2374 22.760 21.263 0.970 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0540 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1251 r_free=0.1547 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=0.1253 r_free=0.1548 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1253 r_free=0.1548 | n_water=258 | time (s): 2.490 (total time: 2.490) Filter (dist) r_work=0.1262 r_free=0.1547 | n_water=252 | time (s): 26.580 (total time: 29.070) Filter (q & B) r_work=0.1265 r_free=0.1546 | n_water=249 | time (s): 3.950 (total time: 33.020) Compute maps r_work=0.1265 r_free=0.1546 | n_water=249 | time (s): 1.930 (total time: 34.950) Filter (map) r_work=0.1282 r_free=0.1552 | n_water=236 | time (s): 3.900 (total time: 38.850) Find peaks r_work=0.1282 r_free=0.1552 | n_water=236 | time (s): 0.750 (total time: 39.600) Add new water r_work=0.1438 r_free=0.1696 | n_water=449 | time (s): 3.970 (total time: 43.570) Refine new water occ: r_work=0.1343 r_free=0.1573 adp: r_work=0.1263 r_free=0.1517 occ: r_work=0.1275 r_free=0.1518 adp: r_work=0.1241 r_free=0.1503 occ: r_work=0.1244 r_free=0.1497 adp: r_work=0.1235 r_free=0.1499 ADP+occupancy (water only), MIN, final r_work=0.1235 r_free=0.1499 r_work=0.1235 r_free=0.1499 | n_water=449 | time (s): 109.450 (total time: 153.020) Filter (q & B) r_work=0.1242 r_free=0.1504 | n_water=429 | time (s): 4.000 (total time: 157.020) Filter (dist only) r_work=0.1242 r_free=0.1504 | n_water=429 | time (s): 40.400 (total time: 197.420) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.878591 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1466.534500 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 0.1236 0.1529 0.0293 0.007 0.9 1.9 0.5 0.0 0 12.939 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.36 15.29 2.93 3.807 23.335 1466.535 0.015 12.06 14.93 2.88 4.233 23.128 1466.535 0.015 Individual atomic B min max mean iso aniso Overall: 8.82 115.13 23.29 2.60 193 1763 Protein: 8.82 115.13 17.74 2.61 0 1519 Water: 10.98 71.87 42.79 N/A 193 236 Other: 25.63 36.96 30.32 N/A 0 8 Chain A: 8.82 115.13 20.47 N/A 0 1763 Chain S: 16.64 69.01 49.08 N/A 193 0 Histogram: Values Number of atoms 8.82 - 19.45 1207 19.45 - 30.08 245 30.08 - 40.71 190 40.71 - 51.34 147 51.34 - 61.98 108 61.98 - 72.61 48 72.61 - 83.24 5 83.24 - 93.87 3 93.87 - 104.50 1 104.50 - 115.13 2 =========================== Idealize ADP of riding H ========================== r_work=0.1206 r_free=0.1494 r_work=0.1206 r_free=0.1493 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1206 r_free = 0.1493 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 = 0.1209 r_free = 0.1488 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.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1209 r_free= 0.1488 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.014004 | | target function (ls_wunit_k1) not normalized (work): 1166.442401 | | target function (ls_wunit_k1) not normalized (free): 102.994515 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1223 0.1209 0.1488 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1620 0.1616 0.1736 n_refl.: 87592 remove outliers: r(all,work,free)=0.1620 0.1616 0.1736 n_refl.: 87592 overall B=0.03 to atoms: r(all,work,free)=0.1625 0.1621 0.1739 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1220 0.1206 0.1482 n_refl.: 87592 remove outliers: r(all,work,free)=0.1219 0.1205 0.1482 n_refl.: 87590 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 93.75 85 5 0.3483 296.969 270.807 0.627 0.938 0.360 11.894-9.307 99.02 97 4 0.1601 478.031 474.938 0.975 0.939 0.337 9.237-7.194 100.00 213 7 0.1622 390.971 391.765 1.047 0.939 0.280 7.162-5.571 100.00 427 22 0.1486 293.402 289.526 1.008 0.939 0.241 5.546-4.326 100.00 867 58 0.0829 402.768 399.809 1.022 0.939 0.223 4.315-3.360 100.00 1859 96 0.0715 383.035 382.240 1.069 0.940 0.220 3.356-2.611 100.00 3867 181 0.0960 251.634 250.996 1.075 0.940 0.150 2.608-2.026 99.99 8198 413 0.0975 166.811 166.367 1.082 0.941 0.000 2.025-1.573 100.00 17313 902 0.1188 81.462 81.644 1.090 0.943 0.000 1.573-1.221 100.00 36679 1900 0.1625 36.123 35.633 1.075 0.946 0.000 1.221-1.150 99.97 13689 708 0.2350 22.760 21.320 1.032 0.948 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0431 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1205 r_free=0.1482 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.1206 r_free=0.1484 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1206 r_free=0.1484 | n_water=429 | time (s): 1.930 (total time: 1.930) Filter (dist) r_work=0.1205 r_free=0.1483 | n_water=427 | time (s): 40.040 (total time: 41.970) Filter (q & B) r_work=0.1205 r_free=0.1483 | n_water=427 | time (s): 1.280 (total time: 43.250) Compute maps r_work=0.1205 r_free=0.1483 | n_water=427 | time (s): 1.570 (total time: 44.820) Filter (map) r_work=0.1248 r_free=0.1495 | n_water=290 | time (s): 3.480 (total time: 48.300) Find peaks r_work=0.1248 r_free=0.1495 | n_water=290 | time (s): 0.520 (total time: 48.820) Add new water r_work=0.1376 r_free=0.1617 | n_water=477 | time (s): 3.610 (total time: 52.430) Refine new water occ: r_work=0.1278 r_free=0.1531 adp: r_work=0.1279 r_free=0.1533 occ: r_work=0.1256 r_free=0.1510 adp: r_work=0.1254 r_free=0.1510 occ: r_work=0.1240 r_free=0.1497 adp: r_work=0.1233 r_free=0.1493 ADP+occupancy (water only), MIN, final r_work=0.1233 r_free=0.1493 r_work=0.1233 r_free=0.1493 | n_water=477 | time (s): 196.170 (total time: 248.600) Filter (q & B) r_work=0.1236 r_free=0.1494 | n_water=448 | time (s): 2.820 (total time: 251.420) Filter (dist only) r_work=0.1236 r_free=0.1493 | n_water=447 | time (s): 38.010 (total time: 289.430) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.035679 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 48.644711 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 0.1239 0.1451 0.0212 0.006 0.9 1.6 0.5 0.0 0 1.018 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.39 14.51 2.12 3.639 22.223 48.645 3.728 12.21 14.06 1.85 4.233 22.009 48.645 3.654 Individual atomic B min max mean iso aniso Overall: 9.24 110.16 21.74 2.33 215 1759 Protein: 9.24 110.16 17.25 2.33 0 1519 Water: 11.64 70.51 36.92 N/A 215 232 Other: 20.66 32.09 26.17 N/A 0 8 Chain A: 9.24 110.16 19.90 N/A 0 1759 Chain S: 15.61 61.04 36.75 N/A 215 0 Histogram: Values Number of atoms 9.24 - 19.33 1236 19.33 - 29.43 271 29.43 - 39.52 215 39.52 - 49.61 141 49.61 - 59.70 78 59.70 - 69.79 20 69.79 - 79.88 7 79.88 - 89.98 3 89.98 - 100.07 1 100.07 - 110.16 2 =========================== Idealize ADP of riding H ========================== r_work=0.1221 r_free=0.1406 r_work=0.1222 r_free=0.1407 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1222 r_free = 0.1407 target_work(ml) = 3.654 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1214 r_free = 0.1403 target_work(ml) = 3.651 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87590 (all), 4.90 % free)------------| | | | r_work= 0.1214 r_free= 0.1403 coordinate error (max.-lik. estimate): 0.06 A | | | | normalized target function (ml) (work): 3.651403 | | target function (ml) not normalized (work): 304139.944231 | | target function (ml) not normalized (free): 16070.555171 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1223 0.1214 0.1403 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1553 0.1551 0.1613 n_refl.: 87590 remove outliers: r(all,work,free)=0.1553 0.1551 0.1613 n_refl.: 87590 overall B=-0.02 to atoms: r(all,work,free)=0.1549 0.1547 0.1610 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1214 0.1205 0.1386 n_refl.: 87590 remove outliers: r(all,work,free)=0.1212 0.1203 0.1386 n_refl.: 87585 ======================== 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 0.3959 296.940 265.438 0.494 0.999 0.357 11.894-9.307 98.04 96 4 0.2433 478.155 457.894 0.845 1.001 0.340 9.237-7.194 99.09 211 7 0.2363 385.522 384.817 0.950 1.002 0.180 7.162-5.571 100.00 427 22 0.2057 293.402 282.563 0.912 1.002 0.163 5.546-4.326 100.00 867 58 0.1102 402.768 398.165 0.950 1.002 0.160 4.315-3.360 100.00 1859 96 0.0925 383.035 380.802 0.996 1.002 0.160 3.356-2.611 100.00 3867 181 0.1155 251.634 249.696 1.000 1.002 0.062 2.608-2.026 99.99 8198 413 0.1056 166.811 165.839 1.012 1.001 0.000 2.025-1.573 100.00 17313 902 0.1023 81.462 81.634 1.028 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1295 36.123 35.716 1.023 0.999 0.000 1.221-1.150 99.97 13689 708 0.2127 22.760 21.401 0.982 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0575 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1203 r_free=0.1386 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1203 r_free=0.1386 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1203 r_free=0.1386 | n_water=447 | time (s): 1.660 (total time: 1.660) Filter (dist) r_work=0.1203 r_free=0.1386 | n_water=447 | time (s): 38.450 (total time: 40.110) Filter (q & B) r_work=0.1203 r_free=0.1386 | n_water=446 | time (s): 3.540 (total time: 43.650) Compute maps r_work=0.1203 r_free=0.1386 | n_water=446 | time (s): 1.740 (total time: 45.390) Filter (map) r_work=0.1230 r_free=0.1393 | n_water=312 | time (s): 2.940 (total time: 48.330) Find peaks r_work=0.1230 r_free=0.1393 | n_water=312 | time (s): 0.560 (total time: 48.890) Add new water r_work=0.1299 r_free=0.1468 | n_water=466 | time (s): 3.110 (total time: 52.000) Refine new water occ: r_work=0.1224 r_free=0.1402 adp: r_work=0.1224 r_free=0.1402 occ: r_work=0.1209 r_free=0.1388 adp: r_work=0.1207 r_free=0.1387 occ: r_work=0.1197 r_free=0.1379 adp: r_work=0.1193 r_free=0.1376 ADP+occupancy (water only), MIN, final r_work=0.1193 r_free=0.1376 r_work=0.1193 r_free=0.1376 | n_water=466 | time (s): 234.730 (total time: 286.730) Filter (q & B) r_work=0.1199 r_free=0.1375 | n_water=434 | time (s): 2.550 (total time: 289.280) Filter (dist only) r_work=0.1199 r_free=0.1375 | n_water=434 | time (s): 36.360 (total time: 325.640) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.963562 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 43.488277 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 0.1202 0.1376 0.0174 0.006 0.9 1.9 0.5 0.0 0 0.982 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.02 13.76 1.74 3.431 21.493 43.488 3.639 11.91 13.70 1.79 3.692 21.417 43.488 3.625 Individual atomic B min max mean iso aniso Overall: 9.31 106.15 21.30 2.17 206 1755 Protein: 9.31 106.15 17.06 2.17 0 1519 Water: 11.63 69.60 36.06 N/A 206 228 Other: 18.20 29.35 24.09 N/A 0 8 Chain A: 9.31 106.15 19.60 N/A 0 1755 Chain S: 16.14 60.53 35.73 N/A 206 0 Histogram: Values Number of atoms 9.31 - 19.00 1234 19.00 - 28.68 281 28.68 - 38.36 195 38.36 - 48.05 142 48.05 - 57.73 71 57.73 - 67.41 24 67.41 - 77.10 9 77.10 - 86.78 2 86.78 - 96.46 1 96.46 - 106.15 2 =========================== Idealize ADP of riding H ========================== r_work=0.1191 r_free=0.1370 r_work=0.1192 r_free=0.1371 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1192 r_free = 0.1371 target_work(ml) = 3.625 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1187 r_free = 0.1369 target_work(ml) = 3.624 | | 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.=87585 (all), 4.90 % free)------------| | | | r_work= 0.1187 r_free= 0.1369 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.623687 | | target function (ml) not normalized (work): 301813.300933 | | target function (ml) not normalized (free): 15940.956480 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1196 0.1187 0.1369 n_refl.: 87585 re-set all scales: r(all,work,free)=0.1539 0.1540 0.1561 n_refl.: 87585 remove outliers: r(all,work,free)=0.1539 0.1540 0.1561 n_refl.: 87585 overall B=-0.02 to atoms: r(all,work,free)=0.1535 0.1536 0.1558 n_refl.: 87585 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1188 0.1371 n_refl.: 87585 remove outliers: r(all,work,free)=0.1193 0.1184 0.1371 n_refl.: 87577 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.3915 289.089 260.027 0.481 0.947 0.293 11.894-9.307 96.08 94 4 0.2397 473.343 456.681 0.891 0.949 0.267 9.237-7.194 97.73 208 7 0.2472 383.602 376.588 0.969 0.949 0.172 7.162-5.571 100.00 427 22 0.2193 293.402 282.059 0.949 0.950 0.142 5.546-4.326 100.00 867 58 0.1126 402.768 398.182 1.004 0.950 0.140 4.315-3.360 100.00 1859 96 0.0941 383.035 380.633 1.050 0.950 0.140 3.356-2.611 100.00 3867 181 0.1152 251.634 249.672 1.056 0.950 0.110 2.608-2.026 99.99 8198 413 0.1030 166.811 165.844 1.068 0.949 0.000 2.025-1.573 100.00 17313 902 0.0980 81.462 81.718 1.085 0.948 0.000 1.573-1.221 100.00 36679 1900 0.1247 36.123 35.747 1.080 0.947 0.000 1.221-1.150 99.97 13689 708 0.2128 22.760 21.381 1.037 0.945 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0605 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1184 r_free=0.1371 After: r_work=0.1185 r_free=0.1370 ================================== NQH flips ================================== r_work=0.1185 r_free=0.1370 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=0.1185 r_free=0.1370 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1185 r_free=0.1370 | n_water=434 | time (s): 1.540 (total time: 1.540) Filter (dist) r_work=0.1185 r_free=0.1370 | n_water=433 | time (s): 36.250 (total time: 37.790) Filter (q & B) r_work=0.1186 r_free=0.1371 | n_water=430 | time (s): 2.910 (total time: 40.700) Compute maps r_work=0.1186 r_free=0.1371 | n_water=430 | time (s): 1.660 (total time: 42.360) Filter (map) r_work=0.1213 r_free=0.1377 | n_water=319 | time (s): 2.780 (total time: 45.140) Find peaks r_work=0.1213 r_free=0.1377 | n_water=319 | time (s): 0.460 (total time: 45.600) Add new water r_work=0.1273 r_free=0.1435 | n_water=490 | time (s): 3.220 (total time: 48.820) Refine new water occ: r_work=0.1201 r_free=0.1380 adp: r_work=0.1201 r_free=0.1380 occ: r_work=0.1188 r_free=0.1372 adp: r_work=0.1187 r_free=0.1371 occ: r_work=0.1178 r_free=0.1366 adp: r_work=0.1174 r_free=0.1364 ADP+occupancy (water only), MIN, final r_work=0.1174 r_free=0.1364 r_work=0.1174 r_free=0.1364 | n_water=490 | time (s): 219.730 (total time: 268.550) Filter (q & B) r_work=0.1183 r_free=0.1365 | n_water=448 | time (s): 2.820 (total time: 271.370) Filter (dist only) r_work=0.1183 r_free=0.1364 | n_water=447 | time (s): 36.720 (total time: 308.090) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.893935 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 39.535631 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1214 0.1391 0.0177 0.007 1.0 1.9 0.5 0.0 0 0.947 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.14 13.91 1.77 3.319 21.263 39.536 3.634 12.21 13.96 1.75 3.701 21.157 39.536 3.631 Individual atomic B min max mean iso aniso Overall: 9.29 101.39 21.05 1.99 221 1753 Protein: 9.29 101.39 16.76 2.00 0 1519 Water: 11.62 68.42 35.62 N/A 221 226 Other: 17.91 25.53 22.09 N/A 0 8 Chain A: 9.29 101.39 19.24 N/A 0 1753 Chain S: 14.82 60.31 35.40 N/A 221 0 Histogram: Values Number of atoms 9.29 - 18.50 1228 18.50 - 27.71 276 27.71 - 36.92 205 36.92 - 46.13 152 46.13 - 55.34 77 55.34 - 64.55 19 64.55 - 73.76 12 73.76 - 82.97 2 82.97 - 92.18 1 92.18 - 101.39 2 =========================== Idealize ADP of riding H ========================== r_work=0.1221 r_free=0.1396 r_work=0.1221 r_free=0.1396 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1221 r_free = 0.1396 target_work(ml) = 3.631 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1215 r_free = 0.1390 target_work(ml) = 3.630 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87577 (all), 4.91 % free)------------| | | | r_work= 0.1215 r_free= 0.1390 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.629621 | | target function (ml) not normalized (work): 302278.470449 | | target function (ml) not normalized (free): 15970.598528 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2919 171 0.1420 0.1434 5.6728 5.6524| | 2: 3.57 - 2.84 1.00 2888 124 0.1155 0.1410 5.2082 5.2523| | 3: 2.83 - 2.48 1.00 2820 163 0.1245 0.1371 5.0158 5.0367| | 4: 2.47 - 2.25 1.00 2825 136 0.1058 0.1192 4.723 4.7705| | 5: 2.25 - 2.09 1.00 2756 127 0.1012 0.1171 4.6602 4.7332| | 6: 2.09 - 1.97 1.00 2846 113 0.0993 0.1167 4.3631 4.4823| | 7: 1.97 - 1.87 1.00 2787 165 0.1020 0.1254 4.0967 4.2054| | 8: 1.87 - 1.79 1.00 2789 144 0.1045 0.1245 4.0125 4.0949| | 9: 1.79 - 1.72 1.00 2745 138 0.0984 0.1341 3.7388 3.9067| | 10: 1.72 - 1.66 1.00 2831 160 0.1018 0.1299 3.6532 3.7999| | 11: 1.66 - 1.61 1.00 2712 147 0.0981 0.1100 3.5853 3.626| | 12: 1.61 - 1.56 1.00 2773 144 0.0946 0.1200 3.3655 3.5171| | 13: 1.56 - 1.52 1.00 2745 130 0.0995 0.1063 3.3512 3.4313| | 14: 1.52 - 1.48 1.00 2803 134 0.1005 0.1103 3.2735 3.3235| | 15: 1.48 - 1.45 1.00 2738 128 0.1038 0.1356 3.1804 3.3461| | 16: 1.45 - 1.42 1.00 2756 161 0.1094 0.1243 3.1611 3.2404| | 17: 1.42 - 1.39 1.00 2785 139 0.1132 0.1311 3.1196 3.2378| | 18: 1.39 - 1.36 1.00 2741 179 0.1160 0.1409 3.0891 3.2734| | 19: 1.36 - 1.34 1.00 2807 134 0.1230 0.1622 3.0989 3.2775| | 20: 1.34 - 1.32 1.00 2696 147 0.1331 0.1484 3.0925 3.1322| | 21: 1.32 - 1.30 1.00 2785 112 0.1426 0.1594 3.0917 3.1493| | 22: 1.29 - 1.27 1.00 2704 152 0.1492 0.1978 3.09 3.3042| | 23: 1.27 - 1.26 1.00 2802 156 0.1574 0.1892 3.1031 3.2133| | 24: 1.26 - 1.24 1.00 2744 132 0.1626 0.1734 3.0943 3.1892| | 25: 1.24 - 1.22 1.00 2733 148 0.1796 0.2298 3.11 3.2831| | 26: 1.22 - 1.21 1.00 2727 135 0.1858 0.1787 3.1209 3.1989| | 27: 1.21 - 1.19 1.00 2814 148 0.2018 0.2109 3.1423 3.1579| | 28: 1.19 - 1.18 1.00 2671 147 0.2153 0.2319 3.1412 3.1659| | 29: 1.18 - 1.16 1.00 2800 134 0.2212 0.2363 3.1251 3.2183| | 30: 1.16 - 1.15 1.00 2739 148 0.2379 0.2510 3.1142 3.1705| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.58 2919 171 0.94 9.18 1.00 0.97 6286.75| | 2: 3.57 - 2.84 2888 124 0.92 13.45 1.01 0.97 6286.75| | 3: 2.83 - 2.48 2820 163 0.89 17.54 0.99 0.98 5277.13| | 4: 2.47 - 2.25 2825 136 0.91 14.66 1.00 0.98 2673.65| | 5: 2.25 - 2.09 2756 127 0.89 16.89 1.01 0.98 2673.65| | 6: 2.09 - 1.97 2846 113 0.91 13.89 1.02 0.98 1583.13| | 7: 1.97 - 1.87 2787 165 0.94 11.07 1.02 0.97 653.07| | 8: 1.87 - 1.79 2789 144 0.91 14.73 1.00 0.97 653.07| | 9: 1.79 - 1.72 2745 138 0.93 11.71 0.98 0.97 352.55| | 10: 1.72 - 1.66 2831 160 0.93 12.56 0.98 0.97 292.36| | 11: 1.66 - 1.61 2712 147 0.92 13.21 0.98 0.97 278.84| | 12: 1.61 - 1.56 2773 144 0.95 9.75 0.99 0.97 151.33| | 13: 1.56 - 1.52 2745 130 0.94 11.35 1.02 0.97 151.33| | 14: 1.52 - 1.48 2803 134 0.94 11.45 1.02 0.97 134.72| | 15: 1.48 - 1.45 2738 128 0.95 10.52 1.01 0.98 104.30| | 16: 1.45 - 1.42 2756 161 0.94 11.73 1.02 0.98 104.30| | 17: 1.42 - 1.39 2785 139 0.94 11.54 1.01 0.98 93.98| | 18: 1.39 - 1.36 2741 179 0.94 11.84 1.01 0.98 88.01| | 19: 1.36 - 1.34 2807 134 0.94 12.39 1.00 0.98 88.01| | 20: 1.34 - 1.32 2696 147 0.94 12.53 0.99 0.97 82.85| | 21: 1.32 - 1.30 2785 112 0.93 13.45 0.99 0.96 82.48| | 22: 1.29 - 1.27 2704 152 0.93 14.03 0.99 0.96 82.66| | 23: 1.27 - 1.26 2802 156 0.92 14.95 0.98 0.95 83.55| | 24: 1.26 - 1.24 2744 132 0.92 15.05 0.97 0.95 83.55| | 25: 1.24 - 1.22 2733 148 0.91 16.48 0.96 0.94 85.12| | 26: 1.22 - 1.21 2727 135 0.90 18.19 1.02 0.93 86.87| | 27: 1.21 - 1.19 2814 148 0.89 18.85 1.02 0.93 86.87| | 28: 1.19 - 1.18 2671 147 0.88 20.41 1.01 0.93 90.31| | 29: 1.18 - 1.16 2800 134 0.88 20.70 0.99 0.93 91.61| | 30: 1.16 - 1.15 2739 148 0.86 22.14 0.98 0.93 91.61| |alpha: min = 0.93 max = 0.98 mean = 0.96| |beta: min = 82.48 max = 6286.75 mean = 986.39| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 90.00 mean = 14.19| |phase err.(test): min = 0.00 max = 89.79 mean = 14.30| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1224 0.1215 0.1390 n_refl.: 87577 re-set all scales: r(all,work,free)=0.1540 0.1540 0.1572 n_refl.: 87577 remove outliers: r(all,work,free)=0.1540 0.1540 0.1572 n_refl.: 87577 overall B=-0.02 to atoms: r(all,work,free)=0.1535 0.1535 0.1569 n_refl.: 87577 bulk-solvent and scaling: r(all,work,free)=0.1224 0.1215 0.1392 n_refl.: 87577 remove outliers: r(all,work,free)=0.1223 0.1214 0.1392 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 0.4057 289.089 261.362 0.445 0.998 0.283 11.894-9.307 94.12 92 4 0.2455 473.549 457.877 0.845 1.000 0.224 9.237-7.194 97.27 207 7 0.2492 383.130 377.344 0.911 1.000 0.170 7.162-5.571 100.00 427 22 0.2214 293.402 281.752 0.899 1.001 0.137 5.546-4.326 100.00 867 58 0.1191 402.768 397.095 0.951 1.001 0.124 4.315-3.360 100.00 1859 96 0.1006 383.035 380.110 0.997 1.001 0.123 3.356-2.611 100.00 3867 181 0.1214 251.634 249.367 1.002 1.001 0.053 2.608-2.026 99.99 8198 413 0.1064 166.811 165.759 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.1001 81.462 81.742 1.028 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1241 36.123 35.785 1.022 1.001 0.000 1.221-1.150 99.97 13689 708 0.2117 22.760 21.390 0.978 1.001 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0644 ================= 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 : 0.2607 0.1968 0.081 5.341 8.8 119.3 19.9 258 0.000 1_bss: 0.1641 0.1795 0.081 5.341 9.1 119.5 20.1 258 0.000 1_settarget: 0.1641 0.1795 0.081 5.341 9.1 119.5 20.1 258 0.000 1_nqh: 0.1641 0.1795 0.081 5.341 9.1 119.5 20.1 258 0.000 1_weight: 0.1641 0.1795 0.081 5.341 9.1 119.5 20.1 258 0.000 1_xyzrec: 0.1214 0.1461 0.007 0.939 9.1 119.5 20.1 258 0.127 1_adp: 0.1249 0.1546 0.007 0.939 8.5 119.0 21.1 258 0.127 1_regHadp: 0.1254 0.1550 0.007 0.939 8.5 119.0 21.1 258 0.127 1_occ: 0.1254 0.1552 0.007 0.939 8.5 119.0 21.1 258 0.127 2_bss: 0.1251 0.1547 0.007 0.939 8.6 119.1 21.3 258 0.127 2_settarget: 0.1251 0.1547 0.007 0.939 8.6 119.1 21.3 258 0.127 2_updatecdl: 0.1251 0.1547 0.007 0.948 8.6 119.1 21.3 258 0.127 2_nqh: 0.1253 0.1548 0.007 0.948 8.6 119.1 21.3 258 0.130 2_sol: 0.1242 0.1504 0.007 0.948 8.6 119.1 23.7 429 n/a 2_weight: 0.1242 0.1504 0.007 0.948 8.6 119.1 23.7 429 n/a 2_xyzrec: 0.1236 0.1529 0.007 0.876 8.6 119.1 23.7 429 n/a 2_adp: 0.1206 0.1494 0.007 0.876 8.8 115.1 23.3 429 n/a 2_regHadp: 0.1206 0.1493 0.007 0.876 8.8 115.1 23.3 429 n/a 2_occ: 0.1209 0.1488 0.007 0.876 8.8 115.1 23.3 429 n/a 3_bss: 0.1205 0.1482 0.007 0.876 8.8 115.2 23.3 429 n/a 3_settarget: 0.1205 0.1482 0.007 0.876 8.8 115.2 23.3 429 n/a 3_updatecdl: 0.1205 0.1482 0.007 0.878 8.8 115.2 23.3 429 n/a 3_nqh: 0.1206 0.1484 0.007 0.878 8.8 115.2 23.3 429 n/a 3_sol: 0.1236 0.1493 0.007 0.878 8.8 115.2 22.1 447 n/a 3_weight: 0.1236 0.1493 0.007 0.878 8.8 115.2 22.1 447 n/a 3_xyzrec: 0.1239 0.1451 0.006 0.920 8.8 115.2 22.1 447 n/a 3_adp: 0.1221 0.1406 0.006 0.920 9.2 110.2 21.7 447 n/a 3_regHadp: 0.1222 0.1407 0.006 0.920 9.2 110.2 21.7 447 n/a 3_occ: 0.1214 0.1403 0.006 0.920 9.2 110.2 21.7 447 n/a 4_bss: 0.1203 0.1386 0.006 0.920 9.2 110.1 21.7 447 n/a 4_settarget: 0.1203 0.1386 0.006 0.920 9.2 110.1 21.7 447 n/a 4_updatecdl: 0.1203 0.1386 0.006 0.919 9.2 110.1 21.7 447 n/a 4_nqh: 0.1203 0.1386 0.006 0.919 9.2 110.1 21.7 447 n/a 4_sol: 0.1199 0.1375 0.006 0.919 9.2 110.1 21.4 434 n/a 4_weight: 0.1199 0.1375 0.006 0.919 9.2 110.1 21.4 434 n/a 4_xyzrec: 0.1202 0.1376 0.006 0.949 9.2 110.1 21.4 434 n/a 4_adp: 0.1191 0.1370 0.006 0.949 9.3 106.1 21.3 434 n/a 4_regHadp: 0.1192 0.1371 0.006 0.949 9.3 106.1 21.3 434 n/a 4_occ: 0.1187 0.1369 0.006 0.949 9.3 106.1 21.3 434 n/a 5_bss: 0.1184 0.1371 0.006 0.949 9.3 106.1 21.3 434 n/a 5_settarget: 0.1184 0.1371 0.006 0.949 9.3 106.1 21.3 434 n/a 5_updatecdl: 0.1184 0.1371 0.006 0.949 9.3 106.1 21.3 434 n/a 5_setrh: 0.1185 0.1370 0.006 0.949 9.3 106.1 21.3 434 n/a 5_nqh: 0.1185 0.1370 0.006 0.949 9.3 106.1 21.3 434 n/a 5_sol: 0.1183 0.1364 0.006 0.949 9.3 106.1 21.2 447 n/a 5_weight: 0.1183 0.1364 0.006 0.949 9.3 106.1 21.2 447 n/a 5_xyzrec: 0.1214 0.1391 0.007 1.048 9.3 106.1 21.2 447 n/a 5_adp: 0.1221 0.1396 0.007 1.048 9.3 101.4 21.1 447 n/a 5_regHadp: 0.1221 0.1396 0.007 1.048 9.3 101.4 21.1 447 n/a 5_occ: 0.1215 0.1390 0.007 1.048 9.3 101.4 21.1 447 n/a end: 0.1214 0.1392 0.007 1.048 9.3 101.4 21.0 447 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_3081210_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_3081210_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.9200 Refinement macro-cycles (run) : 3622.8100 Write final files (write_after_run_outputs) : 57.4600 Total : 3685.1900 Total CPU time: 62.03 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:12:58 PST -0800 (1735452778.02 s) Start R-work = 0.1641, R-free = 0.1795 Final R-work = 0.1214, R-free = 0.1392 =============================================================================== Job complete usr+sys time: 3817.16 seconds wall clock time: 68 minutes 4.56 seconds (4084.56 seconds total)