Starting phenix.refine on Fri Dec 27 17:58:27 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.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3081210.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3081210.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.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 } pdb_interpretation { nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } 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 } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } 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: 2.05, per 1000 atoms: 0.61 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: 0.42 Conformation dependent library (CDL) restraints added in 143.0 milliseconds Time building geometry restraints manager: 0.53 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 1.850 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.777 1.850 nonbonded pdb=" HE2 HIS A 126 " pdb=" O PRO A 184 " model vdw sym.op. 1.804 1.850 x-y,-y,-z-4/3 nonbonded pdb=" H LEU A 10 " pdb=" O ALA A 36 " model vdw 1.833 1.850 ... (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 nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } 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 } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } 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 = 26.304007 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 0.1742 0.1856 0.0113 0.001 0.4 4.5 0.0 0.0 0 0.125 0.1595 0.1726 0.0131 0.001 0.4 3.8 0.0 0.0 0 0.250 0.1444 0.1608 0.0164 0.002 0.5 3.8 0.0 0.0 0 0.500 0.1408 0.1591 0.0183 0.002 0.5 3.5 0.0 0.0 0 0.750 0.1353 0.1552 0.0199 0.002 0.5 3.5 0.0 0.0 0 1.000 0.1353 0.1549 0.0196 0.002 0.5 3.5 0.0 0.0 0 1.000 0.1302 0.1523 0.0221 0.002 0.6 3.5 0.5 0.0 0 2.000 0.1268 0.1494 0.0226 0.003 0.6 3.8 0.5 0.0 0 3.000 0.1260 0.1490 0.0230 0.003 0.7 3.8 0.5 0.0 0 4.000 0.1250 0.1481 0.0231 0.004 0.7 4.2 0.5 0.0 0 5.000 0.1243 0.1475 0.0232 0.004 0.8 3.8 0.5 0.0 0 6.000 0.1237 0.1466 0.0229 0.005 0.8 3.5 0.5 0.0 0 7.000 0.1238 0.1472 0.0234 0.005 0.8 3.8 0.5 0.0 0 8.000 0.1234 0.1468 0.0234 0.006 0.9 4.5 0.5 0.0 0 9.000 0.1232 0.1470 0.0238 0.006 0.9 4.5 0.5 0.0 0 10.000 0.1231 0.1475 0.0244 0.007 0.9 3.8 0.5 0.6 0 11.000 0.1228 0.1472 0.0245 0.007 0.9 4.2 0.5 0.6 0 12.000 0.1227 0.1480 0.0253 0.008 1.0 4.5 0.5 0.6 0 13.152 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1237 0.1466 0.0229 0.005 0.8 3.5 0.5 0.0 0 7.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.37 14.66 2.29 3.013 19.074 2012.685 0.018 12.37 14.66 2.28 2.972 19.074 60.381 0.018 12.44 14.64 2.21 2.657 19.073 251.586 0.018 12.82 15.45 2.63 2.972 19.384 1006.342 0.017 12.64 15.55 2.90 3.407 19.689 2012.685 0.016 12.46 15.43 2.96 3.239 19.589 3019.027 0.016 12.45 15.52 3.07 3.432 19.684 4025.369 0.015 12.42 15.49 3.08 3.392 19.650 5031.711 0.015 12.32 15.42 3.10 3.298 19.602 6038.054 0.015 12.31 15.45 3.14 3.378 19.639 7044.396 0.015 12.30 15.50 3.20 3.499 19.698 8050.738 0.015 12.27 15.48 3.21 3.495 19.680 9057.081 0.015 12.28 15.52 3.25 3.413 19.624 10063.423 0.015 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 251.586 Accepted refinement result: 12.44 14.64 2.21 2.657 19.073 251.586 0.018 Individual atomic B min max mean iso aniso Overall: 9.06 119.45 20.10 3.29 0 1785 Protein: 9.06 114.89 17.01 3.29 0 1519 Water: 11.48 119.45 38.24 N/A 0 258 Other: 19.74 26.62 22.09 N/A 0 8 Chain A: 9.06 119.45 20.10 N/A 0 1785 Histogram: Values Number of atoms 9.06 - 20.10 1270 20.10 - 31.14 229 31.14 - 42.18 125 42.18 - 53.22 94 53.22 - 64.26 42 64.26 - 75.30 11 75.30 - 86.33 7 86.33 - 97.37 4 97.37 - 108.41 1 108.41 - 119.45 2 =========================== Idealize ADP of riding H ========================== r_work=0.1244 r_free=0.1464 r_work=0.1245 r_free=0.1468 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1245 r_free = 0.1468 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1239 r_free = 0.1461 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.22 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= 0.1239 r_free= 0.1461 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.017189 | | target function (ls_wunit_k1) not normalized (work): 1431.825426 | | target function (ls_wunit_k1) not normalized (free): 108.076150 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1250 0.1239 0.1461 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1682 0.1684 0.1693 n_refl.: 87593 remove outliers: r(all,work,free)=0.1682 0.1684 0.1693 n_refl.: 87593 overall B=0.03 to atoms: r(all,work,free)=0.1688 0.1689 0.1697 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1247 0.1236 0.1454 n_refl.: 87593 remove outliers: r(all,work,free)=0.1247 0.1236 0.1454 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 96.88 88 5 0.3598 303.737 279.627 0.660 1.003 0.390 11.894-9.307 99.02 97 4 0.1645 482.472 470.221 0.922 1.003 0.381 9.237-7.194 100.00 213 7 0.1924 394.603 387.524 0.963 1.003 0.350 7.162-5.571 100.00 427 22 0.1838 296.128 290.084 0.936 1.003 0.263 5.546-4.326 100.00 867 58 0.1020 406.510 403.626 0.965 1.003 0.230 4.315-3.360 100.00 1859 96 0.0884 386.594 385.350 1.007 1.003 0.180 3.356-2.611 100.00 3867 181 0.1180 253.972 252.814 1.009 1.002 0.120 2.608-2.026 99.99 8198 413 0.1026 168.360 167.609 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1119 82.218 82.403 1.027 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1462 36.459 35.957 1.020 0.996 0.000 1.221-1.150 99.97 13689 708 0.2263 22.972 21.449 0.983 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0458 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1236 r_free=0.1454 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=0.1238 r_free=0.1456 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1238 r_free=0.1456 | n_water=258 | time (s): 2.010 (total time: 2.010) Filter (dist) r_work=0.1245 r_free=0.1455 | n_water=251 | time (s): 22.000 (total time: 24.010) Filter (q & B) r_work=0.1247 r_free=0.1455 | n_water=248 | time (s): 3.090 (total time: 27.100) Compute maps r_work=0.1247 r_free=0.1455 | n_water=248 | time (s): 1.490 (total time: 28.590) Filter (map) r_work=0.1274 r_free=0.1461 | n_water=221 | time (s): 3.060 (total time: 31.650) Find peaks r_work=0.1274 r_free=0.1461 | n_water=221 | time (s): 0.650 (total time: 32.300) Add new water r_work=0.1423 r_free=0.1624 | n_water=422 | time (s): 2.490 (total time: 34.790) Refine new water occ: r_work=0.1322 r_free=0.1515 adp: r_work=0.1239 r_free=0.1441 occ: r_work=0.1250 r_free=0.1442 adp: r_work=0.1218 r_free=0.1416 occ: r_work=0.1219 r_free=0.1414 adp: r_work=0.1211 r_free=0.1407 ADP+occupancy (water only), MIN, final r_work=0.1211 r_free=0.1407 r_work=0.1211 r_free=0.1407 | n_water=422 | time (s): 66.100 (total time: 100.890) Filter (q & B) r_work=0.1216 r_free=0.1406 | n_water=408 | time (s): 3.460 (total time: 104.350) Filter (dist only) r_work=0.1216 r_free=0.1405 | n_water=407 | time (s): 33.510 (total time: 137.860) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 28.547116 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1485.150295 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 0.1693 0.1803 0.0110 0.001 0.4 7.4 0.0 0.0 0 0.125 0.1549 0.1680 0.0132 0.001 0.4 6.4 0.0 0.0 0 0.250 0.1424 0.1574 0.0151 0.001 0.4 6.1 0.0 0.0 0 0.500 0.1366 0.1527 0.0161 0.002 0.4 5.8 0.0 0.0 0 0.750 0.1343 0.1517 0.0174 0.002 0.5 5.4 0.0 0.0 0 1.000 0.1335 0.1507 0.0172 0.002 0.5 5.4 0.0 0.0 0 1.000 0.1267 0.1460 0.0193 0.002 0.5 4.8 0.5 0.0 0 2.000 0.1240 0.1442 0.0203 0.003 0.6 5.1 0.5 0.0 0 3.000 0.1222 0.1432 0.0211 0.003 0.7 4.8 0.5 0.0 0 4.000 0.1218 0.1436 0.0218 0.004 0.7 4.2 0.5 0.0 0 5.000 0.1208 0.1429 0.0221 0.004 0.7 5.1 0.5 0.0 0 6.000 0.1205 0.1425 0.0220 0.005 0.8 4.2 0.5 0.0 0 7.000 0.1201 0.1419 0.0219 0.005 0.8 4.8 0.5 0.0 0 8.000 0.1198 0.1419 0.0221 0.006 0.8 4.2 0.5 0.0 0 9.000 0.1195 0.1416 0.0221 0.006 0.8 5.1 0.5 0.0 0 10.000 0.1195 0.1418 0.0224 0.007 0.9 4.5 0.5 0.0 0 11.000 0.1196 0.1416 0.0221 0.007 0.9 5.1 0.5 0.0 0 12.000 0.1193 0.1414 0.0221 0.008 0.9 5.1 0.5 0.0 0 13.000 0.1192 0.1417 0.0226 0.008 0.9 5.8 0.5 0.0 0 14.274 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1193 0.1414 0.0221 0.008 0.9 5.1 0.5 0.0 0 13.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.93 14.14 2.21 3.766 21.709 1485.150 0.016 11.93 14.14 2.21 3.766 21.709 44.555 0.016 11.93 14.14 2.21 3.766 21.709 185.644 0.016 12.08 14.56 2.48 3.630 21.711 742.575 0.015 12.10 14.88 2.78 3.555 21.776 1485.150 0.015 11.98 14.86 2.88 3.453 22.043 2227.725 0.014 11.84 14.76 2.92 3.469 22.076 2970.301 0.014 11.77 14.79 3.02 3.505 21.895 3712.876 0.014 11.78 14.73 2.95 3.507 22.051 4455.451 0.014 11.74 14.79 3.05 3.519 22.013 5198.026 0.014 11.73 14.85 3.12 3.540 22.021 5940.601 0.014 11.69 14.82 3.14 3.549 21.994 6683.176 0.014 11.67 14.76 3.09 3.572 22.089 7425.751 0.014 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 44.555 Accepted refinement result: 11.93 14.14 2.21 3.766 21.709 44.555 0.016 Individual atomic B min max mean iso aniso Overall: 9.09 114.92 22.05 3.29 186 1748 Protein: 9.09 114.92 17.04 3.29 0 1519 Water: 11.51 76.69 40.76 N/A 186 221 Other: 19.77 26.65 22.12 N/A 0 8 Chain A: 9.09 114.92 19.39 N/A 0 1748 Chain S: 18.73 60.00 47.01 N/A 186 0 Histogram: Values Number of atoms 9.09 - 19.67 1256 19.67 - 30.26 246 30.26 - 40.84 164 40.84 - 51.42 131 51.42 - 62.01 114 62.01 - 72.59 11 72.59 - 83.17 6 83.17 - 93.76 4 93.76 - 104.34 0 104.34 - 114.92 2 =========================== Idealize ADP of riding H ========================== r_work=0.1193 r_free=0.1414 r_work=0.1193 r_free=0.1414 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1193 r_free = 0.1414 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1194 r_free = 0.1421 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1194 r_free= 0.1421 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.015179 | | target function (ls_wunit_k1) not normalized (work): 1264.358155 | | target function (ls_wunit_k1) not normalized (free): 105.225553 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1205 0.1194 0.1421 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1605 0.1604 0.1654 n_refl.: 87593 remove outliers: r(all,work,free)=0.1605 0.1604 0.1654 n_refl.: 87593 overall B=0.01 to atoms: r(all,work,free)=0.1607 0.1605 0.1656 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1201 0.1190 0.1415 n_refl.: 87593 remove outliers: r(all,work,free)=0.1200 0.1189 0.1415 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 0.3382 299.776 277.090 0.609 1.003 0.370 11.894-9.307 99.02 97 4 0.1539 482.472 475.219 0.916 1.003 0.360 9.237-7.194 100.00 213 7 0.1670 394.603 394.752 0.976 1.003 0.290 7.162-5.571 100.00 427 22 0.1632 296.128 290.861 0.934 1.003 0.233 5.546-4.326 100.00 867 58 0.0897 406.510 403.401 0.960 1.003 0.210 4.315-3.360 100.00 1859 96 0.0793 386.594 385.538 1.006 1.002 0.200 3.356-2.611 100.00 3867 181 0.1086 253.972 253.054 1.011 1.002 0.130 2.608-2.026 99.99 8198 413 0.1016 168.360 167.813 1.020 1.001 0.000 2.025-1.573 100.00 17313 902 0.1105 82.218 82.441 1.030 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1446 36.459 35.991 1.024 0.997 0.000 1.221-1.150 99.97 13689 708 0.2253 22.972 21.478 0.988 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0137 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1189 r_free=0.1415 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1189 r_free=0.1415 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1189 r_free=0.1415 | n_water=407 | time (s): 2.280 (total time: 2.280) Filter (dist) r_work=0.1189 r_free=0.1414 | n_water=404 | time (s): 34.000 (total time: 36.280) Filter (q & B) r_work=0.1189 r_free=0.1414 | n_water=404 | time (s): 1.150 (total time: 37.430) Compute maps r_work=0.1189 r_free=0.1414 | n_water=404 | time (s): 1.690 (total time: 39.120) Filter (map) r_work=0.1224 r_free=0.1406 | n_water=278 | time (s): 2.850 (total time: 41.970) Find peaks r_work=0.1224 r_free=0.1406 | n_water=278 | time (s): 0.550 (total time: 42.520) Add new water r_work=0.1344 r_free=0.1537 | n_water=462 | time (s): 2.750 (total time: 45.270) Refine new water occ: r_work=0.1252 r_free=0.1451 adp: r_work=0.1254 r_free=0.1454 occ: r_work=0.1230 r_free=0.1426 adp: r_work=0.1229 r_free=0.1429 occ: r_work=0.1212 r_free=0.1403 adp: r_work=0.1208 r_free=0.1404 ADP+occupancy (water only), MIN, final r_work=0.1208 r_free=0.1404 r_work=0.1208 r_free=0.1404 | n_water=462 | time (s): 199.000 (total time: 244.270) Filter (q & B) r_work=0.1212 r_free=0.1401 | n_water=431 | time (s): 2.420 (total time: 246.690) Filter (dist only) r_work=0.1212 r_free=0.1399 | n_water=430 | time (s): 35.360 (total time: 282.050) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.724014 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 46.203227 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 0.1247 0.1371 0.0124 0.002 0.6 4.5 0.5 0.0 0 0.086 0.1203 0.1334 0.0130 0.003 0.7 3.5 0.5 0.0 0 0.259 0.1186 0.1326 0.0140 0.004 0.8 3.8 0.5 0.0 0 0.517 0.1177 0.1323 0.0146 0.005 0.9 4.2 0.5 0.0 0 0.776 0.1172 0.1321 0.0148 0.006 1.0 3.8 0.5 0.0 0 1.034 0.1171 0.1320 0.0150 0.007 1.0 3.8 0.5 0.0 0 1.293 0.1169 0.1317 0.0148 0.007 1.0 4.2 0.5 0.0 0 1.552 0.1167 0.1317 0.0150 0.008 1.1 4.2 0.5 0.0 0 1.810 0.1175 0.1321 0.0147 0.005 0.9 4.2 0.5 0.0 0 0.862 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1169 0.1317 0.0148 0.007 1.0 4.2 0.5 0.0 0 1.552 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.69 13.17 1.48 3.769 21.220 46.203 3.625 11.69 13.17 1.48 3.769 21.220 1.386 3.625 11.70 13.17 1.47 3.755 21.220 5.775 3.625 11.74 13.26 1.52 3.707 21.204 23.102 3.619 11.69 13.28 1.59 3.740 21.179 46.203 3.616 11.64 13.28 1.64 3.760 21.158 69.305 3.610 11.60 13.24 1.64 3.773 21.149 92.406 3.605 11.57 13.23 1.67 3.787 21.144 115.508 3.603 11.56 13.26 1.70 3.805 21.132 138.610 3.602 11.56 13.26 1.70 3.823 21.116 161.711 3.601 11.54 13.24 1.70 3.830 21.118 184.813 3.599 11.53 13.24 1.71 3.840 21.115 207.915 3.599 11.52 13.24 1.72 3.850 21.110 231.016 3.598 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.386 Accepted refinement result: 11.69 13.17 1.48 3.769 21.220 1.386 3.625 Individual atomic B min max mean iso aniso Overall: 9.10 114.93 21.15 3.29 211 1746 Protein: 9.10 114.93 17.05 3.29 0 1519 Water: 11.51 76.70 35.62 N/A 211 219 Other: 19.78 26.66 22.12 N/A 0 8 Chain A: 9.10 114.93 19.36 N/A 0 1746 Chain S: 17.02 60.01 35.93 N/A 211 0 Histogram: Values Number of atoms 9.10 - 19.68 1262 19.68 - 30.27 291 30.27 - 40.85 206 40.85 - 51.43 122 51.43 - 62.02 53 62.02 - 72.60 11 72.60 - 83.18 6 83.18 - 93.77 4 93.77 - 104.35 0 104.35 - 114.93 2 =========================== Idealize ADP of riding H ========================== r_work=0.1169 r_free=0.1317 r_work=0.1169 r_free=0.1317 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1169 r_free = 0.1317 target_work(ml) = 3.625 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1158 r_free = 0.1310 target_work(ml) = 3.616 | | occupancies: max = 1.00 min = 0.17 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= 0.1158 r_free= 0.1310 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.615861 | | target function (ml) not normalized (work): 301179.538136 | | target function (ml) not normalized (free): 15852.881907 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1165 0.1158 0.1310 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1513 0.1514 0.1533 n_refl.: 87590 remove outliers: r(all,work,free)=0.1513 0.1514 0.1533 n_refl.: 87590 overall B=-0.01 to atoms: r(all,work,free)=0.1511 0.1512 0.1532 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1161 0.1153 0.1301 n_refl.: 87590 remove outliers: r(all,work,free)=0.1159 0.1151 0.1301 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 92.71 84 5 0.3844 297.086 270.757 0.499 1.001 0.306 11.894-9.307 97.06 95 4 0.2201 475.811 461.301 0.868 1.002 0.289 9.237-7.194 99.09 211 7 0.2301 389.104 387.360 0.946 1.002 0.196 7.162-5.571 100.00 427 22 0.2052 296.128 285.996 0.911 1.002 0.173 5.546-4.326 100.00 867 58 0.1127 406.510 401.998 0.954 1.002 0.155 4.315-3.360 100.00 1859 96 0.0949 386.594 383.945 0.995 1.002 0.143 3.356-2.611 100.00 3867 181 0.1166 253.972 251.917 0.998 1.002 0.053 2.608-2.026 99.99 8198 413 0.0943 168.360 167.491 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0899 82.218 82.496 1.025 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1260 36.459 36.038 1.018 0.998 0.000 1.221-1.150 99.97 13689 708 0.2165 22.972 21.515 0.981 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0242 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1151 r_free=0.1301 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=0.1151 r_free=0.1301 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1151 r_free=0.1301 | n_water=430 | time (s): 2.390 (total time: 2.390) Filter (dist) r_work=0.1151 r_free=0.1300 | n_water=428 | time (s): 44.780 (total time: 47.170) Filter (q & B) r_work=0.1152 r_free=0.1302 | n_water=425 | time (s): 3.820 (total time: 50.990) Compute maps r_work=0.1152 r_free=0.1302 | n_water=425 | time (s): 1.860 (total time: 52.850) Filter (map) r_work=0.1183 r_free=0.1326 | n_water=316 | time (s): 3.850 (total time: 56.700) Find peaks r_work=0.1183 r_free=0.1326 | n_water=316 | time (s): 0.700 (total time: 57.400) Add new water r_work=0.1254 r_free=0.1407 | n_water=486 | time (s): 3.830 (total time: 61.230) Refine new water occ: r_work=0.1174 r_free=0.1321 adp: r_work=0.1174 r_free=0.1325 occ: r_work=0.1159 r_free=0.1305 adp: r_work=0.1159 r_free=0.1308 occ: r_work=0.1147 r_free=0.1291 adp: r_work=0.1144 r_free=0.1293 ADP+occupancy (water only), MIN, final r_work=0.1144 r_free=0.1293 r_work=0.1144 r_free=0.1293 | n_water=486 | time (s): 341.240 (total time: 402.470) Filter (q & B) r_work=0.1150 r_free=0.1300 | n_water=447 | time (s): 3.940 (total time: 406.410) Filter (dist only) r_work=0.1150 r_free=0.1299 | n_water=446 | time (s): 46.090 (total time: 452.500) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.855623 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 38.911168 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 0.1207 0.1335 0.0129 0.002 0.6 3.8 0.5 0.0 0 0.093 0.1173 0.1316 0.0143 0.003 0.8 2.9 0.5 0.0 0 0.278 0.1158 0.1307 0.0149 0.005 0.9 3.8 0.5 0.0 0 0.557 0.1152 0.1302 0.0150 0.006 1.0 3.8 0.5 0.0 0 0.835 0.1149 0.1301 0.0152 0.007 1.0 3.8 0.5 0.0 0 1.113 0.1146 0.1303 0.0157 0.007 1.1 3.8 0.5 0.0 0 1.392 0.1144 0.1298 0.0154 0.008 1.1 4.2 0.5 0.0 0 1.670 0.1143 0.1297 0.0154 0.009 1.1 4.8 0.5 0.0 0 1.948 0.1151 0.1304 0.0154 0.006 1.0 3.8 0.5 0.0 0 0.928 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1143 0.1297 0.0154 0.009 1.1 4.8 0.5 0.0 0 1.948 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.43 12.97 1.54 3.770 21.163 38.911 3.607 11.43 12.97 1.54 3.770 21.163 1.167 3.607 11.43 12.97 1.54 3.770 21.163 4.864 3.607 11.46 13.03 1.57 3.705 21.156 19.456 3.602 11.55 13.20 1.64 3.723 21.125 38.911 3.607 11.46 13.15 1.69 3.749 21.113 58.367 3.600 11.40 13.10 1.70 3.766 21.108 77.822 3.595 11.36 13.07 1.71 3.776 21.108 97.278 3.592 11.36 13.08 1.72 3.789 21.098 116.734 3.591 11.34 13.09 1.74 3.802 21.092 136.189 3.589 11.35 13.11 1.76 3.815 21.081 155.645 3.589 11.33 13.09 1.76 3.826 21.080 175.100 3.588 11.31 13.08 1.77 3.831 21.081 194.556 3.587 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 4.864 Accepted refinement result: 11.43 12.97 1.54 3.770 21.163 4.864 3.607 Individual atomic B min max mean iso aniso Overall: 9.09 114.92 21.05 3.29 230 1743 Protein: 9.09 114.92 17.04 3.29 0 1519 Water: 11.51 76.69 34.71 N/A 230 216 Other: 19.77 26.65 22.12 N/A 0 8 Chain A: 9.09 114.92 19.31 N/A 0 1743 Chain S: 17.04 60.00 34.25 N/A 230 0 Histogram: Values Number of atoms 9.09 - 19.67 1261 19.67 - 30.26 312 30.26 - 40.84 213 40.84 - 51.42 115 51.42 - 62.01 49 62.01 - 72.59 11 72.59 - 83.17 6 83.17 - 93.75 4 93.75 - 104.34 0 104.34 - 114.92 2 =========================== Idealize ADP of riding H ========================== r_work=0.1143 r_free=0.1297 r_work=0.1143 r_free=0.1297 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1143 r_free = 0.1297 target_work(ml) = 3.607 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1137 r_free = 0.1291 target_work(ml) = 3.604 | | occupancies: max = 1.00 min = 0.21 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= 0.1137 r_free= 0.1291 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.604011 | | target function (ml) not normalized (work): 300174.434107 | | target function (ml) not normalized (free): 15807.857030 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1144 0.1137 0.1291 n_refl.: 87585 re-set all scales: r(all,work,free)=0.1478 0.1478 0.1509 n_refl.: 87585 remove outliers: r(all,work,free)=0.1478 0.1478 0.1509 n_refl.: 87585 overall B=-0.01 to atoms: r(all,work,free)=0.1477 0.1477 0.1508 n_refl.: 87585 bulk-solvent and scaling: r(all,work,free)=0.1143 0.1136 0.1295 n_refl.: 87585 remove outliers: r(all,work,free)=0.1141 0.1133 0.1295 n_refl.: 87579 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 90.62 82 5 0.4100 288.276 257.690 0.455 1.000 0.314 11.894-9.307 95.10 93 4 0.2417 471.532 456.166 0.844 1.002 0.260 9.237-7.194 98.18 209 7 0.2390 386.083 381.894 0.921 1.002 0.177 7.162-5.571 100.00 427 22 0.2170 296.128 284.806 0.901 1.002 0.145 5.546-4.326 100.00 867 58 0.1124 406.510 401.968 0.955 1.002 0.116 4.315-3.360 100.00 1859 96 0.0918 386.594 384.329 0.993 1.002 0.100 3.356-2.611 100.00 3867 181 0.1118 253.972 252.100 1.000 1.002 0.034 2.608-2.026 99.99 8198 413 0.0913 168.360 167.671 1.015 1.001 0.000 2.025-1.573 100.00 17313 902 0.0879 82.218 82.529 1.026 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1249 36.459 36.044 1.019 0.997 0.000 1.221-1.150 99.97 13689 708 0.2167 22.972 21.509 0.981 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0190 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1133 r_free=0.1295 After: r_work=0.1135 r_free=0.1294 ================================== NQH flips ================================== r_work=0.1135 r_free=0.1294 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=0.1135 r_free=0.1294 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1135 r_free=0.1294 | n_water=446 | time (s): 2.400 (total time: 2.400) Filter (dist) r_work=0.1135 r_free=0.1294 | n_water=446 | time (s): 42.290 (total time: 44.690) Filter (q & B) r_work=0.1135 r_free=0.1294 | n_water=446 | time (s): 1.400 (total time: 46.090) Compute maps r_work=0.1135 r_free=0.1294 | n_water=446 | time (s): 1.880 (total time: 47.970) Filter (map) r_work=0.1159 r_free=0.1314 | n_water=354 | time (s): 3.840 (total time: 51.810) Find peaks r_work=0.1159 r_free=0.1314 | n_water=354 | time (s): 0.750 (total time: 52.560) Add new water r_work=0.1205 r_free=0.1349 | n_water=502 | time (s): 3.800 (total time: 56.360) Refine new water occ: r_work=0.1152 r_free=0.1297 adp: r_work=0.1152 r_free=0.1299 occ: r_work=0.1141 r_free=0.1284 adp: r_work=0.1140 r_free=0.1287 occ: r_work=0.1133 r_free=0.1275 adp: r_work=0.1131 r_free=0.1277 ADP+occupancy (water only), MIN, final r_work=0.1131 r_free=0.1277 r_work=0.1131 r_free=0.1277 | n_water=502 | time (s): 200.370 (total time: 256.730) Filter (q & B) r_work=0.1139 r_free=0.1287 | n_water=456 | time (s): 3.740 (total time: 260.470) Filter (dist only) r_work=0.1142 r_free=0.1287 | n_water=454 | time (s): 47.630 (total time: 308.100) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.780779 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 44.571474 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 0.1220 0.1335 0.0115 0.004 0.7 6.1 0.0 0.0 0 0.089 0.1176 0.1307 0.0130 0.004 0.8 6.1 0.0 0.0 0 0.267 0.1161 0.1297 0.0137 0.005 0.9 5.4 0.5 0.0 0 0.534 0.1153 0.1292 0.0139 0.006 1.0 5.1 0.5 0.0 0 0.801 0.1148 0.1290 0.0141 0.006 1.1 5.1 0.5 0.0 0 1.068 0.1145 0.1288 0.0143 0.007 1.1 5.1 0.5 0.0 0 1.336 0.1143 0.1287 0.0145 0.008 1.1 4.8 0.5 0.0 0 1.603 0.1142 0.1287 0.0146 0.009 1.1 5.1 0.5 0.0 0 1.870 0.1150 0.1291 0.0140 0.006 1.0 5.1 0.5 0.0 0 0.890 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1143 0.1287 0.0145 0.008 1.1 4.8 0.5 0.0 0 1.603 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.43 12.87 1.45 3.769 21.204 44.571 3.606 11.43 12.87 1.45 3.769 21.204 1.337 3.606 11.43 12.87 1.45 3.765 21.204 5.571 3.606 11.45 12.93 1.48 3.707 21.197 22.286 3.600 11.49 13.05 1.55 3.734 21.162 44.571 3.602 11.43 13.02 1.59 3.754 21.151 66.857 3.597 11.36 12.97 1.61 3.770 21.149 89.143 3.592 11.34 12.98 1.63 3.781 21.144 111.429 3.589 11.31 12.95 1.64 3.788 21.145 133.714 3.587 11.33 13.00 1.67 3.812 21.127 156.000 3.588 11.30 12.98 1.67 3.820 21.128 178.286 3.586 11.29 12.96 1.67 3.828 21.125 200.572 3.585 11.30 12.99 1.69 3.842 21.122 222.857 3.586 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.337 Accepted refinement result: 11.43 12.87 1.45 3.769 21.204 1.337 3.606 Individual atomic B min max mean iso aniso Overall: 9.08 114.91 21.13 3.29 239 1742 Protein: 9.08 114.91 17.03 3.29 0 1519 Water: 11.50 76.68 34.84 N/A 239 215 Other: 19.76 26.64 22.11 N/A 0 8 Chain A: 9.08 114.91 19.30 N/A 0 1742 Chain S: 16.45 60.00 34.49 N/A 239 0 Histogram: Values Number of atoms 9.08 - 19.67 1261 19.67 - 30.25 311 30.25 - 40.83 217 40.83 - 51.42 119 51.42 - 62.00 50 62.00 - 72.58 11 72.58 - 83.16 6 83.16 - 93.75 4 93.75 - 104.33 0 104.33 - 114.91 2 =========================== Idealize ADP of riding H ========================== r_work=0.1143 r_free=0.1287 r_work=0.1143 r_free=0.1287 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1143 r_free = 0.1287 target_work(ml) = 3.606 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1139 r_free = 0.1284 target_work(ml) = 3.604 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87579 (all), 4.91 % free)------------| | | | r_work= 0.1139 r_free= 0.1284 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.603824 | | target function (ml) not normalized (work): 300137.286627 | | target function (ml) not normalized (free): 15792.091732 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2921 171 0.1362 0.1313 5.6862 5.5859| | 2: 3.57 - 2.84 1.00 2888 124 0.1062 0.1439 5.1535 5.2158| | 3: 2.83 - 2.48 1.00 2820 163 0.1113 0.1182 4.939 4.9663| | 4: 2.47 - 2.25 1.00 2825 136 0.0897 0.0945 4.6202 4.6373| | 5: 2.25 - 2.09 1.00 2756 127 0.0871 0.0997 4.5663 4.6251| | 6: 2.09 - 1.97 1.00 2846 113 0.0862 0.1008 4.2604 4.3519| | 7: 1.97 - 1.87 1.00 2787 165 0.0877 0.1097 3.9659 4.0701| | 8: 1.87 - 1.79 1.00 2789 144 0.0911 0.1066 3.876 3.9655| | 9: 1.79 - 1.72 1.00 2745 138 0.0873 0.1195 3.6407 3.8344| | 10: 1.72 - 1.66 1.00 2831 160 0.0914 0.1204 3.5595 3.7137| | 11: 1.66 - 1.61 1.00 2712 147 0.0868 0.1064 3.4946 3.5744| | 12: 1.61 - 1.56 1.00 2773 144 0.0905 0.1140 3.3334 3.4592| | 13: 1.56 - 1.52 1.00 2745 130 0.0955 0.1052 3.3122 3.4078| | 14: 1.52 - 1.48 1.00 2803 134 0.0996 0.1069 3.2472 3.3348| | 15: 1.48 - 1.45 1.00 2738 128 0.1013 0.1228 3.1606 3.2685| | 16: 1.45 - 1.42 1.00 2756 161 0.1059 0.1256 3.1383 3.2405| | 17: 1.42 - 1.39 1.00 2785 139 0.1142 0.1305 3.1204 3.23| | 18: 1.39 - 1.36 1.00 2741 179 0.1204 0.1354 3.1065 3.243| | 19: 1.36 - 1.34 1.00 2807 134 0.1262 0.1547 3.1134 3.2586| | 20: 1.34 - 1.32 1.00 2696 147 0.1371 0.1463 3.1137 3.1497| | 21: 1.32 - 1.30 1.00 2785 112 0.1473 0.1494 3.1151 3.0993| | 22: 1.29 - 1.27 1.00 2704 152 0.1564 0.1981 3.124 3.2914| | 23: 1.27 - 1.26 1.00 2802 156 0.1647 0.1795 3.132 3.2019| | 24: 1.26 - 1.24 1.00 2744 132 0.1712 0.1829 3.128 3.2242| | 25: 1.24 - 1.22 1.00 2733 148 0.1885 0.2131 3.1439 3.2538| | 26: 1.22 - 1.21 1.00 2727 135 0.1909 0.1766 3.1484 3.2031| | 27: 1.21 - 1.19 1.00 2814 148 0.2075 0.2156 3.1713 3.1592| | 28: 1.19 - 1.18 1.00 2671 147 0.2203 0.2300 3.166 3.1732| | 29: 1.18 - 1.16 1.00 2800 134 0.2268 0.2398 3.1481 3.2294| | 30: 1.16 - 1.15 1.00 2739 148 0.2449 0.2452 3.143 3.1687| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2921 171 0.95 8.40 1.00 0.98 5579.46| | 2: 3.57 - 2.84 2888 124 0.93 12.33 1.01 0.98 5579.46| | 3: 2.83 - 2.48 2820 163 0.90 16.20 0.99 0.98 4659.58| | 4: 2.47 - 2.25 2825 136 0.92 13.25 1.00 0.99 2287.50| | 5: 2.25 - 2.09 2756 127 0.91 15.35 1.01 0.99 2287.50| | 6: 2.09 - 1.97 2846 113 0.93 12.19 1.02 0.99 1319.66| | 7: 1.97 - 1.87 2787 165 0.95 9.07 1.02 0.98 494.22| | 8: 1.87 - 1.79 2789 144 0.93 12.37 1.00 0.98 494.22| | 9: 1.79 - 1.72 2745 138 0.94 10.00 0.98 0.98 285.15| | 10: 1.72 - 1.66 2831 160 0.94 11.06 0.98 0.98 243.28| | 11: 1.66 - 1.61 2712 147 0.94 11.69 0.98 0.98 233.25| | 12: 1.61 - 1.56 2773 144 0.95 8.99 0.99 0.98 138.63| | 13: 1.56 - 1.52 2745 130 0.95 10.46 1.03 0.98 138.63| | 14: 1.52 - 1.48 2803 134 0.94 10.84 1.02 0.99 124.52| | 15: 1.48 - 1.45 2738 128 0.95 9.94 1.02 0.99 98.69| | 16: 1.45 - 1.42 2756 161 0.94 11.17 1.02 0.99 98.69| | 17: 1.42 - 1.39 2785 139 0.95 10.97 1.01 0.99 89.54| | 18: 1.39 - 1.36 2741 179 0.94 11.56 1.01 0.99 84.25| | 19: 1.36 - 1.34 2807 134 0.94 11.91 1.00 0.99 84.25| | 20: 1.34 - 1.32 2696 147 0.94 12.11 0.98 0.97 79.81| | 21: 1.32 - 1.30 2785 112 0.94 13.05 0.98 0.97 79.50| | 22: 1.29 - 1.27 2704 152 0.93 13.64 0.98 0.97 79.89| | 23: 1.27 - 1.26 2802 156 0.92 14.81 0.97 0.95 81.87| | 24: 1.26 - 1.24 2744 132 0.92 14.85 0.96 0.95 81.87| | 25: 1.24 - 1.22 2733 148 0.91 16.35 0.96 0.95 83.93| | 26: 1.22 - 1.21 2727 135 0.90 18.10 1.02 0.94 86.21| | 27: 1.21 - 1.19 2814 148 0.89 18.74 1.02 0.94 86.21| | 28: 1.19 - 1.18 2671 147 0.88 20.44 1.01 0.93 90.16| | 29: 1.18 - 1.16 2800 134 0.88 20.56 0.99 0.93 91.65| | 30: 1.16 - 1.15 2739 148 0.86 22.10 0.98 0.93 91.65| |alpha: min = 0.93 max = 0.99 mean = 0.97| |beta: min = 79.50 max = 5579.46 mean = 862.94| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.81 mean = 13.40| |phase err.(test): min = 0.00 max = 88.97 mean = 13.38| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1146 0.1139 0.1284 n_refl.: 87579 re-set all scales: r(all,work,free)=0.1476 0.1477 0.1485 n_refl.: 87579 remove outliers: r(all,work,free)=0.1476 0.1477 0.1485 n_refl.: 87579 overall B=-0.01 to atoms: r(all,work,free)=0.1475 0.1476 0.1485 n_refl.: 87579 bulk-solvent and scaling: r(all,work,free)=0.1146 0.1139 0.1284 n_refl.: 87579 remove outliers: r(all,work,free)=0.1144 0.1137 0.1284 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 0.4127 285.691 242.746 0.436 1.000 0.310 11.894-9.307 93.14 91 4 0.2506 472.653 447.946 0.847 1.002 0.238 9.237-7.194 98.18 209 7 0.2425 386.083 378.354 0.917 1.002 0.170 7.162-5.571 100.00 427 22 0.2174 296.128 284.796 0.905 1.003 0.120 5.546-4.326 100.00 867 58 0.1144 406.510 401.787 0.963 1.003 0.120 4.315-3.360 100.00 1859 96 0.0923 386.594 384.593 1.004 1.002 0.110 3.356-2.611 100.00 3867 181 0.1108 253.972 252.385 1.011 1.002 0.024 2.608-2.026 99.99 8198 413 0.0915 168.360 167.749 1.026 1.001 0.000 2.025-1.573 100.00 17313 902 0.0886 82.218 82.584 1.036 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1256 36.459 36.069 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2170 22.972 21.519 0.990 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0149 ================= 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: 0.1237 0.1466 0.005 0.794 9.1 119.5 20.1 258 0.131 1_adp: 0.1244 0.1464 0.005 0.794 9.1 119.5 20.1 258 0.131 1_regHadp: 0.1245 0.1468 0.005 0.794 9.1 119.5 20.1 258 0.131 1_occ: 0.1239 0.1461 0.005 0.794 9.1 119.5 20.1 258 0.131 2_bss: 0.1236 0.1454 0.005 0.794 9.1 119.5 20.1 258 0.131 2_settarget: 0.1236 0.1454 0.005 0.794 9.1 119.5 20.1 258 0.131 2_updatecdl: 0.1236 0.1454 0.005 0.813 9.1 119.5 20.1 258 0.131 2_nqh: 0.1238 0.1456 0.005 0.813 9.1 119.5 20.1 258 0.134 2_sol: 0.1216 0.1405 0.005 0.813 9.1 114.9 22.1 407 n/a 2_weight: 0.1216 0.1405 0.005 0.813 9.1 114.9 22.1 407 n/a 2_xyzrec: 0.1193 0.1414 0.008 0.922 9.1 114.9 22.1 407 n/a 2_adp: 0.1193 0.1414 0.008 0.922 9.1 114.9 22.1 407 n/a 2_regHadp: 0.1193 0.1414 0.008 0.922 9.1 114.9 22.1 407 n/a 2_occ: 0.1194 0.1421 0.008 0.922 9.1 114.9 22.1 407 n/a 3_bss: 0.1189 0.1415 0.008 0.922 9.1 114.9 22.1 407 n/a 3_settarget: 0.1189 0.1415 0.008 0.922 9.1 114.9 22.1 407 n/a 3_updatecdl: 0.1189 0.1415 0.008 0.926 9.1 114.9 22.1 407 n/a 3_nqh: 0.1189 0.1415 0.008 0.926 9.1 114.9 22.1 407 n/a 3_sol: 0.1212 0.1399 0.008 0.926 9.1 114.9 21.1 430 n/a 3_weight: 0.1212 0.1399 0.008 0.926 9.1 114.9 21.1 430 n/a 3_xyzrec: 0.1169 0.1317 0.007 1.043 9.1 114.9 21.1 430 n/a 3_adp: 0.1169 0.1317 0.007 1.043 9.1 114.9 21.1 430 n/a 3_regHadp: 0.1169 0.1317 0.007 1.043 9.1 114.9 21.1 430 n/a 3_occ: 0.1158 0.1310 0.007 1.043 9.1 114.9 21.1 430 n/a 4_bss: 0.1151 0.1301 0.007 1.043 9.1 114.9 21.1 430 n/a 4_settarget: 0.1151 0.1301 0.007 1.043 9.1 114.9 21.1 430 n/a 4_updatecdl: 0.1151 0.1301 0.007 1.044 9.1 114.9 21.1 430 n/a 4_nqh: 0.1151 0.1301 0.007 1.044 9.1 114.9 21.1 430 n/a 4_sol: 0.1150 0.1299 0.007 1.044 9.1 114.9 21.1 446 n/a 4_weight: 0.1150 0.1299 0.007 1.044 9.1 114.9 21.1 446 n/a 4_xyzrec: 0.1143 0.1297 0.009 1.135 9.1 114.9 21.1 446 n/a 4_adp: 0.1143 0.1297 0.009 1.135 9.1 114.9 21.1 446 n/a 4_regHadp: 0.1143 0.1297 0.009 1.135 9.1 114.9 21.1 446 n/a 4_occ: 0.1137 0.1291 0.009 1.135 9.1 114.9 21.1 446 n/a 5_bss: 0.1133 0.1295 0.009 1.135 9.1 114.9 21.0 446 n/a 5_settarget: 0.1133 0.1295 0.009 1.135 9.1 114.9 21.0 446 n/a 5_updatecdl: 0.1133 0.1295 0.009 1.135 9.1 114.9 21.0 446 n/a 5_setrh: 0.1135 0.1294 0.009 1.135 9.1 114.9 21.0 446 n/a 5_nqh: 0.1135 0.1294 0.009 1.135 9.1 114.9 21.0 446 n/a 5_sol: 0.1142 0.1287 0.009 1.135 9.1 114.9 21.1 454 n/a 5_weight: 0.1142 0.1287 0.009 1.135 9.1 114.9 21.1 454 n/a 5_xyzrec: 0.1143 0.1287 0.008 1.131 9.1 114.9 21.1 454 n/a 5_adp: 0.1143 0.1287 0.008 1.131 9.1 114.9 21.1 454 n/a 5_regHadp: 0.1143 0.1287 0.008 1.131 9.1 114.9 21.1 454 n/a 5_occ: 0.1139 0.1284 0.008 1.131 9.1 114.9 21.1 454 n/a end: 0.1137 0.1284 0.008 1.131 9.1 114.9 21.1 454 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_3081210_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_3081210_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.4200 Refinement macro-cycles (run) : 13497.5300 Write final files (write_after_run_outputs) : 97.0100 Total : 13597.9600 Total CPU time: 3.79 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:05:27 PST -0800 (1735365927.92 s) Start R-work = 0.1641, R-free = 0.1795 Final R-work = 0.1137, R-free = 0.1284 =============================================================================== Job complete usr+sys time: 13780.30 seconds wall clock time: 249 minutes 43.16 seconds (14983.16 seconds total)