Starting phenix.refine on Sun Dec 29 09:24:41 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_1541177.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 Adding command-line PHIL: ------------------------- xray_data.high_resolution=2 ordered_solvent.low_resolution=4 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_1541177.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_1541177.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 2 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.40, per 1000 atoms: 0.41 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: 0.37 Conformation dependent library (CDL) restraints added in 114.5 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.68 - 0.92: 575 0.92 - 1.17: 1067 1.17 - 1.42: 625 1.42 - 1.66: 843 1.66 - 1.91: 43 Bond restraints: 3153 Sorted by residual: bond pdb=" N BGLN A 80 " pdb=" CA BGLN A 80 " ideal model delta sigma weight residual 1.459 1.694 -0.235 1.19e-02 7.06e+03 3.88e+02 bond pdb=" N LYS A 130 " pdb=" CA LYS A 130 " ideal model delta sigma weight residual 1.459 1.692 -0.233 1.19e-02 7.06e+03 3.82e+02 bond pdb=" CA ALA A 61 " pdb=" C ALA A 61 " ideal model delta sigma weight residual 1.523 1.284 0.239 1.35e-02 5.49e+03 3.13e+02 bond pdb=" NE ARG A 145 " pdb=" CZ ARG A 145 " ideal model delta sigma weight residual 1.326 1.518 -0.192 1.10e-02 8.26e+03 3.03e+02 bond pdb=" C ALA A 36 " pdb=" O ALA A 36 " ideal model delta sigma weight residual 1.236 1.436 -0.200 1.22e-02 6.72e+03 2.70e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.72: 3146 4.72 - 9.44: 1861 9.44 - 14.16: 655 14.16 - 18.88: 105 18.88 - 23.60: 10 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O ACYS A 53 " pdb=" C ACYS A 53 " pdb=" N PRO A 54 " ideal model delta sigma weight residual 121.23 140.59 -19.36 8.10e-01 1.52e+00 5.71e+02 angle pdb=" O ILE A 152 " pdb=" C ILE A 152 " pdb=" N ALEU A 153 " ideal model delta sigma weight residual 123.10 142.90 -19.80 1.17e+00 7.31e-01 2.86e+02 angle pdb=" O ILE A 91 " pdb=" C ILE A 91 " pdb=" N LEU A 92 " ideal model delta sigma weight residual 121.83 138.06 -16.23 1.03e+00 9.43e-01 2.48e+02 angle pdb=" C ACYS A 53 " pdb=" N PRO A 54 " pdb=" CA PRO A 54 " ideal model delta sigma weight residual 120.03 104.54 15.49 9.90e-01 1.02e+00 2.45e+02 angle pdb=" CA BLEU A 153 " pdb=" C BLEU A 153 " pdb=" O BLEU A 153 " ideal model delta sigma weight residual 120.30 105.59 14.71 1.07e+00 8.73e-01 1.89e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.51: 1291 16.51 - 33.01: 125 33.01 - 49.52: 49 49.52 - 66.03: 12 66.03 - 82.53: 4 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C ILE A 105 " pdb=" N ILE A 105 " pdb=" CA ILE A 105 " pdb=" CB ILE A 105 " ideal model delta harmonic sigma weight residual -122.00 -144.65 22.65 0 2.50e+00 1.60e-01 8.20e+01 dihedral pdb=" N ILE A 105 " pdb=" C ILE A 105 " pdb=" CA ILE A 105 " pdb=" CB ILE A 105 " ideal model delta harmonic sigma weight residual 123.40 143.79 -20.39 0 2.50e+00 1.60e-01 6.65e+01 dihedral pdb=" C VAL A 186 " pdb=" N VAL A 186 " pdb=" CA VAL A 186 " pdb=" CB VAL A 186 " ideal model delta harmonic sigma weight residual -122.00 -141.95 19.95 0 2.50e+00 1.60e-01 6.37e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.019 - 0.214: 92 0.214 - 0.410: 75 0.410 - 0.605: 43 0.605 - 0.800: 23 0.800 - 0.996: 10 Chirality restraints: 243 Sorted by residual: chirality pdb=" CG BLEU A 153 " pdb=" CB BLEU A 153 " pdb=" CD1BLEU A 153 " pdb=" CD2BLEU A 153 " both_signs ideal model delta sigma weight residual False -2.59 -3.59 1.00 2.00e-01 2.50e+01 2.48e+01 chirality pdb=" CB VAL A 20 " pdb=" CA VAL A 20 " pdb=" CG1 VAL A 20 " pdb=" CG2 VAL A 20 " both_signs ideal model delta sigma weight residual False -2.63 -1.64 -0.99 2.00e-01 2.50e+01 2.46e+01 chirality pdb=" CA ALA A 79 " pdb=" N ALA A 79 " pdb=" C ALA A 79 " pdb=" CB ALA A 79 " both_signs ideal model delta sigma weight residual False 2.48 1.56 0.93 2.00e-01 2.50e+01 2.14e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.029 2.00e-02 2.50e+03 7.00e-02 1.47e+02 pdb=" CG PHE A 164 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.121 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.040 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.085 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.058 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.121 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.123 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.022 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.008 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.025 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " 0.025 2.00e-02 2.50e+03 5.95e-02 1.06e+02 pdb=" CG TYR A 139 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.078 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.118 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.078 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.026 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.026 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " -0.033 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " -0.018 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.107 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.059 2.00e-02 2.50e+03 5.87e-02 1.03e+02 pdb=" CG BTYR A 67 " 0.093 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.002 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " -0.096 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " -0.060 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " -0.043 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " -0.018 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " -0.006 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " 0.003 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " 0.096 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " 0.066 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " 0.027 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.24: 583 2.24 - 2.83: 7551 2.83 - 3.42: 10765 3.42 - 4.01: 15326 4.01 - 4.60: 22349 Nonbonded interactions: 56574 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.655 2.100 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.770 2.100 nonbonded pdb=" H THR A 124 " pdb=" HG1 THR A 154 " model vdw 1.797 2.100 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.847 2.100 nonbonded pdb=" HB2BGLN A 80 " pdb="HE21BGLN A 80 " model vdw 1.849 2.270 ... (remaining 56569 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 2 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 } ordered_solvent { low_resolution = 4 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_1541177_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: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2793 r_free= 0.1840 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.405189 | | target function (ml) not normalized (work): 71553.486197 | | target function (ml) not normalized (free): 3279.412998 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 49.25 - 3.64 1.00 2819 159 0.3209 0.2126 7.5224 5.0159| | 2: 3.63 - 2.88 1.00 2711 122 0.2645 0.1757 4.3345 4.3478| | 3: 2.88 - 2.52 1.00 2682 148 0.2577 0.1695 4.1843 4.1875| | 4: 2.52 - 2.29 1.00 2661 139 0.2535 0.1646 3.4921 3.6583| | 5: 2.29 - 2.13 1.00 2678 122 0.2626 0.1565 3.3954 3.5327| | 6: 2.13 - 2.00 1.00 2692 117 0.2767 0.1839 3.3393 3.3524| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 - 3.64 2819 159 0.88 17.63 0.77 0.23 1304.55| | 2: 3.63 - 2.88 2711 122 0.83 23.94 1.31 0.23 1304.55| | 3: 2.88 - 2.52 2682 148 0.73 33.02 1.28 0.23 1304.55| | 4: 2.52 - 2.29 2661 139 0.93 11.90 1.30 0.26 144.19| | 5: 2.29 - 2.13 2678 122 0.91 14.31 1.32 0.26 144.19| | 6: 2.13 - 2.00 2692 117 0.89 16.99 1.34 0.26 144.19| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 144.19 max = 1304.55 mean = 730.84| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 89.98 mean = 19.63| |phase err.(test): min = 0.00 max = 89.57 mean = 19.71| |-----------------------------------------------------------------------------| ----------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 : 0.082 0.239 1557 Z= 5.520 Angle : 5.413 19.796 2118 Z= 3.892 Chirality : 0.397 0.996 243 Planarity : 0.032 0.090 284 Dihedral : 14.027 82.534 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.16 % Favored : 97.30 % Rotamer: Outliers : 2.48 % Allowed : 1.24 % Favored : 96.27 % Cbeta Deviations : 34.59 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.51), residues: 224 helix: -3.09 (0.37), residues: 108 sheet: -0.73 (0.78), residues: 38 loop : 0.17 (0.70), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.089 0.020 ARG A 98 TYR 0.087 0.038 TYR A 139 PHE 0.138 0.046 PHE A 164 HIS 0.088 0.044 HIS A 115 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 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: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2793 r_free= 0.1840 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.405189 | | target function (ml) not normalized (work): 71553.486197 | | target function (ml) not normalized (free): 3279.412998 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.2955 percent. r_work = 0.2922 r_free = 0.1992 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2868 0.2922 0.1992 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2868 0.2922 0.1992 n_refl.: 17050 remove outliers: r(all,work,free)=0.2160 0.2171 0.1992 n_refl.: 17045 overall B=-0.40 to atoms: r(all,work,free)=0.2134 0.2144 0.1975 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1625 0.1622 0.1679 n_refl.: 17045 remove outliers: r(all,work,free)=0.1625 0.1621 0.1679 n_refl.: 17044 ======================== 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 32.574-12.150 100.00 89 5 0.4077 394.780 361.217 0.638 1.019 0.397 11.894-9.307 99.02 97 4 0.1940 633.634 612.320 0.921 1.019 0.380 9.237-7.194 100.00 213 7 0.2182 518.249 510.469 0.956 1.018 0.340 7.162-5.571 100.00 427 22 0.2359 388.946 376.547 0.917 1.016 0.284 5.546-4.326 100.00 867 58 0.1408 533.961 528.897 0.961 1.013 0.251 4.315-3.360 100.00 1859 96 0.1306 507.802 503.825 1.013 1.007 0.197 3.356-2.611 100.00 3867 181 0.1686 333.597 328.377 1.013 0.998 0.015 2.608-2.000 99.99 8818 434 0.1633 217.448 213.535 1.036 0.982 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.4196 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1621 r_free=0.1679 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.1625 r_free=0.1687 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.502620 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.784285 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1352 0.1644 0.0292 0.009 1.0 1.6 0.5 0.0 0 11.751 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.52 16.44 2.92 3.013 18.461 0.784 0.023 12.79 16.63 3.84 3.602 18.728 0.784 0.021 Individual atomic B min max mean iso aniso Overall: 6.32 113.90 19.99 4.02 1785 0 Protein: 6.32 112.64 17.25 4.03 1519 0 Water: 8.66 113.90 35.96 N/A 258 0 Other: 21.54 36.69 26.46 N/A 8 0 Chain A: 6.32 113.90 19.99 N/A 1785 0 Histogram: Values Number of atoms 6.32 - 17.08 1088 17.08 - 27.84 342 27.84 - 38.60 185 38.60 - 49.35 96 49.35 - 60.11 47 60.11 - 70.87 13 70.87 - 81.63 6 81.63 - 92.39 4 92.39 - 103.14 1 103.14 - 113.90 3 =========================== Idealize ADP of riding H ========================== r_work=0.1279 r_free=0.1663 r_work=0.1283 r_free=0.1672 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1283 r_free = 0.1672 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1277 r_free = 0.1667 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17044 (all), 4.73 % free)------------| | | | r_work= 0.1277 r_free= 0.1667 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.020065 | | target function (ls_wunit_k1) not normalized (work): 325.800579 | | target function (ls_wunit_k1) not normalized (free): 27.581772 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1296 0.1277 0.1667 n_refl.: 17044 re-set all scales: r(all,work,free)=0.1915 0.1914 0.2000 n_refl.: 17044 remove outliers: r(all,work,free)=0.1915 0.1914 0.2000 n_refl.: 17044 overall B=-0.39 to atoms: r(all,work,free)=0.1886 0.1884 0.1984 n_refl.: 17044 bulk-solvent and scaling: r(all,work,free)=0.1296 0.1278 0.1654 n_refl.: 17044 remove outliers: r(all,work,free)=0.1294 0.1276 0.1654 n_refl.: 17042 ======================== 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 0.3539 302.836 279.052 0.625 1.011 0.370 11.894-9.307 99.02 97 4 0.1704 487.064 477.178 0.916 1.011 0.364 9.237-7.194 100.00 213 7 0.1817 398.369 396.102 0.960 1.011 0.341 7.162-5.571 100.00 427 22 0.1829 298.976 294.043 0.929 1.010 0.264 5.546-4.326 100.00 867 58 0.1047 410.447 408.222 0.961 1.008 0.231 4.315-3.360 100.00 1859 96 0.0935 390.339 389.928 1.017 1.005 0.191 3.356-2.611 100.00 3867 181 0.1301 256.430 255.125 1.015 1.000 0.091 2.608-2.000 99.99 8818 434 0.1349 167.149 165.653 1.024 0.991 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.4072 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1276 r_free=0.1654 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1276 r_free=0.1654 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1276 r_free=0.1654 | n_water=258 | time (s): 0.670 (total time: 0.670) Filter (dist) r_work=0.1281 r_free=0.1650 | n_water=253 | time (s): 21.010 (total time: 21.680) Filter (q & B) r_work=0.1282 r_free=0.1650 | n_water=251 | time (s): 1.740 (total time: 23.420) Compute maps r_work=0.1282 r_free=0.1650 | n_water=251 | time (s): 0.530 (total time: 23.950) Filter (map) r_work=0.1313 r_free=0.1636 | n_water=214 | time (s): 1.500 (total time: 25.450) Find peaks r_work=0.1313 r_free=0.1636 | n_water=214 | time (s): 0.510 (total time: 25.960) Add new water r_work=0.1536 r_free=0.1902 | n_water=372 | time (s): 1.860 (total time: 27.820) Refine new water occ: r_work=0.1335 r_free=0.1593 adp: r_work=0.1274 r_free=0.1587 occ: r_work=0.1280 r_free=0.1564 adp: r_work=0.1246 r_free=0.1563 occ: r_work=0.1248 r_free=0.1565 adp: r_work=0.1237 r_free=0.1562 ADP+occupancy (water only), MIN, final r_work=0.1237 r_free=0.1562 r_work=0.1237 r_free=0.1562 | n_water=372 | time (s): 31.830 (total time: 59.650) Filter (q & B) r_work=0.1238 r_free=0.1565 | n_water=366 | time (s): 1.490 (total time: 61.140) Filter (dist only) r_work=0.1239 r_free=0.1568 | n_water=365 | time (s): 28.070 (total time: 89.210) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.563513 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.975446 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1209 0.1609 0.0399 0.008 0.9 2.2 0.5 0.0 0 12.282 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.09 16.09 3.99 4.147 21.111 0.975 0.018 11.93 16.28 4.35 4.232 21.387 0.975 0.017 Individual atomic B min max mean iso aniso Overall: 6.64 107.24 21.43 4.32 1892 0 Protein: 6.64 107.24 17.76 4.31 1519 0 Water: 8.95 68.17 36.37 N/A 365 0 Other: 25.26 45.59 35.74 N/A 8 0 Chain A: 6.64 107.24 19.55 N/A 1741 0 Chain S: 18.48 67.68 43.10 N/A 151 0 Histogram: Values Number of atoms 6.64 - 16.70 1033 16.70 - 26.76 369 26.76 - 36.82 215 36.82 - 46.88 167 46.88 - 56.94 68 56.94 - 67.00 27 67.00 - 77.06 5 77.06 - 87.12 6 87.12 - 97.18 0 97.18 - 107.24 2 =========================== Idealize ADP of riding H ========================== r_work=0.1193 r_free=0.1628 r_work=0.1194 r_free=0.1629 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1194 r_free = 0.1629 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1191 r_free = 0.1632 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17042 (all), 4.74 % free)------------| | | | r_work= 0.1191 r_free= 0.1632 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.016847 | | target function (ls_wunit_k1) not normalized (work): 273.515916 | | target function (ls_wunit_k1) not normalized (free): 25.417534 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1212 0.1191 0.1632 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1756 0.1747 0.1961 n_refl.: 17042 remove outliers: r(all,work,free)=0.1756 0.1747 0.1961 n_refl.: 17042 overall B=-0.38 to atoms: r(all,work,free)=0.1732 0.1723 0.1944 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1207 0.1185 0.1625 n_refl.: 17042 remove outliers: r(all,work,free)=0.1206 0.1184 0.1625 n_refl.: 17041 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3179 299.680 285.859 0.602 1.005 0.350 11.894-9.307 99.02 97 4 0.1499 487.064 483.486 0.915 1.006 0.350 9.237-7.194 100.00 213 7 0.1611 398.369 400.009 0.977 1.006 0.310 7.162-5.571 100.00 427 22 0.1521 298.976 295.163 0.934 1.005 0.243 5.546-4.326 100.00 867 58 0.0859 410.447 407.661 0.959 1.005 0.210 4.315-3.360 100.00 1859 96 0.0822 390.339 389.170 1.015 1.003 0.191 3.356-2.611 100.00 3867 181 0.1202 256.430 255.503 1.011 1.001 0.111 2.608-2.000 99.99 8818 434 0.1330 167.149 166.061 1.017 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.3529 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1184 r_free=0.1625 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1184 r_free=0.1625 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1184 r_free=0.1625 | n_water=365 | time (s): 0.750 (total time: 0.750) Filter (dist) r_work=0.1185 r_free=0.1628 | n_water=364 | time (s): 32.130 (total time: 32.880) Filter (q & B) r_work=0.1185 r_free=0.1630 | n_water=363 | time (s): 1.640 (total time: 34.520) Compute maps r_work=0.1185 r_free=0.1630 | n_water=363 | time (s): 0.780 (total time: 35.300) Filter (map) r_work=0.1257 r_free=0.1645 | n_water=260 | time (s): 1.840 (total time: 37.140) Find peaks r_work=0.1257 r_free=0.1645 | n_water=260 | time (s): 0.490 (total time: 37.630) Add new water r_work=0.1443 r_free=0.1822 | n_water=405 | time (s): 1.730 (total time: 39.360) Refine new water occ: r_work=0.1239 r_free=0.1584 adp: r_work=0.1231 r_free=0.1582 occ: r_work=0.1214 r_free=0.1558 adp: r_work=0.1202 r_free=0.1556 occ: r_work=0.1194 r_free=0.1536 adp: r_work=0.1185 r_free=0.1538 ADP+occupancy (water only), MIN, final r_work=0.1185 r_free=0.1538 r_work=0.1185 r_free=0.1538 | n_water=405 | time (s): 38.080 (total time: 77.440) Filter (q & B) r_work=0.1187 r_free=0.1544 | n_water=397 | time (s): 1.800 (total time: 79.240) Filter (dist only) r_work=0.1187 r_free=0.1544 | n_water=397 | time (s): 30.850 (total time: 110.090) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.879440 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.195780 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1168 0.1543 0.0376 0.009 1.0 4.2 0.5 0.0 0 0.940 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.68 15.43 3.76 4.367 21.491 0.196 4.987 11.47 15.46 3.99 4.963 21.451 0.196 4.962 Individual atomic B min max mean iso aniso Overall: 6.18 105.16 20.86 4.87 1924 0 Protein: 6.18 105.16 17.04 4.86 1519 0 Water: 8.83 65.27 35.24 N/A 397 0 Other: 26.43 47.92 34.26 N/A 8 0 Chain A: 6.18 105.16 18.82 N/A 1737 0 Chain S: 14.64 65.27 39.81 N/A 187 0 Histogram: Values Number of atoms 6.18 - 16.08 1061 16.08 - 25.98 346 25.98 - 35.87 228 35.87 - 45.77 172 45.77 - 55.67 72 55.67 - 65.57 32 65.57 - 75.46 5 75.46 - 85.36 3 85.36 - 95.26 3 95.26 - 105.16 2 =========================== Idealize ADP of riding H ========================== r_work=0.1147 r_free=0.1546 r_work=0.1147 r_free=0.1546 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1147 r_free = 0.1546 target_work(ml) = 4.962 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1140 r_free = 0.1545 target_work(ml) = 4.959 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1140 r_free= 0.1545 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.958536 | | target function (ml) not normalized (work): 80496.878113 | | target function (ml) not normalized (free): 4180.803768 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1160 0.1140 0.1545 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1661 0.1655 0.1838 n_refl.: 17041 remove outliers: r(all,work,free)=0.1661 0.1655 0.1838 n_refl.: 17041 overall B=-0.47 to atoms: r(all,work,free)=0.1629 0.1622 0.1823 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1158 0.1138 0.1546 n_refl.: 17041 remove outliers: r(all,work,free)=0.1157 0.1137 0.1546 n_refl.: 17040 ======================== 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 0.3428 296.122 280.994 0.579 1.007 0.349 11.894-9.307 99.02 97 4 0.1674 487.064 483.675 0.918 1.008 0.349 9.237-7.194 100.00 213 7 0.1806 398.369 399.449 0.984 1.007 0.249 7.162-5.571 100.00 427 22 0.1583 298.976 293.597 0.942 1.007 0.217 5.546-4.326 100.00 867 58 0.0913 410.447 407.054 0.962 1.006 0.201 4.315-3.360 100.00 1859 96 0.0896 390.339 387.877 1.011 1.004 0.188 3.356-2.611 100.00 3867 181 0.1271 256.430 254.311 1.010 1.001 0.142 2.608-2.000 99.99 8818 434 0.1086 167.149 165.699 1.014 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-1.1834 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1137 r_free=0.1546 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN Total number of N/Q/H flips: 1 r_work=0.1139 r_free=0.1538 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1139 r_free=0.1538 | n_water=397 | time (s): 0.690 (total time: 0.690) Filter (dist) r_work=0.1139 r_free=0.1538 | n_water=397 | time (s): 32.970 (total time: 33.660) Filter (q & B) r_work=0.1139 r_free=0.1538 | n_water=397 | time (s): 0.870 (total time: 34.530) Compute maps r_work=0.1139 r_free=0.1538 | n_water=397 | time (s): 0.610 (total time: 35.140) Filter (map) r_work=0.1203 r_free=0.1553 | n_water=312 | time (s): 1.840 (total time: 36.980) Find peaks r_work=0.1203 r_free=0.1553 | n_water=312 | time (s): 0.450 (total time: 37.430) Add new water r_work=0.1349 r_free=0.1684 | n_water=454 | time (s): 1.470 (total time: 38.900) Refine new water occ: r_work=0.1176 r_free=0.1528 adp: r_work=0.1169 r_free=0.1530 occ: r_work=0.1152 r_free=0.1510 adp: r_work=0.1144 r_free=0.1511 occ: r_work=0.1136 r_free=0.1495 adp: r_work=0.1128 r_free=0.1497 ADP+occupancy (water only), MIN, final r_work=0.1128 r_free=0.1497 r_work=0.1128 r_free=0.1497 | n_water=454 | time (s): 28.160 (total time: 67.060) Filter (q & B) r_work=0.1134 r_free=0.1508 | n_water=440 | time (s): 1.870 (total time: 68.930) Filter (dist only) r_work=0.1134 r_free=0.1509 | n_water=439 | time (s): 35.920 (total time: 104.850) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.927027 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.174590 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1118 0.1573 0.0455 0.010 1.0 4.2 0.5 0.0 0 0.964 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.18 15.73 4.55 4.604 21.012 0.175 4.957 11.07 15.70 4.63 4.758 21.034 0.175 4.952 Individual atomic B min max mean iso aniso Overall: 5.86 102.54 20.87 4.94 1966 0 Protein: 5.86 102.54 16.49 4.93 1519 0 Water: 8.37 65.04 35.78 N/A 439 0 Other: 26.81 48.06 34.66 N/A 8 0 Chain A: 5.86 102.54 18.22 N/A 1736 0 Chain S: 16.79 65.04 40.88 N/A 230 0 Histogram: Values Number of atoms 5.86 - 15.52 1046 15.52 - 25.19 368 25.19 - 34.86 216 34.86 - 44.53 189 44.53 - 54.20 96 54.20 - 63.87 33 63.87 - 73.54 9 73.54 - 83.21 3 83.21 - 92.87 3 92.87 - 102.54 3 =========================== Idealize ADP of riding H ========================== r_work=0.1107 r_free=0.1570 r_work=0.1107 r_free=0.1571 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1107 r_free = 0.1571 target_work(ml) = 4.952 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1099 r_free = 0.1575 target_work(ml) = 4.949 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1099 r_free= 0.1575 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.948541 | | target function (ml) not normalized (work): 80329.659379 | | target function (ml) not normalized (free): 4193.059428 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1122 0.1099 0.1575 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1577 0.1563 0.1885 n_refl.: 17040 remove outliers: r(all,work,free)=0.1577 0.1563 0.1885 n_refl.: 17040 overall B=-0.27 to atoms: r(all,work,free)=0.1561 0.1546 0.1877 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1120 0.1097 0.1567 n_refl.: 17040 remove outliers: r(all,work,free)=0.1120 0.1097 0.1567 n_refl.: 17040 ======================== 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 0.3667 296.122 275.439 0.547 1.003 0.328 11.894-9.307 99.02 97 4 0.1700 487.064 484.971 0.923 1.004 0.320 9.237-7.194 100.00 213 7 0.1702 398.369 399.936 0.989 1.005 0.230 7.162-5.571 100.00 427 22 0.1542 298.976 293.435 0.941 1.004 0.210 5.546-4.326 100.00 867 58 0.0891 410.447 407.048 0.962 1.004 0.191 4.315-3.360 100.00 1859 96 0.0856 390.339 388.026 1.006 1.003 0.191 3.356-2.611 100.00 3867 181 0.1245 256.430 254.142 1.003 1.001 0.141 2.608-2.000 99.99 8818 434 0.1029 167.149 165.929 1.000 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.9463 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1097 r_free=0.1567 After: r_work=0.1099 r_free=0.1565 ================================== NQH flips ================================== r_work=0.1099 r_free=0.1565 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=0.1099 r_free=0.1565 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1099 r_free=0.1565 | n_water=439 | time (s): 0.730 (total time: 0.730) Filter (dist) r_work=0.1100 r_free=0.1562 | n_water=438 | time (s): 38.120 (total time: 38.850) Filter (q & B) r_work=0.1100 r_free=0.1562 | n_water=438 | time (s): 0.800 (total time: 39.650) Compute maps r_work=0.1100 r_free=0.1562 | n_water=438 | time (s): 0.640 (total time: 40.290) Filter (map) r_work=0.1172 r_free=0.1556 | n_water=341 | time (s): 1.760 (total time: 42.050) Find peaks r_work=0.1172 r_free=0.1556 | n_water=341 | time (s): 0.430 (total time: 42.480) Add new water r_work=0.1287 r_free=0.1650 | n_water=478 | time (s): 1.410 (total time: 43.890) Refine new water occ: r_work=0.1142 r_free=0.1510 adp: r_work=0.1134 r_free=0.1509 occ: r_work=0.1122 r_free=0.1489 adp: r_work=0.1113 r_free=0.1491 occ: r_work=0.1108 r_free=0.1476 adp: r_work=0.1102 r_free=0.1477 ADP+occupancy (water only), MIN, final r_work=0.1102 r_free=0.1477 r_work=0.1102 r_free=0.1477 | n_water=478 | time (s): 29.670 (total time: 73.560) Filter (q & B) r_work=0.1107 r_free=0.1490 | n_water=466 | time (s): 1.630 (total time: 75.190) Filter (dist only) r_work=0.1107 r_free=0.1490 | n_water=465 | time (s): 38.550 (total time: 113.740) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.871130 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.178014 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1120 0.1518 0.0398 0.011 1.1 4.8 0.5 0.0 0 0.936 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.20 15.18 3.98 4.596 20.844 0.178 4.945 11.08 15.05 3.97 4.635 20.945 0.178 4.934 Individual atomic B min max mean iso aniso Overall: 4.92 101.01 21.08 5.11 1992 0 Protein: 4.92 101.01 16.28 5.08 1519 0 Water: 8.03 67.77 36.55 N/A 465 0 Other: 26.78 46.78 34.78 N/A 8 0 Chain A: 4.92 101.01 17.94 N/A 1735 0 Chain S: 17.25 67.77 42.28 N/A 257 0 Histogram: Values Number of atoms 4.92 - 14.53 984 14.53 - 24.14 407 24.14 - 33.75 210 33.75 - 43.36 186 43.36 - 52.97 147 52.97 - 62.58 32 62.58 - 72.19 16 72.19 - 81.79 2 81.79 - 91.40 4 91.40 - 101.01 4 =========================== Idealize ADP of riding H ========================== r_work=0.1108 r_free=0.1505 r_work=0.1108 r_free=0.1506 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1108 r_free = 0.1506 target_work(ml) = 4.934 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1103 r_free = 0.1509 target_work(ml) = 4.931 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1103 r_free= 0.1509 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.930682 | | target function (ml) not normalized (work): 80039.764691 | | target function (ml) not normalized (free): 4161.601041 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.64 1.00 2810 159 0.1105 0.1384 5.4391 5.6489| | 2: 3.63 - 2.88 1.00 2711 122 0.1090 0.1506 5.208 5.3612| | 3: 2.88 - 2.52 1.00 2681 148 0.1345 0.1653 5.117 5.1766| | 4: 2.52 - 2.29 1.00 2661 139 0.0941 0.1550 4.6317 4.9578| | 5: 2.29 - 2.13 1.00 2678 122 0.0966 0.1502 4.5835 4.896| | 6: 2.13 - 2.00 1.00 2692 117 0.1130 0.1682 4.576 4.7588| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 - 3.64 2810 159 0.95 8.86 1.00 0.96 6190.16| | 2: 3.63 - 2.88 2711 122 0.92 12.69 1.01 0.96 6190.16| | 3: 2.88 - 2.52 2681 148 0.88 18.69 0.99 0.96 6190.16| | 4: 2.52 - 2.29 2661 139 0.93 12.28 1.01 0.97 2143.19| | 5: 2.29 - 2.13 2678 122 0.91 14.29 1.00 0.97 2143.19| | 6: 2.13 - 2.00 2692 117 0.89 16.98 0.99 0.97 2143.19| |alpha: min = 0.96 max = 0.97 mean = 0.96| |beta: min = 2143.19 max = 6190.16 mean = 4187.99| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.98 mean = 13.93| |phase err.(test): min = 0.00 max = 88.18 mean = 13.53| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1123 0.1103 0.1509 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1551 0.1540 0.1805 n_refl.: 17040 remove outliers: r(all,work,free)=0.1551 0.1540 0.1805 n_refl.: 17040 overall B=-0.22 to atoms: r(all,work,free)=0.1539 0.1527 0.1799 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1125 0.1105 0.1508 n_refl.: 17040 remove outliers: r(all,work,free)=0.1125 0.1105 0.1508 n_refl.: 17040 ======================== 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 0.3558 296.122 277.516 0.532 1.003 0.309 11.894-9.307 99.02 97 4 0.1827 487.064 480.885 0.915 1.005 0.293 9.237-7.194 100.00 213 7 0.1694 398.369 401.193 0.990 1.005 0.220 7.162-5.571 100.00 427 22 0.1550 298.976 292.678 0.937 1.005 0.199 5.546-4.326 100.00 867 58 0.0912 410.447 407.205 0.962 1.004 0.197 4.315-3.360 100.00 1859 96 0.0883 390.339 388.099 1.003 1.003 0.171 3.356-2.611 100.00 3867 181 0.1228 256.430 254.247 1.001 1.000 0.121 2.608-2.000 99.99 8818 434 0.1040 167.149 165.792 0.992 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.7718 ================= 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 : 0.2793 0.1840 0.082 5.413 8.8 119.3 19.9 258 0.000 1_bss: 0.1621 0.1679 0.082 5.413 8.4 118.9 19.5 258 0.000 1_settarget: 0.1621 0.1679 0.082 5.413 8.4 118.9 19.5 258 0.000 1_nqh: 0.1625 0.1687 0.082 5.413 8.4 118.9 19.5 258 0.003 1_weight: 0.1625 0.1687 0.082 5.413 8.4 118.9 19.5 258 0.003 1_xyzrec: 0.1352 0.1644 0.009 0.987 8.4 118.9 19.5 258 0.149 1_adp: 0.1279 0.1663 0.009 0.987 6.3 113.9 20.0 258 0.149 1_regHadp: 0.1283 0.1672 0.009 0.987 6.3 113.9 20.0 258 0.149 1_occ: 0.1277 0.1667 0.009 0.987 6.3 113.9 20.0 258 0.149 2_bss: 0.1276 0.1654 0.009 0.987 5.9 113.5 19.6 258 0.149 2_settarget: 0.1276 0.1654 0.009 0.987 5.9 113.5 19.6 258 0.149 2_updatecdl: 0.1276 0.1654 0.009 0.999 5.9 113.5 19.6 258 0.149 2_nqh: 0.1276 0.1654 0.009 0.999 5.9 113.5 19.6 258 0.149 2_sol: 0.1239 0.1568 0.009 0.999 5.9 112.2 20.9 365 n/a 2_weight: 0.1239 0.1568 0.009 0.999 5.9 112.2 20.9 365 n/a 2_xyzrec: 0.1209 0.1609 0.008 0.937 5.9 112.2 20.9 365 n/a 2_adp: 0.1193 0.1628 0.008 0.937 6.6 107.2 21.4 365 n/a 2_regHadp: 0.1194 0.1629 0.008 0.937 6.6 107.2 21.4 365 n/a 2_occ: 0.1191 0.1632 0.008 0.937 6.6 107.2 21.4 365 n/a 3_bss: 0.1184 0.1625 0.008 0.937 6.3 106.9 21.0 365 n/a 3_settarget: 0.1184 0.1625 0.008 0.937 6.3 106.9 21.0 365 n/a 3_updatecdl: 0.1184 0.1625 0.008 0.942 6.3 106.9 21.0 365 n/a 3_nqh: 0.1184 0.1625 0.008 0.942 6.3 106.9 21.0 365 n/a 3_sol: 0.1187 0.1544 0.008 0.942 6.3 106.9 20.9 397 n/a 3_weight: 0.1187 0.1544 0.008 0.942 6.3 106.9 20.9 397 n/a 3_xyzrec: 0.1168 0.1543 0.009 0.963 6.3 106.9 20.9 397 n/a 3_adp: 0.1147 0.1546 0.009 0.963 6.2 105.2 20.9 397 n/a 3_regHadp: 0.1147 0.1546 0.009 0.963 6.2 105.2 20.9 397 n/a 3_occ: 0.1140 0.1545 0.009 0.963 6.2 105.2 20.9 397 n/a 4_bss: 0.1137 0.1546 0.009 0.963 5.7 104.7 20.4 397 n/a 4_settarget: 0.1137 0.1546 0.009 0.963 5.7 104.7 20.4 397 n/a 4_updatecdl: 0.1137 0.1546 0.009 0.962 5.7 104.7 20.4 397 n/a 4_nqh: 0.1139 0.1538 0.009 0.962 5.7 104.7 20.4 397 n/a 4_sol: 0.1134 0.1509 0.009 0.962 5.7 104.7 20.8 439 n/a 4_weight: 0.1134 0.1509 0.009 0.962 5.7 104.7 20.8 439 n/a 4_xyzrec: 0.1118 0.1573 0.010 0.971 5.7 104.7 20.8 439 n/a 4_adp: 0.1107 0.1570 0.010 0.971 5.9 102.5 20.9 439 n/a 4_regHadp: 0.1107 0.1571 0.010 0.971 5.9 102.5 20.9 439 n/a 4_occ: 0.1099 0.1575 0.010 0.971 5.9 102.5 20.9 439 n/a 5_bss: 0.1097 0.1567 0.010 0.971 5.6 102.3 20.6 439 n/a 5_settarget: 0.1097 0.1567 0.010 0.971 5.6 102.3 20.6 439 n/a 5_updatecdl: 0.1097 0.1567 0.010 0.972 5.6 102.3 20.6 439 n/a 5_setrh: 0.1099 0.1565 0.010 0.972 5.6 102.3 20.6 439 n/a 5_nqh: 0.1099 0.1565 0.010 0.972 5.6 102.3 20.6 439 n/a 5_sol: 0.1107 0.1490 0.010 0.972 5.6 102.3 20.9 465 n/a 5_weight: 0.1107 0.1490 0.010 0.972 5.6 102.3 20.9 465 n/a 5_xyzrec: 0.1120 0.1518 0.011 1.057 5.6 102.3 20.9 465 n/a 5_adp: 0.1108 0.1505 0.011 1.057 4.9 101.0 21.1 465 n/a 5_regHadp: 0.1108 0.1506 0.011 1.057 4.9 101.0 21.1 465 n/a 5_occ: 0.1103 0.1509 0.011 1.057 4.9 101.0 21.1 465 n/a end: 0.1105 0.1508 0.011 1.057 4.7 100.8 20.9 465 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_1541177_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_1541177_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.3600 Refinement macro-cycles (run) : 943.3900 Write final files (write_after_run_outputs) : 19.2200 Total : 965.9700 Total CPU time: 16.45 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:28 PST -0800 (1735494088.04 s) Start R-work = 0.1621, R-free = 0.1679 Final R-work = 0.1105, R-free = 0.1508 =============================================================================== Job complete usr+sys time: 1006.80 seconds wall clock time: 17 minutes 9.82 seconds (1029.82 seconds total)